@prefix biotools: . @prefix bsc: . @prefix bsct: . @prefix dcterms: . @prefix edam: . @prefix sc: . @prefix schema: . @prefix xsd: . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3365, edam:topic_3473 ; sc:citation , , , , "pmcid:PMC3042601", "pmcid:PMC3498066", "pmcid:PMC4617611", "pmcid:PMC4750478", "pubmed:20981092", "pubmed:23128226", "pubmed:26432245", "pubmed:26432246" ; sc:description "The 1000 Genomes Project ran between 2008 and 2015, creating a deep catalogue of human genetic variation. The International Genome Sample Resource (IGSR) was set up to ensure the future usability and accessibility of this data." ; sc:featureList edam:operation_0306, edam:operation_3196, edam:operation_3202, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "1000Genomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.internationalgenome.org" ; biotools:primaryContact "Auton A" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2305, edam:format_2306, edam:format_3003, edam:format_3007 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:author "Ensembl team" ; sc:description "Map your data to the current assembly." ; sc:featureList edam:operation_2944 ; sc:name "1000Genomes assembly converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Ensembl Genomes team" ; sc:citation ; sc:description "Get a subset of data from a BAM or VCF file." ; sc:featureList edam:operation_2121 ; sc:name "1000Genomes data slicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3345 ; sc:author "Ensembl team" ; sc:citation ; sc:description "Convert a set of Ensembl IDs from a previous release into their current equivalents." ; sc:featureList edam:operation_3282 ; sc:name "1000Genomes ID history converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199 ; sc:author "Ensembl Genomes team", "Resequencing Informatics" ; sc:citation ; sc:contributor "Resequencing Informatics" ; sc:description "Identify variation patterns in a chromosomal region of interest for different individuals." ; sc:featureList edam:operation_3504 ; sc:name "1000Genomes Variation Pattern Finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199 ; sc:author "Ensembl Genomes team", "Resequencing Informatics" ; sc:contributor "Resequencing Informatics" ; sc:description "Convert a VCF file into a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview." ; sc:featureList edam:operation_0335 ; sc:name "1000Genomes VCF2PED" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://browser.1000genomes.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0593, edam:topic_0749 ; sc:citation ; sc:description "Tool to evaluate 13C chemical shift assignments of RNA." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "13Check_RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BIOS-IMASL/13Check_RNA" ; biotools:primaryContact "A. A. Icazatti", "J. A. Vila" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation "pubmed:25735772" ; sc:description "Webserver that predicts 14-3-3-binding sites by combining predictions from three different classifiers: ANN, PSSM and SVM." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "14-3-3-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/1433pred" ; biotools:primaryContact "The Barton Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0659, edam:topic_2229, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC9580931", "pubmed:36304264" ; sc:description "16S-ITGDB is an integrated database for improving taxonomic classification of 16S ribosomal RNA (rRNA) sequences." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3460 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "16S-ITGDB" ; sc:url "https://github.com/yphsieh/ItgDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0659, edam:topic_3474 ; sc:citation "pubmed:25646627" ; sc:description "Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. It has the unique ability to classify small Hypervariable Regions of 16S rRNA." ; sc:featureList edam:operation_3460 ; sc:name "16S classifier" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://metabiosys.iiserb.ac.in/16Sclassifier/application.php" ; biotools:primaryContact "MetaBioSys Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3301 ; sc:citation ; sc:description "Comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing." ; sc:featureList edam:operation_2454 ; sc:name "16sPIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://16spip.mypathogen.cn/" ; biotools:primaryContact "Wen Zhang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2885, edam:topic_3673 ; sc:description "Cloud-based platform. Providing bioinformatic analysis of bacteria. Species identification (16S, WGS), typing (MLST, cgMLST, SNP), antibiotic resistance profiling, virulence. Possibility to add metadata for transmission analysis." ; sc:featureList edam:operation_3840 ; sc:name "1928 Diagnostics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.1928diagnostics.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305 ; sc:citation ; sc:description "19 and Me: COVID-19 Risk Score Calculator is a tool that synthesizes reported COVID-19 geographic case data and rapidly evolving scientific research to help you ballpark how much risk this disease poses to you." ; sc:featureList edam:operation_2428, edam:operation_3283, edam:operation_3503 ; sc:license "MIT" ; sc:name "19andMe" ; sc:softwareHelp ; sc:url "https://19andme.covid19.mathematica.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Demonstrates Professor Grigoryan's illustration of geometrical interpretation of the 1-D DFT." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Geometrical interpretation of the 1-D DFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29788-geometrical-interpretation-of-the-1-d-dft" ; biotools:primaryContact "Michael Chan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC8180056", "pubmed:34090332" ; sc:description "Mapping-free variant detection from DNA-seq data of matched samples." ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3227, edam:operation_3436, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "2-kupl" ; sc:url "https://github.com/yunfengwang0317/2-kupl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3324, edam:topic_3673 ; sc:citation , "pubmed:33406042" ; sc:description "2019nCoVAS is a web service for different analyses including transmission, genome, and psychological stress." ; sc:featureList edam:operation_0324, edam:operation_2403, edam:operation_2426 ; sc:name "2019nCoVAS" ; sc:url "http://www.combio-lezhang.online/2019ncov/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3175, edam:topic_3474 ; sc:citation , "pubmed:27911828" ; sc:description "2020plus classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene from small somatic variants by using Random Forests." ; sc:featureList edam:operation_0276, edam:operation_0313, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "2020plus" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v1.2.2" ; sc:url "https://github.com/KarchinLab/2020plus" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:encodingFormat edam:format_3547 ; sc:name "Protein structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "A database including visualizations of protein secondary structure via 2D diagrams. The 2D diagrams are based on whole protein family and they take into account 2D structure of the protein family members." ; sc:featureList edam:operation_2486 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "2DProts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://2dprots.ncbr.muni.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_3542 ; sc:citation , "pmcid:PMC6602421", "pubmed:31114904" ; sc:description "Webserver for the comparison of secondary structure algorithms and the secondary structure of protein structures." ; sc:featureList edam:operation_0267, edam:operation_0319, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "2StrucCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://2struccompare.cryst.bbk.ac.uk/index.php" ; biotools:primaryContact "Elliot Drew", "Robert W. Janes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3318, edam:topic_3520 ; sc:citation , , "pmcid:PMC5103804", "pmcid:PMC8832274", "pubmed:27634801", "pubmed:35084336" ; sc:description "2B-Alert Web, an open-access tool for predicting neurobehavioral performance, which accounts for the effects of sleep/wake schedules, time of day, and caffeine consumption, while incorporating the latest scientific findings in sleep restriction, sleep extension, and recovery sleep." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "2B-Alert Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://2b-alert-web.bhsai.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc:description "Two dimensional cepstral spectrum. The present function calculates the cepstral spectrum of image either gray scale or RGB colored. This spectrum is useful for analysis of an image and suitable for pre-processing of an image for machine learning purposes." ; sc:featureList edam:operation_3443, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "2D Image cepstral analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51004-2d-image-cepstral-analysis" ; biotools:primaryContact "Pavel Paunov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154 ; sc:citation "pubmed:20696175" ; sc:description "Web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids." ; sc:featureList edam:operation_0337, edam:operation_2479 ; sc:name "2D-MH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/pplot/2D-MH" ; biotools:primaryContact "Xiao Lab", "Xuan Xiao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1519 ; sc:name "Peptide molecular weights" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2373 ; sc:name "Spot ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0942 ; sc:name "2D PAGE image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "2D-PAGE database." ; sc:featureList edam:operation_0224 ; sc:name "2D-PAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Siena, Italy" ; sc:softwareHelp ; sc:url "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi" ; biotools:primaryContact "Luca Bini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0623, edam:topic_3542 ; sc:citation ; sc:description "Web server for protein secondary structure visualization." ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "2dSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.lcqb.upmc.fr/2dss/" ; biotools:primaryContact "Juliana S.. Bernardes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Algorithms for 2D AR and 2D ARMA parameters estimation." ; sc:isAccessibleForFree true ; sc:name "2D AR and 2D ARMA parameters estimation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29360-2d-ar-and-2d-arma-parameters-estimation" ; biotools:primaryContact "Simona Maggio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:32307725" ; sc:description "2DE-pattern is a database containing data on proteins/isoforms/proteoforms profiles." ; sc:featureList edam:operation_2421 ; sc:name "2DE-pattern" ; sc:url "http://2de-pattern.pnpi.nrcki.ru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC7267828", "pubmed:32108864" ; sc:description """An imputation method that recovers false zeros (known as dropouts) in single cell RNA sequencing (scRNA-seq) data. It features preventing excessive correction by predicting false zeros and imputing their values accurately by making use of the interrelationships between both genes and cells. 2DImpute takes as input a normalized scRNA-seq data matrix (genes in rows and cells in columns) with or without log-transformation. It outputs the imputed data in the same dimension and the same log-transformation.""" ; sc:featureList edam:operation_3435, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "2DImpute" ; sc:url "https://github.com/zky0708/2DImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_3382 ; sc:citation , "pmcid:PMC7011505", "pubmed:32064000" ; sc:description "A toolkit for content-based local image search." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "2DKD" ; sc:url "http://github.com/kiharalab/2DKD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3314, edam:topic_3318 ; sc:citation , "pubmed:36480578" ; sc:description "The 2D semiconductor database (2DSdb) provides an ideal platform for computational modeling and design of new 2D semiconductors and heterostructures in photocatalysis, nanoscale devices, and other applications." ; sc:license "CC-BY-4.0" ; sc:name "2DSdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://materialsdb.cn/2dsdb/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:name "Raw image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_1317 ; sc:citation ; sc:description "A software system designed as a user friendly, platform-independent software package for electron crystallography." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "2DX" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.2dx.unibas.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:25344498" ; sc:description "Algorithm that searches graphs produced from the de novo assembler cortex." ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_3225 ; sc:name "2kplus2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/danmaclean/2kplus2" ; biotools:primaryContact "Team MacLean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC7549647", "pubmed:32138598" ; sc:description "2lpiRNApred is a 2-layer integrated program for identifying piRNAs in the first layer and determining if piRNAs have the function of instructing target mRNA deadenylation in the second layer." ; sc:featureList edam:operation_3936, edam:operation_3937 ; sc:name "2lpiRNApred" ; sc:url "https://github.com/JianyuanLin/2lpiRNApred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing." ; sc:featureList edam:operation_0232, edam:operation_0335, edam:operation_3198, edam:operation_3258, edam:operation_3695 ; sc:license "MIT" ; sc:name "2passtools" ; sc:url "https://github.com/bartongroup/2passtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0749, edam:topic_2269, edam:topic_3299 ; sc:citation , "pmcid:PMC7191778", "pubmed:32349677" ; sc:description """2SigFinder implements multiscale statistical algorithm to predict genomic islands from a single genome. It uses small-scale test with large-scale features to score small region deviating from the host and large-scale statistical test with small-scale features to identify multi-window segments for identification of genomic islands. 2SigFinder is a novel prediction method, the first combined use of small-scale and large-scale statistical testing for genomic island detection. 2SigFinder was tested by genomic island boundary detection and identification of genomic islands or functional features of real biological data. 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Outputs include cell and territorial volume, branch length, and number of branch and end points." ; sc:featureList edam:operation_3450, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3DMorph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ElisaYork/3DMorph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3315, edam:topic_3384 ; sc:citation ; sc:description """3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Related to bio.tools/fossilj.""" ; sc:featureList edam:operation_3443 ; sc:name "3DSlicer" ; sc:softwareHelp ; sc:url "https://www.slicer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3382 ; sc:citation , "pubmed:30886414" ; sc:description "Creates high-quality 3D/4D animations using a natural-language based syntax." ; sc:featureList edam:operation_0250, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "3Dscript" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://imagej.net/3Dscript" ; biotools:primaryContact "Benjamin Schmid" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3308 ; sc:author , , "Dimitri MEISTERMANN", "Philippe Bordron" ; sc:citation , , , , , , , , , "pmcid:PMC5291739", "pmcid:PMC5676863", "pmcid:PMC5783949", "pmcid:PMC5797797", "pmcid:PMC7284977", "pubmed:28194440", "pubmed:29116112", "pubmed:29367672", "pubmed:29445370", "pubmed:32438566" ; sc:contributor ; sc:description """A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. 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Cite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1""" ; sc:featureList edam:operation_0531, edam:operation_2935, edam:operation_3223, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:name "3SRP" ; sc:operatingSystem "Linux" ; sc:provider "BiRD bioinformatics facility" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3320, edam:topic_3517 ; sc:citation , "pubmed:34432052" ; sc:description "An atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues." ; sc:featureList edam:operation_2943, edam:operation_3196, edam:operation_3208, edam:operation_3232, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "3 aQTL-atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wlcb.oit.uci.edu/3aQTLatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "3CAC is a three-class classifier designed to classify contigs in mixed metagenome assemblies as phages, plasmids, chromosomes, or uncertain. 3CAC generates its initial classification by existing classifiers: viralVerify, PPR-Meta, PlasClass, and deepVirFinder. 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It is a part of Elephant." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "3d-SPADE" ; sc:url "https://elephant.readthedocs.io/en/latest/reference/spade.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275 ; sc:citation ; sc:description "The 3D-Beacons Network provides unified programmatic access to experimentally determined and predicted structure models." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "3D-Beacons" ; sc:softwareHelp , , ; sc:softwareVersion "1.0.0" ; sc:url "https://3d-beacons.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_1476, edam:format_3464, edam:format_3874 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0092, edam:topic_3510, edam:topic_3892 ; sc:author "Adam Hospital" ; sc:citation , , "pmcid:PMC6736963", "pmcid:PMC7284151", "pubmed:31506435", "pubmed:32566135" ; sc:contributor "Genís Bayarri" ; sc:description "This workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). 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It is a plugin for Medical Imaging Interaction Toolkit (https://www.mitk.org/)." ; sc:featureList edam:operation_3552 ; sc:name "3D-Cell-Annotator" ; sc:url "http://www.3D-cell-annotator.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "An interactive tool for users to browse through sagittal, axial and coronal views of CT/MRI images." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D CT MRI images interactive sliding viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29134-3d-ct-mri-images-interactive-sliding-viewer" ; biotools:primaryContact "Gang Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0097, edam:topic_0593, edam:topic_1317 ; sc:author ; sc:citation ; sc:description "A web server for generation of 3D-structural DNA models with a defined conformation by providing control over both ‘global’ and ‘local’ conformational features." ; sc:featureList edam:operation_0570, edam:operation_2476, edam:operation_2481 ; sc:isAccessibleForFree true ; sc:name "3D-DART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://milou.science.uu.nl/services/3DDART/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344, edam:topic_3382 ; sc:description "Generate in 3D the diffusion gradient vector field as in Xu and Prince 1998" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D Diffusion gradient" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/31994-diffusion-gradient-vector-field-in-3d" ; biotools:primaryContact "Khaled Khairy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654 ; sc:citation ; sc:description "3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "3d-dna" ; sc:url "https://github.com/aidenlab/3d-dna" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0602, edam:topic_2258, edam:topic_3314 ; sc:citation , "pmcid:PMC5342320", "pubmed:28125221" ; sc:description "Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine." ; sc:featureList edam:operation_2406, edam:operation_2414, edam:operation_3646 ; sc:name "3D-e-Chem-VM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3d-e-chem.github.io/3D-e-Chem-VM/" ; biotools:primaryContact "C. De. Graaf", "Ross Mcguire", "S. Verhoeven" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0157, edam:topic_3534 ; sc:citation "pubmed:19767616" ; sc:description "3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity." ; sc:featureList edam:operation_0321, edam:operation_0478, edam:operation_2997, edam:operation_3561 ; sc:name "3D-Footprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://floresta.eead.csic.es/3dfootprint" ; biotools:primaryContact "3D-Footprint Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3382 ; sc:description "A toolbox for performing image registrations on 4D RTOG files or any other volumetric image." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D Free Form Image Registration Toolbox (GUI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.5.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/21017-3d-free-form-image-registration-toolbox-gui" ; biotools:primaryContact "Daniel Markel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0821, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:18515349" ; sc:description "Software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2487 ; sc:name "3D-Fun" ; sc:url "http://3dfun.bioinfo.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3175, edam:topic_3176, edam:topic_3940 ; sc:citation , "pmcid:PMC7319547", "pubmed:32442297" ; sc:description """3D chromatin organization webserver is a 3D genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. 3D genome organization plays a critical role in its functioning. Alterations of this organization caused by structural variants (SVs) may lead to changes in gene transcription or even to disease. The recent advent of Chromosome Conformation Capture (3C) based techniques such as ChIA-PET and Hi-C allows us to investigate genome spatial organization. The rising volume of sequencing data in turn enables highly accurate identification of structural variation. Combination of those two sources of information can reveal mechanisms of genome regulation.""" ; sc:featureList edam:operation_0481, edam:operation_0570, edam:operation_3196 ; sc:name "3D-GNOME" ; sc:softwareVersion "2.0" ; sc:url "https://3dgnome.cent.uw.edu.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "MATLAB script for converting a image stack into a 3D array." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "3D image stacker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/38788-3d-image-stack-viewer" ; biotools:primaryContact "boyexex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:12761065", "pubmed:12824309", "pubmed:12824423" ; sc:description "3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach." ; sc:featureList edam:operation_0267, edam:operation_0268, edam:operation_0474, edam:operation_0477 ; sc:name "3D-Jury" ; sc:url "http://meta.bioinfo.pl/submit_wizard.pl" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1520 ; sc:name "Peptide hydrophobic moment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Computations of joint angles and displacements, moments and forces (lower / upper limb)" ; sc:featureList edam:operation_0407 ; sc:isAccessibleForFree true ; sc:name "3D Kinematics and Inverse Dynamics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/58021-3d-kinematics-and-inverse-dynamics" ; biotools:primaryContact "Raphael Dumas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0157, edam:topic_0602 ; sc:citation "pubmed:17517763" ; sc:description "Tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes." ; sc:featureList edam:operation_0474, edam:operation_2406, edam:operation_2479, edam:operation_2492, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "3D-partner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gemdock.life.nctu.edu.tw/3d-partner/" ; biotools:primaryContact "Jinn-Moon Yang", "Yu-Shu Lo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3384, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC7082691", "pubmed:32211292" ; sc:description """3D photoacoustic visualization studio. Bio Optics and Acoustics Laboratory.""" ; sc:featureList edam:operation_0297, edam:operation_0337, edam:operation_3443 ; sc:name "3D PHOVIS" ; sc:url "http://www.boa-lab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0160, edam:topic_0736 ; sc:citation "pubmed:10526371", "pubmed:10860755" ; sc:description "Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0303, edam:operation_0474 ; sc:name "3D-pssm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html" ; biotools:primaryContact "Lawrence Kelley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3375 ; sc:citation , "pubmed:31595406" ; sc:description """3D-QSAR is a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets. The underlying idea of any field-based 3-D QSAR is that differences in a target propriety, e.g., biological activity, are often closely related to equivalent changes in shapes and intensities of noncovalent calculated interaction surrounding the molecules (also called molecular interaction fields, MIFs).""" ; sc:featureList edam:operation_0478, edam:operation_3435, edam:operation_3659 ; sc:name "3d-qsar" ; sc:url "http://www.3d-qsar.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:33345702" ; sc:description """3D RNA-seq appA powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. 3D RNA-seq is currently under a dual-licensing model.""" ; sc:featureList edam:operation_0264, edam:operation_2939, edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:name "3D RNA-seq" ; sc:url "https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "3D Shepp-Logan Phantom is a 3D extension of MATLAB's phantom function - generates a phantom consisting of an arbitrary number of ellipsoids in 3D." ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "3D Shepp-Logan Phantom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50974-3d-shepp-logan-phantom" ; biotools:primaryContact "Patrick Bolan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166 ; sc:citation "pubmed:24573477" ; sc:description "3D-SURFER is a web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons." ; sc:featureList edam:operation_2479, edam:operation_3351, edam:operation_3666 ; sc:name "3D-SURFER" ; sc:softwareHelp ; sc:url "http://kiharalab.org/3d-surfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pubmed:33057891" ; sc:description "3D-XGuide is a software framework providing a foundation for rapid prototyping of new approaches in the field of XR navigation guidance. Actual software release offers graphical user interface with basic functionality including data import and handling, calculation of projection geometry and transformations between related coordinate systems, rigid 3D-3D registration, and template-matching-based tracking and motion compensation algorithms in 2D and 3D." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:license "BSD-2-Clause" ; sc:name "3D-XGuide" ; sc:url "https://github.com/ExCaVI-Ulm/3D-XGuide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6747482", "pubmed:31450739" ; sc:description "An Web Server for RNA 3D structure prediction." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:name "3dRNA" ; sc:softwareVersion "v2.0" ; sc:url "http://biophy.hust.edu.cn/3dRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382 ; sc:citation , "pubmed:34743262" ; sc:description "An interactive software for 3D segmentation and analysis of dendritic spines." ; sc:featureList edam:operation_3450, edam:operation_3799 ; sc:name "3D Spine Analysis Software (3dSpAn)" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/3dSpAn/" ; biotools:primaryContact , , "Ewa Baczynska", "Nirmal Das" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3444 ; sc:description "This software contains 2D and 3D Shepp-Logan phantoms in both the image and Fourier domains." ; sc:isAccessibleForFree true ; sc:name "Three Dimensional Analytical Magnetic Resonance Imaging Phantom in the Fourier Domain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/15697-three-dimensional-analytical-magnetic-resonance-imaging-phantom-in-the-fourier-domain" ; biotools:primaryContact "Cheng Guan Koay" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1146 ; sc:name "EMDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_3047, edam:topic_3366 ; sc:author , "Joan Segura" ; sc:citation , , , ; sc:description "Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level." ; sc:featureList edam:operation_0564, edam:operation_0570, edam:operation_2422 ; sc:funder "CORBEL", "CSIC", "Comunidad de Madrid", "EOSC-Life", "Instituto de Salud Carlos III", "Spanish Ministry of Science and Innovation" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "3DBIONOTES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ES", "INB", "cnb.csic.es" ; sc:softwareHelp ; sc:softwareVersion "v3" ; sc:url "http://3dbionotes.cnb.csic.es/ws" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2229, edam:topic_3382, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC8748745", "pubmed:35013443" ; sc:description "A light and robust tool to do 3D cell instance segmentation for cell membrane images. It is useful when the cells clump together." ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "3DCellSeg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AntonotnaWang/3DCellSeg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "3DCOMB is a software which can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments." ; sc:featureList edam:operation_0295, edam:operation_0504 ; sc:name "3DCOMB" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.06" ; sc:url "http://ttic.uchicago.edu/~jinbo/software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC7496221", "pubmed:32859248" ; sc:description """3DeFDR is a statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions""" ; sc:featureList edam:operation_0481, edam:operation_3222, edam:operation_3435 ; sc:license "MIT" ; sc:name "3DeFDR" ; sc:url "https://bitbucket.org/creminslab/5c3defdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0611, edam:topic_3382, edam:topic_3385 ; sc:citation "pubmed:23671335" ; sc:description "3DEM Loupe is a web-server that allows normal mode analysis of any uploaded electron microscopy volume. Results can be explored in 3 dimensions through animations and movies." ; sc:featureList edam:operation_0321, edam:operation_2406, edam:operation_3457 ; sc:name "3DEM Loupe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3demloupe.cnb.csic.es" ; biotools:primaryContact "3DEM Loupe Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation ; sc:description "Robust computational infrastructure capable of supporting the automatic and standardised benchmarking of image processing applications for cryoEM." ; sc:featureList edam:operation_2428 ; sc:name "3DEMBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "cnb.csic.es" ; sc:softwareHelp ; sc:url "http://i2pc.cnb.csic.es/3dembenchmark/LoadHome.htm" ; biotools:primaryContact "Joan Segura" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0769, edam:topic_2814, edam:topic_3400 ; sc:citation , "pmcid:PMC9162058", "pubmed:35664289" ; sc:description "The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space." ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_0570, edam:operation_3663, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "3DFI" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/PombertLab/3DFI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0199, edam:topic_0621, edam:topic_3169, edam:topic_3912 ; sc:citation , "pmcid:PMC9252746", "pubmed:35639501" ; sc:description "A web-server to benchmark computational models for 3D Genomics." ; sc:featureList edam:operation_0475, edam:operation_2483, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "3DGenBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://3dgenbench.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:35511112" ; sc:description "3D graph and text based neural network for drug-drug interaction prediction." ; sc:featureList edam:operation_3625, edam:operation_3927, edam:operation_4009 ; sc:license "Apache-2.0" ; sc:name "3DGT-DDI" ; sc:url "https://github.com/hehh77/3DGT-DDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0602, edam:topic_2275 ; sc:author "Joan Segura" ; sc:citation "pubmed:26772592" ; sc:description "3DIANA (3D Domain Interaction Analysis) is a web based environment designed to integrate bioinformatics-like information for the analysis of protein interactions and quaternary structure modellling" ; sc:featureList edam:operation_2949, edam:operation_3350 ; sc:name "3DIANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3diana.cnb.csic.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:20965963" ; sc:description "Collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The web server visualizes these interfaces along with atomic details of individual interactions using Jmol." ; sc:featureList edam:operation_0246, edam:operation_0248, edam:operation_0303, edam:operation_2492, edam:operation_2949 ; sc:name "3DID database of 3D interacting domains" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3did.irbbarcelona.org/" ; biotools:primaryContact "Patrick Aloy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0621, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:33245777" ; sc:description """3D-Genome Interaction Viewer & database is a comprehensive resource of 3D genome and 3D cancer genome. 3D genome organization is tightly coupled with gene regulation in various biological processes and diseases. 3D Interaction Viewer and Database (3DIV) is a database providing chromatin interaction visualization in a variety of options from one-to-all chromatin interaction with epigenetic annotation to unique dynamic browsing tools allowing examination of large-scale genomic rearrangement mediated impacts in cancer 3D genome.""" ; sc:featureList edam:operation_2429, edam:operation_3208, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "3DIV" ; sc:softwareHelp ; sc:url "http://3div.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_2814, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:20513649" ; sc:description "3DLigandSite is a web server for the prediction of ligand binding sites. 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The membrane model is coupled to a macroscopic model of a single membrane fiber unit to produce lactose concentration profiles, lactose consumption predictions, and performance index estimates." ; sc:featureList edam:operation_0250, edam:operation_0322, edam:operation_0477, edam:operation_2476 ; sc:name "3DMem-enzyme" ; sc:url "http://www.iceht.forth.gr/staff/burganos.html" ; biotools:primaryContact "Vassilios Burganos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3314, edam:topic_3382 ; sc:citation , "pmcid:PMC9416521", "pubmed:25505090", "pubmed:36035779" ; sc:description "Object-oriented, webGL based JavaScript library for online molecular visualization – No Java required! 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Santos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description "ACCOST is a Python script that assigns statistical significance to differences in contact counts in Hi-C experiment." ; sc:license "Apache-2.0" ; sc:name "ACCOST" ; sc:url "https://bitbucket.org/noblelab/accost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6307290", "pubmed:30587115" ; sc:description "Machine learning toolbox for clustering analysis and visualization." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ACES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GrabherrGroup/ACES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2275, edam:topic_3373 ; sc:citation , "pmcid:PMC6882193" ; sc:description "A free tool for drug repurposing using consensus inverse docking strategy." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "ACID" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/ACID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation ; sc:description "ACPP is a Support Vector Machine based tool to predict whether the given peptide is an Anti-cancer peptide or Not. The three different modes include (i) Protein scan with apoptotic domain prediction; (ii) Multiple peptide mode; and (iii) Peptide mutation mode for prediction and design of anti-cancer peptides. Refer: \"ACPP: A Web Server for Prediction and Design of Anti-cancer Peptides.\" International Journal of Peptide Research and Therapeutics 21.1 (2015): 99-106\" for more deatils." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ACPP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/brsaran/ACPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6571645", "pubmed:31121946" ; sc:description "Computational Tool for the Prediction and Analysis of Anticancer Peptides." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ACPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://codes.bio/acpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:31729528" ; sc:description "ACPred-Fuse is a web application that automatically can predict protein sequences with or without anticancer activity in peptide form." ; sc:featureList edam:operation_3092, edam:operation_3631, edam:operation_3767 ; sc:name "ACPred-Fuse" ; sc:url "http://server.malab.cn/ACPred-Fuse/Server.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC8212143", "pubmed:34179848" ; sc:description "A multi-scale resource of biological maps to study disease mechanisms." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0533, edam:operation_2436, edam:operation_3927, edam:operation_3935 ; sc:name "Atlas of Cancer Signalling Network (ACSN)" ; sc:url "https://acsn.curie.fr/ACSN2/ACSN2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:31359028" ; sc:description "Automated Identification of Cell Types in Single Cell RNA Sequencing | Automated Cell Type Identification using Neural Networks | ACTINN (Automated Cell Type Identification using Neural Networks) is a bioinformatic tool to quickly and accurately identify cell types in scRNA-Seq. For details, please read the paper: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz592/5540320 All datasets used in the paper are available here: https://figshare.com/articles/ACTINN/8967116" ; sc:featureList edam:operation_3891 ; sc:name "ACTINN" ; sc:url "https://github.com/mafeiyang/ACTINN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3334, edam:topic_3512 ; sc:citation ; sc:description """a latent Dirichlet model to compare expressed isoform proportions to a reference panel. actor is an R package which takes transcript expression as input and uses a latent Dirichlet model to compare to GTEx tissues. actor provides gene level similarities to the GTEx tissues and identifies collections of genes, or gene classes, which align similarly to GTEx tissues""" ; sc:featureList edam:operation_2499, edam:operation_3196, edam:operation_3658 ; sc:name "ACTOR" ; sc:url "https://github.com/mccabes292/actor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation , "pubmed:31813761" ; sc:description """Automated preprocessing and analysis of actigraphy data. OBJECTIVES:To introduce a novel software-library called Actigraphy Manager (ACTman) which automates labor-intensive actigraphy data preprocessing and analyses steps while improving transparency, reproducibility, and scalability over software suites traditionally used in actigraphy research practice. DESIGN:Descriptive. METHODS:Use cases are described for performing a common actigraphy task in ACTman and alternative actigraphy software. Important inefficiencies in actigraphy workflow are identified and their consequences are described. We explain how these hinder the feasibility of conducting studies with large groups of athletes and or longer data collection periods. Thereafter, the information flow through the ACTman software is described and we explain how it alleviates aforementioned inefficiencies.""" ; sc:name "ACTman" ; sc:url "https://github.com/compsy/ACTman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168 ; sc:citation , "pmcid:PMC6864362", "pubmed:31740563" ; sc:description """A comprehensive web platform of antimicrobial peptides tailored to the user's research. Antimicrobial peptides (AMPs) are part of the innate immune response to pathogens in all of the kingdoms of life. They have received significant attention because of their extraordinary variety of activities, in particular, as candidate drugs against the threat of super-bacteria.""" ; sc:featureList edam:operation_0491, edam:operation_3216, edam:operation_3802 ; sc:name "ADAPTABLE" ; sc:url "http://gec.u-picardie.fr/adaptable/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6612897", "pubmed:31510641" ; sc:description "leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra | Learning molecular vectors for metabolites from spectra-structure pairs] | We propose ADAPTIVE, which has two parts: learning two mappings 1) from structures to molecular vectors and 2) from spectra to molecular vectors" ; sc:featureList edam:operation_3627, edam:operation_3803, edam:operation_3860 ; sc:name "ADAPTIVE" ; sc:url "http://www.bic.kyoto-u.ac.jp/pathway/tools/ADAPTIVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Automated Deconvolution Augmentation of Profiles for Tissue Specific cells." ; sc:featureList edam:operation_2495, edam:operation_3237, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ADAPTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ADAPTS" ; biotools:primaryContact "Samuel A. Danziger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31764991" ; sc:description """a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci. We developed ADDO, a highly-efficient tool designed to detect, classify and visualize quantitative trait loci (QTLs) with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single nucleotide polymorphism (SNP) effects into additive, partial dominance, dominance and overdominance categories. A matrix multiplication approach is used to accelerate the computation: a genome scan on 20 million markers from 836 individuals takes about 8.5 hours with 10 CPUs. Additivity and dominance are the major genetic components underlying variations in complex traits""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3799 ; sc:license "LGPL-3.0" ; sc:name "ADDO" ; sc:url "https://github.com/LeileiCui/ADDO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634 ; sc:citation ; sc:description "Discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "ADEPTUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://adeptus.cs.tau.ac.il/home" ; biotools:primaryContact "Ron Shamir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3334, edam:topic_3419 ; sc:citation , "pubmed:31088588" ; sc:description "Risk calculator to predict ADHD in young adulthood." ; sc:featureList edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ADHD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ufrgs.br/prodah/adhd-calculator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation "pmcid:PMC6890416", "pubmed:31798351" ; sc:description """Bayesian Optimization with Unknown Constraints using ADMM. There exist many problems in science and engineering that involve optimization of an unknown or partially unknown objective function. Recently, Bayesian Optimization (BO) has emerged as a powerful tool for solving optimization problems whose objective functions are only available as a black box and are expensive to evaluate. Many practical problems, however, involve optimization of an unknown objective function subject to unknown constraints. This is an important yet challenging problem for which, unlike optimizing an unknown function, existing methods face several limitations. In this paper, we present a novel constrained Bayesian optimization framework to optimize an unknown objective function subject to unknown constraints.""" ; sc:name "ADMMBO" ; sc:url "https://github.com/SetarehAr/ADMMBO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_3377, edam:topic_3379, edam:topic_3474 ; sc:citation , , "pubmed:31838499", "pubmed:31868917" ; sc:description "Broad-Spectrum Profiling of Drug Safety via Learning Complex Network." ; sc:featureList edam:operation_0478, edam:operation_2426, edam:operation_3435, edam:operation_3439 ; sc:name "ADRAlert" ; sc:url "http://www.bio-add.org/ADRAlert/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3474 ; sc:citation , "pmcid:PMC6855565", "pubmed:31682632" ; sc:description "A novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences." ; sc:featureList edam:operation_2940, edam:operation_3352, edam:operation_3778 ; sc:name "ADS" ; sc:url "http://ekhidna2.biocenter.helsinki.fi/ADS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3303 ; sc:citation , "pmcid:PMC6376756", "pubmed:30764760" ; sc:description "Scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ADS-HCSpark" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/SCUT-CCNL/ADS-HCSpark.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31607216" ; sc:description "A web tool which provides several novel survival analysis approaches. It computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting." ; sc:featureList edam:operation_2495, edam:operation_3435 ; sc:name "Advanced Expression Survival Analysis (AESA)" ; sc:url "http://innovebioinfo.com/Databases/TCGA_Mutation_ExpressionDB/Mutationdb_Search5.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3169, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """A shiny web tool for heatmap generation of genetic expression datasets using R packages. Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a *.CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for interactive expression data visualization that can be easily deployed without any restrictions to any operating system used by any online user""" ; sc:featureList edam:operation_0531, edam:operation_2938, edam:operation_3435, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "AFCMHeatMap" ; sc:url "https://mohammadtarek.shinyapps.io/AFCMHeatMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0208, edam:topic_0625, edam:topic_2830 ; sc:citation , "pubmed:31722398" ; sc:description "The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3431 ; sc:name "The Allele Frequency Net Database (AFND)" ; sc:url "http://www.allelefrequencies.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description """Another Gff Analysis Toolkit (AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.""" ; sc:featureList edam:operation_0362, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AGAT" ; sc:softwareHelp ; sc:softwareVersion "v0.1.0" ; sc:url "https://github.com/NBISweden/AGAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_0736, edam:topic_3912 ; sc:citation , "pubmed:31741225" ; sc:description """A Robot Annotator for Argonaute Proteins. Welcome to AgoNotes home page! AGONOTES is an online service tool to identify Argonaute protein in proteins of all domains of life and annotate the argonaute domains. Users can submit any protein with fasta formation into the input field, or save proteins as a file ended with .faa, .fasta, .fa or .txt and then upload this file""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3096 ; sc:name "AGONOTES" ; sc:url "http://i.uestc.edu.cn/agonotes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3399, edam:topic_3697 ; sc:citation , "pmcid:PMC6727555", "pubmed:31488068" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'ags.sh acn.sh tools', 'AGS', 'ACN' | Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data | Here, we present the ags.sh and acn.sh tools dedicated to the computation of the Average Genome Size (AGS) and 16S rRNA gene Average Copy Number (ACN), respectively. The ags.sh and acn.sh tools compute these metagenomic traits based on the (ultra-fast) annotation of 35 universally distributed single-copy genes in unassembled metagenomic data | Pereira-Flores, E., Glöckner F. O., and Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinformatics. 2019;20(1):453. doi:10.1186/s12859-019-3031-y" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "AGS ACN" ; sc:url "https://github.com/pereiramemo/AGS-and-ACN-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6533287", "pubmed:31123286" ; sc:description "Anti-Inflamamtory Compounds Database for drug discovery." ; sc:featureList edam:operation_2939, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AICD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://956023.ichengyun.net/AICD/index.php" ; biotools:primaryContact "Biaoyan Du", "Jiangyong Gu", "Zaoyuan Kuang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6886511", "pubmed:31694868" ; sc:description """annotation-assisted isoform discovery with high precision. AIDE: annotation-assisted isoform discovery and quantification from RNA-seq data. AIDE is a statistical method which identifies full-length mRNA isoforms from a novel perspective: using the likelihood ratio test to find novel isoforms in a stepwise manner given annotated isoforms, by prioritizing and selectively borrowing information from the annotated isoforms. Please refer to our preprint at Biorxiv for detailed description of our method""" ; sc:featureList edam:operation_0264, edam:operation_0524, edam:operation_3800 ; sc:name "AIDE" ; sc:url "https://github.com/Vivianstats/AIDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC6781298", "pubmed:31590652" ; sc:description """mapping distal regulatory elements using convolutional learning on GPU. BACKGROUND:The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional annotation problem, within the bounds of the hardware constraints and the model's complexity. In our system AIKYATAN, we annotate distal epigenomic regulatory sites, e.g., enhancers. Specifically, we develop a binary classifier that classifies genome sequences as distal regulatory regions or not, given their histone modifications' combinatorial signatures. This problem is challenging because the regulatory regions are distal to the genes, with diverse signatures across classes (e.g., enhancers and insulators) and even within each class (e.g., different enhancer sub-classes)""" ; sc:featureList edam:operation_0417, edam:operation_0438, edam:operation_3443 ; sc:name "AIKYATAN" ; sc:url "https://bitbucket.org/cellsandmachines/aikyatan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:31141141" ; sc:description "Assessing concordance among human, in silico predictions and functional assays on genetic variant classification." ; sc:featureList edam:operation_3225, edam:operation_3431, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AIVAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TopGene/AIvar" ; biotools:primaryContact "Jianfeng Sang", "Jiaqi Luo", "Yujian Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:31112088" ; sc:description "Interactive calculator for Artificial Intelligence (AI) Thyroid Imaging Reporting and Data System (TI-RADS)." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "AI TI-RADS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://deckard.duhs.duke.edu/~ai-ti-rads" ; biotools:primaryContact "Mateusz Buda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_3168 ; sc:citation , "pubmed:31689201" ; sc:description "Jointly integrating VCF-based variants and OWL-based biomedical ontologies in MongoDB." ; sc:featureList edam:operation_3227 ; sc:name "AJIA" ; sc:url "https://github.com/lyotvincent/AJIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:31877126" ; sc:description """Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs. ALACD is to get the drug-lncRNA assoications via bi-level optimization and decoded in R. It includes SVM standard algorithm for argumenting the genes' co-expressed lncRNAs (enhancering-lncRNA-mRNA-coexpression.R), and the optimization procedure for optimal identification of genes aassociated with both lncRNAs and drug to get the drug-lncRNA assoications (optimizating.R). crossvalSVM.R and getperf.R are for SVM cross-validtion and generating the evluation criteria, respectively. It also includes the DEGanalysis.R for differential expression analysis, and survival-analysis.R for surivival analysis of lncRNAs""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3557 ; sc:name "ALACD" ; sc:url "https://github.com/wangyc82/ALACD-v1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3271 ; sc:name "Gene tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_3944 ; sc:citation , "pmcid:PMC5664098", "pubmed:28961181" ; sc:description "Rapid detection of candidate horizontal gene transfers across the tree of life." ; sc:featureList edam:operation_2403, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:name "ALIENNESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://alienness.sophia.inra.fr/cgi/index.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC6686235", "pubmed:31391091" ; sc:description "> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | developing an interactive graph-based visualization for dietary supplement knowledge graph through user-centered design | BACKGROUND:Dietary supplements (DSs) are widely used. However, consumers know little about the safety and efficacy of DSs. There is a growing interest in accessing health information online; however, health information, especially online information on DSs, is scattered with varying levels of quality. In our previous work, we prototyped a web application, ALOHA, with interactive graph-based visualization to facilitate consumers' browsing of the integrated DIetary Supplement Knowledge base (iDISK) curated from scientific resources, following an iterative user-centered design (UCD) process. METHODS:Following UCD principles, we carried out two design iterations to enrich the functionalities of ALOHA and enhance its usability" ; sc:featureList edam:operation_3501 ; sc:name "ALOHA" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31391091" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3474 ; sc:citation , "pmcid:PMC6612814", "pubmed:31510706" ; sc:description "Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype | Deep learning frame for genetic disease | Synthetic data https://drive.google.com/open?id=1Mya0YdT4Hf9wUfbcX6y5mubEFWky6Jg-" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:name "ALS" ; sc:url "https://github.com/byin-cwi/ALS-Deeplearning" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3421, edam:topic_3452 ; sc:citation , "pubmed:31435950" ; sc:description "PURPOSE:The automated segmentation of each lung and trachea in CT scans is commonly taken as a solved problem. Indeed, existing approaches may easily fail in the presence of some abnormalities caused by a disease, trauma, or previous surgery. For robustness, we present ALTIS (implementation is available at http: lids.ic.unicamp.br downloads) - a fast automatic lung and trachea CT-image segmentation method that relies on image features and relative shape- and intensity-based characteristics less affected by most appearance variations of abnormal lungs and trachea. METHODS:ALTIS consists of a sequence of image foresting transforms (IFTs) organized in three main steps: (a) lung-and-trachea extraction, (b) seed estimation inside background, trachea, left lung, and right lung, and (c) their delineation such that each object is defined by an optimum-path forest rooted at its internal seeds" ; sc:name "ALTIS" ; sc:url "http://lids.ic.unicamp.br/downloads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6491633", "pubmed:31068967" ; sc:description "Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis." ; sc:featureList edam:operation_3677, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/xyz5074/AMDA" ; biotools:primaryContact "Xiang Zhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3068, edam:topic_3676 ; sc:citation ; sc:description "A web application for automatic mendelian literature evaluation." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3226 ; sc:name "AMELIE" ; sc:url "http://AMELIE.stanford.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_2330 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pubmed:33821950" ; sc:description """AMICI provides a multi-language (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML or PySB and automatically compiles such models into .mex simulation files (Matlab), C++ executables or Python modules. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood-based output functions. The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but it is also applicable to a wider range of differential equation constrained optimization problems.""" ; sc:featureList edam:operation_2426, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "AMICI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AMICI-dev/AMICI" ; biotools:primaryContact , "Fabian Fröhlich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3366, edam:topic_3572, edam:topic_3697 ; sc:citation , "pmcid:PMC6883642", "pubmed:31779604" ; sc:description """annotation of metabolite origins via networks to integrate microbiome and metabolome data. Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data. It is recommended to install AMON in a conda environment. The environment can be created by first downloading the environment file. A command line tool for predicting the compounds produced by microbes and the host. AMON includes two scripts. extract_ko_genome_from_organism.py takes a KEGG organism flat file and makes a list of KOs present in that file. AMON.py predicts the metabolites that could be produced by the KOs used as input. This can be compared to the KOs present in the host or from some other gene set as well as to as set of KEGG metabolites""" ; sc:featureList edam:operation_2436, edam:operation_3083, edam:operation_3803 ; sc:license "MIT" ; sc:name "AMON" ; sc:url "https://github.com/lozuponelab/AMON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324, edam:topic_3572 ; sc:author ; sc:citation ; sc:contributor ; sc:description "An R Package for Working with Antimicrobial Resistance Data." ; sc:featureList edam:operation_3482 ; sc:license "GPL-2.0" ; sc:name "AMR" ; sc:url "https://msberends.github.io/AMR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0749, edam:topic_2828 ; sc:citation , "pmcid:PMC6688666", "pubmed:31397323" ; sc:description "A GUI-based, open-source system for imaging samples in multi-well plates | Described here are instructions for building and using an inexpensive automated microscope (AMi) that has been specifically designed for viewing and imaging the contents of multi-well plates. The X, Y, Z translation stage is controlled through dedicated software (AMiGUI) that is being made freely available. Movements are controlled by an Arduino-based board running grbl, and the graphical user interface and image acquisition are controlled via a Raspberry Pi microcomputer running Python. Images can be written to the Raspberry Pi or to a remote disk. Plates with multiple sample wells at each row column position are supported, and a script file for automated z-stack depth-of-field enhancement is written along with the images" ; sc:featureList edam:operation_3552 ; sc:name "AMi" ; sc:url "https://doi.org/10.1107/S2053230X19009853" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3474 ; sc:citation , "pubmed:31103790" ; sc:description "Attentive neural cell instance segmentation." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANCIS-Pytorch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/yijingru/ANCIS-Pytorch" ; biotools:primaryContact "Daniel J. Hoeppner", "Dimitris N. Metaxas", "Jingru Yi", "Menglin Jiang", "Pengxiang Wu", "Qiaoying Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3306 ; sc:citation , "pmcid:PMC6547486", "pubmed:31159742" ; sc:description "Atomic angle- and distance-dependent statistical potential for protein structure quality assessment." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANDIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://qbp.hzau.edu.cn/ANDIS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_2330 ; sc:name "Evidence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_2332 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Ontology", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0085, edam:topic_0089, edam:topic_0194, edam:topic_0219, edam:topic_2229, edam:topic_3064, edam:topic_3065, edam:topic_3308, edam:topic_3383, edam:topic_3679 ; sc:citation , , , , ; sc:description """ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). It integrates for each species: i) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; ii) A multispecies genomic browser; iii) a Genomicus gene synteny browser.""" ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_0336, edam:operation_0362, edam:operation_0567, edam:operation_2478, edam:operation_2495, edam:operation_3208, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ANISEED" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:softwareVersion "2019" ; sc:url "https://www.aniseed.fr" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC6694624", "pubmed:31412762" ; sc:description "Additional Neural Matrix Factorization model for computational drug repositioning | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” | This is our implementation for the paper“Additional Neural Matrix Factorization model for Computational drug repositioning. BMC Bioinformatics ” #Author Xin-Xing Yang Southeast University Email:220174323@seu.edu.cn | Open the \"ANMF.py\" file and run it directly. In the Data folder is the test example we provide | We use Keras with Theano as the backend" ; sc:featureList edam:operation_3501 ; sc:name "ANMF" ; sc:url "https://github.com/MortySn/ANMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3474 ; sc:citation , "pmcid:PMC6505829", "pubmed:31067238" ; sc:description "Flux prediction using artificial neural network (ANN) for the upper part of glycolysis." ; sc:featureList edam:operation_3435, edam:operation_3439, edam:operation_3715 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ANN-Glycolysis-Flux-Prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DSIMB/ANN-Glycolysis-Flux-Prediction" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching." ; sc:featureList edam:operation_3627, edam:operation_3755, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ANN-SoLo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bittremieux/ANN-SoLo" ; biotools:primaryContact "Wout Bittremieux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3174 ; sc:citation ; sc:description "Analysis and Performance Assessment of Label-free Proteome Quantification." ; sc:featureList edam:operation_3634, edam:operation_3638, edam:operation_3639 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ANPELA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://idrblab.cn/anpela/" ; biotools:primaryContact "Feng Zhu", "Jianbo Fu", "Jing Tang", "Yunxia Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "AOE (All Of gene Expression) - an integrated index for public gene expression databases." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AOE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://aoe.dbcls.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3343 ; sc:citation , "pmcid:PMC6791490", "pubmed:31487205" ; sc:description "Opportunities and Challenges with in Vitro Testing and Adverse Outcome Pathway Approaches | Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki) | This wiki is hosted by the Society for the Advancement of Adverse Outcome Pathways (SAAOP) and serves as one component of a larger OECD-sponsored AOP Knowledgebase (AOP-KB) effort. The AOP-KB represents the central repository for all AOPs developed as part of the OECD AOP Development Effort by the Extended Advisory Group on Molecular Screening and Toxicogenomics. All AOPs from the AOP Knowledgebase are available via the e.AOP.Portal, which is the primary entry point for the AOP-KB. More information about the AOP-KB efforts, the organizations supporting these efforts, and the other modules of the AOP-KB are available on the About page" ; sc:name "AOP" ; sc:url "https://aopwiki.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3314 ; sc:citation , "pubmed:31453632" ; sc:description "A proposed methodology and inventory of effective tools to link chemicals to adverse outcome pathways | Welcome to the Adverse Outcome Pathway Exploratory Research Assistant (AOPERA)! | AOPERA is designed to identify existing tools that can assist you in the process of linking your chemical to an adverse outcome pathway (AOP). This informational tool is specifically targeted to users with an uncharacterized chemical and limited toxicity information, but can also assist you if you already have information that links your uncharacterized chemical to a molecular initiating event (MIE), a key event (KE), or an adverse outcome (AO), or if you have a characterized chemical" ; sc:featureList edam:operation_3216 ; sc:name "AOPERA" ; sc:url "https://igbb.github.io/AOPERA_HTML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6759716", "pubmed:31620433" ; sc:description """A Sequence-Based Classifier of Antioxidant Proteins Using a Support Vector Machine. AOPs-SVM: Sequence-based Classifier of Antioxidant Proteins Using a Support Vector Machine. Input your sequence:(FASTA format)""" ; sc:featureList edam:operation_0267, edam:operation_0335, edam:operation_0418 ; sc:name "AOPs-SVM" ; sc:url "http://server.malab.cn/AOPs-SVM/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382 ; sc:citation , "pubmed:31684366" ; sc:description "A Python package for adaptive optics modelling and analysis." ; sc:featureList edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "AOtools" ; sc:url "https://github.com/AOtools/aotools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Proteotypic peptide prediction tool by taking the peptide digestibility into consideration." ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_2929 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AP3" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://fugroup.amss.ac.cn/software/AP3/AP3.html" ; biotools:primaryContact "Cheng Chang", "Zhiqiang Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31586392" ; sc:description """decoding alternative polyadenylation across human tissues. The APA atlas refers to " A lternative P oly A denylation atlas in human tissues". Widespread alternative polyadenylation (APA) occurs during cell proliferation and differentiation, exhibits strong tissue specificity. Recent studies have highlighted the important role of APA in transcription regulation. Here we systematically characterize APA profile in 9,475 samples across 53 human tissues from Genotype-Tissue Expression (GTEx) project with two algorisms, and analyzed the association between APA events with traits and mRNA expression. These APA events may uncover novel mechanisms for the transcription regulation, development of tissues and phenotypes""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3196 ; sc:name "APAatlas" ; sc:url "https://hanlab.uth.edu/apa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "APEC (Accessibility Pattern based Epigenomic Clustering) - single cell epigenomic clustering based on accessibility pattern." ; sc:featureList edam:operation_3192, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "APEC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/QuKunLab/APEC" ; biotools:primaryContact "Bin Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3416, edam:topic_3489 ; sc:citation , "pmcid:PMC6822468", "pubmed:31666054" ; sc:description "The APHIRM Toolkit is a set of OHS risk management procedures that target both physical and psychosocial hazards. A participative hazard identification and risk management toolkit for improving the risk management of musculoskeletal disorders." ; sc:name "APHIRM toolkit" ; sc:url "http://www.aphirm.org.au" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:31609085" ; sc:description """An auto-adaptive parentage inference software that tolerates missing parents. Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents. Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions. The main function of this package is the function APIS(), which is the parentage assignment function""" ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "APIS" ; sc:url "https://cran.r-project.org/package=APIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3500 ; sc:citation ; sc:description "APproximate PArallel and stochastic GrAph querying TOol for biological networks." ; sc:featureList edam:operation_0224, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APPAGATO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://profs.scienze.univr.it/~bombieri/APPAGATO/" ; biotools:primaryContact "Federico Busato", "Nicola Bombieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2229, edam:topic_2640, edam:topic_3168 ; sc:citation ; sc:description """Systematic Identification of Novel Cancer Genes through Analysis of Deep shRNA Perturbation Screens. APSiC: Analysis of Perturbation Screens for the Identification of Novel Cancer Genes. A web portal using the Shiny framework in R has been developed to visualize rank profiles of the DRIVE shRNA screen and corresponding gene expression data from TCGA at https://apsic.shinyapps.io/APSiC/""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3501 ; sc:name "APSiC" ; sc:url "https://apsic.shinyapps.io/APSiC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Sequencing-based quantitative mapping of the cellular small RNA landscape. Processing scripts for AQ RNA-seq. This repo contains python processing scripts for AQRNA-seq data analysis. The scripts were used in conjuction with open-source tools/algorithms such as fastxtoolkit and blast as described below""" ; sc:featureList edam:operation_2429, edam:operation_3192, edam:operation_3799 ; sc:name "AQRNA-seq" ; sc:url "https://github.com/dedonlab/aqrnaseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602 ; sc:citation ; sc:description "Tool that facilitates analysis of the behaviour of molecules that penetrate any selected region in a protein." ; sc:featureList edam:operation_0387, edam:operation_2950, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "AQUA-DUCT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://www.aquaduct.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3332, edam:topic_3489 ; sc:citation , "pubmed:31603259" ; sc:description """A database and toolkit for researchers working on environmental mercury geochemistry. AQUA-MER is useful for researchers who want to investigate mercury speciation in defined environments i.e., to which chemical elements and groups it will bind and in what proportions, given an input of concentrations of chemicals.""" ; sc:featureList edam:operation_0224, edam:operation_2476 ; sc:name "AQUA-MER" ; sc:url "https://aquamer.ornl.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3534 ; sc:citation , "pubmed:31141211" ; sc:description "Active and Regulatory site Prediction (AR‐Pred) to identify protein regulatory and functional binding sites." ; sc:featureList edam:operation_2464, edam:operation_3896, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "AR-Pred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sambitmishra0628/AR-PRED_source" ; biotools:primaryContact "Sambit Mishra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6778075", "pubmed:31586139" ; sc:description """accurate, reliable and active histopathological image classification framework with Bayesian deep learning. This repository contains an implementation of ARA-CNN - a Bayesian deep learning model intended for histopathological image classification. ARA stands for Accurate, Reliable and Active. Any method that works on patient data needs to be accurate and reliable, meaning that in addition to very high classification accuracy it should also provide a measure of uncertainty for each prediction. ARA-CNN adheres to these requirements. Moreover, the uncertainty measurement can be used as an acquisition function in active learning, which significantly speeds up the learning process on new histopathological datasets. Uncertainty can also be used to identify mislabelled training images""" ; sc:featureList edam:operation_3283, edam:operation_3443, edam:operation_3553 ; sc:license "MIT" ; sc:name "ARA" ; sc:url "https://github.com/animgoeth/ARA-CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3575, edam:topic_3673 ; sc:citation ; sc:description "comprehensive antibiotic resistance detection from Burkholderia pseudomallei genomes | Comprehensive resistance detection from WGS data | ARDaP - Antimicrobial Resistance Detection and Prediction | ARDaP was written by Derek Sarovich (@DerekSarovich) (University of the Sunshine Coast, Australia) with database construction, code testing and feature design by Danielle Madden (@dmadden9), Eike Steinig (@EikeSteinig) (Australian Institute of Tropical Health and Medicine, Australia) and Erin Price (@Dr_ErinPrice)" ; sc:featureList edam:operation_3196, edam:operation_3431, edam:operation_3482 ; sc:name "ARDaP" ; sc:url "http://github.com/dsarov/ARDaP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:31054477" ; sc:description "Antibiotic Resistance Gene Analyzer." ; sc:featureList edam:operation_0308, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ARGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mem.rcees.ac.cn:8083/" ; biotools:primaryContact "Ye Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3855 ; sc:citation , "pmcid:PMC6643886", "pubmed:31088905" ; sc:description "ARMOR (Automated Reproducible MOdular RNA-seq) Workflow for Preprocessing and Differential Analysis of RNA-seq Data." ; sc:featureList edam:operation_2428, edam:operation_3192, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ARMOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/csoneson/ARMOR" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2269, edam:topic_3318, edam:topic_3421 ; sc:citation , "pmcid:PMC6868867", "pubmed:31752856" ; sc:description """Development and validation of a predictive model for American Society of Anesthesiologists Physical Status. BACKGROUND:The American Society of Anesthesiologists Physical Status (ASA-PS) classification system was developed to categorize the fitness of patients before surgery. Increasingly, the ASA-PS has been applied to other uses including justification of inpatient admission. Our objectives were to develop and cross-validate a statistical model for predicting ASA-PS; and 2) assess the concurrent and predictive validity of the model by assessing associations between model-derived ASA-PS, observed ASA-PS, and a diverse set of 30-day outcomes. METHODS:Using the 2014 American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) Participant Use Data File, we developed and internally cross-validated multinomial regression models to predict ASA-PS using preoperative NSQIP data. Accuracy was assessed with C-Statistics and calibration plots""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3659 ; sc:name "ASA-PS" ; sc:url "https://s-spire-clintools.shinyapps.io/ASA_PS_Estimator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_3305, edam:topic_3390, edam:topic_3474 ; sc:citation , "pubmed:31847188" ; sc:description "The Automated Self-Administered 24-Hour (ASA24) Dietary Assessment Tool is a free web-based tool for collection of automatically coded dietary recalls and/or food records." ; sc:featureList edam:operation_2421, edam:operation_3359, edam:operation_3891 ; sc:name "ASA24" ; sc:url "https://epi.grants.cancer.gov/asa24/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_2545, edam:format_2546, edam:format_2572, edam:format_3590 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3301 ; sc:author ; sc:citation , "pmcid:PMC7077848", "pubmed:32134915" ; sc:description "ASA³P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates." ; sc:featureList edam:operation_0323, edam:operation_0362, edam:operation_0524, edam:operation_3216, edam:operation_3460, edam:operation_3461, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ASA3P" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "https://github.com/oschwengers/asap" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3419, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC6890833", "pubmed:31827430" ; sc:description """A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data. This repository contains the implementation of ASD-DiagNet algorithm""" ; sc:featureList edam:operation_3359, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ASD-DiagNet" ; sc:url "https://github.com/pcdslab/ASD-DiagNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_1317, edam:topic_2640, edam:topic_3360, edam:topic_3382, edam:topic_3400, edam:topic_3500 ; sc:citation , , "pmcid:PMC6917801", "pubmed:31848351", "pubmed:35972352" ; sc:description """Alignment by Simultaneous Harmonization of Layer/Adjacency Registration. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASHLAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://labsyspharm.github.io/ashlar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6709372", "pubmed:31462970" ; sc:description "A Program for Assembling Splice Junctions Analysis | RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and characterizes all splice junctions from high-throughput RNA sequencing (RNA-seq) data. ASJA processes assembled transcripts and chimeric alignments from the STAR aligner and S tringTie assembler. ASJA provides the unique position and normalized expression level of each junction. Annotations and integrative analysis of the junctions enable additional filtering. It is also appropriate for the identification of novel junctions. Implementation and Dependencies" ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_3800 ; sc:name "ASJA" ; sc:url "https://github.com/HuangLab-Fudan/ASJA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_0623, edam:topic_0637, edam:topic_3300 ; sc:citation ; sc:description """classifying functionally diverse protein families using alignment score matrices. the three scripts in this directory comprise ASM-clust, an approach to de novo classify complex protein superfamilies ASM-clust is intended to. ASM-Clust is implemented in bash with two helper scripts in perl, and will take a protein fasta file as the sole input. Fasta files are processed with ASM_clust.sh, which then:""" ; sc:featureList edam:operation_0291, edam:operation_3644 ; sc:name "ASM-Clust" ; sc:url "https://github.com/dspeth/ASM_clust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0610, edam:topic_3500 ; sc:citation , "pmcid:PMC6488576", "pubmed:31036810" ; sc:description "Animal Social Networks Repository - repository of interaction data from published studies of wild, captive, and domesticated animals." ; sc:featureList edam:operation_3562, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ASNR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bansallab.github.io/asnr/" ; biotools:primaryContact "Shweta Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0780, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:31843802" ; sc:description "An online database for exploring over 2,000 Arabidopsis small RNA libraries." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3435 ; sc:name "ASRD" ; sc:url "http://ipf.sustech.edu.cn/pub/asrd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0820, edam:topic_3324, edam:topic_3384 ; sc:citation , "pubmed:31609612" ; sc:description """An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. Welcome to ATB assistant discrimination!. Home Document Datasets Contact Us. Approximately one third of the world's population is infection with Mycobacterium tuberculosis. They are at a high risk progression to active tuberculosis (ATB) during their lifetime, so it is urgent and vital to develop diagnostic methods that can distinguish ATB from latent tuberculosis infection. Please input single sample data in the text form:. Please Cite: Jiangpeng Wu, Jun Bai, Wei Wang, Lili Xi, Pengyi Zhang, Jingfeng Lan, Liansheng Zhang*, Shuyan Li*. ATBdiscrimination: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. J. Chem. Inf. Model., 2019, doi: 10.1021/acs.jcim.9b00678""" ; sc:name "ATBdiscrimination" ; sc:url "http://lishuyan.lzu.edu.cn/ATB/ATBdiscrimination.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_3474 ; sc:citation , "pmcid:PMC6739564", "pubmed:31543820" ; sc:description "Prediction of the Classes of Anatomical Therapeutic Chemicals Using a Network-Based Label Space Partition Method | codes for the drug class prediction paper | Codes and dataset for \"Network-based label space partition for predicting the classes of anatomical therapeutic chemicals\"" ; sc:featureList edam:operation_3502 ; sc:license "GPL-3.0" ; sc:name "ATC-NLSP" ; sc:url "https://github.com/dqwei-lab/ATC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31368481" ; sc:description "And/Or Tree Ensemble for inferring accurate Boolean network topology and dynamics | # Download the development version of ATEN from GitHub: | Note: please note that set.seed() is not suitable for the Package parallel. In order to make the results reproducible, we introduced function clusterSetRNGStream(), more deatails please see the Pacakge parallel | B, the number of And/Or trees in ATEN. This parameter always depends on the size/noise of the data. We suggest you set a higher B for large/noisy networks. If you set a very large B, although it won't affect the results much, but it takes much time.." ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3562 ; sc:license "GPL-2.0" ; sc:name "ATEN" ; sc:url "https://github.com/ningshi/ATEN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3421, edam:topic_3474 ; sc:citation , "pubmed:31468306" ; sc:description "Design a prototype for automated patient diagnosis in wireless sensor networks | It is indeed necessary to design of an elderly support mobile healthcare and monitoring system on wireless sensor network (WSN) for dynamic monitoring. It comes from the need for maintenance of healthcare among patients and elderly people that leads to the demand on change in traditional monitoring approaches among chronic disease patients and alert on acute events. In this paper, we propose a new automated patient diagnosis called automated patient diagnosis (AUPA) using ATmega microcontrollers over environmental sensors. AUPA monitors and aggregates data from patients through network connected over web server and mobile network. The scheme supports variable data management and route establishment. Data transfer is established using adaptive route discovery and management approaches" ; sc:name "AUPA" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31468306" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC6444607", "pubmed:30940067" ; sc:description "Automatic adaptive LASSO for genome-wide prediction." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "AUTALASSO" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/patwa67/AUTALASSO" ; biotools:primaryContact "Patrik Waldmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC7301356", "pubmed:31467448" ; sc:description "Toward automated pathogenic variant evidence retrieval directly from the full-text literature | PURPOSE:Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach. METHODS:Automatic VAriant evidence DAtabase (AVADA) is a novel machine learning tool that uses natural language processing to automatically identify pathogenic genetic variant evidence in full-text primary literature about monogenic disease and convert it to genomic coordinates. RESULTS:AVADA automatically retrieved almost 60% of likely disease-causing variants deposited in the Human Gene Mutation Database (HGMD), a 4.4-fold improvement over the current best open source automated variant extractor" ; sc:featureList edam:operation_2422, edam:operation_3227, edam:operation_3431 ; sc:name "AVADA" ; sc:url "http://bejerano.stanford.edu/AVADA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC6767648", "pubmed:31564248" ; sc:description "Identifying Crohn's disease signal from variome analysis | prediction of individual predisposition to disease x through variation analysis | After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3501 ; sc:name "AVA,Dx" ; sc:url "https://bromberglab.org/project/avadx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_2830 ; sc:citation , "pmcid:PMC6728052", "pubmed:31442220" ; sc:description "An web application that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains." ; sc:featureList edam:operation_3202, edam:operation_3216 ; sc:name "AbLIFT" ; sc:url "http://AbLIFT.weizmann.ac.il" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602 ; sc:citation ; sc:description "AcCNET (Accessory genome Constellation Network) - application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels." ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AcCNET" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/valflanza/accnet" ; biotools:primaryContact "Val F. Lanza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0798, edam:topic_3474, edam:topic_3810 ; sc:citation ; sc:description "AcRanker is a machine learning system developed in python that ranks proteins in a proteome as per their Anti-CRISPR tendencies predicted using sequence features." ; sc:featureList edam:operation_0253, edam:operation_3092, edam:operation_3096 ; sc:name "AcRanker" ; sc:url "https://github.com/amina01/AcRanker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_0821, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC6908459", "pubmed:31832668" ; sc:description "AcetoBase is a dedicated repository and curated database for the analysis of acetogenic bacteria based on the key functional gene formyltetrahydrofolate synthetase (FTHFS/fhs) of Wood-Ljungdahl Pathway for Acetogenesis." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3460 ; sc:name "AcetoBase" ; sc:url "https://acetobase.molbio.slu.se" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_2640, edam:topic_3175 ; sc:citation , "pubmed:23340843" ; sc:description "ActiveDriver is a computational method for identifying post-translational modification (PTM) sites (i.e., active sites) in proteins that are significantly mutated in cancer genomes. ActiveDriver provides signalling-related interpretation of single nucleotide variants (SNVs) identified in cancer genome sequencing." ; sc:featureList edam:operation_2415, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ActiveDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "http://reimandlab.org/software/activedriver/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3315 ; sc:citation ; sc:description "Accurate, Detailed, and Automatic Modelling of Laser-Scanned Trees | AdTree implements the tree reconstruction method described in the following paper: | 3D Trees reconstructed from point clouds" ; sc:featureList edam:operation_3478, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "AdTree" ; sc:url "https://github.com/tudelft3d/adtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "An R package for data Adaptive Robust Estimation in Linear Regression with Application in GTEx Gene Expressions." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "AdaReg" ; sc:url "https://github.com/mwgrassgreen/AdaReg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3407 ; sc:citation , "pubmed:31648087" ; sc:description """A comprehensive bioinformatics knowledge-base for food additive chemicals. A comprehensive food additive database. Supported search options:Text query, Structure, Fragment, Similarity, MCS. Food additives are considered to be the catalysts and headstones of the modern food industry, affecting every step of food production, processing, and storage. Fields searchable in this way are:CAS number,JECFA number,FEMA number,CoE number,Name,InChI,InChI key,INS""" ; sc:featureList edam:operation_2421 ; sc:name "AdditiveChem" ; sc:url "http://www.rxnfinder.org/additivechem/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC6710032", "pubmed:31450236" ; sc:description "An R package for probability distributions and general purpose optimization | Several lifetime distributions have played an important role to fit survival data. However, for some of these models, the computation of maximum likelihood estimators is quite difficult due to presence of flat regions in the search space, among other factors. Several well-known derivative-based optimization tools are unsuitable for obtaining such estimates. To circumvent this problem, we introduce the AdequacyModel computational library version 2.0.0 for the R statistical environment with two major contributions: a general optimization technique based on the Particle Swarm Optimization (PSO) method (with a minor modification of the original algorithm) and a set of statistical measures for assessment of the adequacy of the fitted model" ; sc:name "AdequacyModel" ; sc:url "https://github.com/prdm0/AdequacyModel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description "R-based tool to support topic discovery for systematic and literature reviews." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Adjutant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/amcrisan/Adjutant" ; biotools:primaryContact "Anamaria Crisan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3304 ; sc:description "A Web resource enabling to inspect the neuroanatomy of the fruit fly, equipped with a graphical interface enabling users to color structures on brain sections." ; sc:name "Adult Fruitfly Brain Atlas" ; sc:url "https://fruitfly.tefor.net/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6891986", "pubmed:31801606" ; sc:description """bias adjustment for alignment-free sequence comparison based on sequencing data using neural network regression. Alignment-Free methods Adjusted by Neural Network. Afann (Alignment-Free methods Adjusted by Neural Network) is an alignment-free software that supports fast calculation of different dissimilarity measures including d2star, d2shepp, CVtree, Manhattan, Euclidean and d2. It also adjusts the bias of d2star and d2shepp calculated from sequencing samples""" ; sc:featureList edam:operation_3435, edam:operation_3472, edam:operation_3659 ; sc:name "Afann" ; sc:url "https://github.com/GeniusTang/Afann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3305 ; sc:citation , "pmcid:PMC6529631", "pubmed:31113894" ; sc:description "framework for the analysis of Aspergillus fumigatus isolates based on their microsatellite profile." ; sc:featureList edam:operation_3196, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AfumID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://afumid.shinyapps.io/afumID" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3292, edam:topic_3315, edam:topic_3368 ; sc:citation , "pubmed:31599925" ; sc:description """A mathematical model for the prediction of change in aggregation rate upon point mutation. Protein aggregation is a major unsolved problem in biochemistry with implications for several human diseases (including type II diabetes, corneal dystrophy and most of neurodegenerative disease like Alzheimer's disease, Parkinson's disease, huntington's disease etc.) as well as for biotechnology and bio-material science products (such as human recombinant proteins, monoclonal antibodies, industral enzymes and vaccines). AggreRATE-Pred is a linear regression based tool which can predict the change in aggregation rate upon point mutation for the given protein""" ; sc:featureList edam:operation_0331, edam:operation_2426, edam:operation_3436, edam:operation_3659 ; sc:name "AggreRATE-Pred" ; sc:url "http://www.iitm.ac.in/bioinfo/aggrerate-pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0130, edam:topic_0199 ; sc:citation , "pubmed:30825368" ; sc:description "Package for structure-based prediction of protein aggregation properties and rational design of protein solubility." ; sc:featureList edam:operation_0244, edam:operation_0409, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Aggrescan3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://biocomp.chem.uw.edu.pl/A3D/" ; biotools:primaryContact "Michal Jamroz", "Rafael Zambran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3810 ; sc:description "The RDF Knowledge-based Database for plant molecular networks." ; sc:name "AgroLD" ; sc:url "http://agrold.southgreen.fr/agrold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3810 ; sc:description "Browser for ontologies for agricultural science based on NBCO BioPortal." ; sc:name "AgroPortal" ; sc:url "http://agroportal.lirmm.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6437997", "pubmed:30917859" ; sc:description "Tool introducing a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data." ; sc:featureList edam:operation_2495, edam:operation_3200, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Alevin" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://salmon.readthedocs.io/en/latest/alevin.html#references" ; biotools:primaryContact "A. Srivastava", "Rob Patro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0622, edam:topic_3293, edam:topic_3500 ; sc:citation ; sc:description """AliTV-interactive visualization of whole genome comparisons. Visualize whole genome alignments as linear maps. For the perl part, see AliTV-perl-interface. You do not need to install anything to try the interactive visualization of AliTV. Just navigate to the demo page to try all the features on an example dataset (seven chloroplast genomes). You can also import your own json files on that page. When loading your own data into AliTV it is not transferred to a server but remains on your local machine. Read the documentation at readthedocs""" ; sc:featureList edam:operation_0337, edam:operation_3182, edam:operation_3198, edam:operation_3209 ; sc:license "MIT" ; sc:name "AliTV" ; sc:url "https://github.com/AliTVTeam/AliTV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3360 ; sc:citation , , "pmcid:PMC7141867", "pubmed:31750888" ; sc:description "Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data." ; sc:featureList edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "All-FIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KhiabanianLab/All-FIT" ; biotools:primaryContact "Khiabanian Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3421, edam:topic_3912 ; sc:citation , "pmcid:PMC6694686", "pubmed:31416467" ; sc:description "a tool for personalized and allele-specific sgRNA design | A software tool for personalized and allele-specific CRISPR editing | The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is open-source software that incorporates single nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing one or multiple haplotypes of a sequenced genome, currently supporting eleven Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer" ; sc:featureList edam:operation_0487, edam:operation_3096, edam:operation_3197 ; sc:license "MIT" ; sc:name "AlleleAnalyzer" ; sc:url "https://github.com/keoughkath/AlleleAnalyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6602569", "pubmed:31069394" ; sc:description "Method for the identification and analysis of cancer driver targets." ; sc:featureList edam:operation_0331, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AlloDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mdl.shsmu.edu.cn/ALD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0654, edam:topic_0780, edam:topic_3295 ; sc:citation ; sc:description """Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze 'germline' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze 'somatic' epimutations in the context of plant development and aging""" ; sc:featureList edam:operation_3196, edam:operation_3204, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "AlphaBeta" ; sc:url "http://bioconductor.org/packages/3.10/bioc/html/AlphaBeta.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3454, edam:operation_3557 ; sc:name "AlphaFamImpute" ; sc:url "http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31634848" ; sc:description "A method for sequence discovery with deep reinforcement learning." ; sc:featureList edam:operation_3695 ; sc:name "AlphaSeq" ; sc:url "https://github.com/lynshao/AlphaSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3673 ; sc:citation , "pmcid:PMC6639938", "pubmed:31360240" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'Conclusions:AluMine' | alignment-free method for the discovery of polymorphic Alu element insertions | Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes | git clone https://github.com/bioinfo-ut/AluMine | This GitHub repository stores various scripts required to discover and genotype polymorphic Alu element insertions. There are four different workflows: REF-plus discovery, REF-minus discovery, merging and filtering workflow and genotyping workflow. REF-plus and REF-minus workflows generate text file containing 32-mer pairs that can be subsequently used for genotyping using FastGT package. The scripts are written in PERL and bash | Please cite: Puurand T, Kukuškina V, Pajuste F-D, Remm M. (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA 10:31. [https://doi.org/10.1186/s13100-019-0174-3](doi: https://doi.org/10.1186/s13100-019-0174-3)" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "AluMine" ; sc:url "https://github.com/bioinfo-ut/AluMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6411622", "pubmed:30906832" ; sc:description "R package for copy number variation calling and cancer risk prediction with next-generation sequencing data." ; sc:isAccessibleForFree true ; sc:name "AluScanCNV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hutaobo/AluScanCNV2" ; biotools:primaryContact "Taobo Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3050, edam:topic_3301 ; sc:citation , "pubmed:30910089" ; sc:description "Text mining tool for extracting information about microbial biodiversity in food." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlvisIR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Bibliome/alvisir" ; biotools:primaryContact "Robert Bossy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3365, edam:topic_3489 ; sc:citation ; sc:description """Data architecture and visualization for a large-scale neuroscience collaboration. Database for experimental neuroscience laboratories. Documentation: http://alyx.readthedocs.io. The setup.py script sets up postgres (it creates the database and postgres user), it sets up the alyx/alyx/settings_secret.py file with the postgres database connection information, it creates the Python virtual environment with the dependencies (including django), and it creates all the required SQL tables. Note that the postgres username and password are distinct from Alyx (Django) users and password. There is only one postgres user that is only used locally for maintenance task or by Django""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "Alyx" ; sc:softwareHelp ; sc:url "https://github.com/cortex-lab/alyx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3342 ; sc:citation , "pmcid:PMC6679440", "pubmed:31375105" ; sc:description "Identification of single nucleotide variants using position-specific error estimation in deep sequencing data | Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227 ; sc:name "AmpliSolve" ; sc:url "https://github.com/dkleftogi/AmpliSolve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3316 ; sc:citation , "pmcid:PMC6901069", "pubmed:31816087" ; sc:description """Systematic processing of ribosomal RNA gene amplicon sequencing data. This is the AmpliconTagger home page. AmpliconTagger pipeline - for various types of amplicon sequencing data. By Julien Tremblay - julien.tremblay_at_nrc-cnrc.gc.ca""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3460 ; sc:name "AmpliconTagger" ; sc:url "http://jtremblay.github.io/amplicontagger.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation , "pmcid:PMC6324066", "pubmed:30247677" ; sc:description "This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Paleolithic to roughly Iron Age times, focusing on an Euroasian geographical area. We provide both the mtDNA sequences (in FASTA format), and the metadata for the samples (IDs, dates, geolocation, site, culture, mtDNA haplogroup etc., available to download in a tab-delimited text file)." ; sc:featureList edam:operation_0226 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AmtDB" ; sc:operatingSystem "Linux" ; sc:provider "Institute of Molecular Genetics AS CR" ; sc:softwareHelp ; sc:softwareVersion "v1.007" ; sc:url "https://amtdb.org" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3407 ; sc:citation , "pubmed:31094220" ; sc:description "Collection of amyloidoses and other clinical disorders related to amyloid deposition." ; sc:featureList edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AmyCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.biol.uoa.gr/amyco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489 ; sc:citation , "pmcid:PMC6790968", "pubmed:31608948" ; sc:description "A software designed for the analysis of binding curves with which to evaluate the interactions of biomolecules." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3778 ; sc:license "MIT" ; sc:name "Anabel" ; sc:url "https://skscience.org/anabel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0780, edam:topic_3452 ; sc:citation , "pmcid:PMC6395764", "pubmed:30816109" ; sc:description "Software package for quantitative analysis of plant ER architecture and dynamics." ; sc:featureList edam:operation_3216, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "AnalyzER" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "https://markfricker.org/77-2/software/er-network-analysis/" ; biotools:primaryContact "Dr M.D. Fricker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation , "pubmed:30567711" ; sc:description "Package for trans-cell type prediction of transcription factor binding sites." ; sc:featureList edam:operation_0417, edam:operation_0445, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "Anchor" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GuanLab/Anchor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305 ; sc:citation , "pubmed:31106350" ; sc:description "Estimating the number of people in hidden populations is needed for public health research, yet available methods produce highly variable and uncertain results. The Anchored Multiplier calculator uses a Bayesian framework to synthesize multiple population size estimates to generate a consensus estimate." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Anchored Multiplier Calculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://anchoredmultiplier.ucsf.edu/" ; biotools:primaryContact "Paul D. Wesson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6580570", "pubmed:31208319" ; sc:description "Web-based exploration of numerical chromosomal variation in single cells." ; sc:featureList edam:operation_1812, edam:operation_3233, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Aneuvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dpique.shinyapps.io/aneuvis/" ; biotools:primaryContact "Daniel Pique" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3500, edam:topic_3518, edam:topic_3673 ; sc:citation , "pubmed:31584087" ; sc:description "A comprehensive database with multiple animal reference panels for genotype imputation." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3661 ; sc:name "Animal-ImputeDB" ; sc:url "http://gong_lab.hzau.edu.cn/Animal_ImputeDB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3867 ; sc:name "Trajectory data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3892 ; sc:citation , "pmcid:PMC6482212", "pubmed:31058167" ; sc:description "Anncolvar builds a feed-forward neural network for approximation of a collective variable of a molecular system. Molecular simulations are slow due to fact that a studied system tends to stay in local energy minima. Methods such as metadynamics address this problem by application of artificial forces acting on collective variables. Collective variables are some descriptors of the state of the molecular system. For example, when simulation binding of a ligand to protein it is possible to use their distance as a collective variable and by applying force onto this collective variable you can accelerate binding and unbinding. However, some sophisticated collective variables are difficult to calculate. For this purpose we developed Anncolvar to approximate such collective variables using artificial neural network." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Anncolvar" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "v0.2", "v0.3", "v0.4", "v0.5", "v0.6" ; sc:url "https://github.com/spiwokv/anncolvar" ; biotools:primaryContact "Vojtech Spiwok" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0821 ; sc:citation , "pmcid:PMC6511854", "pubmed:31081040" ; sc:description "Interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data." ; sc:featureList edam:operation_0558, edam:operation_0567, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AnnoTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://annotree.uwaterloo.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0203, edam:topic_0219, edam:topic_3518 ; sc:citation , "pmcid:PMC6824123", "pubmed:31675914" ; sc:description """a Django-based sample, reagent, and experiment metadata tracking system. Annot and information about what Annot is can be found here: https://gitlab.com/biotransistor/annot . This here is just tutorial material for the tutorial described here: http://annot.readthedocs.io/en/latest/man_tutorial.html . Welcome to Annotamentum’s Documentation. — Annot 5 documentation. Welcome to Annotamentum’s Documentation.¶. Django admin based sample, reagent and experiment metadata tracking. Summary: Annot is a web application, developed for biological wetlab experiment layout, sample and reagent logging, so that data is ready for sharing and analysis. On its core annot makes use of the acpipe_anjson library and acjson - assay coordinate json - file format. The use of controlled vocabulary from ontologies for sample and reagent annotation is enforced. Annot’s modular implementation can be adapted to a variety of experimental paradigms""" ; sc:featureList edam:operation_0361, edam:operation_0558, edam:operation_2422, edam:operation_3553 ; sc:name "Annot" ; sc:softwareHelp , ; sc:url "https://gitlab.com/biotransistor/annot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_3053, edam:topic_3168, edam:topic_3175 ; sc:citation , ; sc:description "Integrated tool for annotation and ranking of structural variations." ; sc:featureList edam:operation_0226, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AnnotSV" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://lbgi.fr/AnnotSV/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3315, edam:topic_3474 ; sc:citation "pubmed:31797628" ; sc:description """Generative Adversarial Networks for Anonymizing Private Medical Data. Scikit-learn library package (version 0.18). Keras library package (version 2.0.6)""" ; sc:featureList edam:operation_3283 ; sc:name "AnomiGAN" ; sc:url "https://github.com/hobae/AnomiGAN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description """Automating the design of oligonucleotides for capture/enrichment technologies. AnthOligo is a web-based application developed to automatically generate oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. It automates the complex process of checking multiple applications so that the oligos selected successfully pass certain specific parameter criteria and then get shortlisted as a possible use case for RSE (region specific extraction) processes""" ; sc:featureList edam:operation_0308, edam:operation_0309, edam:operation_0335 ; sc:name "AnthOligo" ; sc:url "http://antholigo.chop.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_0821, edam:topic_3303 ; sc:citation , "pubmed:31661960" ; sc:description """A Web Application for Predicting Antibacterial Activity of Chemical Compounds. Predict Targets for Drawn Structure. Discovery of novel antibacterial agents is the high-priority task because the existing therapy do not provide the necessary safety and sufficient long-term efficacy due to the emerging resistance [1]. The process may be optimized using (Q)SAR methods based on the accumulated experimental data in the field. Nowadays, data on antibacterial action of chemical compounds are well represented in public domain. ChEMBL database [2], for example, contains records on activity of chemical compounds against 1386 bacteria. We extracted bioactivity records on minimum inhibitory concentrations (MICs) of chemical compounds from ChEMBL_24 and prepared them as follows:. antiBac-Pred allows user to predict the fact that chemical compound can inhibit the growth of one or more of 353 bacteria in concentration below the 10000 nM""" ; sc:featureList edam:operation_0417, edam:operation_3860 ; sc:name "AntiBac-Pred" ; sc:url "http://www.way2drug.com/antibac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336 ; sc:citation , "pubmed:31418763" ; sc:description "Web-resource for in silico prediction of anti-HIV/AIDS activity | MOTIVATION:Identification of new molecules promising for treatment of HIV-infection and HIV-associated disorders remains an important task in order to provide safer and more effective therapies. Utilization of prior knowledge by application of computer-aided drug discovery approaches reduces time & financial expenses and increases the chances of positive results in anti-HIV R&D. To provide the scientific community with a tool that allows estimating of potential agents for treatment of HIV-infection and its comorbidities, we have created a freely-available web-resource for prediction of relevant biological activities based on the structural formulae of drug-like molecules" ; sc:name "AntiHIV-Pred" ; sc:url "http://www.way2drug.com/hiv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0623, edam:topic_0749 ; sc:citation , "pmcid:PMC6748703", "pubmed:31529106" ; sc:description "The comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors | Despite significant progress in apicomplexan genome sequencing and genomics, the current list of experimentally validated transcription factors (TFs) in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and transcription-associated co-factors (TcoFs). We have performed a systematic bioinformatics-aided prediction of TFs and TcoFs in apicomplexan genomes and developed the ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TcoFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1292 TFs which includes experimentally validated and computationally predicted TFs, representing 20 distinct families across 14 apicomplexan species" ; sc:featureList edam:operation_2492 ; sc:name "ApicoTFdb" ; sc:url "http://bioinfo.icgeb.res.in/PtDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2830, edam:topic_3297 ; sc:citation , "pmcid:PMC6602511", "pubmed:31069385" ; sc:description "Web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models." ; sc:featureList edam:operation_0272, edam:operation_0394, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AppA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mspc.bii.a-star.edu.sg/minhn/appa.html" ; biotools:primaryContact "Chandra S Verma", "Minh N Nguyen", "Pingyu Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC6817610", "pubmed:31695717" ; sc:description """A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. AppleMDO is a multi-dimensional omics database. Users can submit locus IDs to quickly search for co-expression networks, functional modules, chromatin states and enriched epigenetic marks. For gene lists in search results, gene expression profiling analysis and functional enrichment analysis tools are provided to systematically extract biological themes from gene lists. Additionally, the basic structural and functional annotations of each gene can be obtained, such as gene families, KEGG annotations, GO terms, orthologues in thirteen species and Pfam domains. In addition, some functional support toolkits are also provided, such as GO analysis, blast, motif analysis, ID conversion, sequence extraction and the UCSC genome browser. We hope that AppleMDO will benefit apple research communities and serve as a reference for other fruit trees""" ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3672 ; sc:name "AppleMDO" ; sc:url "http://bioinformatics.cau.edu.cn/AppleMDO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description "Assembly based variant calling package for stLFR and hybrid assembly for linked-reads | Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads | Install through Bioconda (The updated version 1.2.11): | Aquila_stLFR_assembly_based_variants_call --help | (Please ensure channels are properly setup for bioconda before installing) | Aquila_stLFR utilizes Python3 (+ numpy, pysam, and scipy), SAMtools, and minimap2. To be able to execute the above programs by typing their name on the command line, the program executables must be in one of the directories listed in the PATH environment variable (\".bashrc\")" ; sc:featureList edam:operation_0487, edam:operation_0525, edam:operation_3227 ; sc:name "Aquila_stLFR" ; sc:url "https://github.com/maiziex/Aquila_stLFR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3557 ; sc:citation , "pmcid:PMC6446796", "pubmed:30679268" ; sc:description "Proteome-wide structure-based prediction of protein-protein interactions in Arabidopsis." ; sc:featureList edam:operation_0478, edam:operation_2497, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "Arabidopsis Interactions Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bar.utoronto.ca/interactions2/" ; biotools:primaryContact "Nicholas Provart" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931, edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3320, edam:topic_3512 ; sc:description "Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge." ; sc:featureList edam:operation_3199, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Arriba" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/suhrig/arriba/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3673, edam:topic_3676 ; sc:citation , ; sc:description "ArrowSAM is an in-memory Sequence Alignment/Map (SAM) representation which uses Apache Arrow framework (A cross-language development platform for in-memory data) and Plasma (Shared-Memory) Object Store to store and process SAM columnar data in-memory." ; sc:featureList edam:operation_2409, edam:operation_3182 ; sc:name "ArrowSAM" ; sc:url "https://github.com/abs-tudelft/ArrowSAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3068, edam:topic_3673 ; sc:citation , "pmcid:PMC6905352", "pubmed:31825479" ; sc:description """An automation system for a sequencing core facility. StackStorm packs to automate sequencing center operations. Event-driven sequencing center automation. It forms the core of the Arteria automation system, which you can read about on our website or preprint. This pack integrates with a series of bioinformatic micro-services, which can be found at https://github.com/arteria-project. This pack provides re-usable units for automating tasks at a sequencing core facility using the StackStorm event-driven automation platform. Handling sequencing data from massive parallel sequencing can be a daunting task! And while the process of handling sequencing data will share many of its characteristics across centers, the current norm is one center one solution. This creates a situation where reuse is difficult to achieve and the wheel is invented over and over again. This is a situation that we hope can be remedied in the form of the Arteria project""" ; sc:featureList edam:operation_1812, edam:operation_3431, edam:operation_3436 ; sc:license "MIT" ; sc:name "Arteria" ; sc:url "https://arteria-project.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31373612" ; sc:description "Computational validation of fusion gene detection tools without relying on simulated reads | MOTIVATION:Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, real world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. RESULTS:Here we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore can be applied to any RNA-seq dataset without the need for any simulated reads" ; sc:name "ArtiFuse" ; sc:url "https://github.com/TRON-Bioinformatics/ArtiFusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780 ; sc:citation ; sc:description "A complete network for ascorbic acid (including associated pathways) with a list of the identified genetic variants in tomato genome through a methodology that integrates gene annotations and transcriptome. It represents the only available collection, exhaustive and detailed, on ascorbic acid network in tomato." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AsANet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/asanet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3399, edam:topic_3577 ; sc:citation ; sc:description "a web server for allele-specific sgRNA design in precision medicine | Abstract Allele-specific targeting by CRISPR provides a point of entry for personalized gene therapy of dominantly inherited diseases, by selectively disrupting the mutant alleles or disease-causing single nucleotide polymorphisms (SNPs), ideally while leaving normal alleles intact. Despite unprecedented specificity and tremendous therapeutic utility of allele-specific targeting by CRISPR, few bioinformatic tools have been implemented for the allele-specific purpose. We thus developed AsCRISPR ( A llele- s pecific CRISPR ), a web tool to aid the design of guide sequences that can discriminate between alleles. It can process with query sequences harboring single-base or short insertion-deletion (indel) mutations, as well as heterozygous SNPs deposited in the dbSNP database. Multiple CRISPR nucleases and their engineered variants including newly-developed Cas12b and CasX are included for users’ choice" ; sc:featureList edam:operation_3096, edam:operation_3431 ; sc:name "AsCRISPR" ; sc:url "http://www.genemed.tech/ascrispr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0780, edam:topic_3172 ; sc:citation , "pubmed:31111606" ; sc:description "Whole-genome annotation and functional analyses based on RNA expression data." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AspWood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aspwood.popgenie.org/aspwood-v3.0/" ; biotools:primaryContact "Ewa Mellerowicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation ; sc:description "Web analytics tool for the detection of variants from an assembly." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Assemblytics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://assemblytics.com/" ; biotools:primaryContact "Maria Nattestad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:31532487" ; sc:description "Combining evolutionary conservation and proteomics to assess prokaryotic gene predictions | MOTIVATION:A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy. RESULTS:Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer, and Prodigal on genomes spanning the prokaryotic tree of life" ; sc:featureList edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "AssessORF" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/AssessORF.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3512 ; sc:citation , "pmcid:PMC6732846", "pubmed:31523128" ; sc:description "Assembling Exon Using Gene Capture Data | Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3644 ; sc:name "Assexon" ; sc:url "https://github.com/yhadevol/Assexon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_3512 ; sc:citation ; sc:description "A new method for studying the spatial distribution of mRNA in astrocytes | Abstract Cells with a complex shape often use mRNA distribution and local translation to regulate distal functions. These mechanisms have recently been described in astrocytes, the processes of which contact and functionally modulate neighbouring synapses and blood vessels. In order to study the distribution of mRNA in astrocytes, we developed a three-dimensional histological method that combines mRNA detection via in situ hybridization with immunostaining of the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP). Three-dimensional confocal images were analyzed using AstroDot, a custom Image J plug-in developed in-house for the identification and quantification of mRNAs in GFAP-immunolabelled astrocyte somata, large processes and fine processes" ; sc:featureList edam:operation_2495, edam:operation_3629 ; sc:name "AstroDot" ; sc:url "https://doi.org/10.1242/jcs.239756" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3591 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2333 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3474 ; sc:citation ; sc:description "An event-based tool for analyzing and quantifying calcium or glutamate imaging data." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Astrocyte Quantification and Analysis (AQuA)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yu-lab-vt/aqua" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_1775, edam:topic_3168 ; sc:citation , "pubmed:31562099" ; sc:description "Cross-Species Protein Function Prediction with Asynchronous-Random Walk | Description :This page includes the codes of AsyRW which are implemented and tested on Matlab2015b version by Ms. Zhao (YingWen Zhao, Email: ywzhao@email.swu.edu.cn) and free for academic usage. You can run it at your own risk. For other purposes, please contact the corresponding author Dr. Yu (Guoxian Yu, Email: gxyu@swu.edu.cn). If you have any problem on using these codes, just contact Dr. Yu or Ms. Zhao via Email" ; sc:featureList edam:operation_1777 ; sc:name "AsyRW" ; sc:url "http://mlda.swu.edu.cn/codes.php?name=AsyRW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6323297", "pubmed:30624648" ; sc:description "Database of fusion transcripts in Arabidopsis thaliana." ; sc:featureList edam:operation_0224, edam:operation_0495, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "AtFusionDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nipgr.ac.in/AtFusionDB/" ; biotools:primaryContact "Dr. Shailesh Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3169, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc:description """A deep convolutional neural network toolkit for epigenomics. SDK for deep learning based processing of Atac-seq data. AtacWorks is a deep learning toolkit for track denoising and peak calling from low-coverage or low-quality ATAC-Seq data. AtacWorks trains a deep neural network to learn a mapping between noisy (low coverage/low quality) ATAC-Seq data and matching clean (high coverage/high quality) ATAC-Seq data from the same cell type. Once this mapping is learned, the trained model can be applied to improve other noisy ATAC-Seq datasets""" ; sc:featureList edam:operation_0438, edam:operation_3222, edam:operation_3436 ; sc:name "AtacWorks" ; sc:url "https://github.com/clara-genomics/AtacWorks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3300, edam:topic_3697 ; sc:citation , "pubmed:31535335" ; sc:description "a platform of the microbiome of the Atacama Desert | The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information" ; sc:featureList edam:operation_0337 ; sc:name "Atacama Database" ; sc:url "https://www.atacamadb.cl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_2830 ; sc:citation , "pmcid:PMC6658830", "pubmed:31372196" ; sc:description "A Robust Sequence-Based Prediction of Anti-Tubercular Peptides Using Extremely Randomized Trees | Welcome to the Home Page of AtbPpred | AtbPpred is a web based two-layer prediction server for anti-tubercular peptides. In the first layer, we applied a two-step feature selection procedure and identified the optimal feature set individually for nine different feature encodings, whose corresponding models were developed using extremely randomized tree (ERT). In the second-layer, the predicted probability of AtbPs from the above nine models were considered as input features to ERT and developed the final predictor. For a given peptide, AtbPpred predicts its class and probability values" ; sc:name "AtbPpred" ; sc:url "http://thegleelab.org/AtbPpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC5581536", "pubmed:28875074" ; sc:description """specific, sensitive, and speedy trimming of sequencing reads. An NGS read trimming tool that is specific, sensitive, and speedy. (production). Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer (https://github.com/marcelm/cutadapt, DOI:10.14806/ej.17.1.200), with the primary improvements being:""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3219, edam:operation_3472 ; sc:name "Atropos" ; sc:url "https://github.com/jdidion/atropos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:32690972" ; sc:description """Cell type prioritization in single-cell data. Augur is an R package to prioritize cell types involved in the response to an experimental perturbation within high-dimensional single-cell data. The intuition underlying Augur is that cells undergoing a profound response to a given experimental stimulus become more separable, in the space of molecular measurements, than cells that remain unaffected by the stimulus. Augur quantifies this separability by asking how readily the experimental sample labels associated with each cell (e.g., treatment vs. control) can be predicted from molecular measurements alone. This is achieved by training a machine-learning model specific to each cell type, to predict the experimental condition from which each individual cell originated. The accuracy of each cell type-specific classifier is evaluated in cross-validation, providing a quantitative basis for cell type prioritization""" ; sc:featureList edam:operation_2428, edam:operation_3450, edam:operation_3799 ; sc:license "MIT" ; sc:name "Augur" ; sc:url "https://github.com/neurorestore/Augur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2830, edam:topic_3314 ; sc:citation , "pubmed:31545316" ; sc:description "Hierarchical and Programmable One-Pot Oligosaccharide Synthesis | Auto-CHO is a free-to-use software for providing glycan synthetic solutions by one-pot approach | Auto-CHO is an open source (MIT License) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis | Auto-CHO is an open source (MIT Licence) and free-to-use software developed by Academia Sinica for providing solutions of hierarchical one-pot glycan synthesis" ; sc:license "MIT" ; sc:name "Auto-CHO" ; sc:url "https://sites.google.com/view/auto-cho/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6923820", "pubmed:31856727" ; sc:description "Integrate multi-omics data with biological interaction networks using Multi-view Factorization AutoEncoder (MAE)." ; sc:featureList edam:operation_2492, edam:operation_3439, edam:operation_3659 ; sc:license "MIT" ; sc:name "AutoEncoder" ; sc:url "https://github.com/BeautyOfWeb/Multiview-AutoEncoder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_2275 ; sc:citation , "pubmed:31436329" ; sc:description "Improvements on AutoDock Affinity Maps and Associated Software Tools | Precomputed affinity maps are used by AutoDock to efficiently describe rigid biomolecules called receptors in automated docking. These maps greatly speed up the docking process and allow users to experiment with the forcefield. Here, we present AutoGridFR (AGFR): a software tool facilitating the calculation of these maps. We describe a new version of the AutoSite algorithm that improves the description of binding pockets automatically detected on receptors, and an algorithm for adding affinity gradients which help search methods optimize solution using fewer evaluations of the scoring functions. AGFR supports the calculation of maps for various advanced docking techniques such as covalent docking, hydrated docking, and docking with flexible receptor sidechains" ; sc:featureList edam:operation_0482, edam:operation_3216, edam:operation_3899 ; sc:name "AutoGridFR" ; sc:url "http://adfr.scripps.edu/AutoDockFR/agfr.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3168, edam:topic_3320 ; sc:citation ; sc:description "An automatic classification tool for PVS1 interpretation of null variants | Abstract Null variants are prevalent within human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion (PVS1) for pathogenicity in the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG AMP) guidelines. The refinement may improve interpretation consistency, but it also brings hurdles to biocurators because of the complicated workflows and multiple bioinformatics sources required. To address these issues, we developed an automatic classification tool called AutoPVS1 to streamline PVS1 interpretation. We assessed the performance of AutoPVS1 using 56 variants manually curated by ClinGen’s SVI Working Group and achieved an interpretation concordance of 95% (53 56)" ; sc:featureList edam:operation_3225 ; sc:name "AutoPVS1" ; sc:url "http://autopvs1.genetics.bgi.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC7310949", "pubmed:32212641" ; sc:description "Autotuner is a used to identify proper parameters during metabolomics data processing." ; sc:featureList edam:operation_3215 ; sc:license "MIT" ; sc:name "AutoTuner" ; sc:url "https://github.com/crmclean/Autotuner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3361, edam:topic_3678 ; sc:citation ; sc:description "A complete, open-source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Autopilot enables qualitatively greater experimental flexibility by allowing arbitrary numbers of hardware components to be combined in arbitrary experimental designs." ; sc:license "MPL-2.0" ; sc:name "Autopilot" ; sc:url "https://github.com/wehr-lab/autopilot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3518, edam:topic_3810 ; sc:citation , "pmcid:PMC6498479", "pubmed:31046664" ; sc:description "Axiom Analysis Suite advances genotyping data analysis with a single-source software package to enable complete genotyping analysis of all Axiom arrays and copy number analysis on select Axiom arrays." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Axiom Analysis Suite" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://www.thermofisher.com/dk/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/axiom-analysis-suite.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3474 ; sc:citation ; sc:description "An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors | Behavioral segmentation of open field in DeepLabCut, or B-SOID (\"B-side\"), is an unsupervised learning algorithm written in MATLAB that serves to discover behaviors that are not pre-defined by users | B-SOID: Behavioral segmentation of open field in DeepLabCut" ; sc:featureList edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "B-SOiD" ; sc:url "https://github.com/YttriLab/B-SOiD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31554957" ; sc:description "High-throughput detection and tracking of cells and intracellular spots in mother machine experiments | BACteria in Mother Maching Analyzer (BACMMAN) is a software allowing fast and reliable automated image analysis of high-throughput 2D/3D time-series images from mother machine. Mother machine is a very popular microfluidic device allowing investigating biological processes in bacteria at the single-cell level | BACMMAN: BACteria in Mother Machine Analyzer | BACMMAN was designed to analyse data from Mother machine experiments" ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "BACMMAN" ; sc:softwareHelp ; sc:url "https://github.com/jeanollion/bacmman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:31702789" ; sc:description """A Bayesian Hierarchical Model Approach for Gene Set Enrichment Analysis. Bayesian Analysis of Gene Set Enrichment. This repository contains the software package BAGSE designed for gene set enrichment analysis. BAGSE performs both enrichment (hypothesis) testing and quantification. It requires gene-level association evidence (in forms of either z-scores or estimated effect sizes with corresponding standard errors) and pre-defined gene set annotations as input""" ; sc:featureList edam:operation_2436, edam:operation_3658, edam:operation_3659, edam:operation_3799 ; sc:name "BAGSE" ; sc:url "https://github.com/xqwen/bagse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3518 ; sc:citation ; sc:description "Tool that determines if two BAM files came from the same sample or patient by comparing common SNP positions." ; sc:featureList edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "BAM-matcher" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/sacgf/bam-matcher/src/master/" ; biotools:primaryContact "Paul P.S. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6456731", "pubmed:30967541" ; sc:description "Bayesian mixture model for single-cell sequencing (BAMM-SC) method for clustering droplet-based single cell transcriptomic data from population studies." ; sc:featureList edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "BAMM-SC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/lichen-lab/BAMMSC" ; biotools:primaryContact "Li Chen", "Zhe Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "Automated checkup tool for matched sample pairs in NGS cohort." ; sc:featureList edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "BAMixChecker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/heinc1010/BAMixChecker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation ; sc:description "Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty | BANDITS: Bayesian ANalysis of DIfferenTial Splicing | BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts" ; sc:featureList edam:operation_0264, edam:operation_3223, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "BANDITS" ; sc:url "https://bioconductor.org/packages/BANDITS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6683345", "pubmed:31387612" ; sc:description "cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis | Software required for Bart-Seq technology – a cheap technology to analyze (single) cells using forward and reverse barcoding for target genes | Demultiplexing pipeline for BARTSeq | Software required for Bart-Seq – a cost-effective target enrichment technology using forward and reverse barcoding to analyze selected set of genes in single cells and/or bulk RNA/DNA samples | The pipeline can be run via snakemake [-j 4] [-s …/bartseq/Snakefile] [-d …/mydata], where -j specifies the number of threads, and the other parameters default to ./Snakefile and ., respectively" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3200 ; sc:license "GPL-3.0" ; sc:name "BART-Seq" ; sc:url "https://github.com/theislab/bartSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0593, edam:topic_3538 ; sc:citation , "pmcid:PMC6290515", "pubmed:30537929" ; sc:description "Tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins." ; sc:featureList edam:operation_0250, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BASILIScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://basilisc.com/" ; biotools:primaryContact "M. Barski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:31665503" ; sc:description """an expression atlas of blood-based biomarkers in the early diagnosis of cancers. The early detection of cancer holds the key to combat and control the increasing global burden of cancer morbidity and mortality. Blood-based screenings using circulating DNAs (ctDNAs), circulating RNA (ctRNAs), circulating tumor cells (CTCs) and extracellular vesicles (EVs) have shown promising prospects in the early detection of cancer. Recent high-throughput gene expression profiling of blood samples from cancer patients has provided a valuable resource for developing new biomarkers for the early detection of cancer. However, a well-organized online repository for these blood-based high-throughput gene expression data is still not available""" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3435 ; sc:name "BBCancer" ; sc:url "http://bbcancer.renlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation , "pubmed:29695703" ; sc:description "BCIgePred (Linear B cell IgE Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell IgE epitopes." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BCIgEPred" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/brsaran/BCIgePred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3047, edam:topic_3172, edam:topic_3343 ; sc:citation , "pubmed:31593245" ; sc:description """A Customized Biosynthetic Chemical Space Explorer with Multifunctional Objective Function Analysis. Select all Deselect all Toggle select. ( Note:The less enzymes/biotransformations you select, the shorter the runtime is.)""" ; sc:featureList edam:operation_3564 ; sc:name "BCSExplorer" ; sc:url "http://www.rxnfinder.org/bcsexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121, edam:topic_2828 ; sc:citation , "pubmed:31603511" ; sc:description """An Interpretable Sequence-Based Protein Crystallization Predictor. The training set is readily available for ease of use at: https://drive.google.com/file/d/1FRWIcs4xvK2O5OCqhg7u5g_4qm2zJn2d/view and can be used in combination with Step 2 to generate the BCrystal model""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0410, edam:operation_0420, edam:operation_3454 ; sc:name "BCrystal" ; sc:url "https://github.com/raghvendra5688/BCrystal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description "Prediction of Homolytic Bond Dissociation Enthalpies for Organic Molecules at near Chemical Accuracy with Sub-Second Computational Cost." ; sc:featureList edam:operation_0394, edam:operation_0417, edam:operation_3439 ; sc:name "BDE" ; sc:url "https://ml.nrel.gov/bde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168, edam:topic_3343 ; sc:citation , "pubmed:30635653" ; sc:description "Pipeline for processing barcode sequencing data from multiplexed experiments. Applicable to any experiment in which pools of genetically barcoded cells are grown under different conditions, with the resulting barcode DNA isolated from those cells combined into one 2nd-gen sequencing run via the use of indexed PCR primers." ; sc:featureList edam:operation_3192, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "BEAN-counter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/csbio/BEAN-counter" ; biotools:primaryContact "Myers Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3063 ; sc:citation , "pmcid:PMC6602520", "pubmed:31114876" ; sc:description "Tool for Biomedical Entity Expansion, Ranking, and Exploration." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "BEERE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://discovery.informatics.uab.edu/beere/" ; biotools:primaryContact "Jake Y Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3855 ; sc:citation , "pmcid:PMC6301338", "pubmed:30576488" ; sc:description "Environment for exploration and analysis of networks encoded in Biological Expression Language." ; sc:featureList edam:operation_1812, edam:operation_3083, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BEL Commons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bel-commons.scai.fraunhofer.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6691531", "pubmed:31405383" ; sc:description "a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes | BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data | BERMUDA: Batch Effect ReMoval Using Deep Autoencoders" ; sc:featureList edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "BERMUDA" ; sc:url "https://github.com/txWang/BERMUDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC6806563", "pubmed:31647030" ; sc:description "BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs." ; sc:featureList edam:operation_2421, edam:operation_3096, edam:operation_3461 ; sc:license "MIT" ; sc:name "BEable-GPS" ; sc:url "http://www.picb.ac.cn/rnomics/BEable-GPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3523 ; sc:citation , "pmcid:PMC6704634", "pubmed:31438847" ; sc:description "Prediction of regulatory targets of alternative isoforms of the epidermal growth factor receptor in a glioblastoma cell line | Bayesian Gene Selection Criterion (BGSC) approach | The datasets analyzed during the current study are available in the BGSC repository. The raw data files are in the folder rawdata including the Einzelanalyse_nonorm_nobkgd_SF767-1.txt.gz and ControlProbeProfile_SF767-1.txt.gz. The lists of genes predicted for all of the four classes can be found in the folder PredectionResult" ; sc:featureList edam:operation_3223 ; sc:name "BGSC" ; sc:url "https://github.com/GrosseLab/BGSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3125, edam:topic_3534 ; sc:citation , "pubmed:31553288" ; sc:description "Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites | AIM AND OBJECTIVE:The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. MATERIALS AND METHODS:In this study, we aim to relieve the negative impact of class imbalance by boosting multiple granular support vector machines (BGSVM). In BGSVM, each base SVM is trained on a granular training subset consisting of all minority samples and some reasonably selected majority samples" ; sc:featureList edam:operation_0482, edam:operation_2575 ; sc:name "BGSVM-NUC" ; sc:url "http://202.119.84.36:3079/BGSVM-NUC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description "An integrated Web-database for bovine sequencing variations and selective signatures." ; sc:featureList edam:operation_0487, edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3208 ; sc:name "Bovine Genome Variation Database (BGVD)" ; sc:url "http://animal.nwsuaf.edu.cn/code/index.php/BosVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation , "pubmed:30718882" ; sc:description "BItsliced Genomic Signature Index (BIGSI) searches a collection of raw (fastq/bam), contigs or assembly for genes, variant alleles and arbitrary sequence." ; sc:featureList edam:operation_3211, edam:operation_3431, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BIGSI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bigsi.io/" ; biotools:primaryContact "Phelim Bradley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6734328", "pubmed:31500560" ; sc:description "Computationally inferring a gene regulatory network for Mycobacterium abscessus | BINDER (BayesIan gene regulatory Networks inferreD via gene coExpression and compaRative genomics) is a hybrid approach, integrating coexpression and comparative genomics to infer prokaryotic regulons | Code, data and results for 'BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus'" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "BINDER" ; sc:url "http://github.com/ptrcksn/BINDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2269 ; sc:citation , "pubmed:31368479" ; sc:description "Bayesian Estimation of Genetic Regulatory Effects in High-throughput Reporter Assays | Bayesian Inference of Regulatory Differences | Photo by Bill Majoros. Used with permission | [6/16/2018] First version of BIRD released - The first version of BIRD has been released on GitHub at https://github.com/bmajoros/BIRD | [8/23/2018] Experiment design web tool released - A web tool is now available for power and sample size estimation: http://67.159.92.22:8080/ | BIRD (Bayesian Inference of Regulatory Differences) is a software suite for identifying regulatory variants in data from STARR-seq and other massively parallel reporter assays (MPRAs)" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3227 ; sc:name "BIRD" ; sc:url "http://www.geneprediction.org/bird" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology term" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1731 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Ontology concept definition" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Workflow metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3669 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Training material" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3063, edam:topic_3298, edam:topic_3382 ; sc:contributor , , , , , "Chong Zhang" ; sc:description "BIII (BioImage Informatics Index, biii.eu) is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis. Software tools are organized as either a full protocol of analysis (workflow), a specific component to construct a workflow, or a software platform or library (collection). They are described using EDAM-bioimaging. All entries are exposed following FAIR principles and accessible for other usage with ODC-By v1.0 license." ; sc:featureList edam:operation_0224, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BIII (BioImage Informatics Index, biii.eu)" ; sc:provider "NEUBIAS Network of Bioimage Analysts" ; sc:softwareHelp , , , , ; sc:url "https://biii.eu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , , "pubmed:33040404" ; sc:description "Brain tISue segmentatiON pipeline using T1-weighted magnetic resonance images and a random forests classifier | Abstract Introduction Accurate differentiation of brain tissue types from T1-weighted magnetic resonance images (MRIs) is a critical requirement in many neuroscience and clinical applications. Accurate automated tissue segmentation is challenging due to the variabilities in the tissue intensity profiles caused by differences in scanner models and acquisition protocols, in addition to the varying age of the subjects and potential presence of pathology. In this paper, we present BISON (Brain tISue segmentatiON), a new pipeline for tissue segmentation. Methods BISON performs tissue segmentation using a random forests classifier and a set of intensity and location priors obtained based on T1-weighted images" ; sc:name "BISON" ; sc:url "http://nist.mni.mcgill.ca/?p=2148" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3316 ; sc:citation , "pmcid:PMC6923898", "pubmed:31861980" ; sc:description """An efficient and scalable RNAseq analysis workflow with interactive report generation. BISR-RNAseq pipeline submitted for ICIBM-2019. Submission files for the ICIBM2019 conference""" ; sc:featureList edam:operation_0337, edam:operation_3211, edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "BISR-RNAseq" ; sc:url "https://code.bmi.osumc.edu/gadepalli.3/BISR-RNAseq-ICIBM2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_3512 ; sc:citation , , "pubmed:32492257" ; sc:description "A comprehensive tool for the identification and annotation of gene families in genome assemblies | BITACORA: A Bioinformatics tool for gene family annotation | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families in the genomes of non-model organisms | BITACORA: A pipeline for the identification and annotation of gene families in genome assemblies | Genome annotation is a critical bottleneck in genomic research, especially for the rigorous and comprehensive study of gene families" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "BITACORA" ; sc:url "http://www.ub.edu/softevol/bitacora" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:31359834" ; sc:description "A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates | Liu, Y., Chen, X., & Li, G. (2019). A new joint screening method for right-censored time-to-event data with ultra-high dimensional covariates. Statistical methods in medical research, 0962280219864710 | This program implements the BJASS joint screening method for DLBCL data (stored in matlab.mat) described in Section 4 of the paper" ; sc:featureList edam:operation_3501, edam:operation_3557, edam:operation_3659 ; sc:name "BJASS" ; sc:url "https://github.com/yiucla/BJASS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602 ; sc:citation ; sc:description "Basic Local Alignment for Networks Tool." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BLANT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/waynebhayes/BLANT" ; biotools:primaryContact "Wayne B. Hayes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC6365300", "pubmed:30535326" ; sc:description "Package for the next level of genome-wide association studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BLINK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Menggg/BLINK" ; biotools:primaryContact "Meng Huang", "Yao Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6819473", "pubmed:31660858" ; sc:description """Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. A R package to perform genome-wide allele-specific expression. BLMRM: A Bayesian Logistic Regression Model for Genome-Wide Detection of Allele-Specific Gene Expression. This R package provide a powerful and flexiable method (BLMRM) to detect ASE genes and detect ASE variation within genes simultaneously while maintaining low computational requirements""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659 ; sc:name "BLMRM" ; sc:url "https://github.com/JingXieMIZZOU/BLMRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_3306, edam:topic_3314, edam:topic_3315 ; sc:citation , , , , ; sc:description """Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo. Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling. BLUES: Binding modes of Ligands Using Enhanced Sampling. Gill, S; Lim, N. M.; Grinaway, P.; Rustenburg, A. S.; Fass, J.; Ross, G.; Chodera, J. D.; Mobley, D. L. “Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo” - Journal of Physical Chemistry B. February 27, 2018""" ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3899 ; sc:license "MIT" ; sc:name "BLUES" ; sc:url "http://github.com/MobleyLab/blues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2840, edam:topic_3315, edam:topic_3360 ; sc:citation , "pubmed:31833558" ; sc:description "Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays." ; sc:featureList edam:operation_3435, edam:operation_3503, edam:operation_3799 ; sc:name "BMCeasy" ; sc:softwareHelp ; sc:url "http://invitrotox.uni-konstanz.de/BMC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3173 ; sc:citation , , "pmcid:PMC7049249", "pubmed:32097025" ; sc:description "Exploring Integrative Analysis using the BioMedical Evidence Graph | A graph database for merging and analyzing connected data | Discover The BMEG is a graph database that collects data from over 20 different large scale resources and aggregates them into a single coherent resource. Sources include:" ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3501 ; sc:name "BMEG" ; sc:url "http://bmeg.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3518 ; sc:citation ; sc:description "Software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BMRF-Net" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/bmrfcjava/" ; biotools:primaryContact "Jianhua Xuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3315 ; sc:citation , "pubmed:31035759" ; sc:description "Automated BioModel Selection System for gene circuit designs, supports bio-model automated fitting and selection processes, providing a means to efficiently derive the best model candidate that could capture the transient (time-series) dynamic profiles of a bio-part or device using characterization data." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BMSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioeng.nus.edu.sg/engbio/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3810, edam:topic_3855 ; sc:citation , "pubmed:30819822" ; sc:description "R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction." ; sc:featureList edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "BMTME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=BMTME" ; biotools:primaryContact "Francisco Javier Luna-Vazquez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3377, edam:topic_3379 ; sc:citation , "pmcid:PMC6612853", "pubmed:31510658" ; sc:description "Drug repositioning based on bounded nuclear norm regularization | BNNR is a novel computational method, which utilizes Bounded Nuclear Norm Regularization algorithm to identify potential novel indications for known or new drugs. The code in this package implements Bounded Nuclear Norm Regularization (BNNR) for drug repositioning, which is implemented in Matlab2014a" ; sc:name "BNNR" ; sc:url "https://github.com/BioinformaticsCSU/BNNR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602 ; sc:citation , "pmcid:PMC6323831", "pubmed:30616557" ; sc:description "Model to detect and classify relations in text, representing each entity of domain-specific ontologies as the sequence of its ancestors in the ontology. 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It can be applied to help uncover underlying relationships in biological data. Please see our publication for more information: [insert eventual publication here]" ; sc:featureList edam:operation_2497, edam:operation_3501, edam:operation_3562 ; sc:name "BONITA" ; sc:url "https://github.com/thakar-lab/BONITA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc:description "BOOSTER is an alternative method for calculating the branch supports of phylogenetic trees, using the bootstrap. With large trees and moderate phylogenetic signal, BOOSTER tends to be more informative than the standard Felsenstein bootstrap method." ; sc:name "BOOSTER" ; sc:url "https://booster.pasteur.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3305, edam:topic_3324 ; sc:citation , , "pmcid:PMC7363093", "pubmed:32667952" ; sc:description """BORIS: R package for Bayesian Outbreak Reconstruction Inference and Simulation. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates.""" ; sc:featureList edam:operation_0451, edam:operation_3660 ; sc:license "GPL-2.0" ; sc:name "BORIS" ; sc:url "https://github.com/sfires/BORIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3300, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:33216147" ; sc:description "The Brain Predictability toolbox (BPt) is a Python based Machine Learning library designed for working with Neuroimaging data. This library is particularly suited towards working with large neuroimaging datasets, where a large number of subjects with potentially multimodal data are avaliable." ; sc:featureList edam:operation_0224, edam:operation_3359, edam:operation_3659 ; sc:license "MIT" ; sc:name "Brain Predictability toolbox" ; sc:softwareHelp ; sc:url "https://github.com/sahahn/BPt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830 ; sc:citation ; sc:description "Software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing." ; sc:featureList edam:operation_0230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BRAPeS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YosefLab/BRAPeS" ; biotools:primaryContact "Shaked Afik" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3475 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , ; sc:description "Bayesian method for estimating splicing isoform proportions from single cell RNA-seq data." ; sc:featureList edam:operation_2499, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BRIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://brie.readthedocs.io/en/latest/index.html" ; biotools:primaryContact "Yuanhua Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_3518 ; sc:citation , "pmcid:PMC6525352", "pubmed:31101000" ; sc:description "Systems biology web tool for microRNA and omics data integration." ; sc:featureList edam:operation_0463, edam:operation_1812, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cbb.pnnl.gov/brm/" ; biotools:primaryContact , "Katrina M. Waters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2269, edam:topic_2885 ; sc:citation , "pubmed:31742317" ; sc:description "Block Regression Mapping (BRM) is a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Block Regression Mapping (BRM)" ; sc:url "https://github.com/huanglikun/BRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3316, edam:topic_3336 ; sc:citation , "pubmed:31074975" ; sc:description "HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases." ; sc:featureList edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "BRUSELAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bio-hpc.ucam.edu/Bruselas/" ; biotools:primaryContact "Horacio Pérez-Sánchez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6571488", "pubmed:31141611" ; sc:description "Web-based quantitative trait locus linkage analysis and bulk segregant analysis of yeast sequencing data." ; sc:featureList edam:operation_0282, edam:operation_1812, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BSA4Yeast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bsa4yeast.lcsb.uni.lu" ; biotools:primaryContact "Zhi Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access. On this website we provide access to our annotation integration efforts for Bacillus subtilis 168. We integrated the gene annotations from BsubCyc, Rfam, RefSeq, SubtiWiki, and some additional resources (see manuscript for details). Each gene indicates from which reources its annotation stem from, and links to the respective resources are provided where applicable. The integration overall improved the annotation of non-coding RNAs (ncRNA) in B. subtilis. Based on public transcription start sites (TSS) and termination sites (TTS), we created a comprehensive annotation of operons, transcripts, and transcriptional units (TU) for 93% of the genes in the genome. We provide the BSGatlas in form of a UCSC browser hub, a downloadable GFF3 file, and as a light-weight interactive quick browser directly on this side""" ; sc:featureList edam:operation_0362, edam:operation_0435, edam:operation_2422 ; sc:name "BSGatlas" ; sc:url "http://rth.dk/resources/bsgatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3068 ; sc:citation , "pmcid:PMC6805536", "pubmed:31640567" ; sc:description """an R package to facilitate the conduct and reporting of Bayesian network Meta-analyses. Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis”]. BUGSnet: Bayesian inference Using Gibbs Sampling to conduct NETwork meta-analysis. [Home] [Installation] [RStudio Server] [Vignettes]. BUGSnet is a new feature-rich R package to conduct high-quality Bayesian NMA analyses and facilitate compliance with best practice guidelines and reporting. Bayesian analyses are conducted with JAGS (BUGS code is automatically generated by the package based on the user’s inputs.) Outputs are highly customizable and include network plots, tables of network characteristics, data plots, league tables and league heat plots, SUCRA plots, rankograms, forest plots, leverage plots, traceplots and posterior mean deviance comparison plots""" ; sc:featureList edam:operation_2238, edam:operation_3436 ; sc:name "BUGSnet" ; sc:url "https://bugsnetsoftware.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31073610" ; sc:description "> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/pymzml (GITHUB.COM) | > CORRECT NAME OF TOOL COULD ALSO BE 'BUStools suite', 'BUStools suite tools', 'BUS' (bio.tools/bus), 'kallisto' (bio.tools/kallisto) | The Barcode, UMI, Set format and BUStools | Materials associated with the manuscript \"The Barcode, UMI, Set format and BUStools\" by Páll Melsted, Vasilis Ntranos and Lior Pachter | Tools for working with BUS files | R vignettes for processing BUS format single-cell RNA-seq files" ; sc:featureList edam:operation_3200, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "BUStools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://BUStools.github.io/" ; biotools:primaryContact "Lior Pachter", "Páll Melsted", "Vasilis Ntranos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , , "pmcid:PMC7141418", "pubmed:32240182" ; sc:description "A R package for genomic selection and its application to a wheat breeding programme | Abstract We developed an integrated R library called BWGS to enable easy computation of Genomic Estimates of Breeding values (GEBV) for genomic selection. BWGS relies on existing R-libraries, all freely available from CRAN servers. The two main functions enable to run 1) replicated random cross validations within a training set of genotyped and phenotyped lines and 2) GEBV prediction, for a set of genotyped-only lines. Options are available for 1) missing data imputation, 2) markers and training set selection and 3) genomic prediction with 15 different methods, either parametric or semi-parametric. The usefulness and efficiency of BWGS are illustrated using a population of wheat lines from a real breeding programme. Adjusted yield data from historical trials (highly unbalanced design) were used for testing the options of BWGS" ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:name "BWGS" ; sc:url "https://cran.r-project.org/web/packages/BWGS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_2269, edam:topic_3172, edam:topic_3517 ; sc:citation , "pubmed:31593215" ; sc:description """Bayesian weighted Mendelian randomization for causal inference based on summary statistics. BWMR (Bayesian Weighted Mendelian Randomization). Code for the experiments in BWMR. BWMR (Bayesian Weighted Mendelian Randomization), is an efficient statistical method to infer the causality between a risk exposure factor and a trait or disease outcome, based on GWAS summary statistics. 'BWMR' package provides the estimate of causal effect with its standard error and the P-value under the test of causality""" ; sc:featureList edam:operation_3435, edam:operation_3658, edam:operation_3659 ; sc:name "BWMR" ; sc:url "https://github.com/jiazhao97/BWMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Application designed to view the frequency content of recorded brainwave files. It uses wavelets rather than a conventional FFT to analyse the data for maximum flexibility and resolution." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "BWView" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://uazu.net/bwview/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0736, edam:topic_0798, edam:topic_3324 ; sc:citation , "pubmed:31665505" ; sc:description """A database to assess the relevance of bacterial genes during host infection. Bacterial Fitness In infecTion dataBase. Host species Any host species Cow (Bos taurus) Chicken (Gallus gallus) Mouse (Mus musculus) Rabbit (Oryctolagus cuniculus) Pig (Sus scrofa) Pathogen Any pathogen Acinetobacter baumannii ATCC 17978 Campylobacter jejuni subsp. jejuni 81-176 Escherichia coli CFT073 Escherichia coli M12 Escherichia coli O157:H7 str. EDL933 Haemophilus influenzae Rd KW20 Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 KPPR1 Mycobacterium avium subsp. paratuberculosis K10 Porphyromonas gingivalis ATCC 33277 Salmonella enterica Serovar Typhimurium SL1344 Salmonella enterica Serovar Typhimurium ST4 74 Serratia marcescens Strain UMH9 Streptococcus pyogenes M1 5448 Vibrio cholerae O1 biovar El Tor str. N16961 Vibrio parahaemolyticus RIMD 2210633""" ; sc:featureList edam:operation_0418, edam:operation_0435, edam:operation_2421 ; sc:name "BacFITBase" ; sc:url "http://www.tartaglialab.com/bacfitbase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6924045", "pubmed:31856735" ; sc:description "A gene Expression Browser for RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics." ; sc:featureList edam:operation_0524, edam:operation_3196, edam:operation_3258 ; sc:name "BacHBerryEXP" ; sc:url "http://www.bachberryexp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC6501397", "pubmed:31060512" ; sc:description "Pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BacTag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://git.lumc.nl/l.khachatryan/BacTag" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "an R package for integrating, analyzing and visualizing bacterial microscopy data | Abstract High-throughput analyses of single-cell microscopy data is a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP ( Bac terial t oolbox for M icroscopy A nalysis & P lotting), a software package that allows researchers to transform cell segmentation and spot detection data generated by different programs automatically into various plots" ; sc:name "BactMAP" ; sc:url "https://veeninglab.com/bactmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC6562250", "pubmed:31099741" ; sc:description "Tool to identify SNPs among bacterial isolates. BactSNP can detect SNPs and create a simple TSV file with SNP information as well as an alignment FASTA file containing reconstructed pseudo-genomes of the target isolates in a one-step process." ; sc:featureList edam:operation_0484, edam:operation_3216, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BactSNP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/IEkAdN/BactSNP" ; biotools:primaryContact "Takehiko Itoh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:31521251" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'genetic algorithm Bagging-SVM', 'druggable', '93.78' | Accurate prediction of potential druggable proteins based on genetic algorithm and Bagging-SVM ensemble classifier | Discovering and accurately locating drug targets is of great significance for the research and development of new drugs. As a different approach to traditional drug development, the machine learning algorithm is used to predict the drug target by mining the data. Because of its advantages of short time and low cost, it has received more and more attention in recent years. In this paper, we propose a novel method for predicting druggable proteins. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC), dipeptide composition (DPC) and reduced sequence (RS), getting the 591 dimension of drug target dataset" ; sc:name "Bagging-SVM" ; sc:url "https://github.com/QUST-AIBBDRC/GA-Bagging-SVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_3420 ; sc:citation ; sc:description "Robust and window-insensitive mixture model approaches for localizing balancing selection." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BalLeRMix" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.personal.psu.edu/mxd60/ballermix.html" ; biotools:primaryContact "Michael DeGiorgio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3308, edam:topic_3810 ; sc:author ; sc:citation , ; sc:description "A Next-Generation Information System for Musa genomics" ; sc:featureList edam:operation_0338, edam:operation_2403, edam:operation_3208 ; sc:funder "ANR" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Banana Genome Hub" ; sc:softwareHelp , , ; sc:softwareVersion "v2" ; sc:url "https://banana-genome-hub.southgreen.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:30420522" ; sc:description "Software for analysis of nucleic acid structures and trajectories." ; sc:featureList edam:operation_0249, edam:operation_0279, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Barnaba" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/srnas/barnaba" ; biotools:primaryContact "Small RNAs in silico" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325, edam:topic_3673, edam:topic_3676 ; sc:author "Riku Katainen" ; sc:citation , , "pubmed:30323186" ; sc:description "Large-scale discovery tool for potential causative mutations in human coding and noncoding genome." ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BasePlayer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://baseplayer.fi/" ; biotools:primaryContact "Riku Katainen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6343306", "pubmed:30669962" ; sc:description "Integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "BatMeth2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GuoliangLi-HZAU/BatMeth2" ; biotools:primaryContact "Guoliang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3308 ; sc:citation ; sc:description "A hierarchical Bayesian deconvolution model with stochastic search variable selection | Bayesian deconvolution model for intracellular component exploration (BayICE)" ; sc:featureList edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "BayICE" ; sc:url "https://github.com/AshTai/BayICE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_2640 ; sc:citation , "pmcid:PMC6454009", "pubmed:31001324" ; sc:description "Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts." ; sc:featureList edam:operation_0477, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:name "BayesPI-BAR2" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://folk.uio.no/junbaiw/BayesPI-BAR2/" ; biotools:primaryContact "Junbai Wang", "Kirill Batmanov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:citation , "pmcid:PMC6711387", "pubmed:31456910" ; sc:description "Application of Bayesian predictive probability for interim futility analysis in single-arm phase II trial | The tool provides futility interim analysis plan using the Bayesian predictive design in single arm early phase II clinical trial. It also generates statistical plan so clinicians could easily incorporate it into the clinical trial protocol. (reference: Application of Bayesian predictive probability for interim analysis in single-arm early phase II trial. Chen et al; submitted) | devtools::install_github(\"dungtsa/BayesianPredictiveFutility\",force = TRUE) | The shiny applictaion provides futility interim analysis plan for the Bayesian predictive design design in single arm early phase II clinical trial and generates a statistical plan to be easily incorporated into the clinical trial protocol | Simply run the following from an R console:" ; sc:featureList edam:operation_3454 ; sc:name "BayesianPredictiveFutility" ; sc:url "https://github.com/dungtsa/BayesianPredictiveFutility" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pmcid:PMC6472072", "pubmed:30999943" ; sc:description "Method for read extraction and realignment of high-throughput sequencing data." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "Bazam" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ssadedin/bazam" ; biotools:primaryContact "Simon Sadedin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pubmed:31808510" ; sc:description """self-correction of short reads via mapping on de Bruijn graphs. de Bruijn graph cOrrectiOn from graph aLignment. Bcool clone and compile Bcalm2 Bgreat2 Btrim and Ntcard""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3195, edam:operation_3198, edam:operation_3472 ; sc:license "AGPL-3.0" ; sc:name "BCOOL" ; sc:url "http://github.com/Malfoy/BCOOL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0196, edam:topic_3068, edam:topic_3306, edam:topic_3385 ; sc:citation ; sc:description """simple alignment tool for optical systems. BeamDelta is called from the command line using the following format:. A simple GUI interface for python-microscope which allows a compatible camera (see python-microscope compatibility list) to be used for optical alignment purposes. The GUI will display live images, calculate and mark beam centroids and then store an alignment centroid position. Once a position is stored the live centroid then displays a pixel based delta position to allow precise alignment between the marked position and the new beam. We include a suggested parts list in BeamDelta-parts-list.csv which enables the construction of a two camera alignment setup. This hardware configuration will allow both lens alignment and co-aligning two beams and has a small footprint so can relatively easily be mounted within an existing setup""" ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "BeamDelta" ; sc:url "https://github.com/MicronOxford/BeamDelta" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A mine with common bean data from the Legume Info tripal.chado database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "BeanMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/beanmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6787812", "pubmed:31624564" ; sc:description """The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. Bellerophon is a pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies. The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate""" ; sc:featureList edam:operation_0450, edam:operation_0524, edam:operation_2428, edam:operation_3258, edam:operation_3644 ; sc:name "Bellerophon" ; sc:url "https://github.com/JesseKerkvliet/Bellerophon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3517 ; sc:citation , "pmcid:PMC6556976", "pubmed:31056107" ; sc:description "Benchmarking gene and variant prioritization algorithms for GWAS data." ; sc:featureList edam:operation_0488 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Benchmarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RebeccaFine/benchmarker" ; biotools:primaryContact "Joel N. Hirschhorn", "Rebecca Fine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0611 ; sc:citation ; sc:description "Program for reconstruction of amyloid structures containing adjacent β-arches." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "BetaSerpentine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://bioinfo.montp.cnrs.fr/b-serpentine" ; biotools:primaryContact "Andrey V. Kajava", "Stanislav A. Bondarev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure." ; sc:featureList edam:operation_0278, edam:operation_0491, edam:operation_0502 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BiAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/s-will/BiAlign" ; biotools:primaryContact "Ivo L. Hofacker", "Maria Waldl", "Michael T. Wolfinger", "Sebastian Will" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0091, edam:topic_0102, edam:topic_3172, edam:topic_3697 ; sc:citation , "pmcid:PMC6917865", "pubmed:31768033" ; sc:description """A computational framework to explore large-scale biosynthetic diversity. Biosynthetic Genes Similarity Clustering and Prospecting Engine. Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency... BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" ; sc:featureList edam:operation_0303, edam:operation_0496, edam:operation_3432 ; sc:name "BiG-SCAPE" ; sc:url "https://bigscape-corason.secondarymetabolites.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3293, edam:topic_3407 ; sc:citation , "pubmed:31696234" ; sc:description """BiGG Models is a website for browsing gold-standard genome-scale models, multi-strain genome-scale models and expansion across the phylogenetic tree. BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3660 ; sc:name "BiGG Models" ; sc:softwareHelp , ; sc:url "http://bigg.ucsd.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6288881", "pubmed:30526492" ; sc:description "Spark-based highly scalable aligner for bisulfite sequencing data." ; sc:featureList edam:operation_3186, edam:operation_3198, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BiSpark" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bhi-kimlab/BiSpark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description """Bipartite Tight Spectral Clustering (BiTSC) Algorithm for Identifying Conserved Gene Co-clusters in Two Species. Yidan Eden Sun, Heather J. Zhou and Jingyi Jessica Li. $ python3 BiTSC.py ./data/orthologs_data_uniq.csv ./data/dm_timecourse_FPKMs.csv ./data/ce_timecourse_FPKMs.csv 30 10 100 0.8 10 10 ./data/result 0.90 0.95 1.00""" ; sc:featureList edam:operation_0313, edam:operation_2454, edam:operation_3501 ; sc:name "BiTSC" ; sc:url "https://github.com/edensunyidan/BiTSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6876073", "pubmed:31760932" ; sc:description """A novel algorithm based on bi-random walks to identify disease-related lncRNAs. EMAIL: jhu@nwpu.edu.cn, yiqun.gao@nwpu-bioinformatics.com. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. BiWalkLDA.m: BiwalkLDA framework to predict potential lncRNA-disease association. normFun.m: Laplacian normalization""" ; sc:featureList edam:operation_3435 ; sc:license "Other" ; sc:name "BiWalkLDA" ; sc:url "https://github.com/screamer/BiwalkLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2258, edam:topic_3071, edam:topic_3336, edam:topic_3343 ; sc:citation ; sc:description "A Comprehensive Database for Biased GPCR Ligands | A manually curated database of biased GPCR ligands | BiasDB[1] is a manually curated database containing all published biased GPCR ligands. BiasDB currently contains 615 bias cases of signaling bias representing 481 individual ligands for 61 receptors. We provide information about the chemical structure, target receptor, type of bias, assay categories used for bias determination, reference ligand and literature source. BiasDB is a resource for medicinal chemists, pharmacologists and researchers interested in biased GPCR signaling" ; sc:featureList edam:operation_0337, edam:operation_0482 ; sc:isAccessibleForFree true ; sc:name "BiasDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biasdb.drug-design.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31384047" ; sc:description "Reconstructing high-resolution image datasets of cleared and expanded samples | ImgLib2/BDV implementation of Stitching for large datasets | The BigStitcher is a software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes. The software supports images of almost arbitrary size ranging from very small images up to volumes in the range of many terabytes, which are for example produced when acquiring cleared tissue samples with lightsheet microscopy" ; sc:featureList edam:operation_0232, edam:operation_3552, edam:operation_3629 ; sc:license "GPL-2.0" ; sc:name "BigStitcher" ; sc:url "https://imagej.net/BigStitcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601 ; sc:citation , "pmcid:PMC6923822", "pubmed:31856704" ; sc:description """phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. Phosphoglycerylation prediction using evolutionary information of amino acids. Run the file Bigram_PGK.m to obtain statistical measures of the Bigram_PGK predictor. The algorithm runs on the train and test data to obtain the values. Preprocessing_BigramPGK.m file was used to carry out preprocessing for Bigram_PGK predictor, which includes feature extraction for segment size of ±32, filtering, and construction of train and test sets for 10-fold cross-validation. Everytime the algorithm is executed, it will have a slightly different combination of samples for train and test sets. Nevertheless, the performance will be similar""" ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3755 ; sc:name "Bigram-PGK" ; sc:url "https://github.com/abelavit/Bigram-PGK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3174 ; sc:citation ; sc:description "Software for fast genome distance estimation on a typical personal laptop." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BinDash" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zhaoxiaofei/BinDash" ; biotools:primaryContact "XiaoFei Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6717532", "pubmed:31406384" ; sc:description "BindSpace decodes transcription factor binding signals by large-scale sequence embedding | The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data from hundreds of TFs and embedding over 1 M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance, in vitro and in vivo, and can distinguish between signals of closely related TFs" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_3222 ; sc:name "BindSpace" ; sc:url "https://bitbucket.org/hy395/bindspace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3172 ; sc:citation , "pubmed:31642507" ; sc:description """Binner is a Java application for deep annotation of untargeted LC-MS metabolomics data. It takes a numerical feature table obtained from any preprocessing software (e.g. XCMS, MZmine) as input and outputs a file with clusters of closely eluting, highly correlated metabolite features that are most related, along with their pairwise correlations, mass differences, and putative annotations.""" ; sc:featureList edam:operation_3432 ; sc:name "Binner" ; sc:url "http://binner.med.umich.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2258, edam:topic_3372 ; sc:citation ; sc:description "A web-based tool for data and algorithms integration." ; sc:featureList edam:operation_2422 ; sc:name "Bio-DIA" ; sc:url "https://ucrania.imd.ufrn.br/biodia-app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_2258 ; sc:citation ; sc:description "Integration of Structured Biological Data Sources using Biological Expression Language." ; sc:featureList edam:operation_0533, edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Bio2BEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bio2bel" ; biotools:primaryContact "Charles Tapley Hoyt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3303 ; sc:citation , "pubmed:31501885" ; sc:description "A pre-trained biomedical language representation model for biomedical text mining | BioBERT: a pre-trained biomedical language representation model | This repository provides pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details | This repository provides fine-tuning codes of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. Please refer to our paper BioBERT: a pre-trained biomedical language representation model for biomedical text mining for more details. This project is done by DMIS-Lab" ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:name "BioBERT" ; sc:url "https://github.com/naver/biobert-pretrained" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:31119364" ; sc:description "Tool for converting cell lineage data from SIMI BioCell to MaMuT (Fiji)." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BioCell2XML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guleom/BioCell2XML" ; biotools:primaryContact "Carsten Wolff", "Günther Loose", "Markus Pennerstorfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0593, edam:topic_3474 ; sc:citation ; sc:description """Efficient Ensemble Refinement by Reweighting. BioEn - Bayesian Inference Of ENsembles. BioEn integrates a broad range of experimental data to refine ensembles of structures. For a detailed description of the procedures and the algorithm, we refer to [Hummer2015]""" ; sc:featureList edam:operation_0337, edam:operation_2425, edam:operation_2476, edam:operation_3799, edam:operation_3891 ; sc:name "BioEn" ; sc:url "http://github.com/bio-phys/BioEn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:description "Visual designer for biofeedback. Provides environment and tools to create various types of processing tasks." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioEra" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bioera.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Program for real-time biophysical data acquisition, processing, and display." ; sc:isAccessibleForFree false ; sc:license "Other" ; sc:name "BioExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7" ; sc:url "http://www.cyberevolution.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "BioFabric is an open-source network visualization tool." ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_3083 ; sc:name "BioFabric" ; sc:url "https://github.com/wjrl/BioFabric" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pmcid:PMC6324058", "pubmed:30476227" ; sc:description "BioGRID ORCS is an open repository of CRISPR screens compiled through comprehensive curation efforts. Our current index searches more than 49 publications and 58,161 genes to return more than 895 CRISPR screens from 3 major model organism species and 629 cell lines.All screen data are freely provided through our search index and available via download in a wide variety of standardized formats." ; sc:featureList edam:operation_0224, edam:operation_1777, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:name "BioGRID Open Repository of CRISPR Screens (ORCS)" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://orcs.thebiogrid.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128 ; sc:citation , "pmcid:PMC7703768", "pubmed:31710663" ; sc:description "A triple store with RDF graphs obtained from various curated databases, queryable by SPARQL and through the Cytoscape plugin BioGateway App." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "BioGateway" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.0" ; sc:url "https://www.biogateway.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3300, edam:topic_3314, edam:topic_3315, edam:topic_3407 ; sc:citation , "pmcid:PMC6813930", "pubmed:31681022" ; sc:description "BioGears® is a open source, comprehensive human physiology engine that will drive medical education, research, and training technologies." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "BioGears Engine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biogearsengine.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2258, edam:topic_3168, edam:topic_3336 ; sc:citation , "pubmed:31885044" ; sc:description """an R/CRAN package for integrated data analysis pipeline in biomedical study. generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions. The BioMedR package offers an R package for generating various molecular descriptors for chemicals, proteins, DNAs RNAs and their interactions. Calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA/RNA descriptors from nucleotide sequences, and six types of interaction descriptors using three different combining strategies""" ; sc:featureList edam:operation_0262, edam:operation_2929, edam:operation_3894 ; sc:license "GPL-2.0" ; sc:name "BioMedR" ; sc:url "https://CRAN.R-project.org/package=BioMedR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_1975 ; sc:name "Genome map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1860 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "QTL map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3055 ; sc:citation ; sc:description "BioMercator is a software that provides a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis, graphical representation of large datasets. User may import sequence and genome annotations datasets within the software in order to display functional annotation related to QTL and meta-QTL." ; sc:featureList edam:operation_0282, edam:operation_2944 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioMercator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.2.3" ; sc:url "https://sourcesup.renater.fr/projects/biomercator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:30799505" ; sc:description "R package for Biological interpretation of DNA methylation data in the TCGA cancers context." ; sc:featureList edam:operation_0533, edam:operation_3207, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "BioMethyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yuewangpanda/BioMethyl" ; biotools:primaryContact "Chao Cheng", "Yue Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0084, edam:topic_0154, edam:topic_0621 ; sc:citation ; sc:description """A database for metazoan biomineralization proteins. Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and proteins, which give them extra hardness and special attributes. Biomineralization proteins are also known to be associated with multiple bone disorders and are therefore of biomedical importance. Herein we describe BioMine-DB, a biomineralization centric protein database. Availability and implementation: BioMine-DB can be accessed at http: biomine.net, SQL dump, FASTA files and source code are available for download as well at https: github.com bishoyh biomineDB \"""" ; sc:name "BioMine-DB" ; sc:url "http://biomine.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0769, edam:topic_2259, edam:topic_3473 ; sc:citation , ; sc:description """The biological network mining workflow identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language (SBML). The repository contains the scripts for a workflow that identifies frequent structural patterns in biochemical reaction networks encoded in the Systems Biology Markup Language.""" ; sc:featureList edam:operation_0239, edam:operation_2422, edam:operation_3660 ; sc:name "BioNet-Mining" ; sc:url "https://github.com/FabienneL/BioNet-Mining" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:description "Bioinformatics workflows in the functional Nix language" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "BioNix" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://github.com/PapenfussLab/bionix" ; biotools:primaryContact "Mailing list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_2830 ; sc:citation ; sc:description "Python tool for integration of protein structure and sequence-based features." ; sc:featureList edam:operation_0302, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BioStructMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://biostructmap.burnet.edu.au" ; biotools:primaryContact "Andrew Guy", "Dr. Paul Ramsland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070 ; sc:citation , "pubmed:31609384" ; sc:description """A tool for the detection of bistability and multi-steady state behaviour in signaling and gene regulatory networks. https://sites.google.com/view/bioswitch. BioSwitch is a Matlab software tool for detection of multi-steady state behaviour in biochemical reaction networks (specially suited for signaling and gene regulatory networks)""" ; sc:featureList edam:operation_2497, edam:operation_3799 ; sc:name "BioSwitch" ; sc:url "https://sites.google.com/view/bioswitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3489, edam:topic_3500 ; sc:citation ; sc:description "A tool to search and map bioinformatics identifiers and special keywords | A bioinformatics tool to search and map identifiers and special keywords | Biobtree is a bioinformatics tool which process large datasets effectively and provide uniform search and mapping functionalities with web interface and web services for genomic research" ; sc:featureList edam:operation_2422 ; sc:license "BSD-3-Clause" ; sc:name "Biobtree" ; sc:url "https://www.github.com/tamerh/biobtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0218, edam:topic_3473 ; sc:citation , "pmcid:PMC6584971", "pubmed:31249680" ; sc:description "Package that facilitates access to extensive metadata in computable form covering the Bioconductor package ecosystem, facilitating downstream applications such as custom reporting, data and text mining of Bioconductor package text descriptions, graph analytics over package dependencies, and custom search approaches." ; sc:featureList edam:operation_0306, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BiocPkgTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioconductor.org/packages/BiocPkgTools" ; biotools:primaryContact "Sean Davis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3697, edam:topic_3810 ; sc:citation ; sc:description "A software tool for quantitative image analysis of microbial biofilm communities | Software tool for quantitative analysis of microbial biofilm images | Developed by Raimo Hartmann, Hannah Jeckel, Eric Jelli, Knut Drescher | Analysis supports any biofilm type" ; sc:featureList edam:operation_3196, edam:operation_3552, edam:operation_3799 ; sc:name "BiofilmQ" ; sc:url "https://drescherlab.org/data/biofilmQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Suite", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0121, edam:topic_0622, edam:topic_3293 ; sc:author , , ; sc:description "A collection of 40+ well-documented Docker images of commonly used bioinformatics applications and pipelines." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_2403, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "Bioinformatics Docker Images Project" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://pegi3s.github.io/dockerfiles/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0780, edam:topic_3174, edam:topic_3500 ; sc:citation , "pubmed:31599923" ; sc:description """A database for construction and analysis of functional interaction networks for any species with a sequenced genome. Earth BioGenome Project has been officially launched in November 2018 with the goal of decoding genomes of Earth’s biome over a period of 10 years. For every sequenced species, genome annotation will be followed by functional annotation for individual genes and pathways. Network biology can facilitate functional annotations of genomes in the context of collaborative interactions between genes. BiomeNet is a database of scored functional networks enabling network biology for every sequenced genome of Earth’s biome. With protein sequences of target species submitted by users, BiomeNet will transfer co-functional links between orthologous proteins from 95 source networks (comprising ~8 million links), which were previously constructed and validated for 18 species (5 animals, 6 plants, 5 bacteria, and 2 fungi)""" ; sc:featureList edam:operation_0277, edam:operation_0525, edam:operation_3439, edam:operation_3672 ; sc:name "BiomeNet" ; sc:url "http://kobic.re.kr/biomenet/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3746 ; sc:name "Database search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "A Shiny R app for microbiome visualization, built around the \"microbiome\" package." ; sc:featureList edam:operation_0337 ; sc:name "Biome-Shiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9" ; sc:url "https://github.com/BioData-PT/Biome-Shiny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:author "Vid Podpečan" ; sc:citation ; sc:contributor "Hannu Toivonen", "Kristina Gruden", "Nada Lavrač", "Živa Ramšak" ; sc:description """Biomine Explorer is a web application that enables interactive exploration of selected publicly available biological knowledge. It is based on the results of the Biomine project that develops methods for the analysis of public biological data sources (annotated sequences, proteins, domains, and orthology groups, genes and gene expressions, gene and protein interactions, scientific articles, and ontologies). All information is handled as networks and Biomine provides probabilistic network search algorithms to automatically extract the most relevant subnetworks. The most prominent feature of Biomine Explorer is interactive exploration of its large probabilistic networks by using an interactive network visualisation interface. Network editing features and private network repositories are also available as well as a repository of publicly available graphs. All links to Biomine graphs are permanent so they can be used in scientific publications or published on the web.""" ; sc:featureList edam:operation_0337, edam:operation_3927 ; sc:name "Biomine Explorer" ; sc:provider "Jožef Stefan Institute, Department of Knowledge Technologies" ; sc:softwareHelp ; sc:url "https://biomine.ijs.si/" ; biotools:primaryContact "Vid Podpečan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102 ; sc:citation , "pmcid:PMC6755254", "pubmed:31544213" ; sc:description "Demonstrating and facilitating best practices for bioinformatics command-line software | Demonstrating best practices for bioinformatics command line tools | Bionitio provides a template for command line bioinformatics tools in various programming languages | The purpose of the tool is to provide an easy-to-understand working example that is built on best-practice software engineering principles. It can be used as a basis for learning and as a solid foundation for starting new projects. We provide a script called bionitio-boot.sh for starting new projects from bionitio, which saves time and ensures good programming practices are adopted from the beginning (see below for details)" ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "Bionitio" ; sc:url "https://github.com/bionitio-team/bionitio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description """A Fast and Accurate Exhaustive Higher-Order Epistasis Search. BitEpi: An exhaustive search of higher-order epistatic interactions. BitEpi is software for an exhaustive search of higher-order epistatic interactions between genomic variants (SNPs) given a binary phenotype (Case/Control). BitEpi performs an exhaustive search that means it tests all possible combinations of SNPs. For example, the 4-SNP search of 50 SNPs (data.csv) requires to test all "4 out of 50" 4-SNP combinations (230300 4-SNP combinations)""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3196 ; sc:name "BitEpi" ; sc:url "https://github.com/aehrc/BitEpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3855 ; sc:citation , "pmcid:PMC6509165", "pubmed:31073241" ; sc:description "Building machine learning models for predicting the bitter and sweet taste of small molecules." ; sc:featureList edam:operation_3216, edam:operation_3280, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BitterSweet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cosylab.iiitd.edu.in/bittersweet/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3325 ; sc:citation , "pmcid:PMC8256816", "pubmed:34165986" ; sc:description """A Bioconductor and Bioconda package for differential extreme value analysis. A tool for differential extreme-value analysis. Differential extreme outlier analysis using Blacksheep. https://blacksheep.readthedocs.io/en/master/. conda install -c bioconda blksheep. Requirements (automatically taken care of with pip and conda)""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2495, edam:operation_3223, edam:operation_3436 ; sc:license "MIT" ; sc:name "BlackSheep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ruggleslab/blackSheep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_3500 ; sc:citation , , "pmcid:PMC7144090", "pubmed:32071071" ; sc:description "BlobToolKit Viewer is a genome-scale dataset visualistion tool developed as part of the blobtoolkit project to allow browser-based identification and filtering of target and non-target data in genome assemblies." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_1812, edam:operation_3216, edam:operation_3431 ; sc:license "MIT" ; sc:name "BlobToolKit" ; sc:url "https://blobtoolkit.genomehubs.org/view" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31452088" ; sc:description "A cloud-based peptide search engine for MS/MS sequencing." ; sc:featureList edam:operation_2929, edam:operation_3645, edam:operation_3646 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Bolt" ; sc:url "http://www.optystech.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated data warehouse for the Bovine Genome Database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "BovineMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "http://genomes.missouri.edu/bovinemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "A random forest model for inferring higher-order trait interactions associated with complex biological phenotypes." ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:name "BowSaw" ; sc:url "https://github.com/ddimucci/BowSaw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Bio and Neurofeedback Application, designed to work with various Electroencephalography (EEG) amplifiers. It supports Human-Computer-Interface functions and NeuroServer Software Framework to transmit live recordings via Internet or LAN." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BrainBay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.4" ; sc:url "http://www.shifz.org/brainbay/" ; biotools:primaryContact "Chris Veigl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3334, edam:topic_3384 ; sc:citation , , "pmcid:PMC7058611", "pubmed:32139786" ; sc:description "a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets | BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets : available in both Python and Matlab : | Welcome to BrainSpace’s documentation! — BrainSpace 0.1.0 documentation | Free document hosting provided by Read the Docs" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "BrainSpace" ; sc:softwareHelp ; sc:url "http://github.com/MICA-MNI/BrainSpace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3304 ; sc:citation , "pmcid:PMC6838536", "pubmed:31677479" ; sc:description """Systematic Identification of Cell-Cell Communication Networks in the Developing Brain. Since the generation of cell-type specific knockout models, the importance of inter-cellular communication between neural, vascular, and microglial cells during neural development has been increasingly appreciated. However, the extent of communication between these major cell populations remains to be systematically mapped. Here, we describe EMBRACE (embryonic brain cell extraction using FACS), a method to simultaneously isolate neural, mural, endothelial, and microglial cells to more than 94% purity in ∼4 h. Utilizing EMBRACE we isolate, transcriptionally analyze, and build a cell-cell communication map of the developing mouse brain. We identify 1,710 unique ligand-receptor interactions between neural, endothelial, mural, and microglial cells in silico and experimentally confirm the APOE-LDLR, APOE-LRP1, VTN-KDR, and LAMA4-ITGB1 interactions in the E14.5 brain""" ; sc:featureList edam:operation_2429, edam:operation_3446 ; sc:name "Brain Interactome Explorer" ; sc:url "https://mpi-ie.shinyapps.io/braininteractomeexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3399, edam:topic_3408 ; sc:citation ; sc:description "Interactive, web-based tool for testing hypotheses and developing predictive models." ; sc:featureList edam:operation_3359, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Branch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/sulab/biobranch/src/default/" ; biotools:primaryContact "Andrew I. Su", "Benjamin M. Good" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3293, edam:topic_3474 ; sc:citation , , "pubmed:32602888" ; sc:description """combining phylogenetic and network analyses for orthology assignment. orthology assignment using phylogenetic and network analyses. Broccoli, a user-friendly pipeline designed to infer with high precision orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm (label propagation). Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups""" ; sc:featureList edam:operation_0327, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "Broccoli" ; sc:url "https://github.com/rderelle/Broccoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_0749 ; sc:citation , "pmcid:PMC6851476", "pubmed:31365149" ; sc:description "Deep-learning contact-map guided protein structure prediction in CASP13 | contact-guided protein structure prediction | C-I-TASSER (Contact-guided Iterative Threading ASSEmbly Refinement) is a composite approach that uses contact information to enhance the accuracy of protein structure and function predictions | [View example output] [Check previous jobs] [Server statistics] [Help] [Forum]" ; sc:featureList edam:operation_0272, edam:operation_0476, edam:operation_3350 ; sc:name "C-I-TASSER" ; sc:url "https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3292 ; sc:citation ; sc:description "C-InterSecture (Computional tool for InterSpecies analysis of genome architecture) - pipeline to cross-species comparison of Hi-C map. C-InterSecture was designed to liftover contacts between species, compare 3-dimensional organization of defined genomic regions, such as TADs, and analyze statistically individual contact frequencies." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "C-InterSecture" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/NuriddinovMA/C-InterSecture" ; biotools:primaryContact "M. Nuriddinov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:31732979" ; sc:description """Powerful rare variant association testing in a copula-based joint analysis of multiple phenotypes. Copula-Based Joint Analysis of Multiple Phenotypes. We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2019, submitted)""" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:license "GPL-2.0" ; sc:name "C-JAMP" ; sc:url "https://cran.r-project.org/web/packages/CJAMP/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6818389", "pubmed:31465854" ; sc:description "Consensus Cancer Driver Gene Caller | Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C3), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results" ; sc:name "Consensus Cancer driver gene Caller (C3)" ; sc:url "http://drivergene.rwebox.com/c3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc:description "Cross Cell-type Correlation in DNaseI hypersensitivity (C3D) - tool to predict 3D genomic interactions between cis-regulatory elements." ; sc:featureList edam:operation_0441 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "C3D" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/LupienLab/C3D" ; biotools:primaryContact "Tahmid Mehdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3957 ; sc:citation , , "pmcid:PMC6933849", "pubmed:31682301", "pubmed:31733137" ; sc:description "A web application for flexible protein-peptide docking." ; sc:featureList edam:operation_0480, edam:operation_0482, edam:operation_2575, edam:operation_3631, edam:operation_3899 ; sc:name "CABS-dock" ; sc:url "http://biocomp.chem.uw.edu.pl/CABSdock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3474 ; sc:citation , "pubmed:31382223" ; sc:description "An interactive machine-learning approach for sex estimation with the pelvis | The pelvis is consistently regarded as the most sexually dimorphic region of the human skeleton, and methods for sex estimation with the pelvic bones are usually very accurate. In this investigation, population-specific osteometric models for the assessment of sex with the pelvis were designed using a dataset provided by J. A. Serra (1938) that included 256 individuals (131 females and 125 males) from the Coimbra Identified Skeletal Collection and 38 metric variables. The models for sex estimation were operationalized through an online application and decision support system, CADOES. Different classification algorithms generated high accuracy models, ranging from 85% to 92%, with only three variables; and from 85.33% to 97.33%, with all 38 variables" ; sc:name "CADOES" ; sc:url "http://osteomics.com/CADOES/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6718774", "pubmed:31443860" ; sc:description "The semi-automated open-source calcium imaging analyzer | CalciumImagingAnalyser is free software for the extraction and analysis of calcium imaging footage. Designed to be fast, user-friendly and portable, it includes such functions as spatiotemporal and network analysis | CALciumIMagingAnalyser (CALIMA) is a free application for the extraction and analysis of calcium imaging data. Read more below or go straight to the download section" ; sc:featureList edam:operation_3450, edam:operation_3660 ; sc:name "CALIMA" ; sc:url "https://aethelraed.nl/calima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0637 ; sc:citation ; sc:description "Codon Aversion Motifs for Alignment-free Phylogenies." ; sc:featureList edam:operation_0284, edam:operation_2962, edam:operation_2964 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ridgelab/cam" ; biotools:primaryContact "Justin Miller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0610, edam:topic_0625, edam:topic_2269 ; sc:citation , "pmcid:PMC6912896", "pubmed:31871640" ; sc:description """Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation. Community Assembly Model Inference. For full Installation instructions and initial uses, refer to vignette ‘CAMI_Installation.Rmd’. Briefly, you can install the R package using devtools::install_github("ruffleymr/CAMI")""" ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_3659, edam:operation_3695 ; sc:name "Community Assembly Model Inference (CAMI)" ; sc:url "https://github.com/ruffleymr/CAMI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6368784", "pubmed:30736849" ; sc:description "Software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CAMISIM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CAMI-challenge/CAMISIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31838143" ; sc:description """Comparative analysis of metabolic network decomposition based on previous and two new criteria. Metabolic networks can model the behavior of metabolism in the cell. Since analyzing the whole metabolic networks is not easy, network modulation is an important issue to be investigated. Decomposing metabolic networks is a strategy to obtain better insight into metabolic functions. Additionally, decomposing these networks facilitates using computational methods, which are very slow when applied to the original genome-scale network. Several methods have been proposed for decomposing of the metabolic network. Therefore, it is necessary to evaluate these methods by suitable criteria.""" ; sc:featureList edam:operation_0337, edam:operation_3660 ; sc:name "CAMND" ; sc:url "http://eslahchilab.ir/softwares/dmn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC6499410", "pubmed:30304439" ; sc:description "R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis." ; sc:featureList edam:operation_0337, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CANDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://candi.nextgenhealthcare.org/" ; biotools:primaryContact "M. A. Badgeley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2275, edam:topic_3336, edam:topic_3379 ; sc:citation , , "pubmed:32515949" ; sc:description "CANDO is a open-source, unique computational drug discovery, design, and repurposing platform." ; sc:featureList edam:operation_0477, edam:operation_0478, edam:operation_2575 ; sc:license "BSD-3-Clause" ; sc:name "Computational Analysis of Novel Drug Opportunities (CANDO)" ; sc:url "https://github.com/ram-compbio/CANDO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063 ; sc:citation , "pubmed:31714219" ; sc:description """Cross-disease Attention Network for Joint Diabetic Retinopathy and Diabetic Macular Edema Grading. Diabetic retinopathy (DR) and diabetic macular edema (DME) are the leading causes of permanent blindness in the working-age population. Automatic grading of DR and DME helps ophthalmologists design tailored treatments to patients, thus is of vital importance in the clinical practice. However, prior works either grade DR or DME, and ignore the correlation between DR and its complication, i.e., DME. Moreover, the location information, e.g., macula and soft hard exhaust annotations, are widely used as a prior for grading. Such annotations are costly to obtain, hence it is desirable to develop automatic grading methods with only image-level supervision. In this paper, we present a novel cross-disease attention network (CANet) to jointly grade DR and DME by exploring the internal relationship between the diseases with only image-level supervision""" ; sc:featureList edam:operation_3659 ; sc:name "CANet" ; sc:url "https://github.com/xmengli999/CANet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3384, edam:topic_3474, edam:topic_3676 ; sc:citation , , "pmcid:PMC7446154", "pubmed:32831124" ; sc:description "A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3461 ; sc:name "CAPICE" ; sc:url "https://molgenis43.gcc.rug.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2885, edam:topic_3174, edam:topic_3305, edam:topic_3673 ; sc:citation , "pubmed:31665441" ; sc:description "Antibiotic resistome surveillance with the comprehensive antibiotic resistance database." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_3196, edam:operation_3461, edam:operation_3482 ; sc:name "The Comprehensive Antibiotic Resistance Database (CARD)" ; sc:softwareHelp ; sc:url "https://card.mcmaster.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0749, edam:topic_3308, edam:topic_3422 ; sc:citation , "pmcid:PMC6848167", "pubmed:31728204" ; sc:description """contextualizing large signaling networks with CARNIVAL. CAusal Reasoning for Network Identification with integer VALue programming in R. CARNIVAL is an R-package providing a framework to perform causal reasoning to infer a subset of signalling network from transcriptomics data. This work was originally based on Melas et al. with a number improved functionalities comparing to the original version. Transcription factors’ (TFs) activities and pathway scores from gene expressions can be inferred with our in-house tools DoRothEA & PROGENy, respectively. TFs’ activities and signed directed protein-protein interaction networks +/- drug targets and pathway scores are then used to derive a series of linear constraints to generate integer linear programming (ILP) problems. An ILP solver (CPLEX) is subsequently applied to identify the sub-network topology with minimised discrepancies on fitting error and model size""" ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3439 ; sc:name "CARNIVAL" ; sc:url "https://github.com/saezlab/CARNIVAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3292, edam:topic_3315, edam:topic_3452 ; sc:citation , "pmcid:PMC6716611", "pubmed:31474782" ; sc:description "The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation | Colored Abstract Simplicial Complex Library | Colored Abstract Simplicial Complex (CASC) Library | CASC is a modern and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes with user-defined classes stored directly on the simplices at each dimension. This is achieved by taking advantage of the combinatorial nature of simplicial complexes and new C++ code features such as: variadic templates and automatic function return type deduction. Essentially CASC stores the full topology of the complex according to a Hasse diagram. The representation of the topology is decoupled from interactions of user data through the use of metatemplate programming" ; sc:license "LGPL-2.1" ; sc:name "Colored Abstract Simplicial Complex (CASC)" ; sc:url "https://github.com/ctlee/casc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC7141873", "pubmed:31750900" ; sc:description """Distance Measures for Tumor Evolutionary Trees. MOTIVATION:There has been recent increased interest in using algorithmic methods to infer the evolutionary tree underlying the developmental history of a tumor. Quantitative measures that compare such trees are vital to a number of different applications including benchmarking tree inference methods and evaluating common inheritance patterns across patients. However, few appropriate distance measures exist, and those that do have low resolution for differentiating trees or do not fully account for the complex relationship between tree topology and the inheritance of the mutations labeling that topology.""" ; sc:featureList edam:operation_0326, edam:operation_0540, edam:operation_0557, edam:operation_3799 ; sc:name "CASet" ; sc:url "https://bitbucket.org/oesperlab/stereodist/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0209, edam:topic_0749 ; sc:citation , "pmcid:PMC6910964", "pubmed:31836830" ; sc:description """A robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome. Cosolvent Analysis Toolkit (CAT). Authors: Frances Sabanes Zariquiey, Joao V. de Souza, Agnieszka K. Bronowska.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_2492, edam:operation_2575, edam:operation_3891 ; sc:license "LGPL-3.0" ; sc:name "Cosolvent Analysis Toolkit (CAT)" ; sc:url "https://github.com/ammvitor/CAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:author "Cheng-Kai Shiau" ; sc:citation ; sc:description "Tool for generating comprehensive annotations of alternative transcript events." ; sc:featureList edam:operation_0264, edam:operation_1812, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CATANA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/shiauck/CATANA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0102 ; sc:citation , "pubmed:31790141" ; sc:description """A novel threading algorithm with predicted contacts. CATHER is a threading algorithm for template-based modeling. It uses an iterative algorithm to combine both sequential information and contact maps to improve the threading performance. For a submitted query protein sequence, the returned results include the predicted structure""" ; sc:featureList edam:operation_0272, edam:operation_0302, edam:operation_0474 ; sc:name "CATHER" ; sc:url "http://yanglab.nankai.edu.cn/CATHER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2830, edam:topic_3170 ; sc:citation , , "pubmed:32399561" ; sc:description "An ultrasensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data | An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data | HomePage: http://bioinfo.life.hust.edu.cn/CATT | An ultra-sensitive and accurate tool for characterizing T cell receptor sequence in bulk and single cell TCR-Seq and RNA-Seq data. The tool can be found in: | CATT(CharActerzing TCR repertoires) is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq, scRNA-seq and any TCR contained sequencing data)" ; sc:featureList edam:operation_3192 ; sc:name "CATT" ; sc:url "http://bioinfo.life.hust.edu.cn/CATT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31691819" ; sc:description """A database for disease/trait causal variants identified using summary statistics of genome-wide association studies. A GWAS fine-mapping pipeline used in CAUSALdb. CAUSALdb integrates large numbers of GWAS summary statistics and identifies credible sets of causality by uniformly processed fine-mapping""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3791 ; sc:name "CAUSALdb" ; sc:url "http://mulinlab.org/causaldb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6534331", "pubmed:31060045" ; sc:description "Spiking Neural Network of cortico-basal ganglia-thalamus (CBGT) pathways." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CBGT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CoAxLab/CBGT" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6907873", "pubmed:31790386" ; sc:description "Controllability based Biological Network Analysis (CBNA) is a tool to uncover coding and non-coding cancer drivers (i.e. miRNA cancer drivers)." ; sc:featureList edam:operation_0463, edam:operation_3202, edam:operation_3792 ; sc:name "CBNA" ; sc:url "https://github.com/pvvhoang/CancerDriver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6737777", "pubmed:31551994" ; sc:description "Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding | A pipeline for completing circular bacterial genomes using a sampling strategy | Since CCBGpipe implements many analytical tools, we strongly recommend you to run it with Docker. Alternatively, you can install all dependencies as listed in the Installation section | This pipeline is designed to complete circular bacterial genomes using a sampling strategy from a sinlge MinION with barcoding" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "CCBGpipe" ; sc:url "https://github.com/jade-nhri/CCBGpipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3315, edam:topic_3382 ; sc:citation , "pubmed:31870986" ; sc:description "CCC-Tool (Charting Continuous Colormaps) is a tool for creating, editing, and analyzing such application-specific colormaps." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3435 ; sc:name "CCC-Tool" ; sc:url "https://ccctool.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3518 ; sc:citation , , "pubmed:32510568" ; sc:description """an accurate method and web server for cancer cell line authentication using gene expression profiles. Abstract Cancer cell lines (CCLs) as important model systems play critical roles in cancer researches. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphisms, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication, http: bioinfo.life.hust.edu.cn web CCLA ) to authenticate 1,291 human CCLs of 28 tissues using gene expression profiles. CCLA curated CCL-specific gene signatures and employed machine learning methods to measure overall similarities and distances between the query sample and each reference CCL""" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3227 ; sc:name "Cancer Cell Line Authentication (CCLA)" ; sc:url "http://bioinfo.life.hust.edu.cn/web/CCLA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3697 ; sc:citation , "pmcid:PMC6719681", "pubmed:31482150" ; sc:description "Software-as-a-service approach for fully-automated microbiome profiling | Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https: ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface" ; sc:name "CCMP" ; sc:url "https://ccmp.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation ; sc:description "Pipeline to classify organisms in metagenomes or metatranscriptomes accurately." ; sc:featureList edam:operation_3460, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CCMetagen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cge.cbs.dtu.dk/services/ccmetagen/" ; biotools:primaryContact "Vanessa R. Marcelino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3169 ; sc:citation ; sc:description """Clusters of Colocalized Sequences. Abstract 0.1 Motivation Potential transcription factor (TF) complexes may be identified by testing whether the binding sequences of individual TF proteins form clusters with each other. These clusters may also indicate TF inhibition due to competitive occupancy of enhancer regions. Genome annotation data containing the coordinates of enhancer sequences is highly accessible via position-weight matrix tools. 0.2 Results An algorithm called CCSeq (Clusters of Colocalized Sequences) was developed for identifying clusters of sequences along a one-dimensional line, such as a chromosome, given genome annotation files and a cut-off distance as inputs.""" ; sc:featureList edam:operation_0291, edam:operation_0362, edam:operation_3695 ; sc:name "CCSeq" ; sc:url "https://cran.r-project.org/web/packages/colocalized/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0637 ; sc:citation , "pmcid:PMC6726630", "pubmed:31485005" ; sc:description "An Online Package for Evaluation of Complex Detection Methods | Complex Detection Analyzer Package (CADP) helps you to execute protein complex detection methods and compare their results in a quick and compact ways. It computes a wide range of evaluation criteria and visualize the comparison of methods in tables and multiplots. It assists you in filtering detected clusters by providing a protein name (STRING ID) as a query and by setting constraint on maximum and minimum number of proteins in detected clusters. The list of methods for detecting protein complexes is as follows: | You may look for the values of evaluation criteria for a specific threshold. This can also be done by CDAP. The PPI datasets are: | You can also upload the result of any other method for evaluating its results. The valid format for uploaded file is described here | The list of evaluation criteria is as follows:" ; sc:featureList edam:operation_2492, edam:operation_3501 ; sc:name "CDAP" ; sc:url "http://www.eslahchilab.ir/softwares/cdap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3379, edam:topic_3401 ; sc:citation , , "pubmed:31077078", "pubmed:31087257" ; sc:description "Common Data Elements for Unruptured Intracranial Aneurysm and Subarachnoid Hemorrhage Clinical Research." ; sc:featureList edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cde.nlm.nih.gov/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC6693031", "pubmed:31411687" ; sc:description "Clinical Drug Experience Knowledgebase | Washington University in St. Louis | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | The Clinical Drug Experience Knowledgebase (CDEK) is a platform intended to explore every active pharmaceutical ingredient (API) with evidence of clinical testing | YOU AGREE THAT THE INFORMATION PROVIDED ON THIS WEBSITE IS PROVIDED “AS IS”, WITHOUT ANY WARRANTY OF ANY KIND, EXPRESSED OR IMPLIED, INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR NON-INFRINGEMENT OF ANY THIRD-PARTY PATENT, COPYRIGHT, OR ANY OTHER THIRD-PARTY RIGHT | Build your own query by selecting various table columns and a filtration predicate; then press the to launch the query" ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:name "Clinical Drug Experience Knowledgebase (CDEK)" ; sc:softwareHelp ; sc:url "http://cdek.wustl.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3053 ; sc:citation , "pubmed:31769930" ; sc:description """Modeling multilocus selection in an individual-based, spatially-explicit landscape genetics framework. An individual-based, eco-evolutionary model for spatially-explicit simulation of population viability in landscape demogenetics. Welcome to the CDMetaPOP v1.0 release! This release includes installation instructions, version notes, some examples, and technical documentation. Baseline Requirements. CDMetaPOP requires the Python2.7.x interpreter, NumPy package, and SciPy package. Remember that Python modules usually require particular Python interpreters, so be sure the version ID for any external Python module or package (e.g. NumPy or others) matches the version of your Python interpreter (normally v2.7.x). aTo avoid Python installation errors, we highly recommend installing Python from any number of the freely available bundlers, e.g., Canopy, ActiveState, Anaconda.""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3659 ; sc:name "CDMetaPOP" ; sc:url "https://github.com/ComputationalEcologyLab/CDMetaPOP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6449719", "pubmed:30759968" ; sc:description "Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CDRgator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cdrgator.ewha.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269, edam:topic_3170, edam:topic_3300 ; sc:citation , , "pmcid:PMC6907860", "pubmed:31790389" ; sc:description """A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data. CDSeq MATLAB code. CDSeq is a novel computational complete deconvolution method for dissecting tissue heterogeneity. CDSeq: A complete deconvolution method for dissecting tissue heterogeneity. Added data-dilution option to speed up the algorithm. We provided explaination in the manuscript which you can find on bioRxiv. Check out the demo.m in CDSeq_012 for details""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "CDSeq" ; sc:url "https://github.com/kkang7/CDSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3174, edam:topic_3810 ; sc:citation , "pmcid:PMC6751219", "pubmed:31592221" ; sc:description "A portal for geographic reference data for the Amazon." ; sc:featureList edam:operation_2428 ; sc:name "CEBA geoportail" ; sc:url "http://vmcebagn-dev.ird.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3325, edam:topic_3376 ; sc:citation "pubmed:20841733" ; sc:description "Collection of continuous and complete records of patients with rare diseases, and their follow-up through a web-based Information System." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "CEMARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cemara.org/presentation/show.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC6792302", "pubmed:31649733" ; sc:description """A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. There are two comparison strategies for the NMI and ARI depending on the availability of true labels of patients. If you upload an empirical pre-determination of subtypes for samples by experts or clinicians based on clinical phenotypes, images or experience, CEPICS will take it as gold standard to compare. If you don’t have any subtype information, CEPICS will calculate NMI and ARI between the results of every two methods for each k, and then calculated the average NMI and ARI for each method at each k""" ; sc:featureList edam:operation_0531, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "CEPICS" ; sc:url "https://github.com/GaoLabXDU/CEPICS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC6364436", "pubmed:30727967" ; sc:description "Software pipeline and associated machine-learning framework for identifying regulatory single nucleotide polymorphisms (rSNPs) in the noncoding genome for post-analysis of genetic regions identified in genome-wide association studies (GWAS)." ; sc:featureList edam:operation_0484, edam:operation_2495, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CERENKOV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v0.1-alpha" ; sc:url "https://github.com/ramseylab/cerenkov" ; biotools:primaryContact "Stephen Ramsey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3444 ; sc:citation , ; sc:description "Library of model implementations for sharing deep-learning image segmentation and outcomes models | Deep learning-based auto-segmentation of swallowing and chewing structures in CT | Matlab based platform for Radiological Research | CERR (pronounced 'sir'), stands for Computational Environment for Radiological Research. CERR is MATLAB based software platform for developing and sharing research results using radiation therapy treatment planning and imaging informatics. CERR has a wide variety of dose, imaging, and structure analysis and comparison tools. CERR is open-source and GNU GPL copyrighted" ; sc:featureList edam:operation_3096 ; sc:license "LGPL-2.1" ; sc:name "Computational Environment for Radiological Research (CERR)" ; sc:softwareHelp ; sc:url "https://www.github.com/cerr/CERR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0625, edam:topic_3308 ; sc:citation , "pmcid:PMC6821211", "pubmed:31552418" ; sc:description "Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction | Transcriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature-viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time" ; sc:featureList edam:operation_3501, edam:operation_3642, edam:operation_3891 ; sc:name "CEVIChE" ; sc:url "https://saezlab.shinyapps.io/ceviche/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_0130, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC6818797", "pubmed:31622328" ; sc:description """Detecting distant-homology protein structures by aligning deep neural-network based contact maps. fold recorgnition by eigen-decomposition of contact map. CEthreader (Contact Eigenvector-based threader) is a new threading algorithm that combines contact-map with profile-based alignments for protein fold recognition.""" ; sc:featureList edam:operation_0272, edam:operation_0300, edam:operation_0303, edam:operation_0476, edam:operation_0477 ; sc:name "CEthreader" ; sc:url "https://zhanglab.ccmb.med.umich.edu/CEthreader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation , "pubmed:31518497" ; sc:description "A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals | Chassis selection from 70 candidate orgainisms for more than 6,000 target molecules production | CF-Targrter: We present CF-Targeter to solve several biological problems, including host organism selection, biosynthetic pathway design and quantitative evaluations of pathways. It is very useful for those who plan to biosynthesize a target molecule but do not know which host organism should be selected, what the heterologous pathway is or what maximum theoretical yields could be achieved | Tips: please choose a search type" ; sc:featureList edam:operation_3799, edam:operation_3803 ; sc:name "CF-targeter" ; sc:url "http://www.rxnfinder.org/cf_targeter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """A statistical method for identifying consistently important features across samples. (software for the manuscript "A statistical method for identifying consistently important features across conditions"). CFD itself is implemented in Go (source code is in the go/src/ directory), and figures for the manuscript were generated in Python, using the produce_manuscript_figures.py code""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3630 ; sc:name "Conserved Feature Discovery (CFD)" ; sc:url "https://github.com/Kingsford-Group/cfd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3173, edam:topic_3176 ; sc:citation , "pmcid:PMC6943076", "pubmed:31428785" ; sc:description "A cell-free epigenome atlas in human diseases | Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species | Welcome to CFEA (Cell-Free Epigenome Atlas) | The cell-free DNA (cfDNA) was shown to be a powerful tool for the noninvasive diagnosis of various diseases and accumulating evidence suggests large-scale epigenetic alterations such as cfDNA methylation (5mC), cfDNA hydroxymethylation (5hmC) and cfDNA nucleosome positioning (NP) can sensitively detect and classify cancers. The CFEA (Cell-Free Epigenome Atlas) data portal is the first database dedicated to human cell-free epigenomes" ; sc:featureList edam:operation_0432, edam:operation_2428, edam:operation_3192 ; sc:name "Cell-Free Epigenome Atlas (CFEA)" ; sc:url "http://www.bio-data.cn/CFEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6612823", "pubmed:31510662" ; sc:description "Rotation equivariant and invariant neural networks for microscopy image analysis | Conic Convolution and DFT Network (CFNet) combines a novel rotation equivariant convolution scheme, called conic convolution, and the DFT to aid networks in learning rotation-invariant tasks. This network has been especially designed to improve performance of CNNs on automated computational tasks related to microscopy image analysis" ; sc:featureList edam:operation_3443 ; sc:name "CFNet" ; sc:url "https://github.com/bchidest/CFNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3382 ; sc:citation , "pmcid:PMC6315083", "pubmed:30602526" ; sc:description "Analyzes images of cell colonies that emit a luminescent/fluorescent signal in the form of a luminescent halo around the colony. Automatically identifies both the colonies and their emitted luminescent halos and returns quantitative data on features" ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CFQuant-automatic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.energylabtau.com/cfquant" ; biotools:primaryContact "Eyal Dafni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0625, edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:author "In-Hee Lee", "Jose A. Negron" ; sc:citation , "pubmed:31691385" ; sc:contributor ; sc:description """An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition. Clinical Genome & Ancestry Report (CGAR) enables users to identify and prioritize phenotype-associated variants from genome sequencing with a user-friendly and interactive online platform.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "Clinical Genome and Ancestry Report (CGAR)" ; sc:softwareHelp ; sc:url "https://tom.tch.harvard.edu/apps/cgar/" ; biotools:primaryContact "Sek-Won Kong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pubmed:31443042" ; sc:description "Developing the Web Server for CpG Island related Density and LAUPs (Lineage-associated Underrepresented Permutations) Study | WA web server for CpG Island study:CpG Island related density and LAUPs (Lineage-associated Underrepresented Permutations) analysis" ; sc:featureList edam:operation_0430, edam:operation_0440, edam:operation_3431 ; sc:name "CGIDLA" ; sc:url "http://www.combio-lezhang.online/cgidla/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC6700431", "pubmed:31400611" ; sc:description "Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells | Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors in the development and progression of cancer | However, detection of genetic interactions in the cancer genome is a major obstacle in the research of identifying biomarkers for cancer cell drug resistance and sensitivity" ; sc:featureList edam:operation_3501 ; sc:name "CGIdb" ; sc:url "http://www.medsysbio.org/CGIdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_3542 ; sc:citation , "pubmed:31860059" ; sc:description "A contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm." ; sc:featureList edam:operation_0476, edam:operation_0481, edam:operation_3454 ; sc:name "CGLFold" ; sc:url "https://github.com/iobio-zjut/CGLFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31704313" ; sc:description """Splice sites detection using chaos game representation and neural network. Email: hoangthanhtungvn@gmail.com. Project description: We propose to use chaos game representation and neural network for splice sites detection. DNA sequences are mapped to numerical sequences using chaos game representation. Numerical sequences are used as feature inputs to neural networks for splice sites classification""" ; sc:featureList edam:operation_0232, edam:operation_0446, edam:operation_2871 ; sc:name "CGR" ; sc:url "https://github.com/thoang3/portfolio/tree/SpliceSites_ANN_CGR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3068 ; sc:author "Ramil Nugmanov" ; sc:citation , "pubmed:31063394" ; sc:description "Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing | CGRs, molecules and reactions manipulation." ; sc:featureList edam:operation_0394, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "CGRtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cimm-kzn/CGRtools" ; biotools:primaryContact "Alexandre Varnek", "Ramil Nugmanov", "Timur Madzhidov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0153 ; sc:citation , , , , "pubmed:18351591", "pubmed:25130509", "pubmed:26631602", "pubmed:30525595" ; sc:description "Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans." ; sc:featureList edam:operation_0417, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CHARMM-GUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.charmm-gui.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199 ; sc:citation , "pmcid:PMC6323790", "pubmed:30616525" ; sc:description "Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC) - tools to pick causative mutation from bulks segregant sequencing." ; sc:featureList edam:operation_0524, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CHERIPIC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.2.6" ; sc:url "https://github.com/shyamrallapalli/cheripic" ; biotools:primaryContact "Shyam Rallapalli" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated database for Cricetulus griseus and CHO cells" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "CHOmine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "https://chomine.boku.ac.at/chomine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "Web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets." ; sc:featureList edam:operation_0438, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CHiCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.chicp.org/" ; biotools:primaryContact "O. S. Burren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC4739640", "pubmed:25822800" ; sc:description "The Role of Circular RNA CDR1as/ciRS-7 in Regulating Tumor Microenvironment | CIBERSORT is an analytical tool developed by Newman et al. to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data | Absolute mode (beta) is now available" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3792 ; sc:name "CIBERSORT" ; sc:url "https://cibersort.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0749, edam:topic_3169, edam:topic_3170 ; sc:citation , "pubmed:31701125" ; sc:description """a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Causal Inference and Directional Enrichment Methods on Biological Networks. Launching Causal Inference Engine... CIE is a platform for inference of active transcriptional regulators of differential gene expression. CIE provides a user-friendly web-app and an R-package to run inference queries on casual regulatory netowrks. Several regulatory networks are provided in the platform, including a TF-gene intraction network constructed from ChIP-seq and tissue specific gene expression data, a netowrk based on STRING-DB, and curated TF-gene interaction networks such as TRRUST and TRED. The R-package provides functionality for custom networks as well. Causal Inference Engine: Directional Enrichment Analysis on Biological Networks.""" ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3083, edam:operation_3439 ; sc:name "Causal Inference Enrichment (CIE)" ; sc:url "https://umbibio.math.umb.edu/cie/app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:30239607" ; sc:description "Central Informative Nodes in Network Analysis (CINNA) package gathers all required functions for centrality analysis in weighted/unweighted and directed/undirected networks." ; sc:featureList edam:operation_2497, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CINNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.53" ; sc:url "https://cran.r-project.org/package=CINNA" ; biotools:primaryContact "Minoo Ashtiani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3320, edam:topic_3512 ; sc:author "Li Yang", "Xiao-Ou Zhang" ; sc:citation , "pubmed:30539552" ; sc:description "Genome-wide annotation of circRNAs and their alternative back-splicing/splicing." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CIRCexplorer2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://circexplorer2.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6339429", "pubmed:30660194" ; sc:description "CircRNA Identifier. A de novo circular RNA identification tool." ; sc:featureList edam:operation_0443, edam:operation_3644, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CIRI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/ciri" ; biotools:primaryContact "Fangqing Zhao", "Jinyang Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3379 ; sc:citation , "pubmed:31119495" ; sc:description "Tool for Predicting Cross-interaction or Self-interaction of Monoclonal Antibodies Using Sequences." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CISI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://i.uestc.edu.cn/eli/cgi-bin/cisi.pl" ; biotools:primaryContact "Jian Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1022 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence feature label" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3033 ; sc:name "Nucleic acid report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3750 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3308 ; sc:description "Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment." ; sc:featureList edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CITE-seq-Count" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hoohm.github.io/CITE-seq-Count/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0219, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , , "pmcid:PMC6891984", "pubmed:31796060" ; sc:description "CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset." ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_3778 ; sc:license "MIT" ; sc:name "CIViCmine" ; sc:url "http://bionlp.bcgsc.ca/civicmine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3379, edam:topic_3400 ; sc:citation , ; sc:description "A Python software development and analysis toolkit for the CIViC knowledgebase | Clinical Interpretations of Variants in Cancer | CIViCpy — civicpy 1.0.0-rc1 documentation | A python interface for the CIViC db application | Sorry, something went wrong. Reload? | Sorry, we cannot display this file | CIViCpy is an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase | You have reached the code repository for CIViCpy, a python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC) | Sorry, this file is invalid so it cannot be displayed | CIViCpy lets you pull data from CIViC using the civic module and interact with records as dynamic objects. With the aid of caching, it is easy to explore relationships between CIViC records (e.g. assertions, genes, variants) without worrying about querying CIViC more than once for the same data" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3197 ; sc:license "MIT" ; sc:name "CIViCpy" ; sc:url "https://docs.civicpy.org/en/1.1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_2229 ; sc:author ; sc:description "CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases." ; sc:featureList edam:operation_2233 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CLASTR" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://web.expasy.org/cellosaurus-str-search/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3372, edam:topic_3382 ; sc:citation , "pubmed:31740823" ; sc:description """GPU-accelerated image processing for everyone. CLIJ is an OpenCL - ImageJ bridge and a Fiji plugin allowing users with entry-level skills in programming to build GPU-accelerated workflows to speed up their image processing. Increased efforts were put on documentation, code examples, interoperability, and extensibility. CLIJ is based on ClearCL, JOCL, Imglib2, ImageJ and SciJava""" ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:name "CLIJ" ; sc:softwareHelp , ; sc:url "https://clij.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3168, edam:topic_3382 ; sc:citation , "pmcid:PMC6819642", "pubmed:31660851" ; sc:description "CLINE (Comparison of bioLogIcal deNdrogram structurEs), is a web-tool specifically designed for the visual comparison of dendrograms, with an emphasis on the display of matching clusters that, even when not isomorphic, can be perceived as having the same biological meaning." ; sc:featureList edam:operation_0570, edam:operation_2938, edam:operation_3432 ; sc:license "MIT" ; sc:name "CLINE" ; sc:softwareHelp , ; sc:url "http://mizuguchilab.org/cline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3794 ; sc:description "Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to the iCLIP workflows also FLASH, and uvCLAP." ; sc:name "CLIP-Explorer" ; sc:url "https://clipseq.usegalaxy.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3063, edam:topic_3379, edam:topic_3794 ; sc:citation , , "pmcid:PMC7500653", "pubmed:32946464" ; sc:description """An interactive retrieval system for clinical trial studies with context-dependent protocol elements. Clinical trial protocol includes all the steps that should be conducted in clinical trial and all clinical trial start with development of the protocol. The purpose of our study is to provide context-dependent protocol element selection system for the development of objective and successful clinical trial protocols. We have developed a database and search application for protocol structure retrieval""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3891 ; sc:name "CLIPS" ; sc:url "https://corus.kaist.edu/clips" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3376, edam:topic_3474 ; sc:citation , "pubmed:31454273" ; sc:description "Open Source Infrastructure for Health Care Data Integration and Machine Learning Analyses | PURPOSE:We have created a cloud-based machine learning system (CLOBNET) that is an open-source, lean infrastructure for electronic health record (EHR) data integration and is capable of extract, transform, and load (ETL) processing. CLOBNET enables comprehensive analysis and visualization of structured EHR data. We demonstrate the utility of CLOBNET by predicting primary therapy outcomes of patients with high-grade serous ovarian cancer (HGSOC) on the basis of EHR data. MATERIALS AND METHODS:CLOBNET is built using open-source software to make data preprocessing, analysis, and model training user friendly. The source code of CLOBNET is available in GitHub" ; sc:license "BSD-2-Clause" ; sc:name "CLOBNET" ; sc:url "https://github.com/isoviita/CLOBNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3794 ; sc:citation ; sc:description "Chlamydomonas Library Project (CLiP) provides access to a collection of mutant strains in the green alga Chlamydomonas reinhardtii, a powerful model system for studying a broad range of fundamental processes including the biology of chloroplasts, photosynthesis, cilia/flagella, eyespots, and algal lipid accumulation." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CLiP Chlamydomonas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.chlamylibrary.org/" ; biotools:primaryContact "Jonikas lab", "Matt Laudon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3379, edam:topic_3400 ; sc:citation , "pmcid:PMC6701018", "pubmed:31429750" ; sc:description "A simple classification scheme for data elements of clinical data based on semantics" ; sc:featureList edam:operation_2422, edam:operation_3352, edam:operation_3559 ; sc:name "Clinical MetaData Ontology (CMDO)" ; sc:url "http://www.snubi.org/software/CMDO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0804, edam:topic_3324, edam:topic_3421, edam:topic_3489 ; sc:citation , "pubmed:31813095" ; sc:description """A Public Omics Database for Systematic and Comparable Information of CMV. Cytomegalovirus is a double-stranded DNA virus in the same family as herpesvirus found every where,infect people of all ages. Cytomegalovirus Treatment & Management Kauser Akhter, MD Assistant Professor, Department of Internal Medicine, Florida State University College of Medicine; Associate Program Director, Infectious Diseases Fellowship Program, Orlando Health; Updated: Jan 05, 2017""" ; sc:featureList edam:operation_0308, edam:operation_0477, edam:operation_2421 ; sc:name "CytoMegaloVirus DataBase (CMVdb)" ; sc:url "http://shaktisahislab.com/include/CMV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation , "pubmed:31581092" ; sc:description """A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. [Source] CNAPE: A Software for Copy Number Alteration Prediction from Gene Expression in Human Cancers. Copy number alterations (CNAs) are important features of human cancer. While the standard methods for CNA detection (CGH arrays, SNP arrrays, DNA sequencing) rely on DNA, occasionally DNA data are not available, especially in cancer studies (e.g. biopsies, legacy data). CNAPE comes into play by predicting CNAs based on gene expression data from RNA-seq""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3435 ; sc:name "CNAPE" ; sc:url "https://github.com/WangLabHKUST/CNAPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CNAtra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AISKhalil/CNAtra" ; biotools:primaryContact "Ahmed Khalil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6874599", "pubmed:31758002" ; sc:description """Convolutional neural network for efficient estimation of regional brain strains. Three pretrained CNN neural network models are provided based on all of the brain response samples available in the published study (N=3069). They correspond to the peak maximum principal strain (MPS) of the whole brain (WB), MPS of the corpus callosum (CC), and fiber strain (FS) of the CC, all assessed at the 95th percentile levels""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "CNN" ; sc:url "https://github.com/Jilab-biomechanics/CNN-brain-strains" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6838336", "pubmed:31700141" ; sc:description """Problems with homepage (January 6th, 2021) | CNN-SuccSite is a web server for characterization and identification succinylation sites based on deep learning method.""" ; sc:featureList edam:operation_0417, edam:operation_3755 ; sc:name "CNN-SuccSite" ; sc:url "http://csb.cse.yzu.edu.tw/CNN-SuccSite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3172, edam:topic_3474, edam:topic_3542 ; sc:citation , "pubmed:31860715" ; sc:description """Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. CNN-based Annotation of Bacterial Type IV Secretion System Effectors. The CNN-T4SE is a tool that can be run in windows and linux operating systems. It is used to identify effector proteins through the amino acid sequence, evolutionary information in the form of a position-specific scoring matrix, secondary structure and solvent accessibility information of the proteins.""" ; sc:featureList edam:operation_0267, edam:operation_2476, edam:operation_2488 ; sc:name "CNN-T4SE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://idrblab.org/cnnt4se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3673 ; sc:citation , , "pubmed:32219377" ; sc:description """Copy Number Variation Detection in Bacterial Circular Genome. Abstract Motivation Whole genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. Results We show that the replication bias is widespread using ~200 bacterial WGS data. We develop CNV-BAC that can properly normalize the replication bias as well as other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementation CNV-BAC is available at https: github.com LinjieWu CNV-BAC. Contact ruibinxi@math.pku.edu.cn""" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "CNV-BAC" ; sc:url "https://github.com/LinjieWu/CNV-BAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:31392308" ; sc:description "association analysis of CNVs with gene expression and quantitative phenotypes | Summarization and expression/phenotype association of CNV ranges | The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes" ; sc:featureList edam:operation_0484, edam:operation_3232, edam:operation_3800 ; sc:license "Artistic-2.0" ; sc:name "CNVRanger" ; sc:url "http://bioconductor.org/packages/CNVRanger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6887803", "pubmed:31832011" ; sc:description """Visually Exploring Copy Number Aberrations in Cancer Genomes. CNVScope interchromosomal heatmaps. A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization. Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps. CNVScope is a visualization toolkit for seeing copy number data in a relationship fashion, both utilizing tools that find regions of interest (much like domains in Hi-C terminology), visualize the relationships in vibrant color (blue for negative association, red for positive), and integrates several different relevant types of data (RNASeq, sample information, Cancer Gene Census data, and structural variants)""" ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3196, edam:operation_3659 ; sc:license "BSD-3-Clause" ; sc:name "CNVScope" ; sc:url "http://cnvscope.nci.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:31141125" ; sc:description "Multi-omics Approach to Detecting Clinically Associated, Combinatory Genomic Signatures." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bsml320/CNet" ; biotools:primaryContact "Zhongming Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0602, edam:topic_3360 ; sc:citation , "pmcid:PMC6396937", "pubmed:30779739" ; sc:description "Component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications." ; sc:featureList edam:operation_1781, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "COAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ChengF-Lab/COAC" ; biotools:primaryContact "ChengF-Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_3172 ; sc:citation ; sc:description "Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COBRA Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "3.0" ; sc:url "https://opencobra.github.io/cobratoolbox/" ; biotools:primaryContact "Ronan Fleming on behalf of the COBRA Toolbox Development Community" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3300, edam:topic_3407 ; sc:citation , "pmcid:PMC6538558", "pubmed:31138123" ; sc:description "Context-specific biological knowledge representation for systemic physiology analysis." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CODA-ML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MijinKwon/CODA-ML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3444 ; sc:citation , , "pubmed:31463859", "pubmed:32073269" ; sc:description "Automated Tools for the Analysis of 1D-NMR and 2D-NMR Spectra | COLMARm 13C-1H HSQC, HSQC-TOCSY and TOCSY Query and Verification | Visit a step by step how-to with figures here | Bingol, K.; Li, DW.; Zhang, B.; Brüschweiler, R.; Comprehensive metabolite identification strategy using multiple two-dimensional NMR spectra of a complex mixture implemented in the COLMARm web server; Anal. Chem; 2016, 88, 12411-12418;" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3803 ; sc:name "COLMARm" ; sc:url "http://spin.ccic.ohio-state.edu/index.php/colmarm/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31121098" ; sc:description "Data-Analysis Package for Combinatorial Materials Science." ; sc:featureList edam:operation_1812, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "COMBIgor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.COMBIgor.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6348648", "pubmed:30691411" ; sc:description "Web-based application used to download, collect and manage gene expression data from public databases." ; sc:featureList edam:operation_2495, edam:operation_3431, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COMMAND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/marcomoretto/command" ; biotools:primaryContact "Marco Moretto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , , "pmcid:PMC7520036", "pubmed:32399572" ; sc:description """A tool to explore and visualize intercellular communication. Abstract Intercellular communication plays an essential role in multicellular organisms and several algorithms to analyse it from single-cell transcriptional data have been recently published, but the results are often hard to visualize and interpret. We developed COMUNET (Cell cOMmunication exploration with MUltiplex NETworks), a tool that streamlines the interpretation of the results from cell-cell communication analyses. COMUNET uses multiplex networks to represent and cluster all potential communication pathways between cell types. The algorithm also enables the search for specific patterns of communication and can perform comparative analysis between two biological conditions. To exemplify its use, here we apply COMUNET to investigate cell communication patterns in single-cell transcriptomic datasets from mouse embryos and from an acute myeloid leukemia patient at diagnosis and after treatment""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3802 ; sc:name "COMUNET" ; sc:url "https://github.com/ScialdoneLab/COMUNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6624895", "pubmed:31300005" ; sc:description "CCA (canonical correlation analysis) ON Features for INter-dataset Effect Detection." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "CONFINED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cozygene/CONFINED" ; biotools:primaryContact "Mike Thompson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3810 ; sc:citation ; sc:description "COPO is a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "COPO" ; sc:url "http://copo-project.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3382 ; sc:citation , "pubmed:31702166" ; sc:description "The CORDERLY software analyses colloidal ordering via the 2D fast Fourier transform, the radial distribution function, the spatial distribution function, and the angular distribution. The spatial distribution function plots the resulting analysis in Cartesian and polar coordinates (angular distribution)." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "CORDERLY" ; sc:url "https://github.com/adrena-lab/CORDERLY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_2640 ; sc:citation , "pubmed:30378070" ; sc:description "Cores of Recurrent Events (CORE) is software tool for delineating regions of recurrent DNA copy number alteration in cancer." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "CORE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://cran.r-project.org/package=CORE" ; biotools:primaryContact "Guoli Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3407 ; sc:citation , "pmcid:PMC6302372", "pubmed:30577744" ; sc:description "CORGi (COmplex Rearrangement detection with Graph-search), a method for the detection and visualization of complex local genomic rearrangements." ; sc:featureList edam:operation_0452, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CORGi" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zstephens/CORGi" ; biotools:primaryContact "J. P. Kocher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:32384242" ; sc:description "COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats." ; sc:featureList edam:operation_3637, edam:operation_3649, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "COSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/compomics/COSS" ; biotools:primaryContact "Computational Omics and Systems Biology Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0203, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC6934141", "pubmed:31800035" ; sc:description """A Normalized Measure of Codon Usage Preferences. COUSIN is a bioinformatic tool which aims to calculate the Codon Usage Preferences (CUPrefs) of sequences using a novel index named COUSIN. In addition, numerous functions are proposed to enhance your CUPrefs analysis experience !""" ; sc:featureList edam:operation_0284, edam:operation_0285, edam:operation_0335, edam:operation_2962, edam:operation_3435 ; sc:name "Codon Usage Similarity Index (COUSIN)" ; sc:url "http://cousin.ird.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , , "pmcid:PMC7198273", "pubmed:32132097" ; sc:description "Genome-wide association analysis of age-at-onset traits using Cox mixed-effects models | Abstract Age-at-onset is one of the critical phenotypes in cohort studies of age-related diseases. Large-scale genome-wide association studies (GWAS) of age-at-onset can provide more insights into genetic effects on disease progression, and transitions between different stages. Moreover, proportional hazards or Cox regression generally achieves higher statistical power in a cohort study than a binary trait using logistic regression. Although mixed-effects models are widely used in GWAS to correct for population stratification and family structure, application of Cox mixed-effects models (CMEMs) to large-scale GWAS are so far hindered by intractable computational intensity. In this work, we propose COXMEG, an efficient R package for conducting GWAS of age-at-onset using CMEMs" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3891 ; sc:name "COXMEG" ; sc:url "https://CRAN.R-project.org/package=coxmeg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6602467", "pubmed:31066451" ; sc:description "Integrated plastome sequence annotator and analyzer." ; sc:featureList edam:operation_0464, edam:operation_0484, edam:operation_0526 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CPGAVAS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.herbalgenomics.org/cpgavas2" ; biotools:primaryContact "Chang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC6469151", "pubmed:30991962" ; sc:description "R package for p-value adjustment when looking for an optimal transformation of a single explanatory variable in generalized linear models." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CPMCGLM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://cran.r-project.org/package=CPMCGLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3343, edam:topic_3892 ; sc:citation , "pubmed:31580670" ; sc:description """An Open-Source C++ and Python Library for Polarizable Embedding. C++ and Python library for Polarizable Embedding. CPPE is an open-source, light-weight C-Plus-Plus library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field calculations and post-SCF methods. A convenient Python interface is also available""" ; sc:license "LGPL-3.0" ; sc:name "CPPE" ; sc:url "https://github.com/maxscheurer/CPPE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2640, edam:topic_3168, edam:topic_3360, edam:topic_3577 ; sc:author , ; sc:citation , "pubmed:34310709" ; sc:contributor ; sc:description "The Cancer Predisposition Sequencing Reporter (CPSR) is a computational workflow that interprets and classifies germline DNA variants identified from next-generation sequencing in the context of cancer predisposition and inherited cancer syndromes. The workflow can also report incidental findings (ACMG v3.0) as well as the genotypes of common germline variants associated with cancer risk, as reported in the NHGRI-EBI GWAS catalog." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226, edam:operation_3661, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cancer Predisposition Sequencing Reporter (CPSR)" ; sc:softwareHelp , , , , ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/sigven/cpsr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3300, edam:topic_3810, edam:topic_3855 ; sc:citation , ; sc:description """whole plant modelling framework for the simulation of water and carbon related processes. Output of CPlantBox-PiafMunch coupling. Simulation output of CPlantBox-PiafMunch coupling. Example 2-4""" ; sc:featureList edam:operation_2426, edam:operation_3454, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "CPlantBox" ; sc:url "https://github.com/Plant-Root-Soil-Interactions-Modelling/CPlantBox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3173 ; sc:citation ; sc:description "K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment | CQF-deNoise enables fast k-mer counting with memory usage nearly unaffected by sequencing errors" ; sc:featureList edam:operation_0524, edam:operation_3198, edam:operation_3472 ; sc:name "CQF-deNoise" ; sc:url "https://github.com/Christina-hshi/CQF-deNoise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0219 ; sc:citation , "pubmed:31725864" ; sc:description "The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset." ; sc:featureList edam:operation_2421, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "CRAFT" ; sc:url "https://github.com/UCDenver-ccp/CRAFT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:31288758" ; sc:description "Software package for conditional robustness analysis of cancer systems biology models in MATLAB." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "CRA toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gitlab.ict4life.com/SysBiOThe/CRA-Matlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3500 ; sc:description "CRB-Anim is the online catalog of biological resources of the french national infrastructure supporting research on domestic animals." ; sc:name "CRB-Anim" ; sc:url "https://www.crb-anim.fr/crb-anim_eng/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269, edam:topic_2640 ; sc:citation ; sc:description "Conditional Robust Calibration (CRC) - Bayesian method for nonlinear model calibration and robustness analysis using omics data." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/fortunatobianconi/CRC" ; biotools:primaryContact "Fortunato Bianconi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc:description "Colo-Rectal Cancer Risk Prediction (CRCRpred) webserver can be used to distinguish high risk CRC patients from low risk CRC patients given the protein concentration of one or more apoptotic proteins (Bak, Bax, Bcl2, BclXL or Mcl1) involved in the process of Mitochondrial Outer Membrane Permeabilization (MOMP), which is defunct in the case of cancer. The risk estimation is based on statistical and survival analysis on recent CRC datasets." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRCRpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/crcrpred" ; biotools:primaryContact "Gajendra P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31432077" ; sc:description "Consensus Reverse Docking System for Target Fishing | Identification of putative drug targets is a critical step for explaining the mechanism of drug action against multiple targets, finding new therapeutic indications for existing drugs, and unveiling the adverse drug reactions. One important approach is to use the molecular docking. However, its widespread utilization has been hindered by the lack of easy-to-use public servers. Therefore, it is vital to develop a streamlined computational tool for target prediction by molecular docking on a large scale. RESULTS:We present a fully automated web tool named CRDS (Consensus Reverse Docking System) which predicts potential interaction sites for a given drug. To improve hit rates, we developed a strategy of consensus scoring" ; sc:featureList edam:operation_0478 ; sc:name "Consensus Reverse Docking System (CRDS)" ; sc:url "http://pbil.kaist.ac.kr/CRDS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6771399", "pubmed:31533978" ; sc:description "Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks | Clustering of Genomic Regions Analysis Method | Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach" ; sc:featureList edam:operation_0441, edam:operation_3432, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "CREAM" ; sc:url "https://cran.r-project.org/web/packages/CREAM/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0736 ; sc:citation ; sc:description "cath-resolve-hits (CRH)- tool that resolves domain matches suspiciously quickly." ; sc:featureList edam:operation_0303, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRH" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/UCLOrengoGroup/cath-tools" ; biotools:primaryContact "Ian Sillitoe", "Tony E Lewis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0749 ; sc:citation ; sc:description "Design tool for CRISPR-mediated gene editing, repression and activation." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRISPR-ERA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crispr-era.stanford.edu/" ; biotools:primaryContact "Honglei Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "Improved CRISPR/Cas9 tool for genome editing in plants" ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRISPR-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://crispr.hzau.edu.cn/CRISPR2/" ; biotools:primaryContact "Kabin Xie", "Ling-Ling Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Suite of web applications for analysing Clustered Regularly Interspaced Short Palindromic Repeats." ; sc:name "CRISPRCas" ; sc:url "https://crisprcas.i2bc.paris-saclay.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0798 ; sc:citation , "pmcid:PMC6030898", "pubmed:29790974" ; sc:description "Easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype." ; sc:featureList edam:operation_3211 ; sc:name "CRISPRCasFinder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.5 - I2BC" ; sc:url "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index" ; biotools:primaryContact "Christine Pourcel", "David Couvin", "Marie Touchon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3512, edam:topic_3912 ; sc:author "Kenian Chen" ; sc:citation , "pmcid:PMC6706119", "pubmed:31453219" ; sc:description "A fast and intuitive tool for designing guide RNA for genome editing | The RNA-guided CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeat-CRISPR-associated 9) system has become a revolutionary technology for targeted genome engineering. The critical step of this technology requires the design of a highly specific and efficient guide RNA (gRNA) that will guide the Cas9 nuclease to the complementary DNA target sequence. CRISPR-Explorer is a new and user-friendly web server for selecting optimal CRISPR sites. It implements the latest scoring schemes of gRNA specificity and efficiency based on published empirical studies. The gRNA design results are generated instantly, thus removing wait times. The user can visualize the high-quality gRNAs with detailed design information through an interactive genome browser. Furthermore, the user can define and specify the parameters for gRNA selection in the Batch Design mode, which recognizes various input formats" ; sc:featureList edam:operation_3096 ; sc:name "CRISPR Explorer" ; sc:url "http://crisprexplorer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation ; sc:description "Software for designing CRISPR/Cas guide RNA with reduced off-target sites." ; sc:featureList edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CRISPRdirect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://crispr.dbcls.jp/" ; biotools:primaryContact "Yuki Naito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3512, edam:topic_3676, edam:topic_3912 ; sc:citation , "pubmed:31764961" ; sc:description """A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.""" ; sc:featureList edam:operation_3096, edam:operation_3211, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "CRISPRitz" ; sc:url "https://github.com/pinellolab/CRISPRitz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_2885 ; sc:citation ; sc:description "Gateway to publicly accessible CRISPRs database." ; sc:name "CRISPRs Database" ; sc:url "http://crispr.i2bc.paris-saclay.fr/crispr/" ; biotools:primaryContact "Christine Pourcel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3452 ; sc:citation , "pubmed:31617571" ; sc:description "A novel constrained reconstruction model towards high-resolution sub-tomogram averaging." ; sc:name "CRM-SIRT" ; sc:url "https://github.com/icthrm/CRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description "Web server for predicting the in vivo structure of RNA molecules." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CROSSalive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://service.tartaglialab.com/new_submission/crossalive" ; biotools:primaryContact "Gian Tartaglia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6709893", "pubmed:31449539" ; sc:description "A tool for the prediction of ancestry in cattle | Added an avenue for data that plink does not have a \"species ID\" for. In this case users, will specify \"NA\" as the plink_species_ID in their input file. It is now required to specify chromosome number for the data in the input | CRUMBLER has now been successfully ran in Pigs, following these updates" ; sc:featureList edam:operation_0335, edam:operation_3196 ; sc:name "CRUMBLER" ; sc:url "https://github.com/tamarcrum/CRUMBLER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0634, edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC6839171", "pubmed:31699133" ; sc:description """A comprehensive framework to predict condition-specific regulatory units. We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.""" ; sc:featureList edam:operation_0438, edam:operation_3439, edam:operation_3463 ; sc:name "CRUP" ; sc:url "https://github.com/VerenaHeinrich/CRUP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3314 ; sc:citation , "pubmed:31077416" ; sc:description "Visualization environment for plotting properties of crystalline solids as computed by means of the CRYSTAL code." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRYSPLOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://crysplot.crystalsolutions.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659 ; sc:citation , "pmcid:PMC6542128", "pubmed:31142266" ; sc:description "Pairwise visual comparison of small RNA secondary structures with base pair probabilities." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CS2BP2-Plot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nrcmonsrv01.nrc.ca/cs2bp2plot" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154, edam:topic_0593 ; sc:citation , "pubmed:31829591" ; sc:description "C2Structure: Extracting Structural Information Directly From NMR Chemical Shifts. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0303, edam:operation_2441 ; sc:license "MIT" ; sc:name "CS2Structure" ; sc:url "https://github.com/atfrank/CS2Structure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0804, edam:topic_3673 ; sc:citation , "pmcid:PMC6486994", "pubmed:31029079" ; sc:description "R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR." ; sc:featureList edam:operation_0308, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CSESA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://cran.r-project.org/package=CSESA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3360, edam:topic_3520 ; sc:citation , "pubmed:31432427" ; sc:description "Essential Features and Use Cases of the Cerebrospinal Fluid Proteome Resource (CSF-PR) | Every year, a large number of published studies present biomarkers for various neurological disorders. Many of these studies are based on mass spectrometry proteomics data and describe comparison of the abundance of proteins in cerebrospinal fluid between two or more disease groups. As the number of such studies is growing, it is no longer straightforward to obtain an overview of which specific proteins are increased or decreased between the numerous relevant diseases and their many subcategories, or to see the larger picture or trends between related diseases" ; sc:featureList edam:operation_0306, edam:operation_3799 ; sc:name "CSF-PR" ; sc:url "https://proteomics.uib.no/csf-pr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:31038684" ; sc:description "Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data." ; sc:featureList edam:operation_3501, edam:operation_3565, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CSHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.andrew.cmu.edu/user/chiehl1/CSHMM/" ; biotools:primaryContact "Ziv Bar-Joseph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3063, edam:topic_3168, edam:topic_3263, edam:topic_3794 ; sc:citation ; sc:description """An Online Platform for Automated NGS Data Analysis and Sharing. CSI NGS Portal is an online platform for fully automated NGS data analysis and sharing . CSI NGS Portal uses a single, randomly generated, persistent, secure and http-only browser cookie for the sole purpose of user recognition for data authorisation.""" ; sc:featureList edam:operation_3096, edam:operation_3222, edam:operation_3799 ; sc:name "CSI NGS Portal" ; sc:url "https://csibioinfo.nus.edu.sg/csingsportal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31626280" ; sc:description """A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples. A computational pipeline for high-resolution profiling of low abundance microbiome in clinical samples using whole genome shotgun sequencing. Computation Subtraction-based Microbiome Discovery (CSMD). CSMD will work with a series of libraries listed in Table 2, including human-related genomes or sequences (21G) and all RefSeq bacteria genomes (150G, as of November 2018). The build process will then require approximately 500GB of additional disk space and 200GB of RAM. These genomes or sequences can be found in DBPATH/hg38/SEQ, DBPATH/AHG/SEQ, DBPATH/EHG/SEQ and DBPATH/RefSeq/bacteria/SEQ, respectively. And the indexed files will be saved in DBPATH/hg38, DBPATH/AHG, DBPATH/EHG and DBPATH/RefSeq/bacteria, respectively""" ; sc:featureList edam:operation_3198, edam:operation_3454, edam:operation_3460 ; sc:name "Computation Subtraction-based Microbiome Discovery (CSMD)" ; sc:url "https://github.com/liuyu8721/csmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation , ; sc:description """A label-free method for dynamic measurement of single-cell volume. Kai Yao, Nash D Rochman, Sean X Sun (*ssun@jhu.edu) @ Johns Hopkins University""" ; sc:featureList edam:operation_3659, edam:operation_3799, edam:operation_3891 ; sc:license "MIT" ; sc:name "Cell Topography Regression Learner (CTRL)" ; sc:url "https://GitHub.com/sxslabjhu/CTRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3360, edam:topic_3517 ; sc:citation ; sc:description "Cross-validated Rank-based Marker Selection for Genome-wide Prediction of Low Heritability | Marker selection for genome-wide prediction | Cross-Validated Rank-based Marker Selection (CVRMS) | CVRMS is an R package designed to extract marker subset from ranked marker dataset induced by genome-wide association study (GWAS) or marker effect analysis for genome-wide prediction" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:name "CVRMS" ; sc:url "https://github.com/gtayana/CVRMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769 ; sc:author "Felix Xavier Amaladoss" ; sc:description "CWL VM environment is a repository which can be deployed on cloud to execute Biobb Mutations Workflow." ; sc:isAccessibleForFree true ; sc:name "Biobb Mutations Workflow" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3395 ; sc:citation , "pmcid:PMC6933651", "pubmed:31881827" ; sc:description """Model-based cell clustering and population tracking for time-series flow cytometry data. CYBERTRACK is an R package for CYtometry-Based Estimation and Reasoning for cell populatiomn TRACKing""" ; sc:featureList edam:operation_2238, edam:operation_3432, edam:operation_3565 ; sc:name "CYBERTRACK" ; sc:url "https://github.com/kodaim1115/CYBERTRACK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3320, edam:topic_3382, edam:topic_3676 ; sc:citation , "pubmed:31674704" ; sc:description """An example of integrative tool for in silico analysis of missense variants identified in Mendelian disorders. Cystic Fibrosis Missense Analysis. Website dedicated to the in silico analysis of missense variants in the CFTR gene. Welcome to the Cystic Fibrosis Missense Analysis Website. Data provided and calculated by CYSMA must be considered as predictions. If you are dealing with the genetics of cystic fibrosis or CFTR-related disorders, you may find this website useful. CYSMA has been developed as a tool to help you to predict the impact of novel uncharacterized missense variants when the information provided by CFTR patient databases such as CFTR-France, CFTR1 and CFTR2 remain insufficient""" ; sc:featureList edam:operation_0331, edam:operation_3197, edam:operation_3461 ; sc:name "CYSMA" ; sc:url "https://cftr.iurc.montp.inserm.fr/cysma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0209, edam:topic_0804 ; sc:citation ; sc:description "CaFE (Calculation of Free Energy) - a VMD plugin for binding affinity prediction using end-point free energy methods." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CaFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/huiliucode/cafe_plugin" ; biotools:primaryContact "Tingjun Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3298, edam:topic_3384, edam:topic_3421, edam:topic_3444 ; sc:citation , , "pmcid:PMC6216519", "pmcid:PMC7113126", "pubmed:32191542" ; sc:description """NIMG-70. QUANTITATIVE IMAGE ANALYSIS AND MACHINE LEARNING TECHNIQUES FOR DISTINGUISHING TRUE PROGRESSION FROM PSEUDOPROGRESSION IN PATIENTS WITH GLIOBLASTOMA. Perelman School of Medicine at the University of Pennsylvania. The Center for Biomedical Image Computing and Analytics (CBICA) was established in 2013, and focuses on the development and application of advanced computational and analytical techniques that quantify morphology and function from biomedical images, as well as on relating imaging phenotypes to genetic and molecular characterizations, and finally on integrating this information into diagnostic and predictive tools in an era of personalized medicine. Center for Biomedical Image Computing & Analytics. Cancer Imaging Phenomics Toolkit (CaPTk). CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer""" ; sc:featureList edam:operation_3443, edam:operation_3659, edam:operation_3799 ; sc:name "CaPTk" ; sc:url "http://www.cbica.upenn.edu/captk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068 ; sc:citation ; sc:description "Calcium Signaling Analyzer (CaSiAn), an open source software tool that allows for quantifying these signal characteristics including individual spike properties and time course statistics in a semi-automated manner." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CaSiAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://r3lab.uni.lu/web/casa" ; biotools:primaryContact "Alexander Skupin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3489 ; sc:citation , "pubmed:26224250" ; sc:description "General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts." ; sc:featureList edam:operation_0224, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Cafe Variome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cafevariome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6548890", "pubmed:31103852" ; sc:description "Early Cancer Detection from Multianalyte Blood Test Results using Artificial Intelligence" ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CancerA1DE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://cancer.cs.cityu.edu.hk/" ; biotools:primaryContact "Ka-Chun Wong" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3242 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602 ; sc:author "Elisa Micarelli", "Prisca Lo SUrdo" ; sc:citation , "pubmed:31598703" ; sc:contributor "Marta Iannuccelli" ; sc:description "CancerGeneNet is a resource that aims at linking genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancers in the cell network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGenNet bridges two interaction layers by connecting proteins whose activities are affected by cancer gene products to proteins that impact on cancer phenotypes. This is achieved by implementing graph algorithms that allow searching for graph path that link any gene of interest to the “hallmarks of cancer\"." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:name "CancerGeneNet" ; sc:provider "Gianni Cesareni" ; sc:url "https://signor.uniroma2.it/CancerGeneNet/" ; biotools:primaryContact "Luana Licata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3173, edam:topic_3375 ; sc:citation , "pmcid:PMC6730898", "pubmed:31490960" ; sc:description "Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles | Liver Heptacellular Carcinoma Stage Prediction | CancerLSP is a web-bench Liver cancer stage prediction Server | Reference: Kaur H et. al., (2019) Classification of early and late stage liver hepatocellular carcinoma patients from their genomics and epigenomics profiles. https://doi.org/10.1371/journal.pone.0221476" ; sc:featureList edam:operation_0417, edam:operation_3206, edam:operation_3207 ; sc:name "CancerLSP" ; sc:url "http://webs.iiitd.edu.in/raghava/cancerlsp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:31110280" ; sc:description "Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer." ; sc:featureList edam:operation_0306, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CancerMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bionlp.bcgsc.ca/cancermine/" ; biotools:primaryContact "Jake Lever" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6823463", "pubmed:31673075" ; sc:description """Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. A Webserver to Predict the Progression of Skin Cancer. This database maintains comprehensive information of short self-assembling peptides forming nanostructures and their structures. Reference: Bhalla, S., Kaur, H., Dhall, A., Raghava, GPS. Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients. Sci Rep 9, 15790 (2019) doi:10.1038/s41598-019-52134-4. https://doi.org/10.1038/s41598-019-52134-4. CancerSPP: A Webserver for predicting the progression of skin cancer. CancerSPP is a web-bench for skin cutaneous melanoma (SKCM) progression prediction""" ; sc:featureList edam:operation_0417, edam:operation_0463, edam:operation_3792, edam:operation_3800 ; sc:name "CancerSPP" ; sc:url "http://webs.iiitd.edu.in/raghava/cancerspp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_2640, edam:topic_3293, edam:topic_3360 ; sc:citation , "pubmed:31701131" ; sc:description """a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity data: 1) Intra-tumor or Intra-metastatic heterogeneity: the presence of multiple subclones within a primary tumor or a single metastatic lesion; 2) Inter-metastatic heterogeneity: the presence of different subclones in different metastatic lesions of the same patient. Somatic mutations and copy number alterations are available in CancerTracer, since both of them are principal factors drive heterogeneity in cancer. The structured heterogeneity data enables researchers to identify trunk mutations in different cancer types and investigate the molecular mechanisms underlying intratumor heterogeneity""" ; sc:featureList edam:operation_0323, edam:operation_0531, edam:operation_2436 ; sc:name "CancerTracer" ; sc:url "http://cailab.labshare.cn/cancertracer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Using existing tools in the Galaxy environment we generated the workflow CandiMeth (CANDIdate feature METHylation). This takes as input a differential methylation table from an R-based package and maps it to a reference genome build. A simple interface then allows the user to query the dataset with inputs as straightforward as lists of gene names, or as detailed as bed files containing specific chromosomal coordinates, for more sophisticated analyses." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CandiMeth" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bit.do/candimeth-github" ; biotools:primaryContact "Colum Walsh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_3292, edam:topic_3343 ; sc:citation ; sc:description "A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3802 ; sc:name "Canvass" ; sc:url "https://tripod.nih.gov/canvass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0634, edam:topic_0654 ; sc:citation , "pmcid:PMC6956725", "pubmed:31840950" ; sc:description """A java tool for designing probes for capture Hi-C applications. Here, we developed CaptureProbe, a user-friendly and graphical Java tool for designing capture probes for Capture Hi-C applications. CaptureProbe is easy-to-use, only need simple input files and provides abundant parameters for designing probes. CaptureProbe can design probes specifically for both genomic sites and genomic regions of interest. Comparisons with existing softwares (HiCapTools and GOPHER) indicated that CaptureProbe has a good design success ratio and better probe specificity. Citation: MA Y F, ADEOLA A C, SUN Y B, et al. 2020. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zool Res [J], 41: 94-96""" ; sc:name "CaptureProbe" ; sc:url "https://sourceforge.net/projects/captureprobe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3300, edam:topic_3375, edam:topic_3377 ; sc:citation , "pubmed:31606584" ; sc:description """A tool for the prediction and visualization of time-concentration profiles of drugs in heart tissue. Cardiac mechanistic physiologically based pharmacokinetic simulation application. User Interface (ui) application which implements PBPK models. Prediction of drug effect is valuable in terms of both safety and efficacy. physiologically based pharmacokinetic-quantitative system. 1) Download the tar.gz archive from the https: sourceforge.net projects cardiacpbpk files or clone github repository (if you have git packages installed in konsole terminal type ‘git clone https: github.com jszlek CardiacPBPK.git’)""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "CardiacPBPK" ; sc:url "https://github.com/jszlek/CardiacPBPK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3318, edam:topic_3335 ; sc:citation , "pmcid:PMC6381356", "pubmed:30666509" ; sc:description "R package for extraction and visualisation of heart rate profiles from wearable fitness trackers." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CardiacProfileR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/VCCRI/CardiacProfileR" ; biotools:primaryContact "Victor Chang Cardiac Research Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3444 ; sc:citation , "pubmed:31076923" ; sc:description "Platform for noninvasive assessment of pulse transit time and pulsatile flow in hyperelastic vascular networks." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CardioFAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YasharVahedein/CardioFAN" ; biotools:primaryContact "Yashar Seyed Vahedein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3303 ; sc:citation ; sc:description "Online tool for assessing genome editing results using NGS data." ; sc:featureList edam:operation_0420, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Cas-analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rgenome.net/cas-analyzer/" ; biotools:primaryContact "Jin-Soo Kim", "Sangsu Bae" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description """A flexible, scalable and easy-to-use amplicon sequence data analysis pipeline. CASCABEL is a pipeline designed to run amplicon sequence analysis across single or multiple read libraries. The objective of this pipeline is to create different output files which allow the user to explore data in a simple and meaningful way, as well as facilitate downstream analysis, based on the generated output files.""" ; sc:featureList edam:operation_0450, edam:operation_3192, edam:operation_3200, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Cascabel" ; sc:url "https://github.com/AlejandroAb/CASCABEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_2229 ; sc:citation , , "pmcid:PMC7155257", "pubmed:32290857" ; sc:description """Inference of Single-Cell Phylogenies from Lineage Tracing Data. A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction. This is a software suite for proecessing data from single cell lineage tracing experiments. This suite comes equipped with three main modules:. Phylogeny Reconstruction: a collection of tools for constructing phylogenies. We support 5 algorithms currently: a greedy algorithm based on multi-state compatibility, an exact Steiner-Tree solver, Cassiopeia (the combination of these two), Neighbor-Joining, and Camin-Sokal Maximum Parsimony. Target Site Sequencing Pipeline: a pipeline for extracing lineage information from raw fastqs produced from a lineage tracing experiment""" ; sc:featureList edam:operation_0326, edam:operation_3478, edam:operation_3745 ; sc:license "MIT" ; sc:name "Cassiopeia" ; sc:url "http://www.github.com/YosefLab/Cassiopeia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3332 ; sc:citation , "pmcid:PMC6538711", "pubmed:31138816" ; sc:description "Web-platform for sharing data and software for computational catalysis research." ; sc:featureList edam:operation_0384, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Catalysis Hub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.catalysis-hub.org" ; biotools:primaryContact "Kirsten Winther", "Thomas Bligaard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3407, edam:topic_3577 ; sc:citation , , "pmcid:PMC4359046", "pubmed:25780776" ; sc:description """Fast inference of causality from complex time series. Causal inference in non-linear dynamics systems. Welcome to CauseMap — CauseMap 0.1.0 documentation. CauseMap is an implementation of Convergent Cross Mapping (CCM), written in Julia. CauseMap is an implementation of Convergent Cross Mapping (CCM) [1], written in Julia""" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:license "MIT" ; sc:name "CauseMap" ; sc:url "http://cyrusmaher.github.io/CauseMap.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3399 ; sc:citation ; sc:description "A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease | ABSTRACT Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge ( http: genomics.senescence.info cells ), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses" ; sc:featureList edam:operation_2942, edam:operation_3463, edam:operation_3501 ; sc:name "CellAge" ; sc:url "https://genomics.senescence.info/cells/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3170 ; sc:citation , "pubmed:31501550" ; sc:description "Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling | Automated, probabilistic assignment of cell types in scRNA-seq data | cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows" ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3891 ; sc:name "CellAssign" ; sc:url "https://github.com/irrationone/cellassign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC7141847", "pubmed:31778143" ; sc:description """R/Bioconductor software for comparing single-cell RNA-seq analysis methods. Construct Benchmarks for Single Cell Analysis Methods. This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods""" ; sc:featureList edam:operation_0244, edam:operation_3557, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "CellBench" ; sc:url "https://bioconductor.org/packages/CellBench" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description """a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. Welcome to CellBender’s documentation! — CellBender documentation. Free document hosting provided by Read the Docs. Stephen J Fleming, John C Marioni, and Mehrtash Babadi. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. bioRxiv 791699; doi: https://doi.org/10.1101/791699.""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "CellBender" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/CellBender" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3292, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """CellCountCV – a web-application for accurate cell counting and automated batch processing of microscopy images using fully-convolutional neural networks. This repository contains the code and examples accompaining our preprint https://doi.org/10.1101/867218. Working_with_CellCounter.ipynb — this notebook contains the examples of pretrained FCNN model usage in Python and through JSON-RPC calls to CellCountCV""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552 ; sc:license "MIT" ; sc:name "CellCountCV" ; sc:url "http://cellcounter.nprog.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3170, edam:topic_3360 ; sc:citation , , , "pmcid:PMC10330642", "pmcid:PMC6615556", "pmcid:PMC6889472", "pubmed:31113817", "pubmed:31733513", "pubmed:37140427" ; sc:description "Web application for exploration and analysis of cancer cell line pharmacogenomic data across different sources." ; sc:featureList edam:operation_0264, edam:operation_3501, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CellMinerCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://discover.nci.nih.gov/cellminercdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3518 ; sc:citation , ; sc:description "Tool for quantifying data from biological images, particularly in high-throughput experiments." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "CellProfiler" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cellprofiler.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3395 ; sc:citation , "pmcid:PMC6399906", "pubmed:30832570" ; sc:description "A software aims to calculate the similarity among different cells and predict their co-regulation networks." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CellSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "http://www.cellsim.nwsuaflmz.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3474 ; sc:citation ; sc:description "Support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort." ; sc:featureList edam:operation_3501, edam:operation_3660, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CellSort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tyolab.northwestern.edu/tools/" ; biotools:primaryContact "Keith E. J. Tyo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6509836", "pubmed:31072405" ; sc:description "Genetic barcode-based sample multiplexing for single-cell genomics." ; sc:featureList edam:operation_1812, edam:operation_3200, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CellTag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/morris-lab/CellTag-Classifier" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3306 ; sc:citation , "pmcid:PMC6481718", "pubmed:31069304" ; sc:description "Platform for interactive, 3D graphical simulation of immunological processes." ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Cell Studio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cellstudio.info" ; biotools:primaryContact "Uri Nevo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6558561", "pubmed:31104596" ; sc:description "Probabilistic census-travel model to predict introduction sites of exotic plant, animal and human pathogens." ; sc:featureList edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Census Travel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epi-models.shinyapps.io/Census_Travel/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Software for interactive visualization of scRNA-seq data." ; sc:featureList edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cerebro" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/romanhaa/Cerebro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444, edam:topic_3473 ; sc:citation , , "pubmed:32305449" ; sc:description "A toolbox for creating Cartesian Geometric Representations with Isometric Dimensions (Cgrids). The Cgrid-toolbox can be used to generate rectangular representations of brain areas." ; sc:featureList edam:operation_0303, edam:operation_3357 ; sc:license "GPL-3.0" ; sc:name "Cgrid" ; sc:url "https://github.com/mathijsraemaekers/Cgrid-toolbox" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_3006 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3173 ; sc:citation , ; sc:description """ChAsE (Chromatin Analysis and Exploration) is a cross platform desktop application that provides an interactive graphical interface for analysis of epigenomic data. Features include: - Exploration and visualization of the data using an interactive heat map and plot interface - Clustering the data automatically or manually by sorting and brushing the heat map - Exporting results for downstream analysis or as high quality images for publications""" ; sc:featureList edam:operation_0337, edam:operation_2451, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "ChAsE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/hyounesy/ChAsE/" ; biotools:primaryContact "Hamid Younesy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6602523", "pubmed:31114921" ; sc:description "Transcription factor enrichment analysis by orthogonal omics integration." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChEA3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://amp.pharm.mssm.edu/ChEA3" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3179 ; sc:citation ; sc:description "Computational package to process the next-generation sequence data generated from ChIA-PET experiments." ; sc:featureList edam:operation_0443, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChIA-PET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3/" ; biotools:primaryContact "Guoliang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3534 ; sc:citation ; sc:description "ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them." ; sc:featureList edam:operation_0445, edam:operation_2464, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChIPSummitDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://summit.med.unideb.hu/summitdb/" ; biotools:primaryContact "Endre Barta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description "A comprehensive user-friendly tool for mining multi-sample ChIP-seq data | a tool for analysing and mining multi-sample ChIP-seq data | ChIPdig is a tool designed for the bulk analysis of ChIP-seq data comprising multiple samples. Its capabilities are organized into four analysis modules: | In the example above, the first command establishes communication with the Bioconductor repository and the second command installs package “edgeR”. Repeat the second command for the remaining Bioconductor packages used by ChIPdig:" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "ChIPdig" ; sc:url "https://github.com/rmesse/ChIPdig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC7523640", "pubmed:31566663" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'RESULTS:ChIPseqSpikeInFree' | A ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in | A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications | We develop ChIPseqSpikeInFree, a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. This method is capable of revealing the similar magnitude of global changes as the spike-in method | Traditional reads per million (RPM) normalization method is inappropriate for the evaluation of ChIP-seq data when the treatment or mutation has the global effect" ; sc:featureList edam:operation_3222, edam:operation_3501, edam:operation_3798 ; sc:license "Apache-2.0" ; sc:name "ChIPseqSpikeInFree" ; sc:url "https://pecan.stjude.cloud/permalink/spikefree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6445533", "pubmed:30897079" ; sc:description "A Python3 framework to simulate read counts in a ChIP-seq experiment." ; sc:featureList edam:operation_0308, edam:operation_0445, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ChIPulate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vishakad/chipulate" ; biotools:primaryContact "Vishaka Datta S" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC6980795", "pubmed:31586868" ; sc:description """An R toolbox for modeling choices and response times in decision-making tasks. BACKGROUND:Decision-making is the process of choosing and performing actions in response to sensory cues to achieve behavioral goals. Many mathematical models have been developed to describe the choice behavior and response time (RT) distributions of observers performing decision-making tasks. However, relatively few researchers use these models because it demands expertise in various numerical, statistical, and software techniques. NEW METHOD:We present a toolbox - Choices and Response Times in R, or ChaRTr - that provides the user the ability to implement and test a wide variety of decision-making models ranging from classic through to modern versions of the diffusion decision model, to models with urgency signals, or collapsing boundaries.""" ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:name "ChaRTr" ; sc:url "https://github.com/mailchand/CHaRTr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749 ; sc:citation , "pubmed:31504177" ; sc:description "improved chaperone binding prediction using position-independent scoring matrices | ChaperISM is an algorithm to identify Hsp70 binding sequences in proteins. It uses a position-independent scoring matrix which was trained on either qualitative or quantitative chemiluminescence data previously published, obtained from interaction between DnaK and different ligands. Both versions of ChaperISM, qualitative or quantitative, resulted in an improved performance in comparison to other state-of-the-art chaperone binding predictors" ; sc:featureList edam:operation_2492, edam:operation_3799 ; sc:name "ChaperISM" ; sc:url "https://github.com/BioinfLab/ChaperISM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:31430151" ; sc:description "Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery | Aggregator Prediction-Webserver-ADMElab | Aggregation is one of the main reasons of false positives in HTS. To build a reliable prediction model, we collected a large dataset of aggregators and drugs to build several models based on the combination of different descriptors and algorithm, ChemAGG is a free webserver that could be used to easily filter out aggregators from potential lead molecules!" ; sc:featureList edam:operation_3216, edam:operation_3436 ; sc:name "ChemAGG" ; sc:url "http://admet.scbdd.com/ChemAGG/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2258, edam:topic_3316, edam:topic_3489 ; sc:citation , "pmcid:PMC6895184", "pubmed:31804487" ; sc:description """Comparative dataset of experimental and computational attributes of UV/vis absorption spectra. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. ChemDataExtractor toolkit tailored towards UV/vis absorption spectroscopy peak data. This work adapts the underlying table extraction mechanics of ChemDataExtractor version 1.3 , for higher precision extraction of maximum absorption peak wavelength data and associated extinction coefficients.""" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0399 ; sc:license "MIT" ; sc:name "ChemDataExtractor" ; sc:softwareHelp ; sc:url "http://chemdataextractor.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC7412753", "pubmed:32831287" ; sc:description """A Fast and Robust Coordination Environment Identification Tool. Coordination or local environments have been used to describe, analyze, and understand crystal structures for more than a century. Here, we present a new tool called ChemEnv< i>, which can identify coordination environments in a fast and robust manner. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen< i> package and the software can as well be used through a web app available on http: crystaltoolkit.org through the Materials Project.""" ; sc:name "ChemEnv" ; sc:url "https://doi.org/10.26434/CHEMRXIV.11294480.V1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation , "pubmed:31514773" ; sc:description "ChemPager is a freely available data analysis tool for analyzing, comparing and improving synthetic routes. Functions include prediction of the cumulative process mass intensity of chemical routes, irrespective of their development status, by comparison with a set of reactions executed on large scale. Along with the prediction of this core green chemistry metric aims to improve existing routes and help the decision-making process among route alternatives without the need for experimental data." ; sc:license "MIT" ; sc:name "ChemPager" ; sc:url "https://www.ingentaconnect.com/content/scs/chimia/2019/00000073/00000009/art00007/supp-data/content-2019_73_9_724" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3474 ; sc:citation , "pubmed:30637953" ; sc:description "Package for chemoinformatics calculations and machine learning." ; sc:featureList edam:operation_2945, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ChemSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://14.139.57.41/chemsuiteweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC6532271", "pubmed:31118054" ; sc:description "Pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data." ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ChiCMaxima" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yousra291987/ChiCMaxima" ; biotools:primaryContact "T. Sexton", "Y. Ben Zouari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3070, edam:topic_3361 ; sc:citation ; sc:description """An open-source automated experimental platform for biological science research. By combining heating, stirring, liquid handling, spectrometry, and optogenetics into a single easy-to-use platform, Chi.Bio can simplify laboratory protocols and drastically reduce equipment costs. No more will tired graduate students need to stay late in the lab to induce experiments, or run samples between incubators and plate readers.""" ; sc:featureList edam:operation_3891 ; sc:name "Chi.Bio" ; sc:url "https://chi.bio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A mine with chickpea data (both desi and kabuli varieties) from the Legume Information Systems (LIS) tripal.chado database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ChickpeaMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/chickpeamine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "Chickspress Genome Browser." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Chickspress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://geneatlas.arl.arizona.edu/" ; biotools:primaryContact "Eric H Lyons", "Fiona M McCarthy", "Shane C Burgess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3489, edam:topic_3500 ; sc:citation , ; sc:description """Open-source software for semi-automated segmentation and analysis of birdsong and other natural sounds. Abstract Audio recording devices have changed significantly over the last 50 years, making large datasets of recordings of natural sounds, such as birdsong, easier to obtain. This increase in digital recordings necessitates an increase in high-throughput methods of analysis for researchers. Specifically, there is a need in the community for open-source methods that are tailored to recordings of varying qualities and from multiple species collected in nature. We developed Chipper, a Python-based software to semi-automate both the segmentation of acoustic signals and the subsequent analysis of their frequencies and durations.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3891 ; sc:name "Chipper" ; sc:url "https://github.com/asearfos/chipper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0797, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC7145651", "pubmed:31665454" ; sc:description """A comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. ChlamDB documentation — ChlamDB 2.0 (June 2019) documentation. A comparative genomics database of the phylum Chlamydiae and other PVC (Planctomycetes, Verrucomicrobia, Lentisphaerae). Problems and errors encountered on the ChlamDB website can be announced on the github page of the website""" ; sc:featureList edam:operation_0303, edam:operation_2421, edam:operation_2422 ; sc:name "ChlamDB" ; sc:softwareHelp ; sc:url "https://chlamdb.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_3697 ; sc:citation , "pubmed:31539022" ; sc:description "A visualisation tool for linking function to phylogeny in microbiomes | Interactive visualisation and data annotation for meta-omics data | Chordomics is a tool to visualize and interpret linked data, such as from metagenomics or metaproteomics where both taxonomic and functional data is obtained | The demonstration version of Chordomics is available at https://kmcd.shinyapps.io/chordomics/. Here, a toy dataset is provided to allow you to see the explorative capabilities Chordomics provides before you need to install it!" ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:license "MIT" ; sc:name "Chordomics" ; sc:url "https://kmcd.shinyapps.io/chordomics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6612838", "pubmed:31510655" ; sc:description "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts | Code for the paper \"Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts\" | ChromDragoNN: cis-trans Deep RegulAtory Genomic Neural Network for predicting Chromatin Accessibility" ; sc:featureList edam:operation_0441, edam:operation_3192, edam:operation_3439 ; sc:license "MIT" ; sc:name "ChromDragoNN" ; sc:url "https://github.com/kundajelab/ChromDragoNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_2815, edam:topic_3293 ; sc:citation , "pmcid:PMC6792252", "pubmed:31615393" ; sc:description """A combined visualisation of phylogenetic and sequence data. Combined visualisation of phylogenetic and sequence data. Please see 'release' tab for executables and documentation below. ChromaClade is a desktop bioinformatics application that produces visualisations combining sequence and phylogenetic data. It annotates taxon names in a phylogenetic tree with amino acids found at individual sites in a corresponding sequence alignment. Residue-specific colour codes enable easy inspection by eye and the resulting trees can be viewed in any of several popular tree-viewing programs""" ; sc:featureList edam:operation_0558, edam:operation_0564, edam:operation_0567 ; sc:license "Apache-2.0" ; sc:name "ChromaClade" ; sc:url "http://github.com/chrismonit/chroma_clade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0798, edam:topic_3382 ; sc:citation , ; sc:description """A scalable whole-genome visualization of structural differences in prokaryotes. Colinear block visualisation tool. To create a fresh environment for chromatiblock to run in do:. Scalable, whole-genome visualisation of structural changes in prokaryotes. Will run chromatiblock on all fasta or genbank files in /path/to/fasta_directory/ and create an interactive webpage of the output. Intermediate files will be created in cb_working_dir""" ; sc:featureList edam:operation_0337, edam:operation_0496, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Chromatiblock" ; sc:url "https://github.com/mjsull/chromatiblock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC4341901", "pubmed:25349306" ; sc:description "Cancer in silico Drug Discovery (CIDD) is a platform to integrate data from the TCGA, Connectivity Map (CMap) and Cancer Cell Line Encyclopedia to facilitate and automate discovery of candidate drug compounds with the ultimate goal for treatment or chemo-prevention of cancer." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CiDD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cidd.scheetlabsoftware.org/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6726224", "pubmed:31483836" ; sc:description "A tool for predicting and analysing transcription factor binding sites | CIIIDER is a user-friendly tool for predicting and analysing transcription factor binding sites, designed with biologists in mind | Transcription factor binding site prediction and visualisation software" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_2464 ; sc:name "CiiiDER" ; sc:url "http://www.ciiider.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6522010", "pubmed:31095607" ; sc:description "An integrated and validated compendium of ciliary genes." ; sc:featureList edam:operation_3501, edam:operation_3629, edam:operation_3638 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CiliaCarta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/" ; biotools:primaryContact , "Martijn A. Huynen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3505 ; sc:encodingFormat edam:format_2330 ; sc:name "Bibliography" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1087 ; sc:encodingFormat edam:format_2196 ; sc:name "Ontology concept ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_3064 ; sc:citation , ; sc:description "The first ontology describing the anatomy and the development of Ciona robusta, based on the Hotta developmental table." ; sc:featureList edam:operation_0226, edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Ciona robusta Anatomy and Development Ontology" ; sc:url "https://www.aniseed.fr/aniseed/anatomy/find_devstage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0092, edam:topic_0203 ; sc:citation , "pmcid:PMC6380029", "pubmed:30777018" ; sc:description "Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space." ; sc:featureList edam:operation_0570, edam:operation_2942, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Circular Gene Ontology (CirGO)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/IrinaVKuznetsova/CirGO.git" ; biotools:primaryContact "Artur Lugmayr", "Irina Kuznetsova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC6795751", "pubmed:31649739" ; sc:description """A Powerful Tool for Identifying circRNA Coding Ability. A Python3-base pipeline for translated circular RNA(circRNA) identification. CircCode is a Python3-base pipeline for translated circular RNA identification. It automatically tandem links sequence in series and processes a given ribosome profile data (including quality control, filtering and alignment). Finally, based on random forest and J48 classification, the final translated circular RNA was predicted. The user only needs to fill in the given configuration file and run the python scripts to get the predicted translated circular RNA""" ; sc:featureList edam:operation_0436, edam:operation_0570, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "CircCode" ; sc:url "https://github.com/PSSUN/CircCode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:author "Dahui Hu", "Ming Chen", "Xianwen Meng" ; sc:citation , "pmcid:PMC6360206", "pubmed:30715276" ; sc:description "Database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "CircFunBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/CircFunBase/" ; biotools:primaryContact "Ming Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Integrated tool for the identification of circRNAs with protein-coding potential." ; sc:featureList edam:operation_0436, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CircPro" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/CircPro/" ; biotools:primaryContact "Ming Chen", "Xianwen Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6709551", "pubmed:31446897" ; sc:description "Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines | The CircRic refers to “circular RNA in cancers”. Circular RNAs (circRNAs) is class of non-coding RNA generated in a “back-splicing”. Recent studies have highlighted the important role of circRNAs in cancer. Here, we systematically characterize circRNAs expression profile in 935 cancer cell lines across 22 cancer lineages from Cancer Cell line Encyclopedia (CCLE), and analyzed the circRNAs biogenesis regulators, effect of circRNAs on drug response and association between circRNAs with mRNA, protein and mutation, and predicted RNA regulatory element in circRNAs" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_2495 ; sc:name "CircRiC" ; sc:url "https://hanlab.uth.edu/cRic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070 ; sc:citation , "pubmed:31588519" ; sc:description """A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms. circacompare is an R package that allows for the statistical analyses and comparison of two circadian rhythms. This work is published here and can be cited as:. Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh, CircaCompare: A method to estimate and statistically support differences in mesor, amplitude, and phase, between circadian rhythms, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz730""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3659 ; sc:name "CircaCompare" ; sc:url "https://github.com/RWParsons/circacompare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6909605", "pubmed:31830908" ; sc:description """Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. A method for circular DNA detection based on probabilistic mapping of ultrashort reads. Welcome to Circle-Map official repository!. Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. The package contains easy to run algorithms for accurately detect circular DNA formed from mappable and non mappable regions of a genome.""" ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "Circle-Map" ; sc:url "https://github.com/iprada/Circle-Map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6602521", "pubmed:31053864" ; sc:description "Web server for functional enrichment analysis of transcription factor ChIP-seq peaks." ; sc:featureList edam:operation_3222, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Cistrome-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://go.cistrome.org/" ; biotools:primaryContact "Clifford A Meyer", "X Shirley Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , , "pubmed:32353146" ; sc:description """CiteFuse enables multi-modal analysis of CITE-seq data. multi-modal analysis of CITE-seq data. CiteFuse is a streamlined package consisting of a suite of tools for pre-processing, modality integration, clustering, differential RNA and ADT expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualization of CITE-seq data""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3799 ; sc:name "CiteFuse" ; sc:url "http://SydneyBioX.github.io/CiteFuse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3293 ; sc:citation , "pubmed:30718334" ; sc:description "Clade Phylogenetic Profiling (CladePP) detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g. mammals, vertebrates, animals, plants) at which coevolution occurred." ; sc:featureList edam:operation_0533, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "CladePP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dolevrahat/CladePP" ; biotools:primaryContact "D. Rahat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3047, edam:topic_3295, edam:topic_3474 ; sc:citation , ; sc:description """Exploring the limit of using a deep neural network on pileup data for germline variant calling. Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling. Clair - Yet another deep neural network based variant caller. Single-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling, complex genome assembly, and epigenetic mark detection""" ; sc:featureList edam:operation_0525, edam:operation_3196, edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "Clair" ; sc:url "https://github.com/HKU-BAL/Clair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Field-scouting software for the identification of wildlife in camera trap images." ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ClassifyMe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://classifymeapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0637, edam:topic_2258, edam:topic_3314 ; sc:citation , "pubmed:31576380" ; sc:description "A webapplication for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy." ; sc:featureList edam:operation_2422, edam:operation_2996, edam:operation_3359 ; sc:name "ClassyFire" ; sc:url "http://classyfire.wishartlab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3517 ; sc:citation , "pmcid:PMC6595587", "pubmed:31391866" ; sc:description "An open cloud-based platform for big pan-cancer data genome-wide association study, visualization and exploration | Click: Do GWAS analysis by yourself by Clicking | More than 30 cancer types, more than 10,000 samples | Including gene expression, copy number variation, methylation and mutation data categories | You are accessing a non-profit web site which is based on GDC data portal hosted by National Cancer Institute, USA. All data was downloaded from GDC public database. Please make sure you are aware of and obey the policy of GDC data portal. Please go to User`s Guide for more information | Beeswarm plot, Manhattan plot, Volcano plot, Mountain plot, Deflection plot, Linear regression analysis, significance test and" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:name "ClickGene" ; sc:softwareHelp ; sc:url "http://www.clickgenome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3518, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """A novel method for allele-specific somatic copy-number alterations detection. Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data. A tool for large-scale CNV and CNA detection.""" ; sc:featureList edam:operation_0452, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "ClinCNV" ; sc:url "https://github.com/imgag/ClinCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3305, edam:topic_3324, edam:topic_3382 ; sc:citation , ; sc:description """An open-access clinical epidemiology database resource encouraging online exploration of complex studies. The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical and epidemiologic studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework. Here we present an intuitive point-and-click website that allows users to visualize and subset data directly in the ClinEpiDB browser and immediately explore potential associations""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "ClinEpiDB" ; sc:url "https://clinepidb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3400 ; sc:description "Visual analytics tool for breast cancer treatment stratification." ; sc:featureList edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ClinOmicsTrail" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://clinomicstrail.bioinf.uni-sb.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3400 ; sc:citation , "pubmed:31038669" ; sc:description "Visual analytics tool for breast cancer treatment stratification." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ClinOmicsTrailbc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://clinomicstrail.bioinf.uni-sb.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC6174354", "pubmed:30220433" ; sc:description "Efficient tool for identifying disease-relevant nonsynonymous single nucleotide variants." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3461 ; sc:name "ClinPred" ; sc:url "https://sites.google.com/site/clinpred/" ; biotools:primaryContact "Jacek Majewski", "Najmeh Alirezaie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0749 ; sc:citation , "pubmed:30765865" ; sc:description "Quick evaluation of the clinical relevance of copy number variants (CNVs) in the context of topologically associated domains (TADs)." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "ClinTAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.clintad.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation , "pubmed:31830259" ; sc:description "Clinical Variant Annotation Pipeline (ClinVAP) creates a genetic report of somatic mutations from a variant call format (VCF) file. Please refer this document for implementation of the pipeline. Documentation of the pipeline is available at Wiki page." ; sc:featureList edam:operation_0310, edam:operation_0331, edam:operation_0337, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "ClinVAP" ; sc:url "https://github.com/PersonalizedOncology/ClinVAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network." ; sc:featureList edam:operation_3798, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CliqueMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.3.2" ; sc:url "https://github.com/osenan/cliqueMS" ; biotools:primaryContact "Oriol Senan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3794 ; sc:citation , , "pmcid:PMC7016857", "pubmed:31947823" ; sc:description """Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Clirc: a user-friendly bioinformatics software to identify RBP-bound circRNAs through analysis of CLIP-Seq data. The Clirc software is designed to identify RBP-bound circRNAs in CLIP-Seq data. The Clirc software internally calls the gsnap aligner for alignment of CLIP-Seq reads. The CLIP-Seq technology comprises of three variants: HITS-CLIP, PAR-CLIP, and iCLIP. The Clirc software works on all three versions of them. It can also work on any type of RNA-Seq data in general, although non-polyA selected RNA-Seq is preferred. The Clirc software is designed to search for known circRNAs in high-throughput sequencing data whose coordinates are provided by users. The users can collect these coordinates from previous publication or their own search using RNA-Seq data. This avoids the common problem of short sequncing reads in CLIP-Seq data. But this approach cannot identify novel circRNAs in CLIP-Seq data""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198 ; sc:name "Clirc" ; sc:url "https://github.com/Minzhe/Clirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_3168 ; sc:citation , , "pmcid:PMC6936074", "pubmed:31888455" ; sc:description """Clonal reconstruction from time course genomic sequencing data. ClonalTREE (Clonal reconstruction in Time couRse long-term Evolution Experiment). Usage: python3 ClonalTREE.py """ ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226 ; sc:license "GPL-3.0" ; sc:name "ClonalTREE" ; sc:url "https://github.com/COL-IU/ClonalTREE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:30649189" ; sc:description "R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics." ; sc:featureList edam:operation_0337, edam:operation_3627, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CluMSID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tdepke/CluMSID/" ; biotools:primaryContact "Tobias Depke" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation ; sc:description "Create Neighbor-joining or UPGMA phylogentic trees from a multiple sequence alignment using ClustalW." ; sc:featureList edam:operation_0323 ; sc:name "ClustalW2 Phylogeny API EBI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=54651945" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:31089956" ; sc:description "R package for the analysis of hierarchical data using generalized linear models with the cluster bootstrap." ; sc:featureList edam:operation_0552, edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ClusterBootstrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://cran.r-project.org/package=ClusterBootstrap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3305, edam:topic_3512, edam:topic_3676 ; sc:citation , , "pubmed:32732227" ; sc:description """Enhanced prediction of gene and missense rare-variant pathogenicity by joint analysis of gene burden and amino-acid residue position. Rare variant association using position and burden signals. This method is designed for case-control studies where the condition under investigation is caused by rare variants in protein-coding regions. This is the case for most Mendelian diseases and therefore this method is relevant for these""" ; sc:featureList edam:operation_2454, edam:operation_3225, edam:operation_3461, edam:operation_3791 ; sc:name "ClusterBurden" ; sc:url "https://github.com/adamwaring/ClusterBurden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation ; sc:description "ClusterScan is a tool to search for genomic clusters starting from genomic feature locations and their annotations. It allows the user to scan an annotation file (BED format with locations of specific features such as gene, transcripts, regulatory regions or anything that can be mapped on a genome) and get clusters coordinates in output. In order to build annotated clusters, ClusterScan needs an additional two-columns file, storing the feature ids and the corresponding categorical information (such as Gene Ontology classes, KEGG, Pfam accessions, etc)." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ClusterScan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "https://github.com/pyrevo/ClusterScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pubmed:28187414" ; sc:description "The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org." ; sc:name "CmPIweb" ; sc:url "http://CmPIweb.CELLmicrocosmos.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Script" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259, edam:topic_3070 ; sc:citation , "pubmed:31359031" ; sc:description "CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models." ; sc:featureList edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoBAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.1.4" ; sc:url "https://github.com/BioSystemsUM/cobamp" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31141144" ; sc:description "Count Corrector for nested genes and multi-mapped reads." ; sc:featureList edam:operation_3563, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3336, edam:topic_3379 ; sc:citation , "pmcid:PMC6637175", "pubmed:31360332" ; sc:description "A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria | Computational Drug Repositioning Score" ; sc:name "CoDReS" ; sc:url "http://bioinformatics.cing.ac.cy/codres" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1963 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_1963 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0128, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:30626316" ; sc:description """CoExpresso is a tool to investigate the behavior of protein subunits in known complexes by comparing their abundance profiles across up to 140 cell types available in ProteomicsDB. Thorough assessment of different randomization methods and statistical scoring algorithms allows determining the significance of concurrent profiles within a complex, therefore providing insights into the conservation of their composition across human cell types as well as the identification of intrinsic structures in complex behavior to determine which proteins orchestrate complex function.""" ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0531, edam:operation_0571, edam:operation_2238, edam:operation_2495, edam:operation_2935, edam:operation_3083, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CoExpresso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/CoExpresso/" ; biotools:primaryContact "Veit Schwämmle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3517 ; sc:citation ; sc:description "Collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoMM-S" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gordonliu810822/CoMM" ; biotools:primaryContact "Jin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Comparative Metatranscriptomics Workflow is a standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads." ; sc:featureList edam:operation_0524, edam:operation_2495, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoMW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/anwarMZ/CoMW" ; biotools:primaryContact "Carsten Suhr Jacobsen", "Muhammad Zohaib Anwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:author "Alexandra Zaharia" ; sc:citation , "pmcid:PMC6327494", "pubmed:30630411" ; sc:description "CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods) - exploration tool for conserved organizational motifs at both the metabolic and genomic level." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoMetGeNe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cometgene.lri.fr" ; biotools:primaryContact "Alexandra Zaharia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0780 ; sc:citation , , "pmcid:PMC7145505", "pubmed:31988262" ; sc:description "Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots | A platform dedicated to the visualization and analysis of plant co-expression and co-function networks" ; sc:featureList edam:operation_0313, edam:operation_3463, edam:operation_3766 ; sc:name "CoNekT-Plants" ; sc:url "http://conekt.plant.tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3520 ; sc:author "Marzieh Ayati", "Mehmet Koyuturk" ; sc:citation , "pmcid:PMC6411229", "pubmed:30811403" ; sc:description "Method for Co-phosphorylation-based Kinase-substrate interaction prediction (CophosK)." ; sc:featureList edam:operation_0417, edam:operation_3501, edam:operation_3639 ; sc:isAccessibleForFree true ; sc:name "CoPhosK" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://compbio.case.edu/omics/software/cophosk/index.html" ; biotools:primaryContact "Mark R. Chance", "Marzieh Ayati" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3957 ; sc:citation , , "pmcid:PMC7356028", "pubmed:32580303" ; sc:description "A pipeline to decrypt the inter protein interfaces from amino acid sequence information | Abstract Computational methods have been devised in the past to predict the interface residues using amino acid sequence information but have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence are different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here we report a new hybrid pipeline for the prediction of protein-protein interaction interfaces from the amino acid sequence information alone based on the framework of Co -evolution, machine learning ( R andom forest) and Ne twork A nalysis named CoRNeA trained specifically on eukaryotic protein complexes" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_2492 ; sc:name "CoRNeA" ; sc:url "https://github.com/krits04/cornea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3520 ; sc:citation , "pubmed:31042389" ; sc:description "Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry." ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoSIMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/ChristopherAMyers/CoSIMS" ; biotools:primaryContact "Alan A. Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3308, edam:topic_3810 ; sc:citation , ; sc:contributor ; sc:description "The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources." ; sc:featureList edam:operation_0292, edam:operation_3184, edam:operation_3559 ; sc:funder "ANR" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Cocoa Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://cocoa-genome-hub.southgreen.fr/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc:description """predictive models for the characterization of mRNA transcripts in Eukaryotes. CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species""" ; sc:featureList edam:operation_0278, edam:operation_0436, edam:operation_0524, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "CodAn" ; sc:url "https://github.com/pedronachtigall/CodAn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2885 ; sc:citation ; sc:description "Computes genomic breeding values using external information on the markers. The package fits a linear mixed model with heteroscedastic random effects, where the random effect variance is fitted using a linear predictor and a log link." ; sc:featureList edam:operation_0282, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CodataGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/CodataGS/index.html" ; biotools:primaryContact "E. F. Mouresan", "Lars Ronnegard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0780 ; sc:description "Coding Sequence optimization for Chlamydomonas reinhardtii" ; sc:isAccessibleForFree true ; sc:name "Coding Sequence Optimization for Chlamydomonas reinhardtii" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65416-iddoweiner-coding-sequence-optimization-for-chlamydomonas-reinhardtii" ; biotools:primaryContact "Iddo Weiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3512 ; sc:citation , "pubmed:23466472" ; sc:description "CODONOME collects the expression value of each codon (just called \"codonome\") and of each aminoacyl-tRNA synthetase (aaRS). To do this, the software is able to count the total mRNA codon number of any organism and to import and integrate any mRNA expression data source in tabulated text format." ; sc:name "Codonome" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apollo11.isto.unibo.it/software/Codonome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780 ; sc:author "Alexis Dereeper", "Gaetan Droc" ; sc:citation , , "pubmed:25392413" ; sc:description "The Coffee Genome Hub is an integrated web-based database providing centralized access to coffee community genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee." ; sc:featureList edam:operation_0361, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Coffee Genome Hub" ; sc:softwareHelp ; sc:url "https://coffee-genome-hub.southgreen.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623 ; sc:citation , , "pmcid:PMC7200068", "pubmed:32100706" ; sc:description """Detecting Significant Associations and Dissociations in Pangenomes. A tool for the identification of coincident (associating and dissociating) genes in pangenomes. input/output files associated with the analysis performed in the manuscript describing coinfinder. Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Coinfinder is written primarily in C++ and is a command line tool which generates text, gexf, and pdf outputs for the user. Written in collaboration with Martin Rusilowicz""" ; sc:featureList edam:operation_2238, edam:operation_2422, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Coinfinder" ; sc:url "https://github.com/fwhelan/coinfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3382 ; sc:citation , "pubmed:31216308" ; sc:description "Python package for the analysis of bacterial fluorescence microscopy data." ; sc:featureList edam:operation_3431, edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ColiCoords" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Jhsmit/ColiCoords" ; biotools:primaryContact "J. H. Smit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC6538547", "pubmed:31138109" ; sc:description "Collaboration of deep neural networks for biomedical named entity recognition." ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CollaboNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wonjininfo/CollaboNet" ; biotools:primaryContact "Jaewoo Kang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0202, edam:topic_0209 ; sc:citation ; sc:description "Tool that allows extracting from the Open PHACTS Discovery platform series of compounds annotated with experimental data that can be used directly for building QSAR predictive models." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Collector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://phi.upf.edu/collector/" ; biotools:primaryContact "Manuel Pastor", "Oriol L. Massaguer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , , "pmcid:PMC7214035", "pubmed:32049317" ; sc:description "artificial intelligence approach to quantify co-localization between mass spectrometry images | Methods for measuring co-localization of ion images | Measuring co-localization of ion images | This repository is devoted to a project on measuring co-localization of mass spectrometry images. The project is carried out by the Alexandrov team at EMBL Heidelberg. We created a webapp for ranking pairs of ion images, engaged external experts to rank images from their public data from METASPACE, consolidated the results into a gold standard set of ranked pairs of ion images, and, finally, developed and evaluated various measures of co-localization | Katja Ovchinnikova: pixel-based co-localization method development, gold standard preparation" ; sc:featureList edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "ColocML" ; sc:url "https://github.com/metaspace2020/coloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC6307751", "pubmed:30589908" ; sc:description "Software tool for the quantification of metastatic colony growth dynamics and size distributions in vitro and in vivo." ; sc:featureList edam:operation_3443, edam:operation_3795, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ColonySizeDistributions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sbhoyar1/ColonySizeDistributions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_3512 ; sc:citation ; sc:description """Community predictions of hubs in gene regulatory networks. Abstract Summary Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been developed to predict individual regulator-gene interactions from gene expression data, few methods focus on inferring these hubs. We have developed ComHub, a tool to predict hubs in GRNs. ComHub makes a community prediction of hubs by averaging over predictions by a compendium of network inference methods. Benchmarking ComHub to the DREAM5 challenge data and an independent data set of human gene expression, proved a robust performance of ComHub over all data sets. Lastly, we implemented ComHub to work with both predefined networks and to do standard network inference, which we believe will make it generally applicable""" ; sc:featureList edam:operation_1781, edam:operation_2454, edam:operation_3439 ; sc:name "ComHub" ; sc:url "https://gitlab.com/Gustafsson-lab/comhub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0780 ; sc:citation ; sc:description "A comparative platform on grapevine and tomato reporting paralog and related ortholog genes identified with an analytical, dedicated, procedure. It provides an update on functional annotations from the two species and it represents an internationally unique platform. It is in expansion in order to include other species, useful to study fruit development." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ComParaLogS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://biosrv.cab.unina.it/comparalogs/gene/search" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3068, edam:topic_3399 ; sc:citation ; sc:description "Tool for interactive analysis of disease comorbidities over large patient datasets." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Comorbidity4j" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comorbidity.eu/comorbidity4web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3372 ; sc:citation , , "pmcid:PMC4845442", "pmcid:PMC6869179", "pubmed:27112575", "pubmed:31747901" ; sc:description """A GUI based tool for comparison of multiple biological interaction networks. Interaction networks are a convenient way of representing the complex nature of multi-component systems. Examples of such complex systems include biological pathways, social interactions, financial markets, management systems, multiple modules in a programming language, etc. Recognizing the similarities and differences between multiple interaction networks becomes easier when aided by proper visualization tools. we present a GUI based network comparison tool CompNet, which allows to visually compare multiple networks based on node and edge similarities. Additionally, the tool can compare individual networks on the basis of general network properties, node neighborhoods and community similarities. CompNet is expected to be a valuable addition in the field of visual data mining especially for users aiming to visually compare more than two interaction networks at the same time""" ; sc:featureList edam:operation_0277, edam:operation_3083 ; sc:name "CompNet" ; sc:url "https://web.rniapps.net/compnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31449403" ; sc:description """Problems with homepage (January 6th, 2021) | CompScore is a web application for boosting structure-based virtual screening performance by incorporating docking scoring function components into consensus scoring.""" ; sc:featureList edam:operation_0482, edam:operation_3501 ; sc:name "CompScore" ; sc:url "http://bioquimio.udla.edu.ec/compscore/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc:description "Simple and fast web tool for everyday list comparison, e.g. of genes. Shows the intersection, union, and Jaccard index. Allows easy copying & pasting of comparison results." ; sc:featureList edam:operation_2424 ; sc:isAccessibleForFree true ; sc:name "Compare Two Lists" ; sc:url "https://compare.tartaglialab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6547514", "pubmed:31159772" ; sc:description "Differential analysis of combinatorial protein complexes." ; sc:featureList edam:operation_3258, edam:operation_3630, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CompleXChange" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/complexchange/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0128, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "ComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps." ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0531, edam:operation_0571, edam:operation_2238, edam:operation_2428, edam:operation_2495, edam:operation_2938, edam:operation_2939, edam:operation_2940, edam:operation_3083, edam:operation_3282, edam:operation_3435, edam:operation_3463, edam:operation_3659, edam:operation_3799 ; sc:name "ComplexBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , ; sc:description "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules. All data is freely available for search and download." ; sc:featureList edam:operation_2422, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Complex Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ebi.ac.uk/complexportal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885 ; sc:citation , "pubmed:29625053" ; sc:description "CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers" ; sc:featureList edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CompositeDriver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/khuranalab/CompositeDriver" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_0798 ; sc:citation , "pmcid:PMC6301336", "pubmed:30576494" ; sc:description "Comprehensive database of transposable elements in conifers." ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ConTEdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genedenovoweb.ticp.net:81/conTEdb/index.php" ; biotools:primaryContact "Fangqun Ouyang", "Fei Yi", "Junhui Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6444814", "pubmed:30935387" ; sc:description "Software for unsupervised discovery of clonal somatic mutations in single cells through read phasing." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Conbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/conbase/conbase" ; biotools:primaryContact "Ezeddin Al Hakim", "Marie Kindblom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description "machine-learning optimized long-range genome analysis workflow for next-generation sequencing | a machine-learning optimized long-range genome analysis workflow for next-generation sequencing | Current human genome sequencing assays in both clinical and research settings primarily utilize short-read sequencing and apply resequencing pipelines to detect genetic variants" ; sc:license "Apache-2.0" ; sc:name "ConnectedReads" ; sc:url "https://github.com/atgenomix/connectedreads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0610, edam:topic_3489 ; sc:citation , "pmcid:PMC6863500", "pubmed:31679497" ; sc:description "A database portal containing esources that can be used to infer baseline species conditions." ; sc:name "Conservation Archive" ; sc:url "https://conservationarchive.shinyapps.io/ConservationArchive/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:encodingFormat edam:format_3475 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:encodingFormat edam:format_3475 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3475 ; sc:name "Evidence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3475 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author ; sc:citation , ; sc:description "Conterminator is an efficient method to detect incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison. It is free open-source GPLv3-licensed software for Linux and macOS." ; sc:featureList edam:operation_2478, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Conterminator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1-c74b5" ; sc:url "https://conterminator.mmseqs.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229 ; sc:citation , "pmcid:PMC6331134", "pubmed:30601802" ; sc:description "Analysis of spatially organized protein expression in high-throughput screens." ; sc:featureList edam:operation_3443, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Context-explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://contextexplorer.readthedocs.io/en/latest/" ; biotools:primaryContact "Joel Ostblom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0176, edam:topic_0611 ; sc:citation , , "pmcid:PMC6933837", "pubmed:31693263", "pubmed:36244611" ; sc:description """Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Plugin to use continuousflex protocols within the Scipion framework. This plugin provides HEMNMA and StructMap protocols and is frequently updated.""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3457, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "ContinuousFlex" ; sc:url "https://pypi.org/project/scipion-em-continuousflex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC6831742", "pubmed:31737032" ; sc:description """Automatic Partial Charge Prediction by Machine Learning. In recent years, machine learning techniques have been widely used in biomedical research to predict unseen data based on models trained on experimentally derived data. In the current study, we used machine learning algorithms to emulate computationally complex predictions in a reverse engineering-like manner and developed ContraDRG, a software that can be used to predict partial charges for small molecules based on PRODRG and Automated Topology Builder (ATB) predictions. Both tools generate molecular topology files, including the partial atomic charge, by using different procedures.""" ; sc:featureList edam:operation_2476, edam:operation_3435, edam:operation_3893 ; sc:name "ContraDRG" ; sc:url "https://cdrg.mathematik.uni-marburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6921240", "pubmed:31767541" ; sc:description """A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network. BACKGROUND:The spatial distributions of different types of cells could reveal a cancer cell's growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key "hallmarks of cancer". However, the process by which pathologists manually recognize and localize all the cells in pathology slides is extremely labor intensive and error prone. METHODS:In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor cell, stromal cell, and lymphocyte classification, and extraction of tumor microenvironment-related features for lung cancer pathology images.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3659 ; sc:name "ConvPath" ; sc:softwareHelp ; sc:url "https://qbrc.swmed.edu/projects/cnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3678 ; sc:citation , "pmcid:PMC6853199", "pubmed:31763041" ; sc:description """Set-based differential covariance testing for genomics. We describe four different summary statistics, to ensure power and flexibility under various settings, including a new connectivity statistic that is sensitive to changes in overall covariance magnitude""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "CorDiff" ; sc:url "https://cran.r-project.org/web/packages/CorDiff/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:31657800" ; sc:description """Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal. Welcome to the CorEx portal for gene expression analysis!. This website began as an extension of work applying the CorEx machine learning algorithm to gene expression data from ovarian cancer tumors as presented in this paper.""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3223 ; sc:name "CorEx" ; sc:url "http://corex.isi.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3855 ; sc:citation , "pmcid:PMC6525400", "pubmed:31101011" ; sc:description "Transcriptomic database for 14 species of scleractinian corals." ; sc:featureList edam:operation_3258, edam:operation_3431, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CoralTBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.comp.hkbu.edu.hk/~db/CoralTBase" ; biotools:primaryContact , "Jianliang Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC6371488", "pubmed:30744586" ; sc:description "Enables extraction of morphomic markers from CT images by non-technically skilled clinicians." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoreSlicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://coreslicer.com/" ; biotools:primaryContact "Louis Mullie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3168 ; sc:citation , , "pmcid:PMC3964939", "pmcid:PMC5727400", "pubmed:24203703", "pubmed:31725859" ; sc:description "A genomics, genetics and breeding web portal for cotton research." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_3196, edam:operation_3208 ; sc:name "CottonGen" ; sc:url "http://cottongen.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382 ; sc:citation , "pmcid:PMC6683572", "pubmed:31404403" ; sc:description "Applications for plant phenotyping | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods | A semiautomated graphic software – applications for plant phenotyping Lianne Merchuk-Ovnat, Ph.D.; Zev Ovnat; Orit Amir-Segev; Yaarit Kutsher; Yehoshua Saranga; Moshe Reuveni Plant Methods 'Coverage.exe' - instructions for use | \"o To exclude everything but the interior of a quadrilateral, position cursor over its 4 vertices and click F1, F2, F3 & F4 in clockwise order:\" \"at top left click F1, at top right click F2, at bottom right click F3, at bottom left click F4.\" \"o Click on radio button 1-10 to select colors to take into account (\"\"Include\"\") and those to dis-count (\"\"Ignore\"\").\" o Not all 10 + 10 selctions need be filled" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "CoverageTool" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/lianneovnat/CoverageTool" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A mine containing both cowpea genetic and genomic data, courtesy UC-Riverside" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "CowpeaMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/cowpeamine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC6927105", "pubmed:31865908" ; sc:description """Interpretable deep neural network for cancer survival analysis by integrating genomic and clinical data. Pathway-based sparse deep neural network for survival analysis. Cox-PASNet is a pathway-based sparse deep neural network for survival analysis""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_2497 ; sc:name "Cox-PASNet" ; sc:url "https://github.com/DataX-JieHao/Cox-PASNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:31808791" ; sc:description """A Python Package for DNA Methylation Analysis. Python package to analyze DNA methylation data. $ pip3 install git+https://github.com/liguowang/cpgtools.git""" ; sc:featureList edam:operation_3204, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "CpGtools" ; sc:url "https://github.com/liguowang/cpgtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2885, edam:topic_3293 ; sc:citation , "pubmed:31453748" ; sc:description "The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas | Welcome to the CpnClassiPhyR Github Page! | a cpn60 universal target-based classification tool for phytoplasma | Phytoplasmas (‘Candidatus Phytoplasma’), first known as mycoplasma-like organisms, are wall-less, insect vectored bacteria that cause disease in more than a thousand different plant hosts, affecting weedy, ornamental and crop plants worldwide | Following the strategy previously used in the phytoplasma classification scheme based on the 16S rRNA gene, we developed a complementary, coherent system to classify phytoplasmas based on RFLP analysis of cpn60 UT sequences with seven endonucleases" ; sc:featureList edam:operation_3192, edam:operation_3460, edam:operation_3891 ; sc:name "CpnClassiPhyR" ; sc:url "http://cpnclassiphyr.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:31099383" ; sc:description "Reference-Based Decompression in Node and the Browser." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cram-JS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GMOD/cram-js" ; biotools:primaryContact "Robert Buels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Software to generate CRISPR guide RNAs against genomes annotated with individual variation." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Crisflash" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/crisflash/crisflash" ; biotools:primaryContact "Margus Lukk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6501434", "pubmed:31058278" ; sc:description "Comprehensive circular RNA resource for crops in response to abiotic stress." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CropCircDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://deepbiology.cn/crop/" ; biotools:primaryContact , "Hongwei Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6330393", "pubmed:30634901" ; sc:description "GUI application for viewing and handling Manhattan Plots. The user can zoom, select and crop Manhattan Plots and generate output both in the graphical and numerical format." ; sc:featureList edam:operation_3222, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Cropper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/cropper" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3308 ; sc:author "Ahmed Hafez", "Hrant Hovhannisyan" ; sc:citation , "pmcid:PMC7049214", "pubmed:31392323" ; sc:description "estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies | General descripiton of Crossmapper | Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific expression studies, and can be extended for the use in large sequencing facilities for resource optimization" ; sc:license "GPL-3.0" ; sc:name "Crossmapper" ; sc:softwareHelp ; sc:softwareVersion "v1.1.1" ; sc:url "https://github.com/Gabaldonlab/crossmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0610 ; sc:citation ; sc:description "A wisdom of the crowd-based Gene Ontology annotation tool | Abstract Motivation Protein function prediction tools vary widely in their methodologies, resulting in different sets of GO terms being correctly predicted. Ideally, multiple tools are combined to achieve a higher recall of GO terms while increasing precision. Results CrowdGO combines input predictions from any number of tools and combines them based on the Gene Ontology Directed Acyclic Graph. Using each GO terms information content, the semantic similarity between GO predictions of different tools, and a Support Vector Machine model, it achieves improved precision and recall compared to each of the tools separately (Figure 1). Availability CrowdGO can be found at https: gitlab.com mreijnders CrowdGO" ; sc:license "GPL-3.0" ; sc:name "CrowdGO" ; sc:url "https://gitlab.com/mreijnders/CrowdGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3305, edam:topic_3474 ; sc:citation , "pmcid:PMC6476276", "pubmed:31037238" ; sc:description "Tracking Health Trends Using Public Social Media Data and Crowdsourcing." ; sc:featureList edam:operation_0560, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Crowdbreaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.crowdbreaks.org/" ; biotools:primaryContact "Marcel Salathé", "Martin Müller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3263 ; sc:citation ; sc:description "Secure encryption tool for genomic data, namely in Fasta, Fastq, VCF, SAM and BAM formats, which is also capable of reducing the storage size of Fasta and Fastq files." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Cryfa" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cobilab/cryfa" ; biotools:primaryContact "Morteza Hosseini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3077, edam:topic_3382 ; sc:citation , , "pubmed:32233514" ; sc:description """Live analysis and reconstruction of single-particle cryo-electron microscopy data with CryoFLARE. CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data. The FMI Live Analysis and Reconstruction Engine. Live analysis of Cryo EM data made easy. Import data from EPU or SerialEM""" ; sc:featureList edam:operation_2422, edam:operation_2940, edam:operation_3457 ; sc:name "CryoFLARE" ; sc:softwareHelp , ; sc:url "http://www.cryoflare.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3452 ; sc:citation , , "pmcid:PMC6400257", "pubmed:30821710" ; sc:description "Software for processing serial crystallography data from an X-ray free-electron laser or a synchrotron light source." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CrystFEL" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "http://www.desy.de/~twhite/crystfel/" ; biotools:primaryContact "Thomas White" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3314, edam:topic_3474 ; sc:citation , "pubmed:31615262" ; sc:description """Automated computation of lattice energies of organic crystals exploiting the many-body expansion to achieve dual-level parallelism. Set of scripts to automate the calculation of crystal lattice energies. Automated calculation of crystal lattice energies with the many-body expansion. CrystaLattE has an interface with the quantum chemistry package PSI4. To run, the code requires a crystallographic information file containing structural information of the crystal and an input file specifying execution details. Work continues in the creation of a CrystaLattE pip package. So, for the moment, the instructions to download and install CrystaLattE and to create a conda environment that includes PSI4 are presented below. CyrstaLattE is a software that automates the computation of crystal lattice energies using the many-body cluster expansion""" ; sc:featureList edam:operation_3432 ; sc:license "LGPL-3.0" ; sc:name "CrystaLattE" ; sc:url "https://github.com/carlosborca/CrystaLattE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3416 ; sc:citation ; sc:description """A cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq. Cumulus WDL workflows and Dockerfiles. Interactive single cell visualization in the cloud or on your desktop. Cumulus WDL workflows and Dockerfiles — Cumulus documentation. Clone the cirrocumulus repository:. Google Cloud Platform (GCP) Deployment Instructions. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_2939, edam:operation_3096, edam:operation_3680 ; sc:license "BSD-3-Clause" ; sc:name "Cumulus" ; sc:softwareHelp ; sc:url "https://github.com/klarman-cell-observatory/cumulus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3379, edam:topic_3400 ; sc:citation , "pubmed:31416842" ; sc:description "A Database of Predicted T-cell Epitopes from Overly Expressed Proteins in Metastatic Cutaneous Melanoma | Browse and download predicted melanoma epitopes with high expected clinical efficacy in anti-cancer immunotherapy | This page acts as a gateway to the Curatopes Melanoma database" ; sc:featureList edam:operation_0416 ; sc:name "Curatopes Melanoma" ; sc:softwareHelp ; sc:url "https://www.curatopes.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC6507062", "pubmed:31072334" ; sc:description "Optimal Equal-HR Method to Find Two Cutpoints for U-Shaped Relationships in Cox Model." ; sc:featureList edam:operation_0490, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CutpointsOEHR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=CutpointsOEHR" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:encodingFormat edam:format_3751 ; sc:name "Pathway or network report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0204 ; sc:author ; sc:citation ; sc:description "CyGenexpi is a Cytoscape plugin for validating/inferring genetic networks from time series expression data. It is based on a ordinary differential equation (ODE) model of gene regulation." ; sc:featureList edam:operation_1781 ; sc:funder "Ministry of Education, Youth and Sports of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "CyGenexpi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0", "1.4.2" ; sc:url "https://github.com/cas-bioinf/genexpi/wiki/CyGenexpi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3360 ; sc:citation , "pmcid:PMC5473464", "pubmed:28663787" ; sc:description "Differential discovery in high-throughput high-dimensional cytometry datasets." ; sc:featureList edam:operation_2938, edam:operation_2939, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CyTOF workflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imlspenticton.uzh.ch/robinson_lab/cytofWorkflow" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3474 ; sc:citation , , "pmcid:PMC3855388", "pmcid:PMC6707396", "pubmed:24340000", "pubmed:31489175" ; sc:description "A flexible solution for network extension in Cytoscape | The CyTargetLinker app extends biological networks with regulatory interactions, for example miRNA-target, TF-target or drug-target interactions | CyTargetLinker website and tutorials | CyTargetLinker - Extend your biological networks in Cytoscape" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "CyTargetLinker" ; sc:softwareHelp , ; sc:url "https://cytargetlinker.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520, edam:topic_3697 ; sc:citation , "pubmed:31864964" ; sc:description """De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. CycloNovo: Algorithm for de novo cyclopeptide analysis of high-resolution tandem mass spectra. CycloNovo is a new algorithm that identifies spectra generated from cyclopeptides in large mass spectrometry datasets. CycloNovo can also de novo sequence the cyclopeptides represented by identified cyclospectra""" ; sc:featureList edam:operation_0524, edam:operation_3644, edam:operation_3860 ; sc:name "CycloNovo" ; sc:url "https://github.com/bbehsaz/cyclonovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3170 ; sc:citation ; sc:description "Package to tackle cell cycle. It provides methods to recover cell cycle information and remove cell cycle factor from the scRNA-seq data." ; sc:featureList edam:operation_2436, edam:operation_3629, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cyclum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KChen-lab/cyclum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3518 ; sc:citation , "pmcid:PMC6739950", "pubmed:31510921" ; sc:description "A web-based tool to convert karyotypes to genomic coordinates | Sequence-Cytogenetic Bulk Conversion | Bulk Sequence - Cytogenetic Conversion Service | Use this page to get cytogenetic locations for features or sequence locations, or get sequence locations for cytogenetic locations | Organism: Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus" ; sc:featureList edam:operation_1812, edam:operation_3196 ; sc:name "CytoConverter" ; sc:url "https://jxw773.shinyapps.io/Cytogenetic__software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3303, edam:topic_3518 ; sc:citation , ; sc:description "CytoGenetic Pattern Sleuth (CytoGPS) - web-enabled karyotype analysis tool for cytogenetics." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CytoGPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.8" ; sc:url "http://cytogps.org/" ; biotools:primaryContact "Institute for Informatics, Washington University School of Medicine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3934 ; sc:citation , "pmcid:PMC7078957", "pubmed:31633883" ; sc:description "A Normalization Algorithm for Cytometry Data. A R library to normalize cytometry data." ; sc:featureList edam:operation_3200, edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:license "GPL-2.0" ; sc:name "CytoNorm" ; sc:softwareHelp ; sc:softwareVersion "0.0.5" ; sc:url "http://www.github.com/saeyslab/CytoNorm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:31114843" ; sc:description "Web-interface for simulating multi-dimensional cell imaging." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CytoPacq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cbia.fi.muni.cz/simulator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3395 ; sc:citation ; sc:description "Single-cell transcriptional diversity is a hallmark of developmental potential" ; sc:featureList edam:operation_2436, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CytoTRACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cytotrace.stanford.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3360, edam:topic_3382 ; sc:citation , "pmcid:PMC6720861", "pubmed:31477013" ; sc:description "A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging | Microscopy Image Cytometry Toolkit | Cytokit is a collection of tools for quantifying and analyzing properties of individual cells in large fluorescent microscopy datasets with a focus on those generated from multiplexed staining protocols. This includes a GPU-accelerated image processing pipeline (via TensorFlow), CLI tools for batch processing of experimental replicates (often requiring conditional configuration, as things tend go wrong when capturing hundreds of thousands of microscope images over a period of hours or days), and visualization UIs (either Cytokit Explorer or CellProfiler Analyst) | Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google | Fortsæt til Google Cloud Platform | Skriv den tekst, du hører eller ser" ; sc:featureList edam:operation_3552, edam:operation_3629 ; sc:license "Apache-2.0" ; sc:name "Cytokit" ; sc:url "https://github.com/hammerlab/cytokit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382 ; sc:citation , "pubmed:30520559" ; sc:description """Tool for collaborative multimodal imaging and our latest software developments to support next-generation digital pathology bridged to molecular investigations.""" ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Cytomine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cytomine.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite", "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3293 ; sc:citation , "pmcid:PMC6717989", "pubmed:31477170" ; sc:description "Cytoscape Automation combines Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio." ; sc:featureList edam:operation_2497, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "Cytoscape Automation" ; sc:url "http://automation.cytoscape.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0659 ; sc:citation , "pmcid:PMC6779407", "pubmed:31390943" ; sc:description "A comprehensive database and analytical platform to dissect the modification of drugs on lncRNA expression" ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:name "D-lnc" ; sc:url "http://www.jianglab.cn/D-lnc/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "Identification of differentially-expressed genes in single-cell RNA sequencing data." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "D3E" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.sanger.ac.uk/science/tools/discrete-distributional-differential-expression-d3e" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6933629", "pubmed:31881937" ; sc:description """a data driven dynamic network construction method to infer gene regulatory networks. Gene regulatory network;Dynamic networks construction;Regression;DREAM challenge. 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In practice, DENOPTIM is meant for building chemical entities by assembling building blocks (i.e., fragments), processing each chemical entity as to produce its figure of merit (i.e., fitness), and designing new entities based on the properties of entities generated before." ; sc:featureList edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "DENOPTIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/denoptim-project/DENOPTIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Densitometry software written for Mathlab." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "DENSIFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46205-densife" ; biotools:primaryContact "Lorena" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:author "Daniele Raimondi", "Ibrahim Tanyalcin" ; sc:citation "pubmed:28498993" ; sc:description "Sequence-based predictor of deleteriousness of amino acid variants in human proteins" ; sc:featureList edam:operation_0331 ; sc:name "DEOGEN2" ; sc:url "http://deogen2.mutaframe.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3308 ; sc:author , , "Eric Charpentier", "Erwan Delage" ; sc:citation , , "pubmed:30977188" ; sc:contributor "Damien Vintache" ; sc:description "Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes." ; sc:featureList edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "DEPIB" ; sc:provider "BiRD bioinformatics facility" ; sc:softwareVersion "1.0" ; sc:url "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline" ; biotools:primaryContact "Eric Charpentier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3334, edam:topic_3538 ; sc:citation , "pubmed:31870849" ; sc:description """Intrinsic disorder and disorder function prediction server. Predictors of disordered regions and their molecular functions - web server from Biomine lab. DEPICTER : DisorderEd PredictIon CenTER""" ; sc:featureList edam:operation_0470, edam:operation_1777, edam:operation_1812, edam:operation_3904 ; sc:name "DEPICTER" ; sc:url "http://biomine.cs.vcu.edu/servers/DEPICTER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0219, edam:topic_3489 ; sc:citation , "pmcid:PMC6911163", "pubmed:31836896" ; sc:description "DEPOD - the human DEPhOsphorylation Database, is a manually curated database collecting human phosphatases, their experimentally verified substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates." ; sc:featureList edam:operation_0417, edam:operation_3083, edam:operation_3208 ; sc:name "Human Dephosphorylation Database (DEPOD)" ; sc:url "http://depod.bioss.uni-freiburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3322, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC6532897", "pubmed:31120982" ; sc:description "Multi-domain tuberculosis data analysis resource." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DEPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://depot.tbportals.niaid.nih.gov" ; biotools:primaryContact "Andrei Gabrielian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3510 ; sc:citation , "pmcid:PMC6735894", "pubmed:31372637" ; sc:description "DESSO is a deep learning-based framework that can be used to accurately identify both sequence and shape regulatory motifs from the human genome." ; sc:featureList edam:operation_0238, edam:operation_0441, edam:operation_0445 ; sc:name "Deep Sequence and Shape Motif (DESSO)" ; sc:url "https://bmbl.bmi.osumc.edu/DESSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170 ; sc:author "Maximilian Hastreiter", "Tim Jeske" ; sc:citation , "pubmed:31228198" ; sc:description "R package for accurate small RNA profiling based on differential expression of unique sequences." ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DEUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ibis.helmholtz-muenchen.de/deus/" ; biotools:primaryContact "Tim Jeske" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:30849608" ; sc:description """DEWE is a software tool to perform genetic differential expression analysis of RNA-Seq data. DEWE offers built-in, easy-to-configure workflows that facilitate the execution of DE analyses. Currently, DEWE provides two differential expression analysis workflows: HISAT2, StringTie and R libraries (Ballgown and edgeR) and Bowtie2, StringTie and R libraries (Ballgown and edgeR).""" ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DEWE: Differential Expression Workflow Executor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://www.sing-group.org/dewe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6399874", "pubmed:30832568" ; sc:description "R package for aggregation and visualization of differential expression data." ; sc:featureList edam:operation_2495, edam:operation_3436, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.0" ; sc:name "DEvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=DEVis" ; biotools:primaryContact "Adam Price" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3407 ; sc:citation , , "pmcid:PMC6571761", "pubmed:31137754", "pubmed:32692571" ; sc:description "DIA-DB is a web server for the prediction of diabetes drugs that uses two different approaches; a) comparison by similarity with a curated database of anti-diabetic drugs and experimental compounds, and b) inverse virtual screening of the input molecules chosen by the users against a set of protein targets identified as key elements in diabetes." ; sc:featureList edam:operation_0394, edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "DIA-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bio-hpc.ucam.edu/dia-db/" ; biotools:primaryContact , "Zeno Apostolides" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:31768060" ; sc:description """Neural networks and interference correction enable deep proteome coverage in high throughput. DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data. None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)""" ; sc:featureList edam:operation_3767, edam:operation_3799, edam:operation_3801 ; sc:name "DIA-NN" ; sc:softwareHelp ; sc:url "https://github.com/vdemichev/diann" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3655, edam:format_3747 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:25599550" ; sc:description "DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3630, edam:operation_3631, edam:operation_3633, edam:operation_3649, edam:operation_3801, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DIA-Umpire" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://sourceforge.net/projects/diaumpire/" ; biotools:primaryContact "Chih-Chiang Tsou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , , "pmcid:PMC7335186", "pubmed:32620816" ; sc:description "Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM. Remove debris-contaminated droplets from single-cell based data" ; sc:featureList edam:operation_0313, edam:operation_2238, edam:operation_3192 ; sc:name "Debris Identification using Expectation Maximization (DIEM)" ; sc:url "https://github.com/marcalva/diem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6612874", "pubmed:31510699" ; sc:description "predicting isoform functions from sequences and expression profiles via deep learning | Deep learning based prediction of IsoForm FUnctions from Sequences and Expression | DIFFUSE is a deep learning based method for predicting isoform functions by integrating the data of isoform sequences, domains and expression profiles." ; sc:featureList edam:operation_0264, edam:operation_3766, edam:operation_3798 ; sc:license "MIT" ; sc:name "DIFFUSE" ; sc:url "https://github.com/haochenucr/DIFFUSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0634, edam:topic_0804, edam:topic_3308 ; sc:citation ; sc:description """Integration of immunome with disease gene network reveals pleiotropy and novel drug repurposing targets. Abstract Immune system is crucial for the development and progression of immune-mediated and non-immune mediated complex diseases. Studies have shown that multiple complex diseases are associated with several immunologically relevant genes. Despite such growing evidence, the effect of disease associated genes on immune functions has not been well explored. Here, we curated the largest immunome (transcriptome profiles of 40 different immune cells) and integrated it with disease gene networks and drug-gene database, to generate a Disease-gene IMmune cell Expression network (DIME). Is a Shiny app.""" ; sc:featureList edam:operation_2495 ; sc:name "Disease-gene Immune cell Expression (DIME)" ; sc:url "https://bitbucket.org/systemsimmunology/dime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0202, edam:topic_0820, edam:topic_3300, edam:topic_3892 ; sc:citation , , "pubmed:32096817" ; sc:description "Exploring and visualizing possible GPCR dimer." ; sc:featureList edam:operation_0269, edam:operation_0337, edam:operation_2995 ; sc:name "DIMERBOW" ; sc:softwareHelp ; sc:url "http://lmc.uab.es/dimerbow/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC3931231", "pubmed:24600385" ; sc:description "DIPY is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments" ; sc:featureList edam:operation_2939, edam:operation_3446, edam:operation_3891 ; sc:name "Diffusion Imaging in Python (DIPY)" ; sc:url "http://dipy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6794908", "pubmed:31615418" ; sc:description """RNA contact predictions by integrating structural patterns. It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0278, edam:operation_0474, edam:operation_2441 ; sc:name "Direct Information Reweighted by Contact Templates (DIRECT)" ; sc:url "https://zhaolab.com.cn/DIRECT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "DISCo-microbe is an easy-to-use command-line program, for creation of diverse communities of organisms that can be distinguished through next-generation sequencing technology" ; sc:featureList edam:operation_3192, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Design of an Identifiable Synthetic Community of Microbes (DISCo-microbe)" ; sc:url "https://github.com/dlcarper/DISCo-microbe" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3242 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3242 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3325 ; sc:author "Alberto Calderone", "Prisca Lo Surdo" ; sc:citation "pubmed:29036667" ; sc:contributor "Gianni Cesareni", "Luana Licata", "Marta Iannuccelli" ; sc:description "A disease-focused resource that uses the causal interaction information annotated in SIGNOR and the protein interaction data in mentha to generate and explore protein interaction networks linking disease genes." ; sc:featureList edam:operation_3083, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "DISNOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:softwareHelp ; sc:url "https://disnor.uniroma2.it/" ; biotools:primaryContact "Livia Perfetto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0123, edam:topic_3538 ; sc:citation , "pmcid:PMC6933862", "pubmed:31642118" ; sc:description "Disorder predictor selection at the protein level. DISOselect accepts either single or multiple protein sequences. The input is limited to 1000 protein sequences. The user should submit the protein sequence(s) in FASTA format" ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_3904 ; sc:name "DISOselect" ; sc:url "http://biomine.cs.vcu.edu/servers/DISOselect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3569 ; sc:citation , "pmcid:PMC6680062", "pubmed:31392032" ; sc:description "The complete analysis of deep sequencing data from the DISSEQT paper is available at the collaborative science platform Synapse here. In order to view and download files you must create a Synapse account. (The scripts are also available in the examples folder for reference, but note that you will need a Synapse account to access the data files.)" ; sc:featureList edam:operation_0487, edam:operation_2939, edam:operation_3196 ; sc:license "MIT" ; sc:name "Distribution-based modeling of Sequence space time dynamics (DISSEQT)" ; sc:url "https://github.com/rasmushenningsson/DISSEQT.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6716629", "pubmed:31469855" ; sc:description "A tool for detecting bipartite motifs by considering base interdependencies | A DNA sequence motif finding program | DIpartite is a tool for detecting bipartite motif based on dinucleotide weight matrix | DIpartite predicts transcription factor binding sites (TFBSs) based on PWM or DWM. Bipartite motif is defined as two conserved blocks separated by variable gaps" ; sc:featureList edam:operation_0239, edam:operation_0445, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DIpartite" ; sc:url "https://github.com/Mohammad-Vahed/DIpartite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3050, edam:topic_3474 ; sc:citation ; sc:description "Modelling the niches of wild and domesticated Ungulate species using deep learning | Abstract Knowledge of global biodiversity remains limited by geographic and taxonomic sampling biases. The scarcity of species data restricts our understanding of the underlying environmental factors shaping distributions, and the ability to draw comparisons among species. Species distribution models (SDMs) were developed in the early 2000s to address this issue. Although SDMs based on single layered Neural Networks have been experimented with in the past, these performed poorly. However, the past two decades have seen a strong increase in the use of Deep Learning (DL) approaches, such as Deep Neural Networks (DNNs). Despite the large improvement in predictive capacity DNNs provide over shallow networks, to our knowledge these have not yet been applied to SDM" ; sc:license "MIT" ; sc:name "DL-SDM" ; sc:url "https://github.com/naturalis/trait-geo-diverse-dl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation , "pmcid:PMC6686496", "pubmed:31392430" ; sc:description "An improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state | DLIGAND2 is a knowledge-based method to predict protein-ligand binding affinity based on a distance-scaled, finite, ideal-gas reference (DFIRE) state" ; sc:featureList edam:operation_0482, edam:operation_3501, edam:operation_3899 ; sc:license "MIT" ; sc:name "DLIGAND2" ; sc:url "https://github.com/sysu-yanglab/DLIGAND2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC6838938", "pubmed:31648791" ; sc:description """DLITE Uses Cell-Cell Interface Movement to Better Infer Cell-Cell Tensions. Cell shapes and connectivities evolve over time as the colony changes shape or embryos develop. Shapes of intercellular interfaces are closely coupled with the forces resulting from actomyosin interactions, membrane tension, or cell-cell adhesions. Although it is possible to computationally infer cell-cell forces from a mechanical model of collective cell behavior, doing so for temporally evolving forces in a manner robust to digitization difficulties is challenging. Here, we introduce a method for dynamic local intercellular tension estimation (DLITE) that infers such evolution in temporal force with less sensitivity to digitization ambiguities or errors. This method builds upon previous work on single time points (cellular force-inference toolkit). We validate our method using synthetic geometries.""" ; sc:name "DLITE" ; sc:softwareHelp ; sc:url "https://github.com/AllenCellModeling/DLITE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0654 ; sc:citation , , "pmcid:PMC7140825", "pubmed:32164155" ; sc:description "DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis | Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture. Results Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering" ; sc:featureList edam:operation_3211, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "DLO Hi-C" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/GuoliangLi-HZAU/DLO-Hi-C-Tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC6726615", "pubmed:31484923" ; sc:description "Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints | Extending genome-scale de novo protein modelling coverage using iterative deep learning-based prediction of structural constraints | See our paper in Nature Communications for more. Please cite the paper if you use DMPfold | You can also run DMPfold via the PSIPRED web server. This is a good way to get models for a few sequences, but if you want to run DMPfold on many sequences we strongly recommend you run it locally. The server version of DMPfold has restrictions on run time and uses parameters that give faster runs, so should not be used to benchmark DMPfold" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DMPfold" ; sc:url "https://github.com/psipred/DMPfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0196, edam:topic_0749, edam:topic_3318, edam:topic_3895 ; sc:citation , , "pmcid:PMC7476404", "pubmed:32995552" ; sc:description """A low-cost, automated DNA assembly platform for synthetic biology. Material for DNA assembly using BASIC on OpenTrons (DNA-BOT). Users looking to implement the DNA-BOT workflow are encouraged to consult the instructions. If you are looking to contribute to this project, please raise an issue or pull request. Otherwise, feel free to reach out to hainesm6""" ; sc:featureList edam:operation_0310, edam:operation_3435 ; sc:license "MIT" ; sc:name "DNA-BOT" ; sc:softwareHelp ; sc:url "https://github.com/BASIC-DNA-ASSEMBLY/dnabot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3314 ; sc:citation , "pmcid:PMC6662285", "pubmed:30576403" ; sc:description "R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DNABarcodeCompatibility" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/comoto-pasteur-fr" ; biotools:primaryContact "Céline Trébeau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0632, edam:topic_0654, edam:topic_3500 ; sc:citation , , "pubmed:32647895" ; sc:description """DNA Chisel - A versatile sequence optimizer. DNA Chisel is a Python library for optimizing DNA sequences with respect to a set of constraints and optimization objectives. It comes with over 15 classes of sequence specifications which can be composed to, for instance, codon-optimize genes, meet the constraints of a commercial DNA provider, avoid homologies between sequences, tune GC content, or all of this at once!""" ; sc:featureList edam:operation_3095, edam:operation_3096 ; sc:license "MIT" ; sc:name "DNA Chisel" ; sc:url "https://edinburgh-genome-foundry.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3173 ; sc:citation , "pubmed:31373608" ; sc:description "An R based visualizer for network analysis of chromatin interaction data | A Shiny App for visualizing genomic data | Welcome to the github repository for DNA Rchitect, a Shiny App for visualizing genomic data | DNA Rchitect is a Shiny App for visualizing genomic data (HiC, mRNA, ChIP, ATAC etc) in bed, bedgraph, and bedpe formats. HiC (bedpe format) data is visualized with both bezier curves coupled with network statistics and graphs (using an R port of igraph). Shiny Apps are interactive web applications built with R using the shiny R package. Shiny apps are built with R wrappers for HTML, CSS, and JS to run R code in a web browser through a dynamic and reactive user interface that is powered by an underlying NodeJS engine. These apps can be locally hosted from an R session or hosted in the cloud through a ShinyServer" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "DNA Rchitect" ; sc:url "http://shiny.immgen.org/DNARchitect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3399 ; sc:citation , "pmcid:PMC6708158", "pubmed:31443728" ; sc:description "A chronological age predictor based on DNA methylation. Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3891 ; sc:name "DNA-methyaltion-based age predictor" ; sc:url "https://github.com/qzhang314/DNAm-based-age-predictor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0154, edam:topic_0166, edam:topic_0654, edam:topic_3542 ; sc:citation , "pubmed:31612957" ; sc:description """An expanded database and web-based tool for structural analysis of DNA-protein complexes. A Database and Web Tool for Structural Analysis of DNA-Protein Complexes. DNAproDB automatically lays out nucleotide and residue interactions maps elegantly. Use the form below to search DNAproDB. DNAproDB is processing pipeline, web server and database which aims to assist researchers in performing structural analysis of DNA-protein complexes. DNAproDB is a database, structure processing pipeline and web-based visualization tool which makes structural analysis of DNA-protein complexes easy""" ; sc:featureList edam:operation_0570, edam:operation_2421, edam:operation_2422, edam:operation_2488, edam:operation_2939 ; sc:name "DNAproDB" ; sc:softwareHelp ; sc:url "https://dnaprodb.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6487045", "pubmed:31029080" ; sc:contributor "Dr Alfredo Iacoangeli", "Dr Stephen J Newhouse" ; sc:description "Personal computer compatible NGS analysis, annotation and visualisation." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DNAscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KHP-Informatics/DNAscan" ; biotools:primaryContact "KCL IoPPN: NIHR BRC-MH Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3174, edam:topic_3474 ; sc:citation , "pubmed:31504181" ; sc:description "Analysis of several key factors influencing deep learning-based inter-residue contact prediction | Deep convolutional neural networks for protein contact map prediction | Web-server and datasets at http://sysbio.rnet.missouri.edu/dncon2/ | We tested in Ubuntu becasue the tool 'FreeContact' is easier to install in a Debian system. If you would like to install DNCON2 in some other operating systems, first test if 'FreeContact' can be installed in it. If, for some reason, you do not have a Ubuntu machine, and cannot install FreeContact, you can still use DNCON2. With just a few code updates you can skip using the FreeContact tool. You will get slightly less precise results" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0476 ; sc:license "GPL-3.0" ; sc:name "DNCON2" ; sc:url "http://sysbio.rnet.missouri.edu/dncon2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0634 ; sc:citation , "pmcid:PMC6929334", "pubmed:31874600" ; sc:description """differential network local consistency analysis. Using Local Moran's I for detection of differential network local consistency""" ; sc:featureList edam:operation_2497, edam:operation_3463 ; sc:license "GPL-2.0" ; sc:name "DNLC" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/DNLC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:31598709" ; sc:description """DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan-meQTL and HACER databases. Overall, DNMIVD mainly contains the following important resources:. DNA methylation is strongly related to cancer, currently, no resource integratively provides the DNA methylation based diagnostic and prognostic models, e-mQTL (expression–methylation quantitative trait loci), pathway-meQTL (pathway activity-methylation quantitative trait loci), differentially variable and differentially methylated CpGs, survival analysis, as well as functional epigenetic modules for different cancers, which are valuable information for researchers to explore DNA methylation profile from different aspects in cancer""" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:name "DNA Methylation Interactive Visualization Database (DNMIVD)" ; sc:url "http://www.unimd.org/dnmivd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3542 ; sc:citation ; sc:description "Improved ab initio protein secondary structure prediction using advanced deep learning architectures." ; sc:featureList edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DNSS2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/multicom-toolbox/DNSS2" ; biotools:primaryContact "Jianlin Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31081635" ; sc:description "Data-Driven Optimization of Mass Spectrometry Methods." ; sc:featureList edam:operation_2428, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DO-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://do-ms.slavovlab.net" ; biotools:primaryContact "Nikolai Slavov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_3308 ; sc:citation , , "pmcid:PMC6602495", "pubmed:27153665", "pubmed:31076763" ; sc:description "Domain-based transcriptome and proteome quality assessment." ; sc:featureList edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DOGMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://domainworld-services.uni-muenster.de/dogma/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3068, edam:topic_3407 ; sc:citation , "pubmed:31581093" ; sc:description """Database Of Reconstructed MetAbolic Networks. We apologize for the inconvenience, but it appears that an internal error has occurred in the Dorman system. If this is the first time you have encountered this message, please use the Back button on your browser and try your last action again. If you are receiving this message repeatedly, please send an e-mail to (aec51 [at] case [dot] edu) with a detailed description of what you were doing when this message occurred so that we may try and resolve this issue. Thank you!""" ; sc:featureList edam:operation_0224, edam:operation_3083, edam:operation_3660 ; sc:name "DORMAN" ; sc:url "http://ciceklab.cs.bilkent.edu.tr/dorman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3423, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC6382494", "pubmed:30450799" ; sc:description "DMD Open-access Variant Explorer (DOVE) - web-based aid for DMD variant interpretation which additionally reports variant-specific predicted molecular eligibility for therapy." ; sc:featureList edam:operation_0446, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DOVE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.dmd.nl/DOVE" ; biotools:primaryContact "Mitch Bailey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31621827" ; sc:description """DPre: Computational identification of differentiation bias and genes underlaying cell type conversions. DPre is a bioinformatic tool that enables the user to explore cell type conversion/ differentiation experiments. DPre may take the expression or the differentially regulated genes of the samples to rate transcriptional similarity with a reference dataset, the targets.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3629 ; sc:license "MIT" ; sc:name "DPre" ; sc:url "https://github.com/LoaloaF/DPre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3379 ; sc:citation , "pmcid:PMC6798577", "pubmed:31390010" ; sc:description "DQueST is a web applciation for reducing information overload for trial seekers using dynamic questionnaires." ; sc:featureList edam:operation_3280 ; sc:name "DQueST" ; sc:url "https://github.com/stormliucong/dquest-flask" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3318, edam:topic_3489 ; sc:citation , "pubmed:31584610" ; sc:description """Thermodynamically Consistent Estimation of Gibbs Free Energy from Data. The DR-thermo algorithm can be used to curate experimental thermodynamic data from different sources to generate reliable data-banks such that all measurements are modified to be thermodynamically consistent and any missing reaction or formation Gibbs energies can be predicted either directly or using group contributions.""" ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3799 ; sc:license "MIT" ; sc:name "DR-thermo" ; sc:url "https://github.com/samansalike/DR-thermo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3301, edam:topic_3379 ; sc:citation , "pmcid:PMC6692298", "pubmed:31409791" ; sc:description "updated data repository of antimicrobial peptides | Browse, Create and Mining Antimicrobial Peptides | 157 new entries are added to in DRAMP. 33 entries are natural AMPs including 31 animal AMPs and 2 plant AMPs. 124 entries are synthetic AMPs | A brief introduction to DRAMP database | DRAMP database is an information portal to biological active peptides. Peptides in this database come from three sources : Public databases (Swiss-Prot, PDB, PubMed), Clinical antimicrobial peptides (preclinical and clinical) and Patents | DRAMP(Data repository of antimicrobial peptides) is an open-access and manually curated database harboring diverse annotations of AMPs including sequences, structures, activities, physicochemical, patent, clinical and reference information | We are responsible for maintaining the website daily and updating the database regularly" ; sc:featureList edam:operation_3431, edam:operation_3482, edam:operation_3646 ; sc:name "DRAMP" ; sc:softwareHelp ; sc:url "http://dramp.cpu-bioinfor.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3673 ; sc:citation , , "pmcid:PMC7179940", "pubmed:32282793" ; sc:description "A tool to Detect and Re-Align Mixed-up Samples based on multi-omics data. Need at least three types of -omics data to run this tool." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3431, edam:operation_3659, edam:operation_3802 ; sc:name "DRAMS" ; sc:url "https://github.com/Yi-Jiang/DRAMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3855 ; sc:citation , "pubmed:31515012" ; sc:description "A user-friendly program for the analyses of radiation-induced biological responses utilizing established deterministic models at cell population and organ scales | PURPOSE:To develop a user-friendly program for biological modeling to analyze radiation-induced responses at the scales of the cell population and organ. METHODS:The program offers five established cell population surviving fraction (SF) models to estimate the SF and the relative biological effectiveness (RBE) from clonogenic assay data, and two established models to calculate the normal tissue complication probability (NTCP) and tumor control probability (TCP) from radiation treatment plans. Users can also verify the results with multiple types of quantitative analyses and graphical representation tools" ; sc:name "DREAP" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31515012" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6685255", "pubmed:31387525" ; sc:description "DRIP-seq optimized peak annotator | DROPA is a fully customizable peak-annotation tool optimized for DRIP-seq peaks, which allows a finest gene annotation based on gene expression information. Its output can easily be integrated into pipelines to perform downstream analyses, while useful and informative summary plots and statistical enrichment tests can be produced. Although it is developed for R-loop mapping, DROPA can also be used to annotate other genomic sequencing data as in the case of Histone marks IP-seq, DNAse-seq, FAIRE-seq" ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3501 ; sc:license "MIT" ; sc:name "DROPA" ; sc:url "https://github.com/marcrusso/DROPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3047, edam:topic_3336 ; sc:citation , "pubmed:31605102" ; sc:description "DRUDIT, Web-Based DRUgs DIscovery Tools to Design Small Molecules as Modulators of Biological Targets." ; sc:featureList edam:operation_3761 ; sc:name "DRUDIT" ; sc:softwareHelp ; sc:url "http://www.drudit.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0166 ; sc:citation , "pubmed:31793988" ; sc:description "DNA Readout Viewer is a free on-line service providing novel and intuitive visualisation modes for displaying sequence specific DNA-protein interactions." ; sc:featureList edam:operation_0239, edam:operation_0337, edam:operation_3894 ; sc:name "DNA Readout Viewer" ; sc:softwareHelp , ; sc:url "https://drv.brc.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3336, edam:topic_3855 ; sc:citation , "pmcid:PMC6528253", "pubmed:31113359" ; sc:description "Tool for the analysis of discrete data from multi-well plate assays." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DRfit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.structuralchemistry.org/pcsb/drfit.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602 ; sc:citation ; sc:description "Drug-Set Enrichment Analysis (DSEA) - computational method based on drug-induced gene expression profiles, which is able to identify the molecular pathways that are targeted by most of the drugs in the set." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "DSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dsea.tigem.it/" ; biotools:primaryContact "Diego Carrella", "Diego di Bernardo", "Francesco Napolitano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "A collection of databases, tools and web servers for structural biology." ; sc:name "DSIMB tools" ; sc:url "http://www.dsimb.inserm.fr/tools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6929406", "pubmed:31874618" ; sc:description """de novo transcriptome assembly by using simplified suffix trees. DTA-SiST: a novel radical framework for de novo transcriptome assembly based on suffix trees. The RNA-seq has revolutionized our ability to transcripts reconstruction""" ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3472 ; sc:name "DTA-SiST" ; sc:url "https://github.com/Jane110111107/DTA-SiST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258 ; sc:citation , , "pmcid:PMC6645132", "pmcid:PMC6645227", "pubmed:31458051", "pubmed:31459245" ; sc:description "How Precise Are Our Quantitative Structure-Activity Relationship Derived Predictions for New Query Chemicals? | QSPR Modeling of the Refractive Index for Diverse Polymers Using 2D Descriptors | QSAR Model Development Using DTC Lab. Software Tools | DTC lab - Software Tools - DTC lab is working in the field of molecular modelling mainly using different QSAR methodologies in various diverse area such as drug designing, toxicity, anti-oxidant studies etc | Drug Theoretics and Cheminformatics Laboratory | *Genetic Algorithm(MAE-based Fitness Function) | *Intelligent Consensus Predictor" ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3891 ; sc:name "DTCLab" ; sc:url "http://teqip.jdvu.ac.in/QSAR_Tools/DTCLab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:31885041" ; sc:description "A cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Drug-target interactions (DTIs) play a crucial role in target-based drug discovery and development" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_3435 ; sc:name "DTI-CDF" ; sc:url "https://github.com//a96123155/DTI-CDF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0749 ; sc:citation , "pubmed:31389563" ; sc:description "DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data | MOTIVATION:RNA molecules can undergo complex structural dynamics, especially during transcription, which influence their biological functions. Recently developed high-throughput chemical probing experiments that study RNA cotranscriptional folding generate nucleotide-resolution 'reactivities' for each length of a growing nascent RNA that reflect structural dynamics. However, the manual annotation and qualitative interpretation of reactivity across these large datasets can be nuanced, laborious, and difficult for new practitioners. We developed a quantitative and systematic approach to automatically detect RNA folding events from these datasets to reduce human bias error, standardize event discovery, and generate hypotheses about RNA folding trajectories for further analysis and experimental validation" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_3799 ; sc:name "DUETT" ; sc:url "https://github.com/BagheriLab/DUETT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6582333", "pubmed:31106330" ; sc:description "Algorithm based on the distance variation allowed by secondary structure (DVASS), which ranks restraints according to their importance to RNA tertiary structure prediction." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DVASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/dokhlab/dvass" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3542 ; sc:citation "pubmed:30209260", "pubmed:31114872" ; sc:description "Web server for the (re-)modeling of loops in homology models. It follows a data-based approach, identifying loop candidates by mining the complete set of experimental structures available in the Protein Data Bank." ; sc:featureList edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "DaReUS-Loop" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::DaReUS-Loop" ; biotools:primaryContact "Pierre Tufféry", "Sjoerd de Vries" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3361 ; sc:citation , "pmcid:PMC6892282", "pubmed:31801633" ; sc:description "Fast and accurate genomic distances using HyperLogLog. dashing sketches and computes distances between fasta and fastq data." ; sc:featureList edam:operation_3211, edam:operation_3472, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Dashing" ; sc:url "https://github.com/dnbaker/dashing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3794 ; sc:author "Natasha Stander" ; sc:citation , "pmcid:PMC6878877", "pubmed:31798364" ; sc:description """A graphical user interface for visualizing and querying large data sets in serial femtosecond crystallography. DatView displays plots of tabular data and syncs selections across plots. It was initially developed for serial crystallography data analysis with CrystFEL output files and includes a frame viewer for displaying 1D and 2D data from HDF5/CXI files.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3436, edam:operation_3695, edam:operation_3802 ; sc:name "DatView" ; sc:softwareHelp , ; sc:url "https://github.com/nstander/DatView" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation , , ; sc:description """DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters. This tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "DataDiscovery" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/data-discovery/" ; biotools:primaryContact "urgi-support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3394, edam:topic_3571 ; sc:author , "Jacek Lebioda", "Kavita Rege", "Yohan Jarosz" ; sc:citation , "pmcid:PMC6892452", "pubmed:31800037" ; sc:contributor , , "Christophe Trefois", "Sandrine Munoz", "Vilem Ded" ; sc:description "DAISY is an open-source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Data Information System (DAISY)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/elixir-luxembourg/daisy" ; biotools:primaryContact , "Regina Becker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605 ; sc:author , , "Jan Slifka" ; sc:citation , , ; sc:contributor , "Rob Hooft" ; sc:description "The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Data Stewardship Wizard" ; sc:softwareHelp , , ; sc:url "https://ds-wizard.org" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0203 ; sc:citation , , "pmcid:PMC7110638", "pubmed:32238171" ; sc:description "Automated Gene Data Integration with Databio | Automated data transformation for bioinformatics | Automated data integration tools | A simple Gene ID mapping service for Bioinformatics. Upload a gene-oriented data set, we'll automatically detect the identifiers in use, and offer to convert them to match other providers in just a few clicks | A web portal that does automated identifier translation for bioinformatics" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3282 ; sc:name "Datab.io" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://datab.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3068 ; sc:citation , "pmcid:PMC6506717", "pubmed:31042286" ; sc:description "Workflow and package for delivering successive versions of 'evolving data' directly into R." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Datastorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/ropenscilabs/datastorr" ; biotools:primaryContact , "Rich FitzJohn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3421, edam:topic_3474 ; sc:author ; sc:citation , "pubmed:31751268" ; sc:description "Generative cooperative networks for joint surgical smoke detection and removal in order to remove surgical smoke and improve the quality of intra-operative imaging and reduce hazards in image-guided surgery. This is a highly desirable post-process for many clinical applications." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "De-smokeGCN" ; sc:url "https://github.com/melights/cnn_desmoke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2275, edam:topic_3047, edam:topic_3303, edam:topic_3474 ; sc:citation , , "pmcid:PMC7189367", "pubmed:32195587" ; sc:description """Deep Generative Models for 3D Compound Design. This repository contains our implementation of Deep Generative Models for 3D Compound Design (DeLinker). We provide two settings of DeLinker. The first setting generates linkers with the same number of atoms as the reference molecule. The second setting generates linkers with a specified number of atoms""" ; sc:featureList edam:operation_3216, edam:operation_3435, edam:operation_3891 ; sc:name "DeLinker" ; sc:url "https://github.com/oxpig/DeLinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31095815" ; sc:description "Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network." ; sc:featureList edam:operation_3450 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeTerm" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/skibbe/DeTerm/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3370, edam:topic_3520 ; sc:citation , "pubmed:31436405" ; sc:description "Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS-Based Untargeted Metabolomics | DecoMetDIA was developed to process SWATH-MS based data for metabolomics." ; sc:featureList edam:operation_3629, edam:operation_3637, edam:operation_3803 ; sc:name "DecoMetDIA" ; sc:url "https://github.com/ZhuMSLab/DecoMetDIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC6472186", "pubmed:30999839" ; sc:description "Tool for detecting contaminating organisms in human unmapped sequences." ; sc:featureList edam:operation_3187, edam:operation_3219, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DecontaMiner" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www-labgtp.na.icar.cnr.it/decontaminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31129958" ; sc:description "On-demand decoy glycopeptide generator that can produce a high volume of decoys with low mass differences." ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DecoyDeveloper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://glycopro.chem.ku.edu/JHome.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6848155", "pubmed:31712594" ; sc:description """Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome. Tissue and Cancer Type Identification using Deep Neural Networks. Authors: Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi""" ; sc:featureList edam:operation_3435, edam:operation_3792 ; sc:name "DeePathology" ; sc:url "https://github.com/SharifBioinf/DeePathology" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31686039" ; sc:description """Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning. DeepZ Plugin Release_v1.3 – Google Drev. Three-dimensional propagation and time-reversal of fluorescence images. Neural network learns fluorescence wave propagation and time-reversal to propagate a 2D fluorescence image onto user-defined 3D surfaces, enabling 3D imaging of fluorescent samples using a single 2D image, without mechanical scanning, additional hardware, or a trade-off of resolution or speed. For details, refer to our publication "Three-dimensional propagation and time-reversal of fluorescence images" [1]. (Video below: 3D reconstruction of a C. elegans using Deep-Z inference)""" ; sc:featureList edam:operation_3450, edam:operation_3457, edam:operation_3552 ; sc:name "Deep-Z" ; sc:softwareHelp , ; sc:url "https://github.com/puppy101puppy/Deep-Z" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc:description """Attention mechanism-based deep learning pan-specific model for interpretable MHC-I peptide binding prediction. Deep learning prediction of MHC-I peptide binding with attention mechanism. Please download the full folder of "DeepAttentionPan_Code" to run the programs, or you may need to configure some directory paths. Usage: the codes can be used to train our models, output results on the testing set, output positional attention weights for chosen group of peptides. And they also can be used to test on single hla-peptide pair input from the command line.""" ; sc:featureList edam:operation_0252, edam:operation_2492, edam:operation_3439 ; sc:name "DeepAttentionPan" ; sc:url "https://github.com/jjin49/DeepAttentionPan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6765103", "pubmed:31400112" ; sc:description "A deep learning genome-mining strategy for biosynthetic gene cluster prediction | BGC Detection and Classification Using Deep Learning | DeepBGC: Biosynthetic Gene Cluster detection and classification | DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. DeepBGC employs a Bidirectional Long Short-Term Memory Recurrent Neural Network and a word2vec-like vector embedding of Pfam protein domains. Product class and activity of detected BGCs is predicted using a Random Forest classifier" ; sc:featureList edam:operation_0306, edam:operation_3803 ; sc:license "MIT" ; sc:name "DeepBGC" ; sc:url "https://github.com/Merck/deepbgc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC6661145", "pubmed:31380152" ; sc:description "A deep learning based method for estimating effective protein-ligand affinity." ; sc:featureList edam:operation_0482 ; sc:license "MIT" ; sc:name "DeepBindRG" ; sc:url "https://github.com/haiping1010/DeepBindRG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3518 ; sc:citation , "pmcid:PMC6697729", "pubmed:31420533" ; sc:description "A novel deep learning-based framework for cancer molecular subtype classification | a deep learning-based framework for cancer classification | After training, now you can use your DeepCC model to classify new sample(s). DeepCC can classify samples in a data set, as well as individual samples. The input data should be in the same format as above gene expression profile(s)" ; sc:featureList edam:operation_2436 ; sc:license "MIT" ; sc:name "DeepCC" ; sc:url "https://cityuhk-compbio.github.io/DeepCC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , , "pmcid:PMC7438055", "pubmed:32699072" ; sc:description """A deep-learning-based Python toolbox for inferring calcium imaging neuronal activity based on movie visualization. Abstract Two-photon calcium imaging is now widely used to indirectly infer multi neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the analysis of highly active neurons in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development. Indeed, the reliable inference of single cell activity is not achieved by the latest analytical tools that often lack proper benchmark measurements. To meet this challenge, we first developed a graphical user interface allowing for a precise manual detection of all calcium transients from detected neurons based on the visualization of the calcium imaging movie. Then, we analyzed our movies using a convolutional neural network with an attention process and a bidirectional long-short term memory network""" ; sc:featureList edam:operation_0337, edam:operation_3450 ; sc:license "MIT" ; sc:name "DeepCINAC" ; sc:softwareHelp , , ; sc:url "https://gitlab.com/cossartlab/deepcinac" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3585 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_4002 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3474, edam:topic_3794 ; sc:author , , "Alexander Gulliver Bjørnholt Grønning" ; sc:citation , ; sc:description "Predicting the effect of mutations on protein-RNA binding with Deep Learning | This repository contains all DeepCLIP Python code | A context-aware neural network for modeling and predicting protein binding to nucleic acids using only sequence input | DeepCLIP is a neural network with shallow convolutional layers connected to a bidirectional LSTM layer" ; sc:featureList edam:operation_0441, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DeepCLIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://deepclip.compbio.sdu.dk" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0204, edam:topic_2640 ; sc:citation , "pubmed:31504186" ; sc:description "Deep Learning-Based Approach to Predict Gene Regulating Effects of Small Molecules | MOTIVATION:Recent advances in the areas of bioinformatics and chemogenomics are poised to accelerate the discovery of small-molecule regulators of cell development. Combining large genomics and molecular data sources with powerful deep learning techniques has the potential to revolutionize predictive biology. In this study, we present Deep Compound Profiler (DeepCOP), a deep learning based model that can predict gene regulating effects of low-molecular weight compounds. This model can be used for direct identification of a drug candidate causing a desired gene expression response, without utilizing any information on its interactions with protein target(s)" ; sc:featureList edam:operation_3501 ; sc:license "MIT" ; sc:name "Deep gene compound profiler (DeepCOP)" ; sc:url "https://github.com/godwinwoo/DeepCOP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3534 ; sc:citation , "pmcid:PMC6694742", "pubmed:31440276" ; sc:description "Precise Prediction of Calpain Cleavage Sites and Their Aberrance Caused by Mutations in Cancer | SWISS-MODEL is a fully automated protein structure homology-modelling server. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide | DeepCalpain is a web server developed for understanding the enzyme-specific cleavage for calpains including m-calpain and μ-calpain" ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0422 ; sc:name "DeepCalpain" ; sc:url "http://deepcalpain.cancerbio.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31077303" ; sc:description "R package for deep learning of the back-splicing code for circular RNA formation." ; sc:featureList edam:operation_0264, edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DeepCirCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioDataLearning/DeepCirCode" ; biotools:primaryContact "Jun Wang", "Liangjiang Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3534 ; sc:citation , "pubmed:31566664" ; sc:description "A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites | Proteases are enzymes that cleave target substrate proteins by catalyzing the hydrolysis of peptide bonds between specific amino acids. While the functional proteolysis regulated by proteases plays a central role in the 'life and death' process of proteins, many of the corresponding substrates and their cleavage sites were not found yet. Availability of accurate predictors of the substrates and cleavage sites would facilitate understanding of proteases' functions and physiological roles. Deep learning is a promising approach for the development of accurate predictors of substrate cleavage events. RESULTS:We propose DeepCleave, the first deep learning-based predictor of protease-specific substrates and cleavage sites. DeepCleave uses protein substrate sequence data as input and employs convolutional neural networks with transfer learning to train accurate predictive models" ; sc:featureList edam:operation_0366, edam:operation_0422 ; sc:name "DeepCleave" ; sc:url "http://deepcleave.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0654, edam:topic_3169, edam:topic_3474 ; sc:citation , ; sc:description "Deep Neural Networks for Identification of DNA-binding Proteins." ; sc:featureList edam:operation_3767, edam:operation_3900, edam:operation_3901 ; sc:name "DeepDBP" ; sc:url "https://github.com/antorkhan/DNABinding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_2815, edam:topic_3474, edam:topic_3796 ; sc:citation , "pmcid:PMC6805717", "pubmed:31639043" ; sc:description "A hybrid convolutional and recurrent neural network for compressing compression human mitochondrial genomes. DeepDNA, a novel unified model called deepDNA that combines the convolutional neural network (CNN) with the long short-term memory network (LSTM) for compressing human mitochondrial genome sequences. The experiment has shown that out method deepDNA is able to learn sequence local features through a convolutional layer, and to learn higher level representations of long-term sequences dependencies through a long short-term memory network (LSTM) layer. We evaluated the learned genome sequences representations model on human mitochondrial genome sequences compressing tasks and achieved a satisfactory result." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3695 ; sc:license "MIT" ; sc:name "DeepDNA" ; sc:url "https://github.com/rongjiewang/DeepDNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:31722485" ; sc:description """A new genome annotation predictor for identifying DNA binding proteins and RNA binding proteins using Convolutional Neural Network and Long Short-Term Memory. In this study, we proposed a new computational predictor called DeepDRBP-2L for identifying DBPs, RBPs and DRBPs. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two kinds of crucial proteins, which are involved in various cellule activities and associated with many diseases""" ; sc:featureList edam:operation_3900, edam:operation_3901 ; sc:name "DeepDRBP-2L" ; sc:url "http://bliulab.net/DeepDRBP-2L" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC6886168", "pubmed:31787076" ; sc:description "A deep learning framework for identifying essential proteins. DeepEP is a deep learning framework to automatically predict essential proteins using PPI network and gene expression data." ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3439 ; sc:license "MIT" ; sc:name "DeepEP" ; sc:url "https://github.com/CSUBioGroup/DeepEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6753114", "pubmed:31537810" ; sc:description "Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning | Core code for the DeepHF prediction tool | SpCas9 & Base Editor Efficiency Prediction | This tool provides guide designs for Wild-type SpCas9, two highly specific Cas9 mutants(eSpCas9 (1.1) and SpCas9-HF1) and base editors (AncBE4max, ABEmax)" ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3216 ; sc:name "DeepHF" ; sc:url "http://www.DeepHF.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6838785", "pubmed:31736974" ; sc:description """A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. DeepHLApan Server – A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. A deep learning approach used for neoantigen prediction. DeepHLApan is a deep learning approach used for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC. The stand-alone software is available in github""" ; sc:featureList edam:operation_0252, edam:operation_0331, edam:operation_0416 ; sc:license "GPL-2.0" ; sc:name "DeepHLApan" ; sc:url "http://biopharm.zju.edu.cn/deephlapan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0605, edam:topic_3382, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc:description """A user-friendly plugin to run deep learning models in ImageJ. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained deep learning models in ImageJ and Fiji. The plugin bridges the gap between deep learning and standard life-science applications. DeepImageJ runs image-to-image operations on a standard CPU-based computer and does not require any deep learning expertise.""" ; sc:featureList edam:operation_3096, edam:operation_3435, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "DeepImageJ" ; sc:url "https://deepimagej.github.io/deepimagej/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6798445", "pubmed:31627739" ; sc:description "An accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data. An accurate and efficient deep learning method for single-cell RNA-seq data imputation." ; sc:featureList edam:operation_2940, edam:operation_3557 ; sc:license "MIT" ; sc:name "DeepImpute" ; sc:url "https://github.com/lanagarmire/DeepImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc:description "A general framework for interpreting wide-band neural activity. DeepInsight is a toolbox for the analysis and interpretation of wide-band neural activity and can be applied on unsorted neural data. This means the traditional step of spike-sorting can be omitted and the raw data can be used directly as input, providing a more objective way of measuring decoding performance." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:license "MIT" ; sc:name "DeepInsight" ; sc:url "https://github.com/CYHSM/DeepInsight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation , "pmcid:PMC6612839", "pubmed:31510651" ; sc:description "An accurate prediction of MHC class I ligands using peptide embedding | The 5-fold cross-validation split used in the paper can be downloaded from here. The DeepLigand model provided in this repository is trained on all the five folds combined" ; sc:featureList edam:operation_0252 ; sc:license "MIT" ; sc:name "DeepLigand" ; sc:url "https://github.com/gifford-lab/DeepLigand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Evaluating the quality of metagenomic assemblies" ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3180 ; sc:license "MIT" ; sc:name "Deep learning for Metagenome Assembly Error Detection (DeepMAsED)" ; sc:url "https://github.com/leylabmpi/DeepMAsED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3308 ; sc:citation , , "pmcid:PMC6933662", "pubmed:31881818" ; sc:description "Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method | Deciphering the Hidden Patterns on Transcriptome Profiles with a Deep Learning Fashion" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "DeepMF" ; sc:url "https://github.com/paprikachan/DeepMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3174, edam:topic_3474 ; sc:citation , "pubmed:31738385" ; sc:description """Constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. deep multiple sequence alignment generation. DeepMSA is a composite approach to generate high quality multiple sequence alignment with large alignment depth and diverse sequence sources by merging sequences from whole-genome sequence databases (Uniclust30 and UniRef90) and from metagenome database (Metaclust). Large-scale benchmark data show that DeepMSA profiles consistently improves contact prediction, secondary structure prediction, and threading over default HHblits or PSI-BLAST profiles""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0292, edam:operation_0303, edam:operation_3192 ; sc:name "DeepMSA" ; sc:url "https://zhanglab.ccmb.med.umich.edu/DeepMSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31529040" ; sc:description "The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry (MS), also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences" ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_2929 ; sc:license "MIT" ; sc:name "DeepMSPeptide" ; sc:url "https://github.com/vsegurar/DeepMSPeptide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3400, edam:topic_3474, edam:topic_3697 ; sc:citation , ; sc:description """Deep representation learning for disease prediction based on microbiome data. DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.""" ; sc:featureList edam:operation_3200, edam:operation_3359, edam:operation_3891 ; sc:license "MIT" ; sc:name "DeepMicro" ; sc:url "https://github.com/minoh0201/DeepMicro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6933638", "pubmed:31881831" ; sc:description "Fast and accurate microRNA search using CNN." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:name "DeepMir" ; sc:url "https://github.com/HubertTang/DeepMir" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0140 ; sc:citation , , "pmcid:PMC6956790", "pmcid:PMC7493403", "pubmed:31218353", "pubmed:32938368" ; sc:description "Predictor of protein sub-mitochondrial localization based on deep learning" ; sc:featureList edam:operation_2489, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DeepMito" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://busca.biocomp.unibo.it/deepmito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31081512" ; sc:description "Deep neural network based polyadenylation site analysis." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0428 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepPASTA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/arefeen/DeepPASTA" ; biotools:primaryContact "Ashraful Arefeen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474, edam:topic_3510, edam:topic_3542 ; sc:citation , "pubmed:31593229" ; sc:description """Protein-protein interaction site prediction through combining local and global features with deep neural networks. PPI sites prediction through combining local and global features with deep neural networks. DeepPPISP: Protein-protein interaction sites prediction through combining local and global features with deep neural networks. You can run the train.py file to train DeepPPISP and use the predcit.py file to see the predictive resluts. If you want to tune some hyper-parameters, you can change some values of hyper-parameters in config.py in utils folder. The PSSMs, raw sequences, secondary structures and labels are given in data_cache folder.""" ; sc:featureList edam:operation_2492, edam:operation_3092, edam:operation_3439, edam:operation_3899 ; sc:license "MIT" ; sc:name "DeepPPISP" ; sc:url "http://bioinformatics.csu.edu.cn/PPISP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6364462", "pubmed:30727941" ; sc:description "Phenotype-based variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-4-Clause" ; sc:name "DeepPVP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/bio-ontology-research-group/phenomenet-vp" ; biotools:primaryContact "Bio-Ontology Research Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3474, edam:topic_3577 ; sc:citation , , "pmcid:PMC7710064", "pubmed:33206638" ; sc:description "DeepPheno is a method for predicting gene-phenotype (HPO classes) associations from gene functional annotations (GO classes). Predicting single gene knockout phenotypes." ; sc:featureList edam:operation_2454, edam:operation_3196, edam:operation_3672 ; sc:license "BSD-3-Clause" ; sc:name "DeepPheno" ; sc:url "https://github.com/bio-ontology-research-group/deeppheno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3304, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC6897514", "pubmed:31570119" ; sc:description """A software toolkit for fast and robust animal pose estimation using deep learning. DeepPoseKit is a software toolkit with a high-level API for 2D pose estimation of user-defined keypoints using deep learning—written in Python and built using Tensorflow and Keras.""" ; sc:featureList edam:operation_0337, edam:operation_3215, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "DeepPoseKit" ; sc:url "https://github.com/jgraving/deepposekit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3511, edam:topic_3512 ; sc:citation , "pubmed:31714956" ; sc:description """Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, more than 160 RNA modifications have been discovered; therefore, accurate identification of RNA-modification sites is fundamental for a better understanding of RNA-mediated biological functions and mechanisms. However, due to limitations in experimental methods, systematic identification of different types of RNA-modification sites remains a major challenge. Recently, more than 20 computational methods have been developed to identify RNA-modification sites in tandem with high-throughput experimental methods, with most of these capable of predicting only single types of RNA-modification sites""" ; sc:featureList edam:operation_0278, edam:operation_0417, edam:operation_0443 ; sc:name "DeepPromise" ; sc:softwareHelp ; sc:url "http://DeepPromise.erc.monash.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0888 ; sc:encodingFormat edam:format_3590 ; sc:name "Structure similarity score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description """DeepRank is a general, configurable deep learning framework for data mining protein-protein interactions (PPIs) using 3D convolutional neural networks (CNNs). DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models.""" ; sc:featureList edam:operation_2996 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DeepRank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.0" ; sc:url "https://github.com/DeepRank/deeprank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_3172, edam:topic_3314, edam:topic_3474 ; sc:citation , "pubmed:31871149" ; sc:description """DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Deepginsen is a lantipeptide that is genomically encoded distantly from its modification enzymes and discovered directly as a result of DeepRiPP within the genome and metabolome of Flavobacterium ginsengiterrae JCM 17337.""" ; sc:featureList edam:operation_0436, edam:operation_3629 ; sc:name "DeepRiPP" ; sc:url "http://deepripp.magarveylab.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3175, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6909530", "pubmed:31830921" ; sc:description """A accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network. Calling deletions using deep convolutional neural. DeepSV, an approach based on deep learning for calling long deletions from sequence reads.DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project. Our work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs""" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3199, edam:operation_3227 ; sc:name "DeepSV" ; sc:url "https://github.com/CSuperlei/DeepSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC6790966", "pubmed:31608949" ; sc:description """A deep learning-based screening web server for accelerating drug discovery. DeepScreening is a useful platform to help drug researchers do virtual screening conveniently and fast through deep learning. DeepScreening is a user-friendly web server for constructing deep learning models using public dataset or user provided dataset, which would help biologist and chemist virtual screening the chemical probes or drugs for a specific target of interest.""" ; sc:featureList edam:operation_3644, edam:operation_3659 ; sc:name "DeepScreening" ; sc:url "http://deepscreening.xielab.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc:description "An interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction. A sequence-based pan model for peptide-MHC II binding affinity prediction." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3439 ; sc:name "DeepSeqPanII" ; sc:url "https://github.com/pcpLiu/DeepSeqPanII" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6923924", "pubmed:31861979" ; sc:description """Estimating isoform-level ribosome abundance and distribution with Ribo-seq data. For the estimation of Isoform-Level Ribosome Abundance and Distribution Accurately which needs Ribo-seq data only.""" ; sc:featureList edam:operation_0492, edam:operation_2495, edam:operation_3800 ; sc:name "DeepShape" ; sc:url "https://github.com/cuihf06/DeepShape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_0209, edam:topic_2840, edam:topic_3379 ; sc:citation ; sc:description "A Deep Learning Framework for Drug Side Effect Prediction. Drug failures due to unforeseen adverse effects at clinical trials pose health risks for the participants and lead to substantial financial losses" ; sc:featureList edam:operation_2495 ; sc:license "MIT" ; sc:name "DeepSide" ; sc:url "http://github.com/OnurUner/DeepSide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_3168 ; sc:citation , , "pmcid:PMC6834390", "pubmed:31723604" ; sc:description "A deep learning-based model with unparalleled generalization performance | We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available at http: deepcrispr.info DeepCas9" ; sc:name "DeepSpCas9" ; sc:softwareHelp ; sc:url "http://deepcrispr.info/DeepSpCas9" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6307148", "pubmed:30591034" ; sc:description "Deep learning based splice junction sequence classifier." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepSplice" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zhangyimc/DeepSplice" ; biotools:primaryContact "Yi Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3360, edam:topic_3384, edam:topic_3444, edam:topic_3577 ; sc:citation , "pmcid:PMC6788344", "pubmed:31636533" ; sc:description """Quantifying Neurodegenerative Progression With DeepSymNet. A data-driven method based that identifies longitudinal changes in 3D structural MRI data without relying on prior brain regions of interest, an atlas, or non-linear registration pipelines.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "DeepSymNet" ; sc:url "https://gitlab.com/lgianca/longitudinal-deepsymnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3068, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "A machine learning approach to gene functional enrichment. Deep functional synthesis: a machine learning approach to gene function enrichment. Deep Functional Synthesis (DeepSyn) is function annotation tool that moves beyond gene function databases to dynamically infer the functions of a gene set from its associated network of literature and data, conditioned on the disease and drug context of the current experiment." ; sc:featureList edam:operation_2454, edam:operation_3501, edam:operation_3672 ; sc:name "Deep Functional Synthesis (DeepSyn)" ; sc:url "http://github.com/wangshenguiuc/DeepSyn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2640, edam:topic_3361 ; sc:citation ; sc:description "Deep Learning Approach to Identifying Breast Cancer Subtypes Using High-Dimensional Genomic Data." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepType" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.acsu.buffalo.edu/~yijunsun/lab/DeepType.html" ; biotools:primaryContact "Yijun Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602 ; sc:citation , "pmcid:PMC6379983", "pubmed:30777029" ; sc:description "Deep Learning Framework for Prediction of Ubiquitination Sites in Proteins." ; sc:featureList edam:operation_0417, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DeepUbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Sunmile/DeepUbi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2840, edam:topic_3047, edam:topic_3336 ; sc:citation , , "pmcid:PMC7318080", "pubmed:32607441" ; sc:description """A Deep Learning Approach for Virtual Screening of Big Chemical Datasets. Drug discovery is an extensive and rigorous process that requires up to 2 billion dollars of investments and more than ten years of research and development to bring a molecule “from bench to a bedside”. While virtual screening can significantly enhance drug discovery workflow, it ultimately lags the current rate of expansion of chemical databases that already incorporate billions of purchasable compounds. This surge of available small molecules presents great opportunities for drug discovery but also demands for faster virtual screening methods and protocols. In order to address this challenge, we herein introduce Deep Docking ( D 2 ) - a novel deep learning-based approach which is suited for docking billions of molecular structures.""" ; sc:featureList edam:operation_0478 ; sc:license "MIT" ; sc:name "Deep Docking" ; sc:url "https://github.com/vibudh2209/D2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6722613", "pubmed:31374967" ; sc:description "Classifying Alternative Splicing Events Using Deep Learning | Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as \"Splicing Codes\". The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5'ss, alternative 3'ss, and constitutively spliced exons based only on the sequence of the exon junctions" ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:name "Deep Splicing Code (DSC)" ; sc:url "https://home.jbnu.ac.kr/NSCL/dsc.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3512 ; sc:citation ; sc:description """Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. DeltaNeTS+ is a major improvement to our previous method DeltaNet. DeltaNeTS+ is a method for inferring direct gene targets of drug compounds and diseases from steady-state and/or time-series transcriptional profiles. DeltaNeTS+ incorporates gene regulatory information (if avaialbe) during the inference. DeltaNeTS+ generates a perturbation score for each gene in every sample. The score magnitude reflects the confidence that the transcription process of this gene was directly affected by the external stimuli. The score sign indicates the nature of the perturbation: positive for gene induction, negative for gene repression""" ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3439, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "DeltaNeTS+" ; sc:url "http://www.github.com/cabsel/deltanetsplus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3399, edam:topic_3405 ; sc:citation , "pubmed:31521901" ; sc:description "Automated longevity and risk factor analysis in dental patient care | BACKGROUND AND OBJECTIVE:During routine patient care practitioners have to document several aspects. However, currently it is difficult to methodically analyze the longevity of therapeutic concepts in dental private practice. Thus, the aim of the present paper was to introduce a software (Dentareport) to compare the success of different treatment options and to identify risk factors for failures in dental patient care. METHODS:Dentareport has a digital interface to automatically collect data of electronic patient files of practice management programs. By using computer-aided routines descriptive analyses of the treatments can be visualized. Dentareport also visually displays a bivariate risk factor analysis of treatment options" ; sc:name "Dentareport" ; sc:url "http://dentareport.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3518 ; sc:citation ; sc:description "Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | The Cancer Dependency Map Project at Broad Institute | A resource of data and computational tools to expose the vulnerabilities of cancer, and for identifying targets for therapeutic development and designing strategies to optimize patient responses | Explore the Cancer Dependency Map | The goal of the Dependency Map (DepMap) portal is to enable the research community to make discoveries related to cancer vulnerabilities by providing free and timely access to the datasets, visualizations, and analysis tools that are being used by the Cancer Dependency Map Project at the Broad Institute" ; sc:featureList edam:operation_3557, edam:operation_3629, edam:operation_3891 ; sc:name "DepMap" ; sc:url "https://depmap.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3321, edam:topic_3518 ; sc:description "Tool to determine the optimal read depth for reduced-representation sequencing." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3230 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DepthFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/jerlar73/depthfinder/src/master/" ; biotools:primaryContact "Jerome Laroche" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description "Tool for designing primers that yields amplicons with distinct signatures." ; sc:featureList edam:operation_0308 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DesignSignatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.decipher.codes/DesignSignatures.html" ; biotools:primaryContact "Kalin H. Vetsigian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation ; sc:description "Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry." ; sc:featureList edam:operation_0252, edam:operation_2929, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Deuteros" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andymlau/Deuteros" ; biotools:primaryContact "Argyris Politis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_2885 ; sc:citation , "pubmed:31056858" ; sc:description "Assembly-free analysis and visualization of mobile genetic element composition." ; sc:featureList edam:operation_0427, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DeviaTE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/W-L/deviaTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3332 ; sc:citation , "pubmed:31702762" ; sc:description """Standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis. DiNGO is a standalone application based on open source code from BiNGO a Java based tool aimed to determine which Gene Ontology (GO) categories are overrepresented in a set of genes. DiNGO is a command line application which is able to do GO and HPO term enrichment on a set of genes or proteins. DiNGO is multithreaded application which offers fast processing of large datasets. In addition, the application offers gene/protein identifiers conversion tool as well as automatic download of HPO and GO annotation resources.""" ; sc:featureList edam:operation_3431, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "DiNGO" ; sc:softwareHelp ; sc:url "https://www.vin.bg.ac.rs/180/tools/DiNGO.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC6509638", "pubmed:31130993" ; sc:description "Interactive and Integrated Web-Based Visualization Tool for Comparing Gene Lists." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DiVenn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://divenn.noble.org/" ; biotools:primaryContact "Liang Sun", "Yinbing Ge", "Zach Robinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "Tool for discovery of new molecules by mass spectrometry." ; sc:featureList edam:operation_3627, edam:operation_3645, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DiagnoProt" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://patternlabforproteomics.org/diagnoprot/" ; biotools:primaryContact "André R.F Silva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593 ; sc:description "Software package able to obtain quantitative self-diffusion data in a very straightforward manner allowing the calculation of radii including different molecular models which is not only restricted to spheres." ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "DiffAtOnce" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.diffatonce.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6527599", "pubmed:31139204" ; sc:description "Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DiffExpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://simplicity.nsilico.com/dea" ; biotools:primaryContact "Cintia C. Palu", "Paul Walsh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6519793", "pubmed:31091224" ; sc:description "Identification of disease-gene-chemical relationships from Medline abstracts." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DigChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gcancer.org/digchem" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation ; sc:description "Web-based database system for flow cell management." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DigestiFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bihealth/digestiflow-server" ; biotools:primaryContact "Manuel Holtgrewe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6824295", "pubmed:31708961" ; sc:description """Deep-Learning on scRNA-Seq to Deconvolute Gene Expression Data. A pipeline to generate a Deep Nerual Network cell type deconvolution model for bulk RNASeq samples from single cell experiment data. A pipeline to generate a Deep Neural Network cell type deconvolution model for bulk RNASeq samples from single cell rna-seq data. The pipeline runs in R 3.51 and python 3.6.8. conda create env -n digitalDLSorter""" ; sc:featureList edam:operation_0560, edam:operation_3629, edam:operation_3800 ; sc:name "Digitaldlsorter" ; sc:url "https://github.com/cartof/digitalDLSorter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3305, edam:topic_3519 ; sc:citation , "pmcid:PMC6735924", "pubmed:31528358" ; sc:description "Rapid viral diagnosis from high-throughput sequencing data | High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method" ; sc:featureList edam:operation_3196, edam:operation_3472 ; sc:name "DisCVR" ; sc:url "https://bioinformatics.cvr.ac.uk/software/discvr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31187352" ; sc:description "Software Package for Assessing Reproducibility of Brain Networks and their Discriminability across Disorders." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DisConICA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.01.1", "1.01.2" ; sc:url "https://bitbucket.org/masauburn/disconica/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6542142", "pubmed:31142265" ; sc:description "Software for HPV detection in RNA sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DisV-HPV16" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/ybq1204/DisV-HPV16" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0769, edam:topic_3063 ; sc:citation , "pubmed:31702788" ; sc:description """An easy-to-use web application and R package for discovering rhythmicity. An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface. Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. DiscoRhythm is available as a web application or an R/Bioconductor package for estimating phase, amplitude, and statistical significance using four popular approaches to rhythm detection (Cosinor, JTK Cycle, ARSER, and Lomb-Scargle). Informative visualizations, interactive modules for quality control, dimensionality reduction, periodicity profiling, and incorporation of experimental replicates make DiscoRhythm a thorough toolkit for analyzing rhythmicity.""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "DiscoRhythm" ; sc:url "https://disco.camh.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:30059974" ; sc:description "R package for multi-omic data driven prediction of synthetic lethality in cancers." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DiscoverSL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/shaoli86/DiscoverSL/releases/tag/V1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3336 ; sc:citation , "pmcid:PMC6688218", "pubmed:31399045" ; sc:description "A classifier for identifying Y chromosome sequences in male assemblies | BACKGROUND:Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references. RESULTS:We develop a k-mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal" ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_0525 ; sc:license "MIT" ; sc:name "DiscoverY" ; sc:url "https://github.com/makovalab-psu/DiscoverY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31879784" ; sc:description "Scripts for disentangling small RNA-sequencing (sRNA-Seq) data for libraries containing information from two interacting organisms to study RNA communication between species." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_3258, edam:operation_3792 ; sc:name "Disentangling sRNA-Seq" ; sc:url "https://github.com/ObedRamirez/Disentangling-sRNA-Seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0736 ; sc:citation , "pubmed:31593887" ; sc:description """Database of amino acid distances in proteins and web application for statistical review of distances. Three-dimensional structure of a protein chain is determined by its amino acid interactions. One approach to the analysis of amino acid interactions refers to geometric distances of amino acid pairs in polypeptide chains. For a detailed analysis of the amino acid distances, the database with three types of amino acid distances in a set of chains was created. Web application Distances of Amino Acids has also been developed to enable scientists to explore interactions of amino acids with different properties based on distances stored in the database. Web application calculates and displays descriptive statistics and graphs of amino acid pair distances with selected properties, such as geometric distance threshold, corresponding SCOP class of proteins and secondary structure types.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2488 ; sc:name "DistAA" ; sc:url "http://andromeda.matf.bg.ac.rs/aadis_dynamic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3518 ; sc:citation ; sc:description "An R Package for Divergence Analysis of Omics Data | Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms" ; sc:featureList edam:operation_2495, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "Divergence" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/divergence.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2333 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc:description "DiversityAgents (DWB-DA) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DA is focused on the management of agents, that means persons and organisations. In this context it is designed to manage names (variant names, different names, academic degrees, standardized abbreviations etc.), bibliographic data, postal addresses, agent relation to projects, resources like images and documents and additional agent-related data including agent IDs and the hierarchy of person-related data." ; sc:featureList edam:operation_2409, edam:operation_3349 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityAgents" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityAgents" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3706 ; sc:name "Biodiversity data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2332, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2332, edam:format_3706 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3050, edam:topic_3071, edam:topic_3299, edam:topic_3301, edam:topic_3382, edam:topic_3500, edam:topic_3678, edam:topic_3679 ; sc:description "DiversityCollection (DWB-DC) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DC is designed for data describing collection events, collections, collection vouchers and specimens, parts of specimens, as well as observation and occurrence data with assigned multimedia objects and documents. It is processing any action concerning the gathering, storage, transaction and treatment of specimens in a collection and is also appropriate to store observation data with analyses added. DC is unique among collection management systems by its focus on biological relations between organisms linked together as one or more specimens or observations (e. g., host, parasite, hyperparasite, symbionts, etc.) and by its interoperability through internal and external services." ; sc:featureList edam:operation_0226, edam:operation_0337, edam:operation_2409, edam:operation_2945, edam:operation_3429, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityCollection" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net/Portal/DiversityCollection" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2350 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2350 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_2350 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2332, edam:format_2350 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3050, edam:topic_3070, edam:topic_3071, edam:topic_3391, edam:topic_3678, edam:topic_3855 ; sc:citation ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc:description "DiversityDescriptions (DWB-DD) is an application of the Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. DD has a generic database model. It is organising descriptions of organisms, taxa, syntaxa and any item, which is object of diversity research. The descriptions are characterized by a triple structure, namely ’item-descriptor-state’. The states can be generalized to one of the presently supported data types (categorical states, quantitative values and measures, molecular sequence data and free-form text). The descriptors (=properties) are not limited to morphological characters and functional traits, but could be physiological, ecological, behavioral , survey parameters, molecular descriptors, descriptors of a lab workflow, descriptors of data content schemes. Sample data and measurement data as gained by ecological field sampling are addressed with own functions." ; sc:featureList edam:operation_2409, edam:operation_2429, edam:operation_2945, edam:operation_3434, edam:operation_3438 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityDescriptions" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityDescriptions" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3071 ; sc:contributor "SNSB, Botanische Staatssammlung München" ; sc:description "DiversityExsiccatae (DWB-DE) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DE is currently used in a core installation at the SNSB, Botanische Staatssammlung München to manage bibliographic information and standardized abbreviations of botanical and mycological exsiccatae in a global index. Exsiccatae are series of specimen collections which are distributed as a publication together with assigned printed matters. They are usually available in multiple copies worldwide. This standard list for Exsiccatal series with unique and stable series identifers is increasing the efficiency of the digitization of botanical and mycological collections." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityExsiccatae" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net/Portal/DiversityExsiccatae" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2333 ; sc:name "Map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2333 ; sc:name "Map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3855 ; sc:description "DiversityGazetteers (DWB-DG) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DG is used to manage and visualize geographical dictionary entries with information about places (particular regions and locations). In conjunction with an automatically created background map, equipped with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines and areas) are displayed in their geographical context. Users with administrator rights may import places from other sources (e. g., ArcView shape files) or create places manually using the integrated Diversity GIS Editor. They may also organise the classification and naming of places." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityGazetteers" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityGazetteers" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333, edam:format_2350 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2330 ; sc:name "Text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc:description "The DiversityImageInspector (DWB-DII) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent tool. The DII is designed to scan a bulk of images for included barcodes and relevant EXIF metadata (e.g., GPS coordinates, date, time) and returns the results in a table. The table can be saved as text file (CSV) along with the corresponding image file names. DII is able to rename the multimedia input files by adding a prefix to the file name to fit, e. g., the naming convention of an image data repository. This feature might be used to organize the multimedia file storage, e. g. on a web server. DII combines the functions of two freeware tools: (a) ExifTool, to extract the search tags from the metadata of an image and (b) ZBar bar code reader, to find barcodes within a picture. The latter software supports barcodes of the following types: EAN-13/UPC-A, UPC-E, EAN-8, Code 128, Code 39, Interleaved 2 of 5 and QR Code." ; sc:featureList edam:operation_2409, edam:operation_3438, edam:operation_3443 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityImageInspector" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:url "https://diversityworkbench.net/Portal/DiversityImageInspector" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_3706 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web service" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3070, edam:topic_3071 ; sc:author "University of Bayreuth, Chair of Databases and Information Systems" ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc:description "DiversityMobile (DWB-DM) is an smartphone app for biologists, ecologists and registered citizen scientists being experienced in recording observation data in the field. Data are entered into the app database which follows the Diversity Workbench (DWB) information model. Mechanisms of automated recording and storage of GPS data and manual recording of multimedia data are included. Data entry might be done offline. The DM virtual environment covers webservices for bidirectional data transfer with an institutional data repository. Features include the recording of research data and metadata with automatic inclusion of GPS data, recording of multimedia data (images, audio, video), data transfer from and to an institutional data repository via Wi-Fi. DM webservices are ready to download standardised pick lists with names of organisms, geographic maps and already available metadata of individual research projects. DM webservices are also used to upload research data to the data repository." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityMobile" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityMobile" ; biotools:primaryContact "SNSB IT Center" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071, edam:topic_3678 ; sc:description "DiversityProjects (DWB-DP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DP is focused on the management of (research) projects, data collections, processed by the other DWB modules. It is managing metadata , labels, descriptors, and descriptions of projects, including data package-specific settings for a metadata standard-compliant publication. DP is organising the storage of (legal) documents, permits, information on publications and multimedia resources. DP is handling roles of persons and organisations involved in collection and research projects. The tool is organising project classification and hierarchy in relation to sister and umbrella projects as well as the storage of each type of stable identifier related to data packages. DP is managing issues on web presentation of data collections." ; sc:featureList edam:operation_2409, edam:operation_2428 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityProjects" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityProjects" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3071 ; sc:description "DiversityReferences (DWB-DR) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DR is focussed on the management of bibliographic data about each kind of scientific publications. The tool is handling literature annotations, abstracts, keywords and any kind of descriptors and publication object identifiers. DR is able to import and export literature citations and is used to organise documents and multimedia resources." ; sc:featureList edam:operation_0226, edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityReferences" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityReferences" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Ecological data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3855 ; sc:description "DiversitySamplingPlots (DWB-DSP) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DSP is focussed on the management of sampling plots. It is a tool designed for biodiversity, geodiversity, ecological and geosciences research projects. In this context it is appropriate to design plots, organise the geographical position of geoobjects and the geometry of the plots as well as of georeferenced objects found on the plots. DSP is able to import sampling plots from other sources and formats (e. g., ArcView shape files) classifying them hierarchically and annotating them. The Diversity GIS Editor is integrated." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversitySamplingPlots" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversitySamplingPlots" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3071, edam:topic_3303, edam:topic_3314, edam:topic_3855 ; sc:description "DiversityScientificTerms (DWB-DST) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DST is focussed on the management of collections of scientific terms and term concepts, i. e., particular domain-specific terminologies, glossaries and vocabularies (e.g. biostratigraphy, anatomical terminology). DST is able to organise terms together with synonyms, common names and equivalent terms ín different languages. The single terms are defined, (hierarchically) classified and referenced, for example, by linking online resources and external identifiers." ; sc:featureList edam:operation_2409 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityScientificTerms" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityScientificTerms" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330, edam:format_2332, edam:format_2376 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3071 ; sc:description "DiversityTaxonNames (DWB-DTN) is an application of Diversity Workbench (DWB). It might be installed as part of a DWB environment, but also as a stand-alone application, e. g., in a local installation. Each DWB module is devoted to a specific data domain. DTN is focused on the management of taxon names. Next to nomenclatural information on zoological, botanical, mycological, palaeontological, bacteriological taxon names like typification with type specimens, homotypic synonyms, basionyms, protologues and references according to the rules of the respective International Codes, it is designed to document taxonomic information. This includes accepted names (current names), heterotypic synonyms, name concepts and classifications as well as the history of changing taxonomic relations. DTN is also used to organise common names in various languages and regional taxon checklists with information on red list status and other taxon-based (ecological and nature conservation) parameters." ; sc:featureList edam:operation_2409, edam:operation_2945, edam:operation_2990, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DiversityTaxonNames" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "https://diversityworkbench.net/Portal/DiversityTaxonNames" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2330, edam:format_2333, edam:format_2350 ; sc:name "Map" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2330, edam:format_2333, edam:format_2350 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071, edam:topic_3855 ; sc:description "The Diversity GIS Editor (DWB-DGE) is a stand-alone application of Diversity Workbench (DWB). It might be installed as an independent module of a DWB environment. Beside this, the DGE is an integrated part of DiversityCollection, DiversityGazetteers and DiversitySamplingPlots. The DGE allows for creating, visualizing, editing and storing samples within a geographical environment. In combination with a background map with world coordinates, collections of Microsoft SQL Geometry Objects (points, lines, areas) may be displayed and edited. The screen and world coordinates of the objects are calculated. Color, thickness and transparency of the elements can be designed. The working area may be shifted or zoomed. The background map could either be loaded from a storage device or created with an online map server tool. Maps without world coordinates may be adjusted to a background map with coordinates by setting reference points. This function allows the georeferencing of historical maps." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2430 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Diversity GIS Editor" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , ; sc:url "https://diversityworkbench.net/Portal/DiversityGisEditor" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3070, edam:topic_3071, edam:topic_3391, edam:topic_3678, edam:topic_3855 ; sc:contributor "Universität Bayreuth, Department of Mycology" ; sc:description "The modularized Diversity Workbench (=DWB) represents a tool suite for the management of life and environmental sciences data. The DWB is handling different kinds of bio- and geodiversity data, taxonomies, terminologies, and facilitates the processing of ecological, molecular biological, observational, collection and taxonomic data. It is capable and flexible enough to be applied as data storage system for institutional data repositories. The DWB is set up on a system of 11 xml-enabled SQL relational databases. The rich clients are installed as desktop applications. The DWB might be run as an intranet solution and provide direct interoperability with clients of interlinked DWB databases including cloud services. DWB installations are flexible in the management of highly structured data, enable sophisticated user administration and allow for user-adapted data entry and data exchange. Further, the DWB design facilitates the dynamic integration of web services and external data resources." ; sc:featureList edam:operation_0226, edam:operation_2409, edam:operation_2425, edam:operation_2945, edam:operation_3429, edam:operation_3434 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Diversity Workbench" ; sc:operatingSystem "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , , ; sc:url "https://diversityworkbench.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3068 ; sc:citation ; sc:description "Bayesian evidence analysis tool for systems biology." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Dizzy-Beats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/bayesevidence/home/Home/" ; biotools:primaryContact "Stuart Aitken" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3306, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6803556", "pubmed:31680924" ; sc:description """Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy. An open source toolbox for reproducible diffusion MRI-based microstructure estimation. Dmipy: Diffusion Microstructure Imaging in Python. The Dmipy software package facilitates the reproducible estimation of diffusion MRI-based microstructure features. It does this by taking a completely modular approach to Microstructure Imaging. Using Dmipy you can design, fit, and recover the parameters of any multi-compartment microstructure model in usually less than 10 lines of code. Created models can be used to simulate and fit data for any PGSE-based dMRI acquisition, including single shell, multi-shell, multi-diffusion time and multi-TE acquisition schemes. Dmipy's main features include:""" ; sc:featureList edam:operation_2425, edam:operation_2426, edam:operation_3629 ; sc:license "MIT" ; sc:name "Dmipy" ; sc:url "https://github.com/AthenaEPI/dmipy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3385, edam:topic_3474 ; sc:citation , "pmcid:PMC6533009", "pubmed:31083649" ; sc:description "Deep architecture for synapse detection in multiplexed fluorescence images." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DoGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kulikovv/dognet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625 ; sc:citation , "pmcid:PMC6602487", "pubmed:31106327" ; sc:description "Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation." ; sc:featureList edam:operation_1812, edam:operation_3280, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Doc2Hpo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://impact2.dbmi.columbia.edu/doc2hpo/" ; biotools:primaryContact , "Kai Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:31578656" ; sc:description """Assessing and improving the performance of consensus docking strategies using the DockBox package. Platform package to simplify the use of docking programs and consensus methods. DockBox is a python wrapper library designed to facilitate the use of standard docking programs either alone or in combination. In addition, DockBox enables to rescore the generated docking poses with different popular scoring algorithms as well as to analyze the results using different consensus docking/scoring strategies""" ; sc:featureList edam:operation_0482, edam:operation_3659, edam:operation_3899 ; sc:name "DockBox" ; sc:url "https://pypi.org/project/dockbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc:description "Web Services for Molecular Docking Simulations | A Free Web Server for Protein-ligand Docking | Add missing hydrogen atoms, complete side chains, change protonation states. Simple and easy!" ; sc:featureList edam:operation_0249, edam:operation_0482, edam:operation_3899 ; sc:name "DockThor" ; sc:url "https://dockthor.lncc.br/v2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pmcid:PMC6982331", "pubmed:31906249" ; sc:description """It is a new work-flow designed for a comprehensive analysis of circRNAs composed of: the circRNAs prediction, their classification and annotation using public databases, the back-splicing sequence reconstruction, the internal alternative structure definition, the alignment-free circRNAs quantification from RNA-Seq reads, and their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNA analysis thanks to its containerization and an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into an docker image following guideline provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/).""" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Docker4Circ" ; sc:operatingSystem "Linux" ; sc:softwareVersion "version 1" ; sc:url "https://github.com/kendomaniac/docker4seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0130, edam:topic_0736 ; sc:citation , "pmcid:PMC6816169", "pubmed:31660857" ; sc:description """domain-oriented orthology inference. BACKGROUND:Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains. RESULTS:This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories""" ; sc:featureList edam:operation_0303, edam:operation_0327, edam:operation_3435, edam:operation_3767 ; sc:name "Domainoid" ; sc:url "https://bitbucket.org/sonnhammergroup/domainoid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3500, edam:topic_3679 ; sc:citation , "pubmed:31816295" ; sc:description """Dominance, Sharing, and Assessment in an Iterated Hawk-Dove Game. Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting is followed by the submission of subordinates. Although models have been developed to analyze specific strategies for resolving conflicts over resources, little work has focused on trying to understand why particular strategies are more likely to arise in certain situations. In this paper, we use a model based on an iterated Hawk-Dove game to analyze how resource holding potentials (RHPs) and other factors affect whether sharing, dominance relationships, or other behaviours are evolutionarily stable""" ; sc:featureList edam:operation_2426 ; sc:name "Dominance Sharing Assessment" ; sc:url "https://bitbucket.org/CameronLHall/dominancesharingassessmentmatlab/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3572 ; sc:description "Detection of doublets (technical errors) in single-cell RNA-seq count matrices." ; sc:featureList edam:operation_0337, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DoubletDetection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JonathanShor/DoubletDetection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3318, edam:topic_3892 ; sc:citation , "pubmed:31542001" ; sc:description "Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models | Stochastic drift-diffusion (DrDiff) framework can evaluate free energy, drift and diffusion coefficients, transition path and first passage times using trajectory time traces | Drift-diffusion (DrDiff) framework" ; sc:featureList edam:operation_0244 ; sc:license "GPL-3.0" ; sc:name "DrDiff" ; sc:url "https://github.com/ronaldolab/DrDiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:31691822" ; sc:description """A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic species. Phase separation, or liquid-liquid phase separation (LLPS), is a ubiquitous and important mechanism for the formation of membraneless condensates in cells""" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3454 ; sc:name "DrLLPS" ; sc:softwareHelp ; sc:url "http://llps.biocuckoo.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31710658" ; sc:description """Rendering glycans and annotating glycopeptide mass spectra. Render glycans and glycopeptides with fragmentation info. using the Symbolic Nomenclature for Glycans [SNFG]. Virtual Glycome Release notes FAQ. IUPAC-condensed Input (glycan or glycopeptide):. If you use this software, please cite: Cheng, K. et al., 'DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information', Glycobiology 27(3): 200-205, 2017 ( Abstract & Full Text )""" ; sc:featureList edam:operation_0337, edam:operation_3646, edam:operation_3755 ; sc:license "GPL-3.0" ; sc:name "DrawGlycan-SNFG" ; sc:softwareHelp ; sc:url "https://virtualglycome.org/drawglycan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_0659, edam:topic_2640, edam:topic_3173 ; sc:citation , "pubmed:31701128" ; sc:description "DriverDBv3 is a cancer omics database which incorporates somatic mutation, RNA expression, miRNA expression, methylation, copy number variation and clinical data in addition to annotation bases." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3207 ; sc:name "DriverDBv3" ; sc:url "http://ngs.ym.edu.tw/driverdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2640, edam:topic_3518, edam:topic_3577 ; sc:citation , "pubmed:31626284" ; sc:description """Inferring subgroup specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication. Developer: Jianing Xi xjn@nwpu.edu.cn. Instructions to DriverSub (version 1.0.0). After the raw data are loaded, the script ./GenerateInputData.m with function ./bin/P02_GenerateMutData.m can generate the mutation matrix of BRCA and BLCA as ./InputData/D01_brca.mat and ./InputData/D02_blca.mat. The two generated .mat files are the input data of DriverSub""" ; sc:featureList edam:operation_2454, edam:operation_3435, edam:operation_3439 ; sc:name "DriverSub" ; sc:url "https://github.com/JianingXi/DriverSub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6602441", "pubmed:31066443" ; sc:description "> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/predrbr (DENGLAB.ORG), bio.tools/deepsacon (DENGLAB.ORG), bio.tools/predhs (DENGLAB.ORG) | an integrative cancer drug combination data portal | DrugComb is an open-access, community-driven data portal where the results of drug combination screening studies for a large variety of cancer cell lines are accumulated, standardized and harmonized. An actively expanding array of data visualization and computational tools is provided for the analysis of drug combination data | Please pay attention that the template header format is changed. Analysis function is also updated | response column should be renamed to inhibition as in the template file | Sharing data leads to novel knowledge | Start analyzing your own drug combination data by uploading | File should be a comma separated value(csv)" ; sc:featureList edam:operation_2929, edam:operation_3431, edam:operation_3894 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DrugComb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://drugcomb.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2640, edam:topic_3336, edam:topic_3375 ; sc:citation , "pubmed:31665429" ; sc:description "DrugCombDB is a comprehensive database dedicated to integrating drug combinations from various data sources, include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature." ; sc:featureList edam:operation_2421, edam:operation_3659, edam:operation_3799 ; sc:name "DrugCombDB" ; sc:softwareHelp ; sc:url "http://drugcombdb.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:31096089" ; sc:description "Database for drug repurposing, combination therapy, and replacement therapy." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DrugR+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.drugr.ir" ; biotools:primaryContact "Ali Masoudi-Nejad", "Massoud Amanlou", "Yadollah Omidi", "Yosef Masoudi-Sobhanzadeh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3379 ; sc:citation , "pmcid:PMC6602481", "pubmed:31106379" ; sc:description "Web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning." ; sc:featureList edam:operation_0420, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Drug ReposER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mfrlab.org/drugreposer/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3374 ; sc:citation , "pubmed:31368482" ; sc:description "A database protal for drug target predictions based knowledge graph embeddings." ; sc:featureList edam:operation_0463, edam:operation_2489 ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "Drug Targets" ; sc:url "http://drugtargets.insight-centre.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation , "pubmed:31062193" ; sc:description "> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'nondecision', 'DM', 'two-choice' | an R package for analyzing two-choice reaction time data with the D∗M method | The decision process in choice reaction time data is traditionally described in detail with diffusion models. However, the total reaction time is assumed to consist of the sum of a decision time (as modeled by the diffusion process) and the time devoted to nondecision processes (e.g., perceptual and motor processes). It has become standard practice to assume that the nondecision time is uniformly distributed. However, a misspecification of the nondecision time distribution introduces bias in the parameter estimates for the decision model. Recently, a new method has been proposed (called the D∗M method) that allows the estimation of the decision model parameters, while leaving the nondecision time distribution unspecified" ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DstarM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=DstarM" ; biotools:primaryContact "Don van den Bergh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2885 ; sc:citation ; sc:description "Fast calculation of the ABBA-BABA statistics across many populations/species." ; sc:featureList edam:operation_3196, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Dsuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/millanek/Dsuite" ; biotools:primaryContact "Milan Malinsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6383267", "pubmed:30791939" ; sc:description "Tool for identification of different modes of duplicated gene pairs." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "DupGen_finder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/qiao-xin/DupGen_finder" ; biotools:primaryContact "Xin Qiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3337 ; sc:author ; sc:description "Dwarna ('about us' in Maltese) is a blockchain-based dynamic consent application for biobanking. The application, which is served through a WordPress plugin, uses a Hyperledger Fabric blockchain, through Hyperledger Composer, to store research participants' consent changes. In this way, the blockchain stores an immutable consent trail. The application contains functionality to manage research studies, research participants and researchers in WordPress." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Dwarna" ; sc:softwareHelp ; sc:url "https://github.com/NicholasMamo/dwarna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6663215", "pubmed:31410378" ; sc:description "Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis | Geniesse, C., Sporns, O., Petri, G., Saggar, M. (in-press) Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "DyNeuSR" ; sc:url "https://braindynamicslab.github.io/dyneusr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3173 ; sc:citation , "pmcid:PMC6693283", "pubmed:31409281" ; sc:description "A web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks | BACKGROUND:The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because of the dynamic nature of these processes, the analysis of the results is challenging. Therefore, there is a great need for bioinformatics tools that address this problem. RESULTS:Here we present DynOVis, a network visualization tool that can capture dynamic dose-over-time effects in biological networks. DynOVis is an integrated work frame of R packages and JavaScript libraries and offers a force-directed graph network style, involving multiple network analysis methods such as degree threshold, but more importantly, it allows for node expression animations as well as a frame-by-frame view of the dynamic exposure" ; sc:featureList edam:operation_0277, edam:operation_3439 ; sc:name "DynOVis" ; sc:url "https://tjmkuijpers.shinyapps.io/dynovistool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3343 ; sc:citation , "pmcid:PMC6572260", "pubmed:31052310" ; sc:description "Dynamic Retention Time Database for Steroidomics." ; sc:featureList edam:operation_3454, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "DynaStI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dynasti.vital-it.ch" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3518 ; sc:citation , "pubmed:31609429" ; sc:description """Interactive sequence logo with dynamic thresholding of matched quantitative proteomic data. Dynalogo can be run with the following code from within RStudio or deployed on a shiny server. To ensure compatibility, the user can download the current list of packages and Version numbers from the Dynalogo webite by clicking on the "Version Info" text at the top of the application located at https://dynalogo.cam.uchc.edu. Dynalogo: Dynamic Sequence Logos. Dynalogo is a web application which can be used to visualize and explore binding array (ie. peptide array) datasets. It was created to allow the dynamic visualizations of sequence logos for better insight into the relationship between affinity and specificity of binding domains. Please import your dataset or dowlnoad the sample dataset""" ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Dynalogo" ; sc:url "https://dynalogo.cam.uchc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pubmed:31793979" ; sc:description """Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances/dissimilarities of shotgun metagenomes at the species level. Dynamic Meta-Storms calculates comprehensive taxonomic and phylogenetic distances dissimilarities of shotgun metagenomes at the species level.""" ; sc:featureList edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "Dynamic Meta-Storms" ; sc:url "https://github.com/qibebt-bioinfo/dynamic-meta-storms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6701490", "pubmed:31430368" ; sc:description "Scripts used during the genome assembly of Dysdera silvatica." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3501 ; sc:license "MIT" ; sc:name "Dysdera silvatica genome" ; sc:url "https://github.com/molevol-ub/Dysdera_silvatica_genome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0121, edam:topic_0749, edam:topic_2229, edam:topic_3308 ; sc:citation , ; sc:description """Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. vngFCM is a package designed to analyse fluocytometry data of small bacterial cells. Fluocytometer analysis of bacterial cells. install.packages("/path/to/E-Flow", repos=NULL, type="source"). This package has been designed to process FCM data by removing non viable cells, subtracting autofluorescence and reduce the effect of electronic noise coming from the cytometer. It has been designed for the analysis of bacterial cells, where the small dimensions and the low expression pose challanges in the correct interpretation of the data.""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:name "E-Flow" ; sc:url "https://github.com/vanNimwegenLab/E-Flow" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3120 ; sc:author , "Matteo Manfredi" ; sc:citation , "pmcid:PMC9710551", "pubmed:36227117" ; sc:description "E-SNPs&GO is a machine-learning method the pathogenicity of human variations. E-SNPs&GO classify input variations into pathogenic or benign." ; sc:featureList edam:operation_0331 ; sc:isAccessibleForFree true ; sc:name "E-SNPs and GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:url "https://esnpsandgo.biocomp.unibo.it/" ; biotools:primaryContact , , "Matteo Manfredi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "EAGS is a smoothing approach for spatial transcriptome data with ultrahigh resolution. Through the principal component information of the profiling of gene expression and the personally identifiable information between cells, it uses a two-factor adaptive smoothing weight mechanism to determine the neighborhood relationship of cells. Then it uses the self-developed smoothing weight formula to calculate the smoothing contribution and recalculate the gene expression of each cell." ; sc:name "Efficient and Adaptive Gaussian smoothing applied to high-resolved spatial transcriptomics" ; sc:url "https://github.com/STOmics/EAGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6505892", "pubmed:31067213" ; sc:description "Predictive model for flanking gene expression of T-DNA insertion activation-tagged rice mutants by machine learning approaches." ; sc:featureList edam:operation_0441, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EAT-Rice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://predictor.nchu.edu.tw/EAT-Rice" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc:description "Evolutionary-based BIClustering (EBIC), a next-generation biclustering algorithm for mining genetic data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EBIC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/EpistasisLab/ebic" ; biotools:primaryContact "Jason H. Moore", "Patryk Orzechowski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3033 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation , "pmcid:PMC5001598", "pubmed:27207878" ; sc:description "A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data." ; sc:featureList edam:operation_0313, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ECLAIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GGiecold/ECLAIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , , "pubmed:33305308" ; sc:description """Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages. Abstract Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. The increasing amount of genomics data gathered from patients allows for better understanding of gene regulatory mechanisms that occur during disease development at a system level. However, integrating such a large amount of population data is still a challenging task. To address this, we developed an interpretable machine learning model, ECMarker, to predict gene expression biomarkers and regulatory networks specific for disease stages such as early cancer. In particular, ECMarker was built on the semi-restricted Boltzmann machine, a machine learning model with multiple hierarchical layers.""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3439 ; sc:name "ECMarker" ; sc:url "https://github.com/daifengwanglab/ECMarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068 ; sc:citation , "pmcid:PMC6822939", "pubmed:31671102" ; sc:description "A new toolbox for time series analysis and forecasting. Some Features found in a few packages or none at all." ; sc:featureList edam:operation_0337, edam:operation_3565, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "ECOTOOL" ; sc:url "https://github.com/djpt999/ECOTOOL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0194, edam:topic_2269, edam:topic_3293 ; sc:citation , , "pmcid:PMC7743758", "pubmed:32877529" ; sc:description "EDCluster is a method for obtaining stationary distributions that can be used to construct empirical stationary distribution mixture models." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "EDCluster" ; sc:url "https://github.com/dschrempf/edcluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0769, edam:topic_0780, edam:topic_0798 ; sc:citation , "pmcid:PMC6913007", "pubmed:31843001" ; sc:description "The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome." ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3629 ; sc:name "The Extensive de novo TE Annotator (EDTA)" ; sc:url "https://github.com/oushujun/EDTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation , "pmcid:PMC6413114", "pubmed:30781869" ; sc:description "Platform to enable EEG measurements and general purposes Brain Computer Interface experimentations." ; sc:name "Open-Electroencephalography (EEG)" ; sc:url "http://openeeg.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Prototype neurofeedback application." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EEGMIR" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://uazu.net/eegmir/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3334 ; sc:citation , "pmcid:PMC6815881", "pubmed:31381946" ; sc:description """A framework for realistic simulation of EEG scalp data using MRI-based forward models and biologically plausible signals and noise | BACKGROUND:Electroencephalography (EEG) is widely used to investigate human brain function. Simulation studies are essential for assessing the validity of EEG analysis methods and the interpretability of results. NEW METHOD:Here we present a simulation environment for generating EEG data by embedding biologically plausible signal and noise into MRI-based forward models that incorporate individual-subject variability in structure and function. RESULTS:The package includes pipelines for the evaluation and validation of EEG analysis tools for source estimation, functional connectivity, and spatial filtering. EEG dynamics can be simulated using realistic noise and signal models with user specifiable signal-to-noise ratio (SNR). License either MIT or GLP-2.0""" ; sc:name "EEGSourceSim" ; sc:url "https://github.com/svndl/EEGSourceSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3174 ; sc:citation , "pubmed:31553576" ; sc:description "Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways | Enzyme Function Initiative Tools | This website contains a collection of webtools for creating and interacting with sequence similarity networks (SSNs) and genome neighborhood networks (GNNs). These tools originated in the Enzyme Function Initiative, a NIH-funded research project to develop a sequence / structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic / physiological functions of unknown enzymes discovered in genome projects | The Enzyme Function Initiative tools are hosted at the Carl R | If you use the EFI web tools, please cite us: | A \"From The Bench\" article was recently published in Biochemistry and is available on the training resources page" ; sc:featureList edam:operation_0362 ; sc:name "EFI" ; sc:url "https://efi.igb.illinois.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3379 ; sc:citation , "pubmed:31433187" ; sc:description "A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge | Drug Repositioning Drug repositioning, or the identification of new indications for approved therapeutic drugs, has gained substantial traction with both academics and pharmaceutical companies because it reduces the cost and duration of the drug development pipeline and the likelihood of unforeseen adverse events. To date there has not been a systematic effort to identify such opportunities, in part because of the lack of a comprehensive resource for an enormous amount of unsystematic drug repositioning information to support scientists who could benefit from this endeavor | Experimental Knowledge-Based Drug Repositioning Database (EK-DRD) provides a versatile resource for the display, search and analysis of structure, function, pathway, disease, network and related experimentally-validated drug repositioning annotation for 1861 FDA-approved and 102 withdrawn small molecule drugs" ; sc:featureList edam:operation_0224, edam:operation_3454 ; sc:name "EK-DRD" ; sc:url "http://www.idruglab.com/drd/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Ensemble Learning Approach for Stability Prediction of Interface and Core mutations." ; sc:featureList edam:operation_0250, edam:operation_0331, edam:operation_2480 ; sc:name "ELASPIC" ; sc:softwareHelp ; sc:url "http://elaspic.kimlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3324, edam:topic_3489, edam:topic_3519, edam:topic_3577 ; sc:citation , "pubmed:31588775" ; sc:description "The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data. A webapplication for managing, documenting and result analyzing of aPCR Data." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:license "MIT" ; sc:name "ELIMU-MDx" ; sc:url "https://sparclex.github.io/elimu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3305, edam:topic_3489, edam:topic_3810 ; sc:citation ; sc:description """A cross-sectional analysis of the emergency events database from a pediatric perspective. The international disasters database. Disaster group: Two main groups of disasters are distinguished in EM-DAT: natural disasters and technological disasters. This field is automatically linked to the disaster sub-group and the disaster type. There is a third group ‘Complex disasters’ which include some major famine situation for which the drought were not the main causal factor. See Table 1 for the Disasters Classification. In 1988, the Centre for Research on the Epidemiology of Disasters (CRED) launched the Emergency Events Database (EM-DAT).""" ; sc:featureList edam:operation_3557 ; sc:name "EM-DAT" ; sc:url "https://www.emdat.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3174, edam:topic_3512 ; sc:citation , "pmcid:PMC6328100", "pubmed:30629718" ; sc:description "Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. Converts EMBL- or GenBank-formatted flat files to submission-ready checklists for submission to ENA via the interactive Webin submission system." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "EMBL2checklists" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/michaelgruenstaeudl/EMBL2checklists" ; biotools:primaryContact "Michael Gruenstaeudl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3474 ; sc:citation , "pmcid:PMC6760811", "pubmed:31518349" ; sc:description "Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology | EMULSION Manual — EMULSION (Epidemiological Multi-Level Simulation framework) | Framework EMULSION is intended for modellers in epidemiology, to help them design, simulate, and revise complex mechanistic stochastic models, without having to write or rewrite huge amounts of code" ; sc:license "Apache-2.0" ; sc:name "EMULSION" ; sc:softwareHelp ; sc:url "https://sourcesup.renater.fr/www/emulsion-public" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC7145688", "pubmed:31665430" ; sc:description "A manually curated database of experimentally supported enhancers for human and mouse. Enhancers are a class of cis-regulatory elements that can increase gene transcription by forming loops in intergenic regions, introns and exons" ; sc:featureList edam:operation_0224, edam:operation_0440, edam:operation_2495 ; sc:name "ENdb" ; sc:url "http://www.licpathway.net/ENdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC6368480", "pubmed:30165689" ; sc:description "Complete reimplementation of the evolutionary placement algorithm (EPA) that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "EPA-ng" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/Pbdas/epa-ng" ; biotools:primaryContact "Pierre Barbera" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3170 ; sc:citation , "pubmed:31099391" ; sc:description "Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data." ; sc:featureList edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EPEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Cobanoglu-Lab/EPEE" ; biotools:primaryContact "Murat Can Çobanoğlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3375 ; sc:citation ; sc:description "Tool for designing peptide ligand libraries based on epitope–paratope interactions." ; sc:featureList edam:operation_0252, edam:operation_0272, edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EPI-peptide designer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biocomp.icb.ufmg.br/biocomp/software-and-databases/epi-peptide-designer/" ; biotools:primaryContact "Viart Benjamin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6602470", "pubmed:31106358" ; sc:description "Analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EPIC-TABSAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tabsat.ait.ac.at/" ; biotools:primaryContact , "Stephan Pabinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2269 ; sc:citation , , "pmcid:PMC7583457", "pubmed:31975601" ; sc:description "EPIFANY is a protein inference engine based on a Bayesian network." ; sc:featureList edam:operation_3649, edam:operation_3767 ; sc:name "Efficient Bayesian protein inference (EPIFANY)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://OpenMS.de/epifany" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc:description """genome wide transcription unit annotation using a multivariate probabilistic model of histone modifications. EPIGENE models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active transcription units. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network — Epigenomics. Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network. The network is funded by the Canadian Institutes of Health Research (CIHR) and Genome Canada and is run by epigenetics researchers from across Canada. CEEHRC is Canada's contribution to the International Human Epigenome Consortium (IHEC)""" ; sc:featureList edam:operation_0417, edam:operation_0463, edam:operation_3800 ; sc:license "MIT" ; sc:name "EPIGENE" ; sc:url "https://github.com/imbbLab/EPIGENE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3168 ; sc:citation , "pubmed:31410461" ; sc:description "A novel approach for condition-specific enhancer-promoter interaction prediction." ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3901 ; sc:name "EPIP" ; sc:url "http://www.cs.ucf.edu/~xiaoman/EPIP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:31588505" ; sc:description """Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism. EPIVAN(Promoter-Enhancer Interaction predictor with pre-trained Vector and Attention based neural Networks). EPIVAN is a new deep learning method that enables predicting long-range EPIs using only genomic sequences""" ; sc:featureList edam:operation_0440, edam:operation_3435 ; sc:name "EPIVAN" ; sc:url "https://github.com/hzy95/EPIVAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:31751246" ; sc:description """Novel Sequence Insertion Detection by Constructing an Extended Reference. Next generation sequencing technology has led to the development of methods for the detection of novel sequence insertions (nsINS). Multiple signatures from short reads are usually extracted to improve nsINS detection performance. However, characterization of nsINSs larger than the mean insert size is still challenging. This paper presents a new method, ERINS, to detect nsINS contents and genotypes of full spectrum range size. It integrates the features of structural variations and mapping states of split reads to find nsINS breakpoints, and then adopts a left-most mapping strategy to infer nsINS content by iteratively extending the standard reference at each breakpoint. Finally, it realigns all reads to the extended reference and infers nsINS genotypes through statistical testing on read counts. We test and validate the performance of ERINS on simulation and real sequencing datasets.""" ; sc:featureList edam:operation_3196, edam:operation_3199, edam:operation_3435 ; sc:name "ERINS" ; sc:url "https://github.com/BDanalysis/ERINS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3318 ; sc:citation , "pubmed:31125060" ; sc:description "Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search." ; sc:featureList edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EROS-DOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://erosdock.loria.fr" ; biotools:primaryContact "Isaure Chauvot de Beauchêne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3399 ; sc:citation , , , "pmcid:PMC5638550", "pmcid:PMC6735795", "pubmed:28968389" ; sc:description "A unique tool to help understand HIV prevention among high-risk young women in Ukraine | Estimate time since infection from NGS diversity" ; sc:name "ETI" ; sc:url "https://hiv.biozentrum.unibas.ch/ETI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3407, edam:topic_3423 ; sc:citation , "pmcid:PMC6692943", "pubmed:31412866" ; sc:description "Iintegrated Ethiopian traditional herbal medicine and phytochemicals database | ETM-DB is a free, online relational database containing Ethiopian herbal medicine, related compounds and target gene/proteins. Ethiopia is endowed with an affluence of botanical remedies that have proven useful over a long time, especially in the rural areas where modern health care is much less accessible. It is estimated that about 80% of the Ethiopian population, predominantly in the rural areas, use traditional medicine. There are about 6,500-7,500 plant species in Ethiopia, of which an estimated 12% are endemic to Ethiopia" ; sc:featureList edam:operation_3280, edam:operation_3803 ; sc:name "ETM-DB" ; sc:url "http://biosoft.kaist.ac.kr/etm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3855 ; sc:citation ; sc:description "A Low-Cost, Open Source, Self-Contained Bacterial EVolutionary biorEactor (EVE)" ; sc:featureList edam:operation_3798 ; sc:license "MIT" ; sc:name "EVE" ; sc:url "https://github.com/vishhvaan/eve-pi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0654, edam:topic_3810 ; sc:citation , "pmcid:PMC6794827", "pubmed:31615397" ; sc:description "EVR is a chromosome 3D structure reconstruction tool using an Error-Vector Resultant algorithm based on DNA interaction data. With normalized or unnormalized IF matrix as input, the program generate a chromosome 3D structure output in a .pdb file. Using Cython and OpenCL, the program can run on CPUs/GPUS/APUs and thus usually faster than similar tools." ; sc:featureList edam:operation_0335, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "EVR" ; sc:url "https://github.com/mbglab/EVR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0820, edam:topic_2275 ; sc:citation ; sc:description """Proteome-scale discovery of protein interactions with residue-level resolution using sequence coevolution. Evolutionary couplings from protein and RNA sequence alignments. If you are simply interested in using EVcouplings as a library, installing the Python package is all you need to do (unless you use functions that depend on external tools). If you want to run the evcouplings application (alignment generation, model parameter inference, structure prediction, etc.) you will also need to follow the sections on installing external tools and databases. Predict protein structure, function and mutations using evolutionary sequence covariation.""" ; sc:featureList edam:operation_0272, edam:operation_0477, edam:operation_0478, edam:operation_2492 ; sc:license "MIT" ; sc:name "EVcouplings" ; sc:url "https://evcouplings.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation ; sc:description "Predicting functional long non-coding RNAs validated by low throughput experiments." ; sc:featureList edam:operation_0525, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EVlncRNA-pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biophy.dzu.edu.cn/lncrnapred/index.html" ; biotools:primaryContact "Jihua Wang", "Yaoqi Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description "Epigenome-wide association study software." ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioapp.org/ewas/" ; biotools:primaryContact "Fanwu Kong", "Liangde Xu", "Yongshuai Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:31584095" ; sc:description "A resource of DNA methylation array data and metadata." ; sc:featureList edam:operation_2422, edam:operation_3186, edam:operation_3207 ; sc:name "EWAS Data Hub" ; sc:softwareHelp ; sc:url "https://bigd.big.ac.cn/ewas/datahub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_3957 ; sc:citation , "pmcid:PMC6744658", "pubmed:31521132" ; sc:description "A Python script for identifying protein complexes based on an edge weight algorithm and core-attachment structure." ; sc:featureList edam:operation_0277, edam:operation_2492, edam:operation_3439 ; sc:name "EWCA" ; sc:url "https://github.com/RongquanWang/EWCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31100387" ; sc:description "EXPANDER (EXPression ANalyzer and DisplayER) is a comprehensive software package for analysis of expression data." ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EXPANDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/expander/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_2830, edam:topic_3421 ; sc:citation , "pubmed:31750874" ; sc:description """A validated web application suite to reveal the full details of HLA typing. Nomenclature for Factors of the HLA System. The WHO Nomenclature Committee for Factors of the HLA System comprises the following individuals:. EasyMatch-R is a tool designed to find unrelated donors in silico. We aim to improve efficiency by saving time and resources in HLA labs. From a patient’s HLA typing in input, Easymatch-R displays probability of finding a potential unrelated bone marrow donor according to the required matching level. In addition to the number of expected donors, Easymatch-R provides complementary typings recomendations. HLA-Upgrade uses the power of haplotypes to predict full high resolution HLA-A, B, C, DRB1, DQB1 genotypes.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "Easy-HLA" ; sc:url "https://hla.univ-nantes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:31743827" ; sc:description """An easy-to-use toolbox for MEG analysis. an easy-to-use software for MEG analysis based on FieldTrip and Matlab GUI. You can use the editor on GitHub to maintain and preview the content for your website in Markdown files""" ; sc:license "GPL-3.0" ; sc:name "EasyMEG" ; sc:url "https://tonywu2018.github.io/EasyMEG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation , "pubmed:31504183" ; sc:description "A user-friendly tool for building and analysis of simple mathematical models in systems biology" ; sc:featureList edam:operation_2426, edam:operation_3096, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "EasyModel" ; sc:url "https://easymodel.udl.cat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2275, edam:topic_3277 ; sc:citation , "pmcid:PMC6530084", "pubmed:31117939" ; sc:description "Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as well as the constituent RNA-binding domains (RBDs)." ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EcRBPome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/ecrbpome" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3172, edam:topic_3375 ; sc:citation , "pubmed:31047795" ; sc:description "Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies." ; sc:featureList edam:operation_3482, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "EcoPrestMet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zampierigroup.shinyapps.io/EcoPrestMet" ; biotools:primaryContact "Mattia Zampieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6684082", "pubmed:31386677" ; sc:description "Mapping the spatial distribution of pairwise gene expression intensities | This file details the different codes that we utlized to create the results for EdgeScaping" ; sc:featureList edam:operation_0313, edam:operation_3463, edam:operation_3766 ; sc:license "MIT" ; sc:name "EdgeScaping" ; sc:url "https://github.com/bhusain/EdgeScaping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31119671" ; sc:description "> HOMEPAGE MISSING! | A Fast, Robust, and User-Friendly Mass Spectrometry Data Processing Engine for Metabolomics | Analysis of large metabolomic datasets is becoming commonplace with the increased realization of the role that metabolites play in biology and pathophysiology. While there are many open-source analysis tools to extract peaks from liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and tandem mass spectrometry (LC-MS MS) data, these tools are not very interactive and are suboptimal when a large number of samples are to be analyzed. El-MAVEN is an open-source analysis platform that extends MAVEN and provides fast, powerful, and interactive analysis capabilities especially for datasets containing over 100 samples. The El-MAVEN workflow is easy to use with just four steps from loading data to exporting of the results" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "El-MAVEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31119671" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Program for neurofeedback that supports modularEEG. Uses fast Fourier transform to extract frequency bands from the raw signal." ; sc:isAccessibleForFree true ; sc:name "Electric Guru" ; sc:operatingSystem "Windows" ; sc:url "https://realization.org/old/page/topics/electric_guru.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC6381631", "pubmed:30782135" ; sc:description "Software tool to correct LC-MS data in isotope labeling experiments." ; sc:featureList edam:operation_3629, edam:operation_3632, edam:operation_3638 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ElemCor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/4dsoftware/elemcor" ; biotools:primaryContact "Di Du", "Xiaoyang Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3382, edam:topic_3542 ; sc:citation , "pmcid:PMC6717539", "pubmed:31358979" ; sc:description "Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning | Emap2sec is a computational tool to identify protein secondary structures | Emap2sec is a computational tool using deep learning that can accurately identify protein secondary structures, alpha helices, beta sheets, others (coils/turns), in cryo-Electron Microscopy (EM) maps of medium to low resolution" ; sc:featureList edam:operation_0468, edam:operation_0470, edam:operation_2488 ; sc:license "GPL-3.0" ; sc:name "Emap2sec" ; sc:url "http://www.kiharalab.org/emap2sec/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , , "pmcid:PMC7496207", "pubmed:32938367" ; sc:description "A novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes | Abstract Background In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the number of cells profiled in individual scRNA-seq experiments, there is a demand for novel computational methods for classifying newly-generated scRNA-seq data onto annotated labels. Although several methods have recently been proposed for the cell-type classification of single-cell transcriptomic data, such limitations as inadequate accuracy, inferior robustness, and low stability greatly limit their wide applications. Results We propose a novel en semble approach, named EnClaSC, for accurate and robust cell-type cla ssification of s ingle- c ell transcriptomic data" ; sc:featureList edam:operation_3891 ; sc:name "EnClaSC" ; sc:url "https://github.com/xy-chen16/EnClaSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474 ; sc:citation , "pubmed:31125056" ; sc:description "R package for imputing dropout events in single cell RNA sequencing data via ensemble learning." ; sc:featureList edam:operation_3192, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EnImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Zhangxf-ccnu/EnImpute" ; biotools:primaryContact "Xiao-Fei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31628884" ; sc:description "Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes." ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3192, edam:operation_3258, edam:operation_3501 ; sc:name "EnTAP" ; sc:softwareHelp ; sc:url "https://gitlab.com/EnTAP/EnTAP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3246 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3245 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:30510204" ; sc:description "EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries." ; sc:featureList edam:operation_0335, edam:operation_3215, edam:operation_3631, edam:operation_3646, edam:operation_3649, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EncyclopeDIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.8.1" ; sc:url "https://bitbucket.org/searleb/encyclopedia/" ; biotools:primaryContact "Brian Searle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6344666", "pubmed:30689845" ; sc:description "Database to discover the regulate relationships in the context of enhancers." ; sc:featureList edam:operation_0441, edam:operation_3232, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "EnhancerDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lcbb.swjtu.edu.cn/EnhancerDB/" ; biotools:primaryContact "Z. Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0194, edam:topic_0797, edam:topic_3293 ; sc:citation , "pubmed:19029536" ; sc:description "Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0491, edam:operation_0492, edam:operation_0558, edam:operation_2403, edam:operation_3182, edam:operation_3460, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ensembl Compara" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "e56", "e81" ; sc:url "http://www.ensembl.org/info/genome/compara/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3318 ; sc:citation , "pubmed:30709308" ; sc:description "Library for working with Markov state models (MSMs) that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Enspara" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://enspara.readthedocs.io/en/latest/" ; biotools:primaryContact "Bowman Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3305, edam:topic_3796 ; sc:citation , ; sc:description "Global genomic population structure of Clostridioides difficile" ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3840 ; sc:name "EnteroBase" ; sc:url "http://enterobase.warwick.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_3068 ; sc:citation , "pubmed:31077305" ; sc:description "Python library to dynamically interact with the NCBI Entrez databases." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "Entrezpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/entrezpy/" ; biotools:primaryContact "Jan buchmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3316 ; sc:description "A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. With Eoulsan, users can easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Working either on standalone workstations or cloud computing clusters, Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression." ; sc:featureList edam:operation_3223 ; sc:name "Eoulsan" ; sc:url "http://outils.genomique.biologie.ens.fr/eoulsan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6868350", "pubmed:31511888" ; sc:description "Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context | Estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum | EphaGen - a package to estimate NGS Dataset qualitity in terms of its ability to detect mutations of predefined spectrum" ; sc:featureList edam:operation_2428, edam:operation_2929, edam:operation_3227 ; sc:name "EphaGen" ; sc:url "https://github.com/m4merg/EphaGen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC6712799", "pubmed:31455207" ; sc:description "An approach of epistasis mining based on genetic Tabu algorithm and Bayesian network" ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "Epi-GTBN" ; sc:url "http://122.205.95.139/Epi-GTBN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC6648345", "pubmed:31045217" ; sc:description "Alignment-based bioinformatic tool for comparing chromatin state sequences." ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "EpiAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zzz3639/EpiAlign" ; biotools:primaryContact , "Haowen Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC6602515", "pubmed:31114924" ; sc:description "Alignment of genomic regions with both sequence and epigenomic information." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EpiAlignment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epialign.ucsd.edu/" ; biotools:primaryContact "Sheng Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "Tool to define and explore genomic regions with tissue or cell type-specific epigenomic features." ; sc:featureList edam:operation_0438, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "EpiCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://epigenome.wustl.edu/EpiCompare/" ; biotools:primaryContact "Yu He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315, edam:topic_3324, edam:topic_3375 ; sc:citation , "pubmed:31624039" ; sc:description """Improved inference of time-varying reproduction numbers during infectious disease outbreaks. This web application generates an estimate of infectious disease transmissibility throughout an outbreak. The time-dependent reproduction number (R) is inferred from disease incidence time series and patient data or estimates of the serial interval.""" ; sc:featureList edam:operation_2422, edam:operation_2426, edam:operation_3799 ; sc:name "EpiEstim" ; sc:softwareHelp ; sc:url "https://shiny.dide.imperial.ac.uk/epiestim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:30717649" ; sc:description "R package for large-scale integrated analysis in methylation hotspots linked to genetic regulation." ; sc:featureList edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EpiMethEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/giupardeb/EpiMethEx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6868874", "pubmed:31752933" ; sc:description """EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation. Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels""" ; sc:featureList edam:operation_3186, edam:operation_3207, edam:operation_3222 ; sc:name "EpiMethylTag" ; sc:url "https://github.com/skoklab/EpiMethylTag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3295, edam:topic_3520 ; sc:citation , "pmcid:PMC6581051", "pubmed:31123082" ; sc:description """Analysis of histone post-translational modifications by direct infusion mass spectrometry .""" ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EpiProfileLite" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/zfyuan/EpiProfileLite" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pubmed:31501853" ; sc:description "Sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements | EpiSAFARI: Sensitive Detection of Valley Shaped Patterns in Epigenetic Signal Profiles | EpiSAFARI is a command line tool for detection, annotation, and characterization of the valley shaped patterns within the functional genomics signal profiles. It takes:" ; sc:featureList edam:operation_0441, edam:operation_3222, edam:operation_3501 ; sc:name "EpiSAFARI" ; sc:url "https://github.com/harmancilab/EpiSAFARI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:31466478" ; sc:description "A robust classifier to determine smoking status from DNA methylation data | Aim: Smoking strongly influences DNA methylation, with current and never smokers exhibiting different methylation profiles. Methods: To advance the practical applicability of the smoking-associated methylation signals, we used machine learning methodology to train a classifier for smoking status prediction. Results: We show the prediction performance of our classifier on three independent whole-blood datasets demonstrating its robustness and global applicability. Furthermore, we examine the reasons for biologically meaningful misclassifications through comprehensive phenotypic evaluation. Conclusion: The major contribution of our classifier is its global applicability without a need for users to determine a threshold value for each dataset to predict the smoking status" ; sc:featureList edam:operation_0417 ; sc:name "EpiSmokEr" ; sc:url "https://github.com/sailalithabollepalli/EpiSmokEr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1931 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc:description "Reproducible Epigenomics Analysis pipeline for the analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. The analysis workflow was originally designed to analyze Brassica rapa data." ; sc:featureList edam:operation_3563, edam:operation_3677 ; sc:funder "Agencia Estatal de Investigación" ; sc:license "MIT" ; sc:name "Epigenomics Workflow on Galaxy and Jupyter" ; sc:softwareHelp ; sc:url "https://github.com/wilkinsonlab/epigenomics_pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3674, edam:topic_3794 ; sc:citation , "pubmed:31794005" ; sc:description """quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Episo-quantify Epitranscriptomal RNA m5c at isoform level. Episo is a probabilistic model to quantify Epitranscriptomal RNA m5C at the transcript isoform level. Episo consists of three tools, named mapper, quant and Bisulfitefq, for mapping, quantifying, and simulating RNA-BisSeq data, respectively. Episo needs a working version of Perl and it is run from the command line. Meanwhile, Bowtie, Tophat and Cufflinks need to be installed on your computer. First you need to download a transcript annotation file from the Ensembl or NCBI websites. Episo supports the reference trancriptom sequence files in FastA format, allowed file extensions are either .fa or .fasta. The details see the document Episo_User_Guide.pdf. This pakage is for estimating m5c level by using Kallisto in Episo""" ; sc:featureList edam:operation_0308, edam:operation_2495, edam:operation_3186, edam:operation_3799 ; sc:license "BSD-2-Clause" ; sc:name "Episo" ; sc:url "https://github.com/liujunfengtop/Episo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3398 ; sc:citation ; sc:description "Tool for Model Discovery and Assembly with the Physiome Model Repository." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Epithelial Modelling Platform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epithelial-modelling-platform.nectar.auckland.ac.nz/" ; biotools:primaryContact "Dewan M. Sarwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3407 ; sc:citation , "pubmed:31598631" ; sc:description "ModelExplorer is a metabolic model visualization package that can assist the user in finding blocked parts of the metabolic network as well as finding out why they are blocked." ; sc:featureList edam:operation_0481, edam:operation_3660 ; sc:name "ErrorTracer" ; sc:url "https://github.com/TheAngryFox/ModelExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_0128, edam:topic_0621, edam:topic_2640 ; sc:citation , "pubmed:31598693" ; sc:description "A comprehensive database for eukaryotic RNA binding proteins. EuRBPDB is a comprehensive and user-friendly database for eukaryotic RNA binding proteins (RBPs). It contains 315,222 RBPs (forms 6,368 ortholog groups) from 162 eukaryotic species, including human, mouse, fly, worm and yeast. EuRBPDB provides precise and comprehensive list of RBPs of each eukaryote with annotations collected from various public databases" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3902 ; sc:name "EuRBPDB" ; sc:url "http://EuRBPDB.syshospital.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation , "pubmed:26720812" ; sc:description "Open source software based on a continuous model to evaluate STR DNA profiles from a mixture of contributors with artefacts." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EuroForMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0" ; sc:url "http://www.euroformix.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3301, edam:topic_3305 ; sc:citation , ; sc:description "EventEpi - A Natural Language Processing Framework for Event-Based Surveillance - is a tool to extract the most important entites from a epidemiological text and to analyze them." ; sc:featureList edam:operation_3280 ; sc:name "EventEpi" ; sc:url "https://github.com/aauss/EventEpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6763948", "pubmed:31616466" ; sc:description "A Literature Evidence-Based Miner for Human Microbial Associations. The importance of understanding microbe-microbe as well as microbe-disease associations is one of the key thrust areas in human microbiome research" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0337 ; sc:name "Evidence Based Microbial Associations Miner (EviMass)" ; sc:softwareHelp ; sc:url "https://web.rniapps.net/evimass/evimass/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3517 ; sc:citation , "pmcid:PMC6612835", "pubmed:31510680" ; sc:description "Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation | Ranking methodology of potential Driver genes using multi-view feature sets" ; sc:featureList edam:operation_3436, edam:operation_3501, edam:operation_3766 ; sc:license "Apache-2.0" ; sc:name "EvidenceAggregatedDriverRanking" ; sc:url "https://github.com/Sage-Bionetworks/EvidenceAggregatedDriverRanking" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:name "Evidence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_1209 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0203 ; sc:description "The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system." ; sc:featureList edam:operation_2454 ; sc:name "EvidenceModeler" ; sc:url "https://github.com/EVidenceModeler/EVidenceModeler.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_2814, edam:topic_3170 ; sc:citation , "pmcid:PMC6806525", "pubmed:31640563" ; sc:description "RNA 3D structure prediction guided by independent folding of homologous sequences and multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io." ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0303, edam:operation_0476, edam:operation_2441 ; sc:license "GPL-3.0" ; sc:name "EvoClustRNA" ; sc:softwareHelp ; sc:url "https://github.com/mmagnus/EvoClustRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0736, edam:topic_3318 ; sc:citation , "pubmed:31588495" ; sc:description """Accurate and fast energy function for computational protein design. energy potential for protein design. EvoEF is a composite energy force field that contains two versions. The first version, EvoEF1, includes five energy terms with parameters optimized on two large sets of thermodynamics mutation data (ΔΔGstability and ΔΔGbind), while the second version, EvoEF2, includes nine energy terms and optimized based on recapitulation of protein sequence design. Extensive benchmark and analysis showed that the usefulness of energy functions is highly correlated with the parameter optimization processes. While EvoEF1 performs better than EvoEF2 on ΔΔG estimation, EvoEF2 significantly outperforms EvoEF2 on de novo protein sequence design. Therefore, we suggest users download the two versions according to their own needs.""" ; sc:featureList edam:operation_0303, edam:operation_0480, edam:operation_2492, edam:operation_3644 ; sc:license "MIT" ; sc:name "EvoEF2" ; sc:url "https://zhanglab.ccmb.med.umich.edu/EvoEF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3293 ; sc:citation , , "pmcid:PMC6916070", "pubmed:31842729" ; sc:description "Visualization of the Evolutionary Frequencies of Sequence and Model Data | Evolutionary frequency visualization tool of temporal data | Users have options ot install EvoFreq depending on if they want to use 'devtools'. Below we show two popular methods for installation. You will need a fully operational install of R (≥3.5.0) and, optionally, RStudio | Visualization Package for Evolutionary Dynamics from Sequence and Model Data. biorxiv pre-print here" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "EvoFreq" ; sc:url "https://github.com/MathOnco/EvoFreq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128 ; sc:author , , "Noé Vázquez" ; sc:citation , ; sc:contributor , ; sc:description "EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for the same and distinct species." ; sc:featureList edam:operation_2422 ; sc:name "EvoPPI" ; sc:url "http://evoppi.i3s.up.pt/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3407 ; sc:citation , , "pubmed:31560365", "pubmed:36806474" ; sc:description "EvolClust predicts groups of genes that are conserved in terms of gene order across different species distinguishing it from the background gene order conservation found between species. We define a cluster as a group of homologous proteins that are found grouped together in at least two different genomes and which are more conserved than what is expected for the pair of genomes. The order of the genes inside the cluster is not necessarily conserved. Pairwise clusters are grouped into multi-species families." ; sc:featureList edam:operation_2422, edam:operation_3432 ; sc:name "EvolClust" ; sc:softwareVersion "1.0" ; sc:url "http://evolclustdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0659 ; sc:description "EvryRNA platform is a web server providing various algorithms and bioinformatics tools developed in the laboratory IBISC of UEVE/Genopole, and dedicated to the prediction and the analysis of non-coding RNAs (ncRNAs)." ; sc:name "EvryRNA" ; sc:url "https://evryrna.ibisc.univ-evry.fr/evryrna/evryrna/evryrna_home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31082210" ; sc:description "Integrated Solution for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis." ; sc:featureList edam:operation_2929, edam:operation_3627, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ExMS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hx2.med.upenn.edu/EXms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3068 ; sc:citation ; sc:description "Tool for phylogenomic analyses on supercomputers." ; sc:featureList edam:operation_0547 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ExaML" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://github.com/stamatak/ExaML" ; biotools:primaryContact "Alexandros Stamatakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3068, edam:topic_3292 ; sc:citation , , "pmcid:PMC7291460", "pubmed:32527218" ; sc:description """Exact calculation of stationary solution and parameter sensitivity analysis of stochastic continuous time Boolean models. Abstract Motivation Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all asymptotic solutions. Moreover, these models have timescale parameters (transition rates) that the probability values of stationary solutions depend on in complex ways that have not been analyzed yet in the literature. 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A suite of tools for detecting expansions of short tandem repeats. ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). EHdn is intended for analysis of a collection of BAM/CRAM files containing alignments of short (100-200bp) reads.""" ; sc:featureList edam:operation_0379, edam:operation_3196, edam:operation_3198 ; sc:license "Apache-2.0" ; sc:name "ExpansionHunter Denovo" ; sc:softwareHelp ; sc:url "https://github.com/Illumina/ExpansionHunterDenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation ; sc:description "Suite for single-cell alternative splicing analysis. Consists of outrigger, anchor and bonvoyage." ; sc:featureList edam:operation_2499 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Expedition" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YeoLab/Expedition" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , , "pubmed:32526385" ; sc:description """an image processing pipeline for multi-center ASL perfusion MRI studies. ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators. OSIPI ASL pipelines google forms. 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The database is being actively updated.""" ; sc:featureList edam:operation_2421 ; sc:name "Exposome Explorer" ; sc:softwareVersion "2.0" ; sc:url "http://exposome-explorer.iarc.fr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Easy interface for determining the Clermont 2013 phylotype of an E. coli isolate" ; sc:featureList edam:operation_3478 ; sc:name "EzClermont" ; sc:url "http://ezclermont.hutton.ac.uk/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0632, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6896590", "pubmed:31810454" ; sc:description """A script for fast and consistent environmental DNA processing and identification. Scripts for executing a filtering, clustering and identification pipeline for eDNA samples. Fast And Consistent Environmental-DNA Processing And Identification (& Conversion and Preparation of Reference Sequences). Wahlberg, E. 2019. FACEPAI: a script for fast and consistent environmental DNA processing and identification. BMC Ecology 19: 51, doi:10.1186/s12898-019-0269-1""" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "FACEPAI" ; sc:url "https://github.com/emmawahl/facepai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:citation , "pubmed:31401715" ; sc:description "An interactive tool for geometric modeling of nerve fiber architectures in the brain | The fiber arcitecture constructor (FAConstructor) allows a simple and effective creation of fiber models based on mathematical functions or the manual input of data points. Models are visualized during creation and can be interacted with by translating them in the 3-dimensional space" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "FAConstructor" ; sc:url "https://github.com/3d-pli/FAConstructor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070, edam:topic_3518 ; sc:citation ; sc:description "Two real use cases of FAIR maturity indicators in the life sciences | This repository contains the results of the FAIR Metrics Group | FAIR Maturity Indicators and Tools | [Horizon 2020 Commission expert group on Turning FAIR data into reality](http://ec.europa.eu/transparency/regexpert/index.cfm?do=groupDetail.groupDetail&groupID=3464" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3501 ; sc:license "MIT" ; sc:name "FAIR" ; sc:url "https://github.com/FAIRMetrics/Metrics" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3256 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3956 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3256 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0605 ; sc:author , "Kees burger" ; sc:citation ; sc:contributor , "Kees burger", "Mark Thompson" ; sc:description "FAIRDataPoint is a REST api for creating, storing and servering FAIR metadata. 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Finding appropriate models that provide a systematic description of such biological systems and that help to identify their relevant factors and processes can be challenging given the sheer number of possibilities. Model selection algorithms that evaluate the performance of a multitude of different models against experimental data provide a useful tool to identify appropriate model structures" ; sc:featureList edam:operation_2426, edam:operation_3891 ; sc:license "MIT" ; sc:name "FAMoS" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/FAMoS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6522071", "pubmed:31059559" ; sc:description "Fast And Robust DEconvolution of Expression Profiles (FARDEEP) - machine learning tool for enumerating immune cell subsets from whole tumor tissue samples." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FARDEEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YuningHao/FARDEEP.git" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3512 ; sc:citation , , "pmcid:PMC7415647", "pubmed:32531203" ; sc:description "Improved de novo Rosetta prediction of complex global RNA folds | ROSIE Rosetta server based on www.rosettacommons.org engine | Welcome to ROSIE Rosetta Online Server that Includes Everyone | Please cite the following article when referring to results from our ROSIE server: | Watkins, A. M.; Das, R. \"An automated and customizable RNA fragment assembly protocol in Rosetta. bioRxiv 223305; doi: https://doi.org/10.1101/223305" ; sc:featureList edam:operation_0278, edam:operation_0476, edam:operation_0483 ; sc:name "FARFAR2" ; sc:softwareHelp ; sc:url "https://rosie.rosettacommons.org/farfar2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "FASTA stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison." ; sc:featureList edam:operation_0346, edam:operation_2451 ; sc:name "FASTA API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/sss/fasta_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Bill Pearson" ; sc:citation , ; sc:description "Sequence similarity searching against protein databases. FASTX and FASTY translate a DNA query. Optimal searches with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database)." ; sc:featureList edam:operation_0346, edam:operation_2451 ; sc:name "FASTA (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Virginia" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/fasta" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3400, edam:topic_3421 ; sc:citation , "pmcid:PMC6511155", "pubmed:31077222" ; sc:description "FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics." ; sc:featureList edam:operation_3352, edam:operation_3501, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FASTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioportal.bioontology.org/ontologies/FASTO" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "a Perl module to parse FASTA/FASTQ files" ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "FASTX::Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.6" ; sc:url "https://metacpan.org/pod/FASTX::Reader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_3068 ; sc:citation ; sc:description "Software to analyze Molecular Dynamics simulations of membranes." ; sc:featureList edam:operation_2476, edam:operation_3279 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FATSLiM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fatslim.github.io/" ; biotools:primaryContact "Sébastien Buchoux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation , , "pmcid:PMC7062913", "pubmed:32194545" ; sc:description """FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells. FB5P-seq: FACS-based 5'-end single-cell RNA-seq. Copyright 2019: PMlab, Centre d'Immunologie de Marseille-Luminy This work is distributed under the terms of the GNU General Public License. It is free to use for all purposes. FB5P-seq is a computational pipeline to process single-cell RNA sequencing (scRNAseq) data produced with the FB5P-seq protocol designed by the Milpied lab at Centre d'Immunologie de Marseille-Luminy. The pipeline relies on 5 main softwares:""" ; sc:featureList edam:operation_3200, edam:operation_3680, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "FB5P-seq" ; sc:url "https://github.com/MilpiedLab/FB5P-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3794 ; sc:citation ; sc:description "Fast Bayesian-bound tool to calibrate RNA-seq aligners." ; sc:featureList edam:operation_3198, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FBB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/irenerodriguez/fbb/src/master/" ; biotools:primaryContact "Ramón Huerta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3382 ; sc:author ; sc:citation , "pubmed:31878664" ; sc:description """Optical classification of inland waters based on an improved Fuzzy C-Means method. Water optical clustering based on water color information is important for many ecological and environmental application studies, both regionally and globally. The fuzzy clustering method avoids the sharp boundaries in type-memberships produced by hard clustering methods, and thus presents its advantages. However, to make good use of the fuzzy clustering methods on water color spectra data sets, the determination of the fuzzifier parameter (m) of FCM (fuzzy c-means) is the key factor. Usually, the m is set to 2 by default. Unfortunately, this method assigned some membership degrees to non-belonging water type, failing to obtain the unitarity of cluster structure in some cases, especially in inland eutrophic water.""" ; sc:featureList edam:operation_3432 ; sc:name "FCM-m" ; sc:url "https://github.com/bishun945/FCMm" ; biotools:primaryContact "Yunmei Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3063, edam:topic_3474 ; sc:citation , "pmcid:PMC6818468", "pubmed:31695723" ; sc:description """Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. Fully Convolutional Neural Network model. A demonstration of what can be accomplished visually through CSS-based design. If you want to visit this website, the google browser will be recommended !. The fully convolutional neural network (FCNN) model is a deep learning model based on traditional convolution neural network (CNN) model with a fully connected first layer and combines expression similarities and prior-knowledge similarities as the input""" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3660 ; sc:name "FCNN" ; sc:softwareHelp ; sc:url "https://bmbl.bmi.osumc.edu/FCNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "A calculator of conservation and allele frequency for variant pathogenic prediction." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:name "Frequency Conservation Score (FCS)" ; sc:url "http://bioinfo.cnic.es/FCS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3016 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3796 ; sc:description "File format converter for FImpute" ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FConverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/herrsalmi/FConverter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC6471690", "pubmed:30999847" ; sc:description "Software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing." ; sc:featureList edam:operation_0436, edam:operation_3096, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "FEDRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://math.unipa.it/rombo/FEDRO" ; biotools:primaryContact "Simona E. Rombo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3399, edam:topic_3577 ; sc:citation , "pubmed:31542453" ; sc:description "An Individualized Prediction Model for Long-term Lung Function Trajectory and Risk of COPD in the General Population" ; sc:name "FEV1" ; sc:softwareHelp ; sc:url "http://resp.core.ubc.ca/ipress/FraminghamFEV1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3316 ; sc:citation , , "pubmed:31574354" ; sc:description """The FEniCS Project is a collaborative project for the development of innovative concepts and tools for automated scientific computing, with a particular focus on the solution of differential equations by finite element methods.""" ; sc:name "FEniCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fenicsproject.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_0749 ; sc:citation , "pubmed:31830251" ; sc:description """A Web Server for Transcription Factor and miRNA Feed Forward Loop Analysis in Human. FFLtool is a webserver for analyzing Feed Forward Loop (FFL) regulatory motifs among transcription factors (TFs), microRNAs (miRNAs) and genes. FFLs potentially regulate thousands of target genes in facilitating spatiotemporal avoidance or noise buffering and play important roles in biological processes and diseases (see Refs. PMIDs: 20157565 and 24307685 ). It integrated TF-target data from hTFtarget and miR-target data from several predicted and validated databases. Except for identifying FFLs, FFLtools can also be used to search miR-target and TF-target information""" ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_3792 ; sc:name "FFLtool" ; sc:url "http://bioinfo.life.hust.edu.cn/FFLtool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC6836741", "pubmed:31649055" ; sc:description "Analysis pipeline for FFPEcap-seq. A method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3211, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "FFPEcap-seq" ; sc:url "https://github.com/jeffpkamp/FFPEcap-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0625, edam:topic_3314, edam:topic_3382 ; sc:citation , "pmcid:PMC6822706", "pubmed:31671091" ; sc:description """A tool for quantitatively characterizing the morphology and growth of filamentous fungi. The FFT represents a user-friendly tool that automatically characterizes several fungal phenotypes using images that can be obtained using basic imaging devices. The FFT can be used to study different fungal species, conditions and image scales and resolutions. Relying on simple built-in image analysis functions, the FFT is able to quantitatively characterize conidiation, conidia morphology and different aspects of the mycelium, including the growth area, number of hyphal tips and total length of the hyphae. In addition, we developed a function within the FFT that can detect and count traps developed by nematode-trapping fungi.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "Fungal Feature Tracker (FFT)" ; sc:url "https://github.com/hsueh-lab/FFT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_2885, edam:topic_3293 ; sc:citation ; sc:description "Method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "WTFPL" ; sc:name "FGTpartitioner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tkchafin/FGTpartitioner" ; biotools:primaryContact "Tyler K. Chafin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3324, edam:topic_3400, edam:topic_3489 ; sc:citation , , "pmcid:PMC6784845", "pmcid:PMC6913576", "pubmed:31598581", "pubmed:31621639" ; sc:description "FHIR is a standard for health care data exchange. It is a platform specification that defines a set of capabilities use across the healthcare process, in all jurisdictions, and in lots of different contexts." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3192, edam:operation_3891 ; sc:name "FHIR" ; sc:softwareHelp , ; sc:softwareVersion "4.0.1" ; sc:url "https://www.hl7.org/fhir/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3301 ; sc:citation , , "pmcid:PMC7653809", "pubmed:33172489" ; sc:description "FINET is a software to infer any network. Implemented by Julia with algorithms of stability selection and elastic-net, plus parameter optimization, finet can infer a network fast and accurately from a big data. Additionally, finet is user-friendly, only one single command line to complete all computational processes. Developed under Linux, but finet should work in any OS system. Installing and using finet becomes simple by using following instructions" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "FINET" ; sc:url "https://github.com/anyouwang/finet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6916105", "pubmed:31847917" ; sc:description """finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. FInding REliable Variants without ArTifacts. FIREVAT (FInding REliable Variants without ArTifacts) is an R package that performs variant refinement on cancer sequencing data. FIREVAT uses mutational signatures to identify sequencing artifacts and low-quality variants""" ; sc:featureList edam:operation_3227, edam:operation_3629, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "FIREVAT" ; sc:url "https://github.com/cgab-ncc/FIREVAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3855 ; sc:citation , "pubmed:31443908" ; sc:description "Framework for the Inference of In Situ Interaction Kinetics from Single-Molecule Imaging Data | Recent experimental and computational developments have been pushing the limits of live-cell single-molecule imaging, enabling the monitoring of intermolecular interactions in their native environment with high spatiotemporal resolution. However, interactions are captured only for the labeled subset of molecules, which tends to be a small fraction. As a result, it has remained a challenge to calculate molecular interaction kinetics, in particular association rates, from live-cell single-molecule tracking data. To overcome this challenge, we developed a mathematical modeling-based Framework for the Inference of in Situ Interaction Kinetics (FISIK) from single-molecule imaging data with substoichiometric labeling" ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "FISIK" ; sc:url "https://github.com/kjaqaman/FISIK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3518, edam:topic_3855 ; sc:citation ; sc:description "Statistical modeling tool for transcriptome dynamics under fluctuating field conditions." ; sc:featureList edam:operation_1812, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "FIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.0.6" ; sc:url "https://cran.r-project.org/package=FIT" ; biotools:primaryContact "Koji Iwayama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780 ; sc:description "Integrative database around plant genomes." ; sc:name "FLAGdb" ; sc:url "http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31384046" ; sc:description "A full-length mRNA sequencing reveals principles of poly(A) tail length control | Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs. We report a complementary DNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids and Caenorhabditis elegans we show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample" ; sc:featureList edam:operation_0308, edam:operation_0428, edam:operation_3192 ; sc:name "FLAM-seq analysis pipeline" ; sc:url "https://github.com/rajewsky-lab/FLAMAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC6314628", "pubmed:30543621" ; sc:description "Full-Length Envelope Analyzer (FLEA) - tool for longitudinal analysis of viral amplicons." ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FLEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/veg/flea-pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3372 ; sc:citation , "pubmed:31473443" ; sc:description "A support tool for efficient and seamless experiment data processing to evaluate musculo-articular stiffness | FLEXOR is a multiplatform software tool to simplify traditional complex and manual procedures for MAS analysis" ; sc:license "GPL-3.0" ; sc:name "FLEXOR" ; sc:url "https://github.com/FlexorSoftware/flexor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0736, edam:topic_3318 ; sc:citation , "pubmed:31490691" ; sc:description "Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform | Web Server for Calculating Protein Second Virial Coefficients | PI2PE: Protein Interface/Interior Prediction Engine | FMAPB2 implements FMAP, a method based on fast Fourier transform (FFT), to calculate second virial coefficients ( B 2 ) for proteins represented at the all-atom level in implicit solvent. FMAP stands for F FT-based M odeling of A tomistic P rotein-protein interactions. In FMAPB2, we express terms of the protein-protein inteaction energy as correlation functions, and evaluate them by FFT. These terms include steric repulsion, nonpolar attraction (in the form of a Lennard-Jones potential), and electrostatic interactions (in the form of a Debye-Hückel potential)" ; sc:featureList edam:operation_0409, edam:operation_2929, edam:operation_3454 ; sc:name "FMAPB2" ; sc:url "http://pipe.rcc.fsu.edu/fmapb2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , , "pubmed:33290385" ; sc:description "A 3-dimensional clustering package for single-molecule localization microscopy | Single-molecule localization microscopy (SMLM) yields an image resolution 1-2 orders of magnitude below that of conventional light microscopy, resolving fine details on intracellular structure and macromolecular organization. The massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Density based clustering algorithms, such as DBSCAN, can provide spatial statistics on protein nucleic acid aggregation or dispersion while explicitly identifying macromolecular clusters. The performance of DBSCAN, however, is typically dependent upon an arbitrary, or at least highly subjective, parametric tuning of the algorithm. Moreover, DBSCAN can be computationally expensive, which makes it arduous to evaluate on large image stacks" ; sc:license "GPL-3.0" ; sc:name "FOCAL3D" ; sc:url "https://github.com/MilsteinLab/FOCAL3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3361, edam:topic_3474 ; sc:author ; sc:citation , "pmcid:PMC6895225", "pubmed:31804528" ; sc:description "Computing the statistical significance of optimized communities in networks." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3562 ; sc:license "Apache-2.0" ; sc:name "Fast Optimized Community Significance (FOCS)" ; sc:url "https://github.com/google/fast-optimized-community-significance" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3321, edam:topic_3474 ; sc:citation ; sc:description "Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks." ; sc:featureList edam:operation_2238, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "FORECasT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://partslab.sanger.ac.uk/FORECasT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0202, edam:topic_0769 ; sc:citation ; sc:contributor "Ali Esfahani" ; sc:description "Tool for the systematic comparison of translational drug response modeling pipelines." ; sc:featureList edam:operation_1812, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FORESEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://osf.io/rf6qk/" ; biotools:primaryContact "L. Turnhoff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3676 ; sc:citation , "pmcid:PMC6296055", "pubmed:30558649" ; sc:description "Tool for ranking variants and building an optimal graph genome." ; sc:featureList edam:operation_3211, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FORGe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/langmead-lab/FORGe/tree/v1.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3067, edam:topic_3170 ; sc:citation ; sc:description "A Python package automatic computed fusion of ontologies." ; sc:license "GPL-3.0" ; sc:name "FOntCell" ; sc:url "https://gitlab.com/JavierCabau/fontcell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0607, edam:topic_3077, edam:topic_3572 ; sc:description """FP-LIMS is a LIMS solution specialized on mass spectroscopy measurement equipment. Primary compatible device manufacturers include: Spectro / Ametek,Agilent Technologies,Analytik Jena AG,Bruker,Hitachi / Oxford Instruments,Horiba Jobin Yvon GmbH,Malvern Panalytical,Microtrac GmbH,OBLF,PerkinElmer,Thermo Fisher,Zwick. FP-LIMS was first released in 1993. Its first version was based on spectroscopy-giant Spectro's(Ametek) in-house Laboratory data management solution. Its primarily used in metallurgy & foundry QM-laboratories where it is used for audit-trailing, certification, managing the passing of data from devices to an immutable data-store as well as upwards to systems such as the SAP QM module. FP-LIMS was formerly distributed as [DIA]/DIA2000/DIAPLUS.""" ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "FP-LIMS" ; sc:operatingSystem "Windows" ; sc:provider "Philip Moerke" ; sc:softwareHelp ; sc:url "https://www.fp-lims.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31070725" ; sc:description "Molecular featurizer for learning molecular properties." ; sc:featureList edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FP2VEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wsjeon92/FP2VEC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:30886412" ; sc:description "Community-editable fluorescent protein database, cataloging an expanded range of proteins and parameters, including a new spectra viewer." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FPbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "https://www.fpbase.org/" ; biotools:primaryContact "Talley Lambert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3174 ; sc:citation , "pmcid:PMC6694608", "pubmed:31416440" ; sc:description "A parallel architecture for very high-speed assessment of sequencing quality metrics | BACKGROUND:High throughput DNA RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine but important task. Identification and elimination of low-quality sequence data is crucial for reliability of downstream analysis results. There is a need for a high-speed tool that uses optimized parallel programming for batch processing and simply gauges the quality of sequencing data from multiple datasets independent of any other processing steps. RESULTS:FQStat is a stand-alone, platform-independent software tool that assesses the quality of FASTQ files using parallel programming" ; sc:featureList edam:operation_3180, edam:operation_3218, edam:operation_3359 ; sc:name "FQStat" ; sc:softwareHelp ; sc:url "http://otulab.unl.edu/FQStat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3325, edam:topic_3512 ; sc:author ; sc:citation ; sc:description """Detection of aberrant splicing events in RNA-seq data with FRASER. FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is currently avaiable as preprint here. Accompanying analysis code for the FRASER manuscript. The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use our Colab tutorial at: http://tinyurl.com/RNA-ASHG-colab. This is based on a workshop we presented at ASHG 2019. FRASER: Find RAre Splicing Events in RNA-seq. This folder contains the FRASER paper and supplementary data. This project depends on the python package wBuild and the R package FRASER. Further, we use the Leafcutter adaptation used in the Kremer et al paper, which can be found here""" ; sc:featureList edam:operation_0337, edam:operation_0433, edam:operation_2499, edam:operation_3196 ; sc:license "MIT" ; sc:name "FRASER" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FRASER.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3474 ; sc:author ; sc:citation ; sc:description """Benchmarking machine learning models for the analysis of genetic data using FRESA.CAD Binary Classification Benchmarking | Feature Selection Algorithms for Computer Aided Diagnosis | Contains a set of utilities for building and testing statistical models (linear, logistic,ordinal or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization License: GPL-2, GPL-2.1 and/or GPL-3.""" ; sc:featureList edam:operation_3196 ; sc:license "LGPL-2.0" ; sc:name "FRESA" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=FRESA.CAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3315, edam:topic_3855 ; sc:citation , "pubmed:30580414" ; sc:description "Food Spoilage and Safety Predictor (FSSP)" ; sc:featureList edam:operation_2426, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "FSSP" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fssp.food.dtu.dk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation , "pubmed:31384919" ; sc:description "Topology-independent and global protein structure alignment through an FFT-based algorithm | Fast topology-independent and global structure alignment through an FFT-based algorithm" ; sc:featureList edam:operation_0503, edam:operation_0509, edam:operation_0510 ; sc:name "FTAlign" ; sc:url "http://huanglab.phys.hust.edu.cn/ftalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2229, edam:topic_2640, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31750879" ; sc:description """Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. MOTIVATION:The elucidation of dysfunctional cellular processes that can induce the onset of a disease is a challenging issue from both experimental and computational perspectives. Here we introduce a novel computational method based on the coupling between fuzzy logic modeling and a global optimization algorithm, whose aims are to (1) predict the emergent dynamical behaviors of highly heterogeneous systems in unperturbed and perturbed conditions, regardless the availability of quantitative parameters, (2) determine a minimal set of system components whose perturbation can lead to a desired system response, therefore facilitating the design of a more appropriate experimental strategy. RESULTS:We applied this method to investigate what drives K-ras induced cancer cells, displaying the typical Warburg effect, to death or survival upon progressive glucose depletion""" ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "FUMOSO" ; sc:url "https://github.com/aresio/FUMOSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation , "pmcid:PMC6878879", "pubmed:31798363" ; sc:description """A graphical user interface for the X-ray-diffraction-based determination of crystallite size distributions. Bragg intensities can be used to analyse crystal size distributions in a method called FXD-CSD, which is based on the fast measurement of many Bragg spots using two-dimensional detectors. This work presents the Python-based software and its graphical user interface FXD-CSD-GUI. The GUI enables user-friendly data handling and processing and provides both graphical and numerical crystal size distribution results.""" ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3453 ; sc:name "FXD-CSD-GUI" ; sc:url "https://owncloud.gwdg.de/index.php/s/JGluHlEp0pEUcAH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3399, edam:topic_3500 ; sc:citation , "pubmed:31532469" ; sc:description "Create realistic 3D faces from photos or at random, edit with many controls, export for animation, rendering or 3D printing using a demographically diverse and customizable face space model" ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3891 ; sc:isAccessibleForFree false ; sc:name "FaceGen" ; sc:url "https://facegen.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3794 ; sc:citation ; sc:description "Open source framework for recording facial expressions with head-mounted cameras | The FaceSync toolbox provides 3D blueprints for building the head-mounted camera setup described in our paper. The toolbox also provides functions to automatically synchronize videos based on audio, manually align audio, plot facial landmark movements, and inspect synchronized videos to graph data" ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FaceSync" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cosanlab/facesync" ; biotools:primaryContact "Jin Hyun Cheong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_3047 ; sc:citation ; sc:description "PubChem and ChEMBL Beyond Lipinski." ; sc:featureList edam:operation_0337 ; sc:name "Faerun" ; sc:url "http://faerun.gdb.tools/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3474 ; sc:author ; sc:citation ; sc:description """Faster parallel feature extraction from genome sequences and efficient prediction of DNA N6-methyladenine sites. Faster parallel feature extraction from genome sequence. This is a tool for faster feature extraction from genome sequences and making efficient prediction. To build efficient prediction model, user can go through the following instructions step by step. If user only wants to predict query sequences from our built model, then just go to step Make prediction for query sequences. Currently, FastFeatGen supports text file as shown in dataset.txt file in datasets directory; however, fasta file can also be used with a simple preprocessing""" ; sc:featureList edam:operation_0224, edam:operation_0253 ; sc:name "FastFeatGen" ; sc:url "https://github.com/khaled-rahman/FastFeatGen" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6580563", "pubmed:31208325" ; sc:description "Fast preprocessing of next-generation sequencing reads." ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FastProNGS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Megagenomics/FastProNGS" ; biotools:primaryContact "G. Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Tools to deal with fastq sequences and paired-end reads." ; sc:name "FastqProcessing" ; sc:url "https://bioweb.pasteur.fr/packages/pack@FastqProcessing@0.38.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6500068", "pubmed:31053060" ; sc:contributor "Claudio Lottaz", "Julia Engelmann", "Paula Pérez Rubio" ; sc:description "High-performance preprocessing tool for RNA-seq data." ; sc:featureList edam:operation_3180, edam:operation_3219, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FastqPuri" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jengelmann/FastqPuri" ; biotools:primaryContact "Julia Engelmann" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated Omics data warehouse for FAW, Spodoptera frugiperda" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "FawMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://insectmine.org:8080/fawmine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2350 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3780 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0099 ; sc:description "A Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs" ; sc:featureList edam:operation_0292, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Fcirc" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/WangHYLab/fcirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_3174 ; sc:citation , , "pmcid:PMC7005843", "pubmed:32082281" ; sc:description "a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies | HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes | Please see the Wiki page for introduction and tutorial on how to use this tool | git clone https://github.com/Arkadiy-Garber/FeGenie.git | Easy Installation (if you have Conda installed) | HMM-lib directory can be found within FeGenie's main repository -t 8 means that 8 threads will be used for HMMER and BLAST. If you have less than 16 available on your system, set this number lower (default = 1)" ; sc:featureList edam:operation_0310, edam:operation_3798 ; sc:name "FeGenie" ; sc:url "https://github.com/Arkadiy-Garber/FeGenie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6446290", "pubmed:30943889" ; sc:description "Software for feature selection based on machine learning approaches." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "FeatureSelect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LBBSoft/FeatureSelect" ; biotools:primaryContact "LBBSoft" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3292 ; sc:citation , "pmcid:PMC6656964", "pubmed:31372542" ; sc:description "A web application for new bioactive peptides from food protein" ; sc:featureList edam:operation_0366, edam:operation_0482, edam:operation_3646 ; sc:name "FeptideDB" ; sc:url "http://www4g.biotec.or.th/FeptideDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3676 ; sc:citation ; sc:description "Tool to extract data from the 1000 Genomes Project." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ferret" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://limousophie35.github.io/Ferret/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31362508" ; sc:description "Identifying Fertility-Related Proteins by Incorporating Deep-Gated Recurrent Units and Original Position-Specific Scoring Matrix Profiles | Identifying fertility-related proteins by incorporating GRU and PSSM profiles" ; sc:featureList edam:operation_3639 ; sc:name "Fertility-GRU" ; sc:url "https://github.com/khanhlee/fertility-gru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3067, edam:topic_3444 ; sc:citation , "pmcid:PMC6532268", "pubmed:31118056" ; sc:description "Numerical phantom for fetal cardiovascular magnetic resonance imaging." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Fetal XCMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cwroy/Fetal-XCMR/" ; biotools:primaryContact "Chris Roy", "Christopher K. Macgowan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885 ; sc:citation , "pmcid:PMC6602425", "pubmed:31114899" ; sc:description "Webserver for scoring the impact of single nucleotide variants in the dog genome." ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Fido-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fidosnp.bca.unipd.it/" ; biotools:primaryContact , "Piero Fariselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0632, edam:topic_3855 ; sc:citation , "pubmed:31425088" ; sc:description "Designing for Mobile and Immersive Visual Analytics in the Field | Abstract: Data collection and analysis in the field is critical for operations in domains such as environmental science and public safety" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3501 ; sc:name "FieldView" ; sc:url "https://cmci.colorado.edu/visualab/fieldview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , , "pmcid:PMC3855844", "pmcid:PMC6861648", "pubmed:22743772", "pubmed:31763187" ; sc:description """A quantitative method to analyse F-actin distribution in cells. ImageJ, with "Batteries Included". Fiji: A batteries-included distribution of ImageJ. Fiji bundles together many popular and useful ImageJ plugins for image analysis into one installation, and automatically manages their dependencies and updating.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Fiji" ; sc:url "https://fiji.sc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0196, edam:topic_3474, edam:topic_3542 ; sc:citation , ; sc:description "interpretable supervised contact prediction using inter-domain coevolution." ; sc:featureList edam:operation_0272, edam:operation_0476, edam:operation_2950, edam:operation_3350 ; sc:name "FilterDCA" ; sc:url "http://gitlab.lcqb.upmc.fr/muscat/FilterDCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC6836550", "pubmed:31694722" ; sc:description """whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. FindSV is a structural variation pipeline written in nextflow and python. FindSV performs variant calling using TIDDIT and CNVnator. similar variants are merged, and the variants are annotated using VEP, frequency database, genmod, and custom annotation using the annotator script. FindSV outputs one unfilered vcf file per caller, a merged and unfiltered vcf file (_Combined.vcf), as well as an annotated and filtered vcf file "_FindSV.vcf". In addition, FindSV outputs a ploidy tab file, that describes the ploidy for each chromosome.""" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227, edam:operation_3695 ; sc:name "FindSV" ; sc:url "https://github.com/J35P312/FindSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3673 ; sc:citation ; sc:description "Repeat-aware tool for upgrading de novo assembly using long reads." ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FinisherSC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://kakitone.github.io/finishingTool/" ; biotools:primaryContact "Ka-Kit Lam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3407 ; sc:citation , "pmcid:PMC6364290", "pubmed:30746152" ; sc:description "R package and GUI application for analysis of aquatic respirometry data." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FishResp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.3" ; sc:url "https://fishresp.org/" ; biotools:primaryContact "Sergey Morozov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Digital Filter Design, Viewing and Comparison tool." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Fiview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://uazu.net/fiview/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3673, edam:topic_3794 ; sc:citation ; sc:description """Correcting reference bias from the Illumina Isaac aligner enables analysis of cancer genomes. Code to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file. Support code for NGS copy number algorithms. Takes a file of locations and a [cr:b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). Altered so that it clips all reads by n bases to reduce reference bias. python FixVaf.py [vcf file] [bam file] [fasta file]. The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. Requires python 3 with psam installed. The project previously contained 2 equivalent implementations of allele counting code in perl and C for BAM CRAM processing""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227, edam:operation_3695, edam:operation_3802 ; sc:name "FixVAF" ; sc:url "https://github.com/danchubb/FixVAF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3474 ; sc:citation , ; sc:description """Computing Persistent Homology of Directed Flag Complexes. Computing homology of directed flag complexes (based on https://github.com/Ripser/ripser). Three modified versions of flagser from luetge/flagser. flagser computes the homology of directed flag complexes. For a more detailed description consult the documentation under docs/documentation_flagser.pdf. Copyright © 2017–2018 Daniel Lütgehetmann. For more detailed instructions, see docs/documentation_flagser.pdf. The program flagser-memory is a variant of flagser storing the full directed flag complex in memory, speeding up parts of the computation but requiring more memory""" ; sc:featureList edam:operation_0551, edam:operation_2422 ; sc:license "MIT" ; sc:name "Flagser" ; sc:url "https://github.com/luetge/flagser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31542415" ; sc:description "Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data | Inference of microbial interaction networks from large-scale heterogeneous abundance data | FlashWeave predicts ecological interactions between microbes from large-scale compositional abundance data (i.e. OTU tables constructed from sequencing data) through statistical co-occurrence or co-abundance. It reports direct associations, with adjustment for bystander effects and other confounders, and can furthermore integrate environmental or technical factors into the analysis of microbial systems" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "FlashWeave" ; sc:url "https://github.com/meringlab/FlashWeave.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3172, edam:topic_3336, edam:topic_3390 ; sc:citation , "pmcid:PMC6823394", "pubmed:31696036" ; sc:description """A web-based chemical repository of flavonoid compounds. Flavonoids are richly diverse polyphenolic plant secondary metabolites that are known to be crucial component of human diet. These compounds are attributed with variety of nutritional as well as therapeutic value. Flavonoids are often known for their effective antioxidant nature; however, their various other bioactivities are well established. These bioactivities mainly includes antibacterial, anti-cancer, cardio protective, promotion of immune system, anti-inflammatory and skin protection from ultra violet radiation; these properties are effectively reviewed by Tungmunnithum et al 2018.""" ; sc:featureList edam:operation_0305, edam:operation_3216, edam:operation_3799, edam:operation_3891 ; sc:name "FlavoDb" ; sc:url "http://bioinfo.net.in/flavodb/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6612844", "pubmed:31510682" ; sc:description "Large scale microbiome profiling in the cloud | Main repository of the Flint project for Spark and Amazon EMR | This is the main repository of the Flint project for Amazon Web Services. Flint is a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark's built-in parallelism and streaming engine architecture to quickly map reads against a large reference collection of bacterial genomes" ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3211 ; sc:license "MIT" ; sc:name "Flint" ; sc:softwareHelp , , ; sc:url "https://camilo-v.github.io/flint/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3398, edam:topic_3452 ; sc:citation , "pubmed:31482902" ; sc:description "Flowsculpt is an open-source utility for solving the inverse problem in pillar programming. That is, given a fluid flow shape, what is the pillar sequence and inlet design that will produce such a shape? Our utility uses a customizable genetic algorithm to determine optimal pillar sequence and inlet flow design for a given fluid flow shape." ; sc:license "MIT" ; sc:name "FlowSculpt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.flowsculpt.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_0781, edam:topic_3305 ; sc:citation , "pubmed:31687905" ; sc:description """Tools for Influenza Activity and Surveillance. U.S. Influenza Surveillance System. Overview of Influenza Surveillance in the United States - CDC. Centers for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting People. FluNet is a global web-based tool for influenza virological surveillance first launched in 1997. The virological data entered into FluNet, e.g. number of influenza viruses detected by subtype, are critical for tracking the movement of viruses globally and interpreting the epidemiological data. The data at country level are publically available and updated weekly. The results are presented in various formats including tables, maps and graphs.""" ; sc:featureList edam:operation_0337, edam:operation_2429 ; sc:name "FluNet" ; sc:softwareHelp ; sc:url "https://www.who.int/influenza/gisrs_laboratory/flunet/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3293, edam:topic_3324 ; sc:citation , "pubmed:31774482" ; sc:description "A database for the study of genomic reassortments among influenza viruses." ; sc:featureList edam:operation_0323, edam:operation_0552, edam:operation_3431 ; sc:name "FluReassort" ; sc:url "https://www.jianglab.tech/FluReassort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3305 ; sc:citation , "pubmed:31687905" ; sc:description """Tools for Influenza Activity and Surveillance. The Influenza Division at CDC collects, compiles and analyzes information on influenza activity year-round in the United States. FluView , a weekly influenza surveillance report, and FluView Interactive , an online application which allows for more in-depth exploration of influenza surveillance data, are updated each week. The data presented each week are preliminary and may change as more data is received""" ; sc:featureList edam:operation_0337, edam:operation_2429 ; sc:name "FluView" ; sc:url "https://www.cdc.gov/flu/weekly/fluviewinteractive.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC6493727", "pubmed:31042738" ; sc:description "Algorithm for automated analysis of high-throughput droplet microfluidic data." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FluoroCellTrack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Manibarathi/FluoroCellTrack" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3518 ; sc:citation , , "pmcid:PMC7100978", "pubmed:32126077" ; sc:description "Automated analysis of mosaic imaginal discs in Drosophila | Fly-QMA: Quantitative Mosaic Analysis in Drosophila | Fly-QMA is part of the NU FlyEye platform for studying gene expression in the developing Drosophila eye. The package enables Quantitative Mosaic Analysis (QMA) - that is, it helps users compare expression levels between distinct clonal subpopulations within the eye epithelium" ; sc:featureList edam:operation_2495, edam:operation_3799 ; sc:license "MIT" ; sc:name "Fly-QMA" ; sc:softwareHelp , , ; sc:url "https://www.sbernasek.com/flyqma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3304, edam:topic_3382, edam:topic_3474 ; sc:citation , , "pubmed:21129968", "pubmed:31797265" ; sc:description "FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain." ; sc:featureList edam:operation_2421, edam:operation_2940, edam:operation_3450 ; sc:name "FlyCircuit" ; sc:url "http://www.flycircuit.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3174, edam:topic_3673 ; sc:author "Jeffrey Yuan", "Mikhail Kolmogorov", "Yu Lin" ; sc:citation , , , "pmcid:PMC6807382", "pubmed:30936562", "pubmed:31483244", "pubmed:33020656" ; sc:description "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3730 ; sc:name "Flye" ; sc:url "https://github.com/fenderglass/Flye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3518 ; sc:description "Formal model checking based pathway analysis (FoPA) - tool for identification of perturbed signaling pathways in clinical conditions using formal methods." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:name "FoPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fmansoori/FoPA" ; biotools:primaryContact "Mansoori F." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2828, edam:topic_3047, edam:topic_3068, edam:topic_3489 ; sc:citation , "pubmed:31686102" ; sc:description "The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3454, edam:operation_3695 ; sc:name "FoldamerDB" ; sc:softwareHelp ; sc:url "http://foldamerdb.ttk.hu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3301 ; sc:citation ; sc:description "Data resource collecting taxonomic composition and related metadata of > 2300 food and food-related samples. Data were produced according to a standardized pipeline and each sample is identified according the FoodEx2 classification (developed by the European Food Safety Authority to facilitate the comparison among different studies)." ; sc:name "FoodMicrobionet" ; sc:softwareVersion "3.1" ; sc:url "http://www.foodmicrobionet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3168, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6938691", "pubmed:31851693" ; sc:description """Quality control on genetic variants from next-generation sequencing data using random forest. This classifier uses random forest model to identify good or bad variants from grey variants. $ conda install forestqc -c avallonking. To install the software. This software is compatible with OSX, 64-bit Linux and 64-bit Windows systems. If no HWE p-value file provided, HWE p-value would be computed by ForestQC. Or if ForestQC cannot find HWE p-value for some sites in the provided HWE p-value file, ForestQC would compute HWE p-value for those sites""" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3225, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "ForestQC" ; sc:url "https://github.com/avallonking/ForestQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3489 ; sc:citation , "pmcid:PMC6864098", "pubmed:31745083" ; sc:description "A database for the late quaternary fossil records of Sahul along with data processing scripts." ; sc:name "FosSahul" ; sc:url "https://github.com/GlobalEcologyFlinders/FosSahul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3382 ; sc:citation , ; sc:description "FossilJ is a ImageJ plugin for fossil data acquisition and semi-automatic measurements by image analysis." ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "FossilJ" ; sc:url "https://github.com/fionapye/FossilJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0749, edam:topic_3303 ; sc:citation , "pmcid:PMC6301337", "pubmed:30576493" ; sc:description "Message-oriented, horizontally scalable ETL system for scientific data integration and enhancement." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Foundry" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/biocaddie/Foundry-ES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "Automated tool for animal detection in camera trap images." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "FoxMask" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/edevost/foxmask" ; biotools:primaryContact "Eric Devost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780 ; sc:citation ; sc:description "Graphical tool for assessing fractionation bias following polyploidy." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FractBias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://genomevolution.org/CoGe/SynMap.pl" ; biotools:primaryContact "Eric Lyons" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0593, edam:topic_2258, edam:topic_3314 ; sc:citation , , "pmcid:PMC3961104", "pubmed:24688855" ; sc:description """An efficient Python library to setup quantum chemistry calculations on peptides models. fragbuilder is a tool to create, setup and analyze QM calculations on peptides. FragBuilder will run with most versions of Open Babel, however there was bug in Open Babel which prevented some dihedral angles to be set accurately. If you experience this while using fragbuilder you will have to update your Open Babel""" ; sc:featureList edam:operation_0249, edam:operation_0479, edam:operation_0480 ; sc:license "BSD-Source-Code" ; sc:name "FragBuilder" ; sc:softwareHelp , ; sc:url "https://github.com/jensengroup/fragbuilder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3174, edam:topic_3179 ; sc:citation , "pubmed:31712779" ; sc:description """FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. FreeHi-C pipeline for high fidelity Hi-C data simulation. FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation. FreeHi-C (v1.0) is short for Fragment interactions empirical estimation for fast simulation of Hi-C data. It is a data-driven Hi-C data simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating an interaction distribution of genome fragments and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data. FreeHi-C not only can be used to study and benchmark a wide range of Hi-C analysis methods but also boosts power and enables false discovery rate control for differential interaction detection algorithms through data augmentation""" ; sc:featureList edam:operation_0244, edam:operation_3192, edam:operation_3435 ; sc:license "MIT" ; sc:name "FreeHi-C" ; sc:url "https://github.com/keleslab/FreeHiC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1668 ; sc:encodingFormat edam:format_2331 ; sc:name "Z-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation "pubmed:28336965" ; sc:description "Frela is a web service for computing functional relationships of protein pairs based on Gene Ontology (GO) annotations. It allows very fast calculation of protein functional similarity based on their GO annotations for biological process (BP), molecular function (MF), and cellular component (CC) ontologies using various popular semantic similarity measures that can be combined arbitrarily with a set of widely used mixing strategies." ; sc:featureList edam:operation_1778, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Frela" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://frela.eurac.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0632, edam:topic_3168, edam:topic_3293, edam:topic_3512 ; sc:citation ; sc:description "FrogCap is a modular sequence capture probeset for phylogenomics and population genetics for frogs" ; sc:featureList edam:operation_2419, edam:operation_3192, edam:operation_3196 ; sc:name "FrogCap" ; sc:url "https://github.com/chutter/FrogCap-Sequence-Capture" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31596475" ; sc:description "FullMeSH is a large-scale MeSH indexing method taking advantage of the recent increase in the availability of full text articles. The software is available upon request." ; sc:featureList edam:operation_0306, edam:operation_3435 ; sc:name "FullMeSH" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31596475" ; biotools:primaryContact "Shanfeng Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC6612877", "pubmed:31510685" ; sc:description "identification and prioritization of functional differential m6A methylation genes | A R package used to identify single base resolution m6A and differential m6A methylation site from MeRIP-seq data version 1.0" ; sc:featureList edam:operation_3207, edam:operation_3501 ; sc:name "FunDMDeep-m6A" ; sc:url "https://github.com/NWPU-903PR/DMDeepm6A1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_0602, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31882995" ; sc:description """A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information. Functional potential of bacterial genomes and microbiomes from gene context information. This feature allows the user to input a newly sequenced genome and annotate it using gene context based modules generated using extensive literature mining and manual curation. Users can also carry out comparative analysis (synteny view using parallel coordinates) of the uploaded genome with genomes already sequenced in NCBI using interactive visualizations. This feature allows comparison of functional modules in sequenced genomes obtained from NCBI. Users can interactively select upto five genomes which are compared using a synteny based visualization (parallel coordinates) and circular genomic representations. Information about individual modules in all these genomes can also be viewed as tabular outputs""" ; sc:featureList edam:operation_0306, edam:operation_0362, edam:operation_2495, edam:operation_2939, edam:operation_3208 ; sc:name "FunGeCo" ; sc:url "https://web.rniapps.net/fungeco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0621 ; sc:citation , "pmcid:PMC6376640", "pubmed:30767762" ; sc:description "User-friendly graphical interface that allows to visualize and summarize the functional annotations of one or multiple molecular biology experiments at once." ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FunMappOne" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Greco-Lab/FunMappOne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769 ; sc:citation , "pubmed:31454647" ; sc:description "A systematic pipeline to unravel the convergence patterns of genetic variants in ASD | A Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in Complex Diseases | FunVar (Functional annotation of Variants ) utilizes the existing resources to streamline and to improve the functional enrichment analysis of genetic variants disrupting genes in patients. FunVar, a semi-automated pipeline consist of three different and independent modules" ; sc:featureList edam:operation_3501 ; sc:name "FunVar" ; sc:url "https://github.com/lasigeBioTM/FunVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3473 ; sc:citation , "pmcid:PMC6377781", "pubmed:30770734" ; sc:description "Automated and interactive pattern recognition tool to integrate time with multi-omics assays." ; sc:featureList edam:operation_0531, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "Functional Heatmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-abcc.ncifcrf.gov/Heatmap/" ; biotools:primaryContact "Daniel Watson", "Joshua Williams", "Ruoting Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "The code which segment the retinal blood vessels accurately. The Kirsch's template is used for tracking the larger blood vessels; fuzzy c-means is used to segment smaller blood vessels. The region based active contour method is used for edge detection and Morphoplogical operations are used to remove the background from the foreground fundus image. This methodology is suitable for different fundus image databases captured using different fundus cameras." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Locating Retinal Blood Vessels on Fundus Images by Kirsch s Template and Fuzzy C-Means" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63116-locating-retinal-blood-vessels-on-fundus-images-by-kirsch-s-template-and-fuzzy-c-means" ; biotools:primaryContact "Jemima Jeba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0202, edam:topic_0625 ; sc:citation , "pmcid:PMC6546077", "pubmed:31183256" ; sc:description "R package for QTL mapping using longitudinal phenotypes." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Funmap2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.4.2" ; sc:url "https://github.com/wzhy2000/Funmap2" ; biotools:primaryContact "N. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6808644", "pubmed:31610622" ; sc:description """An accurate prediction of fusion genes from RNA-Seq data. Homepage may be broken as of January 4th, 2021.""" ; sc:featureList edam:operation_2454, edam:operation_3192, edam:operation_3359 ; sc:name "FusionScan" ; sc:url "http://biome.ewha.ac.kr/fusionscan/fusionscan.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3382 ; sc:author "Peter Andrews" ; sc:citation ; sc:description """An interactive genomic graph viewer. G-Graph is a free-software graphical desktop application that allows you to perform efficient exploratory analysis of genomic copy number and other numeric datasets. G-Graph can be installed and runs under the Linux, Mac, and Windows operating systems. G-Graph's features include the ability to easily zoom and scroll the view, alter the visual display properties, display gene annotations, link genes to the UCSC genome browser, and save application views to image and pdf format. G-Graph is also very fast and therefore supports smooth scrolling and zooming of views even for millions of data points""" ; sc:featureList edam:operation_2940 ; sc:license "MIT" ; sc:name "G-Graph" ; sc:url "https://mumdex.com/ggraph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3382 ; sc:citation , "pubmed:31070714" ; sc:description "Galaxy-based platform for collaborative annotation of eukaryotic genomes." ; sc:featureList edam:operation_0525, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "G-OnRamp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gonramp.wustl.edu/" ; biotools:primaryContact "Jeremy Goecks", "Luke Sargent", "Sarah C.R. Elgin", "Wilson Leung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3360, edam:topic_3517 ; sc:citation , , "pmcid:PMC6894795", "pubmed:31805043" ; sc:description "Assessing the performance of genome-wide association studies for predicting disease risk." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:name "G-WIZ" ; sc:url "https://github.com/jonaspatronjp/GWIZ-Rscript/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc:description "Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "G2P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XiaoleiLiuBio/G2P" ; biotools:primaryContact "Xiaolei Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:31393560" ; sc:description "R package to interactively visualize genetic mutation data using a lollipop-diagram." ; sc:featureList edam:operation_0337, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "G3viz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=g3viz" ; biotools:primaryContact "Xin Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0622, edam:topic_0780, edam:topic_3512 ; sc:citation ; sc:description """A Python script for dividing genome annotation files into feature-based files. A python script for extracting genome features from GTF/GFF3.""" ; sc:featureList edam:operation_0362, edam:operation_2478, edam:operation_3800 ; sc:name "GAD" ; sc:url "https://github.com/bio-projects/GAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3056 ; sc:description "Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data" ; sc:name "GADMA" ; sc:url "https://github.com/ctlab/GADMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3474 ; sc:citation , ; sc:description "A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction." ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_0487, edam:operation_3198, edam:operation_3211 ; sc:name "GAEseq" ; sc:url "https://github.com/WuLoli/GAEseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3520 ; sc:citation , "pmcid:PMC6324007", "pubmed:30371822" ; sc:description "Online tool to build 3D models of GAG sequences from GlycoCT codes." ; sc:featureList edam:operation_2422, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GAG builder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycan-builder.cermav.cnrs.fr/gag/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0780 ; sc:citation , "pubmed:30926570" ; sc:description "A Docker-based package for genome analysis and visualization." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "Genome Annotator Light (GAL)" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "https://hub.docker.com/r/cglabiicb/gal" ; biotools:primaryContact "Arijit Panda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3524 ; sc:citation , ; sc:description "GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations." ; sc:featureList edam:operation_2426 ; sc:name "GAMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gama-platform.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3306, edam:topic_3452 ; sc:citation ; sc:description "An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries | Geometry-preserving Adaptive Mesher | GAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others. GAMer has the following main features: | Geometry-preserving Adaptive Mesher — GAMer v2.0.5 documentation | Free document hosting provided by Read the Docs" ; sc:license "LGPL-2.1" ; sc:name "GAMer" ; sc:softwareHelp ; sc:url "http://github.com/ctlee/gamer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "Collection of commands for working with phylogenetic data." ; sc:featureList edam:operation_0325, edam:operation_0567, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GAPPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://github.com/lczech/gappa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6815017", "pubmed:31653208", "pubmed:31744474" ; sc:description """a GPU accelerated sequence alignment library for high-throughput NGS data. GASAL2 - GPU-accelerated DNA alignment library. GASAL2 is an easy-to-use CUDA library for DNA/RNA sequence alignment algorithms. Currently it supports different kind of alignments:. A Linux platform with CUDA toolkit 8 or higher is required, along with usual build environment for C and C++ code. GASAL2 has been tested over NVIDIA GPUs with compute capabilities of 2.0, 3.5 and 5.0. Although lower versions of the CUDA framework might work, they have not been tested""" ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_0496 ; sc:license "Apache-2.0" ; sc:name "GASAL2" ; sc:url "https://github.com/nahmedraja/GASAL2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308, edam:topic_3673 ; sc:citation ; sc:description "Customizable computational tool included in Genome Analysis Toolkit (GATK) for the discovery and identification of microbial sequences in libraries from eukaryotic hosts." ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "GATK PathSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/gatk" ; biotools:primaryContact "Matthew Meyerson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_3050, edam:topic_3277, edam:topic_3303 ; sc:citation , "pmcid:PMC6805691", "pubmed:31656398" ; sc:description "GBIF—the Global Biodiversity Information Facility—is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth." ; sc:featureList edam:operation_2421 ; sc:name "GBIF" ; sc:softwareHelp ; sc:url "https://www.gbif.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0622, edam:topic_2229 ; sc:citation , "pmcid:PMC6828702", "pubmed:31685817" ; sc:description """The Empusa code generator and its application to GBOL. GBOL; Genome Biology Ontology Language. To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). A group is a collection of several projects. If you organize your projects under a group, it works like a folder.""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3559 ; sc:name "GBOL" ; sc:url "http://gbol.life" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3518, edam:topic_3673 ; sc:citation , "pmcid:PMC6683502", "pubmed:31387530" ; sc:description "Screening populations for copy number variation using genotyping-by-sequencing | Detection of deletions and duplications from GBS data | delgbs is an R package which provides tools for detecting copy number variation from genotyping-by-sequencing (GBS) data. delgbs bases its CNV calls on the number of reads per sample in discrete bins (e.g. 1-kb bins) located along a reference genome" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "GBS" ; sc:url "http://github.com/malemay/delgbs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3336, edam:topic_3379 ; sc:citation , "pubmed:30717669" ; sc:description "Galaxy workflow system for predictive model building for virtual screening." ; sc:featureList edam:operation_0482, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GCAC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://toolshed.g2.bx.psu.edu/repository?repository_id=351af44ceb587e54" ; biotools:primaryContact "Andrew M. Lynn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3375, edam:topic_3518 ; sc:citation , "pubmed:31397851" ; sc:description "Graph convolution for predicting associations between miRNA and drug resistance | IMPLEMENT FOR graph convolution for predicting associations between miRNA and drug resistance using raw data" ; sc:featureList edam:operation_0463, edam:operation_3482, edam:operation_3792 ; sc:name "GCMDR" ; sc:url "https://github.com/xyzx2019/GCMDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """Graph convolutional networks for inferring cell-cell interactions. using graph convolutional neural network and spaital transcriptomics data to infer cell-cell interactions. GCNG for extracellular gene relationship inference. (A) GCNG model using spatial single cell expression data""" ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3625 ; sc:name "GCNG" ; sc:url "https://github.com/xiaoyeye/GCNG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0780 ; sc:citation ; sc:description "Web tool for guanylyl cyclase functional centre prediction from amino acid sequence." ; sc:featureList edam:operation_0418, edam:operation_0478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GCPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gcpred.com/" ; biotools:primaryContact "Aloysius Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC6902276", "pubmed:31850053" ; sc:description """Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy. This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species. The gene sequence and genetic feature variation between different individuals are very important for natural variation research""" ; sc:featureList edam:operation_0292, edam:operation_0362, edam:operation_0524, edam:operation_3227, edam:operation_3644 ; sc:license "MIT" ; sc:name "GEAN" ; sc:url "https://github.com/baoxingsong/GEAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC6624217", "pubmed:31100356" ; sc:description "GEnetic Antibiotic Resistance and Susceptibility Database." ; sc:featureList edam:operation_3196, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GEAR-base" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gear-base.com" ; biotools:primaryContact "Andreas E. Posch", "Andreas Keller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6883002", "pubmed:31824573" ; sc:description """Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification. graph embedding deep learning guide microbial biomarkers' identification.""" ; sc:featureList edam:operation_2940, edam:operation_3439 ; sc:name "GEDFN" ; sc:url "https://github.com/MicroAVA/GEDFN.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Accurate Cell Type Quantification from Gene Expression Data | Abstract The cell type composition of heterogeneous tissue samples can be a critical variable in both clinical and laboratory settings. However, current experimental methods of cell type quantification (e.g. cell flow cytometry) are costly, time consuming and can introduce bias. Computational approaches that infer cell type abundance from expression data offer an alternate solution. While these methods have gained popularity, most are limited to predicting hematopoietic cell types and do not produce accurate predictions for stromal cell types. Many are also limited to particular platforms, whether RNA-Seq or specific microarray models. To overcome these limitations, we present the Gene Expression Deconvolution Interactive Tool, or GEDIT. Using simulated and experimental data, we demonstrate that GEDIT produces accurate results for both stromal and hematopoietic cell types" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3800 ; sc:name "GEDIT" ; sc:url "http://webtools.mcdb.ucla.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3314, edam:topic_3489 ; sc:citation , "pmcid:PMC6661976", "pubmed:31404233" ; sc:description "Lessons in Multi-Institution Teamwork Using Collaboration Software | Dashboard to view/download files from segregated Google Shared Drives | Center for Genetically Encoded Materials (C-GEM) | GEM-NET is the home of the Center for Genetically Encoded Materials (C-GEM), an NSF CCI (Center for Chemical Innovation) | Center for Genetically Encoded Materials | C-GEM seeks to establish a fundamentally new way to program chemical matter and transform the way we produce materials and medicines" ; sc:name "GEM-NET" ; sc:url "http://gem-net.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3303, edam:topic_3398 ; sc:citation , "pmcid:PMC6805226", "pubmed:31406981" ; sc:description "a simple and fast global epistatic model predicting mutational effects | The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modelling inter-site dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present GEMME (www.lcqb.upmc.fr GEMME), an original and fast method that predicts mutational outcomes by explicitly modelling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods" ; sc:featureList edam:operation_0331 ; sc:name "GEMME" ; sc:url "http://www.lcqb.upmc.fr/GEMME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3382 ; sc:citation ; sc:description "GEMMER (GEnome-wide tool for Multi-scale Modeling data Extraction and Representation), a web-based data-integration tool that facilitates high quality visualization of physical, regulatory and genetic interactions between proteins/genes in Saccharomyces cerevisiae." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GEMMER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gemmer.barberislab.com" ; biotools:primaryContact "Matteo Barberis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3382, edam:topic_3407 ; sc:citation ; sc:description """Extracting Views into Genome-scale Metabolic Models. The GEMtractor a platform for trimming and extracting genome-scale metabolic models (GEMs).""" ; sc:featureList edam:operation_3192, edam:operation_3280, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "GEMtractor" ; sc:url "http://sbi.uni-rostock.de/gemtractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6796420", "pubmed:31619158" ; sc:description """a shiny web application for gene expression normalization, analysis and visualization. GENAVi (Gene Expression Normalization Analysis and Visualization) is an rshiny web application that provides a GUI based platform for the analysis of gene expression data. GENAVi combines several R packages commonly used for normalizing, clustering, visualizing, and performing differential expression analysis (DEA) on RNA-seq data""" ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:name "GENAVi" ; sc:url "https://junkdnalab.shinyapps.io/GENAVi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0769 ; sc:citation , , , , "pmcid:PMC3431492", "pmcid:PMC7778937", "pubmed:22955987", "pubmed:22955988", "pubmed:30357393", "pubmed:33270111" ; sc:description "Consortium identifying and classifying all gene features in the human and mouse genomes with high accuracy based on biological evidence, and releasing these annotations for the benefit of biomedical research and genome interpretation." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GENCODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , , , ; sc:url "https://www.gencodegenes.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , , ; sc:description "Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time." ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "GENOMICUS" ; sc:softwareHelp ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "An easy-to-use R pipeline for complete pre-processing of RNA-seq data | You're trying to access a page that requires authentication. × | Home: https://bitbucket.org/thomas_wolf/geo2rnaseq/overview | RNA-seq is a method that uses next-generation sequencing to quantify and analyze RNA. It can be used for finding significantly differentially expressed genes (DEGs) in well sequenced organisms. This package is a complete function library for analyzing read files, trimming of raw reads, mapping on reference genomes, counting reads per gene and finding significant DEGs | PRIVACY POLICY : EULA (Anaconda Cloud v2.33.29) © 2019 Anaconda, Inc. All Rights Reserved | Follow us on Twitter Tap To Close Find us on Facebook Tap To Close Follow us on Slideshare Tap To Close Find us on LinkedIn Tap To Close Follow us on Instagram Tap To Close Watch us on YouTube Tap To Close Follow us on GitHub Tap To Close" ; sc:featureList edam:operation_3192, edam:operation_3223, edam:operation_3435 ; sc:name "GEO2RNAseq" ; sc:softwareHelp ; sc:url "https://anaconda.org/xentrics/r-geo2rnaseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0204, edam:topic_0218, edam:topic_0219 ; sc:citation , "pubmed:31617460" ; sc:description """Gene expression regulation database curated by mining abstracts from literature. Gene Expression Regulation Database. Gene Expression Regulation Database (GREDB) has been developed to facilitate systems-level analyses that will provide insights into the question of how genes are regulated that governing a specific biological response. GREDB is a publicly available, manually curated biological database depositing the human gene expression regulation relationships (Links). To date, more than 39,000 Links have been contextual-ly annotated through the review of 53,000 plus abstracts. GREDB has the ability to analyze user-supplied gene expression data using the GEREA bioinformatics tool in a causal analysis oriented manner. The database can be searched use NCBI official gene symbol (eg. CDC42). The new version of GereDB is online for testing, please visit the following link: Run New GereDB online. Huang, Tinghua & Huang, Xiali & Shi, Bomei & Yao, Min. (2019)""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2495, edam:operation_3431 ; sc:name "GEREDB" ; sc:url "http://www.thua45.cn/geredb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293, edam:topic_3299 ; sc:author "Agata Kilar" ; sc:description "GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GERONIMO" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/amkilar/GERONIMO.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0736, edam:topic_2640, edam:topic_3170 ; sc:citation , "pubmed:31630971" ; sc:description """Identification of transcriptional isoforms associated with survival in cancer patient. GESUR performs overall survival (OS) or disease free survival (DFS, also called relapse-free survival and RFS) analysis based on expression of a gene set. GESUR uses Log-rank test, a.k.a the Mantel–Cox test, for hypothesis test. Cohorts thresholds can be adjusted, and gene-pairs can be used. The cox proportional hazard ratio and the 95% confidence interval information can also be included in the survival plot.""" ; sc:featureList edam:operation_0264, edam:operation_2238, edam:operation_2495 ; sc:name "GESUR" ; sc:url "http://gesur.cancer-pku.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3361, edam:topic_3489 ; sc:citation ; sc:description """Exploiting observations and measurement data standard for distributed LTER-Italy freshwater sites. Water quality issues. Geoinformation Enabling ToolkIT starterkit. Geoinformation Enabling ToolkIT starterkit ®. GET-IT allows you to easily share geospatial data on the web with simple actions. Share your maps, measurements, and sensors.""" ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:name "GET-IT" ; sc:url "http://get-it.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3421, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6857918", "pubmed:31730620" ; sc:description """Gene expression based survival prediction for cancer patients. Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. This repository includes source code from the publication Gene Expression based Survival Prediction for Cancer Patients – A Topic Modeling Approach. You can find the code for the MTLR algorithm here http://pssp.srv.ualberta.ca/home/about.""" ; sc:featureList edam:operation_0571, edam:operation_2454, edam:operation_3891 ; sc:name "GE LDA Survival" ; sc:url "https://github.com/nitsanluke/GE-LDA-Survival" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description """An integrative machine learning approach to discovering multi-level molecular mechanisms of obesity using data from monozygotic twin pairs. We combined clinical, cytokine, genomic, methylation and dietary data from 43 young adult monozygotic twin pairs (aged 22 36, 53% female), where 25 of the twin pairs were substantially weight discordant (delta BMI > 3kg m2). These measurements were originally taken as part of the TwinFat study, a substudy of The Finnish Twin Cohort study. These five large multivariate data sets (comprising 42, 71, 1587, 1605 and 63 variables, respectively) were jointly analysed using an integrative machine learning method called Group Factor Analysis (GFA) to offer new hypotheses into the multi-molecular-level interactions associated with the development of obesity. New potential links between cytokines and weight gain are identified, as well as associations between dietary, inflammatory and epigenetic factors""" ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "GFA" ; sc:url "https://cran.r-project.org/web/packages/GFA/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3172 ; sc:citation , "pubmed:31077287" ; sc:description "Exact hypothesis testing for shrinkage based Gaussian Graphical Models." ; sc:featureList edam:operation_2238, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GGMs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/V-Bernal/GGM-Shrinkage" ; biotools:primaryContact "Peter Horvatovich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6517830", "pubmed:31089686" ; sc:description "Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GIDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bmtongji.cn/GIDB/index.html" ; biotools:primaryContact "Xiaoyan Zhang", "Ying Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3315 ; sc:citation ; sc:description "Using Gauss Integrals to identify rare conformations in protein structures | Abstract The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general" ; sc:name "GISA" ; sc:url "https://github.com/ceegeeCode/GISA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3656 ; sc:citation , "pmcid:PMC6364044", "pubmed:30553884" ; sc:description "GITAR (Genome Interaction Tools and Resources) is a standardized, easy to use and flexible solution to manage Hi-C genomic interaction data, from processing to storage and visualization, composed of two modules: HiCtool and a processed data library." ; sc:featureList edam:operation_1812, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GITAR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://genomegitar.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0781, edam:topic_3050, edam:topic_3174 ; sc:citation , "pmcid:PMC6936153", "pubmed:31884971" ; sc:description """Charting the diversity of uncultured viruses of Archaea and Bacteria. Genomic Lineages of Uncultured Viruses of Archaea and Bacteria. Perl script that automates the analyses to establish GL-UVAB (Genomic Lineages of Uncultured Viruses of Archaea and Bacteria). These include: 1) Identification of protein encoding genes with Prodigal. 2) All-versus-all protein search with Diamond. 3) Calculating Dice distances. 4) Building Dice tree using R 5) Identifying lineages based on the user defined criteria""" ; sc:featureList edam:operation_0362, edam:operation_3198, edam:operation_3460 ; sc:name "GL-UVAB" ; sc:url "https://sourceforge.net/projects/gluvab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3304 ; sc:citation , , "pmcid:PMC6914332", "pubmed:31841564" ; sc:description "A Python toolbox for investigating the association between gaze allocation and decision behaviour | A python toolbox for the Gaze Weighted Linear Accumulator Model (GLAM) | GLAMbox is a Python toolbox for investigating the association between gaze allocation and decision behaviour, and applying the Gaze-weighted Linear Accumulator Model (Thomas, Molter et al., 2019, full text available online)" ; sc:featureList edam:operation_3436 ; sc:license "MIT" ; sc:name "GLAMbox" ; sc:url "https://glambox.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc:description "Genomic loci annotation and enrichment tool." ; sc:featureList edam:operation_3197, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLANET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/burcakotlu/GLANET" ; biotools:primaryContact "Burçak Otlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6927135", "pubmed:31870412" ; sc:description """Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Dimension Reduction of Non-Normally Distributed Data. Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.""" ; sc:featureList edam:operation_2939, edam:operation_3563, edam:operation_3891 ; sc:license "Artistic-2.0" ; sc:name "GLM-PCA" ; sc:url "https://cran.r-project.org/web/packages/glmpca/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3174 ; sc:citation ; sc:description "16S subunit related sequences database, identified from metagenomic efforts as part of the Tara Oceans project. It includes a BLAST search tool. The analysis system incorporates the SILVA collection, allowing comparative analyses to identify unclassified sequences and their geographical distribution." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLOSSary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.szn.it/glossary/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0781, edam:topic_3305 ; sc:citation , "pmcid:PMC6299651", "pubmed:30563445" ; sc:description "GLUE (Genes Linked by Underlying Evolution) is data-centric bioinformatics environment for virus sequence data, with a focus on variation, evolution and sequence interpretation." ; sc:featureList edam:operation_0499, edam:operation_0564, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "GLUE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.glue.cvr.ac.uk/#/home" ; biotools:primaryContact "Josh Singer", "Robert Gifford" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3518 ; sc:citation ; sc:description "Web-based tool to visualize, analyze, present and mine glycan microarray data." ; sc:featureList edam:operation_1812, edam:operation_3218, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GLycan Array Dashboard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://glycotoolkit.com/Tools/GLAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31070732" ; sc:description "Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/chaoning/GMA" ; biotools:primaryContact "Jian-Feng Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pubmed:31825885" ; sc:description """Predicting human lncRNA-disease associations based on geometric matrix completion. Recently, increasing evidences have indicated that dysregulations of long non-coding RNAs (lncRNAs) are implicated in various complex diseases. However, only a limited number of lncRNA-disease associations are experimentally verified. Prioritizing potential lncRNA-disease associations is beneficial not only for understanding disease mechanisms at lncRNA level, but also for disease diagnosis. Various computational methods have been proposed, but precise prediction and full use of data's intrinsic structure are still challenging. In this study, we propose a new method, named GMCLDA (Geometric Matrix Completion lncRNA-Disease Association), to infer potential lncRNA-disease associations based on geometric matrix completion.""" ; sc:featureList edam:operation_0346 ; sc:name "GMCLDA" ; sc:url "https://github.com/bioinfomaticsCSU/GMCLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3385, edam:topic_3810 ; sc:citation , "pmcid:PMC6711351", "pubmed:31467803" ; sc:description "Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers | A growth chamber sensing system using the Raspberry Pi as a platform | GMpi: A Growth Chamber Monitoring System Using the Raspberry Pi as a Platform | The GMpi is a cost-effective solution for monitoring the conditions of a growth chamber, greenhouse, or any other facility for which specific conditions (temperature, light, humidity, etc.) need to be maintained" ; sc:name "GMpi" ; sc:url "https://github.com/BrandinGrindstaff/GMpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0625, edam:topic_3174 ; sc:citation , "pubmed:31504765" ; sc:description "a database of curated and consistently annotated human gut metagenomes | GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries" ; sc:featureList edam:operation_0362 ; sc:name "GMrepo" ; sc:url "https://gmrepo.humangut.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:31874639" ; sc:description """transforming GO terms and proteins to vector representations via graph embeddings. BACKGROUND:Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content to estimate the semantic similarity between GO terms; recently some research exploited word embeddings to learn vector representations for GO terms from a large-scale corpus. In this paper, we proposed a novel method, named GO2Vec, that exploits graph embeddings to learn vector representations for GO terms from GO graph. GO2Vec combines the information from both GO graph and GO annotations, and its learned vectors can be applied to a variety of bioinformatics applications, such as calculating functional similarity between proteins and predicting protein-protein interactions""" ; sc:featureList edam:operation_2492, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "GO2Vec" ; sc:url "https://github.com/xszhong/GO2Vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0196, edam:topic_0622, edam:topic_0780, edam:topic_3316 ; sc:citation ; sc:description """Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant Informatics and Computation Lab. Click on the link to learn more. Publicly available GOMAP Datasets. These datasets generated by GOMAP are new high-coverage and reproducible functional annotation sets of protein coding genes based on Gene Ontology (GO) term assignments. Follow the DOI link for more information, access, and download. Check out the main project page (Home on the left) to find out more about how they were generated and how you can use the pipeline yourself.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3672 ; sc:name "GOMAP" ; sc:softwareHelp ; sc:url "https://dill-picl.org/projects/gomap/gomap-datasets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0632, edam:topic_0749 ; sc:citation , "pmcid:PMC6332836", "pubmed:30642251" ; sc:description "Generator of probes for capture Hi-C experiments at high resolution." ; sc:featureList edam:operation_0309, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GOPHER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/TheJacksonLaboratory/Gopher" ; biotools:primaryContact "The Jackson Laboratory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474, edam:topic_3489 ; sc:citation , "pubmed:31804928" ; sc:description """A Large High-Diversity Benchmark for Generic Object Tracking in the Wild. Generic Object Tracking Benchmark. A large, high-diversity, one-shot database for generic object tracking in the wild""" ; sc:featureList edam:operation_3436 ; sc:name "GOT-10k" ; sc:url "http://got-10k.aitestunion.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_3518 ; sc:citation , "pmcid:PMC6330489", "pubmed:30634902" ; sc:description "Tool to navigate through branches of gene ontology hierarchy." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GOTrapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioGeneTools/GOTrapper" ; biotools:primaryContact "Hezha Hassan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_3518 ; sc:citation , "pmcid:PMC6695228", "pubmed:31415589" ; sc:description "Advances in gene ontology utilization improve statistical power of annotation enrichment | Welcome to GOcats’ documentation! — GOcats 1.1.5 documentation" ; sc:featureList edam:operation_3352, edam:operation_3501, edam:operation_3559 ; sc:name "GOcats" ; sc:url "https://gocats.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0602 ; sc:citation , "pmcid:PMC6286514", "pubmed:30526489" ; sc:description "Tool for interactive Gene Ontology analysis." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "GOnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.dice-database.org/GOnet/" ; biotools:primaryContact "Mikhail Pomaznoy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_0593, edam:topic_0820, edam:topic_3892 ; sc:citation ; sc:description """GPCRmd uncovers the dynamics of the 3D-GPCRome. The online resource for GPCR simulations. GPCRmd is an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visualize, inspect, and analyse GPCR molecular dynamics.""" ; sc:featureList edam:operation_0269, edam:operation_2476, edam:operation_2995, edam:operation_3891 ; sc:name "GPCRmd" ; sc:url "http://gpcrmd.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3334 ; sc:citation , "pmcid:PMC6625143", "pubmed:31127708" ; sc:description "Inherited glycophosphatidylinositol deficiency variant database." ; sc:featureList edam:operation_0417, edam:operation_3225, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GPI-anchor biosynthesis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.gpibiosynthesis.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622, edam:topic_0780, edam:topic_3170, edam:topic_3500 ; sc:citation , "pmcid:PMC6929509", "pubmed:31874598" ; sc:description """a Gene PREDiction model accounting for 5 '- 3' GC gradient. a Gene PREDiction model accounting for 5'-3' GC gradient. A new hidden Markov model (HMM)-based ab initio. gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes.""" ; sc:featureList edam:operation_0430, edam:operation_0476, edam:operation_2454 ; sc:name "GPRED-GC" ; sc:url "https://sourceforge.net/projects/gpred-gc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2259, edam:topic_3068 ; sc:citation ; sc:description """A Docker-based Resource for Genomics, Proteomics and Systems biology. Welcome to GPSRdocker A resource for Genomics, Proteomics and Systems biology. GPSRdocker is a docker-based container that provides a resources on Genomics, Proteomics and System Biology""" ; sc:featureList edam:operation_0267, edam:operation_2489, edam:operation_3461 ; sc:name "GPSRdocker" ; sc:url "https://webs.iiitd.edu.in/gpsrdocker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation , "pubmed:31145605" ; sc:description "Implementation of the Molecular Electrostatic Potential over Graphics Processing Units." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GPUAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/gpuam/binaries.git" ; biotools:primaryContact "Jorge Garza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation ; sc:description """A framework for querying General Feature Format (GFF) files and feature expression files in a compressed form”. This is the GPress, a framework for querying GTF, GFF3 and expression files in a compressed form. Here, we will use the test files to provide an example of how to use GPress. We will use GTF file for illustration since the GFF3 file is nearly the same except slight format variations. We will store the compressed GTF file and compressed expression file in a new folder gtf1""" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_2421, edam:operation_2422, edam:operation_3802 ; sc:name "GPress" ; sc:url "https://github.com/qm2/gpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:31608923" ; sc:description """deconvolution of shared pseudo-profiles at single-cell resolution. Code for the GPseudoClust method, including pre- and postprocessing steps. Magdalena E Strauß, Paul DW Kirk, John E Reid, Lorenz Wernisch (2019); GPseudoClust: deconvolution of shared pseudo-trajectories at single-cell resolution""" ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "GPseudoClust" ; sc:url "https://github.com/magStra/GPseudoClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC6742416", "pubmed:31469829" ; sc:description "A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner | GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell type-specific manner" ; sc:featureList edam:operation_0331, edam:operation_0441, edam:operation_3232 ; sc:name "GRAM" ; sc:url "https://github.com/gersteinlab/GRAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3067 ; sc:citation ; sc:description "Generator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GRANAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://granar.github.io" ; biotools:primaryContact "Guillaume Lobet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC3287830", "pubmed:22373025" ; sc:description "GRANVIL (Gene- or Region-based ANalysis of Variants of Intermediate and Low frequency) - performs rare-variant analysis of binary or quantitative phenotypes. The method is based on accumulation of minor alleles of rare or uncommon markers discovered through dense genotyping or resequencing data. Association analyses are based on gene- or other pre-defined regions, determined by analyst." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:name "GRANVIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/granvil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6749106", "pubmed:31530648" ; sc:description "Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes | Genome Relative Abundance to Sequencing Effort: a tool for planning MAG sequencing experiments | grase is a package that estimates the sequencing effort required to achieve a goal of MAG construction. This is based on a model presented in Royalty and Steen (2018)" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "GRASE" ; sc:url "http://adsteen.shinyapps.io/grase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382 ; sc:citation ; sc:description """From photo-geology to 3D geological models. An open source approach. GRASS GIS is a free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.""" ; sc:featureList edam:operation_3431 ; sc:name "GRASS" ; sc:url "http://grass.osgeo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6527554", "pubmed:31110304" ; sc:description "Interactive Web Platform for Re-analyzing Gene Expression Omnibus (GEO) RNA-seq Data." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GREIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://shiny.ilincs.org/grein" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC6416924", "pubmed:30866794" ; sc:description "Guide RNA Identifier for Balancer Chromosome Generation (GRIBCG) - software for selection of sgRNAs in the design of balancer chromosomes." ; sc:isAccessibleForFree true ; sc:name "GRIBCG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bmerritt1762/GRIBCG" ; biotools:primaryContact "B. Merritt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation ; sc:description "Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms | Abstract The gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore help identify novel mechanisms underlying disease, which can lead to new therapies. Reliable inference of GRNs is however still a major challenge in systems biology. To deduce regulatory interactions relevant to cancer, we applied a recent computational inference framework to data from perturbation experiments in squamous carcinoma cell line A431. GRNs were inferred using several methods, and the false discovery rate was controlled by the NestBoot framework. We developed a novel approach to assess the predictiveness of inferred GRNs against validation data, despite the lack of a gold standard" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "GRN" ; sc:url "https://dcolin.shinyapps.io/CancerGRN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3368 ; sc:citation , "pubmed:31065808" ; sc:description "GROMACS to LAMMPS (GRO2LAM) - converter for molecular dynamics software." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GRO2LAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hernanchavezthielemann/GRO2LAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_3068, edam:topic_3295 ; sc:citation , "pmcid:PMC5750854", "pubmed:31725863" ; sc:description """A comprehensive genetic resource of nicotine and smoking. Genetic resources of nicotine and smoking. Genetic Resources Of Nicotine and Smoking (GRONS) is a database devoted to provide a comprehensive and systematic collection of cross-platform genetic data on genes associated with the biological response to nicotine exposure and smoking related behaviors or diseases. By this database, we try to make such information easily accessible and interpretable for investigators in the smoking/nicotine addiction research community""" ; sc:featureList edam:operation_0283, edam:operation_0305, edam:operation_3196, edam:operation_3431 ; sc:name "GRONS" ; sc:url "http://bioinfo.tmu.edu.cn/GRONS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3172, edam:topic_3300, edam:topic_3697 ; sc:citation , "pubmed:31638380" ; sc:description """Strategy for Intercorrelation Identification between Metabolome and Microbiome. Accumulating evidence points to the strong and complicated associations between the metabolome and the microbiome, which play diverse roles in physiology and pathology. Various correlation analysis approaches were applied to identify microbe-metabolite associations. Given the strengths and weaknesses of the existing methods and considering the characteristics of different types of omics data, we designed a special strategy, called Generalized coRrelation analysis for Metabolome and Microbiome (GRaMM), for the intercorrelation discovery between the metabolome and microbiome.""" ; sc:featureList edam:operation_2940, edam:operation_3463, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "GRaMM" ; sc:url "https://github.com/chentianlu/GRaMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0625 ; sc:citation ; sc:description "Gene Set Annotation - an alternative to enrichment analysis for annotating gene sets." ; sc:featureList edam:operation_2942, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GSAn" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gsan.labri.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3410 ; sc:citation , "pubmed:31437915" ; sc:description "The Gender, Sex, and Sexual Orientation (GSSO) Ontology | GSSO is the Gender, Sex, and Sex Orientation ontology, including terms related to gender identity and expression, sexual and romantic identity and orientation, and sexual and reproductive behavior | Gender, Sex, and Sexual Orientation" ; sc:featureList edam:operation_3559 ; sc:license "Apache-2.0" ; sc:name "GSSO" ; sc:url "https://github.com/Superraptor/GSSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC6507172", "pubmed:31072324" ; sc:description "Package for network-weighted gene-set clustering and network visualization." ; sc:featureList edam:operation_2436, edam:operation_2492, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GScluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/unistbig/GScluster" ; biotools:primaryContact , "Seon-Young Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0623, edam:topic_3293 ; sc:citation , "pmcid:PMC6821227", "pubmed:31560374" ; sc:description "GTA_Hunter is a 'support-vector machine' (SVM) classifier that distinguishes gene transfer agent (GTA) genes from their viral homologs | The classifier was developed to detect GTA genes that are homologous to 11 of the genes that encode the GTA in Rhodobacter capsulatus (RcGTA) (see Kogay et al, 2019). However, the classifier can be trained to detect other RcGTA genes, other GTAs, or even other virus-like elements, as long as there is training data available and the two classes have distinct amino acid composition" ; sc:featureList edam:operation_3431, edam:operation_3501 ; sc:license "MIT" ; sc:name "GTA" ; sc:url "https://github.com/ecg-lab/GTA-Hunter-v1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6718126", "pubmed:31507629" ; sc:description "A User-Friendly Framework for Bacterial Comparative Genomics | Backend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | Frontend application for the GTACG project (Gene Tags Assessment by Comparative Genomics) | This project is the frontend part of the GTACG framework (Gene Tags Assessment by Comparative Genomics): a framework for comparative analysis of bacterial genomes | A proper execution of the GTACG pipeline requires at least genomic files (in fasta format) and coding sequences (CDS, faa, gbf, gb, gff) files. Additionally, you can define phenotypes groups. The following command lines can be used to download files with examples of these formats:" ; sc:featureList edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "GTACG" ; sc:url "https://github.com/caiorns/GTACG-backend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:30255462" ; sc:description "Annotation tool for providing image and text annotations to image-based datasets." ; sc:featureList edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "GTCreator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cvc.uab.es/CVC-Colon/index.php/gtcreator/" ; biotools:primaryContact "CVC-Colon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0637, edam:topic_3174 ; sc:citation , , , , "pmcid:PMC8728215", "pubmed:32341564", "pubmed:34155373", "pubmed:34520557" ; sc:description "Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy | Toolkit for establishing, updating, and validating GTDB species clusters" ; sc:featureList edam:operation_0544, edam:operation_3432, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "GTDB" ; sc:url "https://gtdb.ecogenomic.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3489 ; sc:citation , "pubmed:31730192" ; sc:description """a toolkit to classify genomes with the Genome Taxonomy Database. GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).""" ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_3182, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "GTDB-Tk" ; sc:url "https://github.com/ecogenomics/gtdbtk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194 ; sc:citation ; sc:description """Unblended Disjoint Tree Merging using GTM improves species tree estimation. Abstract Phylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods""" ; sc:featureList edam:operation_0325, edam:operation_0546, edam:operation_3478 ; sc:name "GTM" ; sc:url "https://github.com/vlasmirnov/GTM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1285 ; sc:encodingFormat edam:format_1996, edam:format_3285 ; sc:name "Gene map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170 ; sc:citation ; sc:description "Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GUESSmyLT" ; sc:softwareHelp ; sc:softwareVersion "v1.0" ; sc:url "https://github.com/NBISweden/GUESSmyLT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_3382 ; sc:citation ; sc:description "Multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles." ; sc:featureList edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GUV-AP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://github.com/AG-Roemer/GUV-AP" ; biotools:primaryContact "Winfried Römer", "Yves Mély" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3489, edam:topic_3520 ; sc:citation , "pubmed:31829415" ; sc:description """Expanding the capillary electrophoresis based glucose unit database of the GUcal app. GUcal 1.1c - Internal / bracketing standard approach with GlycoStore database""" ; sc:featureList edam:operation_3435 ; sc:name "GUcal" ; sc:url "https://www.gucal.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3315 ; sc:description "GW6 algorithm for multichannel EEG data" ; sc:isAccessibleForFree true ; sc:name "GW6 - Grand-average ERP algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63973-gw6-grand-average-erp-algorithm" ; biotools:primaryContact "marco.bilucaglia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc:description "A GPU accelerated framework for efficient permutation based genome-wide association studies | GPU accelerated GWAS framework based on TensorFlow | GWAS-Flow was written and published in the hope that you might find it useful. If you do and use it for your research please cite the paper published alongside the software, which is currently publicly accessible on the BiorXiv preprint server. https://www.biorxiv.org/content/10.1101/783100v1 doi: 10.1101/783100" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "GWAS-Flow" ; sc:url "https://github.com/Joyvalley/GWAS_Flow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3574 ; sc:citation , "pubmed:31612961" ; sc:description """a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. A database for human genetic variants identified by genome-wide association studies. Enter a study id, dbSNP id, MeSH/HPO phenotype term, keywords, author names, HGNC gene symbols, chromosomal regions or PUBMED identifier. The NHGRI-EBI GWAS Catalog: a curated collection of all published genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. GWAS CENTRAL - INDIA : A Genotype - Phenotype Association Database. GWAS Central - India (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. GWAS Central provides a complete Study metadata file for use in data citation research, tracking researcher contributions, data discovery projects, etc""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3436, edam:operation_3559, edam:operation_3791 ; sc:name "GWAS Central" ; sc:softwareHelp ; sc:url "https://www.gwascentral.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "Non-local prior based iterative SNP selection tool for genome-wide association studies." ; sc:featureList edam:operation_0484, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GWASinlps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://cran.r-project.org/package=GWASinlps" ; biotools:primaryContact "Nilotpal Sanyal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517, edam:topic_3572 ; sc:description "When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GWASinspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.4" ; sc:url "http://gwasinspector.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders | Grey-to-White matter Percent Contrast in Autism Spectrum Disorders | This repository contains the code used for the analyses described in our manuscript \"Increased contrast of the grey-white matter boundary in the motor, visual and auditory areas in Autism Spectrum Disorders\" (Preprint: https://doi.org10.1101/750117) | We used this code to analyse the grey-white contrast in Autism Spectrum Disorder using magnetic resonance imaging from ABIDE 1&2 datasets (http://fcon_1000.projects.nitrc.org/indi/abide/)" ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3659 ; sc:name "GWPC" ; sc:url "https://github.com/neuroanatomy/GWPC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3391 ; sc:description "GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses." ; sc:name "GalaxEast" ; sc:url "http://www.galaxeast.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091 ; sc:description "An online catalog that lists all the tools available on various Galaxy instances and thus allows through a simple web interface to quickly find on which instances a tool is usable." ; sc:name "GalaxyCat" ; sc:url "http://galaxycat.france-bioinformatique.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "A wide variety of tools from the Galaxy instance of Institut Pasteur, France." ; sc:name "Galaxy Pasteur" ; sc:url "https://galaxy.pasteur.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Tools provided by the Galaxy workbench." ; sc:isAccessibleForFree true ; sc:license "AFL-2.0" ; sc:name "Galaxy Tools" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Project" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation ; sc:description "We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a ‘visualise-filter-visualise’ paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data." ; sc:featureList edam:operation_0571, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "Galaxy scater" ; sc:softwareHelp ; sc:url "https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_0780, edam:topic_3673, edam:topic_3810 ; sc:citation , "pmcid:PMC4958008", "pubmed:27547538" ; sc:description "Tools for genotyping gall-causing phytopathogenic bacteria and identifying strains isolated from Agrobacterium or Rhodococcus-induced galls using MLSA and other methods." ; sc:featureList edam:operation_2421, edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Gall-ID" ; sc:url "http://gall-id.cgrb.oregonstate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0798 ; sc:citation ; sc:description "Automated annotation of amino acid biosynthesis | Abstract GapMind is a web-based tool for annotating amino acid biosynthesis in bacteria and archaea ( http: papers.genomics.lbl gov gaps ). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 seconds. To avoid error-prone “transitive” annotations, GapMind relies primarily on a database of experimentally-characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for “best hit” approaches. To improve GapMind’s coverage, we examined genetic data from 35 bacteria that grow in minimal media and we filled many gaps in amino acid biosynthesis pathways." ; sc:featureList edam:operation_0417, edam:operation_3715 ; sc:name "GapMind" ; sc:url "https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3398, edam:topic_3407 ; sc:citation ; sc:description "Efficient random sampling for constraint-based (COBRA) models." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Gapsplit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jensenlab/gapsplit" ; biotools:primaryContact "Paul A. Jensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6791524", "pubmed:31501545" ; sc:description "Supervised classification enables rapid annotation of cell atlases | Garnett - Automated cell type identification" ; sc:featureList edam:operation_2495, edam:operation_3233, edam:operation_3501 ; sc:name "Garnett" ; sc:url "https://cole-trapnell-lab.github.io/garnett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3572 ; sc:citation , "pubmed:31735856" ; sc:description """Development of Open-source Software and Gaze Data Repositories for Performance Evaluation of Eye Tracking Systems. Repository for GazeVisual performance evaluation software tools. The GazeVisual-Lib is a repository of software tools for practical evaluation of eye trackers and gaze data quality. All codes in this repository are released under GNU General Public License v3.0""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "GazeVisual-Lib" ; sc:url "http://github.com/anuradhakar49/GazeVisual-Lib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3322, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description """A consensus Gene-disease Event Extraction System based on frequency patterns and supervised learning. Abstract Motivation The genetic mechanisms involved in human diseases are fundamental in biomedical research. Several databases with curated associations between genes and diseases have emerged in the last decades. Although, due to the demanding and time consuming nature of manual curation of literature, they still lack large amounts of information. Current automatic approaches extract associations by considering each abstract or sentence independently. This approach could potentially lead to contradictions between individual cases. Therefore, there is a current need for automatic strategies that can provide a literature consensus of gene-disease associations, and are not prone to making contradictory predictions""" ; sc:featureList edam:operation_3196, edam:operation_3280 ; sc:name "GeDex" ; sc:url "https://bitbucket.org/laigen/gedex/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC6323745", "pubmed:30616521" ; sc:description "GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information." ; sc:featureList edam:operation_0277, edam:operation_1781 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GeNeCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://lce.biohpc.swmed.edu/geneck" ; biotools:primaryContact "Minzhe Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3298, edam:topic_3517 ; sc:citation ; sc:description "Genome-Phenome Explorer (GePhEx): A tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence." ; sc:featureList edam:operation_0484, edam:operation_2422, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GePhEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gephex.ega-archive.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GemSIM" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/gemsim/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1939 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0622 ; sc:citation ; sc:description "Program for gene presence-absence analysis for series of closely related bacterial genomes from annotated GFF files." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenAPI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MigleSur/GenAPI" ; biotools:primaryContact "Migle Gabrielaite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3344 ; sc:description "Read GenBank-formatted flat file into structure" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "GenBank Flat File Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48999-genbank-flat-file-reader" ; biotools:primaryContact "Turner Conrad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0637 ; sc:description "Utilities for manipulations and visualization tasks on GenBank taxonomic information." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GenBank taxonomy tools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/spond/gb_taxonomy_tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6357466", "pubmed:30704396" ; sc:description "Genome exploration open source tool for variants generated from high-throughput sequencing projects." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GenESysV" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/ubccr/genesysv" ; biotools:primaryContact "Center for Computational Research" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0623, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC6892992", "pubmed:31844835" ; sc:description """A web application and database for gene family-based classification and functional enrichment analysis. Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query.""" ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3672 ; sc:name "GenFam" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31844835" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC6894214", "pubmed:31653197" ; sc:description """a python module for the simple generation and manipulation of genome graphs. A repository for the GenGraph toolkit for the creation and manipulation of graph genomes""" ; sc:featureList edam:operation_0337, edam:operation_0492, edam:operation_0524, edam:operation_3182 ; sc:license "GPL-3.0" ; sc:name "GenGraph" ; sc:url "https://github.com/jambler24/GenGraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3489, edam:topic_3571 ; sc:citation ; sc:description """Genome Integrative Explorer System. Genome Integrative Explorer System (GenIE-Sys). Website : Documentation : Demo : Users. Welcome to GenIE-Sys’s documentation! — GenIE-Sys 0.1 documentation. The Genome Integrative Explorer System(GenIE-Sys) based on a flat files Content Management System which is a dedicative in-house system to facilitate external groups in setting up their own web resource for searching, visualizing, editing, sharing and reproducing their genomic and transcriptomic data while using project raw data(gff3,fasta,fatsq) as an input. This is the Development and the latest version of GenIE-Sys. Our main goal is to add admin interface where users can easily create database plus integrate different types of data, create new pages and menus, configure tools and changing website layout by using Themes. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3096 ; sc:license "BSD-3-Clause" ; sc:name "GenIE-Sys" ; sc:softwareHelp ; sc:url "https://geniesys.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC5787240", "pubmed:29374474" ; sc:description "Genomic Input Output (GenIO) identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner." ; sc:featureList edam:operation_3196, edam:operation_3229 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://bioinformatics.ibioba-mpsp-conicet.gov.ar/GenIO/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3512 ; sc:citation , "pmcid:PMC6442393", "pubmed:30862647" ; sc:description "Integrated resource for analyzing the evolution and function of primate-specific coding genes." ; sc:featureList edam:operation_0487, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GenTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gentree.ioz.ac.cn/index.php" ; biotools:primaryContact "ZhangLab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6360648", "pubmed:30712510" ; sc:description "Machine learning method that utilizes transcriptome-wide gene co-expression to generate a distributed representation of genes." ; sc:featureList edam:operation_0315, edam:operation_3439, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Gene2vec" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/jingcheng-du/Gene2vec" ; biotools:primaryContact "Jingcheng Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:31642496" ; sc:description """an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) provide effective methods for detecting DNMs and prioritizing candidate genes. However, it remains a challenge for scientists, clinicians, and biologists to conveniently access and analyse data regarding DNMs and candidate genes from scattered publications. To fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different degrees of statistical evidence, including 346 genes with false discovery rates <0.05. We then developed a database called Gene4Denovo (http: www.genemed.tech gene4denovo ), which allowed these genetic data to be conveniently catalogued, searched, browsed, and analysed""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3226, edam:operation_3461 ; sc:name "Gene4Denovo" ; sc:url "http://www.genemed.tech/gene4denovo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0203, edam:topic_0621, edam:topic_0625, edam:topic_2229 ; sc:citation , "pmcid:PMC6886503", "pubmed:31754022" ; sc:description """Identifying gene function and module connections by the integration of multispecies expression compendia. Integrative systems analysis identifying the associations between genes and biological process or modules. For analyzed results for a given gene or module/gene set, please visit https://systems-genetics.org/genebridge. Systems analysis toolkit containing Gene-Module Association Determination (G-MAD) and Module-Module Association Determination (M-MAD) to identify the associations between genes and biological process or modules, as well as associations between modules.""" ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "GeneBridge" ; sc:url "https://github.com/lihaone/GeneBridge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621 ; sc:description "Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm (the set should be large enough to permit self-training). A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models. A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher)." ; sc:featureList edam:operation_0310 ; sc:name "GeneMarkS-T" ; sc:url "http://topaz.gatech.edu/GeneMark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6498745", "pubmed:31105932" ; sc:description "Analysis of copy number variation using Illumina Infinium DNA methylation arrays." ; sc:featureList edam:operation_3219, edam:operation_3436, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GenePattern notebook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.genepattern-notebook.org/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6524327", "pubmed:31096927" ; sc:description "Score for estimating gene pathogenicity in individuals using next-generation sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GenePy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/UoS-HGIG/GenePy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0194 ; sc:citation ; sc:description "A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss | GeneRax is a parallel tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss" ; sc:featureList edam:operation_0544, edam:operation_0547, edam:operation_0552 ; sc:license "AGPL-3.0" ; sc:name "GeneRax" ; sc:url "https://github.com/BenoitMorel/GeneRax" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634 ; sc:citation , "pmcid:PMC6503437", "pubmed:31060502" ; sc:description "Network-based identification of disease genes in expression data." ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GeneSurrounder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/sahildshah1/gene-surrounder" ; biotools:primaryContact "Rosemary Braun", "Sahil Shah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc:description """Ordering gene-expression and functional events in single-cell experiments. Data-driven Network Biology Group. The goal of GeneSwitches is to discover the order of gene-expression and functional events during cell state transitions at a single-cell resolution. It works on any single-cell trajectory or pseudo-time ordering of cells to discover the genes that act as on/off switches between cell states and importantly the ordering at which these switches take place.""" ; sc:featureList edam:operation_2495, edam:operation_3659, edam:operation_3890 ; sc:name "GeneSwitches" ; sc:softwareHelp ; sc:url "https://geneswitches.ddnetbio.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325 ; sc:citation , "pmcid:PMC4643620", "pubmed:26209433" ; sc:description "Investigation of the background prevalence (rare, protein altering variants that could be classified as pathogenic) of exonic variation." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GeneVetter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genevetter.org/" ; biotools:primaryContact "Matthew Gordon Sampson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC7852222", "pubmed:33526072" ; sc:description "GeneWalk identifies relevant gene functions for a biological context using network representation learning | GeneWalk determines for individual genes the functions that are relevant in a particular biological context and experimental condition. GeneWalk quantifies the similarity between vector representations of a gene and annotated GO terms through representation learning with random walks on a condition-specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_2436 ; sc:license "BSD-2-Clause" ; sc:name "GeneWalk" ; sc:url "http://github.com/churchmanlab/genewalk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3676 ; sc:author "David Arenillas", "Zach Maurer" ; sc:citation , "pubmed:25703386" ; sc:description "Tool for clinicians to make connections to share genetic data by being matched using phenotype data. It aims to create a portal for clinicians to enter phenotypic case data for individuals who have had exome sequencing without a genetic diagnosis." ; sc:featureList edam:operation_3227, edam:operation_3229, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "GeneYenta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://geneyenta.com/accounts/home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC6602503", "pubmed:31127311" ; sc:description "Set of tools for assisting in highly precise genome editing and engineering." ; sc:featureList edam:operation_0420, edam:operation_3096, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Gene Sculpt Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genesculpt.org" ; biotools:primaryContact , "Jeffrey J. Essner", "Stephen C. Ekker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:encodingFormat edam:format_2330, edam:format_2350 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2848, edam:format_3617, edam:format_3620 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070, edam:topic_3344, edam:topic_3474, edam:topic_3948 ; sc:description """Platform based on Artificial Intelligence Neural Network. Suggest the most probable gene (protein) based on deep learning on million of scientific papers. It also link the input+output to many free research tools to understand what the neural network suggested and why.""" ; sc:featureList edam:operation_2436, edam:operation_3279, edam:operation_3625, edam:operation_3767, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "GeneRecommender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2 stable" ; sc:url "https://www.generecommender.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC6602493", "pubmed:31114885" ; sc:description "search engine for ranking genes from arbitrary text queries | Submit biomedical terms to receive ranked lists of relevant genes | Submit any search terms to Geneshot to receive prioritized genes that are most relevant to the search terms. Geneshot finds publications that mention both the search terms and genes. It then prioritizes these genes using various methods: 1) list of genes from publications; 2) predicted genes using gene-gene similarity matrices derived from a variety of resources ( ARCHS4 : Enrichr : Tagger : AutoRIF : GeneRIF ) | Examples: Wound healing : Hair loss : Trichostatin A : Glioblastoma : Diabetes" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Geneshot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://amp.pharm.mssm.edu/geneshot" ; biotools:primaryContact , "Alexander Lachmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6668410", "pubmed:31366961" ; sc:description "> LOW CONFIDENCE! | Uncovering missed indels by leveraging unmapped reads | Genesis-indel is a computational pipeline to explore the unmapped reads to identify novel mutations that are initially missed in the original alignment. The genes containing such mutations can be investigated to gain important biological insights" ; sc:featureList edam:operation_0452, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "Genesis-indel" ; sc:url "https://github.com/mshabbirhasan/Genesis-indel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3068, edam:topic_3168, edam:topic_3305 ; sc:citation , "pubmed:31670023" ; sc:description """Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel. A tool for genogeographic inference""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3435 ; sc:name "GenoGeographer" ; sc:url "http://genogeographer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0622, edam:topic_2815, edam:topic_3489 ; sc:citation , , "pmcid:PMC6902006", "pubmed:31820804" ; sc:contributor , ; sc:description """GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces are heterogeneous, not interoperable, and with limited capabilities. GenoSurf provides access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of attributes are semantically enriched by making use of the most suited available ontologies. Users provide as input the search terms, set the desired level of ontological enrichment, and obtain as output the identity of matching data files at the various sources. We integrated about 40 million metadata of several major valuable data sources, including four providers of clinical and experimental data (TCGA, ENCODE, 1000 Genomes, and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq).""" ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2422, edam:operation_3436 ; sc:name "GenoSurf" ; sc:softwareHelp , ; sc:url "http://gmql.eu/genosurf/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Database of genomic data related to marine species of biological interest. It allows analyses of reference genome annotations, organising the resources in an integrated way" ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Genoma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.szn.it/genoma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_0769 ; sc:citation , "pubmed:31733063" ; sc:description """integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Genome3D Annotating Genomes with Structures. Search Genome3D find structural annotations for your proteins. Tool to interact with the Genome3D API. Genome3D provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, THREADER, PHYRE. The tool genome3d-api aims to make communicating with the Genome3D API as convenient as possible. However, since the API has been defined using OpenAPI standards, you should be able to point any OpenAPI compatible client to the following specification:""" ; sc:featureList edam:operation_0303, edam:operation_2421, edam:operation_2422, edam:operation_3778 ; sc:license "GPL-3.0" ; sc:name "Genome3D" ; sc:softwareHelp ; sc:url "https://www.genome3d.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654 ; sc:citation ; sc:description "Graphical tool for modeling and analyzing 3D genome structure." ; sc:featureList edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "GenomeFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/jianlin-cheng/GenomeFlow" ; biotools:primaryContact "Jianlin Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_3489 ; sc:citation ; sc:description """Simple containerised setup of a custom Ensembl database and web server for any species. Forked from molluscdb/molluscdb-plugin. Example configurations to set up custom Ensembl sites using GenomeHubs. GenomeHubs example configuration and demo script. Generic Ensembl plugin for genomehubs sites. GenomeHubs is designed to make it easy to set up and host a core set of bioinformatics tools to help research communities share and access genomic datasets for non-model organisms. Sets up a GenomeHubs site hosting a mirror of the core database for the Glanville fritillary, Melitaea cinxia and imports the genome of the winter moth, Operophtera brumata, into a GenomeHubs site from FASTA and GFF.""" ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3208 ; sc:license "MIT" ; sc:name "GenomeHubs" ; sc:softwareHelp ; sc:url "http://GenomeHubs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description """A quality assessment tool for genome assemblies and gene structure annotations. GenomeQC generates descriptive summaries with intuitive graphics for genome assembly and structural annotations. It also benchmarks user supplied assemblies and annotations against the publicly available reference genomes of their choice. It is optimized for small and medium sized genomes (<2.5 Gb) and has pre-computed results for several maize genomes.""" ; sc:featureList edam:operation_0362, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "GenomeQC" ; sc:url "https://genomeqc.maizegdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description """A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome. About Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety Test new features.""" ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3432 ; sc:name "Genome Constellation" ; sc:url "https://bitbucket.org/berkeleylab/jgi-genomeconstellation/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3263 ; sc:citation , "pmcid:PMC6712716", "pubmed:31455387" ; sc:description "Using genetic distance from individuals to public data for genomic analysis without disclosing personal genomes | # 2019 Bioinformatics Methods / GenomicGPS | GenomicGPS is a software package for applying multilateration to genomic data" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:license "MIT" ; sc:name "Genomic GPS" ; sc:url "https://github.com/hanlab-SNU/GenomicGPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3337, edam:topic_3396, edam:topic_3423, edam:topic_3577, edam:topic_3676 ; sc:citation ; sc:description """Advancing clinical cohort selection with genomics analysis on a distributed platform. Highly performant data storage in C++ for importing, querying and transforming variant data with Java/Spark. Used in gatk4. Sparse Array Storage for Genomics. GenomicsDB, originally from Intel Health and Lifesciences, is built on top of a fork of htslib and a tile-based array storage system for importing, querying and transforming variant data. Open source project providing a collaboration to optimizing sparse array storage for genomics. Using high-level APIs provided in C++, Java*, and Spark*, users can both write and read variant records to and from GenomicsDB shared-nothing instances in parallel using multiple processes in a Single Process Multiple Data (SPMD) manner.""" ; sc:featureList edam:operation_0224, edam:operation_3227, edam:operation_3436 ; sc:name "GenomicsDB" ; sc:url "http://www.genomicsdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0780, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , , ; sc:description "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-plants" ; sc:url "https://www.genomicus.biologie.ens.fr/genomicus-plants" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , ; sc:description "Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-fungi" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-fungi/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , ; sc:description "Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-metazoa" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-metazoa/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , , , ; sc:description "Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-protists" ; sc:url "http://www.genomicus.biologie.ens.fr/genomicus-protists/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0797, edam:topic_3299, edam:topic_3943 ; sc:citation , ; sc:description "Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (https://www.aniseed.cnrs.fr) database." ; sc:featureList edam:operation_0224, edam:operation_0490, edam:operation_0567, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genomicus-tunicates" ; sc:url "https://www.genomicus.biologie.ens.fr/genomicus-tunicates" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3308 ; sc:description "A multigenome platform with information on genomes and gene annotations from different tomato cultivars. This platform includes genomes from Heinz 1706, Lucariello and Corbarino (tomato landaraces) with related genome browsers and transcriptomic data. It gives free access to the recently sequenced Italian tomato varieties and offers tools for their comparative analysis. (Tranchida-Lombardo et al., ‎2017; https://doi.org/10.1093/dnares/dsx045)" ; sc:featureList edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "Genotom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/genotom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_0099, edam:topic_0196, edam:topic_3489 ; sc:citation , "pubmed:31584078" ; sc:description """A database of genus characteristics of proteins and RNA. A database of genus characteristics. The Genus database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all protein and RNA structures deposited in the PDB. This database presents also various statistics and extensive information about biological function of analyzed biomolecules. Moreover, users can analyze their own structures""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3431 ; sc:name "Genus biomolecules" ; sc:url "http://genus.fuw.edu.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3489, edam:topic_3855 ; sc:citation ; sc:description """Open source tools to support Integrated Coastal Management and Maritime Spatial Planning. Geospatial tools to support Maritime Spatial Planning. GeoNode is a web-based application and platform for developing geospatial information systems (GIS) and for deploying spatial data infrastructures (SDI). Tools4MSP is a python-based Free and Open Source Software (FOSS) for geospatial analysis in support of Maritime Spatial Planning (MSP) and marine environmental management. Tools4MSP implements models for Cumulative Effects Assessment (CEA), Maritime Use Conflict (MUC) Analysis and Marine Ecosystem Services Threat (MES-Threat) analysis. The package can be used as stand-alone library or as integrated GeoNode Plugin providing additional functionalities to geospatial CMS and enhancing usability through a graphical user interface (GUI). Gallery Quick Start Try the Demo Blog. The webtools (GeoNode integration) analysis workflow follows a four step approach:""" ; sc:featureList edam:operation_3436, edam:operation_3760 ; sc:license "GPL-3.0" ; sc:name "GeoNode-Tools4MSP" ; sc:url "http://geonode.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780 ; sc:citation , "pubmed:31544935" ; sc:description "database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes | Gephebase compiles genotype-phenotype relationships, i.e. associations between a mutation and a phenotypic variation. Gephebase consolidates data from the scientific literature about the genes and the mutations responsible for phenotypic variation in Eukaryotes (mostly animals, yeasts and plants). We plan to include non Eukaryote species in the future. For now, genes responsible for human disease and for aberrant mutant phenotypes in laboratory model organisms are excluded and can be found in other databases ( OMIM , OMIA , FlyBase , etc.). QTL mapping studies that did not identify single genes are not included in Gephebase | If you use Gephebase for your publication, please cite: Martin, A., & Orgogozo, V. (2013). The loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution, 67(5), 1235- 1250" ; sc:featureList edam:operation_0282, edam:operation_3501 ; sc:name "Gephebase" ; sc:url "http://www.gephebase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3411 ; sc:citation , "pubmed:26065375" ; sc:description "German Obstetric Surveillance System (GerOSS) - project to improve the treatment of obstetric rare diseases and complications using a web based documentation and information platform." ; sc:featureList edam:operation_3283 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GerOSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geross.de/Default_en.aspx" ; biotools:primaryContact "Nicholas Lack", "Silvia Berlage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3071 ; sc:citation , , "pmcid:PMC4897896", "pmcid:PMC6511067", "pubmed:27267926", "pubmed:31077313" ; sc:description "The Gigwa application, which stands for “Genotype Investigator for Genome-Wide Analyses”, provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time. Gigwa provides the means to export filtered data into several popular formats and features connectivity not only with online genomic tools, but also with standalone software such as FlapJack or IGV. Additionnally, Gigwa-hosted datasets are interoperable via two standard REST APIs: GA4GH and BrAPI." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3196, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Gigwa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.3" ; sc:url "http://www.southgreen.fr/content/gigwa" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """A fast and memory-efficient tool for rare cell type identification. Rare cell identification tool for single cell datasets. GiniClust is a clustering method specifically designed for rare cell type detection.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3659 ; sc:name "GiniClust3" ; sc:url "https://github.com/rdong08/GiniClust3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6612808", "pubmed:31510661" ; sc:description "Fast and accurate interpretation of nonlinear gapped k-mer SVMs | Accompanying repository for GkmExplain paper | GkmExplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines | This repository accompanies Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer SVMs by Shrikumar*†, Prakash* and Kundaje† (*co-first authors †co-corresponding authors)." ; sc:featureList edam:operation_0238, edam:operation_3472, edam:operation_3501 ; sc:name "GkmExplain" ; sc:url "https://github.com/kundajelab/gkmexplain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3444 ; sc:citation ; sc:description "Tool for generating structural ensembles of partly disordered proteins from chemical shifts." ; sc:featureList edam:operation_0249, edam:operation_0320, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Glutton" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YeeHo/Glutton" ; biotools:primaryContact "Yi He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0203, edam:topic_3518 ; sc:citation , "pubmed:31841142" ; sc:description "Glycan Microarray Database and Analysis Toolset." ; sc:featureList edam:operation_2421, edam:operation_2426, edam:operation_2495 ; sc:name "GlyMDB" ; sc:url "http://www.glycanstructure.org/glymdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3520 ; sc:author "Dr. Ian Walsh" ; sc:citation ; sc:description "Software for automated interpretation of N -glycan profiles after exoglycosidase digestions." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GlycanAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://glycananalyzer.neb.com/" ; biotools:primaryContact "Dr. Christopher H. Taron", "Dr. Ian Walsh", "Prof. Pauline M. Rudd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0152, edam:topic_0154 ; sc:citation ; sc:description "Conversion tool for translating the complexities of glycans." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GlycanFormatConverter" ; sc:operatingSystem "Mac" ; sc:url "https://github.com/glycoinfo/GlycanFormatConverter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2815, edam:topic_3520 ; sc:citation , "pubmed:31384044" ; sc:description "a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | Glyco-DIA is a method for quantitative O-glycoproteomics with in silico-boosted glycopeptide libraries | The Glyco-DIA library consists of sublibraries obtained from human cell lines and human serum, and it currently covers 2,076 O-glycoproteins (11,452 unique glycopeptide sequences) and the five most common core1 O-glycan structures. Applying the Glyco-DIA library to human serum without enrichment for glycopeptides enabled us to identify and quantify 269 distinct glycopeptide sequences bearing up to 5 different core1 O-glycans from 159 glycoproteins in a singleshot analysis. The DIA method is expandable and widely applicable to different glycoproteomes, and it may represent a first step towards direct and comprehensive approach to glycoproteomics" ; sc:featureList edam:operation_0417, edam:operation_3501, edam:operation_3799 ; sc:name "Glyco-DIA" ; sc:url "https://github.com/CCGMS/Glyco-DIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0166, edam:topic_0176, edam:topic_3300 ; sc:citation , "pmcid:PMC6806574", "pubmed:31640540" ; sc:description """a Python framework for the rapid modeling of glycans. Framework for the rapid modeling glycans and glycoproteins. Glycosylator is a Python framework for the identification, modeling and modification of glycans in protein structure. It can be used directly in a Python script through its API or through its Graphical User Interface (GUI). The GUI provides a straightforward 2D rendering of a glycoprotein that allows for a quick visual inspection of the gylcosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific 3D glycans on a protein structure using a library of predefined templates. Glycosylator has been implemented in a generic way allowing the user to expand the library to incorporate other polymers""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_2476, edam:operation_3192 ; sc:name "Glycosylator" ; sc:url "https://github.com/tlemmin/glycosylator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3382, edam:topic_3697 ; sc:citation , "pmcid:PMC6377400", "pubmed:30597007" ; sc:description "Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur." ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GmT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://galaxyproject.org/use/gmt/" ; biotools:primaryContact "Saskia Hiltemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170 ; sc:description "Gmove is a genome annotation tool. This combiner takes as input mapping of RNA-seq or protein or ab initio data." ; sc:featureList edam:operation_0362, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:name "Gmove" ; sc:url "http://www.genoscope.cns.fr/gmove" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2200 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2200 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_1915 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_3000 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1240 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3508 ; sc:name "PCR primers" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_3508 ; sc:name "Protocol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0601, edam:topic_0632, edam:topic_2533, edam:topic_3361, edam:topic_3895 ; sc:author ; sc:citation , , "pmcid:PMC6662682", "pubmed:31358887" ; sc:contributor ; sc:description "The Golden Gate cloning technique has been proven to be a highly efficient toolbox for a variety of cloning setups. Based on its modular concept it is particularly suitable for the use in multiple-site mutagenesis approaches. In this technical note we developed a protocol termed Golden Mutagenesis for the rapid, easy, reliable and cheap formation of mutagenesis libraries. One to five positions could be altered in parallel or simultaneously within two days. To facilitate the implementation of this technique, this R-library has been developed for the automated primer design and the graphical evaluation of sequencing results to determine the quality of the library." ; sc:featureList edam:operation_0308, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "GoldenMutagenesis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.1" ; sc:url "https://msbi.ipb-halle.de/GoldenMutagenesisWeb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269 ; sc:citation ; sc:description "a Julia package for approximate Bayesian computation with Gaussian process emulation | GpABC provides algorithms for likelihood - free parameter inference and model selection using Approximate Bayesian Computation (ABC). Two sets of algorithms are available:" ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "GpABC" ; sc:url "https://github.com/tanhevg/GpABC.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3305, edam:topic_3673 ; sc:author "Sergio Arredondo-Alonso" ; sc:citation , , , , "pmcid:PMC7320608", "pmcid:PMC7816424", "pubmed:32271863", "pubmed:33472670" ; sc:description """A comprehensive tool for plasmid analysis using short-read graphs. gplas: Binning plasmid-predicted contigs using short-read graphs""" ; sc:featureList edam:operation_0524, edam:operation_0525 ; sc:license "GPL-3.0" ; sc:name "Gplas" ; sc:softwareHelp ; sc:softwareVersion "V0.6.0", "V0.7.0" ; sc:url "https://gitlab.com/sirarredondo/gplas.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated database for grapevine data" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "GrapeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://urgi.versailles.inra.fr/GrapeMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc:description """Rapid and Versatile Sequence-to-Graph Alignment. Seed-and-extend program for aligning long error-prone reads to genome graphs. For a description of the bitvector alignment extension algorithm, see https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz162/5372677.""" ; sc:featureList edam:operation_0524, edam:operation_3182, edam:operation_3196, edam:operation_3198, edam:operation_3211 ; sc:license "MIT" ; sc:name "GraphAligner" ; sc:url "https://anaconda.org/bioconda/graphaligner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6897289", "pubmed:31808801" ; sc:description """Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. A pipeline for structural clustering of RNA secondary structures. GraphClust2 is a workflow for scalable clustering of RNAs based on sequence and secondary structures feature. GraphClust2 is implemented within the Galaxy framework and consists a set of integrated Galaxy tools and flavors of the linear-time clustering workflow.""" ; sc:featureList edam:operation_0278, edam:operation_0302, edam:operation_0502, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "GraphClust2" ; sc:url "https://graphclust.usegalaxy.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6396939", "pubmed:30779737" ; sc:description "Tool for calling transcription factor peaks on graph-based reference genomes using ChIP-seq data." ; sc:featureList edam:operation_0487, edam:operation_3215, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Graph Peak Caller" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/uio-bmi/graph_peak_caller" ; biotools:primaryContact "Biomedical Informatics Research Group (BMI)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1 | GraphMap2 - A highly sensitive and accurate mapper for long, error-prone reads | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and | GSNAP: Genomic Short-read Nucleotide Alignment Program | Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget" ; sc:featureList edam:operation_0526, edam:operation_3192, edam:operation_3198 ; sc:license "MIT" ; sc:name "Graphmap2" ; sc:url "https://github.com/lbcb-sci/graphmap2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "Publicly available novel algorithm and software for discovering and genotyping sequence variants." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Graphtyper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DecodeGenetics/graphtyper" ; biotools:primaryContact "Hannes Pétur Eggertsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3318, edam:topic_3334, edam:topic_3375 ; sc:citation , "pmcid:PMC6904991", "pubmed:31822261" ; sc:description """A computational approach based on the colored Petri net formalism for studying multiple sclerosis. BACKGROUND:Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients. Relapsing Remitting Multiple Sclerosis (RRMS) is one of the most common form of MS in adults and is characterized by a series of neurologic symptoms, followed by periods of remission. Recently, many treatments were proposed and studied to contrast the RRMS progression. Among these drugs, daclizumab (commercial name Zinbryta), an antibody tailored against the Interleukin-2 receptor of T cells, exhibited promising results, but its efficacy was accompanied by an increased frequency of serious adverse events.""" ; sc:featureList edam:operation_3359 ; sc:name "GreatSPN" ; sc:url "https://github.com/greatspn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0632 ; sc:citation ; sc:description "Web-based tool that rapidly designs custom CRISPR screens targeting sets of genes defined by the user." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Green listed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://greenlisted.cmm.ki.se/" ; biotools:primaryContact "Fredrik Wermeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3382 ; sc:citation , "pmcid:PMC6764701", "pubmed:31527870" ; sc:description "Predicting gene regulatory interactions based on spatial gene expression data and deep learning | Gene regulatory interaction prediction through Deep Learning | Gene regulatory interaction prediction through Deep Learning By Qingwei Fang, 2018" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "GripDL" ; sc:url "https://github.com/2010511951/GripDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3390, edam:topic_3474 ; sc:citation , "pmcid:PMC6713322", "pubmed:31461459" ; sc:description "A model for studying living resources through digestive efficiency | The neural computational model GrowthEstimate is introduced with focusing on new perspectives for the practical estimation of weight specific growth rate (SGR, % day-1). It is developed using recurrent neural networks of reservoir computing type, for estimating SGR based on the known data of three key biological factors relating to growth" ; sc:name "GrowthEstimate" ; sc:url "https://github.com/RungruangsakTorrissenManoonpong/GrowthEstimate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0218, edam:topic_0602, edam:topic_3518 ; sc:citation ; sc:description """Comprehensive biological interpretation of gene signatures using semantic distributed representation. GsVec (Gene signature Vector) is an analysis method that supports the biological interpretation of Gene signature obtained by gene expression analysis of Bioinformatics. The association between the gene signature to be interpreted and the gene signature of the Pathway / Gene Ontology data base is performed by natural language processing""" ; sc:featureList edam:operation_0277, edam:operation_2436, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "GsVec" ; sc:url "https://github.com/yuumio/GsVec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3343, edam:topic_3369 ; sc:citation , "pmcid:PMC6534830", "pubmed:31127411" ; sc:description "Program for preparing small-molecule libraries for structure-based virtual screening." ; sc:featureList edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Gypsum-DL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://durrantlab.com/gypsum-dl/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3053 ; sc:citation ; sc:description "The ML Glossary developed by H3ABioNet The machine learning glossary for Bioinformaticians | Ready to get started? Build your own site from scratch or generate one for your project | Code repository for the RefGraph project" ; sc:featureList edam:operation_3431, edam:operation_3557, edam:operation_3891 ; sc:name "H3ABioNet" ; sc:url "http://github.io/H3ABionet-SOPs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC6893198", "pubmed:31636085" ; sc:description """Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments. calculate haplotype-derived allele frequencies for pool-seq samples. HAF-pipe is a bash- and R-based pipeline to calculate haplotype-inferred allele frequencies from pool-seq data and founder SNP profiles. To simulate recombination and pooled sequencing data from a panel of sequenced founders, see the scripts HAFpipe-sim.run_forqs.sh and HAFpipe-sim.simulate_poolseq.sh in the simulations folder""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "HAF-pipe" ; sc:url "https://github.com/petrov-lab/HAFpipe-line" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:30539546" ; sc:description "HAMR (High-throughput Annotation of Modified Ribonucleotides) - web application that allows you to detect and classify modified nucleotides in RNA-seq data." ; sc:featureList edam:operation_0484, edam:operation_3185, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HAMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2" ; sc:url "http://tesla.pcbi.upenn.edu/hamr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation ; sc:description "Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma using Large-scale Transcriptomics Data | A webserver to predict Hepatocellular carcinoma (HCC) | Pipeline Differential Expression Analysis | HCCpred is a web-bench for the prediction of tumorous and non-tumorous Hepatocellular Carcinoma (HCC) patients. Our major prediction modules based on the robust biomarkers such as 3-Gene HCC Biomarker, 4-Gene HCC Biomarker, 5-Gene HCC Biomarker. These HCC biomarkers identified using gene expression profiles of a total of 3,961 samples include 2,306 HCC and 1,655 non-tumorous samples. The datasets derived from various profiling platforms such as Affymatrix, Illumina, High-througput and Agilent. The user can also analyse the expression pattern of any of 26 \"core genes of HCC\" in cancerous vs normal conditions" ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3501 ; sc:name "HCCPred" ; sc:url "http://webs.iiitd.edu.in/raghava/hccpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:31403237" ; sc:description "Automated brain extraction of multisequence MRI using artificial neural networks | Brain extraction is a critical preprocessing step in the analysis of neuroimaging studies conducted with magnetic resonance imaging (MRI) and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy brains and thus frequently fail in the presence of pathologically altered brain or when applied to heterogeneous MRI datasets. Here we introduce a new, rigorously validated algorithm (termed HD-BET) relying on artificial neural networks that aim to overcome these limitations" ; sc:name "HD-BET" ; sc:url "https://github.com/NeuroAI-HD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3577 ; sc:citation , "pubmed:31368480" ; sc:description "Gaussian Mixture Copulas for High-Dimensional Clustering and Dependency-based Subtyping | MOTIVATION:The identification of sub-populations of patients with similar characteristics, called patient subtyping, is important for realizing the goals of Precision Medicine. Accurate subtyping is crucial for tailoring therapeutic strategies that can potentially lead to reduced mortality and morbidity. Model-based clustering, such as Gaussian mixture models, provides a principled and interpretable methodology that is widely used to identify subtypes. However, they impose identical marginal distributions on each variable; such assumptions restrict their modeling flexibility and deteriorates clustering performance. RESULTS:In this paper, we use the statistical framework of copulas to decouple the modeling of marginals from the dependencies between them. Current copula-based methods cannot scale to high dimensions due to challenges in parameter inference" ; sc:featureList edam:operation_3891 ; sc:name "HD-GMCM" ; sc:url "https://bitbucket.org/cdal/hdgmcm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats | Data package containing high-dimensional cytometry data sets in SummarizedExperiment and flowSet formats | R code to reproduce example in Figure 1 in our HDCytoData paper | The HDCytoData package is an extensible resource containing a set of publicly available high-dimensional flow cytometry and mass cytometry (CyTOF) benchmark datasets, which have been formatted into SummarizedExperiment and flowSet Bioconductor object formats. The data objects are hosted on Bioconductor's ExperimentHub platform" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3891 ; sc:license "MIT" ; sc:name "HDCytoData" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/HDCytoData" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3295 ; sc:citation , "pubmed:31504171" ; sc:description "New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform | Essential genes are those whose loss of function compromises organism viability or results in profound loss of fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic and regulatory characteristics of human essential genes. First, we found that essential genes act as 'hubs' in protein-protein interaction networks, chromatin structure and epigenetic modification. Second, essential genes represent conserved biological processes across species, although gene essentiality changes differently among species. Third, essential genes are important for cell development due to their discriminate transcription activity in embryo development and oncogenesis" ; sc:featureList edam:operation_0277, edam:operation_2495, edam:operation_3439 ; sc:name "HEGIAP" ; sc:url "http://sysomics.com/HEGIAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384 ; sc:citation , "pubmed:29993993" ; sc:description "Aims to bring together geographically dispersed medical personnel in order to share a common workspace where they can collaborate over medical images in real-time." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HERMES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hermes.grnet.gr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0218, edam:topic_0621 ; sc:citation , ; sc:description """Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures. Hypermap Registry, remote map services made easy for your SDI. Hypermap Registry is a platform that manages OWS, Esri REST, and other types of map service harvesting, and orchestration and maintains uptime statistics for services and layers. Check Hypermap Registry documentation.""" ; sc:featureList edam:operation_2421, edam:operation_2429, edam:operation_3760, edam:operation_3891 ; sc:license "MIT" ; sc:name "HHypermap" ; sc:url "https://github.com/cga-harvard/HHypermap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3305 ; sc:citation , "pubmed:31766582" ; sc:description """A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. The Hearing Impairment Ontology (HIO) is a collaboratively developed resource by a group of experts in different aspects of hearing impairment (HI) to provide a common controlled HI terminology and concepts. The HIO will allow researchers and clinicians alike to readily access standardised HI-related knowledge in a single location and promote collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic and phenotypic information. It is worth noting, this ontology provides an illustration of the adaptability of the Sickle Cell Disease Ontology framework for use in developing a disease-specific ontology.""" ; sc:featureList edam:operation_2422, edam:operation_3559 ; sc:license "GPL-3.0" ; sc:name "HIO" ; sc:url "https://bioportal.bioontology.org/ontologies/HIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3382 ; sc:citation ; sc:description """Inferring Chromosome Radial Organization from Hi-C Data. The included Python scripts (mat2net.py, and predictCTpos.py) contain an implemention of the HIRAC computational technique described in the following manuscript.""" ; sc:featureList edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "HIRAC" ; sc:url "https://github.com/priyojitDas/HIRAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_0804, edam:topic_3324, edam:topic_3400 ; sc:citation ; sc:description """Detection of novel HIV-1 drug resistance mutations by support vector analysis of deep sequence data and experimental validation. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV/SIV vaccine trials. Each of these topics are available through a dedicated database, extensively annotated and with many specialized search and analysis tools. The HIV databases are supported by the NIH and DOE and maintained at the Los Alamos National Laboratory. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes.""" ; sc:featureList edam:operation_2421, edam:operation_3202, edam:operation_3557 ; sc:name "HIV-1" ; sc:url "http://www.hiv.lanl.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3068, edam:topic_3315, edam:topic_3379 ; sc:citation , "pubmed:31513553" ; sc:description "Online, Educational, Clinical Decision Support Tool to Guide Patient-Centered ARV Regimen Selection | HIV-ASSIST (HIV Antiretroviral Selection Support and Interactive Search Tool) is a web-based platform designed at Johns Hopkins University to assist and educate clinicians in personalizing ART regimens for their patients | HIV-ASSIST is an online, interactive, educational tool to inform clinical decision-making for ARV selection" ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "HIV-ASSIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.hivassist.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0804, edam:topic_3168, edam:topic_3379 ; sc:citation ; sc:description """A tool for detecting linked HIV-1 drug resistance mutations in next generation sequencing data. A script detect and calculate Linked HIV drug resistant mutations on single HIV genomes. HIV-DRLink_github.pl is a script that detects and calculates Linked HIV drug resistant mutations on single HIV genomes. The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV SIV vaccine trials. The HIV databases contain comprehensive data on HIV genetic sequences and immunological epitopes""" ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_3202, edam:operation_3482 ; sc:name "HIV-DRLink" ; sc:url "https://hivdb.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC6849208", "pubmed:31718603" ; sc:description "Optimal allocation of HIV resources among geographical regions." ; sc:featureList edam:operation_2426 ; sc:name "HIV-related" ; sc:url "http://hiv.ocds.co" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3474 ; sc:citation , "pubmed:31146118" ; sc:description "Web server for predicting HIV-1 CRF01_AE coreceptor usage." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HIVCoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://codes.bio/hivcor/" ; biotools:primaryContact "Watshara Shoombuatong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885 ; sc:citation , "pubmed:31518964" ; sc:description "Massively parallel sequencing solutions for two common forensically used platforms | HIrisPlex-S Eye, Hair and Skin Colour DNA Phenotyping Webtool | 8px 9px 10px 11px 12px 13px 14px 15px 16px 17px 18px | With the advancement of DNA phenotyping as a tool in Forensic and Anthropological usage, we now provide an easy to use interactive website to predict eye, hair and skin colour from DNA using the IrisPlex, HIrisPlex and HIrisPlex-S systems" ; sc:featureList edam:operation_3196, edam:operation_3894 ; sc:name "HIrisPlex-S" ; sc:url "https://hirisplex.erasmusmc.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation , "pmcid:PMC6884818", "pubmed:31783725" ; sc:description """Human kinase pocket database for drug design. BACKGROUND:The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot be directly used in the kinase drug study. Therefore, a comprehensive database of human kinase protein pockets is urgently needed to be developed. RESULTS:Here, we have developed HKPocket, a comprehensive Human Kinase Pocket database. This database provides sequence, structure, hydrophilic-hydrophobic, critical interactions, and druggability information including 1717 pockets from 255 kinases. We further divided these pockets into 91 pocket clusters using structural and position features in each kinase group. The pocket structural information would be useful for preliminary drug screening""" ; sc:featureList edam:operation_0321, edam:operation_0337, edam:operation_2421 ; sc:name "HKPocket" ; sc:url "http://zhaoserver.com.cn/HKPocket/HKPocket.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31502156" ; sc:description "Using RNA Sequencing to Characterize the Tumor Microenvironment | Using k-mers to call HLA alleles in RNA sequencing data | HLAProfiler uses the k-mer content of next generation sequencing reads to call HLA types in a sample. Based on the k-mer content each each read pair is assigned to an HLA gene and the aggregate k-mer profile for the gene is compared to reference k-mer profiles to determin the HLA type. Currently HLAProfiler only supports paired-end RNA-seq data" ; sc:featureList edam:operation_2495, edam:operation_3630, edam:operation_3800 ; sc:name "HLA" ; sc:url "https://github.com/ExpressionAnalysis/HLAProfiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3421 ; sc:citation ; sc:description "The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues | The HLA Ligand Atlas is a comprehensive, tissue and HLA allele specific collection of HLA ligands, generated from more than 1,000 MS experiments | This website uses cookies to ensure you get the best experience on our website. Learn more | Warning The HLA Ligand Atlas is currently in a beta test phase . Please notice that the data and interface design might undergo frequent changes. You are welcome to contact us at" ; sc:featureList edam:operation_3891, edam:operation_3893 ; sc:name "HLA Ligand Atlas" ; sc:url "http://www.hla-ligand-atlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3474 ; sc:citation , "pubmed:31722090" ; sc:description """A machine learning-based model to identify the hidden labels of m6A candidates. HLMethy: Machine learning-based model to identify the hidden labels of candidate m6A modifications""" ; sc:featureList edam:operation_3222, edam:operation_3435 ; sc:name "HLMethy" ; sc:url "https://github.com/liuze-nwafu/HLMethy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:description "Older version of the HMMER3 program (https://bio.tools/hmmer3) used for searching sequence databases for sequence homologs, and for making sequence alignments." ; sc:featureList edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "HMMER2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.1 - 2.4i" ; sc:url "http://hmmer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0804, edam:topic_3697 ; sc:citation , "pmcid:PMC6650278", "pubmed:31142855" ; sc:description "Collection of workflows that handle processing several different data types assocaited with the IBDMDB (Inflammatory Bowel Disease Multi’omics Database) project." ; sc:featureList edam:operation_3192, edam:operation_3629, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HMP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/biobakery/hmp2_workflows" ; biotools:primaryContact "Curtis Huttenhower", "Ramnik J. Xavier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2275 ; sc:citation , "pmcid:PMC6602492", "pubmed:31114906" ; sc:description "Nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures." ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HNADOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/hnadock/" ; biotools:primaryContact "Lab of Bioinformatics and Molecular Modeling", "Sheng-You Huang", "Yi Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2640, edam:topic_3406 ; sc:citation , "pmcid:PMC6527845", "pubmed:31139565" ; sc:description "Integrated Gene and Drug Database for Head and Neck Cancer." ; sc:featureList edam:operation_0306, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HNCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hncdb.cancerbio.info" ; biotools:primaryContact "Ankui Yang", "Xiaoqing Pei", "Zhixiang Zuo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3306 ; sc:citation ; sc:description "A new software tool for interpreting the cellular and network origin of human MEG/EEG data | The Human Neocortical Neurosolver (HNN) is a software tool that gives researchers/clinicians the ability to develop/test hypotheses on circuit mechanisms underlying EEG/MEG data | Click here to join our Google Group | Human Neocortical Neurosolver (HNN) is a user-friendly software tool that provides a novel solution to this challenge | Electro- and magneto-encephalography (EEG MEG) are among the most powerful technologies to non-invasively record human brain activity with millisecond resolution" ; sc:featureList edam:operation_3891 ; sc:name "HNN" ; sc:url "https://hnn.brown.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6521357", "pubmed:31096906" ; sc:description "HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification." ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "HOME" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ListerLab/HOME" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC6815001", "pubmed:31653226" ; sc:description """A quantitative score reveals pervasive horizontal pleiotropy in human genetic variation is driven by extreme polygenicity of human traits and diseases. Allows to compute the HOrizontal Pleiotropy Score (HOPS) from summary statistics. HOPS (HOrizontal Pleiotropy Score). The HOPS package allows to compute the horizontal pleiotropy score (HOrizontal Pleiotropy Score) from summary statistics. The package includes a shiny visualization tool to visualize and download the full set of HOPS results computed using UK Biobank summary statistics""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3791, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "HOPS" ; sc:url "https://github.com/rondolab/HOPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3674 ; sc:citation , "pmcid:PMC6582337", "pubmed:31114922" ; sc:description "Examining the basis of high-occupancy target regions." ; sc:featureList edam:operation_0417, edam:operation_0445, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BIMSBbioinfo/HOT-or-not-examining-the-basis-of-high-occupancy-target-regions" ; biotools:primaryContact , "Verdan Franske" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3308, edam:topic_3382 ; sc:citation , "pmcid:PMC6734269", "pubmed:31500569" ; sc:description "An R package that facilitates the retrieval and analysis of the Human Protein Atlas data | To access this site please go to: http://alexdussaq.info/jsHPAanalyze | A Bioconductor package to retrieve and analyze data from the Human Protein Atlas | Results: HPAanalyze is an R package for retreiving and performing exploratory data analysis from HPA. It provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as download all staining images of interest. The package is free, open source, and available via Github | Background: The Human Protein Atlas program aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics" ; sc:featureList edam:operation_2422, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "HPAanalyze" ; sc:url "https://github.com/adussaq/jsHPAanalyze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3520 ; sc:citation , "pubmed:31729669" ; sc:description """Collision Cross Section Calculations Using HPCCS. The High Performance Collision Cross Section (HPCCS) is a new software for fast and accurate calculation of CCS for molecular ions. Based on the Trajectory Method (TM), HPCCS was parallelized and optimized to be an user-friendly program. High Performance Collision Cross Section Calculation – HPCCS""" ; sc:featureList edam:operation_0302, edam:operation_2476, edam:operation_3359 ; sc:name "HPCCS" ; sc:url "https://github.com/cepid-cces/hpccs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0203, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc:description """Prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences. Mapping between HPO and GO terms. If you find HPO2GO useful, please consider citing this publication:. Mapping between Human Phenotype Ontology (HPO) and Gene Ontology (GO) terms for the prediction of gene/protein - function - phenotype - disease associations. In this study, a novel approach is proposed for the identification of relationships between biomedical entities by automatically mapping phenotypic abnormality defining HPO terms with biomolecular function defining GO terms, where each association indicates the occurrence of the abnormality due to the loss of the biomolecular function expressed by the corresponding GO term""" ; sc:featureList edam:operation_1777, edam:operation_2429, edam:operation_3280 ; sc:license "GPL-3.0" ; sc:name "HPO2GO" ; sc:url "https://github.com/cansyl/HPO2GO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_2830, edam:topic_3534 ; sc:citation , "pmcid:PMC6872852", "pubmed:31768230" ; sc:description """Discovery of novel helix binding sites at protein-protein interfaces. Helix Positioner a program for locating helix binding sites at protien-protein interfaces.""" ; sc:featureList edam:operation_2464, edam:operation_2476, edam:operation_2492 ; sc:name "Helix Positioner" ; sc:url "https://github.com/proteincraft/HPer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0121, edam:topic_0601, edam:topic_3320 ; sc:citation , "pmcid:PMC8728143", "pubmed:34986596" ; sc:description "The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas" ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Human Proteoform Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://human-proteoform-atlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31758464" ; sc:description """Image-Based Quantitation of Host Cell-Toxoplasma gondii Interplay Using HRMAn. Host Response to Microbe Analysis. HRMAn enables you to automatically analyse parameters of host-pathogen interaction derived from immunofluorescent experiments""" ; sc:featureList edam:operation_3431, edam:operation_3443, edam:operation_3799 ; sc:name "HRMAn" ; sc:url "https://hrman.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC6612810", "pubmed:31510671" ; sc:description "Model-free biomarker detection for ultra-high dimensional data | Versatile Nonlinear Feature Selection Algorithm for High-dimensional Data | Supervised, nonlinear feature selection method for high-dimensional datasets | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a black box (nonlinear) feature selection method considering the nonlinear input and output relationship. HSIC Lasso can be regarded as a convex variant of widely used minimum redundancy maximum relevance (mRMR) feature selection algorithm | pyHSICLasso is a package of the Hilbert Schmidt Independence Criterion Lasso (HSIC Lasso), which is a nonlinear feature selection method considering the nonlinear input and output relationship" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:license "MIT" ; sc:name "HSIC Lasso" ; sc:url "https://github.com/riken-aip/pyHSICLasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts. Code for our work developing and characterizing the HSMRF priors for birth-death processes. This repository contains code for analyses from "Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts" (Magee et al. 2019). In the directory 1_simulation_study is code for simulating a number of trees under a time-dependent birth-death process, inferring diversification rates under the HSMRF-based and GMRF-based models, and processing those results. In the directory 2_empirical_analyses is code for the empirical analyses presented in the manuscript. Both directories contain more extensive readme files.""" ; sc:featureList edam:operation_0324, edam:operation_2426, edam:operation_3658 ; sc:name "HSMRF" ; sc:url "http://github.com/afmagee/hsmrfbdp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6886170", "pubmed:31787073" ; sc:description """A computational method to perform the integrated analysis of multiple heterogeneous time-series data. This program was designed for integrating analysis of multiple heterogeneous time-series gene expression data to identify response genes.""" ; sc:featureList edam:operation_0277, edam:operation_2495, edam:operation_3223 ; sc:name "HTRgene" ; sc:url "http://biohealth.snu.ac.kr/software/HTRgene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6420756", "pubmed:30878035" ; sc:description "Histosketching Using Little Kmers (HULK) - tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis." ; sc:featureList edam:operation_3435, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HULK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/will-rowe/hulk" ; biotools:primaryContact "Will Rowe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC6670167", "pubmed:31366358" ; sc:description "A pan-genome analysis pipeline for human genomes | Human pan-genome analysis pipeline | HUman PAN-genome analysis toolkit | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. It encourages us to build the pan-genome of human population. Previously, our team developed a \"map-to-pan\" strategy, EUPAN, specific for eukaryotic pan-genome analysis. However, due to the large genome size of individual human genome, EUPAN is not suit for pan-genome analysis involving in hundreds of individual genomes. Here, we present an improved tool, HUPAN (HUman Pan-genome ANalysis), for human pan-genome analysis | The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions | We propose HUPAN strategy primarily in the 185 deep sequencing and 90 assembled Han Chinese genomes" ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:name "HUPAN" ; sc:url "http://cgm.sjtu.edu.cn/hupan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3810 ; sc:citation , "pubmed:31415224" ; sc:description "R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean | Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity | Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer, Schachtel's (1999) Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis | The goal of hagis is to provide analysis tools for plant pathogens with gene-for-gene interactions in the R programming language that the original Habgood-Gilmour Spreadsheet, HaGiS, (Herrmann, Löwer and Schachtel) provided" ; sc:featureList edam:operation_0337, edam:operation_3461 ; sc:license "MIT" ; sc:name "HaGiS" ; sc:url "https://openplantpathology.github.io/hagis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3372 ; sc:citation , "pmcid:PMC6793853", "pubmed:31613890" ; sc:description """A modular pipeline for high-throughput sequencing data analysis. High-throughput sequencing pipeline software. HaTSPiL is a a Python pipeline for High-Throughput Sequencing analysis. It has been designed to be used inside our laboratory, the Salvatore Oliviero lab within the HuGef institute, TO (IT). Whoever find it useful or a good starting point to develop his own pipeline is encouraged to use and hack the code""" ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3359, edam:operation_3454 ; sc:license "MIT" ; sc:name "HaTSPiL" ; sc:url "https://github.com/dodomorandi/hatspil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description "Haloarchaeal genomes database." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Haloarchaeal Genomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://halo.umbc.edu/" ; biotools:primaryContact "Shiladitya DasSarma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6444579", "pubmed:30940094" ; sc:description "R package for power and sample size calculations in genetic association analyses of family triads and unrelated controls." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Haplin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "7.1.0" ; sc:url "https://cran.r-project.org/package=Haplin" ; biotools:primaryContact "Hakon K. Gjessing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885 ; sc:citation , "pmcid:PMC3245002", "pubmed:22064851" ; sc:description "Association between DIO2 polymorphism and the risk of Kashin-Beck disease in the Tibetan population | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:name "HaploReg" ; sc:url "https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0769 ; sc:citation , "pubmed:31834373" ; sc:description """a variant-calling pipeline for phased genomes. This is the Haplotypo repository. This repository contains the Haplotypo pipeline. HaploTypo is a pipeline suited to map variants into haplotypes in genetic variation analyses. After mapping and variant calling on a phased reference genome, HaploTypo infers the haplotype correspondence for each heterozygous variant. It also generates two independent FASTA files for each reconstructed haplotype""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3454 ; sc:name "HaploTypo" ; sc:url "https://github.com/gabaldonlab/haplotypo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3305 ; sc:citation ; sc:description "Tool for visualizing haplotype diversity, based on a cluster-based model for haplotype variation" ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Haploscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.4.1" ; sc:url "http://haploscope.scheetlabsoftware.org/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063 ; sc:author "Francesca Cordero", "Marco Becc" ; sc:citation "pubmed:29169317" ; sc:description "it is an easy-to-use and reliable bioinformatics tool that provides B-cells clonality assessment and MRD monitoring over time analyzing data from Next-Generation Sequencing (NGS) technique. The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HashClone" ; sc:operatingSystem "Linux" ; sc:softwareVersion "version 1.2" ; sc:url "http://tanto.unito.it/WebVisual/index.html" ; biotools:primaryContact "Raffaele Calogero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6934854", "pubmed:31882769" ; sc:description """Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.). This is a repository for a analysis of avocado GBS data in R. This is a repository for a analysis of GBS data in R. The R packages used in this repository are shown below:.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:name "Hass" ; sc:url "https://github.com/IHSMFruitCrops/Hass-genotyping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3344, edam:topic_3407, edam:topic_3421 ; sc:citation , "pmcid:PMC6896291" ; sc:description """Web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences. R package that provide interactive graphical interface for metabolic profiling. If you find it useful, please cite this work. to convert R variables into a JSON object and save it as a file. hastaLaVista is developed and tested using Chrome, although it is known to work with other browser. In the case that a feature is not working as expected please try using Chrome before filling an issue""" ; sc:featureList edam:operation_0337, edam:operation_3214, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "HastaLaVista" ; sc:url "https://github.com/jwist/hastaLaVista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_2275 ; sc:citation , "pmcid:PMC6602443", "pubmed:31106357" ; sc:description "Web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA." ; sc:featureList edam:operation_0482, edam:operation_2492, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HawkDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cadd.zju.edu.cn/hawkdock/" ; biotools:primaryContact "Gaoqi Weng", "Tingjun Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_0821 ; sc:citation , "pubmed:31093654" ; sc:description "R package for an Ultra-Fast and Comprehensive Gene Annotation in Plants." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Hayai-Annotation Plants" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kdri-genomics/Hayai-Annotation-Plants" ; biotools:primaryContact "Andrea Ghelfi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6686264", "pubmed:31395005" ; sc:description "A deep learning predictive model for multi-type biological dataset | HetEncs: A Deep Learning Classifier for Integrated Gene Expression Analysis" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3891 ; sc:name "HetEnc" ; sc:url "https://github.com/seldas/HetEnc_Code" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3321 ; sc:citation ; sc:description "A genetic resource database for rubber tree genomic study | Molecular & Genetic Resources for Hevea tree" ; sc:featureList edam:operation_3216, edam:operation_3431, edam:operation_3766 ; sc:name "HeveaDB" ; sc:url "http://hevea.catas.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:31697323" ; sc:description """Building blocks for efficient handling of large Hi-C datasets. Framework for Storing and Accessing Hi-C Data Through HDF Files. HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization""" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "HiCBricks" ; sc:url "http://bioconductor.org/packages/devel/bioc/html/HiCBricks.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3169, edam:topic_3673 ; sc:citation ; sc:description """Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line. An analytical and visualization tool for CNV discovery and contact map correction of Hi-C/3C-seq data of cancer cell lines. HiCNAtra is a MATLAB-based tool that accepts HDF5 files, the output of hiclib after applying the iterative-mapping technique, as input. HiCNAtra pipeline is divided into three modules: 1) computation of the read depth (RD) signal from Hi-C or 3C-seq reads (RD calculator), 2) RD-based detection of copy number events based on CNAtra approach (CNV caller) and 3) bias correction of chromatin interaction matrix introduced by CNVs and other systematic biases (Contact map corrector)""" ; sc:featureList edam:operation_0392, edam:operation_3435, edam:operation_3659 ; sc:name "HiCNAtra" ; sc:url "https://github.com/AISKhalil/HiCNAtra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31056636" ; sc:description "Computational method for resolution enhancement of Hi-C data. It uses a very deep convolutional neural network to learn the mapping between low-resolution and high-resolution Hi-C contact matrices." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HiCNN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://dna.cs.miami.edu/HiCNN/" ; biotools:primaryContact "Zheng Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3382 ; sc:citation , "pmcid:PMC6844183", "pubmed:31749839" ; sc:description """A Novel Shiny App for Hi-C Data Analysis. R package that allows easily performing a complete Hi-C data analysis through a Graphical User Interface. HiCeekR is a novel Shiny based R package for Hi-C data analysis""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3695, edam:operation_3798 ; sc:license "GPL-2.0" ; sc:name "HiCeekR" ; sc:url "https://github.com/lucidif/HiCeekR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31424526" ; sc:description "An Online Application to Aid Matching Peptide Pairs with Isotopically Labelled PTMs | MOTIVATION:Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy light pair are assigned. In such cases, having a pair of MS MS spectra that differ due to an isotopic label can assist in identifying the relevant m z values that support the correct peptide annotation or can be used for de novo sequencing. RESULTS:We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra" ; sc:featureList edam:operation_3638, edam:operation_3644, edam:operation_3755 ; sc:name "HiLight-PTM" ; sc:url "https://harrywhitwell.shinyapps.io/hilight-ptm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3385 ; sc:citation , "pmcid:PMC6283589", "pubmed:30521560" ; sc:description "Gradient-based, GPU-accelerated, high-precision contour-segmentation algorithm with application to cell membrane fluctuation spectroscopy." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HiPFSTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/michaelmell/hipfsta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_2830, edam:topic_3489 ; sc:citation , "pubmed:31855463" ; sc:description """Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data. High-dimensional mass cytometry (Cytometry by Time-Of-Flight; CyTOF) is a multiparametric single-cell approach that allows for more than 40 parameters to be evaluated simultaneously, opening the possibility to dissect cellular heterogeneity and elucidate functional interactions between different cell types. However, the complexity of these data makes analysis and interpretation daunting. We created High-throughput Population Profiler (HiPPO), a tool that reduces the complexity of the CyTOF data and allows homogeneous clusters of cells to be visualized in an intuitive manner. Each subpopulation is mapped to the Population Analysis Database (PANDA), an open-source, manually curated database containing protein expression profiles for selected markers of primary cells, allowing for cell type abundance in the analyzed samples to be monitored.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3432 ; sc:name "HiPPO" ; sc:url "http://www.hippopanda.org/hippo.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2840, edam:topic_3520 ; sc:citation , "pubmed:31095696" ; sc:description "Online Crowd-Sourced HR-MS Database for Suspect and Non-targeted Screening of New Psychoactive Substances." ; sc:featureList edam:operation_2929, edam:operation_3431, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "HighResNPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://HighResNPS.com" ; biotools:primaryContact "Marie Mardal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3293 ; sc:citation , "pmcid:PMC6612880", "pubmed:31510674" ; sc:description "Collaborative intra-tumor heterogeneity detection | An algorithm for collaborative intra-tumor heterogeneity detection | We introduce a method called Hintra for intra-tumor heterogeneity detection | Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult" ; sc:featureList edam:operation_0567, edam:operation_3478, edam:operation_3629 ; sc:name "Hintra" ; sc:url "https://github.com/sahandk/HINTRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:31609046" ; sc:description """Hippocampal segmentation for brains with extensive atrophy using three-dimensional convolutional neural networks. Welcome to HippMapp3r’s documentation! — HippMapp3r documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_3435 ; sc:name "HippMapp3r" ; sc:url "https://hippmapp3r.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2830, edam:topic_3360, edam:topic_3400 ; sc:citation , "pubmed:31725860" ; sc:description """A human immunosuppression gene database. HisgAtlas is the first database that stores a list of immunosuppression genes collected by literature mining and manual curation. 995 human immunosuppression genes and 260 associated diseases are collected in this database. The user needs to log in for the curation. Please refer to our FAQ for detail. HisgAtlas is a manual curation database for human immunosuppression genes.""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2428 ; sc:name "HisgAtlas" ; sc:softwareHelp ; sc:url "http://biokb.ncpsb.org/HisgAtlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation , "pubmed:31816396" ; sc:description """A practical guide for analysis of histone post-translational modifications by mass spectrometry. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0. Workflow to perform data quality checks, filtering, normalization, statistics, and visualization for histone PTM data run through EpiProfile 2.0 or Skyline software. Raw data and example scripts can be found at: doi:10.25345/C5ZQ0F.""" ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3645 ; sc:name "HistoneAnalysisWorkflow" ; sc:url "https://github.com/DenuLab/HistoneAnalysisWorkflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_2229 ; sc:citation , "pubmed:31821723" ; sc:description """A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. The main web resource to explore human mitochondrial variability data and their pathological correlation. HmtVar is a manually-curated database offering variability and pathogenicity information about mtDNA variants. Data are gathered from HmtVar's twin database HmtDB, and further integrated with pathogenicity predictions as well as additional information from several online resources focused on mtDNA, such as MITOMAP, 1000 Genomes Project, MutPred, SNPs&GO and many others.""" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3227, edam:operation_3461, edam:operation_3778 ; sc:name "HmtVar" ; sc:url "https://www.hmtvar.uniba.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0623, edam:topic_3293, edam:topic_3372 ; sc:citation ; sc:description """Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes. Phylogenetic profiling with orthology data. HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient""" ; sc:featureList edam:operation_0539, edam:operation_0540, edam:operation_3478 ; sc:license "MIT" ; sc:name "HogProf" ; sc:url "https://github.com/DessimozLab/HogProf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc:description "Detecting fabrication in large-scale molecular omics data | Fraud is a pervasive problem and can occur as fabrication, falsification, plagiarism or theft. The scientific community is not exempt from this universal problem and several studies have recently been caught manipulating or fabricating data. Current measures to prevent and deter scientific misconduct come in the form of the peer-review process and on-site clinical trial auditors. As recent advances in high-throughput omics technologies have moved biology into the realm of big-data, fraud detection methods must be updated for sophisticated computational fraud | In the financial sector, machine learning and digit-preference are successfully used to detect fraud | See our pre-press article at: https://www.biorxiv.org/content/10.1101/757070v1" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "Holden" ; sc:url "https://github.com/MSBradshaw/Holden" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:encodingFormat edam:format_3983 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation ; sc:description "Graphical tool for development, simulation and analysis of Petri net based models of complex biological systems." ; sc:featureList edam:operation_0244, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "Holmes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html" ; biotools:primaryContact "Piotr Formanowicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , , ; sc:description """A first prototype Python plugin enabling exploratory spatial data analysis into QGIS. A QGIS plugin for hotspot analyis. Hotspot Analysis Plugin for QGIS.""" ; sc:featureList edam:operation_0451, edam:operation_3435 ; sc:name "Hotspot analysis" ; sc:url "https://github.com/danioxoli/HotSpotAnalysis_Plugin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3170, edam:topic_3307, edam:topic_3361, edam:topic_3512, edam:topic_3518, edam:topic_3678 ; sc:citation , "pubmed:32663312" ; sc:description """Redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets. Web-based tools to search tissue specific housekeeping genes.""" ; sc:featureList edam:operation_2424, edam:operation_3799, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:name "Housekeeping and Reference Transcript Atlas" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.housekeeping.unicamp.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pubmed:31504157" ; sc:description "Improved representation of sequence Bloom trees | Sequence Bloom Tree, supporting determined/how split filters | Jellyfish (Version 2.2.0 or later)" ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "HowDe-SBT" ; sc:url "https://github.com/medvedevgroup/HowDeSBT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_0659 ; sc:citation , "pubmed:30999860" ; sc:description "Manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites." ; sc:featureList edam:operation_3501, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "HumCFS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/humcfs/index.html" ; biotools:primaryContact "Dr. Gajendra P. S. Raghava" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "HumanMine integrates many types of data for Homo sapiens and Mus musculus" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "HumanMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "6.0 2019 May" ; sc:url "https://www.humanmine.org/humanmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation , "pmcid:PMC6684253", "pubmed:31388390" ; sc:description "Estimation and sampling for multi-dimensional Hurdle models on a Normal density with applications to single-cell co-expression | A Hurdle model is a modification of a distribution at zero. This package provides routines to estimate and sample from multivariate Hurdle models on a Normal density. These are distributions that are conditionally Normal, but with singularities along the coordinate axes, so generalize a univariate zero-inflated distribution" ; sc:featureList edam:operation_3436, edam:operation_3463, edam:operation_3501 ; sc:name "Hurdle" ; sc:url "https://github.com/amcdavid/HurdleNormal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3315, edam:topic_3673 ; sc:citation ; sc:description "HyAsP (Hybrid Assember for Plasmids) - tool that identifies, bins and assembles plasmid contigs following a hybrid approach based on a database of known plasmids genes and a greedy assembly algorithm." ; sc:featureList edam:operation_0578, edam:operation_3482, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HyAsP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cchauve/HyAsP" ; biotools:primaryContact "Cedric Chauve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0154, edam:topic_0602 ; sc:author "Art FY Poon", "Sergei L Kosakovsky Pond", "Steven Weaver" ; sc:citation , , "pubmed:15509596", "pubmed:30298394" ; sc:description "Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "HyPhy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://hyphy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation ; sc:description """Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "HybPiper" ; sc:url "https://github.com/mossmatters/HybPiper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209 ; sc:citation , "pubmed:31524396" ; sc:description "A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery | Hybrid Molecules is defined as the design of new chemical molecule that hybridizes two or more pharmacophoric moieties from known identical or non-identical bioactive molecules, or two or more known identical or non-identical bioactive molecules directly into a single molecule to obtain better affinity and efficacy or to improve the properties of the parent molecules or to interact with two or multiple targets or to reduce undesirable side effects or to decrease in drug-drug interactions or reduce emergence of drug resistance | Hybrid Molecule Database (HybridMolDB) provides a versatile resource for the display, search, and analysis of the structure, manual-annotated design protocol, the pharmacological data, some physicochemical and ligand efficiency and druglike and ADMET characteristics and the profile of targets of the well-known hybrid molecules" ; sc:featureList edam:operation_0337, edam:operation_3456, edam:operation_3893 ; sc:name "HybridMolDB" ; sc:url "http://www.idruglab.com/HybridMolDB/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3382 ; sc:citation , "pubmed:31569268" ; sc:description """Joint Estimation of Gross Recharge, Groundwater Usage, and Hydraulic Properties within HydroSight. A toolbox for data-driven hydrogeological insights. Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live. Websites for you and your projects. HydroSight is a highly flexible statistical toolbox for quantitative hydrogeological insights. It comprises of a powerful groundwater hydrograph time-series modelling and simulation framework plus a data quality analysis module. Multiple models can be built for one bore, allowing statistical identification of the dominant processes, or 100’s of bores can be modelled to quantify aquifer heterogeneity. This flexibility allows many novel applications such as:.""" ; sc:featureList edam:operation_3096, edam:operation_3431, edam:operation_3799 ; sc:name "HydroSight" ; sc:url "http://peterson-tim-j.github.io/HydroSight/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated data warehouse for the Hymenoptera Genome Database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "HymenopteraMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "http://hymenopteragenome.org/hymenopteramine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc:description "Two hundred million combinatorially complete datasets from a single experiment | Generate all combinatorially complete datasets from the given genotype list | python3 HypercubeME.py -g test_complete_03.txt | Run in the command line following examples: | See the file 'test_complete_03.txt' for input example. Columns are tab-separated, first line is a header which is ignored by HypercubeME. First column (example: '0C:2T') is a column-separated mutation list of a particular mutant variant. Each mutation consists of mutated position and the variant (amino acid residue or RNA/DNA base) where it is mutated. For wild-type HypercubeME uses '0Z', where 'Z' means wild-type variant (amino acid residue or RNA/DNA base); however, in the genotype file wild-type can also be denoted as empty string as in the file 'test_complete_03.txt'. All other columns are ignored by HypercubeME" ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "HypercubeME" ; sc:url "https://github.com/ivankovlab/HypercubeME.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6530038", "pubmed:31117943" ; sc:description "Method to construct module-level three-way interaction networks. The method is able to present integrative uniform hypergraphs to reflect the global dynamic correlation pattern in the biological system, providing guidance to down-stream gene triplet-level analyses." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Hypergraph Dynamic Correlation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yunchuankong/HypergraphDynamicCorrelation" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6878028", "pubmed:31636105" ; sc:description """A Deep Learning-Based Approach for High-Throughput Hypocotyl Phenotyping. A deep learning-based approach for high throughput plant phenotyping. This repository is the companion for the paper A deep learning-based approach for high throughput plant phenotyping, Dobos et al.. The dataset used in the article can be found at this page. Using a trained model for measuring hypocotyls. The pretrained model used in the research article can be downloaded here.""" ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:name "Hypocotyl" ; sc:url "https://github.com/biomag-lab/hypocotyl-UNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3298, edam:topic_3315 ; sc:citation , "pubmed:31647442" ; sc:description """A Scalable Exploratory Framework for Analyzing Complex Phenomics Data. A header only software library helps to visually discover the insights of high dimensional complex data set. We can represent the category of points in a cluster using a pie chart. In our Hyppo-X framework, we have capability to define a category of a point using single or multiple columns of the dataset. Pie chart shows the percentage distribution of points among all categories. For instance, for the above sample dataset, we can define the locaion column named Loc as the category of all the points then we will get following graphs. Here, blue color indicates points those belong in location N and red color indicates points those belong in location K. This graph with pie chart node helps us to understand the behavior of points with respect to two locations. This software library is built to delve the insights of a complex high dimensional dataset""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_1812, edam:operation_3432, edam:operation_3891 ; sc:name "Hyppo-X" ; sc:url "https://xperthut.github.io/HYPPO-X" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A self-consistent method to impute single cell RNA sequencing data | I-Impute is a “self-consistent” method method to impute scRNA-seq data. I-Impute leverages continuous similarities and dropout probabilities and refines the data iteratively to make the final output \"self-consistent\". I-Impute exhibits robust imputation ability and follows the “self-consistency” principle. It offers perspicacity to uncover the underlying cell subtypes in real scRNA-Seq data" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "I-Impute" ; sc:url "https://github.com/xikanfeng2/I-Impute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0769, edam:topic_3056, edam:topic_3574 ; sc:citation , "pubmed:31765831" ; sc:description """A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data. Intuitive Integrative Interpretation (I3) of complex genetic data. 3 Interpreting genetics of gene expression in brains. 1 State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China""" ; sc:name "I3" ; sc:url "http://suprahex.r-forge.r-project.org/I3.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3374, edam:topic_3382 ; sc:citation , "pmcid:PMC6675096", "pubmed:31369634" ; sc:description "A MATLAB framework for efficient microscopy image analysis development, applied to quantifying intracellular transport of internalized peptide-drug conjugate | IA-Lab: a MATLAB-based framework for high throughput custom image analysis | This is the central repo for the IALab software, including parsers of various microscopy experiments, into multidimensional and multichannel images, and core code for segmentation, measurement, export of results and display of images and results . Some example workflows are stored in the Examples directory" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "IA-Lab" ; sc:url "https://github.com/amcorrigan/ia-lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC6602435", "pubmed:31127271" ; sc:description "Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE) - web server designed for network-based genotype-phenotype mapping of clonal populations that display the same focal phenotype." ; sc:featureList edam:operation_3196, edam:operation_3216, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IAMBEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.intec.ugent.be/iambee/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3305, edam:topic_3337 ; sc:citation ; sc:description "iLASH - IBD Estimation Using Locality Sensitive Hashing | iLASH: Ultra-Rapid Detection of IBD Tracts | iLASH divides the genotype data in consecutive slices and then runs LSH algorithm over each slice. Slices (windows) are, thus, the building blocks of IBD tracts. The following parameters control different properties of these slices" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3211 ; sc:name "IBD" ; sc:url "http://github.com/roohy/IBD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3518 ; sc:citation ; sc:description """Attacks on genetic privacy via uploads to genealogical databases. Create figures for "Attacks on genetic privacy via uploads to genealogical databases" by Michael D. Edge and Graham Coop. README for gedmatch figures & emails. The files marked GEDmatch_*_Redacted.pdf are printouts of the display of the GEDmatch 1-to-1 match genome browser.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:name "IBS-privacy" ; sc:url "http://github.com/mdedge/IBS_privacy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0611, edam:topic_2828 ; sc:citation ; sc:description "Tool for integrated sequence and 3D structure analysis of large macromolecular complexes." ; sc:featureList edam:operation_0448 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IBiSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibiss.igbmc.fr/" ; biotools:primaryContact "Bruno P. Klaholz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3172, edam:topic_3308 ; sc:citation , "pmcid:PMC6771121", "pubmed:31500324" ; sc:description "Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets | ICA-in-Cancer-research-review-materials | Jupyter Notebook containing example of Independent Component Analysis (ICA) accompanying the review in Internal Journal of Molecular Sciences (IJMS) | \"Independent Component Analysis of BIg Omics Data\" | BIODICA: Independent Component Analysis for BIg Omics Data | Deconvolution of transcriptome through Immune Component Analysis | BIODICA is a user-friendly pipline for high-performant computation of independent components for omics data, using stability analysis and computing the optimal number of the components from their stabilities, and performing analyses for interpreting the results of ICA application | You can install deconICA from GitHub with: | AN R PACKAGE FOR IDENTIFYING IMMUNE-RELATED SIGNALS IN TRANSCRIPTOME THROUGH DECONVOLUTION OR UNSUPERVISED SOURCE SEPARATION METHODS" ; sc:featureList edam:operation_2939, edam:operation_3629, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "ICA" ; sc:url "https://github.com/sysbio-curie/ICA-in-Cancer-research-review-materials" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0593, edam:topic_3295, edam:topic_3306, edam:topic_3385 ; sc:citation , "pmcid:PMC6895719", "pubmed:31732142" ; sc:description """Nanoscale Distribution of Nuclear Sites by Super-Resolved Image Cross-Correlation Spectroscopy. User-fiendly code for image cross-correlation specroscopy (ICCS) analysis based on the following article:""" ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:name "ICCS" ; sc:url "https://github.com/llanzano/ICCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3500 ; sc:citation , "pmcid:PMC6933885", "pubmed:31878869" ; sc:description """Integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset. BACKGROUND:Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with genome-wide distributed SNPs instead of pedigree. The key step of it is to construct genomic relationship matrix (GRM) via genome-wide SNPs; however, usually the calculation of GRM needs huge computer memory especially when the SNP number and sample size are big, so that sometimes it will become computationally prohibitive even for super computer clusters. We herein developed an integrative algorithm to compute GRM.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3359 ; sc:name "ICGRM" ; sc:url "https://github.com/mingfang618/CLGRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC6592775", "pubmed:31103785" ; sc:description "Automated electroencephalographic independent component classifier, dataset, and website." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ICLabel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://iclabel.ucsd.edu/" ; biotools:primaryContact "Luca Pion-Tonachini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3474 ; sc:citation ; sc:description """Accurate and reproducible prediction of ICU readmissions. The code in this repository was used to produce the results of this paper (awaiting acceptance, link will be updated). A walkthrough can be found in this notebook.""" ; sc:license "GPL-3.0" ; sc:name "ICU readmissions" ; sc:url "http://github.com/deepphong/icu-readmission" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3399 ; sc:citation , "pubmed:31087665" ; sc:description "Web server for adult age estimation of human skeletal remains." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IDADE2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bass.uib.es/~jaume/IDADE2/https/index.html" ; biotools:primaryContact "Allysha Winburn", "Carme Rissech Badallo", "Marta San-Millán" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_1915, edam:format_2333, edam:format_3244, edam:format_3245, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3621 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3301, edam:topic_3336, edam:topic_3697 ; sc:author ; sc:citation , ; sc:description "A MALDI bioinformatics platform for analyzing protein and small molecule MALDI-TOF MS data (with a particular focus on mic organism analysis )" ; sc:featureList edam:operation_0567, edam:operation_2409, edam:operation_2939, edam:operation_3214, edam:operation_3432, edam:operation_3694, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IDBac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.10" ; sc:url "https://chasemc.github.io/IDBac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0736, edam:topic_0749, edam:topic_0780, edam:topic_3306 ; sc:citation , "pmcid:PMC6933863", "pubmed:31642121" ; sc:description """Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. IDDomainSpotter – Section for Biomolecular Sciences. IDDomainSpotter is a sequence-based approach to assess and visualize domain organisation in long intrinsically disordered proteins based on compositional biases""" ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_3904 ; sc:name "IDDomainSpotter" ; sc:url "http://www.bio.ku.dk/sbinlab/IDDomainSpotter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3360 ; sc:citation , "pmcid:PMC6777501", "pubmed:31608326" ; sc:description """An independently validated nomogram for isocitrate dehydrogenase-wild-type glioblastoma patient survival. Background:In 2016, the World Health Organization reclassified the definition of glioblastoma (GBM), dividing these tumors into isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant GBM, where the vast majority of GBMs are IDH-wild-type. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a nomogram for IDH-wild-type patients with newly diagnosed GBM.""" ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659 ; sc:name "IDH-wild-type" ; sc:url "https://gcioffi.shinyapps.io/Nomogram_For_IDH_Wildtype_GBM_H_Gittleman/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_3790 ; sc:name "Query script" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3255, edam:format_3256, edam:format_3261, edam:format_3464, edam:format_3475, edam:format_3752, edam:format_3956 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "SPARQL endpoint", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3343, edam:topic_3369 ; sc:author , ; sc:citation , ; sc:description "Integrated Database of Small Molecules" ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "IDSM" ; sc:softwareHelp ; sc:url "https://idsm.elixir-czech.cz/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3384 ; sc:citation , "pmcid:PMC6663300", "pubmed:31410382" ; sc:description "Large-scale directed network inference with multivariate transfer entropy and hierarchical statistical testing | The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory. IDTxl provides functionality to estimate the following measures:" ; sc:featureList edam:operation_3216, edam:operation_3658 ; sc:license "GPL-3.0" ; sc:name "IDTxl" ; sc:url "https://github.com/pwollstadt/IDTxl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3063, edam:topic_3324 ; sc:citation , "pmcid:PMC6933616", "pubmed:31881820" ; sc:description """Predicting virus-receptor interactions based on similarity and semi-supervised learning. BACKGROUND:Viral infectious diseases are the serious threat for human health. The receptor-binding is the first step for the viral infection of hosts. To more effectively treat human viral infectious diseases, the hidden virus-receptor interactions must be discovered. However, current computational methods for predicting virus-receptor interactions are limited. RESULT:In this study, we propose a new computational method (IILLS) to predict virus-receptor interactions based on Initial Interaction scores method via the neighbors and the Laplacian regularized Least Square algorithm. IILLS integrates the known virus-receptor interactions and amino acid sequences of receptors. The similarity of viruses is calculated by the Gaussian Interaction Profile (GIP) kernel. On the other hand, we also compute the receptor GIP similarity and the receptor sequence similarity.""" ; sc:featureList edam:operation_0303 ; sc:name "IILLS" ; sc:url "http://bioinformatics.csu.edu.cn/IILLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3837 ; sc:citation , "pmcid:PMC6886165", "pubmed:31787095" ; sc:description """Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion. Kernelized Logistic Matrix Factorization based on Similarity Network Fusion for Predicting Virus-host Association. Xingpeng Jiang, xpjiang@mail.ccnu.edu.cn Dan Liu, liudan@mails.ccnu.edu.cn.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3439 ; sc:name "ILMF-VH" ; sc:url "https://github.com/liudan111/ILMF-VH.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_0804, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC8734366", "pubmed:34991455" ; sc:description "The ImmunoDataAnalyzer (IMDA) pipeline provides various methods for analysing immunological next-generation sequencing (NGS) data." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3200, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "ImmunoDataAnalyzer" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://bioinformatics.fh-hagenberg.at/immunoanalyzer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3297, edam:topic_3407 ; sc:citation , "pubmed:31665416" ; sc:description """An update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase. The public IMG/ABC site has limited features and tools.""" ; sc:featureList edam:operation_2454, edam:operation_3216, edam:operation_3432 ; sc:name "IMG-ABC" ; sc:url "https://img.jgi.doe.gov/abc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , "pubmed:10745995", "pubmed:15089751", "pubmed:17949886", "pubmed:21099347", "pubmed:22654892" ; sc:description "IMGT-ONTOLOGY is the first ontology for immunogenetics and immunoinformatics. It provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics and manages the related knowledge, thus allowing the standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. IMGT-ONTOLOGY manages the knowledge through diverse facets relying on seven axioms, \"IDENTIFICATION\", \"CLASSIFICATION\", \"DESCRIPTION\", \"NUMEROTATION\", \"LOCALIZATION\", \"ORIENTATION\" and \"OBTENTION\". These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized." ; sc:featureList edam:operation_3501 ; sc:name "IMGT-ONTOLOGY" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTindex/ontology.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:25378316" ; sc:description """IMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI). Annotation is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224, edam:operation_0564, edam:operation_2416 ; sc:isAccessibleForFree true ; sc:name "IMGT 2Dstructure-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "IMGT Allele-Align" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.imgt.org/Allele-Align/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/CloneSearch is the IMGT® tool allowing the search of a clone in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT CloneSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2331 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation "pubmed:11862387", "pubmed:18208865", "pubmed:21632776", "pubmed:25378316" ; sc:description "IMGT/Collier-de-Perles is the IMGT® tool to draw standardized IMGT 2D graphical representations, or IMGT Colliers de Perles, of variable (V), constant (C), groove (G) domains, starting from the user own domain amino acid sequences. IMGT Colliers de Perles are based on amino acid sequences gapped according to the IMGT-ONTOLOGY concept of IMGT unique numbering." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "IMGT Collier-de-Perles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/Collier-de-Perles.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3510, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:25378316" ; sc:description """IMGT/DomainDisplay is the IMGT® tool for the display of the amino acid sequences of the variable (V), constant (C) and groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainDisplay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainDisplay.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3154 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:19900967", "pubmed:21632775", "pubmed:25378316" ; sc:description "IMGT/DomainGapAlign is the IMGT® tool for the analysis of amino acid sequences of variable (V), constant (C) or groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0491, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainGapAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2331 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation "pubmed:25378316" ; sc:description "IMGT/DomainSuperimpose is the IMGT® tool to superimpose 3D structures of two domains from IMGT/3Dstructure-DB. Domain 3D structures are numbered according to the IMGT-ONTOLOGY concept of IMGT unique numbering." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT DomainSuperimpose" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/cgi/DomainSuperimpose.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15608191", "pubmed:25378316" ; sc:description """IMGT/GENE-DB is the IMGT® database for immunoglobulin (IG) and T cell receptor (TR) genes and alleles (international nomenclature). Annotation is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "IMGT GENE-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://www.imgt.org/genedb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2058 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2331 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2331 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3053, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15972004", "pubmed:16640788", "pubmed:25378316" ; sc:description """IMGT/GeneFrequency is the IMGT® tool providing the frequency usage of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D) and joining (J) genes in Homo sapiens and Mus musculus rearranged sequences from IMGT/LIGM-DB. Analysis is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneFrequency" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/genefrequency/query" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2331 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1278 ; sc:encodingFormat edam:format_2331 ; sc:name "Genetic map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:14681357", "pubmed:16640788", "pubmed:25378316" ; sc:description "IMGT/GeneInfo is the IMGT® tool providing combination (V-J and V-V) information for the human and mouse T cell receptor (TR) loci. Analysis is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:name "IMGT GeneInfo" ; sc:softwareHelp ; sc:url "http://www.imgt.org/GeneInfoServlets/htdocs/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT/GeneSearch is the IMGT® tool allowing the search of a gene in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2331 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description "IMGT® tool providing the view of a gene in IMGT/LocusView. Display is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT GeneView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3779 ; sc:encodingFormat edam:format_3752 ; sc:name "Annotated text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation , "pubmed:22665256", "pubmed:25378316" ; sc:description """IMGT/HighV-QUEST is the IMGT® portal for NGS high-throughput nucleotide sequence analysis of immunoglobulins (IG) and T cell receptors (TR) variable domains, integrates IMGT/JunctionAnalysis and IMGT/Automat. Analysis is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0292, edam:operation_0448, edam:operation_2478, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "IMGT HighV-QUEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/HighV-QUEST/home.action" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2200 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15262823", "pubmed:21632777", "pubmed:25378316" ; sc:description """IMGT/JunctionAnalysis is the IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR). Analysis is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0292, edam:operation_0448, edam:operation_2478 ; sc:isAccessibleForFree true ; sc:name "IMGT JunctionAnalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGT_jcta" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1103 ; sc:encodingFormat edam:format_2330 ; sc:name "EMBL/GenBank/DDBJ ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0804, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:16381979", "pubmed:25378316" ; sc:description """IMGT/LIGM-DB is the IMGT® database for nucleotide sequences with translation of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224, edam:operation_0338, edam:operation_0361, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:name "IMGT LIGM-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/ligmdb/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25972004" ; sc:description """IMGT/LocusView is the IMGT® tool providing a view of immunoglobulin (IG), T cell receptor (TR) and major histocompatibility (MH) loci. Display is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT LocusView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/LocusView/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:15089751", "pubmed:15972004", "pubmed:25378316" ; sc:description """IMGT/PRIMER-DB is the IMGT® database for oligonucleotides (primers) of immunoglobulins (IG) and T cell receptors (TR). Annotation is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0224, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:name "IMGT PRIMER-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTPrimerDB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology concept" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_1929, edam:format_2331 ; sc:name "Sequence alignment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_2331 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:12818634", "pubmed:25378316" ; sc:description """IMGT/PhyloGene is the IMGT® tool to compute and draw phylogenetic trees for immunoglobulin (IG) and T cell receptor (TR) V-REGION nucleotide sequences. Analysis is based on the IMGT-ONTOLOGY concepts.""" ; sc:featureList edam:operation_0292, edam:operation_0499 ; sc:isAccessibleForFree true ; sc:name "IMGT PhyloGene" ; sc:softwareHelp ; sc:url "http://www.imgt.org/IMGTPhylogeny/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3930, edam:topic_3948 ; sc:author "Safa Aouinti" ; sc:citation "pubmed:26540440", "pubmed:26731095" ; sc:description "IMGT/StatClnotype is the IMGT® tool for statistical analysis of sets from IMGT/HighV-QUEST output. IMGT/StatClonotype uses a generic statistical procedure for identifying significant changes in IG and TR differences of proportions of IMGT clonotypes (AA) diversity and expression. It uses the IMGT gene and allele nomenclature and it is based on IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0315, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:name "IMGT StatClonotype" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/StatClonotype/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_2331 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0804 ; sc:citation "pubmed:14681396", "pubmed:15089751", "pubmed:25378316" ; sc:description "IMGT/StructuralQuery is the IMGT® tool to retrieve IMGT/3Dstructure-DB entries using amino acid structural criteria for variable (V), constant (C) or groove (G) domains. Annotation is based on the IMGT-ONTOLOGY concepts." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT StructuralQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.imgt.org/3Dstructure-DB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3400, edam:topic_3930, edam:topic_3948 ; sc:citation "pubmed:25378316" ; sc:description """IMGT/mAb-DB is the IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA). IMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "IMGT mAb-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.imgt.org/mAb-DB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0804, edam:topic_3172, edam:topic_3302 ; sc:citation , "pubmed:31691834" ; sc:description """Extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. IUPHAR Guide to IMMUNOPHARMACOLOGY. The IUPHAR/BPS Guide to IMMUNOPHARMACOLOGY. Description.""" ; sc:featureList edam:operation_0224, edam:operation_0252 ; sc:name "IMMUNOPHARMACOLOGY" ; sc:url "http://www.guidetoimmunopharmacology.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3794 ; sc:citation , "pmcid:PMC6345043", "pubmed:30678641" ; sc:description "Aligner for mapping noisy long reads to the reference genome." ; sc:featureList edam:operation_0337, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "IMOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Mosjava/IMOS" ; biotools:primaryContact "Hadadian Nejad Youesfi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:29993787" ; sc:description "Inferring MiRNA Targets based on Restricted Boltzmann Machines (IMTRBM) for prediction of miRNA-target interactions (MTIs)." ; sc:featureList edam:operation_0463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IMTRBM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liuying201705/IMTRBM" ; biotools:primaryContact "Y. Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3360 ; sc:author "Zhenzhi Li" ; sc:citation , "pmcid:PMC6549230", "pubmed:31179159" ; sc:description "R package for network based differential expression analysis." ; sc:featureList edam:operation_3463, edam:operation_3741, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "INDEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/INDEED.html" ; biotools:primaryContact "Yiming Zuo", "Zhenzhi Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0218, edam:topic_0602 ; sc:citation , "pubmed:31070726" ; sc:description "Interactive pathway modeling using natural language with automated assembly." ; sc:featureList edam:operation_0533, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "INDRA-IPM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pathwaymap.indra.bio/" ; biotools:primaryContact "Peter Sorger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3810 ; sc:citation , "pmcid:PMC6820601", "pubmed:31535162" ; sc:description "Flexible modelling of spatial variation in agricultural field trials with the R package INLA | This is the site for the INLA approach to Bayesian inference within the R project for Statistical Computing | \"Bayesian inference with INLA\" by Virgilio Gómez-Rubio Another book from Virgilio is soon here. While we're waiting for the printed one, the current version is available as a github book; see the book section. May be .." ; sc:featureList edam:operation_2426, edam:operation_3196, edam:operation_3557 ; sc:name "INLA" ; sc:url "http://www.r-inla.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_3474 ; sc:citation , "pubmed:31883904" ; sc:description """Discovering nuclear targeting signal sequence through protein language learning and multivariate analysis. Nuclear localization signals (NLSs) are peptides that target proteins to the nucleus by binding to carrier proteins in the cytoplasm that transport their cargo across the nuclear membrane. Accurate identification of NLSs can help elucidate the functions of nuclear protein complexes. The currently known NLS predictors are usually specific to certain species or largely dependent on prior knowledge of NLS basic residues. Thus, a more general predictor is highly desired to reduce the potentially high false positives or false negatives in discovering new NLSs. Here, we report a new method, INSP (Identification Nucleus Signal Peptide), to effectively identify NLS mainly based on statistical knowledge and machine learning algorithms.""" ; sc:featureList edam:operation_0418, edam:operation_3631, edam:operation_3767 ; sc:name "INSP" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/INSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Software generated to aid in MRS analysis to achieve a specific diagnosis for brain lesions." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "INTERPRET DSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2" ; sc:url "http://gabrmn.uab.es/dss" ; biotools:primaryContact "Biomedical Applications of Magnetic Resonance research group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31509381" ; sc:description "A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships | Integrated Probabilistic Annotation (IPA) - A Bayesian annotation method for LC/MS data integrating biochemical relations, isotope patterns and adduct formation" ; sc:featureList edam:operation_3803 ; sc:name "IPA" ; sc:url "https://github.com/francescodc87/IPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation , "pmcid:PMC6427891", "pubmed:30936940" ; sc:description "R package for iterative pruning to capture population structure." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IPCAPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.5" ; sc:url "https://cran.r-project.org/package=IPCAPS" ; biotools:primaryContact "Kridsadakorn Chaichoompu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0199, edam:topic_0621, edam:topic_2830, edam:topic_3489 ; sc:citation , "pubmed:31641782" ; sc:description """A centralised resource for the study of polymorphism in genes of the immune system. The Immuno Polymorphism Database. IPD was developed in 2003 to provide a centralised system for the study of polymorphism in genes of the immune system. The IPD project was established by the HLA Informatics Group of the Anthony Nolan Research Institute in close collaboration with the European Bioinformatics Institute.""" ; sc:featureList edam:operation_0416, edam:operation_3197, edam:operation_3431 ; sc:name "IPD project" ; sc:url "https://www.ebi.ac.uk/ipd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:description "Software tool to identify prokaryotic and eukaryotic virus-derived sequences in virome using deep learning. Used to calculate a set of scores that reflect the probability that input sequence fragments are prokaryotic and eukaryotic viral sequences." ; sc:featureList edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "IPEV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "V4" ; sc:url "https://github.com/basehc/IPEV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3322 ; sc:citation ; sc:description "Single Cell RNA-seq reveals ectopic and aberrant lung resident cell populations in Idiopathic Pulmonary Fibrosis | Abstract We provide a single cell atlas of Idiopathic Pulmonary Fibrosis (IPF), a fatal interstitial lung disease, focusing on resident lung cell populations. By profiling 312,928 cells from 32 IPF, 29 healthy control and 18 chronic obstructive pulmonary disease (COPD) lungs, we demonstrate that IPF is characterized by changes in discrete subpopulations of cells in the three major parenchymal compartments: the epithelium, endothelium and stroma. Among epithelial cells, we identify a novel population of IPF enriched aberrant basaloid cells that co-express basal epithelial markers, mesenchymal markers, senescence markers, developmental transcription factors and are located at the edge of myofibroblast foci in the IPF lung" ; sc:featureList edam:operation_3501, edam:operation_3629 ; sc:name "IPF" ; sc:url "http://IPFCellAtlas.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6664791", "pubmed:31362694" ; sc:description "An XGBoost model for prediction of internal ribosome entry sites | BACKGROUND:Internal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5' cap-dependent translation initiation mechanism. IRES usually function when 5' cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool. RESULTS:This paper systematically examines the features that can distinguish IRES from non-IRES sequences" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_3472 ; sc:name "IRESpy" ; sc:url "https://irespy.shinyapps.io/IRESpy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0804, edam:topic_3512 ; sc:citation , "pmcid:PMC5091335", "pubmed:31414702" ; sc:description "the database of immunologically relevant non-coding RNAs | git clone git@github.com:sschmeier/irndb2.git irndb2 | IRNdb - Database of immunologically relevant non-coding RNAs | // © Massey University 2014-2018 // v1.5.8" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3501 ; sc:name "IRNdb" ; sc:url "http://irndb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3382, edam:topic_3417 ; sc:citation , "pmcid:PMC6553792", "pubmed:31125331" ; sc:description "Image System Engineering Toolbox for Biology (ISETBIO) is a Matlab toolbox designed for calculating the properties of the front end of biological visual systems." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ISETBIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://isetbio.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3077, edam:topic_3372 ; sc:citation , "pmcid:PMC6832938", "pubmed:31635039" ; sc:description """Semi-Automated Data Analysis for Ion-Selective Electrodes and Arrays Using the R Package ISEtools. Tools for Ion Selective Electrodes. Characterisation and calibration of single or multiple Ion Selective Electrodes (ISEs); activity estimation of experimental samples. Implements methods described in: Dillingham, P.W., Radu, T., Diamond, D., Radu, A. and McGraw, C.M. (2012) and Dillingham, P.W., Alsaedi, B.S.O. and McGraw, C.M. (2017) """ ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "ISEtools" ; sc:url "https://CRAN.R-project.org/package=ISEtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31736404" ; sc:description """Hep G2 cell culture confluence measurement in phase-contrast micrographs. Phase-contrast micrographs are often used for confirmation of proliferation and viability assays. However, they are usually only a qualitative tool and fail to exclude with certainty the presence of assay interference by test substances. The complexity of image analysis workflows hinders life scientists from routinely utilizing micrograph data. Here, we present an open-source software-based, combined ilastik segmentation ImageJ measurement of area (ISIMA) approach for cell monolayer segmentation and confluence percentage measurement of phase-contrast micrographs of Hep G2 cells. The aim of this study is to test whether the proposed approach is suitable for quantitative confirmation of proliferation data, acquired by the 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "ISIMA" ; sc:url "https://www.ilastik.org/download.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3403, edam:topic_3474 ; sc:citation , "pubmed:31430550" ; sc:description "Visually interpretable deep learning for mortality prediction inside the ICU | To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they have been shown by several studies to offer sub-optimal performance. Alternatively, Deep Learning offers state of the art capabilities in certain prediction tasks and research suggests deep neural networks are able to outperform traditional techniques. Nevertheless, a main impediment for the adoption of Deep Learning in healthcare is its reduced interpretability, for in this field it is crucial to gain insight into the why of predictions, to assure that models are actually learning relevant features instead of spurious correlations" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "ISeeU" ; sc:url "https://github.com/williamcaicedo/ISeeU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "Modeling methylation dynamics with simultaneous changes in CpG islands." ; sc:featureList edam:operation_0417, edam:operation_0430, edam:operation_3186 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IWEPoissonPaper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com//statgenlmu//IWEPoissonPaper" ; biotools:primaryContact "Dirk Metzler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0632, edam:topic_0804, edam:topic_3360 ; sc:citation , "pmcid:PMC6901697", "pubmed:31849974" ; sc:description """Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries. GENERATING AND TESTING MIMOTOPE LIBRARIES. Proof of pricniple diagnostic use with feature selection and predictor construction. comparison between IgM reactivity with different peptide libraries.""" ; sc:featureList edam:operation_0291, edam:operation_2421, edam:operation_2495 ; sc:name "IgM" ; sc:url "https://github.com/ansts/IgMimoPap1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3382, edam:topic_3892 ; sc:citation , "pmcid:PMC6834899", "pubmed:31519398" ; sc:description "Software for Biomolecular Illustration | The small program Illustrate generates non-photorealistic images of biological molecules for use in dissemination, outreach, and education. The method has been used as part of the \"Molecule of the Month,\" an ongoing educational column at the RCSB Protein Data Bank (http: rcsb.org). Insights from 20 years of application of the program are presented, and the program has been released both as open-source Fortran at GitHub and through an interactive web-based interface" ; sc:featureList edam:operation_0337 ; sc:name "Illustrate" ; sc:url "https://github.com/ccsb-scripps/Illustrate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31780825" ; sc:description """An open-source computational platform for the deep learning era. ImJoy -- Deep Learning Made Easy!""" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:name "ImJoy" ; sc:softwareHelp ; sc:url "https://imjoy.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_2640, edam:topic_3360, edam:topic_3382 ; sc:citation , "pubmed:31804670" ; sc:description """A multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images. A deep learning model for protein subcellular localization based on immunohistochemistry images""" ; sc:featureList edam:operation_0418, edam:operation_0477, edam:operation_2489, edam:operation_3436, edam:operation_3552 ; sc:name "ImPLoc" ; sc:url "https://github.com/yl2019lw/ImPloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3170, edam:topic_3400 ; sc:citation , "pubmed:31665245" ; sc:description """R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data. R package to quantify CDR3 data for immune repertoire diversity. Author and Maintainer: Martijn Cordes. devtools::install_github("martijn-cordes/ImSpectR"). We also used ImSpectR to score CDR3 data from human TCR sequencing data sequenced with the ImmunoSeq platform. The CDR3 data scored by ImSpectR was data from CMV+ PBMCs published by Suessmuth et al. (Blood, 2015). Tab seperated (tsv) files were dowloaded from the Adaptive Biotech database for immunoSEQ data: https://clients.adaptivebiotech.com/pub/b4ac7a84-1e69-4d60-8254-845720454d7d""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:name "ImSpectR" ; sc:url "https://github.com/martijn-cordes/ImSpectR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_1964, edam:format_3475, edam:format_3752 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1147 ; sc:name "GEO accession number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3308 ; sc:author ; sc:citation , "pubmed:30137226" ; sc:description "ImaGEO is a web tool for gene expression Meta-Analysis that implements a complete and comprehensive meta-analysis workflow starting from Gene Expression Omnibus (GEO) dataset identifiers. The application integrates GEO datasets, applies different meta-analysis techniques and provides functional analysis results in an easy-to-use environment. ImaGEO is a powerful and useful resource that allows researchers to integrate and perform meta-analysis of GEO datasets to lead robust findings for biomarker discovery studies." ; sc:featureList edam:operation_0531, edam:operation_3223, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ImaGEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://imageo.genyo.es" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3056, edam:topic_3474 ; sc:citation , "pmcid:PMC6873651", "pubmed:31757205" ; sc:description """A convolutional neural network to quantify natural selection from genomic data. ImaGene implements a supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Specifically, it uses a convolutional neural network (CNN) which takes as input haplotypes for a population and locus of interest. It outputs confusion matrices as well as point estimates of the selection coefficient along with its posterior distribution and various metrics of confidence""" ; sc:featureList edam:operation_3196, edam:operation_3799, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "ImaGene" ; sc:url "https://github.com/mfumagalli/ImaGene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31714792" ; sc:description """A Tool To Extract and Quantify Data from Microscopy Images. Extract relevant images using ChemDataExtractor. Identify regions corresponding to individual particles""" ; sc:featureList edam:operation_0306, edam:operation_3458, edam:operation_3799 ; sc:license "MIT" ; sc:name "ImageDataExtractor" ; sc:url "http://www.imagedataextractor.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:31388864" ; sc:description "New Software for Viewing Dynamic PET Scans and Extracting Radiomic Parameters from PET Data | Extensive research is currently being conducted into dynamic positron emission tomography (PET) acquisitions (including dynamic whole-body imaging) as well as extraction of radiomic features from imaging modalities. We describe a new PET viewing software known as Imager-4D that provides a facile means of viewing and analyzing dynamic PET data and obtaining associated quantitative metrics including radiomic parameters. The Imager-4D was programmed in the Java language utilizing the FX extensions. It is executable on any system for which a Java w FX compliant virtual machine is available. The software incorporates the ability to view and analyze dynamic data acquired with different types of dynamic protocols. For image display, the program maintains a built-in library of 62 different lookup tables with monochromatic and full-color distributions" ; sc:name "Imager-4D" ; sc:url "https://jeffreyleal.wixsite.com/jleal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC6525208", "pubmed:31101851" ; sc:description "Characterization of inner shell colour variations in Pinctada margaritifera assessed by HSV colour quantification." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ImaginR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ImaginR/index.html" ; biotools:primaryContact "Chin-Long Ky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3400 ; sc:citation ; sc:description "An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets." ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmClass2019" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KlinkeLab/ImmClass2019" ; biotools:primaryContact "David J. Klinke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pmcid:PMC5827693", "pubmed:29485622" ; sc:description "Data repository with analysis tools that is mainly focused on cytometry and immunology." ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmPort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.immport.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168 ; sc:citation ; sc:description """Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. Welcome to the Immcantation Portal! — Immcantation documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_3432, edam:operation_3625 ; sc:license "CC-BY-SA-4.0" ; sc:name "Immcantation" ; sc:url "http://www.immcantation.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2269, edam:topic_2640, edam:topic_3070, edam:topic_3400 ; sc:citation ; sc:description """A unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Copyright © Guo Lab , College of Life Science and Technology , HUST , China. Any comments and suggestions, please contact us""" ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:name "ImmuCellAI" ; sc:url "http://bioinfo.life.hust.edu.cn/ImmuCellAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3517 ; sc:citation , "pmcid:PMC6602512", "pubmed:31114925" ; sc:description "Web-based tool for identifying human immune regulatory elements." ; sc:featureList edam:operation_0441, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmuneRegulation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://immuneregulation.mssm.edu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830 ; sc:citation , "pubmed:31396940" ; sc:description "Structural Modeling of Lymphocyte Receptors and Their Antigens" ; sc:featureList edam:operation_0416, edam:operation_0477, edam:operation_0478 ; sc:name "ImmuneScape" ; sc:url "https://sysimm.org/immune-scape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "Tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImmunomeBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.iedb.org/immunomebrowser/" ; biotools:primaryContact "Sandeep Kumar Dhanda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3376, edam:topic_3419 ; sc:citation , "pmcid:PMC6693182", "pubmed:31412887" ; sc:description "Development, application, feasibility and preliminary evaluation of the implementation science research development (ImpRes) tool and guide | BACKGROUND:Designing implementation research can be a complex and daunting task, especially for applied health researchers who have not received specialist training in implementation science. We developed the Implementation Science Research Development (ImpRes) tool and supplementary guide to address this challenge and provide researchers with a systematic approach to designing implementation research. METHODS:A multi-method and multi-stage approach was employed. An international, multidisciplinary expert panel engaged in an iterative brainstorming and consensus-building process to generate core domains of the ImpRes tool, representing core implementation science principles and concepts that researchers should consider when designing implementation research" ; sc:featureList edam:operation_3435 ; sc:name "ImpRes" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31412887" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3300, edam:topic_3398 ; sc:citation , "pmcid:PMC6462781", "pubmed:31011536" ; sc:description "Python package for writing data analysis workflows to interpret microbial physiology." ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Impact framework" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.0" ; sc:url "https://github.com/lmse/impact" ; biotools:primaryContact "Laboratory for Metabolic Systems Engineering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3474 ; sc:citation ; sc:description "Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices | We introduce two highly accurate machine learning based distance imputation techniques. One of our approaches is based on matrix factorization (MatrixFactorization.py), and the other one is an autoencoder based deep learning technique (Autoencoder.py). We evaluate these two techniques on a collection of simulated and biological datasets, and show that our techniques are more accurate and robust than the best alternate technique for distance imputation. Moreover, our proposed techniques can handle substantial amount of missing data, to the extent where the best alternate method fails | (See the imports in both of the python files) | -python 3.5+ -easygui -pandas -numpy -matplotlib -seaborn -tensorflow -keras" ; sc:featureList edam:operation_0557, edam:operation_3478, edam:operation_3557 ; sc:name "ImputeDistances" ; sc:url "https://github.com/Ananya-Bhattacharjee/ImputeDistances" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3934 ; sc:description "MATLAB script for importing images and metadata using the LOCI Bioformats package." ; sc:isAccessibleForFree true ; sc:name "Imread for multiple life science image file formats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32920-imread-for-multiple-life-science-image-file-formats" ; biotools:primaryContact "Christoph Moehl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6614062", "pubmed:31284879" ; sc:description "Database and software for mitochondrial imperfect interspersed repeats annotation." ; sc:featureList edam:operation_0237, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ImtRDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfodbs.kantiana.ru/ImtRDB/" ; biotools:primaryContact "Konstantin Gunbin", "Viktor Shamansky" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "IndigoMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "http://www.cbrc.kaust.edu.sa/indigo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6777010", "pubmed:31608148" ; sc:description "Python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports | Genome scale copy number inference from discrete reports of gene-level amplifications on somatic cancer NGS testing reports | InferAMP - inferring genome-wide amplicon boundaries from cancer NGS reports | Optimized for Foundation One reports from Foundation Medicine | A working version of the web implementation is at http://inferamp.org" ; sc:license "MIT" ; sc:name "InferAMP" ; sc:url "http://inferamp.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475, edam:format_3620, edam:format_3752, edam:format_3758 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:18453552" ; sc:description "InfernoRDN can perform various downstream data analysis, data reduction, and data comparison tasks including normalization, hypothesis testing, clustering, and heatmap generation." ; sc:featureList edam:operation_0337, edam:operation_0531, edam:operation_2238, edam:operation_2939, edam:operation_3432, edam:operation_3435, edam:operation_3557, edam:operation_3630 ; sc:license "Apache-2.0" ; sc:name "InfernoRDN" ; sc:url "https://omics.pnl.gov/software/infernordn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3360, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:31769783" ; sc:description """Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. R package for DNA methylation analysis. R package for DNA methylation analysis The proposition of cancer cells in a tumor sample, named as tumor purity, is an intrinsic factor of tumor samples and has potentially great influence in variety of analyses including differential methylation, subclonal deconvolution and subtype clustering. InfiniumPurify is an integrated R pa ckage for est imatin g and accoun ting for tum or puri ty based on DNA methylation Infinium 450 k array data. InfiniumPurify has three main functions getPurity, InfiniumDMC and InfiniumClust, which could infer tumor purity, differential methylation analysis and tumor sample c luster accounting for estimated or user-provided tumor purities, respectively. The InfiniumPurify package provides a comprehensive analysis of tumor purity in cancer methylation research.""" ; sc:featureList edam:operation_3204, edam:operation_3435, edam:operation_3629 ; sc:name "InfiniumPurify-R" ; sc:url "https://github.com/Xiaoqizheng/InfiniumPurify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3307 ; sc:citation , "pubmed:31756362" ; sc:description """Multi-model inference of non-random mating from an information theoretic approach. Non-random mating and Information Theory. mate choice, assortative mating, jmating, sexual selection, akaike. Relying on the informational partition of the non-random mating effects, and by modeling mate choice and competition by the mutual propensity parameters, it is possible to identify the necessary and sufficient conditions of random mating and from here, develop and connect different kinds of models producing different effects. These models can be used to generate inferences on the parameters of interest. The software InfoMating implements the methodology to do so""" ; sc:featureList edam:operation_3659 ; sc:name "InfoMating" ; sc:url "http://acraaj.webs6.uvigo.es/InfoMating/Infomating.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3673 ; sc:citation ; sc:description "Comprehensive genetic resource and analysis platform of insects." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "InsectBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.insect-genome.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512, edam:topic_3519 ; sc:citation , "pubmed:31834359" ; sc:description """Platform-integrated mRNA Isoform Quantification. Integrated model for RNA-Seq based transcript quantification. IntMTQ is an integrative method combining isoform expressions from NanoString/Exon-array platforms to provide better quantification of RNA-Seq based transcript abundances. We provide the source code of paper Platform-integrated mRNA Isoform Quantification for bioinformatics submission""" ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "IntMTQ" ; sc:url "https://github.com/CompbioLabUcf/IntMTQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """Deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data. Intelli-NGS:Intelligent NGS, a deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data Preprint: DOI https://doi.org/10.1101/2019.12.17.879403""" ; sc:featureList edam:operation_0484, edam:operation_3227, edam:operation_3675 ; sc:name "Intelli-NGS" ; sc:url "https://www.github.com/aditya-88/intelli-ngs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation ; sc:description """Global Peptide-Protein Docking with Structural Templates. Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming, and because of the disordered nature of the ligand, the interactions are especially difficult to predict through software, requiring specialized solutions. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide-protein interactions. We have previously shown that structural templates can be used to accurately predict peptide-protein binding sites, and that using templates from regular protein-protein interactions will increase the number of sites found""" ; sc:featureList edam:operation_0267, edam:operation_2464, edam:operation_2492, edam:operation_3899, edam:operation_3904 ; sc:name "InterPep2" ; sc:url "http://wallnerlab.org/InterPep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172 ; sc:citation , "pmcid:PMC6648201", "pubmed:31459550" ; sc:description "Integrated Supportive Webtools for Low- and High-Field NMR Analyses Toward Molecular Complexity | Description SpinLIMS Contact Others | Integrated supportive webtools for low- and high-field NMR analysis toward molecular complexities | SENsitivity improvement with Spectral Integration" ; sc:featureList edam:operation_3215, edam:operation_3637, edam:operation_3642 ; sc:name "InterSpin" ; sc:url "http://dmar.riken.jp/interspin/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3305, edam:topic_3411, edam:topic_3418 ; sc:citation , "pmcid:PMC6818104", "pubmed:31648624" ; sc:description """Adding Circumstances Of Mortality CATegories (COMCATs) to deaths investigated by verbal autopsy. files relating to evaluation of InterVA-5 software. Resources relating to InterVA-5 verbal autopsy software. Software for WHO verbal autopsy standards. InterVA provides the leading public-domain resources for interpreting verbal autopsy data. InterVA is a suite of computer models to facilitate interpreting VAs, and the latest versions and information are available on a public-domain basis from this site. This research is based at the Umeå Centre for Global Health Research, in northern Sweden, which also hosted the World Health Organization Collaborating Centre for Verbal Autopsy from 2012 to 2016.""" ; sc:featureList edam:operation_2409, edam:operation_3503 ; sc:license "GPL-3.0" ; sc:name "InterVA-5" ; sc:url "http://www.interva.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc:description """The Case for Sensible Extraction of Interactions in the Era of Machine Learning. Extract meaningful interactions from machine learning models to obtain machine-learning performance with statistical model interpretability. Welcome to InteractionTransformer. Welcome to the InteractionTransformer wiki!. What our package does not do: extract transformations in the data to add them to the design matrix. For those capabilities, please see the SAFE Transformer package (https://github.com/ModelOriented/SAFE). Our package does have an experimental feature that will iteratively call InteractionTransformer and SAFETransformer to develop multi-layer interactions/transformation models, but this is still under development.""" ; sc:featureList edam:operation_0321, edam:operation_3659 ; sc:license "MIT" ; sc:name "InteractionTransformer" ; sc:softwareHelp ; sc:url "https://github.com/jlevy44/InteractionTransformer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC6612871", "pubmed:31510675" ; sc:description "Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues | Spatial Dirichlet Gaussian Mixture Model for single ion images | run W_matrix.R GMM.R k_DGMM.R S_DGMM.R first | run CpG_Sal_mouse brain.R to get results of CpG and Sal preconditioned mouse brain data" ; sc:featureList edam:operation_3891 ; sc:name "IonSpattern" ; sc:url "https://github.com/Vitek-Lab/IonSpattern" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:30903185" ; sc:description "IsoCor is a scientific software dedicated to the correction of low- and high-resolution mass spectrometry (MS) data for naturally occuring isotopes. IsoCor corrects raw MS data (mass fractions) for naturally-occurring isotopes of all elements and purity of the isotopic tracer. The output of IsoCor is the isotopologue distribution of the molecule (i.e. the relative fractions of molecular entities differing only in the number of isotopic substitutions of the tracer). IsoCor also calculates the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IsoCor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MetaSys-LISBP/IsoCor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3315 ; sc:citation , "pmcid:PMC6855200", "pubmed:31737449" ; sc:description """Another look at the eigenvalues of a population matrix model. Theoretical Population Modeling for Understanding Growth Rates. Visualizing how the growth rates responds to alterations in life history traits. Hanley B, Connelly P, & Dennis B. 2019. IsoPOPd: Interactive software to understand how elements in a population matrix model influence the asymptotic population growth rate [Software]. Cornell University Library eCommons Repository. doi: https://doi.org/10.7298/bcmg-7w08""" ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:name "IsoPOPd" ; sc:url "https://cwhl.vet.cornell.edu/tools/isopopd" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2332 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:21067241" ; sc:description "IsobariQ is a program designed for use in quantitative mass spectrometry based proteomics. It is a novel tool for accurate quantification of IPTL, iTRAQ and TMT data, and currently, it is the only freely available tool to analyse IPTL data. It allows the user to examine proteomic data in detail and interactively through a graphical user interface. In addition, it provides the user with advanced statistical analysis, including recently published variance stabilising normalisation (VSN)." ; sc:featureList edam:operation_3435, edam:operation_3630, edam:operation_3635, edam:operation_3639, edam:operation_3641, edam:operation_3694, edam:operation_3705, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "IsobariQ" ; sc:url "http://norwegian-proteomics-society.uio.no/isobariq/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3955 ; sc:citation , "pubmed:15256408", "pubmed:16002431", "pubmed:17000750", "pubmed:31893378" ; sc:description "“C++”-program simulating the dynamics of metabolites and their isotopic isomers in the central metabolic network using a corresponding kinetic model. Supports the final step of 13C assisted the fluxomic analysis: evaluation of metabolic fluxes consistent with a given mass isotopomer distribution. The previous steps are supported by Ramid, Midcor, Isoform." ; sc:featureList edam:operation_2426 ; sc:license "Freeware" ; sc:name "Isodyn" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/seliv55/isodyn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:31893378" ; sc:description "R-program that prepares the corrected mass spectra (supposed to be provided by Midcor) to the final step of the workflow of fluxomic analysis: simulation of dynamics of mass isotopomer distribution in a kinetic model." ; sc:featureList edam:operation_3214 ; sc:license "Freeware" ; sc:name "Isoform" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3577 ; sc:citation , "pmcid:PMC6699389", "pubmed:31467902" ; sc:description "An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs | MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs" ; sc:featureList edam:operation_0331, edam:operation_0463, edam:operation_0484 ; sc:name "IsomiR_Find" ; sc:url "https://github.com/wangying0128/IsomiR_Find" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation , "pmcid:PMC6396427", "pubmed:30674557" ; sc:description "Analysis package for processing counts from genome-wide CRISPR/Cas9 screens." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "JACKS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/felicityallen/JACKS" ; biotools:primaryContact "F. Allen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_3315, edam:topic_3382 ; sc:citation ; sc:description """JACOBI4 software for multivariate analysis of biological data. JACOBI4 является проектом, разработанным для автоматизации статистического многомерного анализа биологических данных. Д.А. Полунин, И.А. Штайгер, В.М. Ефимов Разработка программного комплекса JACOBI 4 для многомерного анализа микрочиповых данных // Вестник НГУ т.12 Вып. 2. – Новосибирск: Редакционно-издательский центр НГУ, 2014. С. 90-98""" ; sc:featureList edam:operation_3629, edam:operation_3659, edam:operation_3891 ; sc:name "JACOBI4" ; sc:url "https://jacobi4.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0632, edam:topic_2275 ; sc:citation , "pubmed:31140800" ; sc:description "Characterization of Hydration Properties in Structural Ensembles of Biomolecules." ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "JAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mspc.bii.a-star.edu.sg/minhn/jal.html" ; biotools:primaryContact "Chandra S. Verma", "Minh N. Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , , "pmcid:PMC5896493", "pubmed:29666773" ; sc:description """Assessing intraspecific genetic diversity from community DNA metabarcoding data. Estimating intraspecific genetic diversity from community DNA metabarcoding data. JAMP - Just Another Metabarcoding Pipeline. JAMP is a modular metabarcoding pipeline, integrating different functions from USEARCH, VSEARCH, CUTADAPT and other programs. The pipeline is run as an R package and automatically generates the needed folders and summary statistics""" ; sc:featureList edam:operation_0450, edam:operation_0487, edam:operation_3192, edam:operation_3196, edam:operation_3200 ; sc:name "JAMP" ; sc:url "https://github.com/VascoElbrecht/JAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC6408804", "pubmed:30849961" ; sc:description "Joint Overlap Analysis (JOA) of multiple genomic interval sets. Takes n interval sets and finds overlapping intervals with no constraints on the given intervals." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "JOA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://joa.readthedocs.org" ; biotools:primaryContact "Burcak Otlu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2258 ; sc:citation , "pmcid:PMC6645593", "pubmed:31457399" ; sc:description "A Python Program of Joback and Reid Method | Python GUI program for a quick estimation of physicochemical properties of molecules | A brief description of JRgui program: | By using the modern object-oriented programming language Python (e.g. tkinter and pandas modules) and a chemoinformatics open source library (RDKit), the classic Joback and Reid group contribution method was revisited and written into a graphical user interface program JRgui" ; sc:featureList edam:operation_1812 ; sc:name "JRgui" ; sc:url "https://github.com/curieshicy/JRgui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3489 ; sc:citation , "pubmed:31882996" ; sc:description """Bioinformatics Pipeline using JUDI. This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!. JUDI - Bioinformatics Pipeline: Just Do It.""" ; sc:license "MIT" ; sc:name "JUDI" ; sc:url "https://github.com/ncbi/JUDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:31390206" ; sc:description "Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics | protein docking using a density-based descriptor for atoms charge and dynamics | JabberDock provides a mechanism to dock two protein STID maps together in conjunction with the POW engine and BioBox | Shipped with this version of JabberDock is a heavily stripped version of biobox containing the functions JabberDock requires. Please move the biobox folder into whatever directory you like (e.g. your home), just make sure it's in your pythonpath There is a readme file in the biobox folder containing instructions on requirements and installation instructions" ; sc:featureList edam:operation_0387, edam:operation_0482, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "JabberDock" ; sc:url "http://github.com/degiacom/JabberDock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2269, edam:topic_3292, edam:topic_3301 ; sc:citation , "pmcid:PMC6929325", "pubmed:31874610" ; sc:description """Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data. Test Similarity Between Binary Data using Jaccard/Tanimoto Coefficients. Calculate statistical significance of Jaccard/Tanimoto similarity coefficients for binary data.""" ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "Jaccard" ; sc:url "https://cran.r-project.org/package=jaccard" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1477, edam:format_1915, edam:format_1929, edam:format_1938, edam:format_1939, edam:format_1947, edam:format_1948, edam:format_1961, edam:format_1982, edam:format_1984, edam:format_1997, edam:format_3015, edam:format_3016, edam:format_3311, edam:format_3313, edam:format_3774 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0886 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_1947, edam:format_1948, edam:format_1961, edam:format_1982, edam:format_1997, edam:format_3015, edam:format_3313, edam:format_3464, edam:format_3774 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_1915, edam:format_2331, edam:format_3466, edam:format_3603, edam:format_3604 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092 ; sc:citation ; sc:description "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation." ; sc:featureList edam:operation_0324, edam:operation_0564, edam:operation_3081 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Jalview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.11.3.2" ; sc:url "https://www.jalview.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3855 ; sc:citation , "pubmed:31310719" ; sc:description "Extensible open-source software package for adaptive quantum mechanics/molecular mechanics (QM/MM) Methods." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Janus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CCQC/janus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170 ; sc:citation , "pubmed:31681943" ; sc:description """a Java pipeline for isomiR characterization in miRNA-Seq Data. MOTIVATION:The existence of complex subpopulations of miRNA isoforms, or isomiRs, is well established. While many tools exist for investigating isomiR populations, they differ in how they characterize an isomiR, making it difficult to compare results across different tools. Thus, there is a need for a more comprehensive and systematic standard for defining isomiRs. Such a standard would allow investigation of isomiR population structure in progressively more refined sub-populations, permitting the identification of more subtle changes between conditions and leading to an improved understanding of the processes that generate these differences. RESULTS:We developed Jasmine, a software tool that incorporates a hierarchal framework for characterizing isomiR populations""" ; sc:featureList edam:operation_3198, edam:operation_3435, edam:operation_3792 ; sc:name "Jasmine" ; sc:url "https://bitbucket.org/bipous/jasmine/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3384 ; sc:citation , "pubmed:31841400" ; sc:description """Joint Multi-Modal Longitudinal Regression and Classification for Alzheimer's Disease Prediction. Code for Joint Multi-Modal Longitudinal Regression and Classification. Joint Multi-Modal Longitudinal Regression and Classification (JMMLRC) Estimator. This repository contains the code for performing a classification and a regression task at the same time on longitudinal data. This work has been applied to the ADNI dataset and has shown state-of-the-art performance in predicting patients with and without Alzheimer's Disease.""" ; sc:featureList edam:operation_3659 ; sc:name "Joint Multi-Modal Longitudinal Regression Classification" ; sc:url "https://github.com/minds-mines/jmmlrc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Aeschynomene evenia genomic data from the Legume Information System" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "JointvetchMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2.1" ; sc:url "https://mines.legumeinfo.org/jointvetchmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "General approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "K-TOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mlpaull/KTOPE" ; biotools:primaryContact "Michael L. Paull", "Patrick S. Daugherty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0632 ; sc:citation ; sc:description "In vitro and in silico PCR analysis tool for high-throughput SNP genotyping." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KASPspoon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon" ; biotools:primaryContact "Dr. Shafik D. Ibrahim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_3172, edam:topic_3173, edam:topic_3298 ; sc:citation , "pmcid:PMC6923931", "pubmed:31856718" ; sc:description """a universal framework for multi-omics data integration and biological discoveries. Towards this, we have expanded our in-house developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean to other organisms via Knowledge Base Commons (KBCommons) without the need for reinventing the wheel. Advancement of next generation sequencing and high-throughput technologies has resulted in generation of multi-level of 'OMICS' data for many organisms""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_2939, edam:operation_2940 ; sc:name "KBCommons" ; sc:url "http://kbcommons.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3375 ; sc:citation , "pubmed:31381336" ; sc:description "A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding | KBbox is developed to be of use to researchers interested in applying these methods in their work. To help with this, KBbox provides an updated list of examples of published work, along with detailed tutorials to guide less experienced researchers" ; sc:name "KBbox" ; sc:url "https://kbbox.h-its.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_2840 ; sc:citation ; sc:description "Novel computational framework for systematic uncovering hidden gene interactions underlying known drug-disease associations | A computational framework for uncovering hidden gene interactions underlying Known Drug-Disease Associations (KDDAs) | To use KDDANet, please refer to the instructions in manual.txt in this subdirectory | This software identifies the hidden gene interactions and modules underlying KDDAs through implementing minimum cost optimization and graph clustering on a unified flow network model" ; sc:featureList edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "KDDANet" ; sc:url "https://github.com/huayu1111/KDDANet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3263, edam:topic_3474 ; sc:citation , "pmcid:PMC6776354", "pubmed:31581246" ; sc:description """A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services. BACKGROUND AND OBJECTIVE:To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment. METHODS:The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:name "KETOS" ; sc:url "https://ketos.ai/hb/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489 ; sc:citation , "pmcid:PMC6790968", "pubmed:31608948" ; sc:description """new binding kinetics database and its integration in an open-source binding analysis software. Kinetics OF Featured Interactions. KOFFI-DB (???) is an article based database for kinetic constants of biomolecular interactions. We focused on interactions between DNA, RNA, proteins and chemical compounds. All datapoints were manually annotated and reviewed based on open source articles available on Europe PMC""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3778 ; sc:name "KOFFI" ; sc:url "http://www.koffidb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC6889754", "pubmed:31794015" ; sc:description """Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information. The first Korean Reference Genome. KOREF_S means KOREF_Single.""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3228 ; sc:name "KOREF" ; sc:url "http://koref.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3421 ; sc:citation , "pmcid:PMC6538268", "pubmed:31054501" ; sc:description "KPDGUI (Kidney Paired Donation Graphical User Interface) - interactive application for optimization and management of a virtual kidney paired donation program." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "KPDGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mathieubray/KPDGUI" ; biotools:primaryContact "Mathieu Bray" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc:description "Hidden Markov Model generator for detecting KEGG PATHWAY-specific genes." ; sc:featureList edam:operation_3092, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KPHMMER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/suecharo/KPHMMER" ; biotools:primaryContact "Hirotaka Suetake" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3295 ; sc:citation ; sc:description "Online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas." ; sc:featureList edam:operation_0420, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "KRAB ZNF explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mi2.mini.pw.edu.pl:8080/KRAB_ZNF/" ; biotools:primaryContact "Urszula Oleksiewicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3379 ; sc:citation ; sc:description "Defining and targeting adaptations to oncogenic KRASG12C inhibition using quantitative temporal proteomics | ABSTRACT Covalent inhibitors of the KRAS G12C oncoprotein have recently been developed and are being evaluated in clinical trials. Resistance to targeted therapies is common and likely to limit long-term efficacy of KRAS inhibitors (KRASi). To identify pathways of adaptation to KRASi and to predict drug combinations that circumvent resistance, we used a mass spectrometry-based quantitative temporal proteomics and bioinformatics workflow to profile the temporal proteomic response to KRAS G12C inhibition in pancreatic and lung cancer 2D and 3D cellular models. We quantified 10,805 proteins across our datasets, representing the most comprehensive KRASi proteomics effort to date. Our data reveal common mechanisms of acute and long-term response between KRAS G12C -driven tumors" ; sc:featureList edam:operation_2436, edam:operation_3799 ; sc:name "KRASi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://manciaslab.shinyapps.io/KRASi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068 ; sc:citation ; sc:description "Kinase-Substrate Enrichment Analysis (KSEA) App - web-based tool for kinase activity inference from quantitative phosphoproteomics." ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KSEA App" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://casecpb.shinyapps.io/ksea/" ; biotools:primaryContact "Danica D. Wiredja", "Mark R. Chance" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830, edam:topic_3301, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description """Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Kaptive reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies. You can also run a graphical version of Kaptive via this web interface (source code). Given a novel genome and a database of known loci (K, O or OC), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:. Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. It takes one or more pre-assembled genomes and for each finds the best matching locus from a reference database. References for Klebsiella pneumoniae species complex and Acinetobacter baumannii are available in Kaptive's web interface""" ; sc:featureList edam:operation_0525, edam:operation_2421, edam:operation_3431, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Kaptive" ; sc:url "http://kaptive.holtlab.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2830, edam:topic_3411, edam:topic_3518, edam:topic_3673 ; sc:citation , "pubmed:31862729" ; sc:description """Multiregion whole-genome sequencing depicts intratumour heterogeneity and punctuated evolution in ovarian clear cell carcinoma. An R package for detecting and visualizing Kataegis events. KataegisPortal is an R package that provides utilities to detect and visualize the Kataegis events from single nucleotide variants (SNVs)""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3891 ; sc:name "KataegisPortal" ; sc:url "https://github.com/MeichunCai/Kataegisportal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:31583639" ; sc:description """De Novo Pathway Enrichment with KeyPathwayMiner. (17E1EF77D1E66C1CFE344BDA3D7945B0). Given a biological network and a set of case-control studies, KeyPathwayMiner efficiently extracts all maximal connected sub-networks. These sub-networks contain the genes that are mainly dysregulated, e.g., differentially expressed, in most cases studied.""" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3501 ; sc:name "KeyPathwayMiner" ; sc:url "https://keypathwayminer.compbio.sdu.dk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:author "Dr. Ehsan Ullah" ; sc:citation ; sc:description "Visualization tool to detect cryptic relatedness in genetic datasets." ; sc:featureList edam:operation_3196, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "KinVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny-vis.qcri.org/public/kinvis/" ; biotools:primaryContact "Dr. Ehsan Ullah", "Dr. Halima Bensmail" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0820, edam:topic_0821, edam:topic_3314, edam:topic_3570 ; sc:citation ; sc:description """Efficient Manipulation and Generation of Kirchhoff Polynomials for the Analysis of Non-equilibrium Biochemical Reaction Networks. Efficient manipulation and compact generation of expressions of Kirchhoff polynomials""" ; sc:featureList edam:operation_0270, edam:operation_2995 ; sc:name "Kirchhoff polynomials" ; sc:url "https://gitlab.com/csb.ethz/KirchPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome." ; sc:featureList edam:operation_3227, edam:operation_3258 ; sc:name "KisSplice" ; sc:url "http://kissplice.prabi.fr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_1975 ; sc:name "Sequence features metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3475 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3665 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1975 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0780, edam:topic_0797, edam:topic_3511 ; sc:author , , , "Markus Schwalbe" ; sc:citation , "pubmed:31823436" ; sc:contributor , "Markus Schwalbe" ; sc:description "Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity." ; sc:featureList edam:operation_0237, edam:operation_0379, edam:operation_0463, edam:operation_2428, edam:operation_2451, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Kmasker" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.1.0", "1.1.1" ; sc:url "https://kmasker.ipk-gatersleben.de/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0780, edam:topic_3673, edam:topic_3912 ; sc:citation , "pubmed:31823436" ; sc:description """A tool for assessing complex sequence space in plant species. Kmasker - a tool for masking and exploring of sequences from plant species. a versatile tool for masking and exploring of sequences from plant species. Kmasker plants is a tool for the automatic detection of sequence regions with meaningful k-mer characteristics. This can be sequences with highly abundant k-mer patterns (repeats), regions with diverging k-mer patterns between two studied WGS samples or segments with high target specificity. The installation instructions are available at: INSTALL.md. There, you find our list of requirements of external tools. Please make sure, that these are in your PATH environemnt if you installed from source. If not please specify them in the 'etc/kmasker.config' file. Kmasker uses an interal repository for reuse of kindex structures.""" ; sc:featureList edam:operation_0368, edam:operation_0525, edam:operation_3196, edam:operation_3211, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Kmasker plants" ; sc:url "https://kmasker.ipk-gatersleben.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:31598675" ; sc:description """A comprehensive human gene expression profile database with knockdown/knockout of transcription factors. We develop a comprehensive human gene expression profile database with TF knockdown/knockout (KnockTF), which provides a large number of available resources of human gene expression profile datasets associated with TF knockdown/knockout and annotates TFs and their target genes in a tissue/cell type-specific manner""" ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_2942 ; sc:name "KnockTF" ; sc:url "http://www.licpathway.net/KnockTF/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pubmed:31504154" ; sc:description "Knot_pull-python package for biopolymer smoothing and knot detection | Python module for knot-like structure detection in biological molecules | KnotPull - a simplifier for 3D structures | KnotPull reduces a user provided 3D structure, to simplify it, while preserving the topology of the chain. It has been successfully used for knot detection in proteins and chromatin chains" ; sc:featureList edam:operation_3890 ; sc:license "GPL-3.0" ; sc:name "Knot_pull" ; sc:url "http://github.com/dzarmola/knot_pull" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0736, edam:topic_3315 ; sc:citation ; sc:description "Tool to study the entanglement of open protein chains using the concept of knotoids." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Knoto-ID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.vital-it.ch/software/Knoto-ID" ; biotools:primaryContact "Julien Dorier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625 ; sc:citation , "pmcid:PMC6690010", "pubmed:31428111" ; sc:description "A Web-Resource Focused on Diversity Data for Pulse Crop Improvement | Welcome to the Public Portal for the University of Saskatchewan Pulse Crop Research Group | ◼ View other species of interest | ◼ View other bioinformatics tools" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:name "KnowPulse" ; sc:url "https://knowpulse.usask.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:31120584" ; sc:description "Rate constant method for prediction of the diffusion of sorbates inside nanoporous materials at different loadings." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KoBra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/kobra/" ; biotools:primaryContact "Panagiotis D. Kolokathis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_0621, edam:topic_0623 ; sc:citation , "pubmed:31742321" ; sc:description """KEGG ortholog assignment based on profile HMM and adaptive score threshold. KofamKOALA - KEGG Orthology Search. K number assignment based on KO-dependent scoring criteria. KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.""" ; sc:featureList edam:operation_0533, edam:operation_2421, edam:operation_3092 ; sc:name "KofamKOALA" ; sc:url "https://www.genome.jp/tools/kofamkoala/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3324, edam:topic_3673, edam:topic_3837 ; sc:citation , "pmcid:PMC6897419", "pubmed:31756192" ; sc:description "Identification and quantitation of clinically relevant microbes in patient samples." ; sc:featureList edam:operation_2428, edam:operation_3460, edam:operation_3472, edam:operation_3799 ; sc:license "MIT" ; sc:name "KrakenUniq" ; sc:url "https://github.com/hurwitzlab/krakenuniq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC4722636", "pubmed:26801218" ; sc:description "Matlab implementation of the Kronecker Regularized Least Squares with multiple kernels algorithm." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "KronRLS-MKL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/andrecamara/kronrlsmkl" ; biotools:primaryContact "André C. A. Nascimento" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6692109", "pubmed:31405451" ; sc:description "Deep learning software for automated kymograph analysis | The AI that analyses your kymographs | The AI that analyses your kymograph | Easy drag and drop software under http://kymobutler.deepmirror.ai | Download KymoButler.nb and open it in Mathematica. Run the first cell to download the necessary neural networks and the KymoButler package. The use the function KymoButler[] to analyse your kymographs" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "KymoButler" ; sc:url "http://kymobutler.deepmirror.ai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31584629" ; sc:description """A tool for accurate locus specific LINE-1 RNA quantification. Estimate locus specific human LINE-1 expression. git clone https://github.com/wmckerrow/L1EM. git (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git). anaconda (https://docs.anaconda.com/anaconda/install/). If necessary, you can specify the path for bwa and samtools in the run_L1EM.sh script. You must use samtools >=1.0. Early version of pysam will not work. I highly recommend that you use bwa 0.7.17. Earlier versions may differ in how they write the XA tag. This will lead to inaccurate results without throwing an error""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "L1EM" ; sc:url "https://github.com/FenyoLab/L1EM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3361 ; sc:citation , "pubmed:31374334" ; sc:description "A new database designed specifically for Lactic Acid Bacteria bacteriocins | Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicrobial peptides (AMPs) is scattered through the literature and databases. Therefore, we developed the LABiocin database, a specialized database on LAB bacteriocins. The database was stored and compiled using MySQL with NetBeans IDE as the platform. Important data are compiled, including bacteriocin name, class, amino acids and nucleic acid sequences, if available. Target microorganisms, origin, status of the producing strains and their culture conditions and extraction and purification methods are also included in this new database. A phylogenetic tree for the mature peptide bacteriocin sequences has also been created" ; sc:name "LABiocin database" ; sc:url "http://labiocin.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_2640, edam:topic_3336 ; sc:citation , "pubmed:31799600" ; sc:description """Integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, a wide range of computational tools have been designed to investigate the important dynamic information in proteins. However, performing and analyzing protein dynamics is still challenging due to the complicated operation steps, giving rise to great difficulty, especially for nonexperts. Moreover, there is a lack of web protocol to provide online facility to investigate and visualize ligand-driven protein dynamics""" ; sc:featureList edam:operation_2476, edam:operation_2495 ; sc:name "LARMD" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/LARMD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pubmed:22682917" ; sc:description "Liege Acromegaly Survey (LAS) database includes anonymous historical and prospective data on liege acromegaly patients, pathophysiology, clinical features, responses to therapy and long term outcomes of acromegaly." ; sc:name "LAS database" ; sc:url "http://catalogue.rd-connect.eu/web/liege-acromegaly-survey-las-database" ; biotools:primaryContact "Patrick Petrossians" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using Multi-Contrast MRI | LASHiS was loosely adapted from the ANTs Longitudinal Cortical Thickness pipeline https://github.com/ANTsX/ANTs/ The ASHS_TSE image slice direction should be z. In other words, the dimension of ASHS_TSE image should be 400x400x30 or something like that, not 400x30x400" ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "LASHiS" ; sc:url "https://github.com/thomshaw92/LASHiS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2229, edam:topic_3047 ; sc:citation , "pmcid:PMC6822780", "pubmed:31634364" ; sc:description """A lattice model for simulating phase transitions of multivalent proteins. Many biomolecular condensates form via spontaneous phase transitions that are driven by multivalent proteins. These molecules are biological instantiations of associative polymers that conform to a so-called stickers-and-spacers architecture. The stickers are protein-protein or protein-RNA interaction motifs and or domains that can form reversible, non-covalent crosslinks with one another. Spacers are interspersed between stickers and their preferential interactions with solvent molecules determine the cooperativity of phase transitions. Here, we report the development of an open source computational engine known as LASSI (LAttice simulation engine for Sticker and Spacer Interactions) that enables the calculation of full phase diagrams for multicomponent systems comprising of coarse-grained representations of multivalent proteins.""" ; sc:featureList edam:operation_2949, edam:operation_3454, edam:operation_3893 ; sc:name "LASSI" ; sc:url "https://github.com/Pappulab/LASSI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_0781, edam:topic_3676 ; sc:citation ; sc:description """a streamlined visualization tool for longitudinal analysis of viral alleles. LAVA: Longitudinal Analysis of Viral Alleles. LAVA analyzes and visualizes minor allele variants in longitudinal sequence data. LAVA takes a reference fasta (normally representing the first sample in your longitudinal analysis), fastq files (for every sample in your analysis), and a metadata sheet (providing information on what day or passage each sample was collected). Output will be displayed as an interactive graph in your web browser. LAVA will only work on Mac and Linux machines""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3192, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "LAVA" ; sc:url "https://github.com/michellejlin/lava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:31038689" ; sc:description "Label Ambiguous Domain Adaptation (LAmbDA) - species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LAmbDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/tsteelejohnson91/LAmbDA" ; biotools:primaryContact "Jie Zhang", "Kun Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:author ; sc:citation , "pubmed:26406767" ; sc:description "LBEEP (Linear B-Cell Exact Epitope Predictor) is a perl based open source tool for the prediction of Linear B-cell epitopes. Please refer the article tilted \"Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-based Feature Descriptor\" for more deatils." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LBEEP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/brsaran/LBEEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31683145" ; sc:description """Learning Cascade Attention for fine-grained image classification. Code for paper "Learning Cascade Attention for Fine-grained Image Classification", which currently under review at Elsevier Journal of Neural Networks(NN). Train/test split for CUB-200-2011 dataset. Rotate training set for data augmentation.""" ; sc:featureList edam:operation_3359 ; sc:name "LCA-CNN" ; sc:url "https://github.com/billzyx/LCA-CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518, edam:topic_3673 ; sc:citation , "pmcid:PMC6889475", "pubmed:31850063" ; sc:description """A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes. Practical program to annotate candidate polymorphism using annotations for genes in genetic linkage in the specific experiment. A bioinformatics tool to automatically provide annotations for genes included in DNA blocks in linkage disequilibrium with candidate SNPs. LD-annot estimates experiment-specific linkage disequilibrium to delineate regions genetically linked to each genetic markers from a list of polymorphisms (most often candidate SNPs from GWAS) and provide coordinates and annotations for genes included or overlapping such regions. Email: jprunier.1@gmail.com or arnaud.droit@crchudequebec.ulaval.ca""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3216, edam:operation_3661 ; sc:license "GPL-3.0" ; sc:name "LD-annot" ; sc:url "https://github.com/ArnaudDroitLab/LD-annot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3314, edam:topic_3520 ; sc:citation , "pmcid:PMC6882832", "pubmed:31780665" ; sc:description """A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Documentation : Forum : Contact. "2,8-Dimethyl-5,7-dimethoxychromone". "5,7-Dihydroxy-2,6,8-trimethylchromone".""" ; sc:featureList edam:operation_0337, edam:operation_3646, edam:operation_3801, edam:operation_3803 ; sc:name "LDB" ; sc:url "https://gnps.ucsd.edu/ProteoSAFe/gnpslibrary.jsp?library=LDB_POSITIVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632 ; sc:citation ; sc:description "Improved read/write cost tradeoff in DNA-based data storage using LDPC codes | LDPC codes for Illumina sequencing-based DNA storage" ; sc:featureList edam:operation_3192 ; sc:name "LDPC" ; sc:url "https://github.com/shubhamchandak94/LDPC_DNA_storage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc:description "Tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LDassoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ldlink.nci.nih.gov/?%20tab=ldassoc" ; biotools:primaryContact "Mitchell J. Machiela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:31584626" ; sc:description """Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs. Source code for LD motif detection. In this repository, we uploaded the necessary files to set up and environment to predict the LD motif from input sequence. We also have a server for LD motif predition : https://www.cbrc.kaust.edu.sa/ldmf/. Users need to run scripts after changing the value of input parameters. The deatils of each parameter is also provide. The code is shared in the folder "src". All external jars are shared in the folder "ExternalJar_Required" There are two files that should be used for Amino Acid index. These files are also shared.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0478 ; sc:name "LDmotif" ; sc:url "https://github.com/tanviralambd/LD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3168, edam:topic_3174, edam:topic_3175, edam:topic_3697 ; sc:citation , "pmcid:PMC6933643", "pubmed:31881904" ; sc:description """A method to construct the local strains at horizontal gene transfer sites in gut metagenomics. It is a software to reconstruct the HGT inserted local strain. It is a software takes use of existing shotgun NGS datasets to detect HGT breakpoints, identify the transferred genome segments, and reconstructs the inserted local strain. usage: python LEMON/Scripts/get_raw_bkp.py [options]. git clone --recursive https://github.com/lichen2018/hgt-detection.git""" ; sc:featureList edam:operation_0495, edam:operation_3228, edam:operation_3359, edam:operation_3802 ; sc:name "LEMON" ; sc:url "https://github.com/lichen2018/LEMON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description """Local event-based analysis of alternative splicing using RNA-Seq data. Local Event-based analysis of alternative Splicing using RNA-Seq. The Local Event-based analysis of alternative Splicing using RNA-Seq (or LESSeq) is a Linux-based processing pipeline for analyzing alternative splicing events from RNA-Seq data""" ; sc:featureList edam:operation_2499, edam:operation_3196, edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "LESSeq" ; sc:url "https://github.com/gersteinlab/LESSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Algorithm for label-free absolute protein quantification, which can correct the biased MS intensities using the predicted peptide quantitative factors for all identified peptides." ; sc:featureList edam:operation_2929, edam:operation_3631, edam:operation_3634 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "LFAQ" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://lfaq.github.io/LFAQ/" ; biotools:primaryContact "Cheng Chang", "Zhiqiang Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31657565" ; sc:description """An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant. A tool for analysing label-free quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. LFQ-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative proteomic datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result output graphics and tables to facilitate statistical and exploratory analysis of label-free quantitative datasets""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3634, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "LFQ-Analyst" ; sc:softwareHelp ; sc:url "https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:citation , "pmcid:PMC6855649", "pubmed:31725736" ; sc:description """A lossless non-reference-based FASTQ compressor. Contribute to sya12005/LFastqC development by creating an account on GitHub. You can’t perform that action at this time""" ; sc:name "LFastqC" ; sc:url "https://github.uconn.edu/sya12005/LFastqC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6837623", "pubmed:31658247" ; sc:description """Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort. An automated script for extracting the scar area, entropy, components, transmurality, radiality and interface length from short axis late gadolinium enhanced cardiac MRI images in nifti format. This repository provides a script that creates a list of metrics quantifying a scar pattern seen in a cardiac short axis late gadolinium enhanced MRI image. The metrics provided are. area - The total area of the scar. radiality - The angular extent of the LGE pattern, with values between 0 and 1. A score of 1 indicates that scars are present in a full 360 degree pattern with respect to the centre of the blood pool, wheras 0 indicates no angular extent of scar.""" ; sc:featureList edam:operation_0244, edam:operation_0455, edam:operation_2426 ; sc:name "LGE" ; sc:url "https://github.com/GabrielBalabanResearch/lgemri_scar_metrics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_2640 ; sc:citation , "pubmed:31621885" ; sc:description """An independently validated survival nomogram for lower grade glioma. BACKGROUND:Gliomas are the most common primary malignant brain tumor. Diffuse low-grade and intermediate-grade gliomas, which together comprise the lower-grade gliomas [LGG] (WHO grades II and III), present a therapeutic challenge to physicians due to the heterogeneity of their clinical behavior. Nomograms are useful tools for individualized estimation of survival. This study aimed to develop and independently validate a survival nomogram for patients with newly diagnosed LGG. METHODS:Data were obtained for newly diagnosed LGG patients from The Cancer Genome Atlas (TCGA) and the Ohio Brain Tumor Study (OBTS) with the following variables: tumor grade (II or III), age at diagnosis, sex, Karnofsky Performance Status (KPS), and molecular subtype (IDH mutant with 1p 19q codeletion [IDHmut-codel], IDH mutant without 1p 19q codeletion [IDHmut-non-codel], IDH wild-type [IDHwt])""" ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659 ; sc:name "LGG" ; sc:url "https://hgittleman.shinyapps.io/LGG_Nomogram_H_Gittleman/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3489 ; sc:citation ; sc:description "LIBR Methamphetamine and Opioid Cue Database (LIBR MOCD) | Repository for the LIBR Meth Opioid Cue Reactivity Database | This project contains two folders:" ; sc:name "LIBR MOCD" ; sc:url "https://github.com/rkuplicki/LIBR_MOCD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0621, edam:topic_2640, edam:topic_3384, edam:topic_3452 ; sc:citation ; sc:description """Standardized representation of the LIDC annotations using DICOM. Scripts for converting TCIA LIDC-IDRI collection derived data into standard DICOM representation from project-specific XML format. This repository contains the script used to convert the TCIA LIDC-IDRI XML representation of nodule annotations and characterizations into the DICOM Segmentation object (for annotations) and DICOM Structured Reporting objects (for nodule characterizations). pylidc is an Object-relational mapping (using SQLAlchemy) for the data provided in the LIDC dataset. This means that the data can be queried in SQL-like fashion, and that the data are also objects that add additional functionality via functions that act on instances of data obtained by querying for particular attributes.""" ; sc:featureList edam:operation_0224, edam:operation_3435, edam:operation_3553 ; sc:name "LIDC" ; sc:url "https://pylidc.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description "Toolkit for Simulating Lignin Biosynthesis." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LIGNIN-KMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/michaelorella/lignin-kmc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:31804675" ; sc:description """A tool for comparing species partition. We are pleased to announce the launch of Limes!.""" ; sc:name "LIMES" ; sc:url "http://www.limes.cnrs.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "A Web service for genome-based identification of microbes as members of crowdsourced taxa | Abstract The development of next generation and third generation DNA sequencing technologies in combination with new efficient algorithms allows scientists to economically, quickly, and precisely identify microbes at all taxonomic levels and even attribute pathogen isolates to specific disease outbreaks. However, current taxonomic practice has not kept up with the sequencing revolution and continues to rely on cumbersome journal publications to describe new species. Here we introduce a Web service that allows any user to genomically circumscribe any monophyletic group of bacteria as a taxon and associate with each taxon a name and short description. Any other user can immediately identify their unknown microbe as a member of any of these crowdsourced taxa using gene or genome sequences. The Web service is called LINbase" ; sc:featureList edam:operation_3840 ; sc:name "LINbase" ; sc:url "http://www.LINbase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0153, edam:topic_3306 ; sc:citation , "pmcid:PMC6541037", "pubmed:31141612" ; sc:description "Web-based ontology enrichment tool for lipidomic data analysis." ; sc:featureList edam:operation_0335, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LION-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lipidontology.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0780 ; sc:citation ; sc:description "Software for identifying lipids in LC-MS/MS-based lipidomics data." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "LIQUID" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/PNNL-Comp-Mass-Spec/LIQUID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0625, edam:topic_3172, edam:topic_3518 ; sc:citation , "pmcid:PMC6902471", "pubmed:31822265" ; sc:description """Longitudinal linear combination test for gene set analysis. LLCT is a two-step self-contained gene-set analysis method which is developed to handle multiple longitudinal outcomes. Analysis of within-subject variation in the first step is followed by examining the between-subject variation utilizing Linear Combination Test (LCT) in the second step. This method is also applicable in analysis of time-course microarray data""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3463, edam:operation_3659 ; sc:name "LLCT" ; sc:url "https://github.com/its-likeli-jeff/LLCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3172, edam:topic_3292, edam:topic_3336, edam:topic_3382, edam:topic_3518 ; sc:citation , , "pmcid:PMC6719194", "pubmed:31443278", "pubmed:33657805" ; sc:description "A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections | LM-GlycomeAtlas v.1.0 is a web tool visualizing the data from Lectin Microarray analyses using 45 lectins by the Kuno Laboratory at AIST | This work was supported by a project for utilizing glycans in the development of innovative drug discovery technologies in the project focused on developing key technology for discovering and manufacturing drugs for next-generation treatment and diagnosis from the Japan Agency for Medical Research and Development (AMED) | CFG(Consortium for Functional Glycomics) Glycan Profilling data | Mapping data of human serum data was from Dr. Shunji Natsuka of Niigata University, Japan" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435, edam:operation_3891 ; sc:name "LM-GlycomeAtlas" ; sc:url "https://glycosmos.gitlab.io/lm-glycomeatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:31860062" ; sc:description """An environment to design bioimage analysis workflows for large and complex fluorescence microscopy data. SUMMARY:Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation & Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "LOBSTER" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31860062" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3325, edam:topic_3360 ; sc:citation , "pmcid:PMC6527418", "pubmed:31119199" ; sc:description "Annotation tool that recommends candidate Human Phenotype Ontology (HPO) terms to a LOINC (Laboratory Observation Identifier Names and Codes) test based on lexical matching between HPO term definitions and the name of a laboratory test." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "LOINC2HPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/monarch-initiative/loinc2hpo" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_3399 ; sc:citation , "pmcid:PMC6602514", "pubmed:31081035" ; sc:description "LOMETS (Local Meta-Threading Server) is meta-threading method for template-based protein structure prediction." ; sc:featureList edam:operation_0267, edam:operation_0302, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LOMETS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://zhanglab.ccmb.med.umich.edu/LOMETS/" ; biotools:primaryContact "Yang Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6722229", "pubmed:31555116" ; sc:description "A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data | LONI Quality Control (LONI QC) is an imaging data review and assessment platform for human neuroimaging research studies involving one or more centers. LONI QC allows users to anonymously download imaging data from the LONI IDA and run a standardized quality control check via an automated pre-processing system specifically designed to generate a range of vector statistics and derived images" ; sc:featureList edam:operation_3180, edam:operation_3218, edam:operation_3431 ; sc:name "LONI-QC" ; sc:url "http://qc.loni.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6786659", "pubmed:31568528" ; sc:description """A single- and multitask machine learning algorithm for the prediction of cancer driver genes. LOTUS is an algorithm for cancer driver gene prediction. This page provides in particular codes to reproduce simulation results. We propose a new computational method called LOTUS to predict new driver genes. LOTUS is a machine-learning based approach which allows to integrate various types of data in a versatile manner, including information about gene mutations and protein-protein interactions. In addition, LOTUS can predict cancer driver genes in a pan-cancer setting as well as for specific cancer types, using a multitask learning strategy to share information across cancer types""" ; sc:featureList edam:operation_2454, edam:operation_3436, edam:operation_3439 ; sc:name "LOTUS" ; sc:url "https://github.com/LOTUSproject/LOTUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3063, edam:topic_3378, edam:topic_3379 ; sc:citation , "pmcid:PMC6918608", "pubmed:31849321" ; sc:description """Combining pre-clinical drug structures and post-market safety reports. Code and Datasets for paper "Towards early detection of adverse drug reactions: combining pre-clinical drug structures and post-market safety reports". This repository contains source code for paper "Towards early detection of adverse drugreactions: combining pre-clinical drug structuresand post-market safety reports" (accepted by BMC Medical Informatics andDecision Making). Please kindly cite the paper if you use the code, datasets or any results in this repo or in the paper:.""" ; sc:featureList edam:operation_3435, edam:operation_3907 ; sc:name "LP-SDA" ; sc:url "https://github.com/ruoqi-liu/LP-SDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31860024" ; sc:description """A latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations. LPM (Latent Probit Model), is an efficient statistical approach to characterize relationship among complex traits using summary statistics from multiple GWASs and functional annotations. 'LPM' package provides model parameter estimation as well as statistical inference""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557, edam:operation_3658, edam:operation_3659 ; sc:name "LPM" ; sc:url "https://github.com/mingjingsi/LPM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196 ; sc:citation ; sc:description "Tool for evaluating Long Reads Correction methods." ; sc:featureList edam:operation_3195, edam:operation_3198, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LRCstats" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cchauve/lrcstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC6902338", "pubmed:31818249" ; sc:description """Improving draft genomes using long noisy reads. Hybrid assembly strategy is a reasonable and promising approach to utilize strengths and settle weaknesses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologies. According to this principle, we here present a new toolkit named LRScaf (Long Reads Scaffolder) by applied TGS data to improve draft genome assembly. The main features are: short running time, accuracy, and being contiguity. To scaffold rice genome, it could be done in 20 mins with minimap mapper. In human, LRScaf could improve the draft assembly NG50 from 127.5 Kb to 10.4 Mb on 20x PacBio CHM1 dataset and NG50 from 115.7 Kb to 17.4 Mb on ~35x Nanopore NA12878 dataset""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:name "LRScaf" ; sc:url "https://github.com/shingocat/lrscaf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3318 ; sc:citation , "pmcid:PMC6879002", "pubmed:31769805" ; sc:description """Assessment of human diploid genome assembly with 10x Linked-Reads data. A program to simulate linked reads sequencing from 10X Chromium System. LRTK-SIM: Linked read simulator for 10X Chromium System. line2 and line3: Path_Fastahap1 and Path_Fastahap2, the two haploid reference serquences. LRTK-SIM allows one or two fasta files to perform haploid and diploid simulation. The diploid reference sequences can be generated by gen_fasta.py that inserting variants to the reference genome (only SNVs for this version). You can remove Path_Fastahap2=XXX in line3 and set Hap=1 in line33 for haploid simulation.""" ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525, edam:operation_3211, edam:operation_3216 ; sc:license "MIT" ; sc:name "LRTK-SIM" ; sc:url "https://github.com/zhanglu295/LRTK-SIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Lesion Segmentation Tool (LST) is an open source toolbox for SPM that is able to segment T2 hyperintense lesions in FLAIR images. Originally developed for the segmentation of MS lesions it has has also been proven to be useful for the segmentation of brain lesions in the context of other diseases, such as diabetes mellitus or Alzheimer's disease." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.statistical-modeling.de/lst.html" ; biotools:primaryContact "Mark Mühlau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31502974" ; sc:description "Progressive Object Transfer Detection | LSTD: A Low-Shot Transfer Detector for Object Detection | Specifically, SSD acts as the region proposal network (RPN) in LSTD. Additionally, we propose Transfer Knowledge (TK) and Background Depression (BD) modules for transfer detection task. More details can be found in LSTD" ; sc:name "LSTD" ; sc:url "https://github.com/Cassie94/LSTD/tree/lstd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31443043" ; sc:description "Predicting microRNA sequence using CNN and LSTM stacked in Seq2Seq architecture | sequence-prediction-using-CNN-and-LSTMs | microRNA sequence prediction using CNN and LSTM" ; sc:featureList edam:operation_0303, edam:operation_0463 ; sc:name "LSTM" ; sc:url "https://github.com/rajkumar1501/sequence-prediction-using-CNN-and-LSTMs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31634636" ; sc:description """Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Large-Scale Transcriptome Analysis Pipeline-Lite on credit card-sized ARM computer. If you use LSTrAP-Lite in your research, please cite: Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Tan and Mutwil, 2019. (https://doi.org/10.1101/661058).""" ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3439 ; sc:license "MIT" ; sc:name "LSTrAP-Lite" ; sc:url "https://github.com/mutwil/LSTrAP-Lite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3500 ; sc:citation , "pmcid:PMC6693147", "pubmed:31409290" ; sc:description "Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference | A script in R to run the LS³ and LS⁴ phylogenetic data subsampling algorithms for reducing lineage rate heterogeneity | LSX is a script in R that runs the LS³ and LS⁴ algorithms of data subsampling for multigene phylogenetic inference" ; sc:license "GPL-3.0" ; sc:name "LSX" ; sc:url "https://github.com/carlosj-rr/LSx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610 ; sc:description "Webpage dedicated to the visualization and management of environmental and planktonic data collected at the LTER-MC station in the Gulf of Naples." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LTER-MARECHIARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://szn.macisteweb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6765121", "pubmed:31372654" ; sc:description "A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data | This repository contains the R codes which could reproduce the results of \"LTMG: A statistical model of transcriptional regulatory states in single cell RNA-Seq data\" by Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Sha Cao, Melissa L. Fishel, Qin Ma, and Chi Zhang" ; sc:featureList edam:operation_0441, edam:operation_2495, edam:operation_3223 ; sc:name "LTMG" ; sc:url "https://github.com/zy26/LTMGSCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6702745", "pubmed:31429720" ; sc:description "Scripts and Data associated with our publication on genomic signatures to discriminate LUAD and LUSC lung cancer types using TCGA data | Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark | Repository associated to the publication: | Different molecular signatures in lung cancer types from integrative bioinformatic analyses of RNASeq data Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo*, bioRxiv, doi: https://doi.org/10.1101/501569" ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "LUAD LUSC" ; sc:url "https://github.com/ELELAB/LUAD_LUSC_TCGA_comparison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3172, edam:topic_3360 ; sc:citation , "pubmed:31504184" ; sc:description "A Latent Unknown Clustering Integrating Multi-Omics Data (LUCID) with Phenotypic Traits | Latent Unknown Clustering with Integrated Data | An implementation for the 'LUCID' method to jointly estimate latent unknown clusters/subgroups with integrated data. An EM algorithm is used to obtain the latent cluster assignment and model parameter estimates. Feature selection is achieved by applying the regularization method" ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "LUCIDus" ; sc:url "https://CRAN.R-project.org/package=LUCIDus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "A flexible pipeline combining bioinformatic correction tools for prokaryotic and eukaryotic metabarcoding | r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding) | The purpose of LULU is to reduce the number of erroneous OTUs in OTU tables to achieve more realistic biodiversity metrics. By evaluating the co-occurence patterns of OTUs among samples LULU identifies OTUs that consistently satisfy some user selected criteria for being errors of more abundant OTUs and merges these. It has been shown that curation with LULU consistently result in more realistic diversity metrics. The required input of LULU is an OTU table and a corresponding matchlist with all the internal matches of OTUs | A r-package for distribution based post clustering curation of amplicon data" ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3797 ; sc:license "LGPL-3.0" ; sc:name "LULU" ; sc:url "https://github.com/tobiasgf/lulu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "Using Transcriptional Signatures to Find Cancer Drivers with LURE | LURE (Learning UnRealized Events)" ; sc:featureList edam:operation_3501 ; sc:name "LURE" ; sc:url "https://sysbiowiki.soe.ucsc.edu/lure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3489 ; sc:citation ; sc:description """The open data geoportal of the Lamma Consortium. In questa categoria sono immagazzinati i dati relativi a bollettini,... In attuazione del decreto legge D. Lgs n. 33 del 14 marzo 2013, che sancisce...""" ; sc:name "LaMMA" ; sc:url "http://dati.lamma.toscana.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pubmed:31653717" ; sc:description """Diverse traits contribute to salinity tolerance of wild tomato seedlings from the Galapagos Islands. Analyzing natural variation in Galapagos tomatoes. La_isla_de_tomato App user guide. The manuscript is currently undergoing submission / revision, but this App is available to explore the data freely. The App can be accessed here or run locally from your machine, by typing the following: library("shiny") shiny::runGitHub("mmjulkowska/La_isla_de_tomato", "mmjulkowska").""" ; sc:featureList edam:operation_2940, edam:operation_3196, edam:operation_3432 ; sc:license "Apache-2.0" ; sc:name "La isla de tomato" ; sc:url "https://github.com/mmjulkowska/La_isla_de_tomato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6526094", "pubmed:31106360" ; sc:description "Integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LanceletDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genome.bucm.edu.cn/lancelet/" ; biotools:primaryContact "Anlong Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description """A web application for interactive genomic summary visualization. Download and Check the official demo input. Additional demo files from the References are provided in the GitHub project. The 'LandScape' visualization is frequently utilized to provide a systematic illustration of integrative data from multiple layers of batch samples, which are always compared to each other on certain attributes, such as genes and biological pathways mutated in cancers. This online 'LandScape' visualization is designed as a fixed part (histogram and gene-panels) with additional panels (e.g., age, gender, and histology). To visualize data, upload a CSV file in the required format and use sidebar options to customize the display""" ; sc:featureList edam:operation_0279, edam:operation_0337, edam:operation_3802 ; sc:name "LandScape" ; sc:url "http://bio.oviz.org/demo-project/analyses/landscape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service", "Workbench" ; sc:author , ; sc:citation , , "pmcid:PMC8574934", "pubmed:34749633" ; sc:contributor , , , ; sc:description "Laniakea is a complete software solution to set up a “Galaxy on-demand” Platform as a Service (PaaS). Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance, and to the underlying virtual machine (VM)." ; sc:license "GPL-3.0" ; sc:name "Laniakea" ; sc:provider "ELIXIR-ITA-INFN" ; sc:softwareHelp ; sc:softwareVersion "2.0.0" ; sc:url "https://laniakea-elixir-it.github.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31425100" ; sc:description "Deep Lasso-Selection of 3D Point Clouds | Zhutian Chen, Wei Zeng, Zhiguang Yang, Lingyun Yu, Chi-Wing Fu, and Huamin Qu IEEE VIS 2019 | Selection is a fundamental task in exploratory analysis and visualization of 3D point clouds" ; sc:name "LassoNet" ; sc:url "https://lassonet.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0780, edam:topic_3172, edam:topic_3308 ; sc:citation , "pubmed:31605615" ; sc:description """An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3625 ; sc:name "LeGOO" ; sc:url "https://www.legoo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:30179717" ; sc:description "MATLAB-toolbox facilitating deep brain stimulation electrode locations and connectomic imaging." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Lead-DBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2" ; sc:url "https://www.lead-dbs.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3337 ; sc:citation ; sc:description "Open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research." ; sc:featureList edam:operation_0224, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "Leaf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/uwrit/leaf" ; biotools:primaryContact "Sean D. Mooney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269 ; sc:citation ; sc:description "A QGIS plugin for automated landscape ecology analysis." ; sc:featureList edam:operation_3799 ; sc:name "LecoS" ; sc:url "http://plugins.qgis.org/plugins/LecoS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3056 ; sc:citation , "pmcid:PMC6819480", "pubmed:31660852" ; sc:description """Estimating population history from genetic data. Estimate population history parameters from site pattern frequencies. Legofit is a computer package that uses counts of nucleotide site patterns to estimate the history of population size, subdivision, and gene flow.""" ; sc:featureList edam:operation_2426, edam:operation_3659 ; sc:name "Legofit" ; sc:url "https://github.com/alanrogers/legofit" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Multi-organism mine integrates data from legume species: string bean, soybean, peanut and barrel medic" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LegumeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "11" ; sc:url "https://mines.legumeinfo.org/legumemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:30552881" ; sc:description "Leishmania Inhibitor Database" ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "LeishInDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://leishindb.biomedinformri.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0820, edam:topic_3474 ; sc:citation ; sc:description """A Computational Method for the Detection and Classification of Ligand-Gated Ion Channels. LiGIoNs: Prediction of Ligand Gated Ion Channels. LiGIoNs is a profile Hidden Markov Model based method capable of predicting Ligand-Gated Ion Channels utilizing their special topological information. The method consists of a library of 35 pHMMs, built from the alignment of transmembrane segments of representative LGIC sequences. In addition, 14 Pfam pHMMs are used to further annotate and correctly classify unknown protein sequences into one of the 10 LGIC subfamilies""" ; sc:featureList edam:operation_0269, edam:operation_0418, edam:operation_2241 ; sc:name "LiGIoNs" ; sc:url "http://bioinformatics.biol.uoa.gr/ligions/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation ; sc:description "Towards gene regulatory network predictions of high-certainty | Abstract Motivation Reverse engineering of gene regulatory networks has for years struggled with high correlation in expression between regulatory elements. If two regulators have matching expression patterns it is impossible to differentiate between the two, and thus false positive identifications are abundant. Results To allow for gene regulation predictions of high confidence, we propose a novel method, LiPLike, that assumes a regression model and iteratively searches for interactions that cannot be replaced by a linear combination of other predictors. To compare the performance of LiPLike with other available inference methods, we benchmarked LiPLike using three independent datasets from the previous DREAM5 challenge" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "LiPLike" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/Gustafsson-lab/liplike" ; biotools:primaryContact "Mika Gustafsson", "Rasmus Magnusson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6354030", "pubmed:30597002" ; sc:description "Scalable k-mer-based tool for massive all-vs-all metagenome comparisons." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Libra" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/iychoi/libra" ; biotools:primaryContact "Illyoung Choi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3723 ; sc:encodingFormat edam:format_2330 ; sc:name "Morphology parameter" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_2331 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1935, edam:format_2330, edam:format_2571 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:encodingFormat edam:format_2331 ; sc:name "Database ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1192 ; sc:encodingFormat edam:format_2331 ; sc:name "Tool name (BLAST)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:encodingFormat edam:format_2331 ; sc:name "Taxon" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_2331 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:encodingFormat edam:format_2331 ; sc:name "Phenotype name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3752 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2331 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1333, edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0622, edam:topic_3071, edam:topic_3302, edam:topic_3387, edam:topic_3810 ; sc:author , "Sea Lice Research Centre (SLRC)", "Wei Zhang" ; sc:description "LiceBase is a genomics database for sea lice (Lepeophtheirus salmonis and Caligus spp.), which are major pathogens affecting the global salmon farming industry. The database contains the genome annotation of the Atlantic salmon louse (L. salmonis) and is designed to help researchers, industry professionals, and other interested parties access and share information about these parasites, with the goal of developing new treatment methods and tools to ensure a sustainable salmon farming industry. LiceBase provides annotated genome reports, genome browsing, RNA interference (RNAi) experiment browsing for several additional species, BLAST search, and in-situ images. The database homepage posts news updates and recent publications related to sea lice and salmonid species." ; sc:featureList edam:operation_0305, edam:operation_0346, edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:funder "The Research Council of Norway" ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "LiceBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Bergen" ; sc:softwareHelp , , , ; sc:url "https://licebase.org/" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_1910 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3299 ; sc:citation ; sc:description "Explorer of the entire tree of life. Lifemap allows visualizing the entire NCBI taxonomy on a single page with a deep zoom interface and performing easy search, mrca detection, subtree download, etc." ; sc:featureList edam:operation_0337, edam:operation_0567, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "Lifemap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://lifemap.univ-lyon1.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3673 ; sc:citation , "pmcid:PMC6513517", "pubmed:31084602" ; sc:description "Multi-view CpG sites detection on single-cell whole genome sequence data." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LightCpG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guofei-tju/LightCpG" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0654 ; sc:citation ; sc:description "Tool to determine DNA profile weight of evidence." ; sc:featureList edam:operation_2937, edam:operation_3196, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LikeLTD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "6.3.0" ; sc:url "https://sites.google.com/site/baldingstatisticalgenetics/" ; biotools:primaryContact "Christopher Steele" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172 ; sc:citation , "pmcid:PMC6290884", "pubmed:30535020" ; sc:description "R package for personalized pathway-based classification modeling using metabolomics data." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Lilikoi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/lilikoi/index.html" ; biotools:primaryContact "Fadhl Alakwaa" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2978 ; sc:encodingFormat edam:format_2330 ; sc:name "Reaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3314, edam:topic_3520 ; sc:citation , "pubmed:33657806" ; sc:description "LinX is a Java language-based program designed for fast assignment, evaluation, and validation of mass spectrometric datasets from chemical cross-linking." ; sc:featureList edam:operation_0389, edam:operation_2945, edam:operation_3767, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LinX" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://peterslab.org/downloads.php" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_3174 ; sc:citation ; sc:description "Linclust is the first clustering algorithm whose runtime scales linearly. With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity." ; sc:featureList edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Linclust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://mmseqs.com" ; biotools:primaryContact "Söding Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3512, edam:topic_3542 ; sc:citation , "pmcid:PMC6681470", "pubmed:31510672" ; sc:description "linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search | The new source code of the LinearFold, linear-time prediction for RNA secondary structures | This codebase replaces the now deprecated version: https://github.com/abentu0101/LinearFold. This version fixes many bugs and design problems in the old version | Add a sequence Paste or type your sequence here (length < 100,000): | GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGG | Choose model(s) LinearFold-C (using CONTRAfold v2.0 machine-learned model, Do et al 2006) | * Liang Huang, **He Zhang, **Dezhong Deng, Kai Zhao, Kaibo Liu, David Hendrix, and David H. Mathews (2019). LinearFold: Linear-Time Approximate RNA Folding by 5’-to-3’ Dynamic Programming and Beam Search. Bioinformatics, Volume 35, Issue 14, July 2019, Pages i295–i304. ISMB 2019" ; sc:featureList edam:operation_0278, edam:operation_0481, edam:operation_1812 ; sc:name "LinearFold" ; sc:url "http://linearfold.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780 ; sc:citation , "pubmed:31738392" ; sc:description """a versatile framework to explore and integrate heterogeneous microbial communities. a versatile approach to integrate heterogeneous datasets. LinkHD: a versatile framework to explore and integrate heterogeneous data. Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. Laura Zingaretti & Yuliaxis Ramayo Caldas. Laura M Zingaretti, Gilles Renand, Diego P Morgavi, Yuliaxis Ramayo-Caldas, Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz862""" ; sc:featureList edam:operation_3501, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Link-HD" ; sc:url "https://github.com/lauzingaretti/LinkHD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation ; sc:description """Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs. Abstract Phosphorylation of specific substrates by protein kinases is a key control mechanism for vital cell-fate decisions and other cellular processes. However, discovering specific kinase-substrate relationships is timeconsuming and often rather serendipitous. Computational predictions alleviate these challenges, but the current approaches suffer from limitations like restricted kinome coverage and inaccuracy. They also typically utilise only local features without reflecting broader interaction context. To address these limitations, we have developed an alternative predictive model.""" ; sc:featureList edam:operation_0269, edam:operation_0417, edam:operation_3439 ; sc:name "LinkPhinder" ; sc:url "https://LinkPhinder.insight-centre.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_2830 ; sc:citation , "pmcid:PMC6571408", "pubmed:31124967" ; sc:description "Publicly available portal that includes multi-omics data from all 32 TCGA Cancer types. It also includes mass spectrometry-based proteomics data generated by the Clinical Proteomics Tumor Analysis Consortium (CPTAC) for TCGA breast, colorectal and ovarian tumors." ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LinkeDomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.linkedomics.org" ; biotools:primaryContact "Xiaohua Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325 ; sc:citation , "pmcid:PMC5682045", "pubmed:29214177" ; sc:description "Connects rare diseases patient registries through a Semantic Web Layer." ; sc:featureList edam:operation_2422, edam:operation_3283 ; sc:isAccessibleForFree true ; sc:name "Linked Registries" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.ua.pt/linked-registries-app/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6921604", "pubmed:31867556" ; sc:description """Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using Liquid Chromatography-Tandem Mass Spectrometry and 31P Nuclear Magnetic Resonance. Matlab Script for automated LC-MS/MS phospholipid analysis. LipMat script is a set of tools for automated LC-MS/MS phospholipid analysis. Paper is in preparation and this section will be updated when it will be published. Matlab Script for automated LC-MS/MS lipid analysis.""" ; sc:featureList edam:operation_3215, edam:operation_3799, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "LipMat" ; sc:url "https://github.com/MarJakubec/LipMat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0736 ; sc:citation , "pubmed:31545554" ; sc:description "The modular structure of α/β-hydrolases | The BioCatNet Database System aims to collect and present comprehensive information about biocatalysators: sequence, structure, educts, products, environmental conditions and kinetics | The Lipase Engineering Database (LED) version4.0.0 | Widmann M., Juhl PB. & Pleiss J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics 11: 123" ; sc:featureList edam:operation_0303, edam:operation_3431, edam:operation_3798 ; sc:name "Lipase Engineering Database" ; sc:url "https://led.biocatnet.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0821, edam:topic_3534 ; sc:citation ; sc:description "Deposit and classification of lipolytic enzymes based on the proposed classification system in Hitch and Clavel (TBP)." ; sc:featureList edam:operation_0483, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Lipase reclassification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/thh32/Lipase_reclassification" ; biotools:primaryContact "Thomas C. A. Hitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3314, edam:topic_3407 ; sc:citation , "pubmed:31729667" ; sc:description """The Use of LipidIMMS Analyzer for Lipid Identification in Ion Mobility-Mass Spectrometry-Based Untargeted Lipidomics. Questions: zhouzw AT sioc.ac.cn, jiangzhu AT sioc.ac.cn. © Zhu lab , Interdisciplinary Research Center on Biology and Chemistry (IRCBC), Chinese Academy of Sciences (CAS). All Rights Reserved.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3860 ; sc:name "LipidIMMS" ; sc:url "http://imms.zhulab.cn/LipidIMMS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3337, edam:topic_3520 ; sc:citation , "pubmed:30500173" ; sc:description "R Package for Lipid Annotation in Untargeted Liquid Chromatography-Data Independent Acquisition-Mass Spectrometry Lipidomics." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://cran.r-project.org/package=LipidMS" ; biotools:primaryContact "M Isabel Alcoriza-Balaguer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC6489209", "pubmed:31035918" ; sc:description "Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values." ; sc:featureList edam:operation_3629, edam:operation_3633, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidMatch Normalizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "http://secim.ufl.edu/secim-tools/lipidmatch-normalizer/" ; biotools:primaryContact "Jason Cochran", "Jeremy Koelmel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0153 ; sc:citation ; sc:description "Lipid Mining and Ontology (Lipid Mini-On) - mining and ontology tool for enrichment analysis of lipidomic data." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "Lipid Mini-On" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://omicstools.pnnl.gov/shiny/lipid-mini-on/" ; biotools:primaryContact "Geremy Clair", "Jennifer E. Kyle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3068 ; sc:citation , "pubmed:31617563" ; sc:description """A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ceRNA regulation. e.g. NEAT1, TP53, hsa-let-7b-5p, rs3825071, COSN13341324, BRCA""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3208, edam:operation_3503, edam:operation_3659 ; sc:name "LnCeVar" ; sc:url "http://www.bio-bigdata.net/LnCeVar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3068 ; sc:citation ; sc:description "ab initio lncRNA identification and functional annotation tool based on deep learning." ; sc:featureList edam:operation_0476, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "LncADeep" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cyang235/LncADeep/" ; biotools:primaryContact "Huaiqiu Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0634, edam:topic_0659 ; sc:citation , "pubmed:31524988" ; sc:description "LncBook accommodates a high-quality collection of human lncRNA genes and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional signatures of lncRNAs in human diseases and different biological contexts." ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_2495, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "LncBook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://ngdc.cncb.ac.cn/lncbook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3295, edam:topic_3360 ; sc:citation , "pubmed:31713618" ; sc:description """A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species. LncTarD provides key lncRNA-target regulations, their influenced functions and lncRNA-mediated regulatory mechanisms in human diseases. Quick Search, start typing keywords, press ESC to close suggestions""" ; sc:featureList edam:operation_2421, edam:operation_3439, edam:operation_3446 ; sc:name "LncTarD" ; sc:url "http://biocc.hrbmu.edu.cn/LncTarD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885 ; sc:citation , , "pubmed:27605101", "pubmed:30539556" ; sc:description "Database of genetic variations associated with long noncoding genes." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "LncVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ibp.ac.cn/LncVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6324239", "pubmed:30401722" ; sc:description "Automated eukaryotic genome annotation based on long-read cDNA sequencing." ; sc:featureList edam:operation_0308, edam:operation_0362, edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LoReAn" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lfaino/LoReAn" ; biotools:primaryContact "Luigi Faino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140, edam:topic_0602, edam:topic_0749, edam:topic_2229 ; sc:citation , "pmcid:PMC6886211", "pubmed:31787091" ; sc:description """Integrating protein localization with automated signaling pathway reconstruction. Are you sure you want to delete this graph?""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:name "LocPL" ; sc:url "http://graphspace.org/graphs/?query=tags:LocPL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated Omics data warehouse for Locust, Locusta migratoria" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LocustMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.2" ; sc:url "http://locustmine.org:8080/locustmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3512, edam:topic_3855 ; sc:citation ; sc:description "Beautiful sequence logos in python | Software for the visualization of sequence-function relationships | beautiful sequence logos in Python — logomaker 0.8 documentation | Logomaker can be installed from PyPI by executing | Software for creating highly customized sequence logos | Free document hosting provided by Read the Docs" ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Logomaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/jbkinney/logomaker" ; biotools:primaryContact "Ammar Tareen", "Justin Kinney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2885 ; sc:citation ; sc:description "de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models." ; sc:featureList edam:operation_3359, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "Look4TRs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/TulsaBioinformaticsToolsmith/Look4TRs" ; biotools:primaryContact "Hani Z. Girgis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0632, edam:topic_2885, edam:topic_3068, edam:topic_3168 ; sc:citation , "pubmed:31674643" ; sc:description """A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA. git clone https://github.com/kaizhao86/loxodontalocalizer. Loxodonta Localizer maps the localities from which mitochondrial DNA sequences have been reported for African elephants, Loxodonta africana and L. cyclotis, using the dataset described in Ishida et al., 2013, updated with additional sequences. #first, install Python 2.7, pip and git""" ; sc:featureList edam:operation_0224, edam:operation_0487, edam:operation_3192 ; sc:name "Loxodonta Localizer" ; sc:url "http://www.loxodontalocalizer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_3067, edam:topic_3172, edam:topic_3382 ; sc:citation , "pmcid:PMC6814058", "pubmed:31651362" ; sc:description """A comparison of alveolar formation and maturation within mouse and human lung. Anatomic Ontology for Mouse Lung Maturation. Cell Ontology for Mouse Lung Maturation. Anatomic Ontology for Human Lung Maturation. Cell Ontology for Human Lung Maturation. Search BREATH to explore the developing lung. LungMAP provides users with a tool to annotate images within the website. This webpage provides instructions on how to annotate an image using the tool. Image annotation to convey specific information about an image, importantly, in the context of the image increases its value exponentially, especially with resolution on the molecular level. LungMAP human and mouse ontologies reference page provides links to the LungMAP Ontology Browser, Release Notes, and text files for the scientific community to view the ontologies.""" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3352, edam:operation_3553 ; sc:name "LungMAP" ; sc:url "http://www.lungmap.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "White and narrow-leaf lupin data from the Legume Information System" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "LupinMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2" ; sc:url "https://mines.legumeinfo.org/lupinmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31719438" ; sc:description """Digital key for Brazilian sand flies (Diptera, Phlebotominae) within an Android App. Here we present an Android mobile application (app) for the identification of Brazilian phlebotomine sand fly species. The app, which is named LutzoDex™, relies on information included in a data source with morphological and morphometrical characters. This tool can present up to seven answer options to a question. Images of morphological structures can be referenced to make identification easier, and users can see a list of possible species based on the features they report. Maps are also used to determine the geographical distribution and whether the species is incriminated or suspected as a vector of Leishmania spp. in Brazil. The app is available free of charge in both English and Portuguese in the Google Play Store at https: play.google.com store apps details?id=max.com.lutzodexhl=pt_BR.""" ; sc:name "LutzoDexTM" ; sc:url "https://play.google.com/store/apps/details?id=max.com.lutzodexhl=pt_BR." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3179, edam:topic_3519 ; sc:citation , "pubmed:31745565" ; sc:description """Global H-NS counter-silencing by LuxR activates quorum sensing gene expression. FileUtil.pm - perl helper module for loading files reformatFasta.pl - perl script the cleans and reformats multi-fasta files findOverlaps.pl - perl script to identify sets of overlapping peaks for Venn diagram getPeakAnno.pl - perl script to add annotation information to Macs2 peaks getGenePeakAnno2.pl - perl script to add peaks to gene information findClosest2.pl - perl script to produce table relating luxR peaks to H-NS double peaks.""" ; sc:featureList edam:operation_0308, edam:operation_0335, edam:operation_0435, edam:operation_0440, edam:operation_3222 ; sc:name "LuxR" ; sc:url "https://github.com/Juliacvk/LuxR_H-NS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pmcid:PMC6823652", "pubmed:31673810" ; sc:description """An Open-Source Lyophilization Process Optimization Tool. This work presents a new user-friendly lyophilization simulation and process optimization tool, freely available under the name LyoPRONTO. This tool comprises freezing and primary drying calculators, a design-space generator, and a primary drying optimizer. The freezing calculator performs 0D lumped capacitance modeling to predict the product temperature variation with time which shows reasonably good agreement with experimental measurements. The primary drying calculator performs 1D heat and mass transfer analysis in a vial and predicts the drying time with an average deviation of 3% from experiments. The calculator is also extended to generate a design space over a range of chamber pressures and shelf temperatures to predict the most optimal setpoints for operation.""" ; sc:featureList edam:operation_2426, edam:operation_3659, edam:operation_3799 ; sc:name "LyoPRONTO" ; sc:url "https://sites.google.com/view/rgdart/Research/lyopronto-lyophilization-processoptimization-tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3295 ; sc:citation , "pubmed:31493278" ; sc:description "Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes | *This document is under developement. Your ideas and suggestions are always welcome! | M-GCTA is an user-friendly software package, which can be used to estimate the proportion of phenotypic variance due to tagged maternal (or paternal) and offspring genetic effects on offspring phenotypes using large studies where genome-wide genotype data are available on mother- (or father-) offspring pairs" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3557 ; sc:name "M-GCTA" ; sc:url "https://github.com/uqzqiao/M-GCTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3295, edam:topic_3300, edam:topic_3382 ; sc:citation ; sc:description """A platform for live cell multiplex imaging reveals cell phenotypic transition dynamics inherently missing in snapshot data. M-TRACK is a live cell imaging analysis tool""" ; sc:featureList edam:operation_3216, edam:operation_3443, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "M-TRACK" ; sc:url "https://github.com/opnumten/M-TRACK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3473, edam:topic_3697 ; sc:citation , "pmcid:PMC6602433", "pubmed:31114912" ; sc:description "Web server for the analysis of large-scale microbial genomics data." ; sc:featureList edam:operation_0306, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "M1CR0B1AL1Z3R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://microbializer.tau.ac.il/" ; biotools:primaryContact "Tal Pupko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6923906", "pubmed:31861972" ; sc:description """A comprehensive model selection for multi-modal single-cell RNA sequencing data. M3S: A user-friendly tool for comprehensive evaluation of multi-modality and statistical model selection for single-cell RNA sequencing data. A large number of single-cell RNA sequencing (scRNA-seq) data set was recently generated to characterize the heterogeneous in cell types or states in a complex tissue or biological process""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3664 ; sc:name "M3S" ; sc:url "https://github.com/zy26/M3S" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3489 ; sc:citation , "pubmed:31634642" ; sc:description """A web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared.""" ; sc:featureList edam:operation_3196 ; sc:name "MAC-INMV-SSR" ; sc:url "http://mac-inmv.tours.inra.fr/0_macinmv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_0199, edam:topic_3306 ; sc:citation , "pmcid:PMC3940602", "pubmed:24624315" ; sc:description """Analyzing Machupo virus-receptor binding by molecular dynamics simulations. Code and data for Meyer et al, Analyzing Machupo virus-receptor binding by molecular dynamics simulations, PeerJ 2:e266 (2014). This file is meant to explain each of the top level directories. There should be a similar readme in the relevant folders. eq_analysis - contains the scripts used to generate the equilibration rmsf plots as well as the plot themselves. fep_config - contains everything necessary to run the dual topology fep.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_2492 ; sc:name "MACV" ; sc:url "https://github.com/clauswilke/MACV_SMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0154, edam:topic_2814 ; sc:citation , "pmcid:PMC6929402", "pubmed:31870277" ; sc:description """An ultra-fast approach for large-scale protein structure similarity searching. Protein similarity search in PDB. Ultra-fast and Large-Scale Protein Structural Neighbor Searching. MADOKA, a webserver features on searching similar protein structures by aligning input structure with the whole PDB library implemented by MADOKA, an algorithm for matching protein structures by two phases.""" ; sc:featureList edam:operation_0360, edam:operation_0491, edam:operation_0503, edam:operation_0510, edam:operation_3454 ; sc:name "MADOKA" ; sc:url "http://madoka.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3518 ; sc:citation ; sc:description "Robust detection of mosaic loss of chromosome Y from genotype-array-intensity data | R package to detect mosaic loss of Y events in SNP array and NGS data | R package to detect mosaic loss of Y events (LOY) from SNP array data" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3501 ; sc:name "MADloy" ; sc:url "https://github.com/isglobal-brge/MADloy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , , , , , "pmcid:PMC3603318", "pmcid:PMC548345", "pubmed:15661851", "pubmed:23329690" ; sc:description "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "BSD-Source-Code" ; sc:name "MAFFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mafft.cbrc.jp/alignment/server/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0097, edam:topic_0154 ; sc:citation , "pmcid:PMC6602451", "pubmed:31062021" ; sc:description "Multiple alignment program for amino acid or nucleotide sequences." ; sc:featureList edam:operation_0503, edam:operation_0504, edam:operation_0509 ; sc:isAccessibleForFree true ; sc:license "GPL-1.0" ; sc:name "MAFFT-DASH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mafft.cbrc.jp/alignment/server/" ; biotools:primaryContact , "Daron M. Standley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "High speed multiple sequence alignment program." ; sc:featureList edam:operation_0492 ; sc:name "MAFFT API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/mafft_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_3334 ; sc:citation , "pmcid:PMC6815046", "pubmed:31653223" ; sc:description """Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Seed-centric method to identify gene modules of similar interaction and co-expression characteristics. Merge A ffected G enes into I ntegrated networks.""" ; sc:featureList edam:operation_3196, edam:operation_3439, edam:operation_3501 ; sc:name "MAGI-S" ; sc:url "https://github.com/jchow32/magi-s" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3174, edam:topic_3316, edam:topic_3697 ; sc:citation , "pubmed:31633780" ; sc:description """Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes. Microbial species play important roles in different environments and the production of high-quality genomes from metagenome datasets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "MAGO" ; sc:url "http://mago.fe.uni-lj.si" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_2885, edam:topic_3676 ; sc:citation ; sc:description """Discovering Subclones in Tumors Sequenced at Standard Depths. MAGOS: Model-based Adaptive Grouping of Subclones""" ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3435 ; sc:name "MAGOS" ; sc:url "https://github.com/liliulab/magos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0798, edam:topic_3301 ; sc:citation ; sc:description "Microbial Assessment by Genome-wide Tn-Seq Analysis (MAGenTA) - Galaxy implemented tool for complete Tn-Seq analysis and data visualization." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MAGenTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://vanopijnenlab.github.io/MAGenTA/" ; biotools:primaryContact "Tim van Opijnen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "Web-tool to interrogate classical and complex splicing variations from RNA-Seq data." ; sc:featureList edam:operation_0308, edam:operation_3237, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MAJIQ-SPEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "http://majiq.biociphers.org/majiq-spel" ; biotools:primaryContact "Yoseph Barash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:31691160" ; sc:description """Supervised machine learning for diagnostic classification from large-scale neuroimaging datasets. Machine Learning in NeuroImaging (MALINI) is a MATLAB-based toolbox used for feature extraction and disease classification using resting state functional magnetic resonance imaging (rs-fMRI) data. 18 different popular classifiers are presented. With slight modifications, it can also be used for any classification problem using any set of features""" ; sc:featureList edam:operation_2428, edam:operation_3283, edam:operation_3435 ; sc:license "MIT" ; sc:name "MALINI" ; sc:url "https://github.com/pradlanka/malini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0602, edam:topic_0736, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC6812854", "pubmed:31648227" ; sc:description """Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online resource that integrates data from KEGG, SCOP and structural phylogenomic reconstruction. The database, which was introduced in 2006, traces the deep history of the structural domains of enzymes in metabolic pathways. Here we release version 3.0 of MANET, which updates data from KEGG and SCOP, links enzyme and PDB information with PDBsum, and traces evolutionary information of domains defined at fold family level of SCOP classification in metabolic subnetwork diagrams.""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3660 ; sc:name "MANET" ; sc:url "http://manet.illinois.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6796874", "pubmed:31636953" ; sc:description """Model-based analysis of proteomic data to detect proteins with significant abundance changes. MAP (Model-based Analysis of Proteomic data), is designed to statistically compare the proteomic profiles generated from different biological samples using the isotope labeling based mass spectrometry (MS) technique and directly identify proteins with significant abundance changes. Unlike many existing tools for this purpose, it does not require parallel/additional technical replicates to fathom technical variations; instead, MAP uses a novel step-by-step regression analysis to directly model technical variations from the profiles under comparison. Therefore, experimental designs and their expenses can be simplified and reduced for more practices""" ; sc:featureList edam:operation_2429, edam:operation_2495, edam:operation_3638, edam:operation_3659 ; sc:name "MAP" ; sc:url "http://bioinfo.sibs.ac.cn/shaolab/MAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6483256", "pubmed:30986246" ; sc:description "MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data." ; sc:featureList edam:operation_2429, edam:operation_3222, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:name "MAPS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ijuric/MAPS" ; biotools:primaryContact "Ivan Juric", "Ming Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500, edam:topic_3524 ; sc:citation , "pmcid:PMC6876843", "pubmed:31765421" ; sc:description """MARGO (Massively Automated Real-time GUI for Object-tracking). Fast object tracking in real time allows convenient tracking of very large numbers of animals and closed-loop experiments that control stimuli for many animals in parallel. We developed MARGO, a MATLAB-based, real-time animal tracking suite for custom behavioral experiments. We demonstrated that MARGO can rapidly and accurately track large numbers of animals in parallel over very long timescales, typically when spatially separated such as in multiwell plates. We incorporated control of peripheral hardware, and implemented a flexible software architecture for defining new experimental routines. These features enable closed-loop delivery of stimuli to many individuals simultaneously. We highlight MARGO's ability to coordinate tracking and hardware control with two custom behavioral assays (measuring phototaxis and optomotor response) and one optogenetic operant conditioning assay.""" ; sc:featureList edam:operation_3435, edam:operation_3450 ; sc:name "MARGO" ; sc:url "https://github.com/de-Bivort-Lab/margo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:31611695" ; sc:description """Predicting HLA class II antigen presentation through integrated deep learning. MARIA is a machine learning tool developed by Chen et al. to predict likelihood of HLA-II peptide ligand presentation given cell HLA alleles, peptide sequences, and source genes of the peptides.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2454, edam:operation_3439 ; sc:name "MARIA" ; sc:url "https://maria.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3520 ; sc:citation , "pubmed:31097673" ; sc:description "Extracting Publication-ready Mass Spectrometry Metadata from RAW Files." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MARMoSET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.molgen.mpg.de/loosolab/MARMoSET_C" ; biotools:primaryContact "Johannes Graumann", "Mario Looso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3306, edam:topic_3810 ; sc:citation ; sc:description """Novel tool for virtual phenotyping of maize root system hydraulic architectures. How to use MARSHAL from the R environment. install_github("MARSHAL-ROOT/marshal"). MAize Root System Hydraulic Architecture soLver. MARSHAL is a maize root system hydraulic architecture solver that combines the root architecture model CRootBox (Schnepf et al. 2018) with the method for solving water flow in RSHA of Meunier et al. (2017) and with the method for computing macroscopic parameter of Couvreur et al. (2012). To load the package, you can use the command:""" ; sc:featureList edam:operation_2426 ; sc:license "Apache-2.0" ; sc:name "MARSHAL" ; sc:url "https://plantmodelling.shinyapps.io/marshal/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_1915, edam:format_2330, edam:format_3651, edam:format_3834 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_1915, edam:format_3244, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332, edam:format_3247, edam:format_3651, edam:format_3681, edam:format_3713, edam:format_3752 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:10612281", "pubmed:12422359", "pubmed:21447708" ; sc:description "The leading software package for protein identification and characterisation using mass spectrometry data." ; sc:featureList edam:operation_2929, edam:operation_3639, edam:operation_3641, edam:operation_3643, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767, edam:operation_3801 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Mascot Server" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.matrixscience.com/server.html" ; biotools:primaryContact "see publication" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0736, edam:topic_3169 ; sc:citation , "pubmed:31742324" ; sc:description """Improved linking of motifs to their TFs using domain information. Improved motif enrichment analysis using protein domain type information. MASSIF - motif association with domain information. MASSIF is a novel method to improve the performance of existing tool that link motifs to TFs relying on TF-associated sequences.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240 ; sc:license "MIT" ; sc:name "MASSIF" ; sc:url "https://github.com/SchulzLab/MASSIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description """an ultra fast algorithm for solving the single individual haplotype assembly problem. Abstract Background Human genomes are diploid, which means they have two homologous copies of each chromosome and the assignment of heterozygous variants to each chromosome copy, the haplotype assembly problem, is of fundamental importance for medical and population genetics. While short reads from second generation sequencing platforms drastically limit haplotype reconstruction as the great majority of reads do not allow to link many variants together, novel long reads from third generation sequencing can span several variants along the genome allowing to infer much longer haplotype blocks""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3196, edam:operation_3211 ; sc:name "MAtCHap" ; sc:url "https://sourceforge.net/projects/matchap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2269, edam:topic_3324 ; sc:citation ; sc:description """Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology. bionomics.cpp: fast functions in C++ to calculate summary statistics of interest from simulation output. trivial-simulation.R: run MBITES on a very simple landscape (used for model comparison) and generate plots to compare with MBDETES. bionomics.R: takes output generated by peridomestic-simulation.R and generates output to make figures""" ; sc:featureList edam:operation_2426, edam:operation_3659 ; sc:name "MBITES" ; sc:url "https://github.com/dd-harp/MBITES/tree/v1.0/MBITES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3673 ; sc:citation , "pubmed:31624841" ; sc:description """An integrated omics knowledgebase for molecular breeding in rice. Rice Phenotype Search and Summary. Rice Genotype Search and Summary. Molecular Breeding Knowledge Database. Created with the Personal Edition of HelpNDoc: News and information about help authoring tools and software. For example: Locus (OsG00048223), RAP Locus (Os03g0407400), MSU Locus (LOC_Os02g44360),. For example(case sensitive): HD, TGW. MBK Nip Locus (OsNipG0313111200.01), MBK R498 Locus (OsR498G0203315700.01). For example(case sensitive): Drought Tolerance, Blast Resistance. Project: All Rice3k MBK Japan174 SubTree Sample >= 20 30 40. Molecular Breeding Knowledgebase (MBKbase) is an integrated database for population next-generation sequencing, germplasm resources, phenotypic and various othergenomics data.""" ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_2429, edam:operation_3196, edam:operation_3227 ; sc:name "MBKbase rice" ; sc:softwareHelp ; sc:url "http://www.mbkbase.org/rice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2830, edam:topic_3315 ; sc:citation , "pmcid:PMC6644659", "pubmed:31458826" ; sc:description "Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions | MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level" ; sc:featureList edam:operation_0478, edam:operation_2492 ; sc:name "MCMap" ; sc:url "http://www.bisb.uni-bayreuth.de/index.php?page=downloads" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6868382", "pubmed:31750523" ; sc:description """A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. added a link to the publication · 92cb2e86. 3rd_party/jemalloc_win_x64_5.1.0""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_2492 ; sc:name "MCOT" ; sc:url "https://gitlab.sysbio.cytogen.ru/academiq/mcot-kernel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC6612898", "pubmed:31510702" ; sc:description "Minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks | Codes and data of competitive methods for finding minimal cut sets of a metabolic network | Files for the work on metabolic networks with Leonid, Tamon, Cedric, Reza, Hooman, and Nafiseh | You need to have licensed MATLAB before running the scripts | There are implemenations of four approaches for enumerating MCSs here. You can run either of them by running its script followed by model name followed by target reaction followed by 1 or 0 which indicates prior network reduction. -1 stands for all reactions" ; sc:featureList edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "MCS2" ; sc:url "https://github.com/RezaMash/MCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "This software provides a clustering module for viewing the relationship of colinear segments in multiple genomes (or heavily redundant genomes). It takes the predicted pairwise segments from dynamic programming (DAGchainer in particular) and then try to build consensus segments from a set of related, overlapping segments." ; sc:name "MCScan" ; sc:url "https://github.com/tanghaibao/mcscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168, edam:topic_3173, edam:topic_3674 ; sc:citation , "pmcid:PMC6795852", "pubmed:31619715" ; sc:description """A reference-free, whole genome profiling system to address cytosine/adenine methylation changes. Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6 mA) at an affordable price. Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6 mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing.""" ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3204 ; sc:name "MCSeEd" ; sc:url "https://bitbucket.org/capemaster/mcseed/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_3315 ; sc:citation , "pmcid:PMC6612807", "pubmed:31510657" ; sc:description "Summarizing the solution space in tumor phylogeny inference by multiple consensus trees | Algorithms for summarizing cancer phylogenies using multiple consensus trees | MCT-Solver - Multiple Consensus Tree Solver | Multiple Consensus Tree (MCT) is a problem that takes a set of input trees on the same set of vertices and an integer k as input, find k consensus trees and a k-clustering of the input trees such that the sum of the distance of each input tree to its corresponding consensus tree is minimized. MCT-Solver contains 3 approaches to this problem, Brute Force, MILP, and Coordinate Ascent" ; sc:featureList edam:operation_0555, edam:operation_0557, edam:operation_3478 ; sc:name "MCT" ; sc:url "https://github.com/elkebir-group/MCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3372 ; sc:citation , "pubmed:31659696" ; sc:description """When global and local molecular descriptors are more than the sum of its parts. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming. …methods and tools for Chem-Bio-Med-Informatic Studies. MD-LOVIs (acronym for Molecular Descriptors from LOcal Vertex Invariants and Related Maps) is a multi-platform software developed in the Java programming language""" ; sc:featureList edam:operation_0394, edam:operation_3436, edam:operation_3659, edam:operation_3891 ; sc:name "MD-LOVIs" ; sc:url "http://tomocomd.com/md-lovis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3047, edam:topic_3335, edam:topic_3512 ; sc:citation , "pmcid:PMC6786093", "pubmed:31632446" ; sc:description """A Computational Model to Predict the Causal miRNAs for Diseases. miRNA-disease causal association predictor. /main.py used for calculate causal miRNA-disease association potential score. /crossvalidation.py used for 10-fold cross validation.""" ; sc:featureList edam:operation_0463, edam:operation_2428, edam:operation_3792 ; sc:name "MDCAP" ; sc:url "https://github.com/cuppeanuts/MDCAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0749 ; sc:citation , "pubmed:30717647" ; sc:description "Web server for identifying glutarylation sites." ; sc:featureList edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "MDDGlutar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/MDDGlutar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2258, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:31745704" ; sc:description """Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. This is a Python implementation of the molecular dynamics fingerprints (MDFP) methodology for building predictive models for phys-chem properties as delineated in our publication. This toolkit is described and applied to the SAMPL6 logP prediction challenge, with the results published here. Visit our documentation to learn details about installation, example workflow and API references.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3893 ; sc:license "MIT" ; sc:name "MDFPtools" ; sc:url "https://github.com/rinikerlab/mdfptools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_3068, edam:topic_3332 ; sc:citation , "pubmed:31660624" ; sc:description """Software Facilitating Performing Molecular Dynamics Simulations. MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins. MDMS: Molecular Dynamics Made Simple. The idea behind MDMS design is that the beginnings should be easy - not exhausting. That is why this program accommodates everything that is required for getting realistic insights about protein/protein-ligand complexes through MD simulations""" ; sc:featureList edam:operation_0477, edam:operation_2476, edam:operation_3893 ; sc:license "MIT" ; sc:name "MDMS" ; sc:url "https://github.com/szymonzaczek/MDMS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3746 ; sc:name "Count matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_3033 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:encodingFormat edam:format_3508 ; sc:name "Histogram" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_2269, edam:topic_3301, edam:topic_3474 ; sc:author ; sc:citation ; sc:contributor ; sc:description "MDPbiome is a software developed in R that uses Markov Decision Processes to create \"policy prescriptions\" for microbiome engineering. MDPbiome performs a variety of analysis describing the robustness of the prescription, as well as a variety of visualizations to assist in manual interpretation of the state transitions and biological understanding of a microbiome's dynamics." ; sc:featureList edam:operation_0004, edam:operation_0335, edam:operation_0337, edam:operation_3432, edam:operation_3480, edam:operation_3695, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MDPBiome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/beatrizgj/MDPbiome" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3170, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31697315" ; sc:description """A model to estimate differential co-occurrence networks in microbiome studies. (Note: This package is currently in development) Microbiome Differential Network Estimation (mdine) allows the estimation of OTU co-occurrence networks within two separate groups, where the networks are defined through precision matrices. The difference between the two precision matrices is also estimated, along with corresponding interval estimates. This work was developed in the Greenwood Lab at McGill University.""" ; sc:featureList edam:operation_3562, edam:operation_3659 ; sc:name "MDiNE" ; sc:url "https://github.com/kevinmcgregor/mdine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0602 ; sc:citation , "pubmed:31418769" ; sc:description "Minimum Energy Path Surface Analysis over n-dimensional surfaces | Molecular Modelling Group. Grupo de Modelado Molecular. Centro de Biologia Molecular 'Severo Ochoa' CBMSO, CSIC-UAM | bioweb: molecular modelling group / grupo de modelado molecular | [ http://www.cbm.csic.es/bioweb ] [ http://bioweb.cbm.uam.es ] | n-dimensional energy surfaces are becoming computationally accessible, yet interpreting their information is not straightforward. We present MEPSAnd, an open source GUI-based program that natively calculates minimum energy paths across energy surfaces of any number of dimensions. Among other features, MEPSAnd can compute the path through lowest barriers and automatically provide a set of alternative paths. MEPSAnd offers distinct plotting solutions as well as direct python scripting" ; sc:featureList edam:operation_1816 ; sc:license "GPL-3.0" ; sc:name "MEPSAnd" ; sc:url "http://bioweb.cbm.uam.es/software/MEPSAnd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_2885, edam:topic_3305 ; sc:citation , "pubmed:31683007" ; sc:description """Visualising molecular epidemiology data combining genetic markers and drug resistance profiles. Molecular epidemiology uses genetic information from bacterial isolates to shed light on the population structure and dynamics of pathogens. Bacterial pathogens can now be studied by whole genome sequencing, but for some well-studied pathogens such as Mycobacterium tuberculosis a wealth of information is also available from other sources such as spoligotyping and multi-locus variable-number-tandem-repeats (VNTR). Isolates are also frequently tested for susceptibility to antibiotics. Methods of analysis are available for each type of data but it would be informative to combine multiple sources of information into a single analysis or visualisation. Here, we propose and implement a simple way to visualise genotypes along with drug resistance profiles for multiple drugs.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3482 ; sc:name "MERCAT" ; sc:url "https://github.com/zaandahl/mercat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6755101", "pubmed:31428793" ; sc:description "Reconstructing complex lineage trees from scRNA-seq data using MERLoT | Reconstruct the lineage topology of a scRNA-seq differentiation dataset | MERLot: A MEthod for Reconstructing Lineage tree Topologies using scRNA-seq data | Benchmark and plotting scripts for the MERLoT paper | MERLot is a tool that can reconstruct the lineage tree topology that explains the emergence of different cell types from a progenitor population. MERLot is an R package than can reconstruct complex lineage tree topologies using coordinates for cells in a given manifold(like diffusion maps) as input | A collection of scripts that was used to generate and benchmark the simulations provided with the tool MERLoT. Download the expression matrices and parameter files via the GWDG FTP server. These will be used as examples for the various scripts | merlot_prosstt_deep_20190424.tar.gz" ; sc:featureList edam:operation_3478, edam:operation_3557, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MERLoT" ; sc:url "https://github.com/soedinglab/merlot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC6602572", "pubmed:31106328" ; sc:description "Web server to prepare and run coarse-grained membrane protein dynamics." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MERMAID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molsim.sci.univr.it/mermaid/" ; biotools:primaryContact "Alejandro Giorgetti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0623, edam:topic_0821 ; sc:citation , "pmcid:PMC6750024", "pubmed:31524991" ; sc:description "Predicting Sequence Features, Function, and Structure of Proteins Using MESSA | MEta-Server for protein Sequence Analysis (MESSA) is a tool that facilitates widespread protein sequence analysis by gathering structural (local sequence properties and three-dimensional structure) and functional (annotations from SWISS-PROT, Gene Ontology terms, and enzyme classification) predictions for a query protein of interest. MESSA uses multiple well-established tools to offer consensus-based predictions on important aspects of protein sequence analysis. Being freely available for noncommercial users and with a user-friendly interface, MESSA serves as an umbrella platform that overcomes the absence of a comprehensive tool for predictive protein analysis. This article reveals how to access MESSA via the Web and shows how to input a protein sequence to analyze using the MESSA web server" ; sc:featureList edam:operation_3092 ; sc:name "MESSA" ; sc:url "http://prodata.swmed.edu/MESSA/MESSA.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc:description """Despite the increasing importance of non-targeted metabolomics to answer various life science questions, extracting biochemically relevant information from metabolomics spectral data is still an incompletely solved problem. Our framework captures potential relationships between spectral features and substructures learned from public spectral libraries. These associations are used to recommend substructures for any unknown mass spectrum. Our method does not require any predefined metabolite candidates, and therefore it can be used for the partial identification of unknown unknowns.""" ; sc:featureList edam:operation_3801, edam:operation_3803 ; sc:name "MESSAR (MEtabolite SubStructure Auto-Recommender)" ; sc:url "https://messar.biodatamining.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3407 ; sc:citation , "pubmed:30657869" ; sc:description "R package for context-specific expression analysis of metabolic gene clusters." ; sc:featureList edam:operation_0313, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "METACLUSTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mbanf/METACLUSTER" ; biotools:primaryContact "EducatedGuess.ai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2640 ; sc:citation , "pubmed:31432076" ; sc:description "Mutual Exclusion and Coverage Based Random Walk to Identify Cancer Modules | This is the original repository for the MEXCOwalk paper | The evaluation file can also be run with multiple models and compared to MEXCOwalk. Simply store the models in 'out/connected_components_isolarge/model_x' and add the model name to the evaluations section in the evaluation file as follows:" ; sc:featureList edam:operation_1812, edam:operation_3501 ; sc:name "MEXCOwalk" ; sc:url "https://github.com/abu-compbio/MEXCOwalk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3308 ; sc:citation , "pmcid:PMC6842160", "pubmed:31703549" ; sc:description """An on-ramp for RESTful query composition. an on-ramp for learning to use the MG-RAST API. MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server provides upload, quality control, automated annotation and comparative analysis for shotgun and amplicon metagenomic samples as well as metatranscriptomes. MG-RAST API Explorer -- an on-ramp for learning to use the MG-RAST API. An object store for scientific data. MG-RAST provides a RESTful API at https: api.mg-rast.org. workflow and resource management system for bioinformatics data analysis.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0362, edam:operation_3192 ; sc:name "MG-RAST API explorer" ; sc:url "https://explorer.mg-rast.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0798 ; sc:citation , "pmcid:PMC6515669", "pubmed:31114637" ; sc:description "Mobile Genetic Elements Retrieving Tool Pipeline (MGERT) for retrieving coding sequences of mobile genetic elements from genome assemblies." ; sc:featureList edam:operation_0427, edam:operation_0525, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MGERT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andrewgull/MGERT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3297, edam:topic_3303, edam:topic_3697, edam:topic_3837 ; sc:citation , ; sc:description """A probabilistic model to recover individual genomes from metagenomes. MGLEX - MetaGenome Likelihood EXtractor. This Python Package provides a probabilistic model to classify nucleotide sequences in metagenome samples. It was developed as a framework to help researchers to reconstruct individual genomes from such datasets using custom workflows and to give developers the possibility to integrate the model into their programs. MGLEX – A Python Package for Probabilistic Modeling and Binning of Metagenomes. We recommend to create a Python virtual installation enviroment for MGLEX. In order to do so, install the venv package for your Python version (e.g. the Debian package python3.4-venv), if not included (or use virtualenv). The following command will make use of the installed system packages""" ; sc:featureList edam:operation_0310, edam:operation_3431, edam:operation_3472, edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "MGLEX" ; sc:url "http://pypi.python.org/pypi/mglex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885 ; sc:citation , "pmcid:PMC9158227", "pubmed:35650523" ; sc:description "Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MGMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zrmacc/MGMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_3293 ; sc:citation , "pubmed:31397853" ; sc:description "The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae | The Methylotroph Gene Order Browser (MGOB) is an online tool for visualising the syntenic context of any gene from several yeast genomes - Copyright Kevin Byrne - ygob@ucd.ie - Wolfe Laboratory, Conway Institute, University College Dublin, Dublin 4, Ireland" ; sc:featureList edam:operation_3208, edam:operation_3216, edam:operation_3501 ; sc:name "MGOB" ; sc:url "http://mgob.ucd.ie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_2229, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31696235" ; sc:description """The microbiome analysis resource in 2020. MGnify (http: www.ebi.ac.uk metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility.""" ; sc:featureList edam:operation_0310, edam:operation_3184, edam:operation_3731 ; sc:name "MGnify" ; sc:url "http://www.ebi.ac.uk/metagenomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0781, edam:topic_0804, edam:topic_3292 ; sc:citation ; sc:description """Multi Epitope Vaccine Prediction Against Aichi Virus using Immunoinformatic Approach. IEDB recommended 2.22 IEDB recommended 2.18 Consensus 2.22 Consensus 2.18 NetMHCIIpan 3.2 NetMHCIIpan 3.1 NN-align 2.3 (NetMHCII 2.3) NN-align 2.2 (NetMHCII 2.2) SMM-align (NetMHCII 1.1) Combinatorial library Sturniolo Help on prediction method selections. Enter protein sequence(s) in FASTA format. Or select file containing sequence(s). or as whitespace-separated sequences.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0482 ; sc:name "MHCII" ; sc:url "http://tools.iedb.org/mhci/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2830 ; sc:citation , "pmcid:PMC6540523", "pubmed:31138107" ; sc:description "Deep neural network model for universal Major Histocompatibility Complex (MHC) binding prediction." ; sc:featureList edam:operation_0252, edam:operation_3227, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MHCSeqNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cmbcu/MHCSeqNet" ; biotools:primaryContact "Computational Molecular Biology Group, Chulalongkorn University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_2830, edam:topic_3520 ; sc:citation , "pubmed:31589052" ; sc:description """Automated and Reproducible Data Analysis for Immunopeptidomics. MHCquant: Identify and quantify peptides from mass spectrometry raw data.""" ; sc:featureList edam:operation_3634, edam:operation_3643, edam:operation_3649 ; sc:name "MHCquant" ; sc:url "https://www.openms.de/mhcquant/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31647522" ; sc:description """Microsatellite instability detection on NGS amplicons data. Workflow for detecting microsatellite instability by next-generation sequencing on amplicons. MIAmS: Microsatellites Instability by AMplicon Sequencing.""" ; sc:featureList edam:operation_3435 ; sc:name "MIAmS" ; sc:url "https://github.com/bialimed/miams" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0610, edam:topic_2269 ; sc:citation , "pmcid:PMC6854112", "pubmed:31832144" ; sc:description """Variable transformation and model selection for species distribution models. A reproducible paper describing the MIAmaxent R package. Read our open-access paper in Ecology and Evolution introducing MIAmaxent: https://doi.org/10.1002/ece3.5654. Maxent software for modeling species niches and distributions. The file 'miamaxent-ms. MIAmaxent is intended primarily for maximum entropy distribution modeling (Phillips et al., 2006; Phillips et al., 2017), and provides an alternative to the standard methodology for training, selecting, and using models. Use this site to download Maxent software for modeling species niches and distributions by applying a machine-learning technique called maximum entropy modeling.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3664 ; sc:name "MIAmaxent" ; sc:url "https://biodiversityinformatics.amnh.org/open_source/maxent/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_0605, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6815465", "pubmed:31655541" ; sc:description """A novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy. The dataset for MIC_Locator can be downloaded from the website (https://pan.baidu.com/s/1dvvyT9OuJUcQYkCxidABDw)""" ; sc:featureList edam:operation_0321, edam:operation_2489, edam:operation_3092 ; sc:name "MIC_Locator" ; sc:url "https://github.com/ProteinLocator/MIC_Locator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0605, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC6829817", "pubmed:31684860" ; sc:description """An interactive web tool for microRNA-target enrichment and network-based analysis. BACKGROUND:miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS:We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis""" ; sc:featureList edam:operation_0463, edam:operation_2436, edam:operation_3792 ; sc:name "MIENTURNET" ; sc:url "http://userver.bio.uniroma1.it/apps/mienturnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3056, edam:topic_3500 ; sc:citation , , "pmcid:PMC6442577", "pubmed:30867282" ; sc:description "Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture." ; sc:featureList edam:operation_0487, edam:operation_0547, edam:operation_3446 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIGRATE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://peterbeerli.com/migrate-html5/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31443048" ; sc:description "Multiple Instance Prediction of Amyloid Proteins | Software and Data Downloads — Personal Webpage documentation | Note: This page will be discontinued. Please visit my new webpage HERE and update your bookmarks | Link to my GitHub profile: HERE Here is a list of the software developed in my lab | AMAP: Antimicrobial activity prediction | MILAMP: Multiple Instance Learning of Amyloid Proteins. Webserver available HERE. Code available HERE" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_2492 ; sc:name "MILAMP" ; sc:url "http://faculty.pieas.edu.pk/fayyaz/software.html#MILAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3489 ; sc:citation , "pmcid:PMC6908718", "pubmed:31831740" ; sc:description """De-identified publicly available database of chest radiographs with free-text reports. If you use the MIMIC-CXR Database in your work, please cite the following publication:. MIMIC-CXR: A large publicly available database of labeled chest radiographs. Johnson AEW, Pollard TJ, Berkowitz S, Greenbaum NR, Lungren MP, Deng C-Y, Mark RG, Horng S. arXiv.. Available from: https://arxiv.org""" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:name "MIMIC-CXR" ; sc:url "https://mimic-cxr.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:31400192" ; sc:description "Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression | Using Multiple Measurements of Tissue to Estimate Subject- And Cell-Type-Specific Gene Expression via Deconvolution | MIND (Multi-measure INdividual Deconvolution) | MIND is a method to glean insights from bulk gene expression. It borrows information across multiple measurements of the same tissue per subject, such as multiple regions of the brain, using an empirical Bayes approach to estimate subject- and cell-type-specific gene expression via deconvolution" ; sc:featureList edam:operation_3232, edam:operation_3629, edam:operation_3658 ; sc:name "MIND" ; sc:url "https://github.com/randel/MIND" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3342, edam:topic_3391 ; sc:citation , , , , , "pmcid:PMC4932659", "pmcid:PMC5516855", "pubmed:27441714", "pubmed:28725475", "pubmed:30991279", "pubmed:31074494", "pubmed:31273380" ; sc:description """MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format, including files produced using CellDesigner or SBGN editors. Visualization of uploaded networks generated by the platform is accessible via a web browser to all viewers with the weblink to the resource. MINERVA is a webservice using the Java Server Faces 2 technology. The server side, including data parsing, integration, annotation and verification, is implemented in Java 8. The platform uses the Postgres SQL database for data storage and the Hibernate framework as a middle layer between web server and database. The user web-interface is generated using JSF and PrimeFaces. The displayed content is visualized by OpenLayers or Google Maps API, dedicated JavaScript and CSS.""" ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MINERVA Platform" ; sc:softwareVersion "13.1.3", "13.2.0", "14.0.13", "15.0.3" ; sc:url "https://minerva-web.lcsb.uni.lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6913132", "pubmed:31624092" ; sc:description """Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution. (m)6A (I)dentification Using (N)anopor(E) (S)equencing. Tombo(v1.4) Commands Prior to MINES:. python cDNA_MINES.py --fraction_modified output_filename.fraction_modified_reads.plus.wig.bed --coverage output_filename.coverage.plus.bedgraph --output m6A_output_filename.bed --ref REF.fa.""" ; sc:featureList edam:operation_0239, edam:operation_0417, edam:operation_3644 ; sc:name "MINES" ; sc:url "https://github.com/YeoLab/MINES.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6923819", "pubmed:31861975" ; sc:description """A webserver for statistical, visual and meta-analysis of RNA editing data in mammals. BACKGROUND:Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS:Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3096 ; sc:name "MIRIA" ; sc:url "https://mammal.deepomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3300, edam:topic_3305, edam:topic_3335, edam:topic_3382 ; sc:citation , "pmcid:PMC6830040", "pubmed:31688939" ; sc:description """A myocardial infarction risk knowledge base. Myocardial Infarction Risk Knowledge Base. MIRKB (the Myocardial Infarction Risk Knowledge Base) is a database that collected single factors, combined factors, and risk models which are article-supported to be associated with the risk assessment, diagnosis, prognosis, and treatment of MI in human. The goal of MIKB was to improve the efficiency of MI research. MI is a common cardiovascular disease and a leading cause of death worldwide. It can be classified into many types according to the disease phase, lesion range, ECG expression, infarction location, and clinical type""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3454 ; sc:name "MIRKB" ; sc:url "http://sysbio.org.cn/MIRKB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0632, edam:topic_2885, edam:topic_3305 ; sc:citation , "pubmed:31603462" ; sc:description """Fast in-silico MIRU-VNTR typing directly from long sequencing reads. In-silico MIRU-VNTR typing using long reads. Identify 24-locus MIRU-VNTR for Mycobacterium tuberculosis complex (MTBC) directly from long reads generated by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). Also work on assembled genome.""" ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "MIRUReader" ; sc:url "https://github.com/phglab/MIRUReader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3375, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6335810", "pubmed:30651067" ; sc:description "Generic open-source framework for model fits and their exploration in medical imaging - design, implementation and application on the example of DCE-MRI." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MITK-ModelFit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mitk.org/wiki/MITK-ModelFit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6721208", "pubmed:31477162" ; sc:description "Inferring features from microbiota time-series data linked to host status | The Microbiome Interpretable Temporal Rule Engine | Input code and results from simulations supporting the MITRE paper | Supporting files for the Microbiome Interpretable Temporal Rule Engine manuscript | MITRE learns predictive models of patient outcomes from microbiome time-series data in the form of short lists of interpretable rules | This repository includes the configuration files used to set up simulations for the MITRE manuscript, and results from those simulations, with a few useful auxiliary files | MITRE will load data from Bokulich, N. A., et al., \"Antibiotics, birth mode, and diet shape microbiome maturation during early life.\" Science Translational Medicine 8(343): 343ra82, which is packaged with MITRE" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "MITRE" ; sc:url "https://github.com/gerberlab/mitre/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6561249", "pubmed:31113885" ; sc:description "Mismatching Isoform eXon Remover." ; sc:featureList edam:operation_0499, edam:operation_0544, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MIXR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/hawkjo/mixr" ; biotools:primaryContact "Sara L. Sawyer", "William H. Press" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3384, edam:topic_3577 ; sc:citation , "pubmed:31693075" ; sc:description """Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. MOTIVATION:The use of human genome discoveries and other established factors to build an accurate risk prediction model is an essential step towards precision medicine. While multi-layer high-dimensional omics data provide unprecedented data resources for prediction studies, their corresponding analytical methods are much less developed. RESULTS:We present a multi-kernel linear mixed model with adaptive lasso (MKpLMM), a predictive modeling framework that extends the standard linear mixed models widely used in genomic risk prediction, for multi-omics data analysis. MKpLMM can capture not only the predictive effects from each layer of omics data but also their interactions via using multiple kernel functions.""" ; sc:name "MKpLMM" ; sc:url "https://github.com/YaluWen/OmicPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_0621 ; sc:citation , "pmcid:PMC6880518", "pubmed:31775608" ; sc:description """Potential based, spatial simulation of dynamically nested particles. Source repository for the publication "Potential based, spatial simulation of dynamically nested particles" in BMV Bioinformatics. ML-Force source code added · 1e971b94.""" ; sc:featureList edam:operation_2476 ; sc:name "ML-Force" ; sc:url "https://git.informatik.uni-rostock.de/mosi/ml-force-publication" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3298, edam:topic_3382 ; sc:citation ; sc:description "A Fast, Accurate and General Approach for Automated Detection and Landmarking of Biological Structures in Images | Machine-learning-based morphometrics | Machine-learning tools for landmark-based morphometrics | Porto & Voje (2019) A fast, accurate and general model for automated landmarking of biological images. Submitted | Also note that while ml-morph can handle multiple image file formats, some care is needed with regards to the presence of special characters in image filenames. So far, we have only had problems with &, but it is possible that other special characters might lead the software to throw out an error" ; sc:name "ML-morph" ; sc:url "https://github.com/agporto/ml-morph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Metric Learning on Expression Data for Gene Function Prediction." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MLC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.github.com/stamakro/MLC" ; biotools:primaryContact "Stavros Makrodimitris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0157, edam:topic_0654 ; sc:citation , "pubmed:31584616" ; sc:description """A Fast and Memory Efficient MLCS Algorithm by Character Merging for DNA Sequences Alignment. This is a fast MLCS algorithm for DNA sequence""" ; sc:featureList edam:operation_0232, edam:operation_0292, edam:operation_0306 ; sc:name "MLCS" ; sc:url "https://github.com/liusen1006/MLCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0654, edam:topic_3474 ; sc:citation ; sc:description "An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis | An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis" ; sc:featureList edam:operation_0337, edam:operation_3460 ; sc:name "MLDSP-GUI" ; sc:url "https://sourceforge.net/projects/mldsp-gui/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749 ; sc:citation , "pubmed:31116391" ; sc:description "Morais-Lima-Martin (MLM) algorithm for data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach." ; sc:featureList edam:operation_3359, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MLM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://figshare.com/articles/MLM_Algorithm/7393517/1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:30653470" ; sc:description "R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MLML2R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.3.2" ; sc:url "https://cran.r-project.org/package=MLML2R" ; biotools:primaryContact "Samara Kiihl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3305, edam:topic_3673, edam:topic_3796 ; sc:citation ; sc:description """Automatic multilocus and core genome sequence typing in R. An easy way of MLSTyping your genomes in R. This R package allows you to easily determine the Multi Locus Sequence Type (MLST) of your genomes. It also works as an interface between PubMLST through their RESTful API, so you don't have to bother downloading and collecting files: the application does it automatically. Today the package works in Unix-based systems. If you use MLSTar in your publications, please cite:. Note: cgMLST and wgMLST are not yet fully supported since the RESTful API interphase for theses cases is a little different than the one for the standard 7 loci schemes. See issues#11 for more details""" ; sc:featureList edam:operation_3227, edam:operation_3431, edam:operation_3840 ; sc:license "MIT" ; sc:name "MLSTar" ; sc:url "http://github.com/iferres/MLSTar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_2885, edam:topic_3519, edam:topic_3673 ; sc:citation , "pmcid:PMC6905556", "pubmed:31825986" ; sc:description """Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae. python-dev (sudo apt-get install python-dev),. regex (https://launchpad.net/ubuntu/+archive/primary/+files/python-regex_0.1.20170117.orig.tar.gz).""" ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_2404 ; sc:name "MLVAType" ; sc:url "https://github.com/dpchris/MLVA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6493971", "pubmed:31042284" ; sc:description "Microbiome Learning Repo (ML Repo) - public repository of microbiome regression and classification tasks" ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ML Repo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://knights-lab.github.io/MLRepo/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3474, edam:topic_3570 ; sc:citation , "pubmed:31219626" ; sc:description "Program package for quantum chemical research assisted by machine learning." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MLatom" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://mlatom.com/" ; biotools:primaryContact "Dr. Pavlo O. Dral" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ML for insightful data analysis and enhance research outcomes. By simplifying and automating various stages of the ML workflow, it enables researchers to allocate more time to their core research tasks, thereby enhancing efficiency and productivity." ; sc:name "MLME: Machine Learning Made Easy" ; sc:url "https://github.com/FunctionalUrology/MLme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31446280" ; sc:description "Evaluation of algorithms for Multi-Modality Whole Heart Segmentation | Multi-Modality Whole Heart Segmentation Challenge | MM-WHS: Multi-Modality Whole Heart Segmentation | Accurate computing, modeling and analysis of the whole heart substructures is important in the development of clinical applications. Segmentation and registration of whole heart images is however challenging and still relies heavily on manual work, which is time-consuming and prone to errors | For evaluation of the test data, the participants should prepare a brief description of their algorithm and email with the segmentation results of the test datasets to the organizers" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:name "MM-WHS" ; sc:url "http://www.sdspeople.fudan.edu.cn/zhuangxiahai/0/mmwhs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """Mother machine image analysis with MM3. Version 3 of Python mother machine analysis code. MM3 at University of California, San Diego. MM3 at University of California, San Diego for Fall 2019 on Piazza, a free Q&A platform for students and instructors. mm3 is a image analysis pipeline for mother machine experiments. It takes as input raw timelapse images and produces as output cell objects containing information such as elongation rate, birth size, etc. There is support for fluorescent planes. Segmentation and tracking software for mother machine experiments. The name Piazza comes from the Italian word for plaza--a common city square where people can come together to share knowledge and ideas. We strive to recreate that communal atmosphere among students and instructors""" ; sc:featureList edam:operation_3443, edam:operation_3454 ; sc:name "MM3" ; sc:url "https://piazza.com/ucsd/fall2019/mm3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3315, edam:topic_3384, edam:topic_3398, edam:topic_3452 ; sc:citation ; sc:description """GPU-accelerated mesh-based Monte Carlo photon transport simulations. ===============================================================================. = Mesh-based Monte Carlo (MMC) =. = Supporting both OpenCL and Multi-threading with SSE4 =. A GPU-accelerated photon transport simulator. Download v2019.4 or Nightly-build. "mmc -L" or "mmclab('gpuinfo')" to list). Designing MATLAB-streamlined MC-based analysis using MCXLAB and MMCLAB.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435 ; sc:name "MMCL" ; sc:url "http://mcx.space/#mmc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2182, edam:format_2200 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_0637, edam:topic_3174 ; sc:citation , , , , , ; sc:description """MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.""" ; sc:featureList edam:operation_0291, edam:operation_0292, edam:operation_0346, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MMseqs2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://mmseqs.com" ; biotools:primaryContact "Söding Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Software and resources for experiments and data analysis of MEG and EEG data | Installation — contents — MNE 0.19.1 documentation | The official home of the Python Programming Language | Notice: While Javascript is not essential for this website, your interaction with the content will be limited. Please turn Javascript on for the full experience | MNE-Python is an open-source Python module for processing, analysis, and visualization of functional neuroimaging data (EEG, MEG, sEEG, ECoG, and fNIRS) | Python is a programming language that lets you work quickly and integrate systems more effectively | Join the official 2019 Python Developers Survey Start the survey!" ; sc:featureList edam:operation_0337 ; sc:license "Proprietary" ; sc:name "MNE-Python" ; sc:softwareHelp ; sc:url "http://python.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3336 ; sc:citation , "pmcid:PMC6589129", "pubmed:31125569" ; sc:description "Mother of All Databases (MOAD) - Polypharmacology Tools and Their Utility in Drug Repurposing." ; sc:featureList edam:operation_0482, edam:operation_2575, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MOAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.BindingMOAD.org" ; biotools:primaryContact "Heather A. Carlson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "Efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MOAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://moat.gersteinlab.org/" ; biotools:primaryContact "Mark Gerstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0623 ; sc:citation , "pubmed:31584171" ; sc:description """Automated Annotation of MOB Relaxases. Please, fill the submission form below and select the FASTA file containing the amino acid sequences. Your data is being processed. 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Swertz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6612815", "pubmed:31510700" ; sc:description "Multi-omics late integration with deep neural networks for drug response prediction | MOTIVATION:Historically, gene expression has been shown to be the most informative data for drug response prediction. Recent evidence suggests that integrating additional omics can improve the prediction accuracy which raises the question of how to integrate the additional omics. Regardless of the integration strategy, clinical utility and translatability are crucial. Thus, we reasoned a multi-omics approach combined with clinical datasets would improve drug response prediction and clinical relevance. RESULTS:We propose MOLI, a multi-omics late integration method based on deep neural networks. MOLI takes somatic mutation, copy number aberration and gene expression data as input, and integrates them for drug response prediction" ; sc:featureList edam:operation_3557 ; sc:name "MOLI" ; sc:url "https://github.com/hosseinshn/MOLI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3360 ; sc:citation ; sc:description "Toolbox integrating top-performing methods for NEtwork MOdularisation." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MONET" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BergmannLab/MONET.git" ; biotools:primaryContact "Mattia Tomasoni", "Sven Bergmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3895 ; sc:citation ; sc:description "Design and assembly of DNA molecules using multi-objective optimisation | A DNA design and assembly method based on multi-objective optimization | MOODA: Multi-Objective Optimization for DNA sequence Design and Assembly | A manufacturing-aware sequence optimizer | Write a MOODA configuration file. A .yaml file defining operators, objective functions, assemblies strategy and their parameters, this is how a MOODA configuration file looks like:" ; sc:featureList edam:operation_2425, edam:operation_3745 ; sc:license "MIT" ; sc:name "MOODA" ; sc:url "http://mooda.stracquadaniolab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3315, edam:topic_3407 ; sc:citation , "pubmed:31504164" ; sc:description "Mathematical explOration of 'Omics data on a MetabolIc Network | MOOMIN is a tool for analysing differential expression data | MOOMIN (Mathematical explOration of Omics data on a MetabolIc Network) is a tool for analysing differential expression data. It takes as its input a metabolic network and the results of a DE analysis: a posterior probability of differential expression and a (logarithm of a) fold change for a list of genes. It then forms a hypothesis of a metabolic shift, determining for each reaction its status as \"increased flux\", \"decreased flux\", or \"no change\". These are expressed as colours: red for an increase, blue for a decrease, and grey for no change. 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Lun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation , "pmcid:PMC6789201", "pubmed:31620462" ; sc:description """Mobile training and support (MOTS) service-using technology to increase Ebola preparedness of remotely-located community health workers (CHWs) in Sierra Leone. As in many African countries, the Community Health Worker (CHW) is the backbone of the healthcare system, and the focus and objective of the Mobile Training and Support (MOTS) project will be strengthening this network to ensure preparedness for Ebola vaccine campaigns and outbreak response. The project will set up a MOTS service that is the veh….""" ; sc:license "Apache-2.0" ; sc:name "MOTS" ; sc:url "https://github.com/motech-implementations/mots" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2269, edam:topic_3474 ; sc:citation , "pubmed:31851308" ; sc:description """A standalone GUI-based package for maximum entropy model inference. Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters. MPF-BML: A standalone GUI-based cross-platform package for maximum entropy model inference. MPF-BML-GUI is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the input data (protein sequence data or data of multiple configura-tions of a complex system with large number of variables) and returns the maximum entropy model parameters inferred using the MPF-BML method""" ; sc:license "MIT" ; sc:name "MPF-BML" ; sc:url "https://github.com/ahmedaq/MPF-BML-GUI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3068, edam:topic_3360, edam:topic_3379 ; sc:citation , "pmcid:PMC6759478", "pubmed:31620162" ; sc:description """Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation. Molecular Prognostic Indicators in Cirrhosis. Database for clinical context-specific in silico prognostic biomarker validation. This is a system that enables quick and easy assessment of user’s prognostic gene signature in various liver disease patient cohorts for a specific clinical outcome""" ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:name "MPIC" ; sc:url "http://www.mpic-app.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6717970", "pubmed:31477158" ; sc:description "Statistical framework for massively parallel reporter assays | Statistical Analysis of MPRA data | MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes" ; sc:featureList edam:operation_3200, edam:operation_3501, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "MPRAnalyze" ; sc:url "https://bioconductor.org/packages/release/bioc/html/MPRAnalyze.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "Web-based tool for the design of massively parallel reporter assay experiments." ; sc:featureList edam:operation_0438 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MPRAnator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.sanger.ac.uk/science/tools/mpranator" ; biotools:primaryContact "Ilias Georgakopoulos-Soares", "Martin Hemberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:31359027" ; sc:description "Robust and non-parametric analysis of massively parallel reporter assays | MPRAscore: Robust and non-parametric analysis of massively parallel reporter assays (MPRA) | MPRAscore infers allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence" ; sc:name "MPRAscore" ; sc:url "https://github.com/abhisheknrl/MPRAscore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:31086984" ; sc:description "Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models." ; sc:featureList edam:operation_0477, edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MPRDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/mprdock/" ; biotools:primaryContact "Lab of Bioinformatics and Molecular Modeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3360 ; sc:citation , "pmcid:PMC4349052", "pubmed:25755929" ; sc:description """Language workbench user interfaces for data analysis. The Domain-Specific Language Creator by JetBrains. Use MPS platform to create your own domain-specific language that speak to your business needs. Use non-textual notation with projectional editing. BDVal for MPS is an MPS plugin designed to help you configure BDVal projects. BDVal for MPS makes it easier to develop and validate predictive models in high-throughput datasets. When the product is highly complex and the developers aren’t experts in your business domain. MPS helps even unfamiliar developers understand the system immediately""" ; sc:featureList edam:operation_3096, edam:operation_3359 ; sc:name "MPS" ; sc:url "http://campagnelab.org/software/bdval-for-mps/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc:description "Applications of the Microphysiology Systems Database for Experimental ADME-Tox and Disease Models | The MPS-Db aggregates MPS data with linked preclinical and clinical databases for analysis in the context of human exposure. Built in tools enable the assessment of the reproducibility and transferability of MPS models, while computational models are being developed to enhance the value of MPS models for understanding disease mechanisms, compound toxicity, and prediction of drug pharmacokinetics (PK)" ; sc:featureList edam:operation_3436 ; sc:name "MPS-Db" ; sc:url "https://mps.csb.pitt.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3517 ; sc:citation , , "pmcid:PMC5976434", "pmcid:PMC6694718", "pubmed:29846171", "pubmed:31448343" ; sc:description "Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes | This repository contains the case studies associated with the manuscript \"Using the MR-Base platform to investigate risk factors and drug targets for thousands of phenotypes\" | 2-sample Mendelian Randomisation | MR-base is a database and analytical platform for Mendelian randomization being developed by the MRC Integrative Epidemiology Unit at the University of Bristol" ; sc:featureList edam:operation_0488, edam:operation_3659 ; sc:license "MIT" ; sc:name "MR-Base" ; sc:url "http://www.mrbase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2885, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc:description """Clustering of genetic variants in Mendelian randomization with similar causal estimates. R package for investigating clustered heterogeneity in Mendelian randomization (MR) analyses. mr_clust_em - performs expectation-maximisation (EM) based model fitting of the MR-Clust mixture model. Genetic variants which recover similar estimates of the causal effect of the risk-factor on the outcome - i.e. their ratio-estimates are similar in direction, magnitude and precision - can form distinct clusters in MR analyses. We call this `clustered heterogeneity'. Each cluster might represent a distinct pathway with which the risk-factor is related to the outcome and hence clustered heterogeneity is interesting to investigate as the identity of the genetic variants in the clusters may reveal information about the risk factor and how it relates to the outcome""" ; sc:featureList edam:operation_3432, edam:operation_3659, edam:operation_3791 ; sc:name "MR-Clust" ; sc:url "https://github.com/cnfoley/mrclust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3517 ; sc:citation ; sc:description "MR-MEGA (Meta-Regression of Multi-Ethnic Genetic Association) - tool to detect and fine-map complex trait association signals via trans-ethnic meta-regression." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MR-MEGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "beta 0.1.5" ; sc:url "https://www.geenivaramu.ee/en/tools/mr-mega" ; biotools:primaryContact "Andrew P Morris", "Reedik Magi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6609486", "pubmed:31037800" ; sc:description "Multi‐Atlas Label Fusion Tool for Neonatal Brain MRI Parcellation and Quantification." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRICloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://braingps.mricloud.org" ; biotools:primaryContact "Kenichi Oishi", "Kumiko Oishi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3384, edam:topic_3422, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC6790816", "pubmed:31607099" ; sc:description """Neural Correlates of Urinary Retention in Lateral Medullary Infarction. MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "MRIcron" ; sc:url "https://www.nitrc.org/projects/mricron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC6602510", "pubmed:31045205" ; sc:description "Tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRPrimerW2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://MRPrimerW2.com" ; biotools:primaryContact , "Min-Soo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3520, edam:topic_3673 ; sc:citation ; sc:description "Tool for de novo peptide sequencing utilizing the hadoop distributed computing framework." ; sc:featureList edam:operation_0476, edam:operation_3202, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MRUniNovo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.hupo.org.cn/MRUniNovo/index.php" ; biotools:primaryContact "Kenli Li", "Tao Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31473352" ; sc:description "A fast, flexible and open software framework for medical image processing and visualisation | MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "MRtrix3" ; sc:url "https://github.com/MRtrix3/mrtrix3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6330434", "pubmed:30634897" ; sc:description "Tool with multiple built-in data processing functions, allowing non-expert users to construct circular proteome maps (CPMs) or in general terms circular plots with a non-genomic basis." ; sc:featureList edam:operation_0417, edam:operation_2939, edam:operation_2940 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS-Helios" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.8" ; sc:url "https://sourceforge.net/projects/ms-helios/" ; biotools:primaryContact "Harald Marx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC6929458", "pubmed:31874640" ; sc:description """Predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. Under construction, we will update it soon. MS2CNN compilation requires the following tools installed on your system Python, Keras==2.0.4 and Tensorflow==1.1.0. Predicting MS/MS spectrum based on protein sequence by Deep Convolutional Neural Networks. Lin YM, Chen CT, Chang JM. MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks. BMC Genomics. 2019;20(Suppl 9):906""" ; sc:featureList edam:operation_3643, edam:operation_3646, edam:operation_3767, edam:operation_3801, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "MS2CNN" ; sc:url "https://github.com/changlabtw/MS2CNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31120050" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'MotifDB' | Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra | Python code for running single file and multi-file LDA | A web application developed in Django+D3 to visualise how topics inferred from Latent Dirichlet Allocation can be used to assist in the unsupervised characterisation of fragmented (LC-MS-MS) metabolomics data | Demo available at www.ms2lda.org (please email us to gain access) | Go to Experiments Quick Decomposition | 25th November 2018: We have introduced many new features to make interpreting Mass2Motifs in MS2LDA.org easier | The last command inserts the gensim lda results into the database" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MS2LDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ms2lda.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , , , "pmcid:PMC4489309", "pmcid:PMC5994937", "pmcid:PMC6602496", "pubmed:24078703", "pubmed:25990723", "pubmed:31028400" ; sc:description "MS²PIP is a tool to predict MS² peak intensities from peptide sequences. This makes it possible to generate in silico predicted spectral libraries for full proteomes. MS²PIP employs the XGBoost machine learning algorithm and is written in Python." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS2PIP Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://iomics.ugent.be/ms2pip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_2885, edam:topic_3305, edam:topic_3489 ; sc:citation , "pubmed:31599331" ; sc:description """A comprehensive, annotated database of microsatellites. Multiple Loci VNTR Analysis databases and software. Multi Locus VNTR Analysis (MLVA) databases and software. MICAS 3.0, Microsatellite Analysis Server is the online repository of All Bacterial Microsatellites. MICAS: Microsatellite Analysis Server 3.0. An Online Repository of All Prokaryotic Microsatellites. with a focus on Viruses of Microbes and Molecular Epidemiology of bacterial pathogens. CRISPRCasdb: database for CRISPRs and associated Cas genes. MICAS: Microsatellite Analysis Server.""" ; sc:featureList edam:operation_0237, edam:operation_0337, edam:operation_0543, edam:operation_3840 ; sc:name "MSDB" ; sc:url "http://minisatellites.u-psud.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2640, edam:topic_3373, edam:topic_3676 ; sc:citation , "pubmed:31802092" ; sc:description """Modular within and between score for drug response prediction in cancer cell lines. Drug response prediction in cancer cell lines is vital to discover new anticancer drugs. However, it's still a challenging task to accurately predict drug responses in cancer cell lines. In this study, we presented a novel computational approach, named as MSDRP (modular within and between score for drug response prediction), to predict drug responses in cell lines. The method is based on a constructed heterogeneous drug-cell line network with multiple information. Compared with other state-of-the-art methods, MSDRP acquired better predictive performance, and identified potential associations between drugs and cell lines, which have been confirmed by the published literature. The source code of MSDRP is freely available at https: github.com shimingwang1994 MSDRP.git""" ; sc:featureList edam:operation_2495, edam:operation_3439 ; sc:name "MSDRP" ; sc:url "https://github.com/shimingwang1994/MSDRP.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description "Tool to visualize biological indices from mass spectrometry imaging data." ; sc:featureList edam:operation_3627, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MSIdV" ; sc:operatingSystem "Windows" ; sc:url "https://sourceforge.net/projects/msidv/" ; biotools:primaryContact "Eisuke Hayakawa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3676 ; sc:citation , "pmcid:PMC6277498", "pubmed:30510242" ; sc:description "Python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MSIpred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wangc29/MSIpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3077, edam:topic_3520 ; sc:citation ; sc:description """Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure. Computational Selection of MSMS to Include in Library (MSMS-Chooser). Open-source Protocol for Community-created Public MS/MS Reference Library (MSMS-Chooser). MSMS-Chooser is a GNPS workflow and open-source protocol to empower the community to collect MS/MS reference data and contribute to the public MS/MS reference library.""" ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3860 ; sc:name "MSMS-Chooser" ; sc:url "https://ccms-ucsd.github.io/GNPSDocumentation/msmschooser/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description "MTB Genome to Test (MTBGT) tool transforms WGS-derived data into laboratory-validated results of the primary RDTs – Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MTBGT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KamelaNg/MTBGT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC6794379", "pubmed:31649730" ; sc:description """Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data. MTGO applied to Single Cell analysis. MTGO analysis applied to Single Cell data version 0.2.0 from GitHub. MTGO-SC is an adaptation for single cell RNA-sequencing (scRNA-seq) of MTGO, a biological network module detection algorithm. MTGO-SC integrates external gene annotations, such as the Gene Ontology terms or Reactome pathways with the gene expression networks obtained from single-cell DGE matrices. This package integrates MTGO (Module detection via Topological information and Gene Ontology (GO) knowledge) to single cell analysis. Effort is made to seamless integration of Seurat results, together with visualization and filtering functions. ne1s0n/MTGOsc: MTGO analysis applied to Single Cell data. Extracting gene modules from single cell RNA-seq cell clusters""" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3432, edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "MTGO-SC" ; sc:url "https://github.com/ne1s0n/MTGOsc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0202, edam:topic_0749, edam:topic_0781, edam:topic_3297 ; sc:citation , "pubmed:31686495" ; sc:description """A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. Code and sequence files used in MTK manuscript""" ; sc:featureList edam:operation_0308, edam:operation_0310 ; sc:name "MTK" ; sc:url "https://github.com/jpfon/MTK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pubmed:31403410" ; sc:description "Multi-Task Deep Model with Margin Ranking Loss for Lung Nodule Analysis | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | This is the pytorch implementation for 《MTMR-Net: Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 | Code for 《Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis》 Project" ; sc:featureList edam:operation_3659 ; sc:name "MTMR-Net" ; sc:url "https://github.com/CaptainWilliam/MTMR-NET" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3814, edam:format_3816 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_3816 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation "pubmed:25855812" ; sc:description "Docking into a user-defined binding site or blind docking using AutoDock 4.2." ; sc:featureList edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MTiAutoDock" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock" ; biotools:primaryContact "Maria A. Miteva" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3814, edam:format_3816 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_3816 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3343 ; sc:citation "pubmed:25855812", "pubmed:31546814" ; sc:description "Automated virtual screening with AutoDock Vina." ; sc:featureList edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MTiOpenScreen" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiOpenScreen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780 ; sc:citation , "pubmed:31061104" ; sc:description "Multivariate analysis application for streamlined data analysis and curation." ; sc:featureList edam:operation_2939, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MVApp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mvapp.kaust.edu.sa/MVApp/" ; biotools:primaryContact "Magdalena Julkowska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6751173", "pubmed:31534156" ; sc:description "Multi-view based integrative analysis of gene expression data for identifying biomarkers | This repository provides some codes for this paper | The widespread applications in microarray technology have produced the vast quantity of publicly available gene expression datasets | If you are interested in it but have doubts about the content, please feel free to contact me | Communication: yangziyi091100@163.com" ; sc:featureList edam:operation_2495, edam:operation_3436 ; sc:name "MVIAm" ; sc:url "https://github.com/must-bio-team/MVIAm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0634, edam:topic_3444 ; sc:citation , "pubmed:31407400" ; sc:description "Myelin Water Fraction and Intra/Extracellular Water Geometric Mean T2 Normative Atlases for the Cervical Spinal Cord from 3T MRI | Normative atlases for the spinal cord using myelin water imaging | Myelin water imaging was applied in 20 healthy spinal cords to create T2 metric healthy population atlases that depict the mean and variation of myelin water fraction (MWF), and intra- and extra-cellular water mobility as described by geometric mean T2 (IEGMT2). The created atlases demonstrated structural variations in the spinal cord consistent with well-known anatomical characteristics. These atlases (in PAM50 space from Spinal Cord toolbox) can be used as a reference to demonstrate areas of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400" ; sc:featureList edam:operation_3501, edam:operation_3799 ; sc:name "MWI" ; sc:url "https://sourceforge.net/projects/mwi-spinal-cord-atlases/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC10046854", "pubmed:36979426" ; sc:description "A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses" ; sc:featureList edam:operation_3214 ; sc:name "MaCProQC" ; sc:softwareVersion "1" ; sc:url "https://workflowhub.eu/workflows/343?version=1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0769, edam:topic_0780, edam:topic_3512 ; sc:citation , "pubmed:31665439" ; sc:description """A functional genomics hub for Malvaceae plants. Pipelines of data analysis for MaGenDB""" ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "MaGenDB" ; sc:url "http://magen.whu.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_2275, edam:topic_3172, edam:topic_3474 ; sc:citation , "pubmed:31819266" ; sc:description """Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning. MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces. MaSIF- Molecular Surface Interaction Fingerprints: Geometric deep learning to decipher patterns in protein molecular surfaces. MaSIF is a proof-of-concept method to decipher patterns in protein surfaces important for specific biomolecular interactions""" ; sc:featureList edam:operation_2492, edam:operation_2929, edam:operation_3092 ; sc:license "Apache-2.0" ; sc:name "MaSIF" ; sc:url "https://github.com/lpdi-epfl/masif" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0821, edam:topic_3421 ; sc:citation , "pmcid:PMC6853642", "pubmed:31681953" ; sc:description """A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI (Mycobacterium ABscessus modELLing INItiative) is a database available to anyone that wishes to know in detail the structural proteome of Mycobacterium abscessus. It contains thousands of models, generated with an unique domain-based methodology and thoroughly annotated with information from UniProt, CATH, SCOP and many more resources. These models are readily available for download, either individually or in bundles. To access them, simply use one of the many available queries or explore the data using our hierarchical interactive sunbursts""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0477, edam:operation_0478 ; sc:name "Mabellini" ; sc:url "http://www.mabellinidb.science" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3382 ; sc:citation , "pmcid:PMC6724615", "pubmed:31555312" ; sc:description "Maize Database of Images and Genomes | MaizeDIG - Maize Database of Images and Genomes. This tool allows users to tag phenotypes in images and link them to specific genes | MaizeDIG the Maize Database of Images and Genomes, a genotypic-phenotypic database, for maize based on BioDIG | There are some prerequisites to set up MaizeDIG system such as installation of Django framework, Database system, Python and related libraries, and other dependencies | The Maize Genetics Executive Committee is reaching out to the global maize genetics, genomics, and breeding research communities to encourage researchers to become a maize cooperator (What is a maize cooperator?) Regions currently underrepresented within the maize cooperators are Africa, Asia, Europe, and Latin America" ; sc:featureList edam:operation_0282, edam:operation_3232, edam:operation_3553 ; sc:name "MaizeDIG" ; sc:url "http://www.maizegdb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated data warehouse for MaizeGDB" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "MaizeMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.3" ; sc:url "http://maizemine.rnet.missouri.edu:8080/maizemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC6861670", "pubmed:31762961" ; sc:description """A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used in the system command line with R installed in the system or be used in the R enviroment. test.snp.RData is the input data to this R script. test.snp.RData is an R data file contained the genotype data of 1210 maize lines across 1000 SNP sites in character matrix. The content of this R data can be viewed in the R enviroment as shown below. MaizeSNPDB is deployed at http://150.109.59.144:3838/MaizeSNPDB/ for online use. The genotypes of 1210 maize lines at 35,370,939 SNP sites are stored using Sparse Matrices in R. MaizeSNPDB is idle until you activate it by accessing the URL. After running the R script, a new R data file named as test.snp. Mat.""" ; sc:featureList edam:operation_0282, edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:name "MaizeSNPDB" ; sc:url "https://github.com/venyao/MaizeSNPDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_3047, edam:topic_3292, edam:topic_3306 ; sc:citation ; sc:description """Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm. The cytoplasm of a cell is sometimes jestingly called a Soup, since it contains many different ingredients. Indeed there is quite a bit of salt and glutamate, the well known flavour enhancing compoud that is used a lot in asian kitchen but also in broth. Read more here: https://en.wikipedia.org/wiki/Glutamate_flavoring. In order to study the cytoplasm of a cell one can use a variety of experimental biochemistry techniques, but also computer simulations, which is the focus of this page. Here we thererfore provide information and python scripts to run computer simulations using http://www.gromacs.org of (quite) realistic models of the cytoplasm. The main work is done here by a few scripts, located in the aptly named scripts directory. They are described briefly in the README.md in that directory""" ; sc:featureList edam:operation_0480, edam:operation_2476, edam:operation_3891 ; sc:name "Making Soup" ; sc:url "http://github.com/dspoel/soup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3305, edam:topic_3518 ; sc:citation ; sc:description """An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Plasmodium falciparum Community Project. Dried blood spot collection. Photo credit: Will Hamilton. HiSeq machines at the Wellcome Trust Sanger Institute. Photo credit: Genome Research Limited. We're working with researchers in malaria-endemic countries to generate large-scale genetic and genomic data on all three malaria genomes: human, parasite, and mosquito. The Plasmodium falciparum Community Project supports groups around the world to integrate parasite genome sequencing into clinical and epidemiological studies of malaria. Our projects provide a framework for malaria researchers around the world to work together on large-scale studies that combine epidemiology with the analysis of genome variation to better understand the evolutionary battle between human hosts, malaria parasites, and the mosquito vector""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3211, edam:operation_3629, edam:operation_3891 ; sc:name "MalariaGEN" ; sc:url "http://www.malariagen.net/projects" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3305 ; sc:citation ; sc:description """An open-source web application for increasing access to malaria information. Preventable diseases still cause huge mortality in low- and middle-income countries. Research in spatial epidemiology and earth observation is helping academics to understand and prioritise how mortality could be reduced and generates spatial data that are used at a global and national level, to inform disease control policy. These data could also inform operational decision making at a more local level, for example to help officials target efforts at a local regional level. To be usable for local decision-making, data needs to be presented in a way that is relevant to and understandable by local decision makers. We demonstrate an approach and prototype web application to make spatial outputs from disease modelling more useful for local decision making.""" ; sc:featureList edam:operation_0337 ; sc:name "Malaria Data District" ; sc:url "https://seantomlinson30.shinyapps.io/shiny-map-prize/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3500, edam:topic_3517 ; sc:citation , "pmcid:PMC6882345", "pubmed:31775616" ; sc:description """Displaying genome-wide association summary statistics with multiple annotation layers. A useful way to summarize genome-wide association data is with a Manhattan plot. This type of plot has a point for every SNP or location tested with the position in the genome along the x-axis and the -log10 p-value on the y-axis""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3661 ; sc:name "Manhattan" ; sc:url "https://genome.sph.umich.edu/wiki/Code_Sample:_Generating_Manhattan_Plots_in_R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6330393", "pubmed:30634901" ; sc:description "Tool for automatically detecting and characterizing peaks from GWAS output files (Manhattan Plots)." ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Manhattan Harvester" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.geenivaramu.ee/en/tools/manhattan-harvester" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description "MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data | MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes | MapCaller: An efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data | MapCaller aligns every NGS short read against a reference genome and collects all the alignment information to deduce sequence variants" ; sc:featureList edam:operation_0452, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "MapCaller" ; sc:url "https://github.com/hsinnan75/MapCaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3382 ; sc:citation ; sc:description "Lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MapOptics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FadyMohareb/mapoptics" ; biotools:primaryContact "Fady Mohareb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3263, edam:topic_3489 ; sc:citation ; sc:description "The opendata geoportal of the Lamma Consortium." ; sc:featureList edam:operation_3454, edam:operation_3695 ; sc:license "CC-BY-4.0" ; sc:name "MapStore" ; sc:url "http://geoportale.lamma.rete.toscana.it/MapStore/public/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3067, edam:topic_3304 ; sc:citation , "pmcid:PMC6663211", "pubmed:31410377" ; sc:description "Topological gene expression networks recapitulate brain anatomy and function | Code for reproducing results in the paper \"Topological gene-expression networks recapitulate brain anatomy and function\" | TDA summary for gene-expression: Mapper Algorithm in 2D | Understanding how gene expression translates to and affects human behaviour is one of the ultimate aims of neuroscience" ; sc:featureList edam:operation_3463, edam:operation_3562, edam:operation_3766 ; sc:name "Mapper" ; sc:url "https://github.com/alpatania/AHBA_microarray_Mapper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc:description """Enhancer prediction in the human genome by probabilistic modeling of the chromatin feature patterns. This package is a PRobabilistic Enhancer PredictIoN Tool PREPRINT. Clone the project to the desired directory, this will be your path_to_dir. https://github.com/MariaOsmala/RFECS_BUG_FIXES.git.""" ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_2575 ; sc:license "MIT" ; sc:name "MariaOsmala" ; sc:url "https://github.com/MariaOsmala/preprint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pubmed:31725857" ; sc:description """Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. We aimed to design a hybrid system for systematic entity recognition and ranking to identify poten-tial biomarkers for liver cancer""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3280 ; sc:name "MarkerHub" ; sc:url "http://markerhub.iis.sinica.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Mascot Daemon is a Microsoft Windows client application that automates the submission of data files to Mascot server." ; sc:featureList edam:operation_3762, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "Mascot Daemon" ; sc:operatingSystem "Windows" ; sc:url "http://www.matrixscience.com/daemon.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_3244, edam:format_3654, edam:format_3710, edam:format_3712, edam:format_3858 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3834 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331, edam:format_2332 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description """Mascot Distiller Workstation offers a single, intuitive interface to a wide range of native (binary) mass spectrometry data files. A unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists. This core functionality can be extended by adding one or more toolboxes. These are optional collections of tools for specific tasks, such as Mascot search result review, automatic and manual de novo sequencing, quantitation, and batch processing. There is also a developer’s package that provides access to the API of the underlying COM library.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3634, edam:operation_3635, edam:operation_3643, edam:operation_3644, edam:operation_3646 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Mascot Distiller" ; sc:operatingSystem "Windows" ; sc:url "http://www.matrixscience.com/distiller.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3713 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Mascot Parser provides an object-oriented Application Programmer Interface (API) to Mascot result files and configuration files, making it easy for programs written in C++, C#, Java, Perl or Python to access Mascot results." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "Mascot Parser" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.matrixscience.com/msparser.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_2814, edam:topic_3520 ; sc:citation , , , "pmcid:PMC4391204", "pmcid:PMC5013318", "pubmed:25242457", "pubmed:27412762", "pubmed:31198032" ; sc:description """An extensible, vendor-agnostic application for mass spectrometry analysis. Current analysis packages include protein-protein crosslinking (XL), hydrogen/deuterium exchange (HX), covalent labelling quantification and normalization (CLEAN).""" ; sc:featureList edam:operation_0321, edam:operation_2409, edam:operation_2492, edam:operation_3694 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Mass Spec Studio" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.3.0" ; sc:url "https://www.msstudio.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0602 ; sc:citation , "pubmed:31423789" ; sc:description "A Package for Constructing Master Equation Models of Molecular Dynamics | Python package for generating Markov state models | MasterMSM is a Python package for generating Markov state models (MSMs) from molecular dynamics trajectories. We use a formulation based on the chemical master equation. This package will allow you to:" ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:license "GPL-2.0" ; sc:name "MasterMSM" ; sc:url "https://github.com/daviddesancho/MasterMSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3047, edam:topic_3170, edam:topic_3316, edam:topic_3512 ; sc:citation ; sc:description """Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets. Nextflow pipeline for analysis of Nanopore reads (from RNA/cDNA/DNA). Please read the documentation here: https://biocorecrg.github.io/master_of_pores/. Nextflow pipeline for analysis of Nanopore data from direct RNA sequencing. This is a joint project between CRG bioinformatics core and Epitranscriptomics and RNA Dynamics research group.""" ; sc:featureList edam:operation_0428, edam:operation_3185, edam:operation_3218 ; sc:license "MIT" ; sc:name "MasterOfPores" ; sc:url "https://github.com/biocorecrg/master_of_pores" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3324, edam:topic_3400 ; sc:citation , "pubmed:31609421" ; sc:description """Comprehensive annotation of mature peptides from polyproteins in five virus families. Annotate a viral polyprotein by projecting reference mature peptide annotation through global alignment. The United States Government Department of Health and Human Services, National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases, owns the copyright to the accompanying software under FAR 52.227-14 (c).""" ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_2421 ; sc:license "MIT" ; sc:name "Mat_Peptide" ; sc:url "https://github.com/VirusBRC/vipr_mat_peptide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3474 ; sc:citation , "pubmed:31621830" ; sc:description """Supervised Learning for High-dimensional Matched Case-Control Studies. This code implements Matched Forest algorithm which aims to find important variables in high-dimensional matched case-control data sets. Please refer to our papers for more details:""" ; sc:featureList edam:operation_2940, edam:operation_3659 ; sc:name "Matched Forest" ; sc:url "https://github.com/NooshinSh/Matched_Forest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3172, edam:topic_3308, edam:topic_3577 ; sc:citation , "pubmed:31851777" ; sc:description """General Analysis Utilities for Dynamic Omics Datasets. MathIOmica is a package for bioinformatics, written in the Wolfram language, that provides multiple utilities to facilitate the analysis of longitudinal data generated from omics experiments, including transcriptomics, proteomics, and metabolomics data, as well as any generalized time series. MathIOmica uses Mathematica's notebook interface, wherein users can import longitudinal datasets, carry out quality control and normalization, generate time series, and classify temporal trends. MathIOmica provides spectral methods based on periodograms and autocorrelations for automatically detecting classes of temporal behavior and allowing the user to visualize collective temporal behavior, and also assess biological significance through Gene Ontology and pathway enrichment analyses. MathIOmica's time-series classification methods address common issues including missing data and uneven sampling in measurements.""" ; sc:featureList edam:operation_3083, edam:operation_3435, edam:operation_3565 ; sc:name "MathIOmica" ; sc:url "https://mathiomica.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0621, edam:topic_2640, edam:topic_3520 ; sc:citation , "pubmed:31586405" ; sc:description "The ECM-protein knowledge database." ; sc:featureList edam:operation_0417, edam:operation_2421, edam:operation_2422, edam:operation_3216, edam:operation_3431, edam:operation_3755 ; sc:license "Not licensed" ; sc:name "MatrisomeDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://matrisomedb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1362 ; sc:encodingFormat edam:format_2064 ; sc:name "Position weight matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0749 ; sc:author ; sc:description "We propose MatrixMotif(MM), a new combinatorial hybrid algorithm allowing qualitative and quantitative analysis of TFBS (Transcription Factor Binding Site) motifs using NGS data originated from DNA extraction and enrichment techniques. MM allows de novo motifs discovery and motifs iteration employing enumerative and probabilistic models based on several types of matrixes. MM primarily utilizes set of sequences from NGS in fasta format as a template for mathematical and statistical modeling. Fasta format can be generated from fastq format (Illumina platform) set of individual enriched sequences. MM generates final motifs as PPM, PWM or TFFM allowing visualization of de novo computed motifs." ; sc:featureList edam:operation_0234, edam:operation_0238, edam:operation_0239, edam:operation_0364, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MatrixMotif" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "https://peterslab.org/downloads.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0749, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC6827219", "pubmed:31679514" ; sc:description """An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the citation details for MaveDB. MaveDB is a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning (DMS) or massively parallel reporter assay (MPRA) experiments. Welcome to our table of Multiplexed Assay of Variant Effect (MAVE) studies. To contribute a study or amend/expand an existing entry, please use the GitHub issue tracker or create a pull request""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3227, edam:operation_3431 ; sc:license "CC-BY-4.0" ; sc:name "MaveDB" ; sc:url "https://www.mavedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3489 ; sc:citation , "pubmed:31504189" ; sc:description "An integrated resource for metalloenzyme-ligand associations | The Metalloenzyme-Ligand Association Database (MeLAD)" ; sc:featureList edam:operation_0482, edam:operation_3501, edam:operation_3898 ; sc:name "MeLAD" ; sc:url "https://melad.ddtmlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "Minimum Error Calibration and Normalization for Genomic Copy Number Analysis | Minimum Error Calibration and Normalization for Copy Number Analysis | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It’s crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale | Mecan4CNA (Minimum Error Calibration and Normalization for Copy Number Analysis) uses an algebraic method to estimate the baseline and the distance between DNA levels (referred to as level distance). It can be used for both single file analysis and multi-file normalization | A copy number profile usually needs to be calibrated for the position of baseline (normal copy numbers) due to sample impurity and measurement bias. It's crucial to normalize CN profiles when comparing them in analysis, because usually each profile has a different signal scale" ; sc:featureList edam:operation_3196, edam:operation_3233, edam:operation_3435 ; sc:license "MIT" ; sc:name "Mecan4CNA" ; sc:url "https://pypi.org/project/mecan4cna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2840, edam:topic_3292, edam:topic_3378 ; sc:citation ; sc:description "Applying knowledge-driven mechanistic inference to toxicogenomics | Mechanistic inference of toxicity from gene expression time series and knowledge graphs | Mechanistic inference for toxicology | This repository provide the code for the publication \"Applying knowledge-driven mechanistic inference to toxicogenomics\" (DOI: xxxxxxxxxxxx) and contains the collection of scripts to reproduce the results obtained. Besides the code, this repository provides: | $ git clone git@github.com:ignaciot/MechSpy.git | You can add new mechanisms of your own to MechSpy by editing mechanisms.py. A mock, commented-out \"M12\" mechanism was added to illustrate where would new mechanisms need to go" ; sc:featureList edam:operation_3501, edam:operation_3642 ; sc:license "MIT" ; sc:name "MechSpy" ; sc:url "https://github.com/ignaciot/MechSpy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "MedicMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.3.0" ; sc:url "http://medicmine.jcvi.org/medicmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation "pmcid:PMC6247925", "pubmed:29931280" ; sc:description """algorithms for analyzing DNA methylation data generated using Infinium HumanMethylation450 or MethylationEPIC BeadChips Epigenome-Wide Association Studies (EWAS)""" ; sc:featureList edam:operation_1812, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "Meffil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/perishky/meffil" ; biotools:primaryContact "Matthew Suderman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6843070", "pubmed:31749830" ; sc:description """Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs. git clone https://github.com/HKU-BAL/megagta.git.""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3731 ; sc:name "MegaGTA" ; sc:url "https://github.com/HKU-BAL/megagta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3175, edam:topic_3673 ; sc:citation , "pubmed:31584621" ; sc:description """Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants. Meltos is a novel approach to estimate the variant allele frequency of somatic SVs from whole genome sequencing (WGS) signals and using these VAFs to identify the phylogenetic relationship between SSVs in a multi-sample cell lineage tree using an SNV-only tree as a basis. Our probabilistic framework allows us to assess multiple types of signals taken from the data simultaneously and more accurately calculate the VAF of SV events. Following the maximum parsimony principle, Meltos uses a novel combinatorial algorithm to assign SV clusters on the branches of the given lineage tree, while modestly augmenting the tree topology if needed""" ; sc:featureList edam:operation_3216, edam:operation_3227, edam:operation_3233, edam:operation_3478 ; sc:license "MIT" ; sc:name "Meltos" ; sc:url "https://github.com/ih-lab/Meltos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_3306 ; sc:citation , "pubmed:31564100" ; sc:description "A Tool for Robust Computation and Characterization of Curved Membranes | MemSurfer is a software tool to compute bilayer membrane surfaces | Biochemical and Biophysical Systems Group | MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations | Advances in simulation methodologies, code efficiency, and computing power have enabled larger, longer, and more-complicated biological membrane simulations" ; sc:license "GPL-3.0" ; sc:name "MemSurfer" ; sc:url "https://bbs.llnl.gov/MemSurfer-data.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1915 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1317 ; sc:author ; sc:citation , , , "pubmed:22038510" ; sc:description "Analysis tool for protein-protein cross-linking using MS-cleavable cross-lining reagents such as DSBU, DSSO, CDI or PIR linker" ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MeroX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0 (2.0.0.7)" ; sc:url "https://www.stavrox.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description """Computational tool for metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. The tool (i) is based on machine learning classifiers, (ii) includes automatic model and feature selection steps, (iii) comprises cross-validation and cross-study analysis, and (iv) uses as features quantitative microbiome profiles including species-level relative abundances and presence of strain-specific markers. It provides also species-level taxonomic profiles, marker presence data, and metadata for 3000+ public available metagenomes.""" ; sc:name "MetAML" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://segatalab.cibio.unitn.it/tools/metaml/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31429549" ; sc:description "Generation of a Molecular Network from Electron Ionization Mass Spectrometry Data by Combining MZmine2 and MetGem Software | Calculation and visualization of molecular networks based on t-SNE algorithm - metgem/metgem | MetGem is an open-source software for tandem mass-spectrometry data visualization. It's key features are standalone molecular networking and t-SNE based projections" ; sc:featureList edam:operation_3431, edam:operation_3501, edam:operation_3629 ; sc:name "MetGem" ; sc:url "https://github.com/metgem/metgem/releases" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation ; sc:description "Complex genetic admixture histories reconstructed with Approximate Bayesian Computations | MetHis is a population genetics forward simulation tool designed to simulate arbitrarily complex admixture histories between two populations" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MetHis" ; sc:url "https://github.com/romain-laurent/MetHis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC6572057", "pubmed:31130635" ; sc:description "Metabolite Pipeline Consisting of Metabolite Identification and Biomarker Discovery Under the Control of Two-Dimensional FDR." ; sc:featureList edam:operation_3659, edam:operation_3803, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jjs3098/CNU-Bioinformatics-Lab" ; biotools:primaryContact "Jaesik Jeong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343 ; sc:citation , "pubmed:31369240" ; sc:description "Computer-Assisted Natural Products Anticipation | a web server for natural products anticipation | Currently running beta version 0.4.2 | \"Essence is a function of the relationship.\" Bachelard 1929 | MetWork used for the identification of bromotryptamine derivatives" ; sc:featureList edam:operation_3627, edam:operation_3629, edam:operation_3803 ; sc:name "MetWork" ; sc:url "https://metwork.pharmacie.parisdescartes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC6540332", "pubmed:31146255" ; sc:description "Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Meta-4mCpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://thegleelab.org/Meta-4mCpred" ; biotools:primaryContact "Balachandran Manavalan", "Gwang Lee", "Leyi Wei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3379, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6888698", "pubmed:31731751" ; sc:description """A Sequence-Based Meta-Predictor for Improving the Prediction of Antiviral Peptides Using Effective Feature Representation. In spite of the large-scale production and widespread distribution of vaccines and antiviral drugs, viruses remain a prominent human disease. Recently, the discovery of antiviral peptides (AVPs) has become an influential antiviral agent due to their extraordinary advantages. With the avalanche of newly-found peptide sequences in the post-genomic era, there is a great demand to develop a sequence-based predictor for timely identifying AVPs as this information is very useful for both basic research and drug development. In this study, we propose a novel sequence-based meta-predictor with an effective feature representation, called Meta-iAVP, for the accurate prediction of AVPs from given peptide sequences. Herein, the effective feature representation was extracted from a set of prediction scores derived from various machine learning algorithms and types of features""" ; sc:featureList edam:operation_0252, edam:operation_3436, edam:operation_3631 ; sc:name "Meta-iAVP" ; sc:url "http://codes.bio/meta-iavp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , , "pmcid:PMC4556158", "pmcid:PMC6662567", "pubmed:26336640", "pubmed:31388474" ; sc:description "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different \"bins\", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3798 ; sc:name "MetaBAT 2" ; sc:url "https://bitbucket.org/berkeleylab/metabat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC5592083", "pubmed:28894651" ; sc:description """Reference-guided extraction of CRISPR spacers from unassembled metagenomes. MetaCRAST: reference-guided CRISPR detection in metagenomes. MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes. Unlike other tools, it uses expected CRISPR direct repeat (DR) sequences from assembled contigs or bacterial genomes to guide metagenomic CRISPR detection. It uses a fast implementation of the Wu-Manber multipattern search algorithm to rapidly select reads that contain an expected DR sequence. It then proceeds through reads identified in the previous step to find DR sequences within acceptable distances of each other (i.e., with acceptable length spacers between them). Spacers between these DRs are then extracted and clustered into a non-redundant set with CD-HIT""" ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "MetaCRAST" ; sc:url "https://github.com/molleraj/MetaCRAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6710874", "pubmed:31451112" ; sc:description "MetaCarvel: A scaffolder for metagenomes | MetaCarvel - Scaffolder for metagenomes | MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2. To run MetaCarvel, you will need Python 2.7.x, Samtools, Bedtools, Networkx(Version < 1.11), NumPy,and OGDF" ; sc:featureList edam:operation_0524, edam:operation_2495, edam:operation_3216 ; sc:license "MIT" ; sc:name "MetaCarvel" ; sc:url "https://github.com/marbl/MetaCarvel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6790056", "pubmed:31604482" ; sc:description """Analysis of single-cell RNA-seq data using K-nn graph partitions. scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We describe a methodology for partitioning scRNA-seq datasets into metacells: disjoint and homogenous groups of profiles that could have been resampled from the same cell. Unlike clustering analysis, our algorithm specializes at obtaining granular as opposed to maximal groups. We show how to use metacells as building blocks for complex quantitative transcriptional maps while avoiding data smoothing. Our algorithms are implemented in the MetaCell R C++ software package.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3799 ; sc:name "MetaCell" ; sc:url "https://tanaylab.github.io/metacell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6807170", "pubmed:31737256" ; sc:description """Galaxy workflow for differential abundance analysis of 16s metagenomic data. You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. This history is empty. You can load your own data or get data from an external source""" ; sc:featureList edam:operation_0232, edam:operation_3219, edam:operation_3435 ; sc:name "MetaDEGalaxy" ; sc:url "http://203.101.224.202/galaxy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0736 ; sc:citation , "pubmed:31116477" ; sc:description "Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains." ; sc:featureList edam:operation_0303, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaDome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://stuart.radboudumc.nl/metadome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0160, edam:topic_0602, edam:topic_3174 ; sc:citation , "pmcid:PMC6803454", "pubmed:31681429" ; sc:description """An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. It bundles essential annotation tasks such as feature prediction, functional annotation with Hidden Markov Model (HMM) searches as well as blast and diamond searches. It estimates and visualizes quantitative taxonomic and pathway compositions of multiple metagenomic and proteomics samples using sequencing coverage and proteomics spectral counts, respectively. For visualization, MetaErg provides a HTML interface, bringing all annotation results together in sortable and searchable tables, collapsible trees, and other graphic representations, enabling intuitive navigation of complex data. Analysis statistics: master.stats.txt. Analysis annotation in gff format: master.gff.txt. MetaErg begins biological feature and element prediction by identifying CRISPR elements and non-coding RNA genes (tRNA, rRNA genes)""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3083, edam:operation_3439, edam:operation_3460 ; sc:name "MetaErg" ; sc:url "https://github.com/xiaoli-dong/metaerg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3174 ; sc:citation , , "pmcid:PMC7126354", "pubmed:32245390" ; sc:description "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics" ; sc:featureList edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaEuk" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1-ea903e5", "2-ddf2742" ; sc:url "https://metaeuk.soedinglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640 ; sc:author "Benjamin Haibe-Kains", "Deena M.A. Gen-doo" ; sc:description "A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium." ; sc:featureList edam:operation_0441, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "MetaGxBreast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/release/data/experiment/html/MetaGxBreast.html" ; biotools:primaryContact "Benjamin Haibe-Kains", "Michael Zon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3295, edam:topic_3308, edam:topic_3390, edam:topic_3407 ; sc:citation ; sc:description """Transcriptomic Profiling of Skeletal Muscle Adaptations to Exercise and Inactivity. Transcriptomics meta-analysis of skeletal muscle response to exercise. Transcriptomics meta-analysis of skeletal muscle response to exercise. The shiny app is available at www.metamex.eu.""" ; sc:featureList edam:operation_2495 ; sc:name "MetaMEx" ; sc:url "http://www.metamex.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3303, edam:topic_3697 ; sc:citation , "pmcid:PMC6787565", "pubmed:31594829" ; sc:description """Linking Microbiota Functions with Medicine Therapeutics. Metagenomics Medicine mapping system (MetaMed), is a novel and integrative system-wide correlation mapping system to link bacteria functions and medicine therapeutics""" ; sc:featureList edam:operation_3432, edam:operation_3660, edam:operation_3803 ; sc:name "MetaMed" ; sc:url "http://metamed.rwebox.com/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_3174, edam:topic_3520, edam:topic_3697 ; sc:citation , "pubmed:31629686" ; sc:description """A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery.""" ; sc:featureList edam:operation_3755, edam:operation_3803 ; sc:name "MetaMiner" ; sc:url "https://github.com/mohimanilab/MetaMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520, edam:topic_3922 ; sc:citation , , "pmcid:PMC6733628", "pubmed:31378069", "pubmed:33683901" ; sc:description "Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data | Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities | MetaMorpheus: Free, Open-Source PTM Discovery | Download the current version here. For first-time Windows users, choose \"MetaMorpheusInstaller.msi\" and install MetaMorpheus. Check out our getting started video on YouTube" ; sc:featureList edam:operation_2421, edam:operation_3215, edam:operation_3629, edam:operation_3631, edam:operation_3649, edam:operation_3755, edam:operation_3767 ; sc:license "MIT" ; sc:name "MetaMorpheus" ; sc:url "https://github.com/smith-chem-wisc/MetaMorpheus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3308 ; sc:citation ; sc:description "Analysis pipeline and browser-based software suite for transcriptomic meta-analysis." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MetaOmics" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/metaOmics/metaOmics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation , "pubmed:31116375" ; sc:description "Integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetaQUBIC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/OSU-BMBL/metaqubic" ; biotools:primaryContact "Qin Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3372, edam:topic_3676 ; sc:citation ; sc:description """Simple, high-level languages for data analysis with the R ecosystem. Simple Data Analysis language built with MPS. Generates R code. Metaprogramming in R, thus the name. MetaR takes advantage of Language Workbench Technology to facilitate data analysis with the R language. It can be used by:. Apache Server at metar.campagnelab.org Port 80. bioinformaticians who wish to package state of the art analysis methods into user friendly metaR analysis language constructs. MetaR can act as a bridge between analysis experts who develop analysis methods in R and wish to distribute these methods to the broadest audience without investing a lot of effort in developing user interfaces.""" ; sc:featureList edam:operation_0555, edam:operation_2422, edam:operation_2495 ; sc:name "MetaR" ; sc:url "http://metaR.campagnelab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0769, edam:topic_3382, edam:topic_3697 ; sc:citation ; sc:description """An integrated, customizable microbial genome evaluation and annotation pipeline. Pipeline for major biological analyses. MetaSanity v1.1.1 - 2020 version. MetaSanity v1.1.1 provides a unified workflow for genome assessment and functional annotation that combines all outputs into a single queryable database – all within an easily distributed Docker image""" ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "MetaSanity" ; sc:url "https://github.com/cjneely10/MetaSanity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Spark-based distributed processing tool to recruit metagenomic reads to reference genomes." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetaSpark:" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/zhouweiyg/metaspark" ; biotools:primaryContact "Beifang Niu", "Jing Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6710406", "pubmed:31481973" ; sc:description "A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries | Metagenomic binning based on Hi-C data | pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator | Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamline the processing and binning of metagenomic 3C datasets | Please refer to the tutorial in order to quickly get the pipeline up and running on example data (or your own), and the metaTOR manual for detailed explanations on the parameters" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "MetaTOR" ; sc:url "https://github.com/koszullab/metaTOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6780920", "pubmed:31533242" ; sc:description "A Flexible Tool for Metabolite Annotation from High-Resolution Data-Independent Acquisition Mass Spectrometry Analysis | Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data | Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis" ; sc:featureList edam:operation_2495, edam:operation_3803 ; sc:license "GPL-2.0" ; sc:name "MetaboList" ; sc:url "https://CRAN.R-project.org/package=MetaboList" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Graphical visualization tool for metabolomics and genomic data within metabolic pathways" ; sc:featureList edam:operation_3660 ; sc:name "MetaboPath View" ; sc:url "https://prf.jcu.cz/mpv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0769, edam:topic_3047, edam:topic_3407 ; sc:citation , "pmcid:PMC6929434", "pubmed:31870296" ; sc:description """Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. The Metabolic Disassembler is a Python package to automatically predict a combination of biosynthetic units in a natural product. This software would help to reveal the starting materials of the target natural product.""" ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_3439 ; sc:license "MIT" ; sc:name "Metabolic Disassembler" ; sc:url "https://github.com/the-metabolic-disassembler/metadisassembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219 ; sc:description "FAIR metadata editor for guiding the user through the creation of FAIR Data Point metadata." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metadata Editor" ; sc:url "https://editor.fair-dtls.surf-hosted.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3174, edam:topic_3407 ; sc:citation ; sc:description """metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species. From annotated genomes to metabolic screening in large scale microbiotas. Metage2metabo is a Python3 (Python >= 3.6) tool to perform graph-based metabolic analysis starting from annotated genomes (reference genomes or metagenome-assembled genomes). It uses Pathway Tools in a automatic and parallel way to reconstruct metabolic networks for a large number of genomes. The obtained metabolic networks are then analyzed individually and collectively in order to get the added value of metabolic cooperation in microbiota over individual metabolism and to identify and screen interesting organisms among all. m2m — metage2metabo documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "Metage2Metabo" ; sc:softwareHelp ; sc:url "https://github.com/AuReMe/metage2metabo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "This code implements a pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in the field of metagenomics" ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metagenomic read binning using sparse coding" ; sc:operatingSystem "Linux" ; sc:url "https://gitlab.com/kyrgyzov/lsa_slurm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC6814207", "pubmed:31623721" ; sc:description """An online software tool for mass spectrometry-based isobaric labeling metabolomics. Metandem - A Data Analysis Tool for Isobaric Labeling-based Metabolomics. Metandem is a free online data analysis platform for mass spectrometry-based isobaric labeling metabolomics. It allows users to upload and process MS or hyphenated MS data files for isobaric-labeling-based quantitative and qualitative metabolomics analyses, including feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, parameter optimization, median normalization, and statistical analysis. Results can be downloaded or visualized online""" ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3803 ; sc:name "Metandem" ; sc:url "http://metandem.com/web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056 ; sc:citation , "pubmed:30362291" ; sc:description "Individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes." ; sc:featureList edam:operation_0282, edam:operation_2426, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Metapop" ; sc:softwareHelp ; sc:url "https://quercusportal.pierroton.inra.fr/index.php?p=METAPOP" ; biotools:primaryContact "Antoine Kremer", "Armel Thöni", "Jean-Paul Soularue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3172 ; sc:citation , "pmcid:PMC6447622", "pubmed:30944313" ; sc:description "Portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Metascape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:url "http://metascape.org/gp/index.html#/main/step1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation ; sc:description "A reference methylome database for different organisms that is created from public BS-seq datasets." ; sc:featureList edam:operation_0564, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MethBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/methbase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:31049595" ; sc:description "Bayesian calibration of methylation levels | This package allows the calibration of methylation levels using MethylCal, a Bayesian calibration tool based on INLA (Rue et al., 2009). The package permits the visualisation of the calibration curve derived from standard controls with known methylation percentages for a selected assay. It also allows the correction of the methylation levels in case and control samples. If cases are provided, MethylCal performs a differential methylation test to detect hyper- and hypo-methylated samples. Besides MethylCal method, the package also includes the calibration and the correction provided by two alternative methods (Warnecke et al., 1997; Moskalev et al., 2011)" ; sc:featureList edam:operation_0417, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MethylCal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lb664/MethylCal" ; biotools:primaryContact "Leonardo Bottolo", "Verena Zuber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:31107532" ; sc:description "Framework for Methyl-Seq genome-wide power calculation and study design issues." ; sc:featureList edam:operation_0417, edam:operation_3186, edam:operation_3206 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MethylSeqDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/liupeng2117/MethylSeqDesign" ; biotools:primaryContact "George Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6923858", "pubmed:31861999" ; sc:description """Identifying SNPs in Illumina DNA methylation array data. Detect SNP patterns in Methylation Array data. This is the developer version of Bioconductor package MethylToSNP. Install in R as:""" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3186, edam:operation_3196, edam:operation_3661 ; sc:name "MethylToSNP" ; sc:url "https://github.com/elnitskilab/MethylToSNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31596440" ; sc:description """A Metabolomics Support Package for Untargeted Mass Spectrometry. A Metabolomics Support Package for Untargeted Mass Spectrometery. MetumpX is a Ubuntu based software package that facilitate easy download and installation of about 89 tools related to standard Untargeted Metabolomics Mass Spectrometery pipeline. Installation • Authors • License • Revision History""" ; sc:featureList edam:operation_3627, edam:operation_3767, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "MetumpX" ; sc:url "https://github.com/hasaniqbal777/MetumpX-bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:31785415" ; sc:description """An extended tool for microarray gene expression analysis. Gene expression microarrays capture a complete image of all the transcriptional activity in a biological sample. Microarrays produce a large amount of data, which becomes a challenge when it comes to exploring and interpreting using modern computational and statistical tools. We propose the Microarray Analysis (MiCA) tool that outperforms other similar tools both in terms of ease of use and statistical features requiring minimal input to conduct an analysis. MiCA is an integrated, interactive, and streamlined desktop software for the analysis of microarray gene expression data. MiCA consists of a complete microarray analysis pipeline including but not limited to fetching data directly from GEO, normalization, interactive quality control, batch-effect correction, regression analysis, surrogate variable analysis and functional annotation methods such as GSVA using known existing R packages.""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3501, edam:operation_3659 ; sc:name "MiCA" ; sc:url "http://irzamsarfraz.com/mica/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC6784143", "pubmed:31480341" ; sc:description "A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors | A high-throughput multiplexed amplicon sequencing workflow to quantify drug resistance mutations (DRMs) against protease, reverse transcriptase and integrase inhibitors. MiDRMpol is computational as well as labor efficient bioinformatics pipeline to detect DRMs from HTS data.The method can be incorporated in large scale surveillance of HIV-1 DRMs" ; sc:featureList edam:operation_3192, edam:operation_3196 ; sc:name "MiDRMpol" ; sc:url "https://github.com/neogilab/MiDRMPol" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2830 ; sc:description "Mapper for full-length T- and B-cell repertoire sequencing." ; sc:featureList edam:operation_2403, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MiGMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mikessh/migmap" ; biotools:primaryContact "Mikhail Shugay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3306, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6842143", "pubmed:31703551" ; sc:description """MicroPeptide identification tool using machine learning. MiPepid is a software specifically for predicting the coding capabilities of sORFs. Given a fasta file containing DNA fasta sequences, for each sequence, MiPepid will find all the sORFs (length <= 303 bp) present in all the 3 translation frames of the sequence, and for each sORF it will return the predicted class label (coding or noncoding) as well as the probability of being in that class. All the results will be written in an output .csv file""" ; sc:featureList edam:operation_0436, edam:operation_3659, edam:operation_3792 ; sc:name "MiPepid" ; sc:url "https://github.com/MindAI/MiPepid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3400, edam:topic_3524 ; sc:citation , "pmcid:PMC6498635", "pubmed:31046789" ; sc:description "Agent-based simulation tool to study the self-nonself discrimination of the adaptive immune response." ; sc:featureList edam:operation_0478, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MiStImm" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kerepesi/mistimm" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2830 ; sc:citation ; sc:description "Software for extraction of T- and B-cell receptor repertoires from any type of sequencing data." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MiXCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://milaboratory.com/software/mixcr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation , "pubmed:30368088" ; sc:description "Software tool for predictive microbiology and microbial risk assessment in foods." ; sc:featureList edam:operation_2426, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MicroHibro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.microhibro.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6683435", "pubmed:31387630" ; sc:description "Using metagenomic unmapped reads to provide insights into human microbiota and disease associations | A microbial profiling framework for metagenomic analysis | MicroPro is a software to perform profiling of both known and unknown microbial organisms for metagenomic dataset. A microbe is considered known/unknown if its whole genome is known/unknown according to the NCBI Reference Sequence Database. MicroPro has two pipelines: MicrobialPip and ViralPip. MicrobialPip considers all the microbial organisms including bacteria, archaea and viruses while ViralPip only extracts known and unknown viruses from the provided metagenomics dataset. More details of MicroPro are provided in the following paper:" ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3730 ; sc:license "GPL-3.0" ; sc:name "MicroPro" ; sc:url "https://github.com/zifanzhu/MicroPro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1098 ; sc:name "RefSeq accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1098 ; sc:name "RefSeq accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1931 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:name "Sequence composition plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1936 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0219, edam:topic_0621, edam:topic_0797, edam:topic_2259, edam:topic_3301 ; sc:author "LABGeM - CEA/Genosocope - UMR8030" ; sc:citation , , , , , , "pubmed:28968784", "pubmed:31647104" ; sc:description "MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts." ; sc:featureList edam:operation_0258, edam:operation_0291, edam:operation_0292, edam:operation_0305, edam:operation_0337, edam:operation_0346, edam:operation_0349, edam:operation_0362, edam:operation_2421, edam:operation_2422, edam:operation_2454, edam:operation_2495, edam:operation_2945, edam:operation_3197, edam:operation_3208, edam:operation_3209, edam:operation_3223, edam:operation_3227, edam:operation_3431, edam:operation_3660, edam:operation_3672, edam:operation_3680, edam:operation_3925, edam:operation_3926, edam:operation_3928, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "MicroScope platform" ; sc:provider "LABGeM - CEA/Genosocope - UMR8030" ; sc:softwareHelp , , ; sc:url "https://mage.genoscope.cns.fr/microscope/" ; biotools:primaryContact "LABGeM - CEA/Genosocope - UMR8030" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "Analysing complex metagenomic data with MicroWineBar | MicroWineBar is a graphical tool for analysing metagenomic sequencing samples | MicroWineBar was designed for species abundance tables from shotgun metagenomics data but can also be used for other types of hierarchical data. The tab-delimited files contain absolute and/or relative abundances with taxonomic annotations (or other hierarchical data). As MicroWineBar is not tight to any specific program which generates species abundance tables, one needs to prepare the input:" ; sc:featureList edam:operation_0362, edam:operation_2939, edam:operation_3891 ; sc:license "MIT" ; sc:name "MicroWineBar" ; sc:url "https://github.com/klincke/MicroWineBar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0780, edam:topic_3324, edam:topic_3697 ; sc:citation ; sc:description """An Expanded Database of Ecological and Phenotypical Features of Microbes. Microbial communities are an incredibly fascinating and genetically diverse set of organisms that live with us, in us, and around us! Explore them all using the Microbe Directory, an inventory that profiles more than 7500 microbes!.""" ; sc:featureList edam:operation_2422, edam:operation_3200 ; sc:name "Microbe Directory" ; sc:url "https://microbe.directory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0610, edam:topic_3063, edam:topic_3810 ; sc:citation ; sc:description """An integrated computational pipeline to infer functional effects of microbiome-host interactions. Abstract Microbiome-host interactions are important to nearly all living organisms, and play important roles in health and disease. Understanding these inter-kingdom cross-talks has a huge potential to advance diverse scientific domains such as the clinical and medical sciences, agriculture, and ecology. Detecting such interactions by experimental techniques remain challenging from a cost and feasibility perspective thus hampering large-scale analyses. Computational approaches not only make the inference of microbiome-host interactions viable but also scalable. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins with host molecular networks.""" ; sc:featureList edam:operation_2492, edam:operation_3439, edam:operation_3461 ; sc:name "MicrobioLink" ; sc:url "https://github.com/korcsmarosgroup/HMIpipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697 ; sc:author ; sc:citation ; sc:description "MicrobiomeR is an R package for microbiome analysis that incorporates phyloseq, metacoder, taxa, and microbiome in order to standardize and simplify common microbiome workflows." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MicrobiomeR" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.1" ; sc:url "https://microbiomer.vallenderlab.science/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3063, edam:topic_3473 ; sc:citation , "pubmed:31531513" ; sc:description "A package for downloading and preprocessing microdata from Brazilian Health Informatics Department (DATASUS)] | Download de dados do DataSUS e pré-processamento no R | O pacote para o R microdatasus apresenta funções para download dos arquivos de microdados do DataSUS (formato DBC), leitura dos arquivos através do pacote read.dbc e pré-processamento para utilização. Nesta última etapa, os rótulos e formato das variáveis são atribuídos e tratados | Plano Diretor de Tecnologia da Informação do Ministério da Saúde, biênio 2017-2018, foi publicada no Diário Oficial da União | Software de gestão hospitalar completo, desenvolvido em tecnologia web que substitui o sistema HOSPUB" ; sc:featureList edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "Microdatasus" ; sc:url "http://datasus.saude.gov.br/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , , "pmcid:PMC5291980", "pubmed:28158972", "pubmed:31893378" ; sc:description "R-program supporting a step of workflow of fluxomic analysis of artificial 13C labeling of metabolites. It designed to correct raw mass spectra (MS) of 13C-labeled metabolites of interest for natural isotopes occurrence. The raw mass spectra are supposed to be extracted from MS recording by Ramid." ; sc:featureList edam:operation_3860 ; sc:license "Freeware" ; sc:name "Midcor" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3293, edam:topic_3301, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC6841976", "pubmed:31704961" ; sc:description """Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology. Workflow and supporting files for Taylor et al: "Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". Companion materials for the manuscript "Taylor et al: Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology". This repository contains the primary Nextflow workflow (minion_bacterial.nf) for bacterial nanopore assembly described in the manuscript and accessory scripts for reproducing the results therein. Workflows for the phylogenetic analysis can be run separately from the phylogenetics directory. The time series analysis can be reproduced using the following steps:.""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3644 ; sc:name "MinION" ; sc:url "https://github.com/jvolkening/minion_bacterial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6314158", "pubmed:30523036" ; sc:description "Alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Minerva" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dcdanko/minerva_barcode_deconvolution" ; biotools:primaryContact "David C. Danko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC6833143", "pubmed:31694525" ; sc:description """De novo Nanopore read quality improvement using deep learning. BACKGROUND:Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS:Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3185, edam:operation_3219, edam:operation_3644 ; sc:name "MiniScrub" ; sc:url "https://bitbucket.org/berkeleylab/jgi-miniscrub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc:citation , "pubmed:30726876" ; sc:description "R Package for Multiple Isotope Labeling Assisted Metabolomics Data Analysis." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Miso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.1" ; sc:url "https://cran.r-project.org/package=Miso" ; biotools:primaryContact "Yonghui Dong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC6732850", "pubmed:31523131" ; sc:description "A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome | Ishiya, K., Mizuno, F., Wang, L., & Ueda, S. (2019). MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome. Bioinformatics and biology insights" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3557 ; sc:license "MIT" ; sc:name "MitoIMP" ; sc:url "https://github.com/omics-tools/mitoimp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3384, edam:topic_3518 ; sc:citation ; sc:description "Snakemake pipeline for imputation of mitochondrial genetic variants using Impute2 Chromosome X protocol." ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MitoImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sjfandrews/MitoImpute" ; biotools:primaryContact "Shea J. Andrews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3697, edam:topic_3855 ; sc:citation , "pmcid:PMC6612855", "pubmed:31510709" ; sc:description "Learning a mixture of microbial networks using minorization-maximization | \"MixMPLN\" is a package written in R, which has two features. First feature is generating a proper synthetic sample-taxa count matrix. Second feature is receiving a sample-taxa count matrix and extracting k(number of components) different interaction networks between taxa | Following packages must be installed and loaded in R environment before using \"MixMPLN\":" ; sc:featureList edam:operation_2937, edam:operation_3192 ; sc:name "MixMPLN" ; sc:url "https://github.com/sahatava/MixMPLN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:30730249" ; sc:description "Image-processing software developed for counting cells in photographs of blood smears." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Mizutama" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://datadryad.org/resource/doi:10.5061/dryad.bk2690n?show=full" ; biotools:primaryContact "Gregorio Moreno-Rueda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3297 ; sc:citation ; sc:description """Modular Breeding Program Simulator. This repository contains our R-package MoBPS and the associated packages (miraculix/RandomFieldsUtils/MoBPSmaps). A manuscript for the package is finally available in preprint (https://www.biorxiv.org/content/10.1101/829333v1)""" ; sc:featureList edam:operation_3196, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MoBPS" ; sc:url "https://github.com/tpook92/MoBPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0654, edam:topic_3399, edam:topic_3518 ; sc:citation , "pmcid:PMC6846495" ; sc:description """CLONAL HEMATOPOIESIS IN A CENTENARIAN COHORT. MOsaic CHromosomal Alterations (MoChA) caller. A bcftools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD). If you use this tool in your publication, please cite the following paper and preprint:. This command will create a list of variants falling within segmental duplications with low divergence (<2%), high levels of missingness (>2%), variants with excess heterozygosity (p<1e-6), and variants that correlate with sex in an unexpected way (p<1e-6).""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:name "MoChA" ; sc:url "https://github.com/freeseek/mocha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3175, edam:topic_3512 ; sc:citation , "pmcid:PMC6833150", "pubmed:31690272" ; sc:description """Modular multi-scale integrated genome graph browser. Long-read sequencing allows for more sensitive and accurate discovery of SVs, which requires to filter and validate thousands of candidates. However, no existing genome browser meets the demand for cancer genomics. Because most visualization tools show an only range of a linear sequence, making them unsuitable for large (over megabase) or nested SVs. Also, no existing genome browsers allow users to simultaneously inspect the read alignments that span the reference allele and an alternative allele caused by a heterozygous SV. Here we present MoMI-G, a graph genome browser to visualize SVs on the variation graph, that provides a graph-based view that displays a genome with branches and alignments on them. Users can filter, visualize with genomic annotations, and inspect SVs with read alignments. A genome graph browser for visualization of structural variants (SVs) as a variation graph:""" ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3208, edam:operation_3227 ; sc:license "MIT" ; sc:name "MoMI-G" ; sc:url "https://github.com/MoMI-G/MoMI-G" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3474, edam:topic_3538 ; sc:citation , "pubmed:31504193" ; sc:description "Identifying Molecular Recognition Features in Intrinsically Disordered Regions of Proteins by Transfer Learning | AVAILABILITY HTML server, please click here. RESTful web server, please click here. (Updated Apr. 10, 2018) Downloadable software, please click here. OVERVIEW A new computational approach for a fast and accurate prediction of MoRFs in protein sequences. MoRFchibi SYSTEM (Malhis et al 2016) includes three different predictors: MoRFCHiBi is most appropriate as a component predictor in other applications. […] | The University of British Columbia" ; sc:featureList edam:operation_0253, edam:operation_0303, edam:operation_3904 ; sc:name "MoRF" ; sc:url "https://gsponerlab.msl.ubc.ca/software/morf_chibi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0749, edam:topic_2269 ; sc:citation , "pmcid:PMC6819637", "pubmed:31660849" ; sc:description """Computational prediction of MoRFs based on protein sequences and minimax probability machine. BACKGROUND:Molecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDRs), and undergo disorder-to-order transitions upon binding to their interaction partners. The functional importance of MoRFs and the limitation of experimental identification make it necessary to predict MoRFs accurately with computational methods. RESULTS:In this study, a new sequence-based method, named as MoRFMPM, is proposed for predicting MoRFs. MoRFMPM uses minimax probability machine (MPM) to predict MoRFs based on 16 features and 3 different windows, which neither relying on other predictors nor calculating the properties of the surrounding regions of MoRFs separately.""" ; sc:featureList edam:operation_0250, edam:operation_0303, edam:operation_3904 ; sc:name "MoRFMPM" ; sc:url "https://github.com/HHJHgithub/MoRFs_MPM/tree/master/github_code_MPM_MoRFs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3520 ; sc:citation , "pubmed:30649115" ; sc:description "Programfor calculation of ion or molecule collision cross sections on parallelized computing architectures." ; sc:featureList edam:operation_0386 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MobCal-MPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://uwaterloo.ca/hopkins-lab/mobcal-mpi" ; biotools:primaryContact "C. Ieritano", "W. S. Hopkins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3407 ; sc:citation , "pubmed:30201314" ; sc:description "Strain design framework for modular cell engineering." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ModCell2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://modcell2.readthedocs.io/en/latest/" ; biotools:primaryContact "TrinhLab - University of Tennessee Knoxville" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_0602, edam:topic_2640, edam:topic_3169 ; sc:citation , "pubmed:31857203" ; sc:description """A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction. Deciphering the network of TF-target interactions with information on mode of regulation (activation vs. repression) is an important step toward understanding the regulatory pathways that underlie complex traits. There are many experimental, computational, and manually curated databases of TF-gene interactions. In particular, high-throughput ChIP-seq datasets provide a large-scale map or transcriptional regulatory interactions. ModEx can be installed using the GitHub repository. All of the dependencies will be installed via setup.py script. Saman Farahmand, Todd Riley, Kourosh Zarringhalam, "ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction", BioRxiv, 2019""" ; sc:featureList edam:operation_0306, edam:operation_1781, edam:operation_3439 ; sc:license "MIT" ; sc:name "ModEx" ; sc:url "https://github.com/samanfrm/modex" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A data warehouse for the modENCODE project" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ModMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "33 28JUL2014" ; sc:url "http://intermine.modencode.org/release-33" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3407 ; sc:citation , "pmcid:PMC6348647", "pubmed:30691403" ; sc:description "Software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ModelExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://almaaslab.nt.ntnu.no/index.php/resources/metabolic-modeling/" ; biotools:primaryContact "Eivind Almaas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3316 ; sc:citation , "pubmed:31432070" ; sc:description "A new and scalable tool for the selection of DNA and protein evolutionary models | ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces" ; sc:featureList edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "ModelTest-NG" ; sc:url "https://github.com/ddarriba/modeltest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0659, edam:topic_2275, edam:topic_3512 ; sc:citation , "pmcid:PMC6900601", "pubmed:31732673" ; sc:description """Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX. ModelX: A toolsuite for molecular modeling. ModelX is a toolsuite for biomolecular modeling inspired on the assumption that Molecular Biology conformational landscape is huge but limited, and also on the fact that interactions between biological entities can be decomposed into small structural motifs that are recycled and reused by nature while shaping new relationships.""" ; sc:featureList edam:operation_3216, edam:operation_3899, edam:operation_3900, edam:operation_3901, edam:operation_3902 ; sc:name "ModelX" ; sc:url "http://modelx.crg.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601 ; sc:citation ; sc:description "MolArt (MOLeculAR structure annoTator) - molecular structure annotation and visualization tool." ; sc:featureList edam:operation_0564, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MolArt" ; sc:softwareHelp ; sc:url "https://cusbg.github.io/MolArt/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_1964 ; sc:name "Compound name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3068, edam:topic_3292, edam:topic_3332 ; sc:author , "Jakub Juračka" ; sc:citation ; sc:contributor , , "Michaela Melíková" ; sc:description "MolMeDB is an open chemistry database about interactions of molecules with membranes." ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:funder "Czech Grant Agency" ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MolMeDB" ; sc:softwareHelp , ; sc:url "http://molmedb.upol.cz" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2814 ; sc:citation , "pubmed:31111152" ; sc:description "Computation of clock violations." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Molecular clock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ugobas/Molecular_clock" ; biotools:primaryContact "Ugo Bastolla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_3390 ; sc:citation , "pubmed:31701156" ; sc:description """An integrative data and analytic platform connecting phenotypes to genotypes across species. Combine genotype and phenotype data across species for patient variant prioritization, functional annotation and pathogenicity determination. Securely share & discuss patients with colleagues all around the world.""" ; sc:featureList edam:operation_0306, edam:operation_3196, edam:operation_3226, edam:operation_3778 ; sc:name "Monarch Initiative" ; sc:url "https://monarchinitiative.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3300 ; sc:citation , "pubmed:31071345" ; sc:description "Software tool for behavioral control and data acquisition." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MonkeyLogic" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://monkeylogic.nimh.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC6394031", "pubmed:30819107" ; sc:description "Monoallelic Gene Inference from Chromatin (MaGIC) - tool to classify genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data." ; sc:featureList edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MaGIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/gimelbrantlab/magic" ; biotools:primaryContact "Alexander Gimelbrant", "Henry Ward", "Sachit Saksena", "Svetlana Vinogradova", "Sébastien Vigneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC6394031", "pubmed:30819107" ; sc:description "Machine learning tool set and web application for monoallelic gene inference from chromatin. Classifies genes into monoallelically expressed (MAE) and biallelically expressed (BAE) using chromatin mark enrichment data." ; sc:featureList edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Monoallelic gene inference from chromatin (MaGIC)" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/gimelbrantlab/magic" ; biotools:primaryContact "Alexander Gimelbrant", "Henry Ward", "Sachit Saksena", "Svetlana Vinogradova", "Sébastien Vigneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:description "MoonDB is a database containing predicted Extreme Multifunctional (EMF) proteins (i.e. proteins with several unrelated functions), as well as a set of manually curated moonlighting proteins. Moonlighting proteins are a subclass of multifunctional proteins." ; sc:name "MoonDB" ; sc:url "http://moondb.hb.univ-amu.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC6487805", "pubmed:31086739" ; sc:description "Multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MorphoCatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://morphocatcher.ru" ; biotools:primaryContact "Fedor V. Shirshikov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0736 ; sc:citation , "pmcid:PMC6863708", "pubmed:31599029" ; sc:description """A computational program to investigate the evolution of PDZ-binding target specificity. PDZ domains bind the extreme C-terminus of target proteins and are critical components of signaling and trafficking pathways. MotifAnalyzer-PDZ identifies enrichment trends for specific amino acids in a PDZ-binding motif-satisfying sequence across multiple organisms""" ; sc:featureList edam:operation_0239, edam:operation_0303, edam:operation_2492 ; sc:name "MotifAnalyzer-PDZ" ; sc:url "http://motifAnalyzerPDZ.cs.wwu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3304, edam:topic_3489 ; sc:citation , "pmcid:PMC6934379", "pubmed:31825307" ; sc:description """Open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment. Mousebytes-An-open-access-high-throughput-pipeline-and-database-for-rodent-touchscreen-based-data. This code is associated with the paper from Beraldo et al., "MouseBytes, an open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment". eLife, 2019. http://dx.doi.org/10.7554/eLife.49630. Quality control (QC) procedure in MouseBytes checks the content of xml files against the potential errors and flag the files that do not meet the criteria (refer to "QC Documents" folder). Such xml files belong to a cognitive task experimented using Bussey-Saksida Mouse Touchscreen System and exported via ABET II software. Note that each xml file must contain the machine-generated (ABET II) features like "Analysis Name", "Schedule Name", "Max_Number_Trials", and "Max_Schedule_Time\"""" ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "MouseBytes" ; sc:url "http://mousebytes.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0654, edam:topic_3298, edam:topic_3300, edam:topic_3500 ; sc:citation , "pubmed:31696236" ; sc:description """A data repository and analysis suite for curated primary mouse phenotype data. Available genotype resources and tools. RESTful API for getting data and metadata. Already have an account? Sign In. ...an integrated resource to explore physiology""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3557 ; sc:name "Mouse Phenome Database" ; sc:softwareHelp ; sc:url "https://phenome.jax.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6805343", "pubmed:31640560" ; sc:description """Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection. Data analysis pipeline used for the assembly and differential abundance analysis of M. rosenbergii transcriptome in response to MrNV infection. Transcriptomic analysis (RNAseq) of Macrobrachium rosenbergii post-larvae in response to Macrobrachium rosenbergii nodavirus (MrNV) infection. Phongthana Pasookhush, Charles Hindmarch, Siwaporn Longyant, Paisarn Sithigorngul, William G. Bendena, Parin Chaivisuthangkura. Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) postlarvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation. BMC Genomics volume 20, Article number: 762 (2019), DOI: 10.1186/s12864-019-6102-6 Article URL""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3258, edam:operation_3800 ; sc:name "MrNV" ; sc:url "https://github.com/prawnseq/Mrosenbergii_MrNV_RNAseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description "Tool for haplotype-phased structural variant detection." ; sc:featureList edam:operation_0525, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MsPAC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/oscarlr/MsPAC" ; biotools:primaryContact "Oscar L. Rodriguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168, edam:topic_3474, edam:topic_3517 ; sc:citation , "pubmed:31693090" ; sc:description """Quantifying Functional Impact of Noncoding Variants with Multi-task Bayesian Neural Network. The python script for MtBNN. The help information can be obtain by""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3226 ; sc:license "MIT" ; sc:name "MtBNN" ; sc:url "https://github.com/Zoesgithub/MtBNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Multiple transformer-based language models for accurate DNA methylation prediction" ; sc:name "MuLan-Methyl" ; sc:softwareVersion "1.02" ; sc:url "http://ab.cs.uni-tuebingen.de/software/mulan-methyl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_3314 ; sc:citation , "pubmed:31663741" ; sc:description """A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic. …methods and tools for Chem-Bio-Med-Informatic Studies. MuLiMs-MCoMPAs software is for the calculation of 3D bio macromolecular (protein and peptide) descriptors based on the two-linear and three-linear algebraic forms""" ; sc:featureList edam:operation_0303, edam:operation_3436, edam:operation_3891 ; sc:name "MuLiMs-MCoMPAs" ; sc:url "http://tomocomd.com/mulims-mcompas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation ; sc:description """Mutation effect estimation on protein-protein interactions using deep contextualized representation learning. This is the repository for "Mutation effect estimation on protein-protein interactions using deep contextualized representation learning" (MuPIPR). This repository contains the source code and links to some datasets used in our paper. (to be updated)""" ; sc:featureList edam:operation_0272, edam:operation_0331, edam:operation_2492 ; sc:name "MuPIPR" ; sc:url "https://github.com/guangyu-zhou/MuPIPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2269, edam:topic_2640 ; sc:citation , "pubmed:22759861" ; sc:description "MuSiC2 ( Mutational Significance in Cancer) is a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events." ; sc:featureList edam:operation_0362, edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MuSiC2" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "0.2" ; sc:url "http://gmt.genome.wustl.edu/packages/genome-music/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Tool for finding connected clusters in multi-parametric networks." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Multi-netclust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinformatics.nl/netclust/" ; biotools:primaryContact "Jack A.M. Leunissen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0988 ; sc:encodingFormat edam:format_3681 ; sc:name "Peptide identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3922 ; sc:description "A plug-in to the Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using a multi-omic proteogenomic approach." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Multi-omics Visualization Platform" ; sc:softwareHelp ; sc:url "https://github.com/galaxyproteomics/mvpapplication-git.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Multi-processing tool for designing CRISPR guide RNA libraries." ; sc:featureList edam:operation_3096, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MultiGuideScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/bioinfomaticsCSU/MultiGuideScan" ; biotools:primaryContact "Jianxin Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3299 ; sc:citation , "pubmed:30206356" ; sc:description "Models discrete and continuous gene flow to reconstruct complex population admixtures." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:name "MultiWaver" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.0" ; sc:url "http://www.picb.ac.cn/PGG/resource.php" ; biotools:primaryContact "Shuhua Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC6358100", "pubmed:30668570" ; sc:description "Set of tools to perform integrative gene mapping studies." ; sc:featureList edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MultiXcan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hakyimlab/MetaXcan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation "pmcid:PMC6927681", "pubmed:31871433" ; sc:description """Community Extraction in Multilayer Networks with Heterogeneous Community Structure. An R package to identify strongly connected vertex-layer communities in multilayer networks. An R package that implements the multilayer extraction algorithm to identify densely connected vertex-layer sets in multilayer networks. multilayer.extraction(): identify densely connected vertex-layer communities within multilayer networks. This is a significance based approach that seeks to optimize a score derived from the strength of connection within multilayer communities. See the above reference for more details.""" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "Multilayer Extraction" ; sc:url "https://github.com/jdwilson4/MultilayerExtraction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6612862", "pubmed:31510656" ; sc:description "Deep learning with multimodal representation for pancancer prognosis prediction | Our model estimates the time-til-death for patients across 20 different cancer types using the vast amount of multimodal data that is available for cancer patients | git clone https://github.com/gevaertlab/MultimodalPrognosis | For more details, see our paper" ; sc:featureList edam:operation_3891 ; sc:name "MultimodalPrognosis" ; sc:url "https://github.com/gevaertlab/MultimodalPrognosis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "This is the dockerized environment for the winning algorithm in the 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3." ; sc:license "GPL-3.0" ; sc:name "Multiple Myeloma survival prediction" ; sc:operatingSystem "Linux" ; sc:url "https://www.synapse.org/#!Synapse:syn11459638" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:31697593" ; sc:description """CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber type-specific histology. Because manual immunohistochemical analysis of features such as skeletal muscle fiber typing, capillaries, myonuclei, and fiber size-related parameters is time consuming and prone to user subjectivity, automatic computational methods could allow for faster and more objective evaluation. Here, we developed Muscle2View, a free CellProfiler-based pipeline that integrates all key fiber-morphological variables, including the novel quantification of the capillary-to-fiber interface, in one single tool. Provided that the images are of sufficient quality and the settings are configured for the specific study, the pipeline allows for automatic and unsupervised analysis of fiber borders, myonuclei, capillaries, and morphometric parameters in a fiber type-specific manner from large batches of images in <10 min tissue sample.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "Muscle2View" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31697593" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC6498474", "pubmed:31053169" ; sc:description "Versatile methodological aid to functional genomics in the neuromuscular field." ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Muscle Gene Sets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sys-myo.com/muscle_gene_sets" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pubmed:31588509" ; sc:description """A multifaceted gateway for exploring integrative pan-cancer genomic data. Somatic mutation and gene expression dysregulation are considered two major tumorigenesis factors. While independent investigations of either factor pervade, studies of associations between somatic mutations and gene expression changes have been sporadic and nonsystematic. Utilizing genomic data collected from 11 315 subjects of 33 distinct cancer types, we constructed MutEx, a pan-cancer integrative genomic database. This database records the relationships among gene expression, somatic mutation and survival data for cancer patients. MutEx can be used to swiftly explore the relationship between these genomic clinic features within and across cancer types and, more importantly, search for corroborating evidence for hypothesis inception.""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3223 ; sc:name "MutEx" ; sc:url "http://www.innovebioinfo.com/Databases/Mutationdb_About.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2269, edam:topic_2640 ; sc:citation , , "pubmed:23770567", "pubmed:24390350" ; sc:description "MutSig stands for \"Mutation Significance\". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes." ; sc:featureList edam:operation_2454, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:name "MutSig2CV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://software.broadinstitute.org/cancer/cga/mutsig" ; biotools:primaryContact "Michael S. Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3173 ; sc:citation ; sc:description "Detection of non-coding mutation hotspots in cancer genomes | Non-coding MUTation hotSPOT dectection in cancer genomes | The MutSpot R package systematically and unbiasedly scans cancer whole genomes to detect mutation hotspots. MutSpot first builds a background mutation model that corrects for covariates of mutation probability, such as local nucleotide context, replication timing and epigenomic features. Then MutSpot evaluates the mutation recurrence of focal DNA regions using a Poisson binomial model to account for varying mutation rates across different tumors. Mutation hotspots identified have significantly higher mutation recurrence compared to the background genomic mutation rate, suggesting positive selection in cancer and involvement in tumorigenesis" ; sc:featureList edam:operation_3202, edam:operation_3798 ; sc:name "MutSpot" ; sc:url "https://github.com/skandlab/MutSpot/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "Variant effect prediction with interpretation at the protein structure level" ; sc:featureList edam:operation_0331, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "MutaFrame" ; sc:url "https://mutaframe.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description "Tool for automated analysis of genomic mutations in gene regulatory networks." ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MutaNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://service.bioinformatik.uni-saarland.de/mutanet/" ; biotools:primaryContact "Volkhard Helms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0601, edam:topic_0821, edam:topic_3297 ; sc:citation ; sc:description """an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles. scripts and facilities for in-silico mutagenesis with FoldX. Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark. MutateX: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles Matteo Tiberti, Thilde Terkelsen, Tycho Canter Cremers, Miriam Di Marco, Isabelle da Piedade, Emiliano Maiani, Elena Papaleo, submitted to biorxiv""" ; sc:featureList edam:operation_0307, edam:operation_0331, edam:operation_0417 ; sc:license "GPL-3.0" ; sc:name "MutateX" ; sc:url "https://github.com/ELELAB/mutatex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0736, edam:topic_3068 ; sc:citation , "pmcid:PMC6519802", "pubmed:31091262" ; sc:description "Tool for plotting complex mutation data with flexibility." ; sc:featureList edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Mutplot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformaticstools.shinyapps.io/lollipop/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0605, edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6882182", "pubmed:31775760" ; sc:description """Privacy-protecting browser-based personal Genome analysis for genomics education and exploration. MySeq is a web-application for privacy-protecting interactive analysis of personal genomes (distributed as compressed-and-indexed VCF files) inspired by GENOtation (previously the Interpretome) and DNA.LAND Compass. MySeq is intended for use as a genomics educational platform. Analyzing the PTC Tasting Phenotype with MySeq. This page is an example analysis of the "bitter tasting" trait using the MySeq application in an embedded context. Here MySeq is used to both query a whole genome VCF for NA12878 (from Genome in a Bottle) by genomic coordinates and predict the bitter tasting phenotype directly. All of the queries demonstrated here are performed "live" in the browser, that is these are not pre-generated results. Try MySeq as a "standalone" application. MySeq is a single-page web application for privacy-protecting personal genome analysis""" ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3196, edam:operation_3227, edam:operation_3283 ; sc:name "MySeq" ; sc:url "https://go.middlebury.edu/myseq-demo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3304, edam:topic_3382 ; sc:citation , "pubmed:31095292" ; sc:description "ImageJ macro for high throughput analysis of myelinating cultures." ; sc:featureList edam:operation_3435, edam:operation_3450 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MyelinJ" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/BarnettLab/MyelinJ" ; biotools:primaryContact "Susan Barnett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0632, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC7004237", "pubmed:32055708" ; sc:description """Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Antibiotic resistance prediction in minutes. Table of Contents generated with DocToc. AMR prediction (Mykrobe predictor). Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:license "MIT" ; sc:name "Mykrobe" ; sc:url "https://github.com/mykrobe-tools/mykrobe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2229, edam:topic_3375, edam:topic_3489 ; sc:citation , "pmcid:PMC6776608", "pubmed:31611808" ; sc:description """A Portal for Signaling Interactions in Muscle Regeneration. myogenesis and regeneration portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. Myogenesis & REGeneration Portal. Myo-REG offers easy access to signaling information in the context of muscle regeneration. The information is organized in two layers: the first concerns cell-cell interactions, while the second layer describes the most relevant signaling pathways underlying the crosstalk between the cell types participating in muscle regeneration. A user-friendly interface allows users to explore, via an interactive model, cell and pathway crosstalk""" ; sc:featureList edam:operation_0224, edam:operation_3096, edam:operation_3562 ; sc:name "Myo-REG" ; sc:url "https://myoreg.uniroma2.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3510 ; sc:citation , "pmcid:PMC6731604", "pubmed:31516400" ; sc:description "A database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping | Not a member? Reigist in www.biomarkercenter.org/nglycositeatlas | Database UniProtKB AC/ID Gene Protein Site Peptide Motif Source Year Reference" ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3646 ; sc:name "N-GlycositeAtlas" ; sc:url "http://nglycositeatlas.biomarkercenter.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC6521780", "pubmed:31143202" ; sc:description "Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "N1PAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/grizant/n1pas/tree/master" ; biotools:primaryContact "Alfred Grant Schissler", "Yves A. Lussier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0632, edam:topic_0659 ; sc:citation , "pubmed:31504159" ; sc:description "An R package for quality control of NanoString nCounter data | NACHO: NAnostring quality Control dasHbOard | NACHO does this by visualising quality control metrics, expression of control genes, principal components and sample specific size factors in an interactive web application" ; sc:featureList edam:operation_0571, edam:operation_2939, edam:operation_3218 ; sc:license "LGPL-3.0" ; sc:name "NACHO" ; sc:url "https://github.com/mcanouil/NACHO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_3474, edam:topic_3534 ; sc:citation , "pmcid:PMC6933864", "pubmed:31654438" ; sc:description """An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence. This is for predicting NAGbinding sites in a protein. A web server for predicting N-Acetylglucosamine (NAG) interacting residues in a protein. Home page of NAGbinder, which is a web based tool developed for predicting of NAG binding residues in a protein. NAGbinder is a Python-based tool for predicting NAG interacting residues in an uncharacterized protein chain. Prediction of NAG interacting residues. Reference: Patiyal et. al. (2019) NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence""" ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_2575 ; sc:name "NAGbinder" ; sc:url "https://webs.iiitd.edu.in/raghava/nagbinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780 ; sc:citation , "pubmed:30945190" ; sc:description "Noncoding Assessment of long RNAs in Magnoliophyta Species." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "NAMS" ; sc:operatingSystem "Linux" ; sc:url "http://sunlab.cpy.cuhk.edu.hk/NAMS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3071 ; sc:citation , "pmcid:PMC6301334", "pubmed:30576482" ; sc:description "Comprehensive repository for semantic data in life sciences." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NBDC RDF Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://integbio.jp/rdf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6693229", "pubmed:31409293" ; sc:description "Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods | Library bias correction for multiplex RNAseq | Library bias correction for multiplex RNAseq. GitHub Gist: instantly share code, notes, and snippets | Instantly share code, notes, and snippets |" ; sc:featureList edam:operation_3200, edam:operation_3258, edam:operation_3766 ; sc:name "NBGLM-LBC" ; sc:url "https://shka.github.io/NBGLM-LBC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3369 ; sc:citation , "pmcid:PMC6524730", "pubmed:31133849" ; sc:description "Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NCATS BioPlanet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tripod.nih.gov/bioplanet/" ; biotools:primaryContact "Ruili Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "domain sequence-NES site" ; sc:name "NCBI-protein" ; sc:url "https://www.ncbi.nlm.nih.gov/protein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pubmed:31686064" ; sc:description """A novel method for human lncRNA-disease association prediction based on network consistency projection. Copyright (C) 2019 Zecheng Huang(2111705162@mail2.gdut.edu.cn),Guobo Xie(xiegb@gdut.edu.cn). This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Type: Package Title: NCPHLDA:A Novel Method for Human LncRNA-Disease Association Prediction Based on Network Consistency Projection. To analyze these data on NCPHLDA to further infer potential associations between lncRNAs and diseases, you should input the appropriate code in the matlab Command Window:""" ; sc:featureList edam:operation_3435, edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "NCPHLDA" ; sc:url "https://github.com/bryanze/NCPHLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0634 ; sc:citation , "pubmed:31730176" ; sc:description """A package for clustering analysis of multilayer omics data. Clustering of Omics Data of Multiple Types with a Multilayer Network Representation. Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), )""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "NCutYX" ; sc:url "https://cran.r-project.org/web/packages/NCutYX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6754439", "pubmed:31541145" ; sc:description "Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity | Link of paper: https://www.nature.com/articles/s41598-019-50121-3 A Novel Method For Predicting Drug-Drug Interaction By Neural Network Due to the great importance of this issue in the economy, industry, and health, proposing appropriate computational methods for predicting unknown DDI with high precision is challenging. We propose a novel machine learning method for predicting unknown DDIs called \"NDD\", using a two-layer fully connected neural network. NDD uses various characteristics of drugs to have comprehensive information. Multiple drug similarities are calculated. NDD integrat various drug similarities with a non-linear similarity fusion method called \"SNF\" to achieve high-level features. Dependency: python version 3.5.3 deep learning lib keras: https://github.com/fchollet/keras/ machine learning lib scikit-learn: https://github.com/scikit-learn/scikit-learn Contact: nasim.rohani74@gmail.com" ; sc:featureList edam:operation_3439, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "NDD" ; sc:url "https://github.com/nrohani/NDD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0196, edam:topic_0602, edam:topic_0821, edam:topic_3512 ; sc:citation ; sc:description """A non-equilibrium simulator for multibody self-assembly at the cellular scale. NonEquilibrium Reaction-Diffusion Self-assembly Simulator. Additional documentation through doxygen can be found within docs/ by opening index.html""" ; sc:featureList edam:operation_0310, edam:operation_2476, edam:operation_3893 ; sc:license "GPL-3.0" ; sc:name "NERDSS" ; sc:url "https://github.com/mjohn218/NERDSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC6738962", "pubmed:31511852" ; sc:description "A Gephi Plugin Towards Social Network Analysis of Network Exposure for Unipartite and Bipartite Graphs | Gephi plugin for network exposure models | NET-EXPO is a Gelphi plugin that computes various types of network exposure metrics for the purpose of visualization exposure within a network for analysis. Currently network exposure model (Marsden, et al. 1993, Burt, 1987, Valente, 1996, 2005), affiliation exposure model (Fujimoto, et al., 2011, 2012), and limited support for decomposition exposure model (Fujimoto, 2012, Fujimoto, et al., 2013) are supported" ; sc:featureList edam:operation_3766, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "NET-EXPO" ; sc:url "https://github.com/UTH-Tuan/NET-EXPO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625 ; sc:author "Samuele Bovo" ; sc:citation ; sc:description "Standard and network-based gene enrichment analysis in human and model organisms | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms | NETGE-PLUS is optimized to be used on a Google Chrome browser | NETGE-PLUS is a web-server for standard and network-based functional interpretation of gene sets of human and model organisms, including S. scrofa, S. cerevisiae, E. coli and A. thaliana" ; sc:featureList edam:operation_2436, edam:operation_3083, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "NETGE-PLUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://net-ge2.biocomp.unibo.it" ; biotools:primaryContact , "ELIXIR-ITA-BOLOGNA", "Samuele Bovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634 ; sc:citation ; sc:description "Network propagation of rare mutations in Alzheimer’s disease reveals tissue-specific hub genes and communities | Source code for network propagation | NETPAGE (NETwork Propagation-based Assessment of Genetic Events) is a novel computational framework for gene-based association testing of rare variants that integrates prior knowledge about tissue-specific gene interaction networks (Scelsi et al., in preparation)" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "NETPAGE" ; sc:url "https://github.com/maffleur/NETPAGE.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_2640 ; sc:citation , "pubmed:31504175" ; sc:description "Bayesian simultaneous network estimation across unequal sample sizes | --> 'Data_generate.m' generates the precision matrices and dataset corresponding to that as described in the simulation study | --> 'NExUS.m' computes the estimated partial correlation matrices corresponding to the dataset.Variable 'Partial_corr_mean' (which is a 3D array) gives the all estimated partial correlation matrices. Variable 'lambda_2_square_mean' provides the similarity index for each pair of categories | --> In case of real data, note that it is recommended to normalize the sample corresponding to each variable in the data to have mean 0 and variance 1" ; sc:featureList edam:operation_3562, edam:operation_3891 ; sc:name "NExUS" ; sc:url "https://github.com/priyamdas2/NExUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6320579", "pubmed:30609936" ; sc:description "Next Generation-Targeted Amplicon Sequencing (NG-TAS) - an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NG-TAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cclab-brca/NGTAS_pipeline" ; biotools:primaryContact "Carlos Caldas's la" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3047, edam:topic_3382 ; sc:citation ; sc:description """CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation. NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations.""" ; sc:featureList edam:operation_0321, edam:operation_0337, edam:operation_3891 ; sc:license "MIT" ; sc:name "NGL" ; sc:url "https://github.com/vbchen/ngl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3474 ; sc:citation ; sc:description "Structured Reviews for Data and Knowledge Driven Research | The NGLY1 Deficiency Knowledge Graph | This is the repository for the NGLY1 Deficiency Knowledge Graph, the reasoning context to support hypothesis discovery for NGLY1 Deficiency-CDDG (DOID:0060728) research. The user can navigate the knowledge in the graph in the Neo4j Browser website. This knowledge graph is a structured review around the research question what is the mechanism underpinning the NGLY1-AQP1 regulation association and explaining the reduced transcriptomic expression of multiple Aquaporins in NGLY1 deficient cells?. The graph v3.2 is the first deployed in the Wikibase application for community contribution and curation" ; sc:name "NGLY1" ; sc:url "http://ngly1graph.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC6547473", "pubmed:31159881" ; sc:description "NGLess is a domain-specific language for NGS (next-generation sequencing data) processing with a focus on metagenomics" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NGLess" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://ngless.embl.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3308 ; sc:citation ; sc:description "Network-augmented Gene Set Enrichment Analysis." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.inetbio.org/ngsea" ; biotools:primaryContact "Insuk Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:31099384" ; sc:description "NGSEP (Next Generation Sequencing Experience Platform) - accurate variant calling across species and sequencing protocols." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NGSEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ngsep.sf.net" ; biotools:primaryContact "Jorge Duitama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31689213" ; sc:description """Guide Subspace Learning for Unsupervised Domain Adaptation. Guided Subspace Learning(GSL demo). In the file, there are multiple .m files. NGSL.m : Core codes of NGSL algorithm. GSL.m : Core codes of GSL algorithm.""" ; sc:name "NGSL" ; sc:url "https://github.com/Fjr9516/GSL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC6690869", "pubmed:31406180" ; sc:description "A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data | NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed" ; sc:featureList edam:operation_0290, edam:operation_3216, edam:operation_3564 ; sc:name "NGSReadsTreatment" ; sc:url "https://sourceforge.net/projects/ngsreadstreatment/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3056, edam:topic_3517, edam:topic_3676 ; sc:citation ; sc:description """Genetic profiling of 2,683 Vietnamese genomes from non-invasive prenatal testing data. VCF file of our variant call set: https://drive.google.com/file/d/1iyeuaz5w6uSVP9UyV6DjSc-GvMrYYMyr/view?usp=sharing. The analysis pipeline can be run following instructions in the Python script pipeline.py.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3227 ; sc:name "NIPT" ; sc:url "https://github.com/nh2tran/NIPT_WGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3411 ; sc:citation , "pmcid:PMC6296037", "pubmed:30558531" ; sc:description "R package for fast and accurate trisomy prediction in non-invasive prenatal testing." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "NIPTeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/molgenis/NIPTeR" ; biotools:primaryContact "Lennart Johansson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3678 ; sc:citation , "pmcid:PMC6444531", "pubmed:30940082" ; sc:description "NITPicker (Next Iteration Time-point Picker) selects optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making, while maximising information about the shape of the underlying curves." ; sc:featureList edam:operation_3565, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NITPicker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://cran.r-project.org/package=NITPicker" ; biotools:primaryContact "Daphne Ezer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:31593244" ; sc:description """Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution. R package for our Nonnegative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID), joint work with Seyoung Park (https://sites.google.com/view/seyoungpark/home). Non-negative Matrix Factorization-based Immune-TUmor MIcroenvironment Deconvolution (NITUMID)""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3659 ; sc:name "NITUMID" ; sc:url "https://github.com/tdw1221/NITUMID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0769 ; sc:citation , "pmcid:PMC6642500", "pubmed:31360216" ; sc:description "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge | A tool for divide-and-conquer tree estimation via a shared distance matrix | NJMerge is a tool for scaling phylogengy estimation methods to large datasets. NJMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). NJMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2018)" ; sc:featureList edam:operation_0544, edam:operation_0546, edam:operation_0548 ; sc:name "NJMerge" ; sc:url "http://github.com/ekmolloy/njmerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3398 ; sc:citation ; sc:description "Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories | This project is to convert user query to SPARQL in the Physiome Model Repository. The information looking by users usually is model entities | Natural Language Interface for Model Entity Discovery (NLIMED) is an interface to search model entities (i.e. flux of sodium across the basolateral plasma membrane, the concentration of potassium in the portion of tissue fluid) in the biosimulation models in repositories. The interface utilises the RDF inside biosimulation models and metadata from BioPortal. Currently, the interface can retrieve model entities from the Physiome Model Repository (PMR, https://models.physiomeproject.org) and the BioModels (https://www.ebi.ac.uk/biomodels/)" ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3435 ; sc:name "NLIMED" ; sc:url "https://github.com/napakalas/NLIMED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc:description """Labelling chest x-ray reports using an open-source NLP and ML tool for text data binary classification. Natural language processing and machine learning of a comma separated value (CSV) file with text data and labels. nlp_ml is a command line script that performs natural language processing and machine learning of a CSV (comma separated value) file with text data and labels. The CSV file must have the columns 'text' and 'class'. The code randomly generates classification pipelines, performs 10-fold cross validation for assessing model performance on the training dataset, and saves the results to a SQLite database. The code uses the SMOTE oversampler to avoid issues with imbalanced datasets. nlp_ml solves supervised binary classification problems using text data. When generating your CSV file, replace commas with spaces in the elements of the text column prior to saving the file.""" ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "NLP ML" ; sc:url "http://github.com/pySRURGS/nlp_ml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2828 ; sc:citation , "pmcid:PMC6767145", "pubmed:31510014" ; sc:description "Normal Mode Analysis as a Routine Part of a Structural Investigation | Webtool for Normal Mode Analysis | Web-server for Normal Mode Analysis of proteins | Are you submitting large files to WEBnma? Provide your email address in the submission box above and we will send you a link that you can visit to inspect your results when they are ready. Alternatively, you can bookmark the URL appearing in your web browser once you have submitted your job. The results can be accessed at this URL within two weeks of your submission date" ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3891 ; sc:name "NMA" ; sc:url "http://apps.cbu.uib.no/webnma/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3360, edam:topic_3382 ; sc:citation , "pubmed:31593222" ; sc:description """Blind spectral unmixing of highly mixed multispectral flow and image cytometry data. Matlab code to spectrally unmix highly mixed multispectral flow and image cytometry data. To use NMF-RI on new data (tissue or flow cytometry) we recommend to use the ´main.m´ code distributed and load new cytometry data to the existing folder hierarchy.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3860 ; sc:name "NMF-RI" ; sc:url "https://github.com/djimenezsanchez/Blind_Unmixing_NMF_RI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0593, edam:topic_3172 ; sc:citation , "pmcid:PMC6837886", "pubmed:31363225" ; sc:description "Single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis | In Vitro Transcription NMR. Protocol, code and examples for the co-transcriptional RNA folding network reconstruction | The protocol describes how to setup and analyse observation of a co-transcriptional RNA folding network by Systems NMR approach. While most experimental approaches can monitor only a single molecule class or reaction type at a time, Systems NMR permits single-sample dynamic quantification of entire “heterotypic” networks – involving different reaction and molecule types. It thus provides a deeper systems-level understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of “omics”" ; sc:featureList edam:operation_0483, edam:operation_2495, edam:operation_3799 ; sc:name "NMR" ; sc:url "http://github.com/systemsnmr/ivtnmr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2640 ; sc:citation ; sc:description "Bayesian semi-nonnegative matrix tri-factorization to identify pathways associated with cancer phenotypes | Bayesian Semi-Nonnegative Matrix Tri-Factorization | BSNMTF is a semi-nonnegative matrix tri-factorization method in the framework of Bayesian learning to identify pathways associated with cancer phenotypes (e.g., cancer sub-types or treatment outcome) from a real-valued input matrix (e.g., copy number alterations or normalized log transformed gene expression data)" ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:name "NMTF" ; sc:url "https://github.com/parks-cs-ccf/BayesianSNMTF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3474 ; sc:citation , "pmcid:PMC6795129", "pubmed:31649723" ; sc:description """Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease. Deep learning enables accurate prediction of interplay between lncRNA and disaeas. ###########################################################################################. NNLDA is implemented in Python 3.5 and use Tensorflow 1.12.0. Package numpy and pandas are also required. The experimental data are downloaded from LncRNADiseas2.0 database""" ; sc:featureList edam:operation_3439, edam:operation_3625 ; sc:name "NNLDA" ; sc:url "https://github.com/gao793583308/NNLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC6777013", "pubmed:31608146" ; sc:description """Network-based Observability and Controllability Analysis of Dynamical Systems. NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox for MATLAB and Octave. Daniel Leitold, Anges Vathy-Fogarassy, and Janos abonyi, NOCAD - Network based Observability and Controlability Analysis of Dynamical Systems toolbox (MATLAB version), 2017.""" ; sc:featureList edam:operation_2497 ; sc:name "NOCAD" ; sc:url "https://github.com/abonyilab/NOCAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3071, edam:topic_3301, edam:topic_3307, edam:topic_3332 ; sc:citation , , , , , ; sc:description "NORINE is a platform that includes a database of nonribosomal peptides together with tools for their analysis." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "NORINE" ; sc:url "http://norine.univ-lille.fr/norine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2840, edam:topic_3308 ; sc:citation , "pmcid:PMC6724309", "pubmed:31481014" ; sc:description "An R package for computing network perturbation amplitudes using gene expression data and two-layer networks | NPA - Network Perturbation Amplitude | R package and data for NPA models | The NPA (Network Perturbation Amplitude) and BIF (Biological Impact Factor) methods allow to understand the mechanisms behind and predict the effect of exposure based on transcriptomics datasets.This approach enables to translate the gene expression fold-changes into differential values for each network node, and to summarize this at the network level to provide aquantitative assessment of the degree of perturbation of the network model, the Network Perturbation Amplitude (NPA).Combining multiple relevant network models, the overall biological impact of a perturbing agent, the Biological Impact Factor (BIF),can be calculated by aggregating individual NPA scores | After package installation, networks are installed with no precomputed data" ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3660 ; sc:name "NPA" ; sc:url "https://github.com/philipmorrisintl/NPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pubmed:31752016" ; sc:description """The Neyman Pearson detection of microsaccades with maximum likelihood estimation of parameters. Neyman–Pearson Detector (NPD) for saccadic eye movements. By default, our algorithm reads in files X.csv and Y.csv, where the X and Y coordinates of the tracked eye-gaze positions are stored in each of the csv files. Data in the X.csv and Y.csv must be square matrices of same dimensions, and each trail of the tracked eye-gaze positions forms the rows of the input file. Our algorithm can perform the NPD on each row of the dataset independently""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "NPD" ; sc:url "https://github.com/hz-zhu/NPD-micro-saccade-detection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_3318, edam:topic_3520 ; sc:citation , "pubmed:31753619" ; sc:description """Quantitative Structural Interpretation of Protein Crosslinks. NRGXL: a tool to compute protein crosslinker conformations and energies""" ; sc:featureList edam:operation_0480, edam:operation_2476, edam:operation_3630 ; sc:name "NRGXL" ; sc:url "https://nrgxl.pasteur.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3176, edam:topic_3295 ; sc:citation , "pmcid:PMC6868436", "pubmed:31665434" ; sc:description """CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. NRLcalc: calculation of the Nucleosome Repeat Length. The NRLcalc app provides a visual interface for the bulk calculation of the Nucleosome Repeat Length (NRL) based on multiple phasograms computed with NucTools (https://github.com/homeveg/nuctools).""" ; sc:featureList edam:operation_2575, edam:operation_3222, edam:operation_3659 ; sc:name "NRL" ; sc:url "https://github.com/chrisclarkson/NRLcalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3382 ; sc:citation , "pubmed:31116382" ; sc:description "software for processing and analysis of terabyte-scale volume images locally or on a computing cluster." ; sc:featureList edam:operation_0232, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NRStitcher" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/arttumiettinen/pi2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0654 ; sc:citation ; sc:description "DNA comparison tool with increased speed, sensitivity and accuracy." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NSimScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/abadona/qsimscan" ; biotools:primaryContact "Denis Kaznadzey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3697, edam:topic_3855 ; sc:citation ; sc:description "Massively Parallel Simulator for Individual-based Modelling of Microbial Communities." ; sc:featureList edam:operation_0337, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NUFEB" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/nufeb/NUFEB" ; biotools:primaryContact "Paolo Zuliani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC6933719", "pubmed:31878873" ; sc:description """Archaic mitochondrial DNA inserts in modern day nuclear genomes. Scripts used to detect archaic NUMTs in NGS data. A pipeline including a collection of scripts used to analyse NUMTs discovered in whole genome paired read data. flanking_region_analysis.py is a script used to calculate match ratios with archaic genomes of a specific genomic region. numt_stats.py is a script to calculate various statistics for discovered NUMTs. mito_variance.py is a script to calculate pariwise differences between all sequences of an alignment.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3359 ; sc:name "NUMT" ; sc:url "https://github.com/robbueck/arcnumt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3293 ; sc:citation , "pubmed:31424551" ; sc:description "Estimating cancer spatial and temporal heterogeneity and evolution through alignment-free methods | NGS tool for Unsupervised analysis of fastQ files using Alignment-free | A software to support an alignment-free sequence comparison of large-scale fastq files using a k-mer counting methods paired with distance metrics, Jensen-Shannon divergence and Hellinger Distance | git clone https://github.com/ARoddy/NUQA.git | NUQA reads in a set of raw fastq files - ideally, these are DNA-seq files produced from multiple samples taken from the same patient. Based on these it will identify differences between the files and produce a distance matrix and a newick tree file | Eigen (where /Eigen file containing the headers is located at /usr/local/include for an example run check file 'Eigen_help.txt')" ; sc:featureList edam:operation_3211, edam:operation_3435, edam:operation_3472 ; sc:name "NUQA" ; sc:url "https://github.com/ACRoddy/NUQA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343 ; sc:citation , "pmcid:PMC6688286", "pubmed:31399811" ; sc:description "A natural products likeness scorer-web application and database | NaPLeS - Natural Product Likeness Score calculator | NaPLeS is an open source web application based fully on open data. Source and installation instructions are available at GitHub. Please submit bug reports, feature requests and general issues through the issues tracker at GitHub. NaPLeS is developed and maintained by the Steinbeck group at the University Friedrich-Schiller in Jena, Germany" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3803 ; sc:name "NaPLeS" ; sc:url "http://naples.naturalproducts.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "NaS is a hybrid approach developped to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions." ; sc:name "NaS" ; sc:url "http://www.genoscope.cns.fr/nas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks. Abstract Background Variant detection from high-throughput sequencing data remains an important, unresolved yet often overlooked problem. Long-read sequencing technologies, such as Oxford Nanopore and PacBio sequencing, present unique advantages to detect SNPs and small indels in genomic regions that short-read sequencing cannot reliably examine (for example, only ∼80% of genomic regions are marked as “high-confidence region” to have SNP indel calls in the Genome In A Bottle project). However, existing software tools for short-read data perform poorly on long-read data; instead, several recent studies showed promising results in variant detection on long-read data by deep learning.""" ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:name "NanoCaller" ; sc:url "https://github.com/WGLab/NanoCaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3295 ; sc:citation , "pmcid:PMC6509807", "pubmed:31072312" ; sc:description "Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly." ; sc:featureList edam:operation_0525, edam:operation_3185, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoDJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/genomicsITER/NanoDJ" ; biotools:primaryContact , "Marcos Colebrook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6803960", "pubmed:31590255" ; sc:description """An Implemented Decision Support Framework for Nanomaterial Identification. Official repository of the NanoDefiner e-tool for nanomaterial classification. This is the official repository for the NanoDefiner e-tool, a decision support framework for the characterisation of potential nanomaterials. It is one of the products delivered by the NanoDefine project.""" ; sc:featureList edam:operation_2428, edam:operation_3457 ; sc:license "MIT" ; sc:name "NanoDefiner" ; sc:url "https://fh.do/nanodefiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6360650", "pubmed:30712508" ; sc:description "Computational tool to detect DNA modifications using Nanopore long-read sequencing data." ; sc:featureList edam:operation_0417, edam:operation_0452, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoMod" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/WGLab/NanoMod" ; biotools:primaryContact "Wang Genomics Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781, edam:topic_3170 ; sc:citation , "pmcid:PMC6377397", "pubmed:30689855" ; sc:description "Web server for nanopore MinION sequencing data analysis." ; sc:featureList edam:operation_0484, edam:operation_3185, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "NanoPipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nanopipe.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pubmed:31071140" ; sc:description "R package to analyze and compare nanopore sequencing data." ; sc:featureList edam:operation_2422, edam:operation_3185, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/davidebolo1993/NanoR" ; biotools:primaryContact "Davide Bolognini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0160, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC6857246", "pubmed:31727106" ; sc:description """Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Dynamic time warping of Oxford Nanopore squiggle data to characterize tandem repeats. Several tools exist to analyze tandem repeats (e.g. tandem-genotypes and RepeatHMM)""" ; sc:featureList edam:operation_0237, edam:operation_3194, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "NanoSatellite" ; sc:url "https://github.com/arnederoeck/NanoSatellite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """RNA modifications detection by comparative Nanopore direct RNA sequencing. RNA modifications detection from Nanopore dRNA-Seq data. Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples. Analyses performed for the nanocompore paper. Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro""" ; sc:featureList edam:operation_0417, edam:operation_0428, edam:operation_3196, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Nanocompore" ; sc:url "https://github.com/tleonardi/nanocompore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0593, edam:topic_3297, edam:topic_3314 ; sc:citation , "pmcid:PMC6891855", "pubmed:31807684" ; sc:description """An Open Access Knowledge Base for Microbial Natural Products Discovery. The Natural Products Atlas Network views of chemical space. The Natural Products Atlas provides a unique tools for exploring natural products chemical space, offering perspective on the position that any molecule occupies""" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3431, edam:operation_3803 ; sc:name "Natural Products Atlas" ; sc:url "http://www.npatlas.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071 ; sc:author "Universität Bayreuth, Department of Mycology" ; sc:contributor "SNSB IT Center" ; sc:description "NaviKey is a tool for querying descriptive data and has been implemented as (a) a Java applet providing the contents of DELTA files (see example with the DELTA sample data files), (b) a stand-alone Java application for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively (c) a module (\"plug-in\") of the Java-based Diversity Navigator database client for accessing DELTA files or PostgreSQL versions of DiversityDescriptions databases, respectively." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "NaviKey" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SNSB IT Center" ; sc:softwareHelp , , ; sc:url "http://www.navikey.net/" ; biotools:primaryContact "Universität Bayreuth, Department of Mycology" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3056 ; sc:citation ; sc:description "NeOGen (genetic Ne for Overlapping Generations analysis; pronounced Neo-gen) is point-&-click genetic effective population size (Ne) and demographic modelling software." ; sc:featureList edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeOGen" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0.6.a1" ; sc:url "http://www.molecularfisherieslaboratory.com.au/neogen-v1-3-0-6-a1-software/" ; biotools:primaryContact "J. R. Ovenden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203 ; sc:citation ; sc:description "Tool for the identification of approximate DNA sequence symmetries." ; sc:featureList edam:operation_0239, edam:operation_3472, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeSSie" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.medcomp.medicina.unipd.it/main_site/doku.php?%20id=nessie" ; biotools:primaryContact "Michele Berselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31755900" ; sc:description """Predicting fusion neoantigens from RNA sequencing data. The Section for Bioinformatrics at the Biocenter of Innsbruck Medical University is commited to the generation, management, integration, and leveraging data from genomics studies. Quantification of the tumor immune contexture. Zlatko Trajanoski awarded with ERC Advanced Grant.""" ; sc:featureList edam:operation_0252, edam:operation_0310, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "NeoFuse" ; sc:url "https://icbi.i-med.ac.at/NeoFuse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0804, edam:topic_2640, edam:topic_3068, edam:topic_3400 ; sc:citation , "pmcid:PMC6901387", "pubmed:31819989" ; sc:description """An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunological resources""" ; sc:featureList edam:operation_0252, edam:operation_2421, edam:operation_3435 ; sc:name "NeoPeptide" ; sc:url "http://www.neopeptide.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC6532147", "pubmed:31117948" ; sc:description "High-throughput neoantigen prediction and recognition potential pipeline." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeoPredPipe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MathOnco/NeoPredPipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:31095279" ; sc:description "R Package for Risk-Gene Networks." ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "NetDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cdal.korea.ac.kr/NetDA/" ; biotools:primaryContact "Minhyeok Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_3474 ; sc:citation , "pmcid:PMC6602452", "pubmed:31106361" ; sc:description "Web server that is able to improve improve large-scale protein function prediction with massive network information." ; sc:featureList edam:operation_0267, edam:operation_1777, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NetGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://issubmission.sjtu.edu.cn/netgo/" ; biotools:primaryContact "Shanfeng Zhu", "Shuwei Yao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:31688914" ; sc:description """Network-based multi-task learning models for biomarker selection and cancer outcome prediction. Network-based transfer learning models for biomarker selection and cancer outcome prediction. Download eight .pk files(sample_breast_expression.pk, sample_breast_label.pk, sample_ov_expression.pk, sample_ov_label.pk, sample_PRAD.pkl, sample_PRAD_label.pkl, sample_ppi.pkl, sample_gene_names.pkl) and two .py files(NetTL_three_domains.py, NetSTL_three_domains.py) into the same fold. Run python command and execute: python3 NetTL(NetSTL)_three_domains.py The results will be exported as txt files in the same fold. sample_OV.pkl: : Ovarian Cancer gene expression data set. The size of the data is 100 x 500, 100 samples and 500 genes.""" ; sc:featureList edam:operation_2426, edam:operation_3463, edam:operation_3501 ; sc:name "NetML" ; sc:url "https://github.com/compbiolabucf/NetML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6746993", "pubmed:31527713" ; sc:description "Neural network identification of RiPP precursor peptides | NeuRiPP (Neural Network Identification of RiPP Precursor Peptides) | NeuRiPP is a neural network framework designed for classifying peptide sequences as putative precursor peptide sequences for RiPP biosynthetic gene clusters. It consists of two modules:" ; sc:featureList edam:operation_3501, edam:operation_3631 ; sc:name "NeuRiPP" ; sc:url "https://github.com/emzodls/neuripp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "A Unified Approach to MEG Source Analysis under the Continuous Stimuli Paradigm | The magnetoencephalography (MEG) response to continuous auditory stimuli, such as speech, is commonly described using a linear filter, the auditory temporal response function (TRF) | This repository contains the implementation of our direct TRF estimation algorithm in python (version 3.6 and above)" ; sc:featureList edam:operation_3629 ; sc:license "BSD-2-Clause" ; sc:name "Neuro-Current Response Functions" ; sc:url "https://github.com/proloyd/neuro-currentRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3304, edam:topic_3474 ; sc:citation , "pubmed:31721688" ; sc:description """A Tool to Predict Cleavage Sites of Neuropeptide Precursors. BACKGROUND:Neuropeptides are a class of bioactive peptides produced from neuropeptide precursors through a series of extremely complex processes, mediating neuronal regulations in many aspects. Accurate identification of cleavage sites of neuropeptide precursors is of great significance for the development of neuroscience and brain science. OBJECTIVE:With the explosive growth of neuropeptide precursor data, it is pretty much needed to develop bioinformatics methods for predicting neuropeptide precursors' cleavage sites quickly and efficiently. METHOD:We started with processing the neuropeptide precursor data from SwissProt and NueoPedia into two sets of data, training dataset and testing dataset. Subsequently, six feature extraction schemes were applied to generate different feature sets and then feature selection methods were used to find the optimal feature set of each""" ; sc:featureList edam:operation_0422 ; sc:name "NeuroCS" ; sc:url "http://i.uestc.edu.cn/NeuroCS/dist/index.html#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description """A toolbox to analyse the dynamics of neuronal encoding in freely-behaving rodents in vivo. NeuroChaT is an open-source neuron characterisation toolbox. MNI: Original conception and design of the software architecture, primary development of algorithms and subsequent implementation in Python, primary user’s manual development, iterative development of software based on user feedback, originator of NeuroChaT acronym""" ; sc:name "NeuroChaT" ; sc:url "https://github.com/shanemomara/NeuroChaT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6499165", "pubmed:31105546" ; sc:description "Software Package for Quantification of Cortical Motor Maps Using Frameless Stereotaxic Transcranial Magnetic Stimulation." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NeuroMeasure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/EdwardsLabNeuroSci/NeuroMeasure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0157, edam:topic_3510 ; sc:author "Prof. Jian Huang" ; sc:citation , "pubmed:29525981" ; sc:description "Tool for the prediction of neuropeptide precursors based on optimal sequence composition." ; sc:featureList edam:operation_0253, edam:operation_0418, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NeuroPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/neuropeptide/neuropp/home.html" ; biotools:primaryContact "Prof. Jian Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3421 ; sc:citation , "pmcid:PMC6901659", "pubmed:31849818" ; sc:description """The Effect of Medication and Deep Brain Stimulation on Posture in Parkinson's Disease. NeuroPostureApp©, Klinik für Neurologie, UKSH Campus Kiel. WebApp to measure bending angle in camptocormia patients. Based on the article **to be published** from Nils Margraf and Günther Deuschl et al.""" ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:name "NeuroPostureApp" ; sc:url "http://www.neuroimaging.uni-kiel.de/NeuroPostureApp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description """A free Python toolbox for fast multi-modal and reproducible brain connectivity pipelines. Neuropycon package of functions for electrophysiology analysis, can be used from graphpype and nipype. Neuropycon — ephypype 0.1dev0 documentation. Neuropycon — graphpype 0.1dev0 documentation. Neuropycon is an open-source multi-modal brain data analysis kit which provides Python-based pipelines for advanced multi-thread processing of fMRI, MEG and EEG data, with a focus on connectivity and graph analyses. Neuropycon is based on Nipype, a tool developed in fMRI field, which facilitates data analyses by wrapping many commonly-used neuro-imaging software into a common python framework.""" ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3454 ; sc:name "NeuroPycon" ; sc:url "https://neuropycon.github.io/ephypype/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Standard Electroencephalography (EEG) server that mediates between the raw EEG devices and all the various EEG applications that the user may wish to run to analyse the incoming EEG data." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeuroServer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://openeeg.sourceforge.net/neuroserver_doku/" ; biotools:primaryContact "Rudi Cilibrasi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:31831521" ; sc:description """Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes. Transcriptomics of cortical excitatory and inhibitory neurons""" ; sc:featureList edam:operation_2495, edam:operation_2499, edam:operation_3223, edam:operation_3891 ; sc:name "NeuronSubtypeTranscriptomes" ; sc:url "http://research-pub.gene.com/NeuronSubtypeTranscriptomes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3474 ; sc:description "Implementation of Neutrosophic Recommender System" ; sc:isAccessibleForFree true ; sc:name "Neutrosophic Recommender System for Medical Diagnosis Based on Algebraic Neutrosophic Measures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/55239-a-neutrosophic-recommender-system-for-medical-diagnosis-based-on-algebraic-neutrosophic-measures" ; biotools:primaryContact "pham viet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3314, edam:topic_3489 ; sc:citation , "pubmed:31600445" ; sc:description """An Open, Up-to-Date Resource for the Molecular Sciences Community. A repository for quantum chemistry basis sets. The new Basis Set Exchange (BSE) for Quantum Chemistry. If you are looking for the Basis Set Exchange website (which can be used to browse and download this data in a more user-friendly way), visit https://www.basissetexchange.org. This project is a library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data. This library is used to form the backend of the new Basis Set Exchange website. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community Benjamin P. Pritchard, Doaa Altarawy, Brett Didier, Tara D. Gibson, and Theresa L. Windus J. Chem. Inf. Model. 2019, 59(11), 4814-4820 doi:10.1021/acs.jcim.9b00725. A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community""" ; sc:featureList edam:operation_2422, edam:operation_3283 ; sc:license "BSD-3-Clause" ; sc:name "New Basis Set Exchange" ; sc:softwareHelp ; sc:url "https://www.basissetexchange.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3168, edam:topic_3308 ; sc:citation ; sc:description "Gene Expression platform to investigate gene expression and functionalities in the tomato genome. It includes expression data from cultivated specie/variety Heinz 1706, Ailsa Craig e Solanum pimpinellifolium." ; sc:featureList edam:operation_0315, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NexGenEx-Tom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://140.164.45.142/NexGenEx-Tom/expression/exp-search.aspx" ; biotools:primaryContact "Hamed Bostan", "Maria Luisa Chiusano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780 ; sc:citation , "pubmed:31778144" ; sc:description """A fast and efficient genome polishing tool for long read assembly. Fast and accurately polish the genome generated by noisy long reads. NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo""" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3472 ; sc:name "NextPolish" ; sc:url "https://github.com/Nextomics/NextPolish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0621, edam:topic_0736, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:31577193" ; sc:description """A random forest method for prediction of N-Glycosylation sites in eukaryotic protein sequence. N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. It plays a vital role in various biological processes such as protein folding, stability, immunogenicity of different proteins, cell signaling and protein targeting. N-glycosylation predominantly occurs in N-X-[S T] sequon where X is any amino acid other than proline. However, not all N-X-[S T] sequons in proteins are glycosylated. Therefore, accurate prediction of N-glycosylation sites is essential to understand N-glycosylation mechanism. We developed a random forest method, Nglyc, to predict N-glycosylation sites in eukaryotic protein sequences. The method used 315 features derived from a protein sequence and its sequence homologs. Training and testing was performed using a dataset containing 895 N-glycosylation sites and 853 non-glycosylated sites obtained from 846 PDB structures""" ; sc:featureList edam:operation_0417 ; sc:name "Nglyc" ; sc:url "https://github.com/bioinformaticsML/Ngly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3361, edam:topic_3474 ; sc:citation , "pmcid:PMC6795684", "pubmed:31649523" ; sc:description """Inferring Continuous Subjective Ratings With Deep Regression. Data and code of the BrainLinks-BrainTools NiceBot project, manuscript "Human-Compliant Robot Behavior: Combining Continuous Subjective Evaluation with Multimodal Deep Regression Analysis".""" ; sc:featureList edam:operation_3659 ; sc:name "NiceBot" ; sc:url "https://github.com/TNTLFreiburg/NiceBot" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2333 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308 ; sc:citation , , "pubmed:31819264" ; sc:description "A computational method to study intercellular communication. It uses human or mouse gene expression data of interacting cells in order to predict ligand-receptor interactions that might drive gene expression changes in cells of interest." ; sc:featureList edam:operation_2423, edam:operation_2428, edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NicheNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/saeyslab/nichenetr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218 ; sc:citation , "pubmed:31478922" ; sc:description "An Open-Source Nursing-Sensitive Natural Language Processing System Based on Word Embedding | This study develops and evaluates an open-source software (called NimbleMiner) that allows clinicians to interact with word embedding models with a goal of creating lexicons of similar terms. As a case study, the system was used to identify similar terms for patient fall history from homecare visit notes (N = 1 149 586) extracted from a large US homecare agency. Several experiments with parameters of word embedding models were conducted to identify the most time-effective and high-quality model. Models with larger word window width sizes (n = 10) that present users with about 50 top potentially similar terms for each (true) term validated by the user were most effective. NimbleMiner can assist in building a thorough vocabulary of fall history terms in about 2 hours" ; sc:featureList edam:operation_3501 ; sc:name "NimbleMiner" ; sc:url "https://github.com/mtopaz/NimbleMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc:description "Predicting and Designing therapeutics against the Nipah virus." ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Nipah" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cospi.iiserpune.ac.in/Nipah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0602, edam:topic_3306, edam:topic_3336 ; sc:citation , "pmcid:PMC6831641", "pubmed:31690758" ; sc:description """Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Release Notes for NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis with Multi-State Equilibrium Binding Models. Please download, install, and start NmrLineGuru according to the repo page:. Before you use NmrLineGuru for your own data or project, please repeat the example simulations/fittings in the tutorials and make sure you can reproduce the example results. Feng C, Kovrigin EL, Post CB (2019) NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Scientific Reports 9:16023. [DOI]""" ; sc:featureList edam:operation_0244, edam:operation_2426, edam:operation_3799 ; sc:name "NmrLineGuru" ; sc:softwareHelp ; sc:url "https://github.com/stonefonly/NmrLineGuru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3379 ; sc:citation , "pmcid:PMC6452590", "pubmed:31057324" ; sc:description "Online tool to predict the survival rate in non-small cell lung cancer patients." ; sc:featureList edam:operation_3557 ; sc:name "Nomogram Prognostic Model" ; sc:url "http://lce.biohpc.swmed.edu/lungcancer/nomogram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation , "pubmed:31106635" ; sc:description "Interactive tool for presenting cervical cancer screening indicators in the Nordic countries." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "NordScreen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nordscreen.org/" ; biotools:primaryContact "Veli-Matti Partanen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6503164", "pubmed:31114611" ; sc:description "Framework for researchers to select the best method for the normalization of their gene expression data based on the evaluation of different methods in the principle of the consistency of metrics and the consistency of datasets." ; sc:featureList edam:operation_0571, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "NormExpression" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/NormExpression/index.html" ; biotools:primaryContact "Shan Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3305, edam:topic_3418 ; sc:citation , "pmcid:PMC6704660", "pubmed:31438883" ; sc:description "Genetic diversity and epidemiology of Genogroup II noroviruses in children with acute sporadic gastroenteritis in Shanghai, China, 2012-2017 | BACKGROUND:Noroviruses (NoVs) are considered an important cause of acute gastroenteritis (AGE) across all age groups, especially in children under 5 years of age. We investigated the epidemiology of noroviruses in outpatient children from the Children's Hospital of Fudan University in Shanghai, China. METHODS:Stool specimens were collected between January 2012 and December 2017 from 1433 children under 5 years of age with acute gastroenteritis. All samples were analysed by conventional reverse transcription-polymerase chain reaction (RT-PCR) for genogroup II NoVs amplifying both the RNA-dependent RNA polymerase (RdRp) and partial capsid genes" ; sc:featureList edam:operation_0308, edam:operation_3196 ; sc:name "Norovirus" ; sc:url "https://www.rivm.nl/mpf/typingtool/norovirus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_2830, edam:topic_3306 ; sc:citation , "pmcid:PMC6893490", "pubmed:31771451" ; sc:description """Modelling cell surface dynamics and cell-cell interactions using Cell Studio. A Notch-Delta receptor binding process agent-based model using Unity 3D. The simulation was built and tested on Unity version 4.6.1, which is freely available for download at https://unity3d.com/get-unity/download/archive. To use the simulation, download the repository from GitHub, save it to a new folder (e.g. notch-delta-model), and create a project in Unity by clicking “create a new project” and select that folder (it should contain only the Assets folder and the readme file). Do not import any package. Then, load one of the scenes in the Assets folder by double clicking it.""" ; sc:featureList edam:operation_0321, edam:operation_2426, edam:operation_3096 ; sc:name "Notch" ; sc:url "https://github.com/asafl/NotchDelta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0621, edam:topic_0654, edam:topic_3295, edam:topic_3656 ; sc:citation ; sc:description """Web-based Resources to Simulate and Analyze the Three-Dimensional Genome. A web platform to simulate and browse the three-dimensional architecture of genomes. In NDB user can find data for 3D genome structures and also computational tools for simulating the genome. The server is also made for visualization the structures and dynamics of the genome, allowing users to explore the 3D organization of chromosomes from their computer. This platform enables users to visualize and annotate the 3D chromosome structures with experimental tracks from ENCODE or with their own data, allowing for an integrative experience for all genome scientists.""" ; sc:featureList edam:operation_0570, edam:operation_2476, edam:operation_3208 ; sc:name "Nucleome Data Bank" ; sc:url "https://ndb.rice.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3176, edam:topic_3308 ; sc:citation , "pmcid:PMC6765203", "pubmed:31504766" ; sc:description "A new tool for the dynamic analysis of nucleosome positioning | R package for nucleosome architecture comparison | Nucleosome Dynamics - Singularity | Nucleosome Dynamics Singularity image is a containerized implementation of 'Nucleosome Dynamics suite' | Nucleosome Dynamics Docker Container | Nucleosome Dynamics - docker implementation | This repository includes the set of R programs implementing 'Nucleosome Dynamics' analyses | Nucleosome positioning plays a major role in transcriptional regulation and most DNA-related processes | Nucleosome positioning plays a major role in transcriptional regulation DNA replication and DNA repair | R package aimed at comparing the reads of two MNase-seq experiments for nucleosome positioning and detecting significant inclusions, evictions and shifts" ; sc:featureList edam:operation_0244, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "Nucleosome Dynamics" ; sc:url "http://mmb.irbbarcelona.org/NucleosomeDynamics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3390, edam:topic_3518 ; sc:citation , "pmcid:PMC6821151", "pubmed:31665759" ; sc:description """a nutrigenomics exploratory and analytical platform. Nutrigenomics data mining platform. Nutrigenomics is defined as the science studying the role of nutrients and bioactive food compounds on gene expression. Whereas the idea of modulating human health by food intake is a millenial concept, the increasing number of research efforts on this field is pointing out that nutrition may exert its impact on health outcomes by directly affecting the expression of genes involved in critical metabolic pathways. Nowadays its widely accepted that cellular processes spanning from gene expression to protein synthesis can be regulated by dietary compounds. However there is a limited understanding of the underlying molecular mechanisms which are involved. NutriGenomeDB makes use of publicly available gene expression data obtained from nutrigenomics experiments in order to bring a the first platform for nutrigenomics data exploration""" ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_2436, edam:operation_3223 ; sc:name "NutriGenomeDB" ; sc:url "http://nutrigenomedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31599833" ; sc:description """Development and Validation of a Machine Learning Algorithm for Predicting Response to Anticholinergic Medications for Overactive Bladder Syndrome. Prediction of Response to Anti-Cholinergic Medication for Overactive Bladder. Number of Previously Failed Medications 0 ≥1.""" ; sc:featureList edam:operation_2428 ; sc:name "OAB" ; sc:url "https://oabweb.herokuapp.com/app/pre/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3335, edam:topic_3400, edam:topic_3421 ; sc:citation , , "pmcid:PMC6876873", "pubmed:31765395" ; sc:description """Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. Detect prescription of oral anticoagulants (OAC) in clinical text using regular expressions. Developed and used in Bean et al. (2019 submitted) "Semantic Computational Analysis of Anticoagulation Use in Atrial Fibrillation from Real World Data".""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3435 ; sc:name "OAC" ; sc:url "https://github.com/CogStack/OAC-NLP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2828, edam:topic_3314 ; sc:citation , "pmcid:PMC6774380", "pubmed:31579260" ; sc:description """Building Open Access to Research (OAR) Data Infrastructure at NIST. The NIST Open Access to Research (OAR) Public Data Repository (PDR) system software. Publishing Data Repository (oar-pdr). The oar-metadata package is a prerequisite which is configured as git sub-module of this package. This means after you clone the oar-pdr git repository, you should use git submodule to pull in the oar-metadata package into it:""" ; sc:featureList edam:operation_3435 ; sc:name "OAR" ; sc:url "https://github.com/usnistgov/oar-pdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3316, edam:topic_3337 ; sc:citation , "pmcid:PMC6325911", "pubmed:30482799" ; sc:description "Out-of-Core Matrices Analyzer (OCMA) uses state-of-the-art computational techniques that can nimbly perform eigen and Singular Value Decomposition (SVD) analyses." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OCMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "gamma 0.1" ; sc:url "https://github.com/precisionomics/OCMA" ; biotools:primaryContact "Quan Long", "Zhi Xiong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC6905554", "pubmed:31825992" ; sc:description """A novel one-class classification approach to accurately predict disease-gene association in acute myeloid leukemia cancer. Disease causing gene identification is considered as an important step towards drug design and drug discovery. In disease gene identification and classification, the main aim is to identify disease genes while identifying non-disease genes are of less or no significant. Hence, this task can be defined as a one-class classification problem. Existing machine learning methods typically take into consideration known disease genes as positive training set and unknown genes as negative samples to build a binary-class classification model. Here we propose a new One-class Classification Support Vector Machines (OCSVM) method to precisely classify candidate disease genes.""" ; sc:featureList edam:operation_0315, edam:operation_2454 ; sc:name "OCSVM" ; sc:url "https://github.com/imandehzangi/OCSVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0208, edam:topic_2640, edam:topic_3577 ; sc:citation ; sc:description """An open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. All files can be found on the Chen Lab RNA-Seq server: /home/ubuntu/chenlab_v2/proj/PatrickN/desktop_pipeline_v0.1/. OCTAD:Open Cancer Therapeutic Discovery. Bin Chen, PhD. MSU. contact: Bin.Chen@hc.msu.edu. This version includes some new data files, so be sure to download those from the above directory. The pipeline is configured to run within the folder structure as found in the above directory. William Zeng. MD Candidate. UCSF. contact: billy.zeng@ucsf.edu. Please contact Patrick: patrick.newbury@hc.msu.edu with any issues. https://s3-us-west-2.amazonaws.com/chenlab-data-public/octad In the parent folder for this pipeline, create a folder named "data". Place all files from this download into this data folder. Consolidated many data files into new files: CCLE_OCTAD.RData, metadata.RData""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3463 ; sc:name "OCTAD" ; sc:url "http://octad.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0593, edam:topic_0749 ; sc:citation ; sc:description """A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data. Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy data. OCTAVVS is a set of graphical tools for high-throughput preprocessing and analysis of vibrational spectroscopy data. Currently, the preprocessing is primarily geared towards images from infrared absorption spectroscopy with focal plane array detectors""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3443 ; sc:license "MIT" ; sc:name "OCTAVVS" ; sc:url "http://pypi.org/project/octavvs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3168, edam:topic_3382 ; sc:citation , "pubmed:31658504" ; sc:description """Open-source add-on kit for automation of zone elution in planar chromatography. Follow this link to download an image of raspbian with the OC_manager set-up, last update: 20180605. Shiny app to operate apparatus of office chromatography.""" ; sc:featureList edam:operation_3799 ; sc:name "OC_manager" ; sc:url "https://github.com/OfficeChromatography/OC_manager" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0209, edam:topic_3399 ; sc:citation , "pmcid:PMC6509876", "pubmed:31074377" ; sc:description "Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions." ; sc:featureList edam:operation_3280, edam:operation_3431, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ODAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ODAE-ontology/ODAE" ; biotools:primaryContact "Oliver He" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3475 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3475 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3604 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071, edam:topic_3473, edam:topic_3678 ; sc:author ; sc:citation , "pubmed:33319910" ; sc:description "ODAM (Open Data for Access and Mining) is an Experiment Data Table Management System (EDTMS) that makes research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ODAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1.2" ; sc:url "https://inrae.github.io/ODAM/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC6882730", "pubmed:31781773" ; sc:description """A manually curated database of noncoding RNAs associated with orthopedics. Harbin Medical University, China""" ; sc:featureList edam:operation_2421 ; sc:name "ODNA" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/ODNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0769 ; sc:citation , "pmcid:PMC6501302", "pubmed:31060495" ; sc:description "Consistency pipeline for hierarchies of orthologous groups (OGs) based on subsampling and tree reconciliation." ; sc:featureList edam:operation_0544, edam:operation_0555, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OG" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/meringlab/og_consistency_pipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0804, edam:topic_3400 ; sc:citation , "pubmed:31566225" ; sc:description "A reference database of inferred immune receptor genes | Welcome to OGRDB - the curated Open Germline Receptor Database! | OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly" ; sc:featureList edam:operation_3196, edam:operation_3431 ; sc:name "OGRDB" ; sc:url "https://ogrdb.airr-community.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3293 ; sc:citation , "pubmed:31612943" ; sc:description """A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vertebrate Genomes. OHNOLOGS version 2.0 is now live with more genomes and more genome duplications!. Singh P.P. and Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Singh PP & Isambert H. (2019) OHNOLOGS v2: A comprehensive resource for the genes retained from whole genome duplication in vertebrates. Nucleic Acids Research. Full text.""" ; sc:featureList edam:operation_0224, edam:operation_0310 ; sc:name "OHNOLOGS v2" ; sc:url "http://ohnologs.curie.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0622, edam:topic_3293, edam:topic_3697 ; sc:citation ; sc:description """Estimating Natural Selection to Predict Functional Overlapping Genes. Program for estimating dN/dS in overlapping genes (OLGs). OLGenie is a Perl program for estimating dN/dS to detect selection and function in overlapping genes (OLGs). It relies on no external dependencies, facilitating maximum portability. Just download and run""" ; sc:featureList edam:operation_0362, edam:operation_2454, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "OLGenie" ; sc:url "https://github.com/chasewnelson/OLGenie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_2269 ; sc:citation , "pubmed:31688931" ; sc:description """Determining significance of total overlap length between genomic regions sets. MOTIVATION:Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive p-value. RESULTS:Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported.""" ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "OLOGRAM" ; sc:url "https://github.com/dputhier/pygtftk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885 ; sc:citation ; sc:description "Alignment tool for optical mapping using a seed-and-extend approach." ; sc:featureList edam:operation_0491, edam:operation_3216, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMBlast" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/TF-Chan-Lab/OMBlast" ; biotools:primaryContact "Kevin Y. Yip", "Ting-Fung Chan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3174 ; sc:citation , "pmcid:PMC6612865", "pubmed:31510667" ; sc:description "Locality-sensitive hashing for the edit distance | We have provided the resources necceasary to generate the figures from ``Locality sensitive hashing for the edit distance'' by Guillaume Marçais, Dan DeBlasio, Prashant Pandey, and Carl Kingsford. Which is to appear inthe proceedings of ISMB/ECCB 2019 | The two main directories contain the necceasry code to produce the phylogeny figures (is_trees) and the random sequences figure (random_sequences). All of the figure generation is performed in a combination of perl and python. The omh_compute directory contains the code neccesary for the figure generation and is written in c++. This directory needs to be compiled before anything can be run in the other two" ; sc:featureList edam:operation_0310, edam:operation_3096 ; sc:name "OMH" ; sc:url "http://github.com/Kingsford-Group/omhismb2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6444640", "pubmed:30940089" ; sc:description "Method for the statistical analysis of RNA-Seq paired design data." ; sc:featureList edam:operation_3223, edam:operation_3436, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:name "OMICfpp" ; sc:url "http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15473683" ; sc:description "The Open Mass Spectrometry Search Algorithm (OMSSA) is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. It is developed at the National Center for Biotechnology Information." ; sc:name "OMSSA" ; sc:url "https://pubchem.ncbi.nlm.nih.gov/omssa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3174 ; sc:citation ; sc:description "Ontology-based, data-driven metadata tracking system." ; sc:featureList edam:operation_2422, edam:operation_3352, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JCVenterInstitute/OMeta-Public" ; biotools:primaryContact "J. Craig Venter Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3334, edam:topic_3512 ; sc:citation , "pmcid:PMC6734442", "pubmed:31500643" ; sc:description "516 unique variants and 831 patients registered in an updated centralized Variome database | OPA1 (optic atrophy 1 (autosomal dominant)) | Autosomal dominant optic atrophy (DOA, Kjer type, MIM#165500) is characterized by moderate to severe loss of visual acuity with insidious onset in early childhood, blue-yellow dyschromatopsia and central scotoma" ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3431 ; sc:name "OPA1" ; sc:url "https://www.lovd.nl/OPA1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3421, edam:topic_3855 ; sc:citation ; sc:description "Open Source Solution for Real-time Peri-event Time Histogram Based on Open Ephys | Online Peri-Event Time Histogram for open ephys | Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them | conda create --name opeth --file requirements.txt python" ; sc:name "OPETH" ; sc:url "https://github.com/hangyabalazs/opeth.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3981 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:author , ; sc:citation , "pubmed:19714772" ; sc:description "OPRA (Optimal Protein-RNA Area) is useful for identifying potential RNA-binding sites on proteins and can help to model protein-RNA interactions of biological and therapeutic interest." ; sc:featureList edam:operation_3902 ; sc:name "OPRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Barcelona Supercomputing Center" ; sc:softwareHelp , ; sc:url "https://life.bsc.es/pid/opra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3407, edam:topic_3421 ; sc:citation , "pubmed:31720757" ; sc:description """High nodal FDG uptake increases risk of distant metastasis in patients with oropharyngeal squamous cell carcinoma. BACKGROUND:The purpose of this study was to investigate if FDG uptake metrics in primary tumor and lymph node metastases in patients with oropharyngeal squamous cell carcinoma (OPSCC) has a prognostic value beyond UICC8 staging in a multiple endpoint model. METHODS:Patients with OPSCC treated with primary radiotherapy at Rigshospitalet in the period 2010-2017 were included. All patients had a pretreatment FDG PET CT scan performed. Four cause-specific Cox regression models were built for the hazard ratios (HR) of recurrence in T-, N-, M-site, and death with no evidence of disease (NED), respectively. The following variables were included: T-, N-stage, p16 status, metabolic tumor volume, and FDG uptake in both primary tumor and lymph nodes.""" ; sc:featureList edam:operation_3659 ; sc:name "OPSCC" ; sc:url "https://rasmussen.shinyapps.io/OPSCCmodelFDG_PET/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6521604", "pubmed:30819774" ; sc:description "Algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis." ; sc:featureList edam:operation_0415, edam:operation_3196, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OPTIMIR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/FlorianThibord/OptimiR" ; biotools:primaryContact "Florian Thibord" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6832278", "pubmed:31623266" ; sc:description """Accurate and Robust Monocular SLAM with Omnidirectional Cameras. A real-time robust monocular visual SLAM system based on ORB-SLAM for fisheye cameras, without rectifying or cropping the input images. We develop an improved monocular visual SLAM system by using omnidirectional cameras. Our method extends the ORB-SLAM2 framework with the enhanced unified camera model (EUCM) as a projection function, which can be applied to catadioptric systems and wide-angle fisheye cameras. Without rectifying or cropping the input images, the proposed system can use the full area of the images even with strong distortion.""" ; sc:featureList edam:operation_2429, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "ORB-SLAM" ; sc:url "https://github.com/lsyads/fisheye-ORB-SLAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3500 ; sc:citation , "pmcid:PMC6389317", "pubmed:30517749" ; sc:description "Automatic web tool for phylogenetically inferring bilaterian orthogroups with user-selected taxa." ; sc:featureList edam:operation_0544, edam:operation_0552, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ORTHOSCOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.orthoscope.jp" ; biotools:primaryContact "Jun Inoue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3172, edam:topic_3295 ; sc:citation , "pmcid:PMC6537380", "pubmed:31138268" ; sc:description "OSCA (OmicS-data-based Complex trait Analysis) is a software tool for the analysis of complex traits using multi-omics data." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OSCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cnsgenomics.com/software/osca/#Overview" ; biotools:primaryContact "Futao Zhang", "Jian Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0632, edam:topic_2885 ; sc:citation , "pmcid:PMC6482647", "pubmed:31040636" ; sc:description "Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer." ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OSTRFPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/vivekmathema/OSTRFPD" ; biotools:primaryContact "Mallika Imwong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC6817837", "pubmed:31749633" ; sc:description """Gene Expression-Based Survival Analysis Web Tool For Adrenocortical Carcinoma. Gene expression profiling data with long-term clinical follow-up information are great resources to screen, develop, evaluate and validate prognostic biomarkers in translational cancer research. However, an easy-to-use interactive online tool is needed to analyze these profiling and clinical data. In the current work, we developed OSacc (Online consensus Survival analysis of ACC), a web tool that provides rapid and user-friendly survival analysis based on seven independent transcriptomic profiles with long-term clinical follow-up information of 259 ACC patients gathered from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. OSacc allows researchers and clinicians to evaluate the prognostic value of genes of interest by Kaplan-Meier (KM) survival plot with hazard ratio (HR) and log-rank test in ACC.""" ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:name "OSacc" ; sc:url "http://bioinfo.henu.edu.cn/ACC/ACCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31512935" ; sc:description "An online survival analysis web server to evaluate the prognostic value of biomarkers in cervical cancer | Aim: To establish a web server that can mutually validate prognostic biomarkers of cervical cancer. Methods: Four datasets including expression profiling and relative clinical follow-up data were collected from Gene Expression Omnibus and The Cancer Genome Atlas. The web server was developed by R software. Results: The web server was named OScc including 690 patients and can be accessed at http: bioinfo.henu.edu.cn CESC CESCList.jsp. The Kaplan-Meier survival curves with log-rank p-value and hazard ratio will be generated of interested gene in OScc. Compared with previous predictive tools, OScc had the advantages of registration-free, larger sample size and subgroup analysis. Conclusion: The OScc is highly valuable to perform the preliminary assessment and validation of new or interested prognostic biomarkers for cervical cancer" ; sc:name "OScc" ; sc:url "http://bioinfo.henu.edu.cn/CESC/CESCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3360, edam:topic_3379 ; sc:citation , "pubmed:31646691" ; sc:description """An interactive online consensus survival tool for uveal melanoma prognosis analysis. Uveal melanoma (UM) is a rare, aggressive, but the most frequent primary intraocular malignancy in adults, and up to 50% of patients develop a tendency of liver metastases. Great efforts have been made to develop biomarkers that facilitate diagnosis, prediction of the risk, and response to treatment of UM. However, a biologically informative and highly accurate gold standard system for prognostic evaluation of UM remains to be established. To facilitate assessment of the prognosis of UM patients, we established a user-friendly Online consensus Survival tool for uveal melanoma, named OSuvm, by which users can easily estimate the prognostic values of genes of interest by the Kaplan-Meier survival plot with hazard ratio and log-rank test.""" ; sc:featureList edam:operation_2495, edam:operation_3503 ; sc:name "OSuvm" ; sc:url "http://bioinfo.henu.edu.cn/UVM/UVMList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3292, edam:topic_3895 ; sc:citation , "pmcid:PMC6660583", "pubmed:31372451" ; sc:description "An overlapping DNA fragments generator for molecular cloning and synthetic biology | Reference: Ferreira-Junior, J.R.S. ; Digiampietri, L.A. . OVERFRAG: an Overlapping Fragments Generator for Molecular Cloning and Synthetic Biology. Proceedings of the XLII Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (SBBq), pp. 2, 2013" ; sc:name "OVERFRAG" ; sc:url "http://www.each.usp.br/digiampietri/overfrag" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Quercus robur annotation database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "OakMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2.3" ; sc:url "https://urgi.versailles.inra.fr/OakMine_PM1N" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_3464 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929, edam:format_3464 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1138 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Pfam accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:encodingFormat edam:format_1370 ; sc:name "Hidden Markov model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508, edam:format_3579, edam:format_3603, edam:format_3604 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1984 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_3752 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3174, edam:topic_3387, edam:topic_3941 ; sc:citation , "pubmed:29788376" ; sc:description """The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.""" ; sc:featureList edam:operation_0292, edam:operation_0567, edam:operation_0573, edam:operation_3478, edam:operation_3799 ; sc:funder "OCEANOMICS" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Ocean Gene Atlas" ; sc:provider "MIO" ; sc:softwareHelp , ; sc:url "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3068, edam:topic_3489, edam:topic_3500 ; sc:citation ; sc:description """An online database for the dragonflies and damselflies of Bangladesh. Welcome to the Odonata of Bangladesh, database of the dragonflies and damselflies of Bangladesh. Situated in the South-east Asia, Bangladesh is gifted with the rich network of water resources like ponds, lakes, marshes, rivers, streams and mangrove swamps. This diverse range of water bodies along with many tropical forest patches has generated suitable habitat for many Odonata species. Till date, nearly hundred species of Odonates have been recorded from Bangladesh. The current project, supported by Rufford Small Grant, is designed to assemble and disseminate information of diversity, ecology and behavior of the Bangladeshi dragonflies and damselflies.""" ; sc:name "OdoBD" ; sc:url "http://www.odobd.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0625, edam:topic_0637, edam:topic_3293, edam:topic_3489 ; sc:citation , "pmcid:PMC6908694", "pubmed:31831730" ; sc:description """New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical information collected from various sources. Complete Database Variable Definitions""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196, edam:operation_3431 ; sc:name "Odonate Phenotypic Database" ; sc:url "http://www.odonatephenotypicdatabase.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_1775, edam:topic_3063, edam:topic_3325 ; sc:author "Alexandre Renaux" ; sc:citation ; sc:description "ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques." ; sc:featureList edam:operation_0331, edam:operation_3083, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Oligogenic resource for variant analysis (ORVAL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Interuniversity Institute of Bioinformatics in Brussels" ; sc:softwareHelp , ; sc:softwareVersion "3.0.0" ; sc:url "https://orval.ibsquare.be" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3050 ; sc:citation , "pmcid:PMC6783963", "pubmed:31443503" ; sc:description "High Biodiversity Arises from the Analyses of Morphometric, Biochemical and Genetic Data in Ancient Olive Trees of South of Italy | Multivariate analysis of data and geographic display of results | OliveR is an R package containing a shiny application that provides a vast series of statistical tools for exploring and analyzing both quantitative (such as morphometric or biochemical) and genetic data that can be associated to geographical coordinates. Through the use of shapefiles, the application allows visualizing both data and results of a statistical analysis directly on a geographical basis" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "OliveR" ; sc:url "https://github.com/nicocriscuolo/OliveR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3172 ; sc:citation ; sc:description "Utilizing Omics Data to Explore and Visualize Kinase-Substrate Interactions | Protein phosphorylation is one of the most prevalent post-translational modifications where kinases phosphorylate their selected substrates to maintain proper signal transduction in order to regulate cellular processes. Omic-Sig is developed to stratify phospho-substrates and their associated kinases by computing and ranking the differential abundances between paired samples (e.g., Tumor and its adjacent normal tissue). The differential abundances are calculated using mass spectrometry-based phosphoproteomics and global proteomics data as well as transcriptome data from RNA-Seq. Omic-Sig also provides visualization of the computational results" ; sc:featureList edam:operation_0417 ; sc:license "Apache-2.0" ; sc:name "Omic-Sig" ; sc:url "https://github.com/hzhangjhu/Omic-Sig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC6842565", "pubmed:31720124" ; sc:description """Competing endogenous RNA (ceRNA) hypothetic model based on comprehensive analysis of long non-coding RNA expression in lung adenocarcinoma. OmicShare Tools为完全免费开放生物信息云工具网站。OmicShare Tools云平台所涵盖的生物信息基础工具全面,云平台中所有工具皆为基迪奥开发,操作简单方便,工具输出结果可直接用于SCI文章发表。. 如果您在数据处理过程中,使用了OmicShare Tools完成了分析或在OmicShare Forum得到了有价值的帮助,我们期望您在论文发表时,在方法学部分或致谢部分引用或提及OmicShare平台。例如:XXXX analysis was performed using the OmicShare tools,a free online platform for data analysis (http://www.omicshare.com/tools)。这样便于更多的同行了解和分享OmicShare平台。.""" ; sc:featureList edam:operation_2495, edam:operation_3083, edam:operation_3799 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "OmicShare" ; sc:url "http://www.omicshare.com/tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC6839229", "pubmed:31703610" ; sc:description """A R package for integration of multi-omics datasets via association rules mining. tool for the analysis of multimodal high-throughput data. OmicsARules is a tool for the analysis of multi-omics high-throughput data based on the use of association rules mining. OmicsARules supports to identify recurrent and associated patterns, and provides a new dimension for exploring single or multiple omics data across sequencing platforms or across samples. Besides, a new rule-interestingness measure Lamda3 is embeded in OmicsARules, it can be used to evaluate the association rules and identify biologically significant patterns. Association rule mining and visualizing were implemented in R environment using package arules and ggplot2""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2495 ; sc:name "OmicsARules" ; sc:url "https://github.com/BioinformaticsSTU/OmicsARules" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_3172 ; sc:citation ; sc:description "Associate Omics Data with Phenotypes in One-Click | a tool kit for visualization and analysis of omics data | click here or paste the repo URL:https://github.com/huizhanglab-jhu/OmicsOne.git to https://gke.mybinder.org/ as below: | Try without installation via mybinder.org" ; sc:featureList edam:operation_2939, edam:operation_3501, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "OmicsOne" ; sc:url "https://github.com/huizhanglab-jhu/OmicsOne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3174 ; sc:citation ; sc:description "A web server for integrated OMICS analysis | OmicsX is a user-friendly web server for integration and comparison of different omic datasets with optional sample annotation information. The tool includes four modules for gene-wise correlation, sample-wise correlation, subtype clustering, and differential expression. OmicsX provides researchers the analysis results including inter-omics correlations, conservative clusters, differential expressions, enriched biological pathways and associated phenotypes with visualization, searching, and data downloading, thus help to suggest the biological indications from the comparison of different omic data" ; sc:featureList edam:operation_2436, edam:operation_3891 ; sc:name "OmicsX" ; sc:url "http://bioinfo.wilmer.jhu.edu/OmicsX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation ; sc:description "A comprehensive integrated resource of signaling pathways in activity flow representation, enzyme-substrate interactions in protein post-translational modifications, protein complexes, protein annotations and protein roles in inter-cellular signaling." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "OmniPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://omnipathdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Unifying single-cell annotations based on the Cell Ontology. Single cell typing based on cell ontology. please see the document of OnClass at https://onclass.readthedocs.io/en/latest/""" ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:name "OnClass" ; sc:url "https://onclass.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC6918570", "pubmed:31847870" ; sc:description """Hierarchical domain structure reveals the divergence of activity among TADs and boundaries. An Optimized Nested TAD caller for Hi-C data. OnTAD is an Optimized Nested TAD caller for Hi-C data. OnTAD [-penalty ] [-maxsz ] [-minsz ] [-ldiff ] [-lsize ] [-bedout ] [-log2] [-o output_file]""" ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_3435 ; sc:license "MIT" ; sc:name "OnTAD" ; sc:url "https://github.com/anlin00007/OnTAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6881748", "pubmed:31828101" ; sc:description """Bioinformatics Analysis Identified Key Molecular Changes in Bladder Cancer Development and Recurrence. Here you can link TCGA survival data to mRNA, miRNA, or lncRNA expression levels. To get started simply input either a Tier 3 TCGA mRNA, miRNA, or MiTranscriptome beta lncRNA. More information can be found at this publication, youtube, or Omnes Res. News. A pan-cancer analysis using data in OncoLnc: OncoRank.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:name "OncoLnc" ; sc:url "http://www.oncolnc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0128, edam:topic_0202, edam:topic_2640 ; sc:citation , "pubmed:31583637" ; sc:description """Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of new mechanisms to control tumorigenesis through the integration of genomic, pharmacological, clinical, and structural data with the network of cancer-associated protein-protein interactions experimentally detected in cancer cells.""" ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3083, edam:operation_3439 ; sc:name "OncoPPi" ; sc:url "http://oncoppi.emory.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3421, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC6836658", "pubmed:31699073" ; sc:description """An authentic learning approach to teaching cancer genomics. On this site you can both (a) make and upload, and (b) download and analyse simulated patient case studies.""" ; sc:featureList edam:operation_3216, edam:operation_3283, edam:operation_3907 ; sc:name "OncoWiki" ; sc:url "https://www.oncowiki.co.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation , "pubmed:31369060" ; sc:description "A sequence-based clustering method to identify cancer drivers" ; sc:license "GPL-3.0" ; sc:name "OncodriveCLUSTL" ; sc:url "https://bitbucket.org/bbglab/oncodriveclustl/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3314 ; sc:citation , "pubmed:31846323" ; sc:description """An Ontology for Chemical Kinetic Reaction Mechanisms. A knowledge-graph built with the integration of semantic technologies and software agents for enhancing the experience of chemists in querying chemical kinetic reaction mechanisms. This User Interface (UI) demonstrates the query capability of OntoKin""" ; sc:featureList edam:operation_0224, edam:operation_3280, edam:operation_3454 ; sc:name "OntoKin" ; sc:url "http://www.theworldavatar.com/kb/ontokin/ontokin.owl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3500 ; sc:citation ; sc:description """Musculoskeletal optimal control. OpenSim Moco solves optimal control problems with musculoskeletal models defined in OpenSim, using direct collocation. OpenSim Moco is a software toolkit to solve optimal control problems with musculoskeletal models defined in OpenSim, including those with kinematic constraints. Using the direct collocation method, Moco can solve a wide range of problems, including motion tracking, motion prediction, and parameter optimization. The design of Moco focuses on ease-of-use, customizability, and extensibility. Just like OpenSim itself, Moco has interfaces in XML/command-line, Matlab, Python, Java, and C++.""" ; sc:featureList edam:operation_2426 ; sc:name "Open-Sim Moco" ; sc:url "https://simtk.org/projects/opensim-moco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC6398228", "pubmed:30832730" ; sc:description "Tool for assessing taxonomic metagenome profilers. Implements commonly used performance metrics together with convenient visualizations." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Open-community Profiling Assessment tooL (OPAL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CAMI-challenge/OPAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6355034", "pubmed:30657753" ; sc:description "Open-source and scalable computer-assisted sperm analysis (CASA) tool. Allows users to study three classical sperm quality parameters: motility, morphometry and membrane integrity (viability) and offers the possibility of analyzing the guided movement response of spermatozoa to different stimuli or different motile cells." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OpenCASA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/calquezar/OpenCASA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0634, edam:topic_0769, edam:topic_2640 ; sc:citation ; sc:description """Open source collaborative platform for the annotation of human genetic variation. A modular annotation tool for genomic variants. Open-CRAVAT is a python package that performs genomic variant interpretation including variant impact, annotation, and scoring. It has a modular architecture with a wide variety of analysis modules that are developed both by the CRAVAT team and the broader variant analysis community. Open-CRAVAT is a product of the Karchin Lab at Johns Hopkins University in collaboration with In Silico Solutions with funding provided by the National Cancer Institute's ITCR program. Open Custom Ranked Analysis of Variants Toolkit. CRAVAT 5 is in GRCh38/hg38. If you need to annotate GRCh37/hg19 variants, check the hg19 box under Input section or use CRAVAT 4 which is in GRCh37/hg19. Documentation and Getting Started. Get started with OpenCRAVAT here or with `pip install open-cravat`.""" ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "OpenCRAVAT" ; sc:url "https://opencravat.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0634, edam:topic_3382 ; sc:citation ; sc:description """Robotic microscopy for everyone. The OpenFlexure project, which aims to make high precision mechanical positioning available to anyone with a 3D printer - for use in microscopes, micromanipulators, and more. http://openflexure.org.""" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:name "OpenFlexure" ; sc:url "https://gitlab.com/openflexure/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6860425", "pubmed:31738777" ; sc:description """Improved cortical boundary registration for locally distorted fMRI scans. An MRI analysis toolbox, primarily for laminar analysis. In order to protect your privacy, we only use cookies that are essential for the functioning of this website. Many of the functions for general fMRI preprocessing are wrappers for existing well-established neuroimaging tools. The wrappers should be seen as a consistent MATLAB command line interface to these functions, not as a reimplementation. A large part of these functions are written for my own convenience. A substantial part is new method development, mainly regarding laminar analysis. From this project root, run tvm_installLaminarAnalysisToolbox.m in MATLAB.""" ; sc:featureList edam:operation_3435, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "OpenFmriAnalysis" ; sc:url "https://github.com/TimVanMourik/OpenFmriAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:description "A PyTorch framework for tertiary protein structure prediction." ; sc:featureList edam:operation_0474, edam:operation_0477 ; sc:license "MIT" ; sc:name "OpenProtein" ; sc:softwareVersion "0.0.1" ; sc:url "https://openprotein.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3246, edam:format_3475 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3245, edam:format_3710 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3621, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475, edam:format_3621, edam:format_3833 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3621, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:24727770" ; sc:description "OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS." ; sc:featureList edam:operation_0335, edam:operation_3203, edam:operation_3215, edam:operation_3628, edam:operation_3649 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "OpenSWATH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "OpenMS 2.4.0" ; sc:url "http://www.openswath.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data." ; sc:featureList edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "OpenSegSPIM" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://opensegspim.weebly.com/" ; biotools:primaryContact "Laurent Gole", "Sohail Ahmed", "Weimiao Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3067, edam:topic_3068, edam:topic_3300, edam:topic_3304 ; sc:citation , "pmcid:PMC5007758", "pubmed:27635225" ; sc:description """Unit testing, model validation, and biological simulation. Unified, simple data access python library for data & facts about C. elegans anatomy. A data access layer in Python which integrates disparate structures and representations for C. elegans anatomy and physiology. Enables a simple Python API for asking various questions about the cells of the C. elegans and enabling data sharing for the purpose of building a data-to-model pipeline for the OpenWorm project. OpenWorm is an open source project dedicated to creating a virtual C. elegans nematode in a computer. The web client of a Geppetto application. We're exploring the development of the worm via DevoWorm, an interdisciplinary project under the OpenWorm umbrella, focused on developmental processes in Nematodes and other forms of life through data analysis, visualization, and simulation.""" ; sc:featureList edam:operation_2422, edam:operation_2426, edam:operation_2428 ; sc:license "MIT" ; sc:name "OpenWorm" ; sc:url "http://www.openworm.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pubmed:28289778" ; sc:description "Open Source Registry System for Rare Diseases (OSSE) - software for the creation of patient registries. Necessary interoperability between different registries is supported from the start and allows to federate those registries on a national and international level." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "OSSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "https://www.osse-register.de/en/" ; biotools:primaryContact "Holger Storf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3336, edam:topic_3391 ; sc:description """Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritise drug targets. Through large-scale genomic experiments and the development of innovative computational techniques, the partnership aims to help researchers select the best targets for the development of new therapies. At the heart of Open Targets is a consortium of complementary partner institutions that bring their respective expertise and capabilities to collaborative experimental and informatics projects. Bridging the gap between academic research and pharmaceutical drug development, Open Targets has made significant contributions to understanding the relationships between targets and diseases, established leading informatics tools in the Open Targets Platform and Open Targets Genetics, and contributed to global initiatives such as the Cancer Dependency Map.""" ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "Open Targets" ; sc:softwareHelp ; sc:url "https://www.opentargets.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0208, edam:topic_2259, edam:topic_3336, edam:topic_3342, edam:topic_3391, edam:topic_3574 ; sc:citation , , , , "pmcid:PMC5210543", "pmcid:PMC6324073", "pmcid:PMC7779013", "pmcid:PMC9825572", "pubmed:27899665", "pubmed:30462303", "pubmed:33196847", "pubmed:36399499" ; sc:description """The Open Targets Platform is a comprehensive tool that supports systematic identification and prioritisation of potential therapeutic drug targets. By integrating publicly available datasets including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships. The Platform is a freely available resource that is actively maintained with bi-monthly updates. The data can be accessed through an intuitive web user interface, an API, Google BigQuery, and a comprehensive set of datasets available for download in JSON and Parquet formats. The pipeline and infrastructure codebases that support the Platform are open-source and can be used to create a self-hosted private instance of the Platform with custom data.""" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Open Targets Platform" ; sc:softwareHelp , , , , ; sc:url "https://platform.opentargets.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_3385, edam:topic_3452, edam:topic_3794 ; sc:citation , "pmcid:PMC6821862", "pubmed:31666606" ; sc:description """Open-source optical projection tomography of large organ samples. The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice.""" ; sc:featureList edam:operation_0337 ; sc:name "OptiJ" ; sc:url "https://lag-opt.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "An open-source whole slide image analysis tool | Orbit has many build-in image analysis algorithms. Tissue quantification using machine learning techniques, object / cell segmentation, and object classification are the basic ones. Region of interest (ROI) can be defined by manual annotations or via a trainable exclusion map. Everything can be combined | Sophisticated Image Analysis Algorithms" ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:name "Orbit" ; sc:softwareHelp ; sc:url "http://www.orbit.bio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3068 ; sc:citation ; sc:description "Visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples." ; sc:featureList edam:operation_1812, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "Ordino" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ordino.caleydoapp.org/" ; biotools:primaryContact "Caleydo Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0194, edam:topic_0797, edam:topic_3293 ; sc:citation , , "pmcid:PMC4531804", "pubmed:26243257" ; sc:description "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses." ; sc:featureList edam:operation_0324, edam:operation_0540, edam:operation_3182, edam:operation_3209 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OrthoFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/davidemms/OrthoFinder" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , , "pmcid:PMC3196566", "pmcid:PMC403725", "pubmed:12952885", "pubmed:21901743" ; sc:description "Orthologs are homologs seperated by speciation events. Paralogs are homologs separated by duplication events. Detection of orthologs is becoming much more important with the rapid progress in genome sequencing." ; sc:featureList edam:operation_0553, edam:operation_3942 ; sc:name "OrthoMCL" ; sc:url "https://github.com/stajichlab/OrthoMCL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC6602458", "pubmed:31053848" ; sc:description "Web server for whole-genome comparison and annotation of orthologous clusters across multiple species." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "OrthoVenn2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://orthovenn2.bioinfotoolkits.net" ; biotools:primaryContact "Yi Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3360, edam:topic_3399 ; sc:citation , "pmcid:PMC6487800", "pubmed:31086734" ; sc:description "Human osteoporosis-related gene database." ; sc:featureList edam:operation_2495, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "OsteoporosAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biokb.ncpsb.org/osteoporosis/" ; biotools:primaryContact "Dong Li", "Yang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:citation , "pmcid:PMC6923414", "pubmed:31857603" ; sc:description """A novel tool for predicting unconventional protein secretion. OutCyte, as a versatile tool, can predict input proteins as signal-peptide containing, transmembrane-domain containing, intracellular or unconventionally secreted""" ; sc:featureList edam:operation_0269, edam:operation_0418, edam:operation_3767 ; sc:name "OutCyte" ; sc:url "http://www.outcyte.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6717506", "pubmed:31523522" ; sc:description "A visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling | With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial" ; sc:featureList edam:operation_0323, edam:operation_0552, edam:operation_0557 ; sc:name "OutbreakFinder" ; sc:url "https://github.com/skypes/Newton-method-MDS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "Parallel processing pipeline software for automatic analysis of bisulfite sequencing data." ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "P3BSseq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/p3bsseq/wiki/Home/" ; biotools:primaryContact "Marcos J. Araúzo-Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_0623, edam:topic_0736 ; sc:citation , "pubmed:31584628" ; sc:description """Fast and Flexible Coarse-grained Prediction of Protein Folding Routes using Ensemble Modelling and Evolutionary Sequence Variation. Predicting Protein Folding Routes.""" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_0474, edam:operation_2415, edam:operation_3439 ; sc:name "P3Fold" ; sc:url "http://csb.cs.mcgill.ca/P3Fold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6668381", "pubmed:31366994" ; sc:description "Prediction of N4-acetylcytidine (ac4C) modification sites in mRNA | prediction of acetylation sites in mRNA | PACESPrediction of ac4C(N4-acetylcytidine) sites in mRNA | Citation:Zhao W., Zhou Y., Cui Q. & Zhou Y. PACES: prediction of N4-acetylcytidine (ac4C) modification sites in mRNA. Sci Rep 9, 11112, doi:10.1038/s41598-019-47594-7 (2019)" ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3431 ; sc:name "PACES" ; sc:url "http://www.rnanut.net/paces/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_0821 ; sc:citation , "pubmed:31786268" ; sc:description """Characterizing and Predicting Protein Hinges for Mechanistic Insight. PACKMAN: PACKing and Motion ANalysis""" ; sc:featureList edam:operation_0244, edam:operation_1843, edam:operation_2476 ; sc:name "PACKMAN" ; sc:url "https://PACKMAN.bb.iastate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_0820 ; sc:citation , "pubmed:31120747" ; sc:description "Generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PACKMOL-Memgen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ambermd.org/AmberTools.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_1637, edam:format_2585 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:author "Méziane Aite" ; sc:citation , , , "pmcid:PMC5988327", "pubmed:29791443", "pubmed:31744163" ; sc:description "Portable Database for Metabolism. It is a format to centralizes, in a new graph-based PADMet, all information about a metabolic network. It also provides methods to import, to update, to analyse and to export data, in a library." ; sc:featureList edam:operation_2409, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PADMet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/AuReMe/padmet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_0654, edam:topic_3292, edam:topic_3489 ; sc:citation , "pubmed:31620779" ; sc:description """A database of prokaryotic defense systems related genes. Procaryotic Antiviral Defense System. procaryotic database, defense system database, pangenome database. PADS Arsenal A Database of Prokaryotic Defense Systems Related Genes.""" ; sc:featureList edam:operation_0337, edam:operation_0435, edam:operation_2422 ; sc:name "PADS Arsenal" ; sc:url "https://bigd.big.ac.cn/padsarsenal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation ; sc:description "PAFScaff (Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding) is designed for mapping genome assembly scaffolds to a closely-related chromosome-level reference genome assembly. It uses (or runs) Minimap2 to perform an efficient (if rough) all- against-all mapping, then parses the output to assign assembly scaffolds to reference chromosomes." ; sc:featureList edam:operation_0523 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PAFScaff" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "v0.2.1" ; sc:url "https://github.com/slimsuite/pafscaff/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation "pubmed:31797610" ; sc:description """Interpretable and Integrative Deep Learning for Survival Analysis Using Histopathological Images and Genomic Data. A biologically interpretable integrative deep learning model that integrates PAthological images and GEnomic data. PAGE_net_pretrain : code for pretraining and saving the pretrained model. Integration of aggregated pathological images and genomic data""" ; sc:featureList edam:operation_3436 ; sc:name "PAGE-Net" ; sc:url "https://github.com/DataX-JieHao/PAGE-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3047 ; sc:citation ; sc:description """A Pathway Graph Kernel based Multi-Omics Clustering Approach for Discovering Cancer Patient Subgroups. Install dependencies: if using virtual env omit --user parts. pip install -r requirements.txt --user. For mosek set environment variable MOSEKLM_LICENSE_FILE to your license file install mosek package with""" ; sc:featureList edam:operation_3432, edam:operation_3436, edam:operation_3454 ; sc:name "PAMOGK" ; sc:url "https://pypi.org/project/pamogk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2269 ; sc:citation ; sc:description "Tool for statistical analysis and visualization of quantitative proteomics data" ; sc:featureList edam:operation_2939, edam:operation_3557, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "PANDA-view" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/panda-view/" ; biotools:primaryContact "Cheng Chang", "Yunping Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3305, edam:topic_3321, edam:topic_3324, edam:topic_3673 ; sc:citation , "pmcid:PMC6922483", "pubmed:31815935" ; sc:description """Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis-a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance""" ; sc:featureList edam:operation_0484, edam:operation_3198, edam:operation_3227, edam:operation_3432 ; sc:name "PANPASCO" ; sc:url "https://gitlab.com/rki_bioinformatics/panpasco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3306 ; sc:citation ; sc:description "Ultrafast and accurate clustering of phenotypic data of millions of single cells | PARC, “phenotyping by accelerated refined community-partitioning” - is a fast, automated, combinatorial graph-based clustering approach that integrates hierarchical graph construction (HNSW) and data-driven graph-pruning with the new Leiden community-detection algorithm" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "PARC" ; sc:url "https://github.com/ShobiStassen/PARC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621 ; sc:description "Program to Assemble Spliced Alignment. PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments." ; sc:featureList edam:operation_0232, edam:operation_0310 ; sc:name "PASA" ; sc:url "https://sourceforge.net/projects/pasa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6343338", "pubmed:30669970" ; sc:description "R package for analyses of alternative polyadenylation (APA) related gene expression, including the characterization of poly(A) sites, quantification of association between genes with/without repeated measurements, clustering of APA-related genes to infer significant APA specific gene modules, and the evaluation of clustering performance with a variety of indexes." ; sc:featureList edam:operation_0313, edam:operation_2495, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PASCCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/BMILAB/PASCCA" ; biotools:primaryContact "Wenbin Ye", "Yuqi Long" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "PASER for automated analysis of neural signals recorded in pulsating magnetic fields | PASER: Processing and Analysis Schemes for Extracellular Recordings | Currently, PASER can only be used with data saved by Open Ephys GUI [Ref. 4], specifically .continuous files. See https://github.com/open-ephys/plugin-GUI or http://www.open-ephys.org/ for more information" ; sc:featureList edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "PASER" ; sc:url "http://github.com/DepartmentofNeurophysiology/Paser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360, edam:topic_3407 ; sc:citation , "pmcid:PMC6296065", "pubmed:30558539" ; sc:description "Pathway-associated sparse deep neural network for prognosis prediction from high-throughput data." ; sc:featureList edam:operation_0277, edam:operation_3439, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PASNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/DataX-JieHao/PASNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157 ; sc:description "The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features. It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system. It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence." ; sc:name "PASTEClassifier" ; sc:url "https://urgi.versailles.inra.fr/Tools/PASTEClassifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6913009", "pubmed:31842968" ; sc:description """Mapping functional elements at single amino acid resolution in human cells. Identification of functional elements for a protein of interest is important for achieving a mechanistic understanding. However, it remains cumbersome to assess each and every amino acid of a given protein in relevance to its functional significance. Here, we report a strategy, PArsing fragmented DNA Sequences from CRISPR Tiling MUtagenesis Screening (PASTMUS), which provides a streamlined workflow and a bioinformatics pipeline to identify critical amino acids of proteins in their native biological contexts. Using this approach, we map six proteins-three bacterial toxin receptors and three cancer drug targets, and acquire their corresponding functional maps at amino acid resolution""" ; sc:featureList edam:operation_0321, edam:operation_1812, edam:operation_2429, edam:operation_3096, edam:operation_3767 ; sc:name "PASTMUS" ; sc:url "https://figshare.com/articles/PASTMUS_mapping_functional_elements_at_single_amino_acid_resolution_in_human_cells/10435370" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0781 ; sc:citation , "pmcid:PMC6736041" ; sc:description "A10 Presence and frequency of M184V mutation in the MOBIDIP trial | AbstractThe MOBIDIP trial evaluated the simplification by protease (PI r) monotherapy for HIV infection versus dual therapy and boosted protease inhibitor plus lamivudine (PI r + 3TC) in controlled patients under second-line regimens. MOBIDIP was interrupted because of a significant number of patients with virological failure (VF) at week 48 (W48) in PI r (33 133, ∼25%) versus in PI r + 3TC (4 132, ∼3%). At the time of first-line VF, 96 per cent of patients harbored the M184V mutation. The presence of the M184V mutation was related to a protective effect against VF in the PI r + 3TC arm. We developed a methodology that allows to determine the frequency of M184V I mutations in the HIV reverse transcriptase (RT) gene in peripheral blood mononuclear cells (PBMC) obtained before MOBIDIP simplification" ; sc:name "PASeq" ; sc:url "https://www.paseq.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC6606892", "pubmed:31101593" ; sc:description "R package for crosstalk correction in Pathway Deregulation Score (PDS) inferred by Pathifier algorithm." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PATHcrosstalk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fabotao/PATHcrosstalk" ; biotools:primaryContact "Botao Fa", "Zhangsheng Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2269, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC6889196", "pubmed:31791231" ; sc:description """A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. “rectal_table”: All the nonsynonymous mutations in TCGA rectal cancer dataset and its coresponding Polyphen-2 scores. The first column is the sample names, the second column is the mutated genes and the third column is the functional impact score corresponding to each mutations. “CoreGroup2Gene.txt”: contains the mapping of pathways to genes (genes entrez id). The first column is the name of pathways, the second column is genes included in the pathways. The file "example1.R” is an example of R codes which read the data file “rectal_table” and “CoreGroup2Gene.txt” and analyze the 9 pathways in “CoreGroup2Gene.txt” together. The file returns “pairprob.txt” which contains the probabilities of A>B, A a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:31790154" ; sc:description """Fusion detection in assembled transcriptomes. Post-Assembly Variant Finder (PAVFinder). PAVFinder is a Python package that detects structural variants from de novo assemblies (e.g. ABySS, Trans-ABySS). As such, it is able to analyse both genome and transcriptome assemblies:.""" ; sc:featureList edam:operation_0524, edam:operation_3227, edam:operation_3258 ; sc:name "PAVFinder" ; sc:url "https://github.com/bcgsc/pavfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3337 ; sc:citation , "pmcid:PMC6612857", "pubmed:31510689" ; sc:description "Efficient haplotype matching between a query and a panel for genealogical search | Efficient haplotype matching between a query and panel using PBWT-Query | Ardalan Naseri, Erwin Holzhauser, Degui Zhi, Shaojie Zhang" ; sc:featureList edam:operation_0487, edam:operation_2421, edam:operation_3211 ; sc:name "PBWT-Query" ; sc:url "http://genome.ucf.edu/pbwt-query" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6538748", "pubmed:31138829" ; sc:description "Principle Component Analysis-based iterative PAM50 subtyping (PCA-PAM50) improves consistency between breast cancer intrinsic and clinical subtyping reclassifying a subset of luminal A tumors as luminal B." ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PCA-PAM50" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "ftp://ftp.wriwindber.org/" ; biotools:primaryContact "Praveen K. Raj Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_2828 ; sc:citation , "pmcid:PMC6849643", "pubmed:31580061" ; sc:description """An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing molecular dynamics trajectories via a web browser. PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables 'plug-and-play' trajectory visualization. Jacob Durrant software July 29, 2019September 30, 2019""" ; sc:featureList edam:operation_1812, edam:operation_2476, edam:operation_2939, edam:operation_3890, edam:operation_3891 ; sc:name "PCAViz" ; sc:url "http://durrantlab.com/pcaviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3170, edam:topic_3179, edam:topic_3315 ; sc:citation , "pmcid:PMC6933681", "pubmed:31881819" ; sc:description """Topological structure analysis of chromatin interaction networks. Analysis and visualisation tools for PCHi-C interaction networks""" ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "PCHi-C" ; sc:url "https://github.com/IMCS-Bioinformatics/PCHiCNetworkExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3293, edam:topic_3360, edam:topic_3810 ; sc:citation , "pmcid:PMC6835207", "pubmed:31696928" ; sc:description """A database of Plant Chloroplast Inverted Repeats. Plant Chloroplast Inverted Repeats. Welcome to PCIR! Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching, and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21,433 IRs, 113 plants chloroplast genomes, 16,948 functional genes and 21,659 visual maps. This database offers an online prediction tool for detecting IRs based on Chloroplast DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_2421 ; sc:name "PCIR" ; sc:url "http://biodb.sdau.edu.cn/pcir/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2269, edam:topic_3293 ; sc:citation , "pubmed:31805292" ; sc:description """Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. An R-package for specification, simulation and likelihood calculation of phylogenetic comparative models. PCMBase : Simulation and likelihood calculation of phylogenetic comparative methods. Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3891 ; sc:name "PCMBase" ; sc:url "https://github.com/venelin/PCMBase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0219, edam:topic_0602, edam:topic_0634 ; sc:citation , "pubmed:31725861" ; sc:description """A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Database, Volume 2017, 2017, bax098""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3439 ; sc:name "PCOSBase" ; sc:url "http://pcosbase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , "pmcid:PMC6337464", "pubmed:30621295" ; sc:description "Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment." ; sc:featureList edam:operation_0224, edam:operation_0279, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PDBUSQLExtractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zti.polsl.pl/w3/dmrozek/science/pdbusqlext.htm" ; biotools:primaryContact "D. Mrozek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "Parameter fitting toolbox for partial differential equations in Python." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PDEparams" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/systemsmedicine/PDE_params" ; biotools:primaryContact "Esteban A. Hernandez-Vargas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3056, edam:topic_3336 ; sc:citation ; sc:description """Populating Chemical Space with Peptides using a Genetic Algorithm. In drug discovery one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in chemical space marked by a molecule of interest. Herein we report the peptide design genetic algorithm (PDGA, code available at https: github.com reymondgroup PeptideDesignGA), a computational tool capable of producing peptide sequences of various chain topologies (linear, cyclic polycyclic or dendritic) in proximity of any molecule of interest in a chemical space defined by MXFP, an atom-pair fingerprint describing molecular shape and pharmacophores. We show that PDGA generates high similarity analogs of bioactive peptides, including in selected cases known active analogs, as well as of non-peptide targets.""" ; sc:name "PDGA" ; sc:url "https://github.com/reymond-group/PeptideDesignGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:31714620" ; sc:description """A unified gene expression atlas for the model plant Physcomitrella patens. PEATmoss is an interactive tool to visualize gene expression data. These help pages explain several ways to query the expression data and to visualize the results, enabling the comparison of the expression profiles of several genes simultaneously, as well as to visualize co-expression information. One section describes how to download the expression data in a format that is easy to export to spreadsheet software and to generate figures that are ready for presentations or publications.""" ; sc:featureList edam:operation_0224, edam:operation_0315, edam:operation_0571 ; sc:name "PEATmoss" ; sc:softwareHelp ; sc:url "https://peatmoss.online.uni-marburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , , "pmcid:PMC6642660", "pubmed:31081335" ; sc:description "PSI Extended Fasta Format (PEFF) is a proposed unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools." ; sc:featureList edam:operation_0335, edam:operation_0417, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PEFF" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.psidev.info/peff" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3315, edam:topic_3375 ; sc:citation , "pubmed:31589430" ; sc:description """PELE-MSM is a Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies. IIt is a fully automatic platform based on our Monte Carlo algorithm, the Protein Energy Landscape Exploration method (PELE), for the estimation of absolute protein-ligand binding free energies, one of the most significant challenges in computer-aided drug design. Based on a ligand pathway approach, an initial short enhanced sampling simulation is performed to identify reasonable starting positions for more extended sampling. This stepwise approach allows for a significantly faster convergence of the free energy estimation using the Markov State Model (MSM) technique. PELE-MSM was applied on four diverse protein and ligand systems, successfully ranking compounds for two systems. Based on the results, current limitations and challenges with physics-based methods in computational structural biology are discussed.""" ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3896 ; sc:name "PELE-MSM" ; sc:softwareHelp ; sc:url "https://github.com/miniaoshi/MSM_PELE.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1931 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:name "Biodiversity data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3050 ; sc:description "a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes" ; sc:featureList edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PEMA" ; sc:softwareHelp ; sc:url "https://github.com/hariszaf/pema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_0634 ; sc:citation ; sc:description "Identification of pathogenic variant enriched regions across genes and gene families." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PER viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://per.broadinstitute.org" ; biotools:primaryContact "Dennis Lal", "Eduardo Pérez-Palma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_0634, edam:topic_3120, edam:topic_3168 ; sc:citation , "pubmed:31871067" ; sc:description "PERs is a tool for Identification of pathogenic variant enriched regions across genes and gene families." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "PERs" ; sc:url "https://github.com/edoper/PERs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325 ; sc:citation , "pmcid:PMC3742411", "pubmed:23920006" ; sc:description "Portal for Families Overcoming Neurodevelopmental Disorders (PFOND) provides a structured web interface for the information sharing with individuals struggling with the consequences of rare developmental disorders." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PFOND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pfond.cmmt.ubc.ca/index.html" ; biotools:primaryContact "Wasserman Lab" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3827 ; 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Madhusudhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2840, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc:description "PK-DB is a database and web interface for pharmacokinetics data and information from clinical trials as well as pre-clinical research. PK-DB allows to curate pharmacokinetics data integrated with the corresponding meta-information" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "PK-DB" ; sc:url "https://pk-db.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196 ; sc:citation ; sc:description "Web-based tool for plasmid reconstruction from bacterial genomes." ; sc:featureList edam:operation_3195, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PLACNETw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://castillo.dicom.unican.es/upload/" ; biotools:primaryContact "Fernando de la Cruz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0749, edam:topic_3314 ; sc:citation , "pubmed:31363226" ; sc:description "Promoting transparency and reproducibility in enhanced molecular simulations | The public repository of the PLUMED consortium | PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST monitors the compatibility of the provided PLUMED input files with the current and development versions of the code and integrates links from these files to the PLUMED manual | The community-developed PLUgin for MolEcular Dynamics | PLUMED is an open-source, community-developed library that provides a wide range of different methods, which include: | Home News People Download Doc Forum Cite NEST Funding" ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:name "PLUMED" ; sc:url "https://www.plumed-nest.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0821, edam:topic_3297, edam:topic_3489, edam:topic_3697 ; sc:citation , "pmcid:PMC6859810", "pubmed:31738435" ; sc:description "PMBD is a Comprehensive Plastics Microbial Biodegradation Database." ; sc:featureList edam:operation_0305 ; sc:name "PMBD" ; sc:url "http://pmbd.genome-mining.cn/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc:description "PMD-FDR is a Robust and Reproducible Statistical Framework for Removing Low-Accuracy, High-Scoring Hits." ; sc:featureList edam:operation_2929, edam:operation_3216, edam:operation_3644, edam:operation_3645, edam:operation_3649 ; sc:name "PMD-FDR" ; sc:url "https://github.com/slhubler/PMD-FDR-for-paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2830 ; sc:citation ; sc:description "High-dimensional Bayesian phenotype classification and model selection using genomic predictors." ; sc:featureList edam:operation_3659 ; sc:name "PMMLogit" ; sc:url "https://github.com/v-panchal/PMML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2640, edam:topic_3421 ; sc:citation , "pubmed:31073852" ; sc:description "Patient Navigation Barriers and Outcomes Tool™ (PN-BOT™), a new information management and reporting tool for oncology PN programs." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PN-BOTTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bit.ly/AboutPNBOT" ; biotools:primaryContact "Mandi Pratt-Chapman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC6901264", "pubmed:31765387" ; sc:description "The PNC package is to identify personalized driver genes of an individual patient by using network control principle ." ; sc:featureList edam:operation_0277, edam:operation_2454, edam:operation_3223, edam:operation_3439, edam:operation_3463 ; sc:name "PNC" ; sc:url "https://github.com/NWPU-903PR/PNC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3050, edam:topic_3306, edam:topic_3474 ; sc:citation ; sc:description "PNV is an assessment of Machine Learning algorithms for estimating land potential." ; sc:featureList edam:operation_2429, edam:operation_3431, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "PNV" ; sc:url "https://github.com/envirometrix/PNVmaps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3292, edam:topic_3855 ; sc:citation , "pubmed:30945242" ; sc:description "Interactive visual environment for rule-based modelling of biochemical systems." ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PORGY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://porgy.labri.fr/" ; biotools:primaryContact "Bruno Pinaud", "Guy Melancon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_2275 ; sc:citation , "pubmed:31535472" ; sc:description "PPCheck is a bioinformatics tool to identify protein-protein interactions, predict hotspots, perform compuational alanine scanning, predict native-like docking pose and calculate residue conservation for a protein." ; sc:featureList edam:operation_0394, edam:operation_2492, edam:operation_3899 ; sc:name "PPCheck" ; sc:url "http://caps.ncbs.res.in/ppcheck/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_2640, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC6842548", "pubmed:31706268" ; sc:description "Genome-wide prediction and prioritization of human aging genes by data fusion." ; sc:featureList edam:operation_2454, edam:operation_3439, edam:operation_3501 ; sc:name "PPHAGE" ; sc:url "https://cbb.ut.ac.ir/pphage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0218 ; sc:citation , "pubmed:30521143" ; sc:description "Tool for extracting comprehensive protein-protein interaction information." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PPICurator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ppicurator.hupo.org.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0769, edam:topic_3810 ; sc:citation , "pubmed:31529041" ; sc:description "PPNID: a manually curated reference database and identification tool for plant-parasitic nematode." ; sc:license "GPL-3.0" ; sc:name "PPNID" ; sc:softwareHelp ; sc:url "https://github.com/xueqing4083/PPNID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3796 ; sc:citation ; sc:description """A Software Platform for Facilitating Population Genomic Analyses. Installation — PPP 0.1.1 documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0335, edam:operation_3435 ; sc:name "PPP" ; sc:url "https://ppp.readthedocs.io/en/latest/PPP_pages/install.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3382, edam:topic_3473 ; sc:citation , "pmcid:PMC6819326", "pubmed:31664891" ; sc:description """personalized PageRank and semantic similarity measures for entity linking. BACKGROUND:Biomedical literature concerns a wide range of concepts, requiring controlled vocabularies to maintain a consistent terminology across different research groups. However, as new concepts are introduced, biomedical literature is prone to ambiguity, specifically in fields that are advancing more rapidly, for example, drug design and development. Entity linking is a text mining task that aims at linking entities mentioned in the literature to concepts in a knowledge base. For example, entity linking can help finding all documents that mention the same concept and improve relation extraction methods. Existing approaches focus on the local similarity of each entity and the global coherence of all entities in a document, but do not take into account the semantics of the domain. RESULTS:We propose a method, PPR-SSM, to link entities found in documents to concepts from domain-specific ontologies""" ; sc:featureList edam:operation_3096, edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:name "PPR-SSM" ; sc:url "https://github.com/lasigeBioTM/PPRSSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0601, edam:topic_3474 ; sc:citation , "pubmed:31412138" ; sc:description "Boosting phosphorylation site prediction with sequence feature-based machine learning | Index of /~pralay/resources/PPSBoost | Shyantani Maiti, Atif Hassan, Pralay Mitra (In press). Boosting phosphorylation site prediction with sequence feature-based Machine learning. PROTEINS: Structure, Function, and Bioinformatics" ; sc:featureList edam:operation_0417 ; sc:name "PPSBoost" ; sc:url "http://cse.iitkgp.ac.in/~pralay/resources/PPSBoost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3360 ; sc:citation , "pmcid:PMC6460848", "pubmed:31093546" ; sc:description "Novel method for interrogating receiver operating characteristic curves for assessing prognostic tests." ; sc:featureList edam:operation_0337, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PPV NPV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://d4ta.link/ppvnpv/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0623, edam:topic_3174, edam:topic_3305 ; sc:citation ; sc:description "PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3797, edam:operation_3891 ; sc:name "PPanGGOLiN" ; sc:url "https://github.com/labgem/PPanGGOLiN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3305 ; sc:citation , "pubmed:31724381" ; sc:description "PQStat is an application which enables users to carry out a statistical data analysis in a simple and accurate way." ; sc:featureList edam:operation_3432, edam:operation_3658, edam:operation_3891 ; sc:name "PQStat" ; sc:url "http://www.pqstat.pl/en" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0868 ; sc:encodingFormat edam:format_1929 ; sc:name "Profile-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:author ; sc:description "PRALINE 2 is a framework for tailor-made sequence alignments. It allows almost all aspects of a sequence alignment algorithm to be customised, such as the alphabets used (AA, DNA, secondary structure, disorder, motif matches, etc.). Includes a command-line tool for common use cases without writing any custom code." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PRALINE 2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0.0", "1.1.0" ; sc:url "https://github.com/ibivu/PRALINE" ; biotools:primaryContact "Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments." ; sc:featureList edam:operation_0264, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PRAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://bioconductor.org/packages/pram" ; biotools:primaryContact "Peng Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6716675", "pubmed:31425505" ; sc:description "> HOMEPAGE BROKEN! | Predicting functional targets of RNA binding proteins based on CLIP-seq peaks | RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle" ; sc:featureList edam:operation_3222, edam:operation_3901, edam:operation_3902 ; sc:name "PRAS" ; sc:url "https://github.com/ouyang-lab/PRAS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2331 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC6602504", "pubmed:31143927" ; sc:description "PRECOG (Predicting coupling probabilities of G-protein coupled receptors) lets you predict coupling probabilities of Class A GPCRs to 11 G-proteins based on input sequence information (either WT or mutated). It is built by training logistic-regression algorithm on sequence- and structure-based features, derived from a set of Class A GPCRs." ; sc:featureList edam:operation_0337, edam:operation_2423, edam:operation_2990 ; sc:name "PRECOG: Predicting coupling probabilities of G-protein coupled receptors" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.1" ; sc:url "http://precog.russelllab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0623, edam:topic_0749, edam:topic_0820, edam:topic_2814 ; sc:citation ; sc:description """Improved version of Protein Repeat Identification by Graph Spectral Analysis. Protein Repeat Identification by Graph Spectral Analysis. PRIGSA2 is a graph based algorithm which implements knowledge-based and de novo approach for the identification of structural repeats in proteins. The tool takes PDB file as input and gives the periodicity and coordinates as output""" ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0303, edam:operation_0476, edam:operation_3214 ; sc:name "PRIGSA2" ; sc:url "http://bioinf.iiit.ac.in/PRIGSA2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3518, edam:topic_3519, edam:topic_3673 ; sc:citation , "pmcid:PMC6917790", "pubmed:31848453" ; sc:description "PRIMEval is a tool for optimization and screening of multiplex oligonucleotide assays." ; sc:featureList edam:operation_2419, edam:operation_2428, edam:operation_3198 ; sc:license "MIT" ; sc:name "PRIMEval" ; sc:url "https://primeval.ait.ac.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3325 ; sc:citation , "pmcid:PMC5860394", "pubmed:28065902" ; sc:description "Privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PRINCESS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/achenfengb/PRINCESS_opensource" ; biotools:primaryContact "Feng Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6612819", "pubmed:31510697" ; sc:description "> NAME EQUAL TO (PUB. DIFFERENT) bio.tools/prism-ppi | > NAME (PRISM) SIMILAR TO (PUB. DIFFERENT) bio.tools/prism_3 (PRISM 3), bio.tools/prism-primer (PriSM), bio.tools/prism (PrISM) | methylation pattern-based, reference-free inference of subclonal makeup | Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. (v1.0.1) | PRISM requires the mapping result of Bismark, a bisulfite read mapping tool. Also note that PRISM only applies to RRBS data, and unfortunately, the feasibility of PRISM to the data from other methylation profiling techniques such as whole genome bisulfite sequencing (WGBS), methylated DNA immunoprecipitation sequencing (MeDIP-Seq), or methyl-CpG binding domain-based capture sequencing (MBDCap-Seq) has not been verified | BAM file of RRBS reads, aligned by Bismark" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3629 ; sc:license "MIT" ; sc:name "PRISM" ; sc:url "https://github.com/dohlee/prism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:author ; sc:citation , "pubmed:31051038" ; sc:description "Large-scale prediction of binding affinity in protein-small ligand complexes." ; sc:featureList edam:operation_0272, edam:operation_0482, edam:operation_2492 ; sc:funder "European H2020 e-Infrastructure grant, BioExcel, grant no. 675728", "European H2020 e-Infrastructure grant, BioExcel, grant no. 823830", "European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PRODIGY-LIG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider , "University of Utrecht" ; sc:softwareHelp , ; sc:url "http://milou.science.uu.nl/services/PRODIGY-LIG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0196, edam:topic_1317, edam:topic_2828 ; sc:citation ; sc:description "PRODIGY-CRYSTAL (PROtein binDIng enerGY prediction to classify CRYSTALlographic interfaces) is an automatic web server for distinguish crystallographic from biological interfaces in protein complexes." ; sc:featureList edam:operation_0321 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PRODIGY-CRYSTAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bianca.science.uu.nl/prodigy/cryst" ; biotools:primaryContact , "Anna Vangone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc:description "PROMO (Profiler of Multi-Omics data) - interactive tool for analyzing clinically-labeled multi-omic cancer datasets." ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PROMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/promo/" ; biotools:primaryContact "Dvir Netanely", "Ron Shamir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_0780, edam:topic_3295 ; sc:citation , "pmcid:PMC6891001", "pubmed:31796964" ; sc:description """PRP is a comprehensive integrated regulatory information and analysis portal for plant genomes. Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a 'cell system'. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time.""" ; sc:featureList edam:operation_1781, edam:operation_3083, edam:operation_3207, edam:operation_3792 ; sc:name "PRP" ; sc:url "https://scbb.ihbt.res.in/PRP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3400, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description """A Hybrid Model for Predicting Pattern Recognition Receptors using Evolutionary Information. Prediction of pattern recognition receptors. PRRpred is a web server designed for predicting pattern Recognition Receptors (PRRs) and Non-PRRs""" ; sc:featureList edam:operation_0267, edam:operation_0416, edam:operation_2489 ; sc:name "PRRpred" ; sc:url "http://webs.iiitd.edu.in/raghava/prrpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3298, edam:topic_3416, edam:topic_3517 ; sc:citation , "pmcid:PMC6400585", "pubmed:30835202" ; sc:description "Atlas of polygenic burden associations across the human phenome." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mrcieu.mrsoftware.org/PRS_atlas" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3710, edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_3752 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description """PReMiS analyzes mass spectrometric data collected from the 6×5 LC-MS/MS Peptide Reference Mix and calculates quality control metrics for instrument performance. Thermo raw files and AB Sciex wiff files can be analyzed directly. Data in other vendor formats must be converted to mzML prior to analysis. In addition to its general reporting features, PReMiSallows you to track performance over time and compare parameters across instruments.""" ; sc:featureList edam:operation_3635 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "PReMiS" ; sc:operatingSystem "Windows" ; sc:url "https://promega.com/resources/software-firmware/other/6x5-premis-software-download/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6534809", "pubmed:31127811" ; sc:description "Photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PS-Plant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/g2-bernotas/PS-Plant-Framework" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3534 ; sc:citation ; sc:description "Protein Structural Class Prediction." ; sc:featureList edam:operation_0474, edam:operation_0482, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PSCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://brl.uiu.ac.bd/PL/" ; biotools:primaryContact "Swakkhar Shatabda​" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:31135034" ; sc:description "Splicing-detection method for short-read and long-read RNA-seq analysis." ; sc:featureList edam:operation_3680, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PSI-Sigma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wososa/PSI-Sigma" ; biotools:primaryContact "Kuan-Ting Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6612829", "pubmed:31510650" ; sc:description "Fully-sensitive seed finding in sequence graphs using a hybrid index | Graph REad Mapper (C++ implementation) | Google protocol buffer >= v3.0.0" ; sc:featureList edam:operation_0249, edam:operation_0524, edam:operation_3211 ; sc:license "MIT" ; sc:name "PSI" ; sc:url "https://github.com/cartoonist/psi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2640, edam:topic_2885, edam:topic_3489, edam:topic_3810 ; sc:citation , "pubmed:31599098" ; sc:description """An extensive database for pan-species microsatellite investigation and marker development. A Django app for Pan-Species Microsatellite Database. Pan-Species Microsatellite Database. Microsatellites (simple repeat sequences, SSRs or short tandem repeats, STRs), are tandem repeats of short DNA motifs with length of 1-6 bp which have extensively been exploited as powerful genetic markers for diversity applications, and are involved in gene regulation as well as implicated in numerous genetic diseases even in cancers. PSMD was developed as a web-based comprehensive database comprising 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms covered almost all species with available genomic data. PSMD enables scientists to easily browse, filter, compare, download SSRs with relevant information""" ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_2421, edam:operation_3196 ; sc:license "MIT" ; sc:name "PSMD" ; sc:url "http://big.cdu.edu.cn/psmd/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Prediction of FUS-like phase separation proteins" ; sc:featureList edam:operation_3092 ; sc:name "PSPer" ; sc:url "http://bio2byte.com/psp/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC6307140", "pubmed:30587128" ; sc:description "Plant stress RNA-Seq nexus (PSRN) - stress-specific transcriptome database in plant cells." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PSRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://syslab5.nchu.edu.tw/" ; biotools:primaryContact "Systems Biology Lab, National Chung Hsing University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6895799", "pubmed:31717904" ; sc:description "PSSRdt is a novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data." ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_0524, edam:operation_3196, edam:operation_3258 ; sc:name "PSSRdt" ; sc:url "https://github.com/PSSRdt/program" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation ; sc:description """Visualization of the Dynamics of Histone Modifications and Their Crosstalk Using PTM-CrossTalkMapper. R scripts to create crosstalk maps that visualize multi-layered proteoform data. PTM-CrossTalkMapper is a flexible toolkit to visualize multi-layered quantitative post-transcriptional modification (PTM) data. The preprint manuscript can be found on bioRxiv""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3755, edam:operation_3799 ; sc:name "PTM-CrossTalkMapper" ; sc:url "https://github.com/veitveit/CrossTalkMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6555389", "pubmed:31198645" ; sc:description "R package for PTM site localization and motif extraction from proteomic datasets." ; sc:featureList edam:operation_0335, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PTMphinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/jmwozniak/PTMphinder" ; biotools:primaryContact "Jacob M. Wozniak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0203, edam:topic_0659, edam:topic_2640 ; sc:citation "pubmed:31797620" ; sc:description "PTR is an approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomics." ; sc:featureList edam:operation_3431 ; sc:name "PTR" ; sc:url "https://github.com/arunima2/PTRE_PSB_2020" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc:description """PTRBC is a tool for predicting the required pre-surgery blood volume in surgical patients based on machine learning. This clinical data analysis tool can be used to do data cleaning and predict the required transfusion volume of red blood cells in surgical patients based on machine learning methods. Meanwhile, this tool can process the similar classification or regression problems. In other words, a general prediction model can be established for the input data specified.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "PTRBC" ; sc:url "https://github.com/niu-lab/PTRBC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3170, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description """Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis. Probabilistic Transcriptome-wide Association Analysis (PTWAS). This repository contains the software implementations and necessary annotation resources for a suite of statistical methods to perform transcriptome-wide association analysis (TWAS). These methods are designed to perform rigorous causal inference connecting genes to complex traits. The statistical models and the key algorithms are described in the manuscript [1]""" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659, edam:operation_3664, edam:operation_3891 ; sc:name "PTWAS" ; sc:url "https://github.com/xqwen/ptwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3314 ; sc:citation , "pmcid:PMC6688265", "pubmed:31399858" ; sc:description "programmatic access to chemical annotations integrated in PubChem | PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3431 ; sc:name "PUG-View" ; sc:url "https://pubchemdocs.ncbi.nlm.nih.gov/pug-view" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0780, edam:topic_2259, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC6812194", "pubmed:31667383" ; sc:description """parallel variation calling tools. PVCTools is Parallel Variation Calling Tools, which tries to call variation using multiple threads. Basically, the reference genome will be splited into small pieces, and corresponding alignment BAM files will be extracted. Under this way, it will speed up the process of variation calling a lot""" ; sc:featureList edam:operation_3359, edam:operation_3432 ; sc:name "PVCTools" ; sc:url "https://github.com/CNaibon/PVCTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3337, edam:topic_3577 ; sc:citation ; sc:description """Poly-Exposure and Poly-Genomic Scores Implicate Prominent Roles of Non-Genetic and Demographic Factors in Four Common Diseases in the UK. ABSTRACT While polygenic risk scores (PRSs) have been shown to identify a small number of individuals with increased clinical risk for several common diseases, non-genetic factors that change during a lifetime, such as lifestyle, employment, diet, and pollution, have a larger role in clinical prediction. We analyzed data from 459,613 participants of the UK Biobank to investigate the independent and combined roles of demographics (e.g., sex and age), 96 environmental exposures, and common genetic variants in atrial fibrillation, coronary artery disease, inflammatory bowel disease, and type 2 diabetes. We develop an additive modelling approach to estimate and validate a poly-exposure score (PXS) that goes beyond consideration of a handful of factors such as smoking and pollution""" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "PXS" ; sc:url "http://apps.chiragjpgroup.org/pxs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3056 ; sc:citation ; sc:description """Python implementation of likelihood-free inference by ratio estimation. Likelihood-Free Inference by Ratio Estimation (LFIRE). PYLFIRE is a Python package that uses ELFI (Engine for Likelihood-Free Inference) and glmnet for performing Likelihood-Free Inference. PYLFIRE requires Python 3.6 or greater and a Fortran compiler, for Mac users brew install gcc will take care of this requirement or conda install gcc if you are using anaconda. You can install PYLFIRE by typing in your terminal:""" ; sc:featureList edam:operation_3658, edam:operation_3659, edam:operation_3664 ; sc:name "PYLFIRE" ; sc:url "https://github.com/elfi-dev/zoo/tree/master/pylfire" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:31389023" ; sc:description "Python reconstruction operators in neural networks | Python Reconstruction Operators in Neural Networks. High level python API for PYRO-NN-Layers | Implementation of reconstruction operators in CUDA for Tensorflow for the PYRO-NN Framework | Python Reconstruction Operators in Machine Learning (PYRO-NN-Layers) brings state-of-the-art reconstruction algorithms to neural networks integrated into Tensorflow. This repository contains the actual Layer implementation as CUDA kernels and the necessary C++ information control classes according to the Tensorflow API | At this point the geometry is fully setup and can be used to create projections and reconstructions" ; sc:featureList edam:operation_0487, edam:operation_3660, edam:operation_3745 ; sc:license "Apache-2.0" ; sc:name "PYRO-NN" ; sc:url "https://github.com/csyben/PYRO-NN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC6933905", "pubmed:31878881" ; sc:description """Fast and scalable processing of whole exome and targeted sequencing data. PaCBAM_Performance_analysis – Google Drev""" ; sc:featureList edam:operation_2422, edam:operation_3227, edam:operation_3695 ; sc:name "PaCBAM" ; sc:url "http://bcglab.cibio.unitn.it/PaCBAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3315, edam:topic_3512 ; sc:citation ; sc:description "PaSGAL (Parallel Sequence to Graph Aligner) is designed to accelerate local sequence alignment of sequences to directed acyclic sequence graphs (DAGs), e.g., variation graphs, splicing graphs." ; sc:featureList edam:operation_0495, edam:operation_3196, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PaSGAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://alurulab.cc.gatech.edu/PaSGAL" ; biotools:primaryContact "Haowen Zhang", "Srinivas Aluru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC6746931", "pubmed:31551749" ; sc:description "Fast Signal Feature Extraction Using Parallel Time Windows | Motivation: Hand amputations can dramatically affect the quality of life of a person. Researchers are developing surface electromyography and machine learning solutions to control dexterous and robotic prosthetic hands, however long computational times can slow down this process. Objective: This paper aims at creating a fast signal feature extraction algorithm that can extract widely used features and allow researchers to easily add new ones. Methods: PaWFE (Parallel Window Feature Extractor) extracts the signal features from several time windows in parallel. The MATLAB code is publicly available and supports several time domain and frequency features" ; sc:name "PaWFE" ; sc:url "http://ninapro.hevs.ch/node/229" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3168 ; sc:citation , "pmcid:PMC6588853", "pubmed:31226925" ; sc:description "Sequencing simulator for PacBio sequencing with a high fidelity." ; sc:featureList edam:operation_0524, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PaSS" ; sc:operatingSystem "Linux" ; sc:url "http://cgm.sjtu.edu.cn/PaSS/" ; biotools:primaryContact "Wenmin Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc:description "PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. Several standalone tools (e.g. PGAP, PANNOTATOR, PanGP, Roary and BPGA) and web servers (e.g. Panseq, PGAT and PanWeb) dedicated to pangenome analysis have been developed recently and offer the possibility to compute pangenome analysis for genomes provided by a user. For all these tools and servers, users have to collect genomes and manage to run the tools, which implies a significant effort on the user side. To tackle this problem, we developped PanGeneHome, the only web site offering pre-computed pangenome analysis with up-to-date and large scale data. PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest, the analysis being precomputed and available for 615 taxa, covering 182 species and 49 orders. Considering the fast growing number of microbial genomes, the PanGeneHome tool will need to be updated regularly." ; sc:isAccessibleForFree true ; sc:name "PanGeneHome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pangenehome.lmge.uca.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0621, edam:topic_0780, edam:topic_3174 ; sc:citation ; sc:description "PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands." ; sc:featureList edam:operation_0524, edam:operation_3182, edam:operation_3198, edam:operation_3472 ; sc:name "PanTools" ; sc:url "https://git.wur.nl/bioinformatics/pantools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3292, edam:topic_3315, edam:topic_3474 ; sc:citation ; sc:description """Agilely creating multiple document formats for academic manuscripts with Pandoc Scholar. Create beautiful and semantically meaningful articles with pandoc. science pandoc publishing scientific-writing pandoc-scholar. Plain pandoc is already excellent at document conversion, but it lacks in metadata handling. Pandoc scholar offers simple ways to include metadata on authors, affiliations, contact details, and citations. The data is included into the final output as document headers. Additionally all entries can be exported as JSON-LD, a standardized format for the semantic web. Pandoc a universal document converter. Create beautiful, semantically enriched articles with pandoc. If you need to convert files from one markup format into another, pandoc is your swiss-army knife. (← = conversion from; → = conversion to; ↔︎ = conversion from and to).""" ; sc:featureList edam:operation_0335, edam:operation_3431, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "Pandoc Scholar" ; sc:softwareHelp ; sc:url "https://github.com/pandoc-scholar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6742414", "pubmed:31469823" ; sc:description "An iterative clustering method for single-cell RNA sequencing data | Single-cell Panoramic View Clustering (PanoView) | PanoView is an iterative PCA-based method that integrates with a novel density-based clustering, ordering local maximum by convex hull (OLMC) algorithm, to identify cell subpopulations for single-cell RNA-sequencing. For details of the method, please see our paper at PLOS Computational Biology (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007040)" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:license "MIT" ; sc:name "PanoView" ; sc:url "https://github.com/mhu10/scPanoView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3444 ; sc:citation , "pmcid:PMC6267067", "pubmed:30497372" ; sc:description "Time-course network medicine platform integrating molecular assays and pathophenotypic data." ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PanoromiX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinfo-abcc.ncifcrf.gov/panoromics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3303, edam:topic_3304 ; sc:citation , "pmcid:PMC6345070", "pubmed:30678631" ; sc:description "Open-source web-based search and metadata organization of scientific literature." ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PaperBot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://paperbot.ai/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3068 ; sc:citation ; sc:description "Tool for massively parallel model selection and phylogenetic tree inference on thousands of genes." ; sc:featureList edam:operation_0325, edam:operation_0552, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ParGenes" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/BenoitMorel/ParGenes" ; biotools:primaryContact "Benoit Morel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC6923905", "pubmed:31856721" ; sc:description """A hybrid and scalable error correction algorithm for indel and substitution errors of long reads. BACKGROUND:Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads. METHODS:In this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes the k-mer coverage information of high throughput Illumina short-read sequences to rectify the PacBio long-read sequences.""" ; sc:featureList edam:operation_0524, edam:operation_3195, edam:operation_3472 ; sc:name "ParLECH" ; sc:url "https://github.com/arghyakusumdas/GenomicErrorCorrection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "Graph realignment tools for structural variants." ; sc:featureList edam:operation_3196, edam:operation_3228, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Paragraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Illumina/paragraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Paraload is an original utility which ensures job distribution between thousands of processors, according to the type of the data to be analysed." ; sc:name "Paraload" ; sc:url "ftp://doua.prabi.fr/pub/logiciel/paraload" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pubmed:31127303" ; sc:description "Fast inference and visualization of ancestral scenarios. PastML infers ancestral characters on a rooted phylogenetic tree with annotated tips, using maximum likelihood or parsimony. The result is then visualised as a zoomable html map." ; sc:featureList edam:operation_0567, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PastML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pastml.pasteur.fr/" ; biotools:primaryContact "Anna Zhukova", "Olivier Gascuel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description "User-friendly interface to explore evolutionary scenarios." ; sc:featureList edam:operation_0545, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PastView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pastview.org" ; biotools:primaryContact "Francois Chevenet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Catalogue of public databases for molecular typing and microbial genome diversity." ; sc:featureList edam:operation_3840 ; sc:name "Pasteur MLST" ; sc:url "https://pubmlst.org/databases.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1957 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1401 ; sc:encodingFormat edam:format_3752 ; sc:name "Match reward score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_3534 ; sc:citation "pubmed:28282119", "pubmed:31131411" ; sc:description "Identify structurally conserved regions at the protein surfaces." ; sc:featureList edam:operation_3666 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PatchSearch" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PatchSearch" ; biotools:primaryContact "Frédéric Guyon", "Gautier Moroy", "Julien Rey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "The workflow involves a computational technique that employs propagation of drug-protein and protein-protein interactions to predict the biological pathways that are affected by a drug or compound. Reliable, openly available repositories (CHEMBL, TTD, DrugBank, PharmGKB, IUPHAR, Intact, MINT) were used for connecting pharmaceutically relevant compounds to their target proteins in human and the target proteins to their first-degree interactors. Since these databases differ in their architecture and accessibility, diverse sub-workflows with filtering steps were created ensuring the quality of the retrieved data." ; sc:featureList edam:operation_2423 ; sc:name "Path4Drug" ; sc:url "https://www.ebi.ac.uk/transqst/transqstWeb/DRUG_PATHWAY_RESOURCE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2229, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31602464" ; sc:description """A comprehensive pathway database for model organisms. Quantitative metabolomics services for biomarker discovery and validation. Specializing in ready to use metabolomics kits. Your source for quantitative metabolomics technologies and bioinformatics. PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. A Pathway for Every Protein""" ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3083, edam:operation_3799 ; sc:name "PathBank" ; sc:url "http://www.pathbank.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "Efficient pan-cancer whole-slide image classification and outlier detection using convolutional neural networks." ; sc:featureList edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PathCNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sedab/PathCNN" ; biotools:primaryContact "Seda Bilaloglu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2640 ; sc:citation , "pubmed:31583640" ; sc:description """De Novo Pathway-Based Classification of Breast Cancer Subtypes. Breast cancer is a heterogeneous disease for which various subtypes have been identified. If you find this web application useful please cite:. Alcaraz et al., De novo pathway-based classification of breast cancer subtypes (manuscript in preparation).""" ; sc:featureList edam:operation_2495, edam:operation_3282, edam:operation_3439 ; sc:name "PathClass" ; sc:url "https://pathclass.compbio.sdu.dk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3377 ; sc:citation , "pubmed:31114840" ; sc:description "Interaction-network tool to search for the most relevant protein-protein interactions around a drug's target(s), and then analyzes for which phenotypes the network is enriched relative to the entire interaction network." ; sc:featureList edam:operation_3436, edam:operation_3439, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PathFXweb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pathfxweb.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3474 ; sc:citation ; sc:description "A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology | A Convenient High-Throughput Workflow for Preprocessing, Deep Learning Analytics and Interpretation in Digital Pathology | MedRxiv Manuscript: https://www.medrxiv.org/content/10.1101/19003897v1 | Fig. 1. PathFlowAI Framework: a) Annotations and whole slide images are preprocessed in parallel using Dask; b) Deep learning prediction model is trained on the model; c) Results are visualized; d) UMAP embeddings provide diagnostics; e) SHAP framework is used to find important regions for the prediction" ; sc:featureList edam:operation_3891 ; sc:license "MIT" ; sc:name "PathFlowAI" ; sc:url "https://github.com/jlevy44/PathFlowAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6521546", "pubmed:31092193" ; sc:description "Python package that transforms pathway knowledge from three major pathway databases into a unified abstraction using Biological Expression Language as the pivotal, integrative schema." ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PathMe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pathme.scai.fraunhofer.de/" ; biotools:primaryContact "Daniel Domingo-Fernández" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation ; sc:description "Open source software for analyzing spatial navigation search strategies | Search Strategy analysis and more for spatial navigation data in rodents | Morris Water Maze search strategy and entropy analysis | For a more detailed overview of Pathfinder please visit our Wiki | Created by Matthew Cooke at The University of British Columbia, Jason Snyder Lab | The Pathfinder package is a search strategy analysis tool for the Morris Water Maze, and can be expanded for other spatial navigation tasks. The program analyses X-Y coordinate data exported from commercially available tracking software. Pathfinder currently supports outputs from: Ethovision, Anymazy, WaterMaze, and ezTrack. We then calculate the best-fit search strategy for the trial. Trials are fit into one of: Direct Swim, Directed Search, Focal Search, Spatial indirect, Chaining, Scanning, Thigmotaxis, and Random Search" ; sc:license "GPL-3.0" ; sc:name "Pathfinder" ; sc:url "http://github.com/MatthewBCooke/Pathfinder" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_3790 ; sc:name "Query script" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2331, edam:format_2376, edam:format_3261, edam:format_3464, edam:format_3752 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3307 ; sc:citation "pubmed:21071392" ; sc:description "Pathway Commons aims to collect and disseminate biological pathway and interaction data. Data is collected from partner databases and is represented in the BioPAX standard. By representing data in BioPAX, Pathway Commons is able to provide a detailed representation of a variety of biological concepts including: Biochemical reactions; gene regulatory networks; and genetic interactions; transport and catalysis events; and physical interactions involving proteins, DNA, RNA and small molecules and complexes." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "PathwayCommons SPARQL endpoint" ; sc:softwareHelp ; sc:softwareVersion "11" ; sc:url "http://rdf.pathwaycommons.org/sparql/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:encodingFormat edam:format_2330 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1047 ; sc:encodingFormat edam:format_2330 ; sc:name "URI" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3261 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web service" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3307 ; sc:citation "pubmed:21071392" ; sc:description "Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model, which can be queried using our web API (documented below). This API can be used by computational biologists to download custom subsets of pathway data for analysis, or can be used to incorporate powerful biological pathway and network information retrieval and query functionality into websites and software." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:name "PathwayCommons web service API" ; sc:softwareHelp ; sc:softwareVersion "11" ; sc:url "https://www.pathwaycommons.org/pc2/home" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0602 ; sc:citation , "pmcid:PMC6667378", "pubmed:31363752" ; sc:description "Proteoform-centric network construction enables fine-granularity multiomics pathway mapping | PathwayMatcher is a free, open-source software to search for pathways related to a list of genes, proteins or proteoforms in Reactome | PathwayMatcher was benchmarked against different reference datasets covering multiple types of omics data | We present next the Cypher language queries to find the numbers shown in the summary statistics. These can also be used to get the protein-pathway mapping used in PathwayMatcher | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | PathwayMatcher is a standalone command line tool to match human biomedical data to pathways | 7448 valid tools on Nov 10, 2019" ; sc:featureList edam:operation_0277, edam:operation_0417, edam:operation_0533 ; sc:name "PathwayMatcher" ; sc:softwareHelp , , ; sc:url "http://github.com/PathwayAnalysisPlatform/PathwayMatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3895 ; sc:citation ; sc:description "Tool for the transformation of metabolic pathways and the development of pathfinding algorithms that establish relevant links between compounds that are essential to the biofuel production process." ; sc:featureList edam:operation_3501, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Pathways Analyzer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gitlab.com/lvasquezcr/pathways-analyzer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC6724669", "pubmed:31439692" ; sc:description "Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) | St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal | Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore" ; sc:featureList edam:operation_3208, edam:operation_3225, edam:operation_3227 ; sc:name "PeCanPIE" ; sc:url "https://pecan.stjude.cloud/variant/67664" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3510, edam:topic_3512 ; sc:citation , "pubmed:31393553" ; sc:description """Combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. A toolkit for predicting non-classical secreted proteins by combining the gradient boosting machine in an ensemble learning framework . A combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins | In this work, we first constructed a high-quality dataset of experimentally verified “non-classical” secreted proteins, which we then used to create benchmark datasets. Gram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection""" ; sc:featureList edam:operation_0267, edam:operation_0480 ; sc:name "PeNGaRoo" ; sc:url "http://pengaroo.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3295 ; sc:citation ; sc:description "The Software Tool for Peptide Specificity Analysis (PeSA) is an open-source software designed as a tool to use in the analysis of peptide arrays, permutation arrays and OPALs. The analysis can be used to generate motifs to share the results as a position-specific scoring matrix (PSSM)." ; sc:featureList edam:operation_0238, edam:operation_3631, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "PeSA" ; sc:url "http://www.github.com/EmineTopcu/PeSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC6677017", "pubmed:31373570" ; sc:description "Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data | Tool for identifying/classifying solvent molecules in macromolecular x-ray crystal structures | -- Paul Smith, PhD. Assistant Prof. of Chemistry, FordhamUniversity (psmith66@fordham.edu) -- Laurel Jones, PhD Candidate,Northwestern University -- Michael Tynes, Data Sciences GraduateProgram, Fordham University | -- PeakProbe must be run under the \"phenix.python\" environment or be made aware of the locations of all necessary CCTBX imports -- A PDB file and structure factor data are required and can be specified in any order or suitable format as per PHENIX norms -- The program has several modes of operation and many configurable parameters, but the essentials are covered below" ; sc:featureList edam:operation_0417, edam:operation_0480, edam:operation_3891 ; sc:name "PeakProbe" ; sc:url "https://github.com/paulsmith638/PeakProbe.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A mine with peanut data from Legume Information Systems (LIS) PeanutBase" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "PeanutMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/peanutmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3318, edam:topic_3518 ; sc:citation , "pubmed:31860654" ; sc:description """Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. Program to simulate pedigree structures. The method can use sex-specific genetic maps and randomly assigns the sex of each parent (or uses user-specified sexes) when using such maps. ./ped-sim -d -m -o --intf . The above both produce three output files: [out_prefix].seg containing IBD segments, [out_prefix].fam, a PLINK format fam file with all simulated relatives, and [out_prefix].log, a log of what Ped-sim printed to stdout. Sample ids for simulated individuals""" ; sc:featureList edam:operation_0282, edam:operation_2944, edam:operation_3196, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "Ped-sim" ; sc:url "https://github.com/williamslab/ped-sim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3322, edam:topic_3407, edam:topic_3418 ; sc:citation , "pmcid:PMC6883068", "pubmed:31780760" ; sc:description """A pediatric diseases map generated from clinical big data from Hangzhou, China. Freelyavailable pediatric critical care data for researchers. Haomin Li#*,Gang Yu#, Cong Dong, Zheng Jia, Jiye An, Huilong Duan, Qiang Shu*. PedMap: a pediatric diseases map generated from clinical big data from Hangzhou, China. Scientfic Report 2019. DOI : 10.1038/s41598-019-54439-w. A pediatric disease map shows the relationships among the most common pediatric diseases, incidence rates, ages of onset and seasonal patterns in children based on more than 5 million outpatient visits at The Children's Hospital Zhejiang University School of Medicine (ZUCH)""" ; sc:featureList edam:operation_2429, edam:operation_3432, edam:operation_3659 ; sc:name "PedMap" ; sc:url "http://pedmap.nbscn.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31132275" ; sc:description "Software package for semi-automated processing of protein footprinting data." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PepFoot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jbellamycarter/pepfoot" ; biotools:primaryContact "Jedd Bellamy-Carter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0820, edam:topic_2275, edam:topic_3542 ; sc:citation , "pubmed:31793016" ; sc:description "PepPro is a Nonredundant Structure Data Set for Benchmarking Peptide-Protein Computational Docking." ; sc:featureList edam:operation_0480, edam:operation_0482, edam:operation_2488, edam:operation_3899 ; sc:name "PepPro" ; sc:url "http://zoulab.dalton.missouri.edu/PepPro_benchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:30610011" ; sc:description "Peptide-centric search engine for novel peptide identification and validation." ; sc:featureList edam:operation_3647, edam:operation_3649, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "PepQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pepquery.org/" ; biotools:primaryContact "Gitter", "PepQuery Google Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2275 ; sc:citation , "pubmed:31441995" ; sc:description """PepVis tool is a python based GUI pipeline which can be used to model and prepare large-scale peptide structure from the sequence and also to perform large-scale peptide virtual screening. PepVis integrates ModPep and Gromacs for modelling and structure optimization of the peptides, while it integrates AutoDock Vina,ZDOCK, AutoDock CrankPep(ADCP) for performing peptide virtual screening. The protein-peptide complexes can be rescored using ZRANK2 and the flexible refinement of the large protein-peptide complexes can also be performed using FlexPepDock. The parallel job execution has been implemented using GNU parallel and the user can provide inputs using GUI which will produce the bash script based on the customized input provided by the user and can be run in terminal.""" ; sc:featureList edam:operation_0418, edam:operation_0482, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "PepVis" ; sc:url "https://github.com/inpacdb/PepVis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3512, edam:topic_3520 ; sc:citation , "pmcid:PMC6337836", "pubmed:30654742" ; sc:description "Proteogenomics workflow for the expert annotation of eukaryotic genomes." ; sc:featureList edam:operation_2929, edam:operation_3643, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Peptimapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://hub.docker.com/r/dockerprotim/peptimapper/" ; biotools:primaryContact "L. Guillot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0621, edam:topic_0736, edam:topic_0820, edam:topic_3068 ; sc:citation , "pubmed:31629694" ; sc:description """A database for eukaryotic peripheral membrane proteins. The majority of all proteins in cells interact with membranes either permanently or temporarily. Peripheral membrane proteins form transient complexes with membrane proteins and or lipids, via non-covalent interactions and are of outmost importance, due to numerous cellular functions in which they participate. In an effort to collect data regarding this heterogeneous group of proteins we designed and constructed a database, called PerMemDB. PerMemDB is currently the most complete and comprehensive repository of data for eukaryotic peripheral membrane proteins deposited in UniProt or predicted with the use of MBPpred - a computational method that specializes in the detection of proteins that interact non-covalently with membrane lipids, via membrane binding domains. The first version of the database contains 231,770 peripheral membrane proteins from 1009 organisms.""" ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_2492, edam:operation_3431 ; sc:name "PerMemDB" ; sc:softwareHelp ; sc:url "http://bioinformatics.biol.uoa.gr/db=permemdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , "pmcid:PMC6602478", "pubmed:31106365" ; sc:description "Web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pergola-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pergola.crg.eu/" ; biotools:primaryContact "Cedric Notredame", "Julia Ponomarenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "PertInInt is a tool using an integrative approach uncovers genes with perturbed interactions in cancers. The tool enables rapid uncovering of significantly somatically mutated protein functional regions. The goal of the analytical PertInInt method is to rapidly uncover proteins with significant enrichments of somatic Perturbations In Interaction and other functional sites." ; sc:featureList edam:operation_0420, edam:operation_1812, edam:operation_3501 ; sc:name "PertInInt" ; sc:url "http://github.com/Singh-Lab/PertInInt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199 ; sc:citation , "pmcid:PMC6836735", "pubmed:31628256" ; sc:description "PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. If bulk sequencing data is used, we expect that mutations originate from diploid regions of the genome. Due to variance in VAF values, we recommend the use of bulk data in cases when sequencing depth is at least 1000x (haploid coverage). As output, PhISCS reports tree of tumor evolution together with a set of eliminated mutations, where eliminated mutations represent mutations violating Infinite Sites Assumption (due to deletion of variant allele or due to recurrent mutation) or mutations affected by copy number aberrations that were missed during the tumor copy number profiling (e.g. gain of non-variant allele)." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3233 ; sc:name "PhISCS" ; sc:url "https://github.com/sfu-compbio/PhISCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_0736, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:31612960" ; sc:description "PhaSePro is the comprehensive database of proteins driving liquid-liquid phase separation (LLPS) in living cells. LLPS is a molecular process employed by all living organisms to form membraneless organelles, mediating crucial cellular functions. PhaSePro is manually curated, it is solely based on experimentally verified cases of LLPS, integrating a wide range of information on the biophysical driving forces, biological function and regulation of these molecular systems." ; sc:featureList edam:operation_0361, edam:operation_2422, edam:operation_3216, edam:operation_3454 ; sc:name "PhaSePro" ; sc:url "https://phasepro.elte.hu" ; biotools:primaryContact "Rita Pancsa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0121, edam:topic_2229, edam:topic_3068 ; sc:citation , "pubmed:31584089" ; sc:description """PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures that may facilitate phase separation related proteins identification for all human proteins.""" ; sc:featureList edam:operation_2421, edam:operation_3454, edam:operation_3767 ; sc:name "PhaSepDB" ; sc:url "http://db.phasep.pro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "PhagePromoter is a python tool that predicts promoter sequences in phage genomes, using machine learning models." ; sc:isAccessibleForFree true ; sc:name "PhagePromoter" ; sc:url "https://www.bit.do/phagepromoter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2830, edam:topic_3047, edam:topic_3168, edam:topic_3957 ; sc:citation , "pubmed:31712799" ; sc:description "PhageXress us a Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3795 ; sc:name "PhageXpress" ; sc:url "https://github.com/mdcao/phagexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3375, edam:topic_3377, edam:topic_3379 ; sc:citation ; sc:description """PharmOmics is a A Species- and Tissue-specific Drug Signature Database and Online Tool for Toxicity Prediction and Drug Repurposing. It is a Web server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Integration. PharmOmics apps were implemented with Rshiny and depend on javascript. In case of failed loading, please check your antivirus setting and whitelist/temporary disable to solve the issue.""" ; sc:featureList edam:operation_0277, edam:operation_3223, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PharmOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mergeomics.research.idre.ucla.edu/PharmOmics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0632, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC6933858", "pubmed:31576621" ; sc:description "Pharmacophore is a tool for modeling and hit identification based on druggability simulations." ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3891 ; sc:name "Pharmmaker" ; sc:softwareHelp ; sc:url "http://prody.csb.pitt.edu/pharmmaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0153, edam:topic_2885, edam:topic_3298, edam:topic_3517 ; sc:citation , "pubmed:31860083" ; sc:description "PheGWAS is a three-dimensional approach to dynamically visualize GWAS across multiple phenotypes. It does interactive 3D visualization on many variants many phenotypes" ; sc:featureList edam:operation_0337 ; sc:name "PheGWAS" ; sc:url "https://github.com/georgeg0/PheGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3422 ; sc:citation , , "pubmed:31369862", "pubmed:35995107" ; sc:description "PheValuator is a phenotype algorithm evaluator." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PheValuator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/OHDSI/PheValuator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3325 ; sc:citation , "pubmed:25086502" ; sc:description "Combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "Phen-Gen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://phen-gen.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3325, edam:topic_3512 ; sc:citation ; sc:description "Phen2Gene is a phenotype-driven gene prioritization tool, that takes HPO (Human Phenotype Ontology) IDs as inputs, searches and prioritizes candidate causal disease genes. It is distributed under the MIT License by Wang Genomics Lab. Additionally, we have provided a web server and an associated RESTful API service for running Phen2Gene. Finally, a mobile app for Phen2Gene and several other genetic diagnostic tools from our lab is being tested and will be available soon." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3226 ; sc:license "MIT" ; sc:name "Phen2Gene" ; sc:url "https://phen2gene.wglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3517 ; sc:citation , "pmcid:PMC5507752", "pubmed:28079902" ; sc:description "Web catalog of high-priority measures for consideration and inclusion in biomedical and epidemiologic research." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PhenX Toolkit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.phenxtoolkit.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_0780, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC6805894", "pubmed:31641140" ; sc:description """PheonoCam is tracking vegetation phenology across diverse biomes using Version 2.0 of the PhenoCam Dataset. This tool facilitates the retrieval and post-processing of PhenoCam time series. The post-processing of PhenoCam data includes outlier removal and the generation of data products such as phenological transition dates.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:license "AGPL-3.0" ; sc:name "PhenoCam" ; sc:softwareHelp ; sc:url "https://phenocam.sr.unh.edu/webcam/gallery/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3335, edam:topic_3577 ; sc:citation , "pmcid:PMC5785853", "pubmed:29370821" ; sc:description "Database for phenotypic characterization of rare cardiac diseases." ; sc:featureList edam:operation_2422, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "PhenoDis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.helmholtz-muenchen.de/phenodis/" ; biotools:primaryContact "Dr. Andreas Ruepp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6426163", "pubmed:30937222" ; sc:description "Software package for the prediction of flowering phenology." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhenoForecaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/isaacWpark/PhenoForecaster" ; biotools:primaryContact "Isaac W Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3050, edam:topic_3697 ; sc:citation ; sc:description "Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity." ; sc:featureList edam:operation_3431, edam:operation_3557, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoGMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/prubbens/PhenoGMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc:description "Gene/disease prioritization tool that utilizes heterogeneous gene disease network." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PhenoGeneRanker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bozdaglab/PhenoGeneRanker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3298 ; sc:citation , "pmcid:PMC6377398", "pubmed:30535405" ; sc:description "PhenoMeNal (Phenome and Metabolome aNalysis) is a comprehensive and standardised e-infrastructure that supports the data processing and analysis pipelines for molecular phenotype data generated by metabolomics applications." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoMeNal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://portal.phenomenal-h2020.eu/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0625, edam:topic_3295, edam:topic_3574 ; sc:citation , "pubmed:31642469" ; sc:description "PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3799 ; sc:name "PhenoModifier" ; sc:url "https://www.biosino.org/PhenoModifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3295, edam:topic_3298 ; sc:citation ; sc:description "Database of human genotype-phenotype associations." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhenoScanner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://www.phenoscanner.medschl.cam.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3298, edam:topic_3308, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "PhenomeXcan is a tool for mapping the genome to the phenome through the transcriptome." ; sc:featureList edam:operation_2429 ; sc:license "MIT" ; sc:name "PhenomeXcan" ; sc:url "http://apps.hakyimlab.org/phenomexcan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3325 ; sc:citation , "pubmed:28334266" ; sc:description "Open platform for harmonization and analysis of genetic and phenotypic data." ; sc:featureList edam:operation_3226, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Phenopolis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phenopolis.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0089, edam:topic_0625, edam:topic_2275, edam:topic_3067 ; sc:citation , "pubmed:31596473" ; sc:description "Phenoscape is a Logical Model of Homology for Comparative Biology." ; sc:featureList edam:operation_0310, edam:operation_0477, edam:operation_2421 ; sc:license "MIT" ; sc:name "Phenoscape" ; sc:softwareHelp ; sc:url "http://phenoscape.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749, edam:topic_3170 ; sc:citation ; sc:description "PhiMRF is an R package for Poisson Hierarchical Markov Random Field model for analysis of spatial dependency on count data." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3800 ; sc:license "GPL-2.0" ; sc:name "PhiMRF" ; sc:url "https://github.com/ashleyzhou972/PhiMRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3489 ; sc:citation ; sc:description """PhilDB is capable of storing data at any frequency supported by Pandas. At this time only daily data has been extensively tested with some limited sub-daily usage. Timeseries database project is for storing potentially changing timeseries data. For example, hydrological data, like streamflow data, where the timeseries may be revised as quality control processes improve the recorded dataset over time.""" ; sc:featureList edam:operation_2422 ; sc:name "PhilDB" ; sc:softwareHelp ; sc:url "http://github.com/amacd31/phildb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC6753174", "pubmed:31572139" ; sc:description "Phobos is a software for the automated analysis of freezing behavior in rodents. Unlike other programs, it uses manual quantification of a short video to calibrate parameters for optimal freezing detection. Phobos works with 3 user interfaces (UIs) for this purpose. The main user UI is where the user loads videos for quantification, defines an output folder and creates the .xls file with the results. The Video Parameters UI is where the user defines the beginning and end times for freezing detection in the videos and crops the image to restrict the analysis to a specific area. Finally, the Manual Quantification UI is used to manually quantify freezing in a video, which will then be used as a reference for the calibration process." ; sc:featureList edam:operation_2428, edam:operation_3659, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "Phobos" ; sc:url "https://github.com/Felippe-espinelli/Phobos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3473, edam:topic_3520 ; sc:citation ; sc:description "Phoenix Enhancer is an online service/tool for proteomics data mining using clustered spectra." ; sc:featureList edam:operation_3432, edam:operation_3631, edam:operation_3767 ; sc:name "Phoenix Enhancer" ; sc:url "http://enhancer.ncpsb.org.cn/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:31410451" ; sc:description "Phosphoproteome prediction is a tool for predicting phosphorylation levels of the proteome across cancer patients. It integrates four components into itsalgorithm, including (i) baseline correlations between protein and phosphoprotein abundances, (ii) universal protein–protein interactions, (iii) shareable regulatory information across cancer tissues and (iv) associations among multi-phosphorylation sites of the same protein." ; sc:featureList edam:operation_0417, edam:operation_2492, edam:operation_3639 ; sc:name "Phosphoproteome Prediction" ; sc:url "https://github.com/GuanLab/phosphoproteome_prediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_3293 ; sc:citation ; sc:description "PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances." ; sc:featureList edam:operation_0546, edam:operation_3359, edam:operation_3478, edam:operation_3745 ; sc:license "BSD-3-Clause" ; sc:name "PhyChro" ; sc:url "http://www.lcqb.upmc.fr/phychro2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "PhyDL (Phylogenetics by Deep Learning) is a deep learning predictor for phylogenetic reconstruction." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:name "PhyDL" ; sc:url "https://gitlab.com/ztzou/phydl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3293 ; sc:citation ; sc:description "Phylogenetic model selection using likelihood-based criteria. SMS stends for Smart Model Selection." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SMS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.8.4" ; sc:url "http://www.atgc-montpellier.fr/sms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0602, edam:topic_3676 ; sc:citation "pubmed:31797599" ; sc:description """PhySigs uses the input of a phylogeny with nodes representing clones in a patient tumor, a signature matrix containing the set of mutational signatures to use in the analysis, and a feature matrix for the set of mutations introduced in each clone. In particular, the mutational categories in the feature matrix should correspond to the mutational categories used in the signature matrix. PhySigs automatically computes the count matrix, as it is simply a diagonal matrix containing the sum of columns in the feature matrix. PhySigs then solves the Tree-constrained Exposure (TE) problem for all possible clusterings of the clones that correspond to a partition of the phylogeny. The output of the TE problem is a relative exposure matrix composed of groups of identical columns corresponding to clusters of clones with identical exposures (denoted by blue and yellow). Edges between these clusters in the phylogeny are interpreted to be where exposure shifts occurred (denoted by a lightning bolt).""" ; sc:featureList edam:operation_0323, edam:operation_3435 ; sc:name "PhySigs" ; sc:url "https://github.com/elkebir-group/PhySigs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0659, edam:topic_0769, edam:topic_3293 ; sc:citation , "pmcid:PMC6889546", "pubmed:31791235" ; sc:description "PhySpeTree is an automated pipeline for reconstructing phylogenetic species trees." ; sc:featureList edam:operation_0325, edam:operation_0326, edam:operation_0327, edam:operation_0544, edam:operation_3478 ; sc:name "PhySpeTree" ; sc:url "https://pypi.org/project/PhySpeTree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6785678", "pubmed:31616568" ; sc:description "Phydelity, a redesign of PhyCLIP, is a statistically-principled and phylogeny-informed tool capable of identifying putative transmission clusters in pathogen phylogenies without the introduction of arbitrary distance thresholds" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196, edam:operation_3432 ; sc:license "LGPL-3.0" ; sc:name "Phydelity" ; sc:url "https://github.com/alvinxhan/Phydelity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3305 ; sc:citation , "pubmed:31512371" ; sc:description "This tool is a gene database for Phyllosticta citricarpa and sister species." ; sc:featureList edam:operation_3216 ; sc:name "Phyllosticta citricarpa" ; sc:url "https://genome.jgi.doe.gov/Phyllosticta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3512, edam:topic_3517 ; sc:citation , "pubmed:31537640" ; sc:description "PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies). One of PhyloCSF’s main current applications is to help distinguish protein-coding and non-coding RNAs represented among novel transcript models obtained from high-throughput transcriptome sequencing." ; sc:featureList edam:operation_0436, edam:operation_3192, edam:operation_3216 ; sc:license "AGPL-3.0" ; sc:name "PhyloCSF" ; sc:url "https://github.com/mlin/PhyloCSF/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293, edam:topic_3308, edam:topic_3837 ; sc:citation , "pubmed:31647547" ; sc:description "PhyloMagnet provides fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. The tool has a pipeline for screening metagenomes, looking for arbitrary lineages, using gene-centric assembly methods and phylogenetics" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_3258, edam:operation_3460, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "PhyloMagnet" ; sc:softwareHelp ; sc:url "http://github.com/maxemil/PhyloMagnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0602, edam:topic_3293 ; sc:citation , "pmcid:PMC6612858", "pubmed:31510688" ; sc:description "PhyloNet is a tool that applies a divide-and-conquer method for scalable phylogenetic network inference from multilocus data." ; sc:featureList edam:operation_0547, edam:operation_3501, edam:operation_3562 ; sc:name "PhyloNet" ; sc:url "https://bioinfocs.rice.edu/PhyloNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3500 ; sc:citation , "pmcid:PMC6657734", "pubmed:31062861" ; sc:description "A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes." ; sc:featureList edam:operation_3478, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhyloToL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Katzlab/PhyloTOL" ; biotools:primaryContact "L. A. Katz", "Mario Cerón-Romero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3120 ; sc:citation , "pmcid:PMC6597944", "pubmed:31075275" ; sc:description "Dynamic web application that enables the exploration and mapping of genetic variants onto experimental and predicted structures of proteins and protein complexes." ; sc:featureList edam:operation_0302, edam:operation_0331, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PhyreRisk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://phyrerisk.bc.ic.ac.uk" ; biotools:primaryContact "Alessia David" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0749, edam:topic_3318, edam:topic_3512 ; sc:citation , "pubmed:31809797" ; sc:description "PhysMPrePro is an energy model for recognizing the prokaryotic promoters based on molecular structure." ; sc:featureList edam:operation_0372, edam:operation_0440 ; sc:name "PhysMPrePro" ; sc:url "http://202.207.14.87:8032/bioinformation/PhysMPrePro/index.asp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3316 ; sc:citation , , "pmcid:PMC5841829", "pmcid:PMC6690424", "pubmed:29474446", "pubmed:31497314" ; sc:description "PhysiCell is a physics-based cell simulator." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PhysiCell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://physicell.mathcancer.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An InterMine interface to data from Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, which hosts 81 assembled and annotation genomes, from 78 viridiplantae species." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "PhytoMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "13 (phytomine-13.0)" ; sc:url "https://phytozome.jgi.doe.gov/phytomine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC6301341", "pubmed:30576486" ; sc:description "Database of plant protein inter-cultivar variability and function." ; sc:featureList edam:operation_0267, edam:operation_2422, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "PhytoTypeDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phytotypedb.bio.unipd.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data." ; sc:featureList edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PiMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polyomics.mvls.gla.ac.uk/" ; biotools:primaryContact "Karl Burgess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0736, edam:topic_3542 ; sc:citation , "pmcid:PMC6499831", "pubmed:31053765" ; sc:description "Deep-learning method for prediction of Ï€-helices in protein sequences." ; sc:featureList edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PiPred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/labstructbioinf/PiPred" ; biotools:primaryContact "Stanislaw Dunin-Horkawicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3068, edam:topic_3304, edam:topic_3500 ; sc:citation ; sc:description """PiVR is a closed-loop platform to study unrestrained sensorimotor behavior. PiVR has been developed to track a variety of animals in real time and present them with light stimuli.""" ; sc:featureList edam:operation_3431, edam:operation_3435 ; sc:name "PiVR" ; sc:softwareHelp ; sc:url "http://www.PiVR.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3390, edam:topic_3512 ; sc:citation ; sc:description "Single Cell RNA-seq Analysis Tool." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PicturedRocks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/umangv/picturedrocks" ; biotools:primaryContact "Umang Varma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3382, edam:topic_3512 ; sc:citation , "pubmed:30573696" ; sc:description "Application for designing molecular beacons for live cell imaging of endogenous mRNAs." ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_0502 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PinMol" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "beta 1.0" ; sc:url "https://bratulab.wordpress.com/software/" ; biotools:primaryContact "Irina E. Catrina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0798, edam:topic_3512 ; sc:citation ; sc:description "Tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data." ; sc:featureList edam:operation_0427, edam:operation_2495, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PingPongPro" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/suhrig/pingpongpro" ; biotools:primaryContact "Sebastian Uhrig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6896194", "pubmed:31689965" ; sc:description "PipeMEM is a Framework to Speed Up BWA-MEM in Spark with Low Overhead." ; sc:featureList edam:operation_3096, edam:operation_3182, edam:operation_3802 ; sc:name "PipeMEM" ; sc:url "https://github.com/SCUT-CCNL/PipeMEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description "R package for inferring ethnicity from placental DNA methylation microarray data." ; sc:featureList edam:operation_0417, edam:operation_3196, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PlaNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wvictor14/planet" ; biotools:primaryContact "Victor Yuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2259, edam:topic_3489 ; sc:citation , "pmcid:PMC6652102", "pubmed:31363499" ; sc:description "PlaSMo stands for Plant Systems-biology Modelling and the mission of the project was ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow." ; sc:featureList edam:operation_0481, edam:operation_2422, edam:operation_3431 ; sc:license "MIT" ; sc:name "PlaSMo" ; sc:url "https://github.com/SynthSys/PlasmoPortal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1931 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1354 ; sc:encodingFormat edam:format_2069 ; sc:name "Sequence profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1354 ; sc:encodingFormat edam:format_2069 ; sc:name "Sequence profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0798 ; sc:author ; sc:citation , "pubmed:30265232" ; sc:contributor "Mathieu Dubois" ; sc:description "PlaScope is a targeted approach to assess the plasmidome of bacteria." ; sc:featureList edam:operation_0525, edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PlaScope" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.3.1" ; sc:url "https://github.com/labgem/PlaScope" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31647529" ; sc:description "PlanExp is an intuitive integration of complex RNA-seq datasets with planarian omics resources." ; sc:featureList edam:operation_0571, edam:operation_2940, edam:operation_3223, edam:operation_3439 ; sc:name "PlanExp" ; sc:url "https://compgen.bio.ub.edu/PlanNET/planexp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "An integrated web resource of data & tools to mine Planarian biology" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "PlanMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "3.0" ; sc:url "http://planmine.mpi-cbg.de/planmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation ; sc:description "Plant is a website and database provides systematic annotations of all types of endogenous plant small RNA loci." ; sc:featureList edam:operation_3216, edam:operation_3792 ; sc:name "Plant" ; sc:url "http://plantsmallrnagenes.science.psu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31767692" ; sc:description "PlantAPAdb provides a comprehensive and manually curated catalog of APA sites in plants based on a large volume of data from diverse biological samples generated by 3′ seq. Currently, PlantAPAdb contains APA sites in seven plant organisms, including Oryza sativa L. (japonica and indica), Arabidopsis thaliana, Chlamydomonas reinhardtii, Medicago truncatula, Trifolium pratense, Populus trichocarpa and Phyllostachys edulis." ; sc:featureList edam:operation_0428, edam:operation_2421, edam:operation_2422 ; sc:name "PlantAPAdb" ; sc:url "http://www.bmibig.cn/plantAPAdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "Web-based platform of nucleotide sequence alignments of plants." ; sc:featureList edam:operation_0499, edam:operation_3200, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PlantAligDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plantaligdb.portugene.com" ; biotools:primaryContact "Filipe Pereira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC5727401", "pubmed:31725858" ; sc:description "PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables users to retrieve regulatory interactions of interest by circRNAs, miRNAs and mRNAs across eight model species. Sequences search is also available. And an enrichment analysis tool has been provided for Gene Ontology categories of miRNA targets." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3083, edam:operation_3501, edam:operation_3792 ; sc:name "PlantCircNet" ; sc:url "http://bis.zju.edu.cn/plantcircnet/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0749, edam:topic_0780, edam:topic_3169 ; sc:citation , "pubmed:31701126" ; sc:description "PlantRegMap is a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system." ; sc:featureList edam:operation_0438, edam:operation_2422, edam:operation_2429, edam:operation_2575 ; sc:name "PlantRegMap" ; sc:url "http://plantregmap.gao-lab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_2259, edam:topic_3315 ; sc:citation , "pmcid:PMC6805577", "pubmed:31638901" ; sc:description "PlantSimLab is a modeling and simulation web tool for plant biologists." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3891 ; sc:name "PlantSimLab" ; sc:url "http://app.plantsimlab.org/login.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation , ; sc:description """The purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world. The web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Plant DataDiscovery" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/data-discovery/" ; biotools:primaryContact "Support service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0780, edam:topic_3407, edam:topic_3810 ; sc:citation , "pubmed:31680153" ; sc:description "Plant Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of plant pathway knowledge." ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_2436, edam:operation_3083 ; sc:name "Plant Reactome" ; sc:url "https://plantreactome.gramene.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3173, edam:topic_3174 ; sc:citation , "pubmed:31494994" ; sc:description "Plant Regulomics is a data-driven interface for retrieving upstream regulators from plant multi-omics data, which integrates 20,737 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58,112 functional terms and 695,414 protein-protein interactions) from six plant species, namely Arabidopsis thaliana, Oryza sativa, Zea mays, Glycine max, Solanum lycopersicum and Triticum aestivum, along with the orthologous genes from 56 whole-genome sequenced plant species. These data were well-organized to gene modules and further implemented into the same statistical framework." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3501 ; sc:name "Plant Regulomics" ; sc:url "http://bioinfo.sibs.ac.cn/plant-regulomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly." ; sc:featureList edam:operation_0310, edam:operation_2995, edam:operation_3472 ; sc:license "MIT" ; sc:name "PlasClass" ; sc:url "https://github.com/Shamir-Lab/PlasClass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0632, edam:topic_3673 ; sc:citation , "pubmed:31584170" ; sc:description "PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS)." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3840 ; sc:name "PlasmidFinder" ; sc:url "https://cge.cbs.dtu.dk/services/PlasmidFinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0780, edam:topic_3474 ; sc:citation , "pubmed:31120045" ; sc:description "Automatised pharmacophoric deconvolution of plant extracts." ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "CECILL-1.0" ; sc:name "Plasmodesma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plasmodesma.igbmc.science" ; biotools:primaryContact "Marc-André Delsuc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3308 ; sc:author , ; sc:citation , ; sc:description "Protein-Level ASSembler (PLASS): sensitive and precise protein assembler" ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Plass" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1-2e0ef", "2-c7e35", "3-764a3", "4-687d7" ; sc:url "https://plass.mmseqs.com" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation , "pmcid:PMC6528300", "pubmed:31139240" ; sc:description "Software package for rapid, accurate, and flexible batch annotation of plastomes." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Plastid Genome Annotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/quxiaojian/PGA" ; biotools:primaryContact "Xiao-Jian Qu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0798 ; sc:author ; sc:citation , "pubmed:32579097" ; sc:description "Identification and characterization of bacterial plasmid contigs from short-read draft assemblies." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Platon" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.6" ; sc:url "https://github.com/oschwengers/platon" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc:description "Web-based visualization tool for exploring pleiotropy across complex traits." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PleioNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pleionet.com/" ; biotools:primaryContact "X. R. Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3304, edam:topic_3382 ; sc:citation ; sc:description "PlotTwist (Plotting data from Time-lapse experiments With Indicators of conditions at Set Times) is an app for visualizing the data and statistics of continuous data, with a focus on time-dependent measurements. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To facilitate the visualization of individual measurements, the data can be shown as 'small mutliples' or in 'heatmap-style'. To further facilitate the comparison, the mean and 95% CI can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha). Several color blind friendly palettes are available to label the data. The comparison of multiple conditions is enabled by multiple file upload (csv or xls format), where each file represents a condition." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3798 ; sc:name "PlotTwist" ; sc:url "https://huygens.science.uva.nl/PlotTwist" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3474, edam:topic_3500, edam:topic_3520 ; sc:citation , "pubmed:31735706" ; sc:description "MHC-I epitope presentation prediction based on transfer learning." ; sc:featureList edam:operation_0252, edam:operation_0416 ; sc:name "Pluto" ; sc:url "https://github.com/weipenegHU/Pluto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation , "pubmed:31602478" ; sc:description "PmiREN is a comprehensive encyclopedia of plant miRNAs." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3192, edam:operation_3792 ; sc:name "PmiREN" ; sc:url "http://www.pmiren.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0218, edam:topic_3474 ; sc:author "Shubham Vishnoi" ; sc:citation , "pubmed:31483930" ; sc:description "PnGT stand for 'Physicochemical n-Grams Tool'. It is a tool for protein physicochemical descriptor generation . Physicochemical n-Grams Tool (PnGT) is an open source standalone software for calculating physicochemical descriptors of protein developed using the Python scripting language." ; sc:featureList edam:operation_2423, edam:operation_2426, edam:operation_2930 ; sc:name "PnGT" ; sc:softwareHelp ; sc:url "http://14.139.57.41/pngt/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3174, edam:topic_3519, edam:topic_3577, edam:topic_3837 ; sc:citation , "pubmed:31758176" ; sc:description "Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens." ; sc:featureList edam:operation_0337, edam:operation_3200, edam:operation_3431 ; sc:license "MIT" ; sc:name "Pneumocystis" ; sc:url "https://github.com/Yiheng323/clinical_diagnosis_of_pneumocystis.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_0654, edam:topic_3517, edam:topic_3673 ; sc:citation , "pmcid:PMC6834686", "pubmed:31736907" ; sc:description "PointFinder is an Improved Resistance Prediction in Mycobacterium tuberculosis by Better Handling of Insertions and Deletions, Premature Stop Codons, and Filtering of Non-informative Sites." ; sc:featureList edam:operation_3202, edam:operation_3482, edam:operation_3695 ; sc:name "PointFinder" ; sc:url "http://bitbucket.org/genomicepidemiology/pointfinder_db" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0166, edam:topic_0209, edam:topic_3534 ; sc:citation ; sc:description "PointSite is a point cloud segmentation tool for identification of protein ligand binding atoms." ; sc:featureList edam:operation_0482, edam:operation_2575, edam:operation_3767 ; sc:name "PointSite" ; sc:url "https://github.com/PointSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31617559" ; sc:description """PolyASite is a consolidated atlas of polyadenylation sites from 3' end sequencing. A portal to the curated set of poly(A) sites that we inferred in the human, mouse and worm genomes, based on all 3’ end sequencing datasets that we could identify in the SRA nucleotide database as of June 2019.""" ; sc:featureList edam:operation_0363, edam:operation_0428, edam:operation_3208 ; sc:name "PolyASite" ; sc:url "https://polyasite.unibas.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3377 ; sc:citation , "pmcid:PMC5319934", "pubmed:28270862" ; sc:description "PolyPharmacology Browser (PPB) - Web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data" ; sc:featureList edam:operation_2489, edam:operation_2929, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gdbtools.unibe.ch:8080/PPB/" ; biotools:primaryContact "Mahendra Awale", "Prof. Jean Louis Reymond" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3751, edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:encodingFormat edam:format_3604 ; sc:name "Histogram" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3752 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3932 ; sc:encodingFormat edam:format_3752 ; sc:name "Q-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3604 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values." ; sc:featureList edam:operation_3664, edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "PolySTest" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/PolySTest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3325 ; sc:author "Sebastian Roskosch" ; sc:description "A tool for population level deletion calling from short paired-end sequence reads." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PopDel" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "https://github.com/kehrlab/PopDel" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_2640 ; sc:citation ; sc:description """An approach for reproducibly visualizing and assigning population affiliation in genomic samples of uncertain origin. Quick inference of population history. PopInf is a method to infer the major population (or populations) ancestry of a sample or set of samples. Below are steps for running PopInf. PopInf is incorporated into the workflow system snakemake. All necessary files and scripts are in this directory. There are instructions on preparing the reference panel in a folder called "Reference_Panel". There are also instructions on preparing the unknown samples in a folder called "Unknown_Samples\"""" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:name "PopInf" ; sc:url "https://github.com/SexChrLab/PopInf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "Tool for linkage disequilibrium decay analysis based on variant call format files." ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PopLDdecay" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/BGI-shenzhen/PopLDdecay" ; biotools:primaryContact "Wei-Ming He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3796, edam:topic_3810 ; sc:citation , "pubmed:31095319" ; sc:description "Network-Based Web Resource for Exploring Population Structure." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PopNetD3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compsysbio.org/popnetd3" ; biotools:primaryContact "John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0659, edam:topic_2885, edam:topic_3056, edam:topic_3170 ; sc:citation , "pmcid:PMC6790967", "pubmed:31608947" ; sc:description """PopTargs is a database for studying population evolutionary genetics of human microRNA target sites. These are the scripts used to create the MySQL database that is used by PopTargs.essex.ac.uk. The pipeline can be altered to create similar databases with different species, it may need to be adjusted to fit your file names.""" ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_2421 ; sc:license "MIT" ; sc:name "PopTargs" ; sc:url "https://poptargs.essex.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3305, edam:topic_3517 ; sc:citation , "pubmed:31659794" ; sc:description """The Parkinson's Disease Mendelian Randomization Research Portal. iPDGC PD MR Research Portal""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659 ; sc:name "Portal" ; sc:url "https://pdgenetics.shinyapps.io/MRportal/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation , , "pmcid:PMC6710256", "pubmed:31451723" ; sc:description "Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes" ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Porter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5" ; sc:url "http://distilldeep.ucd.ie/porter/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3542 ; sc:citation , , , "pmcid:PMC6710256", "pubmed:31451723" ; sc:description "Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes" ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0469, edam:operation_0470 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Porter5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5" ; sc:url "http://distilldeep.ucd.ie/porter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2885, edam:topic_3517, edam:topic_3676 ; sc:citation , ; sc:description """An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. Potpourri provides a MATLAB interface for ease of use. These instructions will guide you to build and run Potpourri on MATLAB.""" ; sc:featureList edam:operation_0484, edam:operation_2238, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "Potpourri" ; sc:url "https://github.com/gizemcaylak/Potpourri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31552639" ; sc:description "Using the Object-Oriented PowerShell for Simple Proteomics Data Analysis | Scripting languages such as Python and Bash are appreciated for solving simple, everyday tasks in bioinformatics" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3631 ; sc:name "PowerShell" ; sc:url "https://cpm.lumc.nl/yassene/powershell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3304, edam:topic_3401 ; sc:citation , "pmcid:PMC6827337", "pubmed:31449248" ; sc:description "A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits | Gait analysis is used to quantify changes in motor function in many rodent models of disease. Despite the importance of assessing gait and motor function in many areas of research, the available commercial options have several limitations such as high cost and lack of accessible, open code. To address these issues, we developed PrAnCER, Paw-Print Analysis of Contrast-Enhanced Recordings, for automated quantification of gait. The contrast-enhanced recordings are produced by using a translucent floor that obscures objects not in contact with the surface, effectively isolating the rat's paw prints as it walks. Using these videos, our simple software program reliably measures a variety of spatiotemporal gait parameters. To demonstrate that PrAnCER can accurately detect changes in motor function, we employed a haloperidol model of Parkinson's disease (PD)" ; sc:featureList edam:operation_3799 ; sc:name "PrAnCER" ; sc:url "https://github.com/hayleybounds/PrAnCER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3534 ; sc:citation , , "pmcid:PMC6602436", "pubmed:31114880" ; sc:description "Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application." ; sc:featureList edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PrankWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prankweb.cz/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31710075" ; sc:description """Prediction of S-nitrosylation sites by integrating support vector machines and random forest. PreSNO is only available to academic users""" ; sc:featureList edam:operation_0417 ; sc:name "PreSNO" ; sc:url "http://kurata14.bio.kyutech.ac.jp/PreSNO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3912 ; sc:citation , "pubmed:31526842" ; sc:description "Fast prediction of bacteriophage Virion proteins using un-biased multi-perspective properties with recursive feature elimination | Bacteriophage virion proteins (BVPs) are bacterial viruses that have a great impact on different biological functions of bacteria. They are significantly used in genetic engineering and phage therapy applications. Correct identification of BVP through conventional pathogen methods are slow and expensive. Thus, designing a Bioinformatics predictor is urgently desirable to accelerate correct identification of BVPs within a huge volume of proteins. However, available prediction tools performance is inadequate due to the lack of useful feature representation and severe imbalance issue. In the present study, we propose an intelligent model, called Pred-BVP-Unb for discrimination of BVPs that employed three nominal sequences-driven descriptors, i.e" ; sc:name "Pred-BVP-Unb" ; sc:url "https://github.com/Muhammad-Arif-NUST/BVP_Pred_Unb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0736, edam:topic_0820, edam:topic_3474 ; sc:citation , "pubmed:31821684" ; sc:description """Prediction of disease-causing and neutral mutations in human transmembrane proteins. Transmembrane proteins (TMPs) act as a gate to the interior of the cells. A tool to discriminate the disease-causing and neutral mutations of membrane proteins. We have used 4 different type of datasets for developing the classification models and these datasets are available in the follwoing link""" ; sc:featureList edam:operation_0269, edam:operation_0331, edam:operation_2241 ; sc:name "Pred-MutHTP" ; sc:url "https://www.iitm.ac.in/bioinfo/PredMutHTP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation , "pmcid:PMC6688581", "pubmed:31428122" ; sc:description "Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees | Prediction of protein-RNA binding affinity | PredPRBA, a computational method that can effectively predict Protein-RNA Binding Affinity using Machine Learning Algorithm" ; sc:featureList edam:operation_3659, edam:operation_3901, edam:operation_3902 ; sc:name "PredPRBA" ; sc:url "http://PredPRBA.denglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:31070294" ; sc:description "Predicting the change of percent spliced in (delta-PSI or ) caused by genetic variants." ; sc:featureList edam:operation_0433, edam:operation_0446, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PredPSI-SVR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/chenkenbio/PredPSI-SVR" ; biotools:primaryContact "Huiying Zhao", "Yuedong Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_3050, edam:topic_3168, edam:topic_3500 ; sc:citation ; sc:description "PrimerMiner is an R package for the development and validation of DNA metabarcoding COI primers for aquatic invertebrates." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3200, edam:operation_3237 ; sc:name "PrimerMiner" ; sc:url "https://github.com/VascoElbrecht/PrimerMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation , "pmcid:PMC6763777", "pubmed:31408580" ; sc:description "Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities | Prioritizing Cancer Drugs for Interested Cancer | Prioritize candidate cancer drugs for drug repositioning based on the random walk with restart algorithm in a drug-drug functional similarity network. 1) We firstly constructed a drug-drug functional similarity network by integrating pathway activity and drug activity derived from the NCI-60 cancer cell lines. 2) Secondly, we calculated drug repurposing score according to a set of approved therapeutic drugs of interested cancer based on the random walk with restart algorithm in the drug-drug functional similarity network. 3) Finally, the permutation test was used to calculate the statistical significance level for the drug repurposing score" ; sc:featureList edam:operation_2436, edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "PriorCD" ; sc:url "https://cran.r-project.org/web/packages/PriorCD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31713585" ; sc:description """Sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. This server predicts protein-protein binding affinity change upon mutation using sequence-based features and functional class. ProAffiMuSeq shows a correlation of 0.73 and a mean absolute error (MAE) of 0.86 kcal/mol in cross-validation. In the test dataset, the performance remains consistent with a correlation of 0.75 with MAE of 0.94 kcal/mol. In a blind dataset of 473 mutations (Geng et al. 2019, Proteins 87, 110-119) it showed a correlation and MAE of 0.27 and 1.06 kcal/mol, respectively, comparable to structure-based methods. Further, our method showed a MAE of 1.21 kcal/mol, when tested with a set of 552 additional non-redundant interface mutations in 80 complexes deposited in SKEMPI 2.0 (Jankauskaitė et al. 2019, Bioinformatics 35, 462-469)""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3431 ; sc:name "ProAffiMuSeq" ; sc:url "https://web.iitm.ac.in/bioinfo2/proaffimuseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0152, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31598690" ; sc:description """a database of carbohydrate-binding proteins. An open access database ready to answer your sweetest queries. Carbohydrate-binding proteins play crucial roles across all viruses and organisms""" ; sc:featureList edam:operation_0224, edam:operation_0570, edam:operation_3092 ; sc:name "ProCarbDB" ; sc:url "http://www.procarbdb.science/procarb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection | ProGeo-neo requires a Linux operation system (centos6) with Python (V2.7) , Perl and Java installed" ; sc:featureList edam:operation_0252, edam:operation_3211 ; sc:name "ProGeo-neo" ; sc:url "https://github.com/kbvstmd/ProGeo-neo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_2640, edam:topic_3325 ; sc:citation ; sc:description """An online dataset for accelerating the complete characterization of the human protein-phenotype landscape in biomedical literature. Identifying protein-phenotype relations is of paramount importance for applications such as uncovering rare and complex diseases. One of the best resources that captures the protein-phenotype relationships is the biomedical literature. In this work, we introduce ProPheno, a comprehensive online dataset composed of human protein phenotype mentions extracted from the complete corpora of Medline and PubMed Central Open Access. Moreover, it includes co-occurrences of protein-phenotype pairs within different spans of text such as sentences and paragraphs. We use ProPheno for completely characterizing the human protein-phenotype landscape in biomedical literature""" ; sc:featureList edam:operation_0306, edam:operation_3778 ; sc:name "ProPheno" ; sc:url "http://propheno.cs.montana.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation , "pmcid:PMC6602423", "pubmed:31114881" ; sc:description "Web-based application for exploration and analysis of protein structures using network formalism." ; sc:featureList edam:operation_0244, edam:operation_0272, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ProSNEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prosnex-tool.com" ; biotools:primaryContact , "Onur Sercinoglu", "Rasim Murat Aydinkal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pubmed:31070745" ; sc:description "Ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery." ; sc:featureList edam:operation_0238, edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zhengchangsulab/prosampler" ; biotools:primaryContact "Yang Li", "Zhengchang Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3520 ; sc:citation , "pmcid:PMC6915695", "pubmed:31844049" ; sc:description """ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery. Automated online software for anticancer drug target/mechanism deconvolution. . ProTargetMiner is also available directly through this web page: http://protargetminer.genexplain.com. The ProTargetMiner R Shiny package is an automated online software for anticancer drug target mechanism deconvolution""" ; sc:featureList edam:operation_0337, edam:operation_3629, edam:operation_3767 ; sc:name "ProTargetMiner" ; sc:url "http://protargetminer.genexplain.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6830000", "pubmed:31684883" ; sc:description """predictor for cellular protein stability. Tool for classification of protein variations predictor. A benchmark database for variations. Datasets for training and testing cellular protein stability predictor ProTstab:. Stability of biomolecules, especially of proteins, is of great interest and significance. Protein stability has been the major target for protein engineering, mainly to increase the stability, but sometimes also to destabilize proteins . Effects on stability are among the most common consequences for disease-related variations , thus this phenomenon is of interest for variation interpretation to explain the effects of harmful variants. We trained a novel machine learning tool for prediction of protein stability, especially melting temperature Tm. The tool is based on amino acid sequence information and using GBRT (Gradient boosting of regression trees) algorithm.""" ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_2489, edam:operation_3659 ; sc:name "ProTstab" ; sc:url "http://structure.bmc.lu.se/ProTstab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3047 ; sc:citation ; sc:description """Assessing the shared variation among high-dimensional data matrices. Réflexions autour de l'analyse de la variance basée sur une analyse type procuste pour estimé la part de la variance d'un tableau expliquée par un ou plusieurs autres tableaux""" ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3891 ; sc:name "ProcMod" ; sc:url "https://git.metabarcoding.org/lecasofts/ProcMod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3047 ; sc:citation , "pubmed:31678214" ; sc:description """web-based tool for the prediction, deciphering and design of promiscuous peptides that bind to HLA class I molecules. PromPDD :HLA peptide-binding fingerprints : HLAsupE : Publication : Download: tutorial. PromPDD were developed based on the prediction models generated using the average relative binding (ARB) matrix method.PromPDD enables the prediction and deciphering of promiscuous peptides that bind to multiple HLA molecules within or cross HLA supertypes in a simpler and more direct way. We expanded the application of PromPDD to HLA class I alleles with limited experimentally verified data by generating pan-specific matrices using a derived modular method, and more than 2500 HLA molecules encoded by HLA-A and -B genes are available in PromPDD""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3461 ; sc:name "PromPDD" ; sc:url "http://www.immunoinformatics.net/PromPDD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0749, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc:description """sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence. Machine Learning using Multivariate Linear Regression to Predict the Strength of a Promoter.""" ; sc:featureList edam:operation_0321, edam:operation_0440, edam:operation_3659 ; sc:name "PromoterPredict" ; sc:url "https://github.com/PromoterPredict" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3474, edam:topic_3557 ; sc:citation , "pmcid:PMC6602508", "pubmed:31114893" ; sc:description "Integrative tool that employs similarity matching within our customized phage parts library and machine learning of prophage genetic features, to score the probability of a prophage being active." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Prophage Hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pro-hunter.bgi.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31133760" ; sc:description "Proteome-wide prediction of peptide tandem mass spectra by deep learning." ; sc:featureList edam:operation_3627, edam:operation_3649, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Prosit" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.proteomicsdb.org/prosit/" ; biotools:primaryContact "Prof. Dr. Bernhard Küster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0194 ; sc:citation , "pmcid:PMC6436989", "pubmed:30535314" ; sc:description "Alignment-free phylogeny reconstruction based on whole-proteome sequences." ; sc:featureList edam:operation_0289, edam:operation_0557, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Prot-SpaM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jschellh/ProtSpaM" ; biotools:primaryContact "Jendrik Schellhorn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0218, edam:topic_3512 ; sc:citation , "pmcid:PMC6705771", "pubmed:31437145" ; sc:description "A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins | A RESOURCE FOR FUSION PROTEINS AND THEIR INTERACTIONS | Milana Frenkel-Morgenstern's Cancer Genomics and BioComputing Lab at Bar-Ilan University, Israel | Result for the search by Unspecified: | Lars Juhl Jensen's Cellular Network Biology Group at The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark | ProtFus is a resource that has information about fusion proteins and their interactions, based on a text mining approach. \"Tagging\" is a process of registering the mention of given entities in a particular document | Text mining has been an active research topic for decades; however, it is only fairly recently that biomedical text-mining tools have been developed that make it practically applicable to a wide range of problems" ; sc:featureList edam:operation_0306, edam:operation_2492 ; sc:name "ProtFus" ; sc:url "http://protfus.md.biu.ac.il/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_0601, edam:topic_0602 ; sc:citation ; sc:description """Assembling a phosphoproteomic knowledge base using ProtMapper to normalize phosphosite information from databases and text mining. Map amino acid sites of post-translational modifications from models or data to reference positions. Code to generate results and figures relevant to the ProtMapper manuscript. The Protmapper maps references to protein sites to the human reference sequence based on UniProt, PhosphoSitePlus, and manual curation.""" ; sc:featureList edam:operation_0306, edam:operation_0310, edam:operation_0417, edam:operation_3436, edam:operation_3755 ; sc:license "BSD-2-Clause" ; sc:name "ProtMapper" ; sc:url "https://github.com/indralab/protmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3068, edam:topic_3489, edam:topic_3534 ; sc:citation , "pmcid:PMC6813136", "pubmed:31650170" ; sc:description """a database of promiscuous proteins. Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing catalytic promiscuity. ProtMiscuity contains information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 different organisms. It can be searched or browsed by protein names, organisms and descriptions of canonical and promiscuous reactions. Entries provide information on reaction substrates, products and kinetic parameters, mapping of active sites to sequence and structure and links to external resources with biological and functional annotations.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3896 ; sc:name "ProtMiscuity" ; sc:url "http://ufq.unq.edu.ar/protmiscuity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_3520 ; sc:citation , "pmcid:PMC6842221", "pubmed:31706265" ; sc:description """bypassing the imputation of missing values in differential expression analysis of proteomic data. Python package for differential abundance analysis of proteomics data""" ; sc:featureList edam:operation_2495, edam:operation_3557, edam:operation_3741 ; sc:license "GPL-3.0" ; sc:name "ProtRank" ; sc:url "https://github.com/8medom/ProtRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3306, edam:topic_3474 ; sc:citation ; sc:description "Solubility from protein sequence prediction." ; sc:featureList edam:operation_0409, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Protein-sol" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://protein-sol.manchester.ac.uk/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0736 ; sc:citation , "pubmed:31392322" ; sc:description "protein quality control in E. coli | Publicly available database regarding protein quality control in E. coli | You are using an unsupported browser. Please switch to recent version of either Chrome, Firefox, Edge, Opera or Safari" ; sc:featureList edam:operation_2428, edam:operation_3501 ; sc:name "Protein Homeostasis Database" ; sc:url "http://PHDB.switchlab.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1957 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1957 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2628 ; sc:encodingFormat edam:format_1957 ; sc:name "BioGRID interaction ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3464 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1957 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3510 ; sc:description "Integration of structural information with interactomics data." ; sc:featureList edam:operation_0276, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Proteo3Dnet" ; sc:softwareHelp ; sc:softwareVersion "1.02" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Proteo3Dnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc:description """a taxonomic toolkit for multi-species and metaproteomic analysis. ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. What is ProteoClade? — ProteoClade 0.0.1 documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_3644, edam:operation_3767, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ProteoClade" ; sc:softwareHelp ; sc:url "http://github.com/HeldLab/ProteoClade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1775, edam:topic_2259, edam:topic_3360 ; sc:citation , , "pubmed:30852829", "pubmed:34236662" ; sc:description "ProteoRE (Proteomics Research Environment) is a Galaxy-based instance for the functional analysis and the exploration of proteomics and transcriptomics data in biomedical research; ProteoRE comprises 18 tools organized into five subsections for: i) data manipulation; ii) human and iii ) mouse species database annotation; iv) functional analysis; and v) pathway analysis along with graphical representations." ; sc:name "ProteoRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.2" ; sc:url "https://proteore.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3655 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3520, edam:topic_3557 ; sc:description """Fully managed proteomics data analysis. Cloud-based proteomic data analysis that helps users go from raw MS data to results efficiently. Modern app + open source algorithms + powerful analysis tools""" ; sc:featureList edam:operation_3631, edam:operation_3694, edam:operation_3695, edam:operation_3767, edam:operation_3802 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "ProteoWorker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.proteoworker.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2229, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:31690884" ; sc:description "ProteomeHD is an R script for creating a co-regulation map of the human proteome enables identification of protein functions." ; sc:featureList edam:operation_2495, edam:operation_3216, edam:operation_3638, edam:operation_3766, edam:operation_3767 ; sc:name "ProteomeHD" ; sc:url "http://www.proteomeHD.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Web portal dedicated to the diatom Pseudo-nitzschia multistriata. A genome browser, a BLAST service and a download section are available." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Pseudo-nitzschia multistriata genome portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.szn.it/pmultistriata/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6797663", "pubmed:31432329" ; sc:description "Obtaining psychological embeddings through joint kernel and metric learning | A python package for inferring psychological embeddings | PsiZ: A Psychological Embedding Package | Experiments using the PsiZ package published in Behavior Research Methods | PsiZ provides the computational tools to infer a continuous, multivariate stimulus representation using ordinal similarity relations. It integrates well-established cognitive theory with contemporary computational methods. The companion Open Access article is available at https://link.springer.com/article/10.3758/s13428-019-01285-3 | You will need a Python interpretter (>= 3.6) along with the an installation of the psiz package (version 0.1.0) in your preferred environment. You can install the correct version of the psiz package using pip: pip install psiz==0.1.0. You can also find version 0.1.0 on GitHub: https://github.com/roads/psiz/archive/v0.1.0.tar.gz" ; sc:license "Apache-2.0" ; sc:name "PsiZ" ; sc:url "https://github.com/roads/psiz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0199, edam:topic_0749, edam:topic_3320 ; sc:citation , "pubmed:31809863" ; sc:description """An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translational annotations to de novo variants, which are found in subjects but not in their parents, in developmental and neuropsychiatric disorders. Large-scale genomic and proteomic data are integrated into PsyMuKB, including developmental brain expressions, neuronal single-cell transcriptome, regulatory elements, and transcript annotations, protein-protein interactions (PPI) and protein isoform expressions. It aims to provide users with a comprehensive data exploration of de novo variants, such as their genomic locations on alternatively spliced isoforms, expression patterns of the mutation-disrupted genes and/or isoforms, and interaction network of impacted proteins""" ; sc:featureList edam:operation_0337, edam:operation_3227 ; sc:name "PsyMuKB" ; sc:url "http://psymukb.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3303, edam:topic_3473 ; sc:citation , "pmcid:PMC6602571", "pubmed:31114887" ; sc:description "Web-based application that provides computer-annotated biomedical concepts, such as genes and mutations, in PubMed citations and PMC full-text articles." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PubTator Central" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.ncbi.nlm.nih.gov/research/pubtator/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0634 ; sc:citation , "pmcid:PMC6323318", "pubmed:30624653" ; sc:description "Web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records." ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PubTerm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinformatica.mty.itesm.mx:8080/Biomatec/pubterm.html" ; biotools:primaryContact "Victor Trevino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_3308 ; sc:citation ; sc:description "a curated lung disease gene expression database | An accessible R package to download PulmonDB data | PulmonDB is a transcriptomic database of IPF and COPD with curated annotation | PulmonDB is a gene expression database with Chronic Obstructive Pulmonary Diseases (COPD) and Idiopathic Pulmonary Disease (IPF) experiments. It has homogenized values using individual contrast and manual curated annotation that can be download or accessed by http://pulmondb.liigh.unam.mx" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3258 ; sc:name "PulmonDB" ; sc:url "http://pulmondb.liigh.unam.mx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0736, edam:topic_2830, edam:topic_3293 ; sc:citation ; sc:description "Punchline is a tool for identifying and comparing significant Pfam protein domain differences across draft whole genome sequences." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_2454 ; sc:name "Punchline" ; sc:url "https://github.com/LCrossman/punchline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0736 ; sc:citation ; sc:description "Efficient and accurate prediction of transmembrane topology from amino acid sequence only." ; sc:featureList edam:operation_0269, edam:operation_0468, edam:operation_2241 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PureseqTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pureseqtm.predmp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3385, edam:topic_3452 ; sc:citation , "pubmed:31086343" ; sc:description "Software tools for automated transmission electron microscopy." ; sc:featureList edam:operation_1812, edam:operation_3457, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Py-EM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://git.embl.de/schorb/pyem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_3047, edam:topic_3314 ; sc:citation , "pmcid:PMC6776882", "pubmed:31612127" ; sc:description """A Global Optimizer for Nanoclusters. Python program for aggregation and reaction. PyAR stands for "Python program for aggregation and reaction\"""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:name "PyAR" ; sc:url "https://github.com/anooplab/pyar" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "A command-line tool for analysis of big biological data sets for distributed HPC clusters." ; sc:featureList edam:operation_2939, edam:operation_2945, edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyBDA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://pybda.readthedocs.io/en/latest/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "Algorithm for BSA-Seq data analysis." ; sc:featureList edam:operation_0484, edam:operation_3211, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PyBSASeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dblhlx/PyBSASeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2269 ; sc:citation , , "pmcid:PMC6744527", "pubmed:31522114", "pubmed:34986226" ; sc:description "A general-purpose program for parameterizing biological models specified using the BioNetGen rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML)." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PyBioNetFit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bionetfit.nau.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC6438028", "pubmed:30922213" ; sc:description "Python package for easy retrieval of biological data from heterogeneous sources." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Apache-1.0" ; sc:name "PyCellBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.7.1" ; sc:url "https://pypi.org/project/pycellbase/" ; biotools:primaryContact "Daniel Perez-Gil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description """Discontinuous Boundary Elements for Fluid Flow Problems in Discrete Fracture Networks. Modeling fluid flow in three-dimensional (3D) Discrete Fracture Networks (DFNs) is of relevance in many engineering applications, such as hydraulic fracturing, oil gas production, geothermal energy extraction, nuclear waste disposal and CO2 sequestration. A new Boundary Element Method (BEM) technique with discontinuous quadratic elements and a parallel Domain Decomposition Method (DDM) is presented herein for the simulation of the steady-state fluid flow in 3D DFN systems with wellbores, consisting of planar fractures having arbitrary properties and wellbore trajectories. Numerical examples characterized by DFNs of increasing complexity are investigated to evaluate the accuracy and efficiency of the presented technique.""" ; sc:name "PyDFN3D" ; sc:url "https://github.com/BinWang0213/PyDFN3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0749, edam:topic_3512 ; sc:citation ; sc:description "Python-based effective feature generation tool for DNA, RNA and protein sequences." ; sc:featureList edam:operation_0440, edam:operation_3092, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PyFeat" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/mrzResearchArena/PyFeat/" ; biotools:primaryContact "Rafsanjani Muhammod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3489 ; sc:citation , "pmcid:PMC6842186", "pubmed:31703553" ; sc:description """scalable data extraction and analysis for heterogeneous genomic datasets. Python Library for data analysis based on GMQL. The doucumentation can be found at the following link: http://pygmql.readthedocs.io. API for calling interactively the GMQL Engine from Python""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3791 ; sc:license "Apache-2.0" ; sc:name "PyGMQL" ; sc:url "https://github.com/DEIB-GECO/PyGMQL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6894873", "pubmed:31805157" ; sc:description """An open-source Pythonic library to compute landscape metrics. Open-source Python library to compute landscape metrics. Example notebooks of the PyLandStats library. Test and Deploy Your Code with Confidence. Test Coverage History & Statistics. PyLandStats documentation! — PyLandStats 2.0.0a1 documentation. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". PLOS ONE, 14(12), 1-19. doi.org/10.1371/journal.pone.0225734. Citation: Bosch M. 2019. "PyLandStats: An open-source Pythonic library to compute landscape metrics". Preprint available at bioRxiv. https://doi.org/10.1101/715052. Travis CI enables your team to test and ship your apps with confidence. Easily sync your projects with Travis CI and you'll be testing your code in minutes. Test code coverage history for martibosch/pylandstats. Open-source Pythonic library to compute landscape metrics within the PyData stack (NumPy, pandas, matplotlib...)""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "PyLandStats" ; sc:softwareHelp ; sc:url "https://anaconda.org/conda-forge/pylandstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3343, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6698780", "pubmed:31456680" ; sc:description "Python Library to Build Screens in a Declarative Way | Python library to develope paradigms for psychological experiments | PyParadigm is a small library to build paradigms for psychological experiments. It utilizes pygame, and is installable via pip | Welcome to PyParadigm — PyParadigm 0.1 documentation | PyParadigm is a small set of classes and functions designed to make it easy to write psychological paradigms in Python | PyParadigm takes another approach" ; sc:featureList edam:operation_1816 ; sc:license "MIT" ; sc:name "PyParadigm" ; sc:softwareHelp ; sc:url "https://github.com/KnorrFG/pyparadigm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3325, edam:topic_3332 ; sc:citation , "pubmed:31742744" ; sc:description """An improbability drive for rare events. pyretis - Rare Event Simulations with python. PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling .""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3799 ; sc:name "PyRETIS 2" ; sc:url "http://www.pyretis.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0769, edam:topic_2640, edam:topic_3384 ; sc:citation , "pmcid:PMC6916323", "pubmed:31580484" ; sc:description "PyRadiomics is an ontology-guided radiomics analysis workflow (O-RAW)." ; sc:featureList edam:operation_1812, edam:operation_3435, edam:operation_3443 ; sc:name "PyRadiomics" ; sc:url "https://github.com/Radiomics/pyradiomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:31373614" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'AVAILABILITY:PyRanges' | efficient comparison of genomic intervals in Python | (beta) Performant Pythonic GenomicRanges | PyRanges are collections of intervals that support comparison operations (like overlap and intersect) and other methods that are useful for genomic analyses. The ranges can have an arbitrary number of meta-data fields, i.e. columns associated with them | PyRanges is in a beta state. We are extremely responsive to bug-reports, so if you have problems or come across unexpected behavior, please create an issue | GenomicRanges and genomic Rle-objects for Python | Feel free to ask questions of the type \"how do I do X with pyranges?\" on public forums like Stack Overflow, Bioinformatics Stack Exchange or Biostars. You can use endrebak85#gmail.com to point me to the question(s) | \"Finally ... This was what Python badly needed for years.\" - Heng Li" ; sc:featureList edam:operation_3802 ; sc:license "MIT" ; sc:name "PyRanges" ; sc:url "https://pyranges.readthedocs.io/en/master/autoapi/pyranges/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6913930", "pubmed:31841550" ; sc:description """Python framework for rate-based neural simulations. PyRates is a framework for neural modeling and simulations, developed by Richard Gast and Daniel Rose at the Max Planck Institute of Human Cognitive and Brain Sciences, Leipzig, Germany. Max Planck Institute for Human Cognitive and Brain Sciences. Welcome to the PyRates documentation! — PyRates 0.7.1 documentation. Welcome to the PyRates documentation!¶. PyRates is a Python 3 tool for building rate-based neural models and performing numerical simulations of their dynamic behavior. Efficient software solutions for building and analyzing neural models are of tremendous value to the field of computational neuroscience. Open-source Python toolbox for rate-based neural modeling. PyRates requires an installation of Python >=3.6.1""" ; sc:featureList edam:operation_0337, edam:operation_2497, edam:operation_3562, edam:operation_3907 ; sc:license "GPL-3.0" ; sc:name "PyRates" ; sc:softwareHelp ; sc:url "https://www.cbs.mpg.de/departments/neurophysics/software/pyrates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275 ; sc:citation , "pubmed:31117512" ; sc:description "Software developed to generate dynamic molecular interaction fields (dMIFs) and pharmacophore features based on analyzing the protein environment of water molecules in molecular dynamcis simulations." ; sc:featureList edam:operation_0244, edam:operation_0482, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PyRod" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/schallerdavid/pyrod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:31872957" ; sc:description """PySpacell is a Python Package for Spatial Analysis of Cell Images. Technologies such as microscopy, sequential hybridization, and mass spectrometry enable quantitative single-cell phenotypic and molecular measurements in situ. Deciphering spatial phenotypic and molecular effects on the single-cell level is one of the grand challenges and a key to understanding the effects of cell-cell interactions and microenvironment. However, spatial information is usually overlooked by downstream data analyses, which usually consider single-cell read-out values as independent measurements for further averaging or clustering, thus disregarding spatial locations. With this work, we attempt to fill this gap. We developed a toolbox that allows one to test for the presence of a spatial effect in microscopy images of adherent cells and estimate the spatial scale of this effect.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552, edam:operation_3799, edam:operation_3891 ; sc:name "PySpacell" ; sc:url "https://pypi.org/project/pySpacell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_3047 ; sc:citation ; sc:description """a PyMOL plugin for visualization, comparison, and volume calculation of drug-binding sites. volume calculation and segmentation. PyVOL: Protein Pocket Visualization, Segmentation, and Characterization. PyVOL is a python library packaged into a PyMOL GUI for identifying protein binding pockets, partitioning them into sub-pockets, and calculating their volumes""" ; sc:featureList edam:operation_0337, edam:operation_0387, edam:operation_2575 ; sc:license "MIT" ; sc:name "PyVOL" ; sc:url "https://github.com/schlessingerlab/pyvol/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0601 ; sc:citation ; sc:description "A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model Organisms | Pyntheon; A post translational modifications (PTMs) mapping tool for 87 different species, these PTMs are taken from a large array of popular lab specimens | we are presenting, Universal Functional PTMs Mapping Tool (Pyntheon) which maps post translational modifications (PTMs) present in the functional regions of proteins of almost all lab specimens that are popular among research community. From viruses to human, this tool includes 87 species (see species_id.txt) can help mapping the mutations to PTMs sites or give information about the PTMs present for a list of proteins (UniProt ID) of interest" ; sc:featureList edam:operation_0331, edam:operation_0417, edam:operation_3755 ; sc:license "MIT" ; sc:name "Pyntheon" ; sc:url "https://github.com/AhmedArslan/pyntheon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica | Pipeline to automate the processing of amplicon data | PypeAmplicon v1.0: Python pipeline for analysis of amplicon data | Wijeratne S & Pavinato VAC. (2018, November 17). PypeAmplicon: Python pipeline for analysis of amplicon data (Version v1.0). Zenodo. doi: http://doi.org/10.5281/zenodo.1490421" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "PypeAmplicon" ; sc:url "https://github.com/vitorpavinato/PypeAmplicon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31743789" ; sc:description """An automatic pipeline for macaque functional MRI preprocessing. Non-human primate functional MRI (fMRI) is a growing field in neuroscience. However, there is no standardized method for monkey fMRI data analysis, specifically for data preprocessing. The preprocessing of monkey fMRI data is challenged by several technical and experimental specificities of the monkey research such as artifacts related to body movements or to intracranial leads. Here we propose to address these challenges by developing a new versatile pipeline for macaque fMRI preprocessing. We developed a Python module, Pypreclin, to process raw images using state of the art algorithms embedded in a fully automatic pipeline. To evaluate its robustness, we applied Pypreclin to fMRI data acquired at 3T in both awake and anesthetized macaques, with or without iron oxide contrast agent, using single loop or multichannel phased-array coils, combined or not with intracranial implanted electrodes.""" ; sc:name "Pypreclin" ; sc:url "https://github.com/neurospin/pypreclin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc:description "PythonVideoAnnotator is a graphical application written in Python, to analyze and create notes for events in videos. It was developed with the aim of helping neuroscience and ethology researchers to identify animals’ behaviors based on the information extracted from the video." ; sc:featureList edam:operation_0226, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Python Video Annotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.306" ; sc:url "https://pythonvideoannotator.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0634 ; sc:citation , "pubmed:30661589" ; sc:description "Quantitative hyperspectral image unmixing (Q-HIU) method is intended for quantitative data analysis of multi-set and individual Raman micro-spectroscopy images, allowing to efficiently retrieve non-negative spatial concentration maps and non-negative spectral profiles of the images’ chemical constituents (components) with no a priori information, minimum input parameters, and great operation speed." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Q-HIU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LobanovaEG-LobanovSV/Q-HIU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3393, edam:topic_3810 ; sc:citation , "pmcid:PMC6749258", "pubmed:31443603" ; sc:description "Can We Use Satellite-Based FAPAR to Detect Drought? | Quality Assurance for Essential Climate Variables | The FP7 QA4ECV project was initiated in 2014 to demonstrate how reliable and traceable quality information can be provided for satellite and ground-based measurements of climate and air quality parameters. The project developed and applied a Quality Assurance framework on new and improved multi-decadal data records of the Land ECVs Albedo, Leaf Area Index (LAI), and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), and of the Atmosphere ECVs nitrogen dioxide (NO2), formaldehyde (HCHO), and carbon monoxide (CO) | We encourage you to browse through the website and survey the scope of QA4ECV activities" ; sc:name "QA4ECV FAPAR" ; sc:url "http://www.qa4ecv.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC6602471", "pubmed:31114870" ; sc:description "Quantitative predictions of transcription factor binding changes due to sequence variants." ; sc:featureList edam:operation_0331, edam:operation_0445, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "QBiC-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://qbic.genome.duke.edu" ; biotools:primaryContact "Raluca Gordân" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_2330 ; sc:name "Quality control report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A tool for real-time quality control assessment of mass spectrometry-based proteomics data." ; sc:featureList edam:operation_2238, edam:operation_2940 ; sc:name "QC-ART" ; sc:url "https://ascm.shinyapps.io/bas_QCART/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31099962" ; sc:description "Web-Tool for Performance Diagnosis and Prediction of liquid chromatography-mass spectrometry (LC-MS) Systems." ; sc:featureList edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "QCMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://shiny.maths.usyd.edu.au/QCMAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3489 ; sc:citation , , ; sc:description "QGIS is a free and open source Geographic Information System." ; sc:featureList edam:operation_0387, edam:operation_3454, edam:operation_3565 ; sc:name "QGIS" ; sc:url "http://qgis.osgeo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6385979", "pubmed:30541929" ; sc:description "Statistical procedure for genome-wide detection of QTL hotspots using public databases." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "QHOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.stat.sinica.edu.tw/chkao/RQTL/download.htm" ; biotools:primaryContact "Chen-Hung Kao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:31697312" ; sc:description """Distance Constraints Applied on Model Quality Estimation. QMEAN, the Qualitative Model Energy ANalysis, is a composite scoring function assessing the major geometrical aspects of protein structures. Estimates of structure quality are provided for full structures as well as on a local per residue scale. QMEAN Qualitative Model Energy ANalysis. QMEAN - Qualitative Model Energy ANalysis. Reference for the QMEANDisCo scoring function:. For optimum performance, please add the SEQRES of your model here. Merge branch 'release-3.1.0' · 3c2b6012. Local quality is either estimated using the raw QMEAN scoring function or one of the two specialized functions QMEANBrane and QMEANDisCo. They all provide scores in range [0,1] with one being good. Reference for the QMEAN scoring function:""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3435 ; sc:name "QMEANDisCo" ; sc:url "https://swissmodel.expasy.org/qmean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_0625, edam:topic_0749, edam:topic_3519 ; sc:citation , "pubmed:31683036" ; sc:description "The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure." ; sc:featureList edam:operation_2497, edam:operation_3223, edam:operation_3799 ; sc:name "QPA" ; sc:url "https://github.com/github-gs/QPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3337, edam:topic_3384, edam:topic_3399 ; sc:citation , "pubmed:31868683" ; sc:description """A Researcher-Patient Matching Platform and Multimodal Biorepository. WELCOME TO QUEBEC PARKINSON NETWORK. Quebec Parkinson Network now allows researchers, clinicians and patients to regroup. Promoting collaboration of different actors in the fight against Parkinson's disease, the Network wants to be the new leader of the research on the disease. Support, act and help researchers and clinicians in the fight against Parkinson's disease by participating in research projects. For more information, visit the Participants section. Congress of the “Société Francophone Posture, Équilibre et Locomotion” (SOFPEL) – December 4 & 5, 2019""" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "QPN" ; sc:url "http://rpq-qpn.ca/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3335, edam:topic_3422, edam:topic_3577 ; sc:citation ; sc:description """an unofficial research purposed implementation of ClinRisk’s QRISK3 algorithm into R. 10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017). This function aims to calculate risk of developing cardiovascular disease of individual patients in next 10 years. The package was based on published risk prediction algorithm . A QRISK3 R package implements QRISK3 algorithm into R. Validation of CRAN R package "QRISK3". This respiratory provides the validation programs including QRISK3 SAS macro and original C function for CRAN package "QRISK3" for transparency and replication. Welcome to the QRISK ® 3-2018 risk calculator https://qrisk.org/three. This calculator is only valid if you do not already have a diagnosis of coronary heart disease (including angina or heart attack) or stroke/transient ischaemic attack""" ; sc:featureList edam:operation_2428, edam:operation_3283 ; sc:license "GPL-3.0" ; sc:name "QRISK3" ; sc:url "https://cran.r-project.org/web/packages/QRISK3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3335, edam:topic_3399 ; sc:citation "pubmed:15140353" ; sc:description "General practice database for research." ; sc:featureList edam:operation_3283, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "QResearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.qresearch.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0637, edam:topic_3293 ; sc:citation , "pmcid:PMC6667645", "pubmed:31396256" ; sc:description "Reconstructing Phylogenetic Networks Based on Quartet and Sextet | User Manual for QS-Net Introduction The QS-Net is a phylogenetic network reconstruction method taking advantage of information on the relationship among six taxa" ; sc:featureList edam:operation_0548, edam:operation_3478, edam:operation_3660 ; sc:license "MIT" ; sc:name "QS-Net" ; sc:url "https://github.com/Tmyiri/QS-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC6815455", "pubmed:31655545" ; sc:description """Comprehensive ensemble in QSAR prediction for drug discovery. There exist a new type of QSAR individual classifier that is an end-to-end neural network model based on 1D-CNN and RNN. It extracts sequential features automatically from the SMILES.""" ; sc:featureList edam:operation_3436, edam:operation_3659, edam:operation_3799 ; sc:name "QSAR" ; sc:url "http://data.snu.ac.kr/QSAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3343 ; sc:citation , "pubmed:31083984" ; sc:description "Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QSAR-Co" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/qsar-co" ; biotools:primaryContact "Pravin Ambure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3400, edam:topic_3444 ; sc:citation , "pmcid:PMC6814493", "pubmed:31379055" ; sc:description "Clinical Integration of Automated Processing for Brain Quantitative Susceptibility Mapping | Cornell MRI Research Lab Research Interests | Quantitative Susceptibility Mapping | Quantitative Susceptibility Mapping (QSM) provides a map of local tissue magnetic susceptibility" ; sc:featureList edam:operation_3454, edam:operation_3629, edam:operation_3799 ; sc:name "QSM" ; sc:url "http://pre.weill.cornell.edu/mri/pages/qsm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3673 ; sc:citation , "pubmed:31388943" ; sc:description "A Bulked Segregant Analysis and Visualization Pipeline for QTL-seq | In recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic trait values, has gained increasing popularities in research community. However, there is no publicly available user friendly software for the identification and visualization. Hence, we developed a tool named QTL-BSA (QTL-bulked segregant analysis and visualization pipeline), which could facilitate the rapid identification and visualization of candidate QTLs from QTL-seq. As a proof-of-concept study, we have applied the tool for the rapid discovery and the identification of genes related with the partial blast resistance in rice" ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3232 ; sc:name "QTL-BSA" ; sc:url "https://github.com/sanlengjing/QTL-BSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3173, edam:topic_3517, edam:topic_3518 ; sc:citation , "pubmed:31598699" ; sc:description """an integrative resource for quantitative trait loci across multiple human molecular phenotypes. QTLbase curates and compiles genome-wide QTL summary statistics for many human molecular traits across over 70 tissue/cell types. The database comprises tens of millions significant genotype-molecular trait associations under different conditions. Users can visualize QTL results in phenome-wide and tissue-wide levels, and annotate their biological functions through comprehensive genomic features and functional evidence. QTLbase provides a one-stop shop of QTLs retrieval and comparison across multiple tissues and multiple layers of molecular complexity, and it will greatly help researchers interrogate the biological mechanism of causal variants and guide the direction of functional validation""" ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_2422, edam:operation_3232, edam:operation_3799 ; sc:name "QTLbase" ; sc:url "http://mulinlab.org/qtlbase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3810 ; sc:citation ; sc:description "R package for random-effect multiple quantitative trait loci (QTL) mapping in autopolyploids." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QTLpoly" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/guilherme-pereira/qtlpoly" ; biotools:primaryContact "Guilherme da Silva Pereira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_3047 ; sc:citation ; sc:description """Automating the Derivation of Force Field Parameters from Quantum Mechanics.

Modern molecular mechanics force fields are widely used for modelling the dynamics and interactions of small organic molecules using libraries of transferable force field parameters. For molecules outside the training set, parameters may be missing or inaccurate, and in these cases, it may be preferable to derive molecule-specific parameters. Here we present an intuitive parameter derivation toolkit, QUBEKit (QUantum mechanical BEspoke Kit), which enables the automated generation of system-specific small molecule force field parameters directly from quantum mechanics. QUBEKit is written in python and combines the latest QM parameter derivation methodologies with a novel method for deriving the positions and charges of off-center virtual sites.""" ; sc:featureList edam:operation_2476, edam:operation_3893 ; sc:name "QUBEKit" ; sc:url "https://github.com/cole-group/QuBeKit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:31503285" ; sc:description "A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data | A novel biclustering algorithm for analyses of transcriptomic data | QUBIC2 is a novel biclustering algorithm for analyses of gene expression data from bulk and single-cell RNA-Sequencing. This introductory vignette provides an overview of installation and usage" ; sc:featureList edam:operation_3501 ; sc:name "QUBIC2" ; sc:url "https://github.com/OSU-BMBL/QUBIC2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31436990" ; sc:description "> HOMEPAGE MISSING! | An Automated Protocol for Free Energy Calculations of Protein Mutations in Q | Predicting the effect of single-point mutations on protein stability or protein-ligand binding is a major challenge in computational biology. Free energy calculations constitute the most rigorous approach to this problem, though the estimation of converged values for amino acid mutations remains challenging. To overcome this limitation, we developed tailored protocols to calculate free energy shifts associated with single-point mutations. We herein describe the QresFEP protocol, which includes an extension of our recent protocols to cover all amino acids mutations, based on the latest versions of the OPLS-AA force field. QresFEP is implemented in an application programming interface framework and the graphic interface QGui, for the molecular dynamics software Q" ; sc:featureList edam:operation_0480, edam:operation_0482 ; sc:name "QresFEP" ; sc:url "https://github.com/qusers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description """Overcoming computational bottlenecks in sequence quality control. Abstract With the recent torrent of high throughput sequencing (HTS) data the necessity for highly efficient algorithms for common tasks is paramount. One task for which the basis for all further analysis of HTS data is initial data quality control, that is, the removal or trimming of poor quality reads from the dataset. Here we present QuAdTrim, a quality control and adapter trimming algorithm for HTS data that is up to 57 times faster and uses less than 0.06% of the memory of other commonly used HTS quality control programs. QuAdTrim will reduce the time and memory required for quality control of HTS data, and in doing, will reduce the computational demands of a fundamental step in HTS data analysis. Additionally, QuAdTrim impliments the removal of homopolymer Gs from the 3’ end of sequence reads, a common error generated on the NovaSeq, NextSeq and iSeq100 platforms""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3237 ; sc:license "BSD-3-Clause" ; sc:name "QuAdTrim" ; sc:url "https://bitbucket.org/arobinson/quadtrim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6895564", "pubmed:31849692" ; sc:description """A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology. QuantiMus is a machine-learning based program used for histological analysis of skeletal muscle. Developed as a plugin for the image analysis tool flika, QuantiMus is a versatile, fast, and precise to complete histological analysis. QuantiMus is written in Python and is open-source""" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "QuantiMus" ; sc:url "https://quantimus.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:31070704" ; sc:description "Decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery." ; sc:featureList edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "QuantileBootstrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/owatson/QuantileBootstrap" ; biotools:primaryContact "James A. Watson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3570 ; sc:citation , "pmcid:PMC6287823", "pubmed:30532140" ; sc:description "Modern general-purpose multi-threaded quantum computing library." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Quantum++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/vsoftco/qpp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:31470430" ; sc:description "an integrated platform of electronic and atomic-scale modelling tools | QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals" ; sc:featureList edam:operation_3216, edam:operation_3891 ; sc:name "QuantumATK" ; sc:url "https://docs.quantumatk.com/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293 ; sc:citation , "pubmed:31504977" ; sc:description "Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence | Code for computing various support scores for internodes | See http://www.biorxiv.org/content/early/2017/07/27/168526 for the preprint | If you cannot find our supplementary text, please download it from here: https://github.com/lutteropp/QuartetScores/issues/4" ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0552 ; sc:license "GPL-3.0" ; sc:name "QuartetScores" ; sc:url "https://github.com/lutteropp/QuartetScores" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:author "James E. Johnson" ; sc:citation , "pmcid:PMC6248266", "pubmed:30519459" ; sc:description "Query Tabular is a Galaxy-based tool which manipulates tabular files. Query Tabular automatically creates a SQLite database directly from a tabular file within a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_2409, edam:operation_3695 ; sc:license "CC-BY-4.0" ; sc:name "Query Tabular" ; sc:url "https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3855 ; sc:citation , "pubmed:30637945" ; sc:description "Collection of C++ code snippets, that can be picked and combined to build complex, spatially explicit population genetics simulators and inference frameworks." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Quetzal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://becheler.github.io/pages/quetzal.html" ; biotools:primaryContact "Arnaud Becheler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3710, edam:format_3712, edam:format_3858 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_3508, edam:format_3752 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """QuiC generates quality control metrics for liquid chromatography and mass spectrometry in near real-time from raw files from various vendors and bottom-up proteomics workflows using a commercially available standard. Requires Biognosys iRT Kit to enable automated, fast and accurate QC monitoring of your data sets.""" ; sc:featureList edam:operation_2428, edam:operation_3628 ; sc:name "QuiC" ; sc:url "https://biognosys.com/software/quic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:author "Neural Systems Laboratory" ; sc:citation , "pmcid:PMC6541252", "pubmed:31141518" ; sc:description "Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems." ; sc:featureList edam:operation_3552 ; sc:funder "Horizon 2020" ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "QuickNII" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.nitrc.org/projects/quicknii" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0601 ; sc:citation ; sc:description "Tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome." ; sc:featureList edam:operation_0417, edam:operation_3659, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Quokka" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://quokka.erc.monash.edu/" ; biotools:primaryContact "Fuyi Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0632, edam:topic_0659, edam:topic_2258 ; sc:citation , "pmcid:PMC6925312", "pubmed:31589399" ; sc:description """An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. R-BIND: The RNA-Targeted BIoactive ligaNd Database. The dataset includes only bioactive ligands with demonstrated activity in cell culture and/or animal models. This database is expected to expedite the discovery of RNA chemical probes. R-BIND was created by the Hargrove Lab at Duke University""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "R-BIND" ; sc:url "https://rbind.chem.duke.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0622, edam:topic_3518 ; sc:citation , "pmcid:PMC6831549", "pubmed:31737636" ; sc:description "R2 is a biologist friendly web based genomics analysis and visualization application" ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3463 ; sc:name "R2" ; sc:url "http://r2.amc.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC6893003", "pubmed:31802128" ; sc:description """a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. Recently, the success of AlphaFold on creating 3D protein models demonstrates sequence-dependent inference plays a crucial role in computational proteomics. A web server of reduced amino acid alphabet for sequence-dependent inference""" ; sc:featureList edam:operation_0267, edam:operation_0418, edam:operation_0477 ; sc:name "RAACBook" ; sc:url "http://bioinfor.imu.edu.cn/raacbook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:31410804" ; sc:description "RACE-SEQ and Population-Wide Polymorphism Susceptibility Testing for Endonucleolytically Active, RNA-Targeting Therapeutics | Pipeline for the downstream analysis of 5-RACE Next Generation Sequencing experiments | This is a custom R script for the downstream analysis of RACE-seq data | To run the RACE-SEQ-lite script you will need to have an R version ( >=3.4) installed on your system. All the necessary R packages will get installed and loaded automatically" ; sc:featureList edam:operation_0465, edam:operation_2008, edam:operation_3192 ; sc:name "RACE-SEQ" ; sc:url "https://github.com/pantastheo/RACE-SEQ-lite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3169, edam:topic_3170, edam:topic_3179, edam:topic_3316 ; sc:citation , "pmcid:PMC6819487", "pubmed:31664892" ; sc:description """rapid analysis of ChIP-Seq data for contig based genomes. RACS: Rapid Analysis of ChIP-Seq data for contig based genomes -- repository""" ; sc:featureList edam:operation_3192, edam:operation_3211, edam:operation_3216, edam:operation_3222, edam:operation_3431 ; sc:name "RACS" ; sc:url "https://gitrepos.scinet.utoronto.ca/public/?a=summary&p=RACS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3419 ; sc:citation , "pmcid:PMC6694732", "pubmed:31373275" ; sc:description "Open Source Mobile Health Platform for Collecting, Monitoring, and Analyzing Data Using Sensors, Wearables, and Mobile Devices | BACKGROUND:With a wide range of use cases in both research and clinical domains, collecting continuous mobile health (mHealth) streaming data from multiple sources in a secure, highly scalable, and extensible platform is of high interest to the open source mHealth community. The European Union Innovative Medicines Initiative Remote Assessment of Disease and Relapse-Central Nervous System (RADAR-CNS) program is an exemplary project with the requirements to support the collection of high-resolution data at scale; as such, the Remote Assessment of Disease and Relapse (RADAR)-base platform is designed to meet these needs and additionally facilitate a new generation of mHealth projects in this nascent field" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3431 ; sc:name "RADAR-base" ; sc:url "https://radar-base.org/index.php/documentation/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3673, edam:topic_3796 ; sc:citation , "pubmed:30312001" ; sc:description "Computationally efficient de novo locus assembler for population studies using RADseq data." ; sc:featureList edam:operation_0476, edam:operation_3196, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RADProc" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/beiko-lab/RADProc" ; biotools:primaryContact "Dr. Beiko's Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3071, edam:topic_3512 ; sc:citation , "pmcid:PMC6323319", "pubmed:30624654" ; sc:description "Database of enhancers identified by high-throughput reporter assays." ; sc:featureList edam:operation_0224, edam:operation_0438, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "RAEdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.computationalbiology.cn/RAEdb/index.php" ; biotools:primaryContact "Dr. Yousong Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:31373604" ; sc:description "Webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:name "RAG" ; sc:url "http://tslab10.chem.nyu.edu:7000/ragtop/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3308 ; sc:citation , "pubmed:31609411" ; sc:description "A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae." ; sc:featureList edam:operation_2426 ; sc:name "RAM-ESVM" ; sc:url "http://server.malab.cn/RAM-ESVM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_3277 ; sc:citation , "pmcid:PMC6724667", "pubmed:31413151" ; sc:description "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Alu', 'III-transcribed', 'Pol III-transcribed', 'III-transcribed Alu' | Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function | Pipeline to identify expressed Alu elements using RAMPAGE | A schematic flow shows the pipeline" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_3232 ; sc:license "MIT" ; sc:name "RAMPAGE" ; sc:url "https://github.com/kepbod/rampage_alu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3293 ; sc:citation ; sc:description "Tool for node label ranking and classification in biological networks." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RANKS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=RANKS" ; biotools:primaryContact "Giorgio Valentini" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3272 ; sc:name "Species tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:author "Benjamin Linard" ; sc:citation ; sc:description "RAPPAS stands for Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences. It uses an alignment-free approach for phylogenetic placement, thus removing the hurdle of query sequence alignment." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "RAPPAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.atgc-montpellier.fr/RAPPAS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:description """RARe is a research infrastructure registered on the french national roadmap that brings together five networks of BRCs conserving genetic, genomic, and biological resources assembled and characterized by research on domestic animals, model or cultivated plants, wild species related to domestic animals, forest trees, micro-organisms of agronomic or agri-food interest, micro-organisms and environmental organisms. The purpose of this web portal is to facilitate the discoverability of these data. RARe search is an implementation of DataDiscovery.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "RARe" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/rare/" ; biotools:primaryContact "Support service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description """An RNA-Seq Analysis Workflow with Snakemake. RASflow: RNA-Seq Analysis Snakemake Workflow""" ; sc:featureList edam:operation_3258, edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "RASflow" ; sc:url "https://github.com/zhxiaokang/RASflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2830 ; sc:citation ; sc:description "R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework." ; sc:featureList edam:operation_0487, edam:operation_0495, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "RAbHIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.1.1" ; sc:url "https://yaarilab.bitbucket.io/RAbHIT/" ; biotools:primaryContact "Ayelet Peres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293, edam:topic_3810 ; sc:citation ; sc:description "Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion." ; sc:featureList edam:operation_0547, edam:operation_0552 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RAxML-NG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.8.0 beta" ; sc:url "https://raxml-ng.vital-it.ch/" ; biotools:primaryContact "Vital-IT helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3320, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6348990", "pubmed:30413564" ; sc:description "Enables robust generation of splicing regulatory maps and rapid query of regulatory patterns of RNA binding protein (RBP) of interest." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RBP-Maps" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/YeoLab/rbp-maps" ; biotools:primaryContact "Yeo LAB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_3047, edam:topic_3520 ; sc:citation , "pmcid:PMC6926210", "pubmed:31835171" ; sc:description "RBP atlas is an interactive online data mining tool." ; sc:featureList edam:operation_0303, edam:operation_2436, edam:operation_3196 ; sc:name "RBPome" ; sc:url "http://shiny.cecad.uni-koeln.de:3838/celegans_rbpome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3518, edam:topic_3577, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6858463", "pubmed:31729446" ; sc:description """tool for prioritising copy number variations in germline conditions. Validating copy number variants from using allele balance from NGS data. RBV: Read Balance Validator is a corroborates copy number variants (CNV) from whole exome and whole genome sequence data. It uses the relative reads for the reference and alternative allele at a given position (the read balance) to determine the probability that a putative CNV is real""" ; sc:featureList edam:operation_2428, edam:operation_3226, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "RBV" ; sc:url "https://github.com/whitneywhitford/RBV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_0749 ; sc:citation , "pmcid:PMC6929455", "pubmed:31874608" ; sc:description "RCMF is a robust collaborative matrix factorization method to predict miRNA-disease associations." ; sc:featureList edam:operation_3435 ; sc:name "RCMF" ; sc:url "https://github.com/cuizhensdws/L21-GRMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_3295, edam:topic_3336, edam:topic_3518 ; sc:citation , "pubmed:31774912" ; sc:description "RCSM(Recommended Connectivity-map Scoring Methods) is a comprehensive evaluation of connectivity methods for L1000 data." ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:name "RCSM" ; sc:url "https://github.com/Jasonlinchina/RCSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3172, edam:topic_3325 ; sc:citation , "pmcid:PMC5584330", "pubmed:28870259" ; sc:description "Extends the RDF import and export functionality in Semantic MediaWiki (SMW) to enable using SMW as a collaborative platform for editing semantic data." ; sc:featureList edam:operation_0337, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "RDFIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pharmb.io/project/rdfio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_3047 ; sc:citation ; sc:description "RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel." ; sc:featureList edam:operation_0475, edam:operation_1844, edam:operation_2476 ; sc:name "RDKit" ; sc:url "http://www.rdkit.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3673 ; sc:citation , "pmcid:PMC6555534", "pubmed:19657104", "pubmed:31136576" ; sc:description """> TOOL (matuskalas) | Comprehensively benchmarking applications for detecting copy number variation | The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group Note: (matuskalas): Lumpy (or lumpy-sv) is a completely different tool, atm missing in bio.tools (https://github.com/arq5x/lumpy-sv)""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RDXplorer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/rdxplorer/" ; biotools:primaryContact "Makarov V." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3417, edam:topic_3474 ; sc:citation , "pubmed:31630011" ; sc:description """A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs. The goal of the Retinal Fundus Glaucoma Challenge (REFUGE) is to evaluate and compare automated algorithms for glaucoma detection and optic disc/cup segmentation on a common dataset of retinal fundus images.""" ; sc:featureList edam:operation_3283, edam:operation_3443, edam:operation_3553 ; sc:name "REFUGE Challenge" ; sc:url "https://refuge.grand-challenge.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3295, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """A database for exploring N6-methyladenosine methylome. REPIC (RNA Epitranscriptome Collection) is a database dedicated to provide a new resource to investigate potential functions and mechanisms of N6-adenosine methylation (m6A) modifications. Currently, The database includes about 700 samples of 50 public studies that were reprocessed by our refined pipeline. The database also contains ENCODE histone ChIP-seq and DNase-seq data to correlate m6A modifications. It provided multi-dimensional information (e.g. cell or tissue specificity) to query m6A modification relevance in cellular processes. In addition, a built-in modern genome browser presented a comprehensive atlas of m6A modifications which is helpful to visualize m6A modification sites between different samples and conditions.""" ; sc:featureList edam:operation_0224, edam:operation_3208, edam:operation_3222 ; sc:name "REPIC" ; sc:url "https://repicmod.uchicago.edu/repic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625 ; sc:author "Amanda Kowalczyk", "Maria Chikina", "Nathan Clark", "Raghavendran Partha", "Weiguang (Wayne) Mao", "Wynn Meyer" ; sc:citation , "pubmed:31192356" ; sc:description "R package for associating evolutionary rates with convergent traits." ; sc:featureList edam:operation_0547, edam:operation_0554, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RERconverge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nclark-lab/RERconverge" ; biotools:primaryContact "Maria Chikina", "Nathan Clark", "Raghavendran Partha", "Weiguang (Wayne) Mao", "Wynn Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2830, edam:topic_3360, edam:topic_3382, edam:topic_3518 ; sc:citation ; sc:description "Robust intEnSiTy nORmalization mEthod for Multiplexed Imaging." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:name "RESTORE" ; sc:url "https://gitlab.com/Chang_Lab/cycif_int_norm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736 ; sc:citation , "pmcid:PMC6802825", "pubmed:31634369" ; sc:description "Random Forest Quality Assessment to identify a predicted protein structure in the correct fold." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0321, edam:operation_0474 ; sc:name "RFQAmodel" ; sc:url "https://github.com/clarewest/RFQAmodel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6697926", "pubmed:31419933" ; sc:description "a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression | RF model and functions to estimate tumor purity using methylation data | Install minfi and RF_purify package from GitHub | R-package to predict ABSOLUTE and ESTIMATE tumor purity using a Random Forest regression model trained on TCGA Illumina 450k DNA-methylation array data. Purity prediction functions can be applied to 450k and 850k array data preprocessed with the Bioconductor package minfi" ; sc:featureList edam:operation_0430, edam:operation_3233, edam:operation_3659 ; sc:name "RF_Purify" ; sc:url "https://github.com/mwsill/RFpurify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC6364042", "pubmed:30583062" ; sc:description "Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes." ; sc:featureList edam:operation_0525, edam:operation_3209, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RGAAT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/wushyer/RGAAT_v2" ; biotools:primaryContact "Qiang Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6836459", "pubmed:31694536" ; sc:description "RGADE is a tool with genomic features and differential expression of the innate immune system from a smut-resistant genotype." ; sc:featureList edam:operation_0303, edam:operation_0524, edam:operation_3196, edam:operation_3432 ; sc:name "RGADE" ; sc:url "http://github.com/hugorody/rga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0654, edam:topic_3293 ; sc:citation , "pmcid:PMC6828935", "pubmed:31737036" ; sc:description """RGRPT is a New Algorithm for Identifying Genome Rearrangements in the Mammalian Evolution. Genome rearrangements are the evolutionary events on level of genomes. It is a global view on evolution research of species to analyze the genome rearrangements. We introduce a new method called RGRPT (recovering the genome rearrangements based on phylogenetic tree) used to identify the genome rearrangements. We test the RGRPT using simulated data. The results of experiments show that RGRPT have high sensitivity and specificity compared with other tools when to predict rearrangement events. We use RGRPT to predict the rearrangement events of six mammalian genomes (human, chimpanzee, rhesus macaque, mouse, rat, and dog). RGRPT has recognized a total of 1,157 rearrangement events for them at 10 kb resolution, including 858 reversals, 16 translocations, 249 transpositions, and 34 fusions fissions.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3745 ; sc:name "RGRPT" ; sc:url "https://github.com/wangjuanimu/data-of-genome-rearrangement" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3173, edam:topic_3512 ; sc:citation , "pmcid:PMC6917511", "pubmed:31848596" ; sc:description """a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progression of cancer, such as breast cancer, lung cancer and so on. RHPCG serves as a valuable resource for understanding the roles of Hippo signaling pathway in carcinogenesis. The features of RHPCG contain: (i) the landscape of Hippo gene alterations at multiple omics level; (ii) quick search Hippo regulatory motifs by mRNA, lncRNA, circRNA or miRNA; and (iii) all the Hippo related motifs can be visualized as network and be downloaded freely""" ; sc:featureList edam:operation_0239, edam:operation_2495, edam:operation_3083, edam:operation_3439 ; sc:name "RHPCG" ; sc:url "http://www.medsysbio.org/RHPCG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3474 ; sc:citation , "pmcid:PMC6806664", "pubmed:31640541" ; sc:description """The RICE-GUARD project will develop a wireless sensor network comprised of low-cost measurement nodes that will be capable of transmitting readings of the relevant in-field site-specific environmental variables in real-time to a central server. Rice blast is the most serious disease of cultivated rice. It is caused by the fungus Magnaporthe grisea (Pyricularia oryzae Cav.), which in favourable conditions can produce yield losses of up to 100 %. Although rice blast is present wherever rice is cultivated, its intensity (incidence and severity of disease) is highly variable and depends on cropping system and climate.""" ; sc:featureList edam:operation_3435 ; sc:name "RICE-GUARD" ; sc:url "http://multisite.iris.cat/riceguard/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3517 ; sc:citation , "pubmed:31393554" ; sc:description "Rapid Imputation for COnsortias PIpeLIne | Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies | RICOPILI: Rapid Imputation and COmputational PIpeLIne for Genome-Wide Association Studies by Stephan Ripke is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Based on a work at https://sites.google.com/a/broadinstitute.org/ricopili/download" ; sc:featureList edam:operation_3557, edam:operation_3891 ; sc:name "RICOPILI" ; sc:url "https://sites.google.com/a/broadinstitute.org/RICOPILI/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:31089974" ; sc:description "Medical Imaging Dataset Annotation Tool for and with Deep Learning." ; sc:featureList edam:operation_2422, edam:operation_3553, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "RIL-Contour" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/Philbrick/rilcontour" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0736 ; sc:citation , , "pmcid:PMC5860209", "pmcid:PMC5998007", "pubmed:29028877", "pubmed:29946443" ; sc:description "Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions." ; sc:featureList edam:operation_0248, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "RINspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "http://apps.cytoscape.org/apps/rinspector" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3407 ; sc:citation ; sc:description "Transcriptomic analyses of bacteria have become instrumental to our understanding of their responses to changes in their environment." ; sc:featureList edam:operation_3629, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RIPTiDe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mjenior/riptide" ; biotools:primaryContact "Matthew L. Jenior" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3794 ; sc:citation , "pmcid:PMC6714961", "pubmed:31523495" ; sc:description "web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations | The RIPper is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in genome sequences of Ascomycota | The RIPper was built using Asp.Net Core with an AngularJs based front-end and uses session storage to keep a users files for a defined amount of time. The RIPper has no account or database requirements" ; sc:featureList edam:operation_3216, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "RIPper" ; sc:url "http://theripper.hawk.rocks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3295 ; sc:citation , "pmcid:PMC7924719", "pubmed:33816903" ; sc:description "drawing SVG graphics to visualize and map genome-wide data on the idiograms | Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms | For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species | RIdeogram is a R package to draw SVG graphics to visualize and map genome-wide data on idiograms (Scalable Vector Graphics http://tutorials.jenkov.com/svg/index.html)" ; sc:featureList edam:operation_0575, edam:operation_2429 ; sc:license "Artistic-2.0" ; sc:name "RIdeogram" ; sc:url "https://cran.r-project.org/web/packages/RIdeogram/" ; biotools:primaryContact "Guangchuang Yu", "Jinhui Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_3512 ; sc:description "Tool for RNA–RNA interaction extraction from the literature." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RIscoper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rna-society.org/riscoper/" ; biotools:primaryContact "Wang Dong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC5753293", "pubmed:29040692" ; sc:description "Database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs, as well as their relationships with microRNA binding events, disease-related SNPs and RNA-binding proteins (RBP)." ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RMBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://rna.sysu.edu.cn/rmbase/index.php" ; biotools:primaryContact "Jian-Hua Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC6694479", "pubmed:31416413" ; sc:description "Multiple-kernel learning for genomic data mining and prediction | Multiple Kernel Learning for Classification or Regression Problems | Provides R and C++ function that enable the user to conduct multiple kernel learning (MKL) and cross validation for support vector machine (SVM) models. Cross validation can be used to identify kernel shapes and hyperparameter combinations that can be used as candidate kernels for MKL. There are three implementations provided in this package, namely SimpleMKL Alain Rakotomamonjy et. al (2008), Simple and Efficient MKL Xu et. al (2010), and Dual augmented Lagrangian MKL Suzuki and Tomioka (2011) . These methods identify the convex combination of candidate kernels to construct an optimal hyperplane" ; sc:featureList edam:operation_0306, edam:operation_0463, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "RMKL" ; sc:url "https://CRAN.R-project.org/package=RMKL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_3336 ; sc:citation , "pmcid:PMC6424452", "pubmed:30889216" ; sc:description "R package for a Boolean sensitivity analysis against various types of mutations." ; sc:featureList edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RMut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/csclab/RMut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """A transcriptional toolbox for exploring peripheral neuro-immune interactions. Abstract Correct communication between immune cells and peripheral neurons is crucial for the protection of our bodies. Its breakdown is observed in many common, often painful conditions, including arthritis, neuropathies and inflammatory bowel or bladder disease. Here, we have characterised the immune response in a mouse model of neuropathic pain using flow cytometry and cell-type specific RNA sequencing (RNA-seq). We found few striking sex differences, but a very persistent inflammatory response, with increased numbers of monocytes and macrophages up to 3½ months after the initial injury. This raises the question of whether the commonly used categorisation of pain into “inflammatory” and “neuropathic” is one that is mechanistically appropriate. Finally, we collated our data with other published RNA-seq datasets on neurons, macrophages and Schwann cells in naïve and nerve injury states""" ; sc:featureList edam:operation_3563, edam:operation_3565, edam:operation_3800 ; sc:name "RNA-seq" ; sc:url "http://rna-seq-browser.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:31593214" ; sc:description """discovering somatic coding indels from tumor RNA-Seq data. Somatic indel discovery tool for tumor RNA-Seq data. RNAIndel calls coding indels from tumor RNA-Seq data and classifies them as somatic, germline, and artifactual. You can also use RNAIndel as a postprocessor to classify indels called by your own caller. RNAIndel supports GRCh38 and 37""" ; sc:featureList edam:operation_0226, edam:operation_0452, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RNAIndel" ; sc:softwareHelp ; sc:softwareVersion "2.2.2" ; sc:url "https://github.com/stjude/RNAIndel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0154 ; sc:citation , "pmcid:PMC6482512", "pubmed:31023239" ; sc:description "Fixed-parameter tractable sampling for RNA design with multiple target structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNARedPrint" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/yannponty/RNARedPrint" ; biotools:primaryContact "Yann Ponty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3382 ; sc:citation , "pubmed:31769800" ; sc:description """visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix. A pipeline to detect sample mix-ups in RNASeq data. Generate a sample similarity matrices from RNASeq data. Sample confusion is a common laboratory problem. In RNASeq this is frequently tested for by checking whether sex-specific genes (e.g. those located on the Y chromosome or the X inactivation gene) are congruent with the sex listed for that sample in the metadata. However, this method cannot be used to detect sample confusion between patients of the same sex, and is less sensitive when the phenotype skews the sex ratio of samples away from 1:1. Here we present a tool that leverages RNASeq reads to call genomic SNPs, and use that to generate a similarity matrix between all samples to detect sample confusion. git clone https://github.com/nicokist/RNASeq_similarity_matrix""" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "RNASeq_similarity_matrix" ; sc:url "http://www.github.com/nicokist/RNASeq_similarity_matrix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6612824", "pubmed:31510698" ; sc:description "Prediction of mRNA subcellular localization using deep recurrent neural networks | RNATracker is a deep learning approach to learn mRNA subcellular localization patterns and to infer its outcome. It operates on the cDNA of the longest isoformic protein-coding transcript of a gene with or without its corresponding secondary structure annnotations. The learning targets are fractions/percentage of the transcripts being localized to a fixed set of subcellular compartments of interest" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "RNATracker" ; sc:url "https://www.github.com/HarveyYan/RNATracker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0659, edam:topic_0749, edam:topic_3047, edam:topic_3512 ; sc:citation , "pubmed:31799597" ; sc:description """a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associations between drug sensitivity and RNA molecules including mRNAs, lncRNAs and miRNAs at four molecular levels (expression, copy number variation, mutation and methylation) from integrated analysis of three large-scale pharmacogenomic databases (GDSC, CellMiner and CCLE). Currently, RNAactDrug contains more than 4924200 RNA molecules-drug sensitivity associations at multidimensional molecular levels covering more than 19770 mRNAs, 11119 lncRNAs, 438 miRNAs and 4155 drugs. RNAactDrug aims to help make use of the full breadth and depth of existing large-scale pharmacogenomic data by making this knowledge accessible to both basic researchers""" ; sc:featureList edam:operation_0224, edam:operation_3792 ; sc:name "RNAactDrug" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/RNAactDrug" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2725 ; sc:name "Ensembl transcript ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3752 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , "pmcid:PMC6324028", "pubmed:30445601" ; sc:contributor ; sc:description """Protein–RNA interaction predictions for model organisms with supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise interactions, reflecting nearly 120 years of computation time on the CRG's high-performance computing cluster. It combines experimentally identified interactions (e.g. from ENCODE) with ab initio predictions, enabling full coverage of the RNA-binding proteome.""" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "RNAct" ; sc:softwareHelp ; sc:url "https://rnact.tartaglialab.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:31751879" ; sc:description "RNAdemocracy is an ensemble method for RNA secondary structure prediction using consensus scoring." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:name "RNAdemocracy" ; sc:url "https://github.com/beskidmore/RNAdemocracy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0632, edam:topic_3168, edam:topic_3308 ; sc:citation , "pubmed:31669269" ; sc:description """An online tutorial and data portal for the RNA structurome era. This is an animated dialog which is useful for displaying. Timeline of HTS-associated RNA structure probing methods""" ; sc:featureList edam:operation_0295, edam:operation_0502, edam:operation_2441 ; sc:name "RNAdt" ; sc:url "http://www.zhounan.org/rnadt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3372 ; sc:citation ; sc:description """RNAfamProb Program, Program for Estimations of Posterior Probabilities on RNA Structural alignment. NeoFold Program, Program for Maximum-expected-accuracy Estimations of RNA Secondary Structures with Incorporating Homologous-RNA sequences. This project provides the RNAfamProb program, a program for estimations of posterior probabilities on RNA structural alignment. This project provides the NeoFold Program, a program for the maximum-expected-accuracy estimations of RNA secondary structures with incorporating homologous-RNA sequences. This project has been written in mainly Rust, a systems programming language.""" ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0502 ; sc:name "RNAfamProb Plus NeoFold" ; sc:url "https://github.com/heartsh/rnafamprob" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6859278", "pubmed:31726390" ; sc:description """Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition. RNAm5CPred: A webserver for RNA 5-methylcytosine sites prediction. A webserver for RNA 5-methylcytosine sites prediction. RNAm5CPred was developed by using support vector machine based on three different kinds of nucleotide composition features including KNF (K-nucleotide frequencies), KSNPF (K-spaced nucleotide pair frequencies) and pseDNC (pseudo dinucleotide composition). The input for the server is the RNA sequence. More details can be found in the tutorial""" ; sc:featureList edam:operation_0224, edam:operation_0526 ; sc:name "RNAm5CPred" ; sc:url "http://zhulab.ahu.edu.cn/RNAm5CPred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1254 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0659, edam:topic_3308, edam:topic_3391, edam:topic_3474 ; sc:citation ; sc:description "RNAsamba is a tool for computing the coding potential of RNA sequences using a neural network classification model. It can be used to identify mRNAs and lncRNAs without relying on database searches." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNAsamba" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.4" ; sc:url "https://rnasamba.lge.ibi.unicamp.br/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0820, edam:topic_3474 ; sc:citation , "pubmed:31472418" ; sc:description "Efficient utilization on PSSM combining with recurrent neural network for membrane protein types prediction | RNN-for-membrane-protein-types-prediction | This repo includes the implementation of preprocessing for proteins and network architecture for training" ; sc:featureList edam:operation_2474, edam:operation_2475, edam:operation_3439 ; sc:name "RNN" ; sc:url "https://github.com/YellowcardD/RNN-for-membrane-protein-types-prediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3421 ; sc:citation , "pmcid:PMC6708148", "pubmed:31462928" ; sc:description "RNSCLC-PRSP software to predict the prognostic risk and survival in patients with resected T1-3N0-2 M0 non-small cell lung cancer | Background:The clinical outcomes of patients with resected T1-3N0-2M0 non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic prediction tools have been reported in many published studies, a convenient, accurate and specific prognostic prediction software for clinicians has not been developed. The purpose of our research was to develop this type of software that can analyze subdivided T and N staging and additional factors to predict prognostic risk and the corresponding mean and median survival time and 1-5-year survival rates of patients with resected T1-3N0-2M0 NSCLC. Results:Using a Cox proportional hazard regression model, we determined the independent prognostic factors and obtained a prognostic index (PI) eq" ; sc:name "RNSCLC-PRSP software" ; sc:url "http://www.rnsclcpps.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3173 ; sc:citation , "pmcid:PMC4530010", "pubmed:25693563" ; sc:description "Data repository of NIH Roadmap Epigenomics Mapping Consortium containing genome-wide maps of histone modifications, chromatin accessibility, DNA methylation and mRNA expression across 100s of human cell types and tissues." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ROADMAP epigenomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://egg2.wustl.edu/roadmap/web_portal/index.html" ; biotools:primaryContact "Jin Wook Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3855 ; sc:citation , "pubmed:31410449" ; sc:description "An Abstraction Layer and User Interface for Knowledge Graphs to Support Question Answering | ROBOKOP is a tool for reasoning over structured biomedical knowledge databases as part of the NCATS translator and reasoner programs. The ROBOKOP system consists of a web based user interface, an API server, and several worker servers. The code is separated into three separate repositories" ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "ROBOKOP" ; sc:url "http://robokop.renci.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3382 ; sc:citation , "pubmed:31769676" ; sc:description "ROBOKOP KG is an Integrated Knowledge Graphs from Federated Sources." ; sc:featureList edam:operation_0224 ; sc:name "ROBOKOP KG" ; sc:url "http://robokopkg.renci.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6664714", "pubmed:31357927" ; sc:description "A Tool for Automating Ontology Workflows | ROBOT is a tool for working with Open Biomedical Ontologies | R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019 | ROBOT is a tool for working with Open Biomedical Ontologies. It can be used as a command-line tool or as a library for any language on the Java Virtual Machine | If no --reasoner is provided, ROBOT will default to ELK. The following other reasoner options are supported: | ROBOT will always perform a logical validation check prior to automatic classification | Equivalent Classes (--equivalent-classes-allowed) | Generated Axioms(--axiom-generators)" ; sc:featureList edam:operation_2428, edam:operation_3280, edam:operation_3559 ; sc:license "BSD-3-Clause" ; sc:name "ROBOT" ; sc:url "http://robot.obolibrary.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Joint inference of Runs of Homozygosity and rates of heterozygosity" ; sc:name "ROHan" ; sc:operatingSystem "Linux" ; sc:url "http://grenaud.github.io/ROHan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC6525397", "pubmed:31101001" ; sc:description "Powerful analysis strategy for LC-MS metabolomic datasets." ; sc:featureList edam:operation_3628, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ROIMCR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://mcrals.wordpress.com/download/roimcr/" ; biotools:primaryContact "Romà Tauler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_3063, edam:topic_3303, edam:topic_3489 ; sc:citation , "pmcid:PMC6800657", "pubmed:31633087" ; sc:description """a light-weight R package for interfacing with OMOP-formatted electronic health record data. R package to easily interface with OMOP-formatted EHR data. ROMOP, please wait... This may take a minute or two. Launching ROMOP, please wait... This may take a minute or two. ... ROMOP is a flexible R package to interface with the Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model. Briefly, OMOP is a standardized relational database schema for Electronic Health Record (EHR) or Electronic Medical Record (EMR) data (i.e., patient data collected during clinical visits to a health system). The main benefit of a standardized schema is that it allows for interoperability between institutions, even if the underlying EHR vendors are disparate. Benjamin S. Glicksberg 9/14/2018""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3435 ; sc:license "MIT" ; sc:name "ROMOP" ; sc:url "http://romop.ucsf.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0625, edam:topic_3293 ; sc:citation , "pubmed:31682272" ; sc:description "RPAND is an R package for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade–clade competitive effects or the effect of species richness on phenotypic divergence." ; sc:featureList edam:operation_0399, edam:operation_3745 ; sc:name "RPANDA" ; sc:url "https://github.com/hmorlon/PANDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_3518 ; sc:citation , "pmcid:PMC6846243", "pubmed:31712826" ; sc:description "RPGeNet v2.0 - Retinitis Pigmentosa Gene Network: interacting with the network of genes related to retinitis pigmentosa genes." ; sc:featureList edam:operation_0224, edam:operation_3083, edam:operation_3439 ; sc:name "RPGeNet" ; sc:softwareVersion "2.0" ; sc:url "https://compgen.bio.ub.edu/RPGeNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6429152", "pubmed:30832218" ; sc:description "Hierarchical deep learning model for predicting ncRNA-protein interaction." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RPITER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Pengeace/RPITER" ; biotools:primaryContact "C. Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation , "pubmed:31648100" ; sc:description """Heart rate variability analysis software. BACKGROUND AND OBJECTIVES:Heart rate variability (HRV) has increasingly been linked to medical phenomena and several HRV metrics have been found to be good indicators of patient health. This has enabled generalised treatment plans to be developed in order to respond to subtle personal differences that are reflected in HRV metrics. There are several established HRV analysis platforms and methods available within the literature; some of which provide command line operation across databases but do not offer extensive graphical user interface (GUI) and editing functionality, while others offer extensive ECG editing but are not feasible over large datasets without considerable manual effort""" ; sc:featureList edam:operation_3096, edam:operation_3799 ; sc:name "RR-APET" ; sc:url "https://gitlab.com/MegMcC/rr-apet-hrv-analysis-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "Reduced representation bisulfite sequencing simulator for next-generation sequencing." ; sc:featureList edam:operation_0430, edam:operation_3186, edam:operation_3206 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RRBSsim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/xwBio/RRBSsim" ; biotools:primaryContact "Xiwei Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0176 ; sc:citation ; sc:description "UCSF Chimera tool for viewing and comparing protein distance maps." ; sc:featureList edam:operation_2937, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RRDistMaps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html" ; biotools:primaryContact "Conrad C. Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0623, edam:topic_0736 ; sc:citation , "pmcid:PMC6334006", "pubmed:30649297" ; sc:description "Evolutionary-oriented database of RNA recognition motif sequences." ; sc:featureList edam:operation_0239, edam:operation_0246, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:name "RRMdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://iimcb.genesilico.pl/rrm/" ; biotools:primaryContact "S. Dunin-Horkawicz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3500 ; sc:citation , "pmcid:PMC6934287", "pubmed:31881075" ; sc:description """A new, fast method to search for morphological convergence with shape data. The goal of RRphylo is to compute phenotypic evolutionary rates, estimate ancestral states, locate rate shifts on the tree, and compare vectors of phenotypes and evolutionary rates among species. RRphylo is not based on any evolutionary model, and is best suited to work with phylogenies of fossil species.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0551 ; sc:name "RRphylo" ; sc:url "https://github.com/pasraia/RRphylo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:author ; sc:citation , "pmcid:PMC102588", "pubmed:10648794" ; sc:description "Detect oligomers (k-mers) whose positional distribution significantly discard from a homogeneous distribution." ; sc:featureList edam:operation_0238, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT position-analysis" ; sc:operatingSystem "Linux", "Mac" ; sc:provider ; sc:softwareHelp , , , , ; sc:url "http://teaching.rsat.eu/position-analysis_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1942, edam:format_1957 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204 ; sc:author ; sc:citation , "pubmed:10641039" ; sc:description "Starting from a list of genes, returns upstream or downstream sequences." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "RSAT - Retrieve Sequence" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://pedagogix-tagc.univ-mrs.fr/rsat/retrieve-seq_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3500, edam:topic_3517 ; sc:citation ; sc:description "Accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding." ; sc:featureList edam:operation_0239, edam:operation_0438, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RSAT Var-tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rsat.eu" ; biotools:primaryContact "Alejandra Medina-Rivera", "Jacques van Helden" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:author ; sc:citation , "pmcid:PMC102821", "pubmed:10734201" ; sc:description "Detect over- or under-represented dyads (spaced pairs of k-mers) in sequences." ; sc:featureList edam:operation_0238, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT dyad-analysis" ; sc:operatingSystem "Linux", "Mac" ; sc:provider ; sc:softwareHelp , , , , ; sc:url "http://teaching.rsat.eu/dyad-analysis_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3398 ; sc:citation , "pubmed:31114928" ; sc:description "Regulostat Inferelator (RSI) - network biology platform to uncover molecular devices that predetermine cellular response phenotypes." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rsi.hulilab.org/" ; biotools:primaryContact "Hu Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3047, edam:topic_3382 ; sc:citation , "pubmed:31626286" ; sc:description "Topological data analysis quantifies biological nano-structure from single molecule localization microscopy." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "RSMLM" ; sc:softwareHelp ; sc:url "https://github.com/JeremyPike/RSMLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC6732981", "pubmed:31516576" ; sc:description "Bioinformatics and functional analyses of key genes in smoking-associated lung adenocarcinoma | Embeds the 'SQLite' database engine in R and provides an interface compliant with the 'DBI' package. The source for the 'SQLite' engine is included" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3659 ; sc:license "LGPL-2.0" ; sc:name "RSQLite" ; sc:url "http://CRAN.R-project.org/package=RSQLite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173 ; sc:citation , "pmcid:PMC6724675", "pubmed:31434679" ; sc:description "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'RT', 'TRNs', 'TRNs RT', 'provocative' | Replication timing networks reveal a link between transcription regulatory circuits and replication timing control | Create community RT network For RT Networks visualization. It will return None, but creates txt file for the input for the SAFE algorithm | > pip install -r requirements.txt | Before running below do_something.py, please edit parameters in each file" ; sc:featureList edam:operation_0277, edam:operation_0443, edam:operation_3439 ; sc:name "RT networks" ; sc:url "https://github.com/sebkim/RTNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0749, edam:topic_0798, edam:topic_3673 ; sc:citation , "pmcid:PMC6771411", "pubmed:31575651" ; sc:description "RUFUS is a Pedigree-based estimation of human mobile element retrotransposition rates." ; sc:name "RUFUS" ; sc:url "https://github.com/jandrewrfarrell/RUFUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6614807", "pubmed:31114909" ; sc:description "Removing Unwanted Variation-III (RUV-III) - normalization for Nanostring nCounter gene expression data." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RUV-III" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=ruv" ; biotools:primaryContact , "Johann Gagnon-Bartsch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2258, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description "RXN is a unique tool for digital chemistry, based on the Molecular Transformer, using a simple Ketcher drawing interface and made it available on IBM Cloud to perform a variety of tasks: converting Experimental Protocols into Action Sequences, predicting Chemical Reactions, Retrosynthesis Pathways, Experimental Procedures and automating the compilation and execution of Chemical Syntheses." ; sc:featureList edam:operation_0337, edam:operation_3439, edam:operation_3454 ; sc:name "RXN" ; sc:url "https://rxn.res.ibm.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6366910", "pubmed:30591514" ; sc:description "Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Rqtl2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://kbroman.org/qtl2/" ; biotools:primaryContact "Karl Broman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_2229, edam:topic_3168 ; sc:citation , "pmcid:PMC6816165", "pubmed:31661016" ; sc:description """fast and accurate reference-guided scaffolding of draft genomes. Fast Reference-Guided Scaffolding of Genome Assembly Contigs. Index of /shares/schatzlab/www-data/ragoo. A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome. Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17. Contigs and reference fasta files may now be gzipped. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:""" ; sc:featureList edam:operation_0525, edam:operation_3182, edam:operation_3192, edam:operation_3216 ; sc:license "MIT" ; sc:name "RaGOO" ; sc:url "https://github.com/malonge/RaGOO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation , "pubmed:31730197" ; sc:description "RaNA-Seq is an open bioinformatics tool for the quick analysis of RNA-Seq data. It performs a full analysis in minutes quantifying FASTQ files, calculating quality control metrics, running differential expression analyses and enabling the interpretation of results with functional analyses. Our analysis pipeline integrates cutting edge bioinformatics tools and simplify its application with a friendly Web interface designed for non-experienced users in these analyses. Each analysis can be customized setting up input parameters and applies generally accepted and reproducible protocols. Analysis results are presented as interactive graphics and reports, ready for their interpretation and publication." ; sc:featureList edam:operation_2436, edam:operation_3680, edam:operation_3800 ; sc:name "RaNA-Seq" ; sc:url "https://ranaseq.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC6724115", "pubmed:31390788" ; sc:description """Consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.""" ; sc:featureList edam:operation_0523, edam:operation_0525 ; sc:license "MIT" ; sc:name "Racon" ; sc:url "https://github.com/isovic/racon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_3500 ; sc:citation , "pubmed:30019526" ; sc:description "Identification of radical amino acid changes in multiple sequence alignments." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RadAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sciseim/RadAA" ; biotools:primaryContact "Inge Seim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3474, edam:topic_3510 ; sc:citation , "pubmed:31508799" ; sc:description "Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R | Filter plant hydroxyproline rich glycoproteins | ragp - hydroxyproline aware filtering of hydroxyproline rich glycoprotein sequences | ragp is an R package primarily designed for mining and analysis of plant hydroxyproline rich glycoproteins. It incorporates a novel concept with an additional analysis layer where the probability of proline hydroxylation is estimated by a machine learning model. Only proteins predicted to contain hydroxyprolines are further analysed for HRGP characteristic motifs and features. ragp can also be used for protein annotation by obtaining predictions for several protein features based on sequence (secretory signals, transmembrane regions, domains, glycosylphosphatidylinositol attachment sites and disordered regions). Additionally ragp provides tools for visualization of the mentioned attributes" ; sc:featureList edam:operation_0417, edam:operation_0418, edam:operation_3501 ; sc:license "MIT" ; sc:name "Ragp" ; sc:url "https://github.com/missuse/ragp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3056 ; sc:citation , "pubmed:31180862" ; sc:description """RainBio is a visual tool for comparing gene sets or protein sets, in a proportional way. RainBio is an alternative to the classical Venn diagrams and Euler diagrams. In particular, RainBio can compare up to 15 sets, while Venn diagrams are limited to 6, and proportional Venn diagram are approximated above 4 sets. RainBio can perform the exact proportional visualization of up to 6 sets, and support intersection clustering, allowing to visualize up to 15 sets. RainBio uses the same file format that InteractiVenn. Several demo datasets are available on the website.""" ; sc:featureList edam:operation_3209, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "RainBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lesfleursdunormal.fr/static/appliweb/rainbio/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3407 ; sc:citation "pubmed:12542423" ; sc:description "Rare Metabolic Diseases Database: platform independent, web-based information system for rare metabolic diseases based on filed case reports." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "Ramedis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ramedis.de" ; biotools:primaryContact "Thoralf Töpel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3360, edam:topic_3422 ; sc:citation , "pmcid:PMC6764656", "pubmed:31560690" ; sc:description "Spectral characteristics of urine specimens from healthy human volunteers analyzed using Raman chemometric urinalysis (Rametrix) | Raman chemometric urinalysis (Rametrix™) was used to analyze 235 urine specimens from healthy individuals. The purpose of this study was to establish the \"range of normal\" for Raman spectra of urine specimens from healthy individuals. Ultimately, spectra falling outside of this range will be correlated with kidney and urinary tract disease. Rametrix™ analysis includes direct comparisons of Raman spectra but also principal component analysis (PCA), discriminant analysis of principal components (DAPC) models, multivariate statistics, and it is available through GitHub as the Rametrix™ LITE Toolbox for MATLAB®. Results showed consistently overlapping Raman spectra of urine specimens with significantly larger variances in Raman shifts, found by PCA, corresponding to urea, creatinine, and glucose concentrations" ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:name "RametrixTM" ; sc:url "https://github.com/SengerLab/RametrixLITEToolbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_2269 ; sc:citation , "pmcid:PMC6777641", "pubmed:31611898" ; sc:description """An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi. A package for arbuscular mycorrhyzal fungi colonization. Marco Chiapello , Debatosh Das, Caroline Gutjahr. Ramf: An open-source R package for statistical analysis and display of quantitative root colonization by arbuscular mycorrhiza fungi. _Frontiers Plant Science_. **In press**. If you use the package, please cite it:""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:name "Ramf" ; sc:url "https://github.com/mchiapello/Ramf" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3650 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3835 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3955 ; sc:citation , "pubmed:31893378" ; sc:description "R-program supporting the initial step of the workflow of 13C assisted fluxomic analysis: extraction of mass spectra (MS) of 13C-labeled metabolites of interest from raw mass spectrometer recordings saved in NetCDF files." ; sc:featureList edam:operation_2409 ; sc:license "Freeware" ; sc:name "Ramid" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1.0" ; sc:url "https://github.com/seliv55/ramidcor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2830, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6929103", "pubmed:31816915" ; sc:description """A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics. RankerGUI platform for the comparison of differential expression profiles using a rank-based statistical approach. RankerGUI automates the analysis of complex gene expression signatures. The Pipeline is easy to use and freely available to the scientific community. Users can upload data via a web page and can be notified of the analysis completion by email. The output includes detailed data analysis reports and diagrams. Documentation provides full information on used methods""" ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_2436, edam:operation_3223, edam:operation_3802 ; sc:name "RankerGUI" ; sc:url "http://watson.na.icar.cnr.it/rankergui/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3298 ; sc:citation , "pmcid:PMC6823239", "pubmed:31708940" ; sc:description """Measuring Rapid A-Ci Curves in Boreal Conifers. R scripts for automatic correction of Rapid A-Ci curves. An R package for the batch treatment of Rapid carbon dioxide response curves (A-Ci) generated by the LI-COR® portable photosynthesis systems. The Rapid A-Ci measurement method (RACiR™) can save a lot of time characterising photosynthetic capacity of multiple plants. devtools::install_github("ManuelLamothe/RapidACi"). If, later on, you need to adjust leaf area values, you need to provide a dataframe containing at least one column for the unique sample identifier (named: “sample_ID”), and one column with the leaf area in mm2 (named: “LeafArea_mm2”)""" ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:name "RapidACi" ; sc:url "https://github.com/ManuelLamothe/RapidACi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:31583631" ; sc:description "A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning." ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3439, edam:operation_3899 ; sc:name "RaptorX-ComplexContact" ; sc:url "http://raptorx.uchicago.edu/ComplexContact/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2885, edam:topic_3172, edam:topic_3325 ; sc:citation , "pmcid:PMC6830269", "pubmed:31688938" ; sc:description """a manually curated database of lysosomal enzymes associated with rare diseases. RareLSD: Database for Human Lysosomal Enzymes. RareLSD: A Database for Human Lysosomal Enzymes. RareLSD is a manually curated database of 63 lysosomal enzymes present in the humans. Deficiency or malfunctioning of any enzyme leads to accumulation of toxic metabolites and thus, various storage defects. 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It provides command-line and Python interfaces to download pre-built reference genome \"assets\", like indexes used by bioinformatics tools. It can also build assets for custom genome assemblies. Refgenie provides programmatic access to a standard genome folder structure, so software can swap from one genome to another." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "refgenie" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://refgenie.databio.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3855 ; sc:citation , "pmcid:PMC6612893", "pubmed:31510694" ; sc:description "Reconstructing signaling pathways using regular language constrained paths | Connect the dots in protein interaction networks ... using regular expressions! | RegLinker is an algorithm for the automated curation of signaling pathways. Given a signaling pathway and a background interactome, RegLinker will automatically rank the interactions in the background interactome as candidates for inclusion into the signaling pathway | Connect the dots in protein interaction networks... using regular expressions!" ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "RegLinker" ; sc:url "https://github.com/Murali-group/RegLinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0634, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6883696", "pubmed:31779641" ; sc:description """a computational framework for predicting pathogenic impact of intronic single nucleotide variants. Predict disease-causing probability of human intronic SNVs. regSNP-intron is a tool which predicts disease-causing probability of human intronic single nucleotide variants (iSNVs). regsnp-intron predicts the disease-causing probability of intronic single nucleotide variants (iSNVs) based on both genomic and protein structural features. ANNOVAR (>= 2016Feb01): Follow the instructions at http://annovar.openbioinformatics.org/en/latest to install, and prepare Ensembl gene annotation. Or paste input here (use example). Or upload a file size limit: 10K rows""" ; sc:featureList edam:operation_0417, edam:operation_2499, edam:operation_3461 ; sc:license "MIT" ; sc:name "RegSNPs-intron" ; sc:url "https://regsnps-intron.ccbb.iupui.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3172, edam:topic_3517 ; sc:citation , "pmcid:PMC4293375", "pubmed:24008273" ; sc:description "Performance of fast association analysis between allele frequencies and continuous traits. Uses linear regression to estimate marker effects on continuous traits." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RegScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.5" ; sc:url "https://www.geenivaramu.ee/en/tools/regscan" ; biotools:primaryContact "T. Haller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325 ; sc:citation , "pubmed:31106382" ; sc:description """RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Phenotypic data can be used to focus on likely disease genes.""" ; sc:featureList edam:operation_3225 ; sc:isAccessibleForFree true ; sc:name "RegulationSpotter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.regulationspotter.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0780, edam:topic_0798, edam:topic_3168 ; sc:citation , "pmcid:PMC5274521", "pubmed:28149701" ; sc:description """a high resolution transposable element insertion site mapping tool for population resequencing. This tool is for mapping TEs from resequencing data: Stajich lab. RelocaTE2: a high resolution transposable element insertion sites mapping tool for population resequencing. RelocaTE2 is an improved version of RelocaTE (Robb et al., 2013). RelocaTE2 is highly sensitive and accurate in mapping transposable elements (TE) polymorphisms at single base pair resolution. RelocaTE2 uses the reads associated with TEs as seeds to cluster the read pairs on chromosomes. It automatically detects the target site duplication (TSD) of a TE insertion from alignments in each cluster, which enable high resolution mapping of TE polymorphisms. Unlike parallel searching of multi-TE elements in RelocaTE, RelocaTE2 searches all TEs in one cycle, which enables us find polymorphisms of thousands of TEs in an individual genome or large population in a reasonable timeframe without losing sensitivity and specificity""" ; sc:featureList edam:operation_0452, edam:operation_3192, edam:operation_3196 ; sc:license "MIT" ; sc:name "RelocaTE2" ; sc:url "https://github.com/stajichlab/RelocaTE2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0821, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:31800321" ; sc:description """Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets. Venue - Responsive HTML5 Template. Tool to identify Bioremediation enzymes from. RemeDB aims at identifying Pollutant Degrading Enzymes (PDE) from metagenomic sequences. A hassle-free tool to predict bioremediation enzymes from metagenomic datasets""" ; sc:featureList edam:operation_0417, edam:operation_2421 ; sc:name "RemeDB" ; sc:url "https://www.niot.res.in/Remedb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6883653", "pubmed:31783882" ; sc:description """reference-free orientation of nanopore cDNA reads with deep learning. Transcriptome long-read orientation with Deep Learning. ReorientExpress is a program to create, test and apply models to predict the 5'-to-3' orientation of long-reads from cDNA sequencing with Nanopore or PacBio using deep neural networks for samples without a genome or a transcriptome reference. For details on the benchmarkings and analyses performed with this program, please see our publication: https://www.ncbi.nlm.nih.gov/pubmed/31783882""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3472 ; sc:license "MIT" ; sc:name "ReorientExpress" ; sc:url "https://github.com/comprna/reorientexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2885, edam:topic_3399 ; sc:citation , "pubmed:30598392" ; sc:description "Web server to extract sequence repeats from protein and DNA sequences." ; sc:featureList edam:operation_0237 ; sc:isAccessibleForFree true ; sc:name "RepEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserver2.physics.iisc.ac.in/RepEx/" ; biotools:primaryContact "Professor K. Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0749, edam:topic_0798 ; sc:citation ; sc:description "RepeatFiller incorporates newly-detected repeat-overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in the chains, which makes it feasible to consider all seeds including those that overlap repetitive regions." ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_3182 ; sc:name "RepeatFiller" ; sc:url "https://github.com/hillerlab/GenomeAlignmentTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0196, edam:topic_0621, edam:topic_0798, edam:topic_3673 ; sc:citation ; sc:description "RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data." ; sc:featureList edam:operation_0362, edam:operation_0525, edam:operation_3644 ; sc:name "RepeatModeler" ; sc:url "https://github.com/Dfam-consortium/RepeatModeler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:15961478" ; sc:description "RepeatScout is a tool to discover repetitive substrings in DNA." ; sc:featureList edam:operation_3472 ; sc:name "RepeatScout" ; sc:url "http://bix.ucsd.edu/repeatscout/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Repeats intermine database" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "RepetDB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://urgi.versailles.inra.fr/repetdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31484108" ; sc:description "A New Multi-scale Backbone Architecture | A New Multi-scale Backbone Architecture – 程明明教授主页 | Figure 1. We propose a novel building block for CNNs, namely Res2Net, by constructing hierarchical residual-like connections within one single residual block. The Res2Net represents multi-scale features at a granular level and increases the range of receptive fields for each network layer. The proposed Res2Net block can be plugged into the state-of-the-art backbone CNN models, e.g., ResNet, ResNeXt, BigLittleNet, and DLA. We evaluate the Res2Net block on all these models and demonstrate consistent performance gains over baseline models" ; sc:featureList edam:operation_0479, edam:operation_3436 ; sc:name "Res2Net" ; sc:url "https://mmcheng.net/res2net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3053 ; sc:citation , "pubmed:31845517" ; sc:description """An R package for fine-scale mapping of resistance to dispersal. Management of biological invasions and conservation activity in the fight against habitat fragmentation both require information on how ongoing dispersal of organisms is affected by the environment. However, there are few landscape genetic programs that map resistance to dispersal at small spatiotemporal scales. To facilitate such analyses, we present an R package named ResDisMapper for the mapping of resistance to dispersal at small spatiotemporal scales, without the need for prior knowledge on environmental features or intensive computation. Based on the concept of isolation by distance (IBD), ResDisMapper calculates resistance using deviations of each pair of samples from the general IBD trend (IBD residuals). The IBD residuals are projected onto the studied area, which allows construction and visualization of a fine-scale map of resistance based on spatial accumulation of positive or negative IBD residuals""" ; sc:featureList edam:operation_0282, edam:operation_2950 ; sc:name "ResDisMapper" ; sc:url "https://github.com/takfung/ResDisMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31070716" ; sc:description "Algorithm for protein residue-residue contact-map prediction." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ResPRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanglab.ccmb.med.umich.edu/ResPRE" ; biotools:primaryContact "Yang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3538 ; sc:citation , "pmcid:PMC6748046", "pubmed:31411026" ; sc:description "Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder | Many proteins contain regions of intrinsic disorder, not folding into unique, stable conformations. Numerous experimental methods have been developed to measure the disorder of all or select residues. In the absence of experimental data, computational methods are often utilized to identify these disordered regions and thus gain a better understanding of both structure and function. Many freely available computational methods have been developed to predict regions of intrinsic disorder from the primary sequence of a protein, including our recently developed Rosetta ResidueDisorder. While these methods are very useful, they are only designed to predict intrinsic disorder from the sequence" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_3904 ; sc:name "ResidueDisorder" ; sc:url "https://www.rosettacommons.org/docs/latest/ResidueDisorder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0081 ; sc:citation , "pubmed:31799624" ; sc:description "Programs can use RestraintLib's API to calculate restraints programmatically without interacting with this web page. To see the format of the requests, check the API documentation." ; sc:featureList edam:operation_0249, edam:operation_1844, edam:operation_2518 ; sc:name "RestraintLib" ; sc:url "http://achesym.ibch.poznan.pl/restraintlib/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3398, edam:topic_3407 ; sc:citation , "pmcid:PMC6734243", "pubmed:31500573" ; sc:description "determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms | The overaching goal of RetSynth is to streamline the arduous and complex step of selecting enzyme/reactions pairs to produce a target compound for bioengineering microbial organisms" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3660 ; sc:license "BSD-2-Clause" ; sc:name "RetSynth" ; sc:url "https://github.com/sandialabs/RetSynth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0749 ; sc:citation ; sc:description "Pathogenicity prediction of human missense variants based on protein sequence, structure and dynamics | computationally predicting effects of saturation mutagenesis | In silico saturation mutagenesis | perform a complete scan of all possible 19 amino acid substitutions at each site on a human sequence. See example: H-Ras" ; sc:featureList edam:operation_0331, edam:operation_0477, edam:operation_3461 ; sc:name "Rhapsody" ; sc:url "http://rhapsody.csb.pitt.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0196, edam:topic_0203, edam:topic_0659, edam:topic_2229 ; sc:citation ; sc:description "RiboFlow is an ecosystem for analyzing ribosome profiling data at read length resolution." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboFlow" ; sc:url "https://github.com/ribosomeprofiling/riboflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0196, edam:topic_0203, edam:topic_0659, edam:topic_2229 ; sc:citation ; sc:description "RiboPy is an ecosystem for analyzing ribosome profiling data at read length resolution." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboPy" ; sc:url "https://ribopy.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "Ribo Ecosystem is a set of software tools, built around the ribo file format, to facilitate analyzing ribosome profiling data at ribosome protected footprint length resolution. It consists of a pipeline, RiboFlow, and two interfaces RiboR and RiboPy." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3436 ; sc:name "RiboR" ; sc:url "https://ribosomeprofiling.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:31777932" ; sc:description """a computational framework for visualization, quality control and statistical analysis of ribosome profiling data. Visualization, Quality and Statistics for Ribosome Profiling. This is package RiboVIEW for Visualization, Quality and Statistics for Ribosome Profiling""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_2495, edam:operation_3192, edam:operation_3891 ; sc:name "RiboVIEW" ; sc:url "https://github.com/carinelegrand/RiboVIEW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "Web tool for bacterial classification through m/z data from ribosomal proteins." ; sc:featureList edam:operation_2929, edam:operation_3460, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Ribopeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ribopeaks.com." ; biotools:primaryContact "Rafael Mazer Etto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0623, edam:topic_3293 ; sc:citation , "pmcid:PMC6764101", "pubmed:31560050" ; sc:description "a genomic database of rice relatives for rice research | Welcome to RiceRelativesGD, a genomic database of rice relatives for rice research! | The cultivated rice (Oryza sativa) is one of the most important crops in the world" ; sc:featureList edam:operation_0553, edam:operation_3431, edam:operation_3501 ; sc:name "RiceRelativesGD" ; sc:url "http://ibi.zju.edu.cn/ricerelativesgd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6527052", "pubmed:31107941" ; sc:description "Open resource for plant science." ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "Rice Galaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://13.250.174.27:8080/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3321, edam:topic_3366 ; sc:description "An open source database(s) for genetics, genomics and functional research in rice species" ; sc:featureList edam:operation_0292, edam:operation_0337 ; sc:funder "CRP Rice" ; sc:isAccessibleForFree true ; sc:name "Rice Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://rice-genome-hub.southgreen.fr/" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'PQN', 'Windham', 'eGTEx' | Model-Based Robust Normalization for High-Throughput Proteomics from Mass Spectrometry Platform | Abstract Motivation In the analysis of proteomics data from mass spectrometry (MS), normalization is an important preprocessing step to correct sample-level variation and make abundance measurements for each specific protein comparable across different samples. Under heterogeneous samples such as in the Phase I study of the Enhancing Genotype-Tissue Expression (eGTEx) project (Jiang, et al., 2019), the samples coming from 32 different tissues, and without prior housekeeping protein information or spike-ins, how to robustly correct the bias but keep tissue internal variations becomes a challenging question. Majority of previous normalization methods cannot guarantee a robust and tissue adaptive correction" ; sc:featureList edam:operation_3454, edam:operation_3557, edam:operation_3639 ; sc:name "RobNorm" ; sc:url "https://github.com/mwgrassgreen/RobNorm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0736, edam:topic_0749 ; sc:citation , "pubmed:31800008" ; sc:description """A standalone GUI-based package for robust co-evolutionary analysis of proteins. RocaSec is a standalone cross-platform package which features an easy-to-use GUI. The package only requires the multiple sequence alignment data of a protein for inferring the underlying co-evolutionary sectors. In addition, when information on the protein biochemical domains is provided, RocaSec returns the corresponding statistical association between inferred sectors and biochemical domains""" ; sc:featureList edam:operation_3658, edam:operation_3767 ; sc:license "MIT" ; sc:name "RocaSec" ; sc:url "https://github.com/ahmedaq/RocaSec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31634130" ; sc:description "RBM ( Restricted Boltzmann Machine ) is an unsupervised Rotation Factorization in Restricted Boltzmann Machines." ; sc:name "RBM" ; sc:url "https://bitbucket.org/tuttoweb/rotinvrbm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC6814140", "pubmed:31651257" ; sc:description "Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish." ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_3216, edam:operation_3799 ; sc:name "RsHSF" ; sc:url "http://www.cibiv.at/services/hsf/info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description """correlation of expressed SNVs with splicing using RNA-sequencing data. RsQTL: correlation of expressed SNVs with splicing patterns using RNA-sequencing data. This toolkit contains the required scripts to transform sequencing files into RsQTL input files and run the MatrixEQTL R package to identify significant variation-splicing relationships""" ; sc:featureList edam:operation_2939, edam:operation_3800, edam:operation_3891 ; sc:name "RsQTL" ; sc:url "https://github.com/HorvathLab/RsQTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation , "pubmed:30945241" ; sc:description "tool for drawing graphs that can be represented by the BioNetGen language, which is used to formulate mathematical, rule-based models of biochemical systems." ; sc:featureList edam:operation_2426, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RuleBuilder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/RuleWorld/RuleBuilder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0821, edam:topic_2258, edam:topic_3314 ; sc:citation ; sc:description "Tool computes reaction similarity based on the molecular signatures of participating molecules." ; sc:featureList edam:operation_2929, edam:operation_3502 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RxnSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=RxnSim" ; biotools:primaryContact "Anirban Bhaduri", "Tae Yong Kim", "Varun Giri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3314 ; sc:citation ; sc:description """Alignment-free gapped mapping of noisy long reads. Spaced context based Locality Sensitive Hashing. Spaced context based Locality Sensitive Hashing (S-conLSH) is a new mapper that facilitates gapped mapping of noisy long reads to the corresponding target locations of a reference genome, with multiple spaced patterns. Spaced-context based Locality Sensitive Hashing""" ; sc:featureList edam:operation_0491, edam:operation_3198, edam:operation_3211 ; sc:license "GPL-3.0" ; sc:name "S-conLSH" ; sc:url "https://github.com/anganachakraborty/S-conLSH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC6448907", "pubmed:30908487" ; sc:description "Searching algorithm for Type IV effector proteins (S4TE) - software package developed for the prediction of Type IV effector proteins and the analysis of their genomic context." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "S4TE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://sate.cirad.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0202, edam:topic_3520 ; sc:citation , "pubmed:31612721" ; sc:description """Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. SAAVpedia is a platform for identification, functional annotation, retrieval of single amino-acid variants from proteomic and genomic data. Home Y.-M. Kang 2019-12-24T08:52:37+00:00. S ingle A mino- A cid V ariant Encyclo pedia :. User Guide Y.-M. Kang 2018-11-28T11:06:16+00:00. The SAAVpedia is a comprehensive proteogenomic interpretation platform that identifies, annotates, and retrieves SAAVs from proteomic and genomic sequence data to discover true pathogenic variant candidates. SAAVpedia provides a proteogenomic analysis pipeline to prioritize and interpret SAAVs. The SAAVpedia is a platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. Identification, functional annotation, and retrieval of single amino-acid variants for proteogenomic interpretation""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3226, edam:operation_3436 ; sc:license "Apache-2.0" ; sc:name "SAAVpedia" ; sc:softwareHelp ; sc:url "https://www.SAAVpedia.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3370 ; sc:citation , "pubmed:31462040" ; sc:description "Open Source Software for the Real-Time Control, Processing, and Visualization of High-Volume Electrochemical Data | This repository contains the master script for the SACMES program and all updates | All updates for the Standard Operating Procedure (SOP) can be viewed here: https://www.dropbox.com/preview/NetzLab%20SACMES%20SOP/2019_11_13%20SACMES%20SOP.docx?role=personal" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3431 ; sc:name "SACMES" ; sc:url "https://github.com/netzlab/SACMES.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3277 ; sc:citation ; sc:description "SAD contains efficient algorithms for sampling feasible sets of abundance distributions." ; sc:name "SAD" ; sc:url "https://github.com/klocey/partitions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6704125", "pubmed:31434941" ; sc:description "High-speed device synchronization in optical microscopy with an open-source hardware control platform | Check out the preprint at https://doi.org/10.1101/533349 for more details | This project has been developed in house by the Paszek and Zipfel labs at Cornell University over a few years and several revisions. The primary developer has been Marshall Colville (mjc449@cornell.edu) with assistance from Warren Zipfel and Matt Paszek | Given the scope of the project, the multiple revisions and adaptations that the hardware and software have gone through, and the fact that we are not electrical or software engineers the code tends to change styles and not follow typical conventions" ; sc:name "SAIM" ; sc:url "https://github.com/mjc449/SAIMscannerV3.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3125 ; sc:citation , "pmcid:PMC6719893", "pubmed:31433799" ; sc:description "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "SALSA" ; sc:url "https://github.com/machinegun/SALSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3335, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc:description """classifying clinical short notes using background knowledge from unlabeled data. Short and Long Text Classifier using clustering-based enrichment. .. :Travis: image:: https://travis-ci.com/bagheria/saltclass.svg?token=fYbdQUbpnoucyHyb3fs2&branch=master .. _Travis: https://travis-ci.com/bagheria/saltclass. saltclass (Short and Long Text Classifier) is a Python module for text classification built under the MIT license. The project was started in 2018 at the Department of Methodology & Statistics, Utrecht University""" ; sc:featureList edam:operation_1812, edam:operation_3432, edam:operation_3625 ; sc:license "MIT" ; sc:name "SALTClass" ; sc:url "https://pypi.org/project/saltclass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC6803637", "pubmed:31636330" ; sc:description """Denoising of Aligned Genomic Data. Universal denoiser for genomic sequencing. SAMDUDE is a genomic sequence denoiser that operates on aligned SAM files. It both denoises individual bases in reads as well as updates the corresponding quality scores""" ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3227, edam:operation_3675, edam:operation_3802 ; sc:name "SAMDUDE" ; sc:url "https://github.com/ihwang/SAMDUDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31777938" ; sc:description """Single-cell Aggregated Clustering via Mixture Model Ensemble. SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. SAMEclustering (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data. Although several methods have been recently developed to cluster single-cell RNA-seq (scRNA-Seq) data, they utilize different characteristics of data and yield varying results in terms of both the number of clusters and actual cluster assignments""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3436 ; sc:name "SAME-clustering" ; sc:url "https://github.com/yycunc/SAMEclustering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC6886563", "pubmed:31824393" ; sc:description "SAMIRIX is a custom-developed intraretinal segmentation pipeline. It modularly includes import filters for OCT data, a 3rd-party segmentation algorithm, a user interface for controlling and correcting segmentation results, and batch-operations for processing multiple OCT images." ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "SAMIRIX" ; sc:url "https://github.com/neurodial/am_SAMIRIX.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0602, edam:topic_3068, edam:topic_3407 ; sc:citation , "pubmed:31851289" ; sc:description """A Semi-Automated Tool for the Visualization of Metabolic Networks. Semi-Automated Metabolic Map Illustrator. SAMMI is a web-based tool for the visualization of metabolic networks and related data. Networks can be uploaded directly from KEGG annotated pathways or using constraint-based metabolic reconstructions""" ; sc:featureList edam:operation_0573, edam:operation_1812, edam:operation_3083, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "SAMMI" ; sc:url "http://www.SammiTool.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_3534 ; sc:citation ; sc:description "Web server for predicting SAM binding residues of a protein from its amino acid sequence." ; sc:featureList edam:operation_0272, edam:operation_0417, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SAMbinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://webs.iiitd.edu.in/raghava/sambinder/" ; biotools:primaryContact "G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3474 ; sc:citation ; sc:description "A Machine Learning Recommendation Method and Webtool for the Prediction of Functional Post-Translational Modifications | ABSTRACT Post-translational Modifications (PTMs), chemical or proteinaceous covalent alterations to the side chains of amino acid residues in proteins, are a rapidly expanding feature class of significant importance in cell biology. Due to a high burden of experimental proof and the lack of effective means for experimentalists to prioritize PTMs by functional significance, currently less than ~2% of all PTMs have an assigned biological function. Here, we describe a new artificial neural network model, SAPH-ire TFx for the functional prediction of experimentally observed eukaryotic PTMs. Unlike previous functional PTM prioritization models, SAPH-ire TFx is optimized with both receiver operating characteristic (ROC) and recall metrics that maximally capture the range of diverse feature sets comprising the functional modified eukaryotic proteome" ; sc:featureList edam:operation_0417, edam:operation_0480, edam:operation_3755 ; sc:name "SAPH-ire TFx" ; sc:url "https://saphire.biosci.gatech.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31095298" ; sc:description "Matlab package for incorporating spatial-anatomical similarity into the VGWAS framework to detect significant biomarkers in both genetic and imaging data of neurodegenerative diseases." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SASM-VGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Meiyan88/SASM-VGWAS" ; biotools:primaryContact "Meiyan Huang", "Qianjin Feng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3752 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3752 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474 ; sc:citation ; sc:description "SAUCIE is a python object that loads data from a numpy matrix and produces numpy matrix output for the reconstruction, visualization, and/or clusters." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3557, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SAUCIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KrishnaswamyLab/SAUCIE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:31471617" ; sc:description "Data denoising with transfer learning in single-cell transcriptomics | R package for transfer learning of single-cell RNA-seq denoising | SAVER-X – Laboratory for single Cell data science | R package for transfer learning of scRNA-seq denoising. Take a look at our free SAVER-X web-server for the transfer learning online computation! We also encourage you to read our pre-print manucript for more information. You can also refer to our earlier denoising method SAVER | Laboratory for single Cell data science | Where Statistics, Biology and Computer Science Meet | Uploading Data is as Easy as 1-2-3: | Researchers can directly upload their data of UMI counts to the web portal as a (gene x cell) matrix stored in a .csv, .txt or .rds file. Our cloud service does not store the user’s data or use it for any other purpose besides denoising | In most single cell transcriptomics (scRNA-seq) studies, the data are extremely sparse and noisy, hindering downstream analyses" ; sc:featureList edam:operation_3501, edam:operation_3557 ; sc:name "SAVER-X" ; sc:url "http://singlecell.wharton.upenn.edu/saver-x/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0196, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:31860156" ; sc:description """Modeling multidomain protein structures using small-angle X-ray scattering data. This is a bioinformatics tool to use SAXS data to assemble protein domain structures into full-length structural models. Installation (tested on CentOS Linux 7 (Core)). (3) Compile SAXSDom from source code (required). running /data/jh7x3/SAXSDom/db_tools/tools/cmake-2.8.12.2/bin/cmake -E create_symlink "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" "/data/jh7x3/SAXSDom/installation/Mocapy++-1.07/examples/data" 2>&1""" ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_0321, edam:operation_0476, edam:operation_0477 ; sc:name "SAXSDom" ; sc:url "https://github.com/jianlin-cheng/SAXSDom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , , , "pubmed:31452098", "pubmed:31452104", "pubmed:31452110" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'statistical analysis docking results', 'affinity', 'protein-targeted', 'machine-learning' | A Computational Tool for Docking | Molegro Virtual Docker for Docking | Machine Learning to Predict Binding Affinity | Make molecular docking reliable, fast, easy, free, and funny with SAnDReS. It is the easiest way to run dependable protein-ligand docking simulations. SAnDReS takes a different approach to docking; it focuses on the simulation of a system composed of an ensemble of crystallographic structures for which ligand binding affinity data is available" ; sc:featureList edam:operation_0482, edam:operation_3659, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "SAnDReS" ; sc:url "https://github.com/azevedolab/sandres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31081037" ; sc:description "Coordinate Descent Approach for Sparse Bayesian Learning in High Dimensional QTL Mapping and Genome-wide Association Studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MeiyueComputBio/sbl/tree/master/R%20packge" ; biotools:primaryContact "Meiyue Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3512 ; sc:citation , "pmcid:PMC6743255", "pubmed:31559017" ; sc:description "Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models | SBM-for-correlation-based-networks" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:license "GPL-3.0" ; sc:name "SBM" ; sc:url "https://gitlab.com/biomodlih/sbm-for-correlation-based-networks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3314, edam:topic_3379, edam:topic_3407 ; sc:citation , "pubmed:31738386" ; sc:description "SBML2Modelica is a tool which translates biochemical models written in System Biology Markup Language (SBML) Version 3 Level 2 into well-structured, user-intelligible, easily-modifiable Modelica models." ; sc:featureList edam:operation_0337, edam:operation_3562 ; sc:name "SBML2Modelica" ; sc:url "https://bitbucket.org/mclab/sbml2modelica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3292, edam:topic_3306 ; sc:citation ; sc:description "SBMLLint is a collection of tools for linting reactions. The initial focus is detecting mass balance errors. The tool takes as input a model expressed in either SBML (Systems Biology Markup Language, a standard format for biochemical models) or the Antimony language (a human readable representation of chemical reaction models)." ; sc:featureList edam:operation_3096, edam:operation_3660 ; sc:license "MIT" ; sc:name "SBMLLint" ; sc:url "https://github.com/ModelEngineering/SBMLLint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq | Code for producing the analysis in the \"Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq\" manuscript | Code for producing the analysis in the \"Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq\" by Valentine Svensson, Eduardo Beltrame and Lior Pachter | The workflow has 4 steps. The output data after each step can be downloaded from CaltechDATA at https://data.caltech.edu/records/1276 | 1) FASTQ Subsampling and processing with kallisto bus" ; sc:featureList edam:operation_3223, edam:operation_3230, edam:operation_3800 ; sc:name "SBP_2019" ; sc:url "https://github.com/pachterlab/SBP_2019/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC6783552", "pubmed:31594952" ; sc:description """SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Single-cell ATAC-seq analysis via Latent feature Extraction. SCALE neural network is implemented in Pytorch framework. Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang & Qiangfeng Cliff Zhang. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, (2019).""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "SCALE" ; sc:url "https://github.com/jsxlei/SCALE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Set of tools for SCoring, ANnotating and VISualizing splice junctions using annotation details (gencode or other)." ; sc:featureList edam:operation_2939 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SCANVIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.99.15" ; sc:url "https://github.com/nygenome/SCANVIS" ; biotools:primaryContact "Phaedra Agius" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description "An Open Source Physical Layer for the DARPA Spectrum Collaboration Challenge." ; sc:featureList edam:operation_3215 ; sc:name "SCATTER PHY" ; sc:url "https://github.com/zz4fap/scatter-phy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3474 ; sc:citation , "pmcid:PMC6878945", "pubmed:31769834" ; sc:description "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD and 3) link to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM." ; sc:featureList edam:operation_3096, edam:operation_3435 ; sc:name "SCDO" ; sc:url "http://scdontology.h3abionet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6775478", "pubmed:31611909" ; sc:description """A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes. PRESDB:pig RNA Editing database""" ; sc:featureList edam:operation_2495, edam:operation_3096, edam:operation_3223 ; sc:name "SCDevDB" ; sc:url "https://scdevdb.deepomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2814, edam:topic_2830, edam:topic_3489 ; sc:citation , "pmcid:PMC6785892", "pubmed:31601176" ; sc:description "SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database (IEDB) and clusters them based on antigens, receptors and epitopes to generate benchmark datasets. Users can customize structural quality and clustering parameters (e.g. resolution, R free factors, antigen or epitope sequence identity) to generate these datasets based on their need." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3432 ; sc:name "SCEptRe" ; sc:url "http://tools.iedb.org/sceptre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621, edam:topic_3174 ; sc:citation , "pubmed:31764940" ; sc:description """consensus approach to contig filtering and genome prediction from single cell sequencing libraries of uncultured eukaryotes. SCGid, a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries. Please note that this version of SCGid constitutes an early-release version that is currently under active development toward a stable version coinciding with the release of the accepted manuscript introduing it. I am now porting SCGid to python 3 and stabilizing it for full release as SCGid (v1.0) within the next few weeks. This development is taking place on a separate branch. In the mean time, this beta version is working and available for use. I am available to assist with any problems you run into while using this branch of SCGid as well as patch bugs. If you encounter a bug or confusing error while running the beta version of SCGid, please open an issue on this repositiory""" ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "SCGid" ; sc:url "http://www.github.com/amsesk/SCGid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Schema is a general algorithm for integrating heterogeneous data modalities, with application to multi-modal single-cell biological datasets." ; sc:featureList edam:operation_3435, edam:operation_3561, edam:operation_3891 ; sc:name "SCHEMA" ; sc:url "http://schema.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6612866", "pubmed:31510696" ; sc:description "Inference of clonal selection in cancer populations using single-cell sequencing data | Single Cell Inference of FItness Landscape | We propose a computational method for in vivo inference of clonal selection and estimate of fitness landscapes of heterogeneous cancer cell populations from single cell sequencing data | matlab -nodisplay -nodesktop -r \"n=;m=;gv_file='';output='';method='';nRep=;theta=;SCIFIL\"" ; sc:featureList edam:operation_0487, edam:operation_3478, edam:operation_3799 ; sc:license "MIT" ; sc:name "SCIFIL" ; sc:url "https://github.com/compbel/SCIFIL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3810, edam:topic_3855 ; sc:citation , "pubmed:31494409" ; sc:description "Identifying critical source areas using multiple methods for effective diffuse pollution mitigation | A framework for modelling and mapping diffuse pollution risk across landscapes | SCIMAP - Diffuse Pollution Risk Mapping | To identify the locations that are a problem, we developed SCIMAP. This project was originally jointly developed between Durham and Lancaster Universities. SCIMAP is supported by the U.K.’s Natural Environment Research Council, the Eden Rivers Trust, the Department of the Environment, Food and Rural Affairs and the Environment Agency. Following this project SCIMAP has been supported by Durham University, the Rivers Trust and the Environment Agency" ; sc:featureList edam:operation_2429, edam:operation_3501 ; sc:name "SCIMAP" ; sc:url "http://www.scimap.org.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31770586" ; sc:description "Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach." ; sc:featureList edam:operation_0524, edam:operation_1781, edam:operation_3258 ; sc:name "SCMVTDb" ; sc:url "http://webtom.cabgrid.res.in/scmvtdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6837541", "pubmed:31658262" ; sc:description """Ab initio marker selection for single cell transcriptome profiling. Marker gene selection from scRNA-seq data. SCMarker performs cell-type-specific marker selection from single cell RNA sequencing data. It provides users a tool for selecting features from tens of thousands of genes for further cell-type clustering analysis""" ; sc:featureList edam:operation_0313, edam:operation_3501 ; sc:name "SCMarker" ; sc:url "https://github.com/KChen-lab/SCMarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0780, edam:topic_2885, edam:topic_3170 ; sc:citation , "pmcid:PMC6853641", "pubmed:31680133" ; sc:description """a genomics portal for the soybean cyst nematode (Heterodera glycines). All supporting analyses required for SCNBase data""" ; sc:featureList edam:operation_0362, edam:operation_0433, edam:operation_2421 ; sc:name "SCNBase" ; sc:url "http://SCNBase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3068, edam:topic_3387, edam:topic_3489 ; sc:citation , "pmcid:PMC6820755", "pubmed:31664032" ; sc:description "SCOC database is a large, open, and global database with sediment community oxygen consumption rates." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:name "SCOC database" ; sc:url "http://data.eol.ucar.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "SCOM applies three criteria (significantly synergistic competition for mRNAs, significantly positive correlation, and significantly sensitive correlation conditioning on synergistically competed mRNAs) to predict ncRNA synergistic competition network from gene (ncRNAs acting as ceRNAs, and target mRNAs) expression data and predicted ncRNA-related ceRNA networks." ; sc:featureList edam:operation_0313, edam:operation_2437, edam:operation_2495, edam:operation_3463, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/zhangjunpeng411/SCOM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0820, edam:topic_3517 ; sc:citation , "pmcid:PMC5225593", "pubmed:28077070" ; sc:description "Software for COrrelated Phenotype Analysis." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SCOPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.14" ; sc:url "https://www.geenivaramu.ee/en/tools/scopa" ; biotools:primaryContact "Andrew P Morris", "Reedik Magi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:citation ; sc:description "Tool for sample size calculations for single-cell sequencing experiments." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SCOPIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://alexdavisscs.shinyapps.io/scs_power_multinomial/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_3542 ; sc:citation , "pubmed:31742326" ; sc:description "SCOT is a tool for secondary structure Classification on Turns." ; sc:featureList edam:operation_0249, edam:operation_0267, edam:operation_0319, edam:operation_2488, edam:operation_2996 ; sc:name "SCOT" ; sc:url "https://this-group.rocks/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6501316", "pubmed:31060596" ; sc:description "Single-cell RNA-seq imputation constrained by bulk RNA-seq data." ; sc:featureList edam:operation_3436, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCRABBLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://rdrr.io/cran/SCRABBLE/" ; biotools:primaryContact "Tao Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data. Please run Rscript --vanilla fitSCRIBE.R [expression file] [batch index file] [biological group index file] [output file]""" ; sc:featureList edam:operation_2495, edam:operation_3557 ; sc:name "SCRIBE" ; sc:url "https://github.com/YiliangTracyZhang/SCRIBE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_2275 ; sc:citation , "pmcid:PMC6612887", "pubmed:31510679" ; sc:description "accurate and partner type-specific prediction of protein-binding residues from proteins sequences | SCRIBER - web server from Biomine lab" ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3899 ; sc:name "SCRIBER" ; sc:url "http://biomine.cs.vcu.edu/servers/SCRIBER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31584615" ; sc:description "SCSsim is a tool designed for emulating single-cell genome sequencing data. It consists of three modules: 1) “simuVars” module aims to generate single cell genome from a given reference sequence by inserting user-defined genomic variations into genomic loci; 2) “learnProfile” component is developed to infer sequencing platform dependent profiles from real data; 3) “genReads” utility is provided to mimic single-cell genome amplification and read generation procedures based on the results of “simuVars” and “learnProfile”." ; sc:featureList edam:operation_0296, edam:operation_3198 ; sc:license "BSD-3-Clause" ; sc:name "SCSsim" ; sc:url "https://github.com/qasimyu/scssim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pubmed:31116393" ; sc:description "Statistical test of structured continuous trees based on discordance matrix." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SCTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XQBai/SCTree-test" ; biotools:primaryContact "Liang Ma", "Lin Wan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3308 ; sc:citation ; sc:description "Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing | Abstract A single neuron and its synapses define the fundamental structural motif of the brain but the underlying gene expression programs that specify individual neuron types are poorly understood. To address this question in a model organism, we have produced a gene expression profile of >90% of the individual neuron classes in the C. elegans nervous system, an ensemble of neurons for which both the anatomy and connectivity are uniquely defined at single cell resolution. We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system. Detailed analysis revealed molecular signatures that further subdivide identified classes into specific neuronal subtypes" ; sc:featureList edam:operation_2495, edam:operation_3891 ; sc:name "SCeNGEA" ; sc:url "https://cengen.shinyapps.io/SCeNGEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_2828, edam:topic_3318 ; sc:citation ; sc:description """A web-based platform for analyzing Small-Angle Scattering curves of lyotropic liquid crystals. Small Angle Scattering Crystallographic Peak Treatment and Analysis. To access SCryPTA, click here . The instructions to use SCryPTA can be found here""" ; sc:featureList edam:operation_3454 ; sc:name "SCryPTA" ; sc:url "http://www.if.usp.br/scrypta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3399 ; sc:citation ; sc:description "Adding noise to Markov cohort state-transition models." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rowaniskandar/SDE" ; biotools:primaryContact "Rowan Iskandar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3512 ; sc:citation ; sc:description "Splice graph based differential transcript expression analysis tool for population data." ; sc:featureList edam:operation_2495, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SDEAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ewyang089/SDEAP/wiki" ; biotools:primaryContact "Ei-Wen Yang", "Tao Jian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3489 ; sc:citation ; sc:description "A Sequence Distance Graph framework for genome assembly and analysis | Sequence Distance Graph framework: graph + reads + mapping + analysis | The Sequence Distance Graph (SDG) is a framework to work with genome graphs and sequencing data. It provides a workspace built around a Sequence Distance Graph, datastores for paired, linked and long reads, read mappers, and k-mer counters. It can be used to perform different types of sequence analyses | Index of /opendata/data/sdg_datasets | Welcome to SDG’s documentation! — SDG documentation | Websites for you and your projects, hosted directly from your GitHub repository. Just edit, push, and your changes are live | Websites for you and your projects | Hosted directly from your GitHub repository. Just edit, push, and your changes are live | Ready to get started? Build your own site from scratch or generate one for your project" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "MIT" ; sc:name "SDG" ; sc:softwareHelp ; sc:url "https://github.com/bioinfologics/sdg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6796762", "pubmed:31542696" ; sc:description "A Web-Based Integrative Machine-Learning Framework for Predicting 6mA Sites in the Rice Genome | Welcome to the Home Page of SDM6A | For the convenience of users, particularly for the vast majority of experimental scientists, a publicly accessible web-server for SDM6A has been established. Moreover, to maximize users' convenience, given below a step-by-step guide on how to use it to get the desired results without the need to through the above mathematical details" ; sc:featureList edam:operation_3501 ; sc:name "SDM6A" ; sc:softwareHelp ; sc:url "http://thegleelab.org/SDM6A" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068 ; sc:citation ; sc:description """A GRASS tool for the Sediment Delivery Ratio mapping. This work involves a tool implementation for evaluating Sediment Delivery Ratio (SDR) in a river basin, through GRASS GIS software. The definition of a spatially distributed value of SDR is a very important task as the sediment routing can affects solid transport in stream channels, water quality degradation, and frequency increase of natural disasters such as debris flows and mudflows. For such reason the SDR evaluation, coupled with GIS approach, has been extensively used in scientific literature. Geographic information systems provide a fundamental support for a better prediction of SDR, since it can consider the space variability of factors influencing the sediment routing processes. Actually a specific GIS module to estimate the spatial variability of SDR does not exist.""" ; sc:featureList edam:operation_2429 ; sc:name "SDR" ; sc:url "https://github.com/pierluigiderosa/r.sdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3305, edam:topic_3322, edam:topic_3519 ; sc:citation , "pmcid:PMC6795434", "pubmed:31618236" ; sc:description "The Swine Disease Reporting System (SDRS) consists of multiple projects that aggregates data from participating veterinary diagnostic laboratories (VDLs) in the United States of America, and reports the major findings to the swine industry." ; sc:featureList edam:operation_3196, edam:operation_3283, edam:operation_3436 ; sc:name "SDRS" ; sc:url "http://www.fieldepi.org/SDRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749 ; sc:citation , "pmcid:PMC6686515", "pubmed:31390979" ; sc:description "> MEDIUM CONFIDENCE! | > HOMEPAGE MISSING! | A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations | BACKGROUND:The detection of protein complexes is of great significance for researching mechanisms underlying complex diseases and developing new drugs. Thus, various computational algorithms have been proposed for protein complex detection. However, most of these methods are based on only topological information and are sensitive to the reliability of interactions. As a result, their performance is affected by false-positive interactions in PPINs. Moreover, these methods consider only density and modularity and ignore protein complexes with various densities and modularities" ; sc:featureList edam:operation_2492, edam:operation_3501 ; sc:name "SE-DMTG" ; sc:url "https://github.com/RongquanWang/SE-DMTG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3489, edam:topic_3678 ; sc:citation , "pmcid:PMC6817659", "pubmed:31673594" ; sc:description "Relative sea-level data from the SEAMIS database compared to ICE-5G model predictions of glacial isostatic adjustment." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SEAMIS" ; sc:url "https://github.com/Alerovere/SEAMIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:31598718" ; sc:description """the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis results are downloadable, you can provide the given link here, in order to upload the output to this system and compare them with publically available datasets. SEA (also SEAweb) is a searchable database for the expression of small RNA (miRNA, piRNA, snoRNA, snRNA, siRNA) and pathogens. Publically available sRNA sequencing datasets were analysed with Oasis 2 pipelines and the results are stored here for easy and comparable search. Our curated, ontology connected metadata enables powerful searches within this database. Learn more in the documentation and publication""" ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:name "SEAweb" ; sc:url "http://sea.ims.bio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3168, edam:topic_3293, edam:topic_3512 ; sc:citation , ; sc:description """A bioinformatics pipeline for the rapid and user-friendly processing of Illumina sequences, from raw reads to alignments. A bioinformatics pipeline for the rapid and user-friendly alignment of hybrid enrichment sequences, from raw reads to alignments. Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics. SEquence CApture PRocessor (SECAPR). Sorry, something went wrong. Reload?. Sorry, we cannot display this file. We are now teaching a free 1-week intensive course on target enrichment data, including practical exercises for all functionalities of the SECAPR pipeline. See course overview from last year and contact tobias.andermann@bioenv.gu.se in case you are interested. Sorry, this file is invalid so it cannot be displayed""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3198, edam:operation_3454 ; sc:license "MIT" ; sc:name "SECAPR" ; sc:softwareHelp ; sc:url "http://www.github.com/AntonelliLab/seqcap_processor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0623 ; sc:citation ; sc:description "Webserver and deep neural network design tool for hierarchical biological sequence classification." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SECLAF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pitgroup.org/seclaf/" ; biotools:primaryContact "Balázs Szalkai", "Vince Grolmusz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3315, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """A Simulator of Copy Number Variants and Whole-Exome Sequences from Reference Genomes. A tool for simulating CNVs for WES data. It simulates rearranged genome(s), short reads (fastq) and BAM file(s) automatically in one single command. SECNVs 2.7.1 (SimulateCNVs 2.7.1). SECNVs (Simulator of Exome Copy Number Variants) is a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome""" ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3227, edam:operation_3228 ; sc:license "MIT" ; sc:name "SECNVs" ; sc:url "https://github.com/YJulyXing/SECNVs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3474 ; sc:citation , "pmcid:PMC6612825", "pubmed:31510691" ; sc:description "Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors | SED: Screening for Lasso of ECFPs and Deep Neural Nets | SED was developed to predict ligand bioactivities and to recognize key substructures associated with GPCRs through the coupling of screening for Lasso of long extended-connectivity fingerprints (ECFPs) with deep neural network training" ; sc:featureList edam:operation_0482 ; sc:name "SED" ; sc:url "https://zhanglab.ccmb.med.umich.edu/SED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation ; sc:description "SEGAN is a novel diversity-generated image inpainting adversarial network with a newly designed style extractor for diversity image inpainting tasks. For a single input image with missing regions, our model can generate numerous diverse results with plausible content. Experiments on various datasets have shown that our results are diverse and natural, especially for images with large missing areas." ; sc:featureList edam:operation_3443 ; sc:name "SEGAN" ; sc:url "https://github.com/vivitsai/SEGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199 ; sc:citation ; sc:description "SELVa (Simulator of Evolution with Landscape Variation) - simulator of sequence evolution that allows the fitness landscape to vary according to user-specified rules." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SELVa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bazykinlab/SELVa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2640, edam:topic_3473 ; sc:citation , "pubmed:31070723" ; sc:description "> COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/gddp (RESEARCH.CCHMC.ORG) | > CORRECT NAME OF TOOL COULD ALSO BE 'CONCLUSION:SEMA' | Graphical data mining of cancer mechanisms with SEMA | SEMA is a graphical hypothesis testing platform for multidimensional cancer genomics data | SEMA is a graphical hypothesis testing platform for multidimensinoal cancer genomics data, written in R Shiny and JavaScript. SEMA uses Structural Equation Modeling (SEM) for the analyses of graphical models | Free HTML5 Template by FreeHTML5.CO | Graphical data mining from cancer genomic datasets" ; sc:featureList edam:operation_0306, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SEMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sema.research.cchmc.org/" ; biotools:primaryContact "Kakajan Komurov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169 ; sc:citation , "pubmed:31373606" ; sc:description "Predicting the effects of SNPs on transcription factor binding affinity | MOTIVATION:GWAS have revealed that 88% of disease associated SNPs reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). RESULTS:SEMpl estimates transcription factor binding affinity by observing differences in ChIP-seq signal intensity for SNPs within functional transcription factor binding sites genome-wide. By cataloging the effects of every possible mutation within the transcription factor binding site motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci" ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_3661 ; sc:name "SEMpl" ; sc:url "https://github.com/Boyle-Lab/SEM_CPP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1755 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein atom" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_2814, edam:topic_3306 ; sc:citation , ; sc:description "Now to predict the experimentally measured affinity between protein monomers in solution, we just need the 3D structure of the suggested PBP on one subunit of the proposed dimer." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "SEPAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "SEPAS_V1, Dec 2019" ; sc:url "http://biophysics.ir/affinity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_2640, edam:topic_3174, edam:topic_3316 ; sc:citation , "pmcid:PMC6805339", "pubmed:31639030" ; sc:description """benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines. SEPATH template pipelines optimised for UEA high performance computing cluster. SEPATH - Searching for Pathogens Computational Pipeline. A repository containing scripts and results required for the SEPATH manuscript. SEPATH is a software designed to obtain accurate taxonomic classifications from within host tissue sequences. It is implemented in python 3 and relies on the Snakemake workflow management system. SEPATH was produced specifically to provide researchers with the ability to conduct ultra high throughput metagenomic studies from raw data to classification and has been benchmarked on simulated human cancer whole genome sequence datasets""" ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_0337, edam:operation_3192, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "SEPATH" ; sc:url "https://github.com/UEA-Cancer-Genetics-Lab/sepath_tool_UEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3168, edam:topic_3489 ; sc:citation , "pmcid:PMC6857306", "pubmed:31807141" ; sc:description "SEQdata-BEACON is a comprehensive database of sequencing performance and statistical tools for performance evaluation and yield simulation in BGISEQ-500." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3659 ; sc:name "SEQdata-BEACON" ; sc:url "http://seqbeacon.genomics.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation ; sc:description """web-based visualization of Arabidopsis thaliana iCLIP and RNA-seq data in an interactive python framework. SEQing: interactive web-based tool for visualization of iCLIP and RNA-seq data. The file requirements.txt can be used to install all needed needed dependencies for the project. Python 3.5 or higher is required and we recommend to setup a virtual environment for this project. If your current python points to a python2 version, please put python3 instead of just python before running SEQing""" ; sc:featureList edam:operation_0337, edam:operation_2499 ; sc:license "MIT" ; sc:name "SEQing" ; sc:url "https://github.com/malewins/SEQing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC6383233", "pubmed:30786880" ; sc:description "Modularized and customizable pipeline framework for NGS processing in R package." ; sc:featureList edam:operation_3192, edam:operation_3211, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SEQprocess" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/omicsCore/SEQprocess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3308 ; sc:citation ; sc:description "SEQualyzer (Structure-profiling Experiment Quality Analyzer ) - interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SEQualyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bme.ucdavis.edu/aviranlab/SEQualyzer" ; biotools:primaryContact "Sharon Aviran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_0798, edam:topic_3301, edam:topic_3895 ; sc:citation , "pubmed:31740968" ; sc:description "The Standard European Vector Architecture (SEVA) platform is a web-based resource and a material clone repository to assist the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes." ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_3431, edam:operation_3435 ; sc:name "SEVA" ; sc:softwareVersion "3.0" ; sc:url "http://seva-plasmids.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:31605112" ; sc:description "SF-Matching(SubFragment-Matching) is a machine-learning based approach to predict compounds from tandem mass spectra." ; sc:featureList edam:operation_3431, edam:operation_3797, edam:operation_3803, edam:operation_3860 ; sc:name "SF-Matching" ; sc:url "http://www.bork.embl.de/Docu/sf_matching" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6901457", "pubmed:31819106" ; sc:description "SFLA IWSSr is an Efficient hybrid filter-wrapper metaheuristic-based gene selection method for high dimensional datasets." ; sc:featureList edam:operation_3454, edam:operation_3695, edam:operation_3891 ; sc:name "SFLA IWSSr" ; sc:url "https://github.com/jimy2020/SFLA_IWSSr-Feature-Selection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "a comprehensive and interactive database of the silkworm | Silkworm Genome Informatics Database | e.g. FIBH or KWMTBOMO15365 or BGIBMGA005111 or silk fibroin heavy chain  Browse in Gene Lists | Search by sequence alignment against genomes or genes | With the Exponential increasing of sequencing data in genomics, transcriptomics and epigenetics, and the development of data analysis methods, a serious of informatics database with integrated analysis tools have been constructed, like the Flybase and TAIR. Silkworm, as a domesticated insect, lacks an online analysis platform. On the basis of previous efforts, including Silkbase, SilkDB and Ensembl Insects, we constructed the silkworm genome informatics database, SGID. Hopefully, it will assist to bioinformatics analysis of silkworms in the future" ; sc:featureList edam:operation_0313, edam:operation_0533, edam:operation_3501 ; sc:name "SGID" ; sc:url "http://sgid.popgenetics.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3303, edam:topic_3518 ; sc:citation , "pubmed:31786183" ; sc:description """A novel method for tumor classification via support vector machine with sparse group Lasso. At present, with the in-depth study of gene expression data, the significant role of tumor classification in clinical medicine has become more apparent. In particular, the sparse characteristics of gene expression data within and between groups. Therefore, this paper focuses on the study of tumor classification based on the sparsity characteristics of genes. On this basis, we propose a new method of tumor classification-Sparse Group Lasso (least absolute shrinkage and selection operator) and Support Vector Machine (SGL-SVM). Firstly, the primary selection of feature genes is performed on the normalized tumor datasets using the Kruskal-Wallis rank sum test. Secondly, using a sparse group Lasso for further selection, and finally, the support vector machine serves as a classifier for classification. We validate proposed method on microarray and NGS datasets respectively""" ; sc:featureList edam:operation_3435 ; sc:name "SGL-SVM" ; sc:url "https://github.com/QUST-AIBBDRC/SGL-SVM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_3304 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | A graphical tool for generating hybrid ground-truth spiking data for evaluating spike sorting performance | SHYBRID is a graphical user interface that allows for the easy creation of hybrid ground truth extracellular recordings. This README file contains information on how to install the program, as well as information on how to get started making extracellular spiking ground truth data. If you have any further questions feel free to contact me" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SHYBRID" ; sc:url "https://github.com/jwouters91/shybrid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3375 ; sc:citation ; sc:description "Software for Structural Identifiability ANalysis of ODE models." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SIAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pogudingleb/SIAN" ; biotools:primaryContact "Gleb Pogudin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:31713070" ; sc:description """SIIM is a professional organization at the nexus of medical imaging informatics and healthcare technologies. SIIM provides an unparalleled opportunity to not only hear from the best, brightest and most forward thinkers in imaging space but talk to them face to face in a collegial setting.""" ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:name "SIIM" ; sc:url "https://siim.org/general/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6868744", "pubmed:31752668" ; sc:description """a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. SIMLIN: an improved bioinformatics approach based on multi-stage ensemble learning model for S-sulphenylation prediction""" ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_0417 ; sc:name "SIMLIN" ; sc:url "http://simlin.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2640, edam:topic_3320 ; sc:citation ; sc:description "Survival-significant Isoform Networks By Altered Domain-inclusion." ; sc:featureList edam:operation_2499, edam:operation_3359, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SINBAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/scwest/SINBAD" ; biotools:primaryContact "Sean West" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3500 ; sc:citation ; sc:description "Tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SINE_scan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/maohlzj/SINE_Scan" ; biotools:primaryContact "Hao Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2546, edam:format_2572 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0860 ; sc:name "Sequence signature data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3895, edam:topic_3912 ; sc:description "Accurate consensus sequence from nanopore reads of a DNA gene library. SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences of variants identified by a barcode, needing only a few reads per variant." ; sc:featureList edam:operation_2403, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SINGLe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rocioespci/single" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation ; sc:description "Robust Moiety Model Selection Using Mass Spectrometry Measured Isotopologues." ; sc:featureList edam:operation_3629, edam:operation_3660, edam:operation_3803 ; sc:name "SIRM" ; sc:url "https://pypi.org/project/moiety-modeling/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830, edam:topic_3305, edam:topic_3500, edam:topic_3673 ; sc:citation , "pubmed:31862714" ; sc:description "The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SISTR" ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/phac-nml/sistr_cmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3518 ; sc:citation ; sc:description "Scalable software tool for gene network reverse engineering from big data." ; sc:featureList edam:operation_2495, edam:operation_2497, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SJARACNe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jyyulab/SJARACNe" ; biotools:primaryContact "Yu Lab in the Department of Computational Biology at St. Jude Children's Research Hospital" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3676 ; sc:citation ; sc:description """Computing Skin Cutaneous Melanoma Outcome from the HLA-alleles and Clinical Characteristics. Skin Cutaneous Melanoma High-Risk Prediction(SKCMhrp) webserver can be used to distinguish high risk SKCM patients from low risk SKCM patients from their HLA-superallele and clinical characteristics. The risk estimation is based on statistical and survival analysis on recent SKCM datasets. See general section for more information.""" ; sc:featureList edam:operation_0252, edam:operation_3503, edam:operation_3659 ; sc:name "SKCMhrp" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/skcmhrp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_3070, edam:topic_3384 ; sc:citation , "pmcid:PMC4121546", "pubmed:25097821" ; sc:description """Facilitating knowledge discovery in life sciences by machine-aided skim reading. SKIMMR - a research prototype for machine-aided skim reading (includes back-end code for generating a graph-like knowledge base from texts and a standalone HTTP server-based UI)""" ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "SKIMMR" ; sc:url "https://github.com/vitnov/SKIMMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6528199", "pubmed:31109287" ; sc:description "Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis." ; sc:featureList edam:operation_0484, edam:operation_2495, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SLAM-DUNK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://t-neumann.github.io/slamdunk" ; biotools:primaryContact , "Philipp Rescheneder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation ; sc:description "Simple Local Alignment Search Tool." ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_2421 ; sc:name "SLAST" ; sc:url "https://www.dnaservic.es/dnaresult?ob=2&min=0.5&id=5191&qid=BdZIQbHRnfIsdH0O&tkt=&code=" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3360, edam:topic_3518 ; sc:citation , "pubmed:31598632" ; sc:description "Single-sample landscape entropy reveals the imminent phase transition during disease progression." ; sc:featureList edam:operation_3435, edam:operation_3439, edam:operation_3454 ; sc:name "SLE" ; sc:url "https://github.com/rabbitpei/SLE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3512 ; sc:citation ; sc:description "Systems-Level Interactive Data Exploration (SLIDE) - web-based tool for interactive visualization of large-scale – omics data." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "SLIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/soumitag/SLIDE" ; biotools:primaryContact "Hyungwon Choi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6381720", "pubmed:30782112" ; sc:description "Web application for the reproducible processing of environmental DNA metabarcoding data." ; sc:featureList edam:operation_0450, edam:operation_3185, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://trtcrd.github.io/SLIM/" ; biotools:primaryContact "Yoann Dufresne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description "a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme | A scaffold assemble pipeline for stLFR reads | This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds | git clone --recursive https://github.com/BGI-QingDao/SLR-superscaffolder.git YOUR-DOWNLOAD-DIR --depth 10 | Here is an illustration of this pipeline:" ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3798 ; sc:name "SLR-superscaffolder" ; sc:url "https://github.com/BGI-Qingdao/SLR-superscaffolder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2840, edam:topic_3343 ; sc:citation , "pmcid:PMC6509116", "pubmed:31073139" ; sc:description "Database of Chemical Constitutents of Smokeless Tobacco Products." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SLTChemDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bic.icmr.org.in/sltchem" ; biotools:primaryContact "Harpreet Singh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0610, edam:topic_3299 ; sc:citation , , , ; sc:description "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Includes a graphical modeling environment." ; sc:featureList edam:operation_0230, edam:operation_0550, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLiM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "4.2" ; sc:url "https://messerlab.org/slim/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Using Python® language for the validation of the CCI soil moisture products via SM2RAIN." ; sc:featureList edam:operation_2428 ; sc:name "SM2RAIN" ; sc:url "http://hydrology.irpi.cnr.it/research/sm2rain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6354025", "pubmed:30698691" ; sc:description "SMAGEXP (Statistical Meta-Analysis for Gene EXPression) - galaxy tool suite for transcriptomics data meta-analysis." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SMAGEXP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sblanck/smagexp" ; biotools:primaryContact "Samuel Blanck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC6894252", "pubmed:31805986" ; sc:description """an interactive web application for comprehensive DNA methylation analysis and visualization. BACKGROUND:Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. RESULTS:To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3204 ; sc:name "SMART App" ; sc:url "http://www.bioinfo-zs.com/smartapp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Ultra-fast de novo assembler using long noisy reads" ; sc:featureList edam:operation_0524 ; sc:name "SMARTdenovo" ; sc:url "https://github.com/ruanjue/smartdenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3399, edam:topic_3421 ; sc:citation , "pubmed:31531896" ; sc:description "A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes | R codes for sample size calculation to detect dynamic treatment regime (DTR) effects based on changes in CAL outcomes from a non-surgical chronic periodontitis treatments study. The experiment is performed under a SMART design. The clustered tooth (sub-unit) level CAL outcomes are skewed, spatially-referenced, and non-randomly missing. The imple… | A SMART design for non-surgical treatments of chronic periodontitis with spatially-referenced and non-randomly missing skewed outcomes | devtools::install_github(\"bandyopd/SMARTp\") | # Install from CRAN (when available)" ; sc:featureList edam:operation_3557 ; sc:name "SMARTp" ; sc:url "https://github.com/bandyopd/SMARTp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3292, edam:topic_3336 ; sc:citation , , "pubmed:31603667" ; sc:description "Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative." ; sc:featureList edam:operation_2476, edam:operation_3893 ; sc:name "SMIRNOFF99Frosst" ; sc:url "https://github.com/openforcefield/smirnoff99Frosst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070 ; sc:citation , "pubmed:31483262" ; sc:description "> HOMEPAGE MISSING! | > NAME EQUAL TO (PUB. DIFFERENT) bio.tools/smog | A Lightweight Tool for Object-Spreadsheet Mapping | In the life science domain, experts are usually familiar with spreadsheet software and often use it in their daily work to collect and structure required domain knowledge. The processing and analysis of spreadsheet data is an important task that must be supported by efficient software solutions. A typical application scenario is for example an integration of spreadsheet data (specified or derived) in an ontology to provide reasoning or search. Different converter tools were developed to support a spreadsheet-to-ontology transformation. Such tools allow often only a relatively simple structure of the spreadsheet template or they require complex mapping processes to map the spreadsheet and ontological entities" ; sc:name "SMOG" ; sc:url "https://github.com/Onto-Med/SMOG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC6885704", "pubmed:31591261" ; sc:description """Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. Sequence-Mask-Search framework and SMSNet model for de novo peptide sequencing. SMSNet's predictions for HLA peptidome and human phosphoproteome datasets. SMSNet's training datasets (WCU-MS-BEST, DeepNovo, ProteomeTools). SMSNet's training datasets (WCU-MS-ALL). Two models for SMSNet are provided here. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and phosphoproteome dataset (PRIDE accession PXD009227) can be found on FigShare. SMSNet's predicted amino acid sequences for a public HLA peptidome dataset (MassIVE accession MSV000080527) and human phosphoproteome dataset (PRIDE accession PXD009227)""" ; sc:featureList edam:operation_3359, edam:operation_3643, edam:operation_3644, edam:operation_3646 ; sc:license "Apache-2.0" ; sc:name "SMSNet" ; sc:softwareHelp , ; sc:url "https://figshare.com/articles/SMSNet_s_trained_models/8259122" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3304, edam:topic_3334 ; sc:citation ; sc:description "Identifying Brain Region Connectivity using Steiner Minimal Tree Approximation and a Genetic Algorithm Web-based tool to find a connectivity path among a given set of brain regions. Specifically, this tool uses a genetic algorithm to find a better connectivity path among the brain regions than SMT-Neurophysiology." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SMT-Genetic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dewancse/SMT-Genetic" ; biotools:primaryContact "Dewan Sarwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31099385" ; sc:description "Multi-SNP mediation intersection-union test." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SMUT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=SMUT" ; biotools:primaryContact "Wujuan Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6334411", "pubmed:30646838" ; sc:description "R package for visualization and analysis of single-molecule localization microscopy data." ; sc:featureList edam:operation_3457, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "SMoLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maartenpaul/SMoLR" ; biotools:primaryContact "Maarten Paul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description "a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing | SNAPPy is a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing | This is the repository for SNAPPy, a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing. SNAPPy allows high-throughput HIV-1 subtyping locally while being resource efficient and scalable. This pipeline was constructed using Snakemake , and it uses MAFFT and for multiple sequence alignment, BLAST for similarirty querys, IQ-TREE for phylogenetic inference, and several Biopython modules for data parsing an analysis. For in-depth information on how the tool works please visit the documentation page. SNAPPy was design for Linux based operative systems | Welcome to snappy’s documentation! — SNAPPy-HIV1-Subtyping 1.0.0 documentation | Free document hosting provided by Read the Docs" ; sc:featureList edam:operation_1812, edam:operation_3192, edam:operation_3196 ; sc:license "MIT" ; sc:name "SNAPPy" ; sc:softwareHelp ; sc:url "https://github.com/PMMAraujo/snappy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3325, edam:topic_3337 ; sc:citation "pubmed:17911793" ; sc:description "Web-based browser with comprehensive, scientifically validated clinical healthcare terminology. Enables consistent representation of clinical content in electronic health records." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SNOMED CT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.snomed.org/snomed-ct/five-step-briefing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31511885" ; sc:description "> HOMEPAGE BROKEN! | a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers | Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3' untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3'UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified" ; sc:featureList edam:operation_0428, edam:operation_3196 ; sc:name "SNP2APA" ; sc:url "http://gong_lab.hzau.edu.cn/SNP2APA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275 ; sc:citation , "pmcid:PMC6448223", "pubmed:30943891" ; sc:description "Modular workflow for standardizing molecular simulation and functional analysis of protein variants." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "SNP2SIM" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/mccoymd/SNP2SIM" ; biotools:primaryContact "Matthew McCoy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0208, edam:topic_0625, edam:topic_2885, edam:topic_3303 ; sc:citation ; sc:description "SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence." ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3661 ; sc:name "SNPector" ; sc:url "https://github.com/peterhabib/SNPector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3173, edam:topic_3517, edam:topic_3673 ; sc:citation ; sc:description """high-throughput tissue-specific functional annotation of single nucleotide variants. Tissue-specific variant annotation pipeline. This pipeline annotates variants based on multiple sources of prior knowledge, including the GWAS literature, tissue-specific open chromatin, tissue-specific modulation of gene expression, and clinical pathogenicity. To download and prepare annotation files""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3778 ; sc:name "SNPnotes" ; sc:url "https://github.com/shraddhapai/SNPNotes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL | By using SNP-Seek, you abide by the data use license stated | Query for SNPs from the 3000 genome project | - Mansueto, et al. Rice SNP-seek database update: new SNPs, indels, and queries . Nucl. Acids Res. (2017) 45 (D1): D1075-D1081. doi: 10.1093/nar/gkw1135 This paper describes new features and datasets added to SNP-Seek in 2015-2017 as well as software and database updates | This site provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.)" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:name "SNPs" ; sc:url "http://snp-seek.irri.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0194, edam:topic_0610, edam:topic_2885 ; sc:citation ; sc:description """Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data. SNiPlay is a web_based tool for SNP analysis: SNP detection, haplotype reconstruction, diversity analysis and linkage disequilibrium. SNiPloid assumes that short reads datasets (i.e. samples) derived from distinct accessions (diploid or polyploid) have been separately preprocessed as described here.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3219 ; sc:name "SNiPlay" ; sc:url "http://sniplay.southgreen.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3068, edam:topic_3168, edam:topic_3895 ; sc:citation ; sc:description """Synthetic Oligo Library Quality Control Tool. SOLQC - Synthetic Oligo Quality Control tool. SOLQC is a novel analysis tool, which enables fast and comprehensive analysis of synthetic oligo libraries enabling the user comprehensive information and insights about the quality and state of the library""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "SOLQC" ; sc:url "https://app.gitbook.com/@yoav-orlev/s/solqc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_3474 ; sc:citation , "pubmed:31603466" ; sc:description "SOLart is a fast and accurate method for predicting the protein solubility of a target protein whose experimental or modeled structure is available. It yields a scaled solubility score with values close to zero indicating aggregate-prone proteins, while values close to 130 designate soluble proteins." ; sc:featureList edam:operation_0409, edam:operation_3436 ; sc:name "SOLart" ; sc:url "http://babylone.ulb.ac.be/SOLART/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "Python library implementing the full self-organizing map (SOM) analysis workflow." ; sc:featureList edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/bougui505/SOM" ; biotools:primaryContact "Guillaume Bouvier", "Michael Nilges" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3306 ; sc:citation ; sc:description "Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models." ; sc:featureList edam:operation_3435, edam:operation_3450, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SONATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AllenInstitute/sonata" ; biotools:primaryContact "Anton Arkhipov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3316, edam:topic_3673 ; sc:citation , "pmcid:PMC6805285", "pubmed:31639049" ; sc:description """Using Apache Spark on genome assembly for scalable overlap-graph reduction. Scalable Overlap-Graph Reduction Algorithms for Genome Assembly using Apache Spark on Cloud. Please go to the Wiki pages, https://github.com/BioHPC/SORA/wiki, to learn about SORA""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "SORA" ; sc:softwareHelp ; sc:url "https://github.com/BioHPC/SORA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3673 ; sc:citation ; sc:description "SPAG is a tool for predicting the spatial distribution of adaptive genetic variants under future climatic conditions." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3891 ; sc:name "SPAG" ; sc:url "https://github.com/estellerochat/SPAG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC6488671", "pubmed:31036850" ; sc:description "Efficient algorithm on Apache Spark for aligning multiple similar DNA/RNA sequences with supervised learning." ; sc:featureList edam:operation_0323, edam:operation_0491, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SPARK-MSNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/spark-msna/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0621 ; sc:citation ; sc:description "A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3432 ; sc:name "SPARQL" ; sc:url "https://sparql.orthodb.org/sparql" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31598633" ; sc:description "SPARSim is a count data simulator for scRNA-seq data." ; sc:featureList edam:operation_2426, edam:operation_2429, edam:operation_3799 ; sc:name "SPARSim" ; sc:url "https://sysbiobig.dei.unipd.it/software/sparsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174 ; sc:citation ; sc:description "> HOMEPAGE MISSING! | Alignment of Long Diverged Molecular Sequences to Assembly Graphs | A bstract Background Graph-based representation of genome assemblies has been recently used in different applications from gene finding to haplotype separation. While most of these applications are based on the alignment of molecular sequences to assembly graphs, existing software tools for finding such alignments have important limitations. Results We present a novel SPAligner tool for aligning long diverged molecular sequences to assembly graphs and demonstrate that SPAligner is an efficient solution for mapping third generation sequencing data and can also facilitate the identification of known genes in complex metagenomic datasets. Conclusions Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525 ; sc:name "SPAligner" ; sc:url "http://cab.spbu.ru/software/spaligner/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2851 ; sc:encodingFormat edam:format_3814 ; sc:name "Drug structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1696 ; sc:name "Drug report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314 ; sc:citation , ; sc:description "Structural and physico-chemical interpretation of QSAR models" ; sc:featureList edam:operation_2426, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "SPCI" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://qsar4u.com/pages/sirms_qsar.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_3120, edam:topic_3168 ; sc:citation , "pubmed:31738401" ; sc:description "Data Model for Variants and Applications at NCBI." ; sc:featureList edam:operation_0525, edam:operation_3197, edam:operation_3436 ; sc:name "SPDI" ; sc:url "https://api.ncbi.nlm.nih.gov/variation/v0/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3070, edam:topic_3373 ; sc:citation , "pubmed:31377536" ; sc:description "Learning-to-rank technique based on ignoring meaningless ranking orders between compounds | SPDRank is stochastic pairwise descent RankSVM method with ignoring meaningless ranking orders that used on Learning-to-Rank Technique based on Ignoring Meaningless Ranking Orders between Compounds" ; sc:featureList edam:operation_0482 ; sc:license "MIT" ; sc:name "SPDRank" ; sc:url "https://github.com/akiyamalab/SPDRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6677810", "pubmed:31375721" ; sc:description "A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data | Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry" ; sc:featureList edam:operation_3644, edam:operation_3645, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "SPECTRUM" ; sc:url "https://github.com/BIRL/SPECTRUM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3384 ; sc:citation , "pmcid:PMC6498854", "pubmed:31057203" ; sc:description "Tool that computes point-based models using a parametric boundary description for the computing of Shape analysis." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SPHARM-PDM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.nitrc.org/projects/spharm-pdm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "Disentangling microbial associations from hidden environmental and technical factors via latent graphical models." ; sc:featureList edam:operation_2495, edam:operation_3625, edam:operation_3891 ; sc:name "SPIEC-EASI" ; sc:url "https://github.com/zdk123/SpiecEasi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0736, edam:topic_0798, edam:topic_3168 ; sc:citation , "pubmed:31745561" ; sc:description """Targeted insertional mutagenesis libraries for deep domain insertion profiling. SPINE: Saturated Programmable INsertion Engineering. Protein domain insertion via programmed oligo libraries""" ; sc:featureList edam:operation_0284, edam:operation_0303, edam:operation_0308 ; sc:license "MIT" ; sc:name "SPINE" ; sc:url "https://github.com/schmidt-lab/SPINE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3056 ; sc:citation , "pubmed:31077292" ; sc:description "Simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SPLATCHE3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.splatche.com/splatche3" ; biotools:primaryContact "Mathias Currat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation "pubmed:266227768" ; sc:description "Statistical Parametric Mapping (SPM) software for the analysis of brain imaging data sequences." ; sc:featureList edam:operation_3435, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SPM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.fil.ion.ucl.ac.uk/spm/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:name "RNA secondary structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , "pmcid:PMC6881452", "pubmed:31776342" ; sc:description "RNA secondary structure predictor" ; sc:featureList edam:operation_0278 ; sc:isAccessibleForFree true ; sc:name "SPOT-RNA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sparks-lab.org/jaswinder/server/SPOT-RNA/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0123, edam:topic_0130, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31800243" ; sc:description """To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. Protein sequence profile prediction aims to generate multiple sequences from structural information to advance the protein design. Protein sequence profile can be computationally predicted by energy-based method or fragment-based methods. By integrating these methods with neural networks, our previous method, SPIN2 has achieved a sequence recovery rate of 34%. However, SPIN2 employed only one dimensional (1D) structural properties that are not sufficient to represent 3D structures. In this study, we represented 3D structures by 2D maps of pairwise residue distances. and developed a new method (SPROF) to predict protein sequence profile based on an image captioning learning frame. To our best knowledge, this is the first method to employ 2D distance map for predicting protein properties.""" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0474, edam:operation_2492, edam:operation_2575 ; sc:license "MIT" ; sc:name "SPROF" ; sc:url "https://github.com/biomed-AI/SPROF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2209 ; sc:name "Mutation ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description """SPROUTS has two general functions. The first is to provide existing mutation data given a protein specified by a PDB ID. This is Query mode. The second is to generate new mutation data based on a new PDB ID or a user input. This is Submit mode.""" ; sc:featureList edam:operation_0224 ; sc:name "SPROUTS" ; sc:softwareVersion "1.0" ; sc:url "http://sprouts.rpbs.univ-paris-diderot.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC6298046", "pubmed:30010780" ; sc:description "R package for filtering of spatially related peaks in mass spectrometry imaging data." ; sc:featureList edam:operation_3215 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPUTNIK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/paoloinglese/SPUTNIK" ; biotools:primaryContact "Paolo Inglese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3169 ; sc:citation , "pubmed:31116370" ; sc:description "SPar-K (Signal Partitioning using K-means) is a modified version of a standard K-means algorithm designed to cluster vectors containing a sequence of signal (that is, the order in which the elements appear in the vectors is meaningful). In order to detect a possible phase shift or orientation inversion between two vectors, this program allows computing distances between two vectors by shifting and flipping them." ; sc:featureList edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPar-K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/romaingroux/SPar-K" ; biotools:primaryContact "Philipp Bucher", "Romain Groux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:31752589" ; sc:description "Streamlined particle quantification (SParQ) plug-in is an automated fluorescent vesicle quantification plug-in for particle quantification in Fiji/ImageJ." ; sc:featureList edam:operation_3454, edam:operation_3458, edam:operation_3799 ; sc:name "SParQ" ; sc:url "https://github.com/sparq-plugin/sparq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC6739102", "pubmed:31506264" ; sc:description "High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data | A python application for MALDI-TOF MS dereplication | python SPeDE.py [-d ] [-c ] [-l ] [-m ] [ -o \\] [-p ] [-n ] [-q ] [-v] [-e] | Command driven processing (Windows and Linux supported, MacOS unknown) | This program cannot be run on a Linux subsystem in Windows" ; sc:featureList edam:operation_3627, edam:operation_3637, edam:operation_3860 ; sc:license "MIT" ; sc:name "SPeDE" ; sc:url "https://github.com/LM-UGent/SPeDE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "SProCoP is a set of statistical process control aids for visualize, detect, and identify of assignable causes of variation in chromatographic performance (e.g., retention time reproducibility, peak asymmetry, and resolution); and mass spectrometric performance (targeted peptide ion intensity and mass measurement accuracy for high resolving power instruments) via control charts and boxplots." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:name "SProCoP" ; sc:url "https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=SProCoP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293 ; sc:citation , "pubmed:31536115" ; sc:description "The Prevalence and Impact of Model Violations in Phylogenetic Analysis | tests of stationarity, reversibility, and homogeneity for sequence alignments | This just deletes (with rm -rf, so be careful), /data/srh/processed_data/SRH_tables/ and /data/srh/processed_data/IQtree/ | All scripts have hard-coded input and output destinations. If you want to run them for yourself, you will need to adjust these destinations in each script as you go | This will calculate SRH stats and IQtree input files for all datasets in SRHtests/datasets. It requires python 3.6.x or higher and dependencies as in the header of srh.py. Input and output files are hardcoded near the end of the script, change them if you need to. This script creates two output folders, each of which contains one folder for each dataset in SRHtests/datasets" ; sc:featureList edam:operation_0325, edam:operation_0551, edam:operation_3478 ; sc:name "SRH" ; sc:url "https://github.com/roblanf/SRHtests" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:31504202" ; sc:description "> MEDIUM CONFIDENCE! | Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) for autofluorescence-contaminated micrographs | Semi-blind Sparse Affine Spectral Unmixing (SSASU) | Spectral unmixing methods attempt to determine the concentrations of different fluorophores present at each pixel location in an image by analyzing a set of measured emission spectra" ; sc:name "SSASU" ; sc:url "https://github.com/brossetti/ssasu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3306 ; sc:citation , "pmcid:PMC6903780", "pubmed:31570166" ; sc:description """SSEThread is an Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method.""" ; sc:featureList edam:operation_0302, edam:operation_0320, edam:operation_0479 ; sc:name "SSEThread" ; sc:url "https://github.com/salilab/SSEThread" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_3318 ; sc:citation , "pubmed:31830252" ; sc:description """accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. binding affinity change estimation. SSIPe is a method to calculate binding affinity changes (ΔΔGbind) of protein-protein interactions (PPIs) upon mutations at protein-protein interface. Please direct questions and inquiries to our Service System Discussion Board or contact Dr. Estimation of binding affinity change upon mutations at protein-protein interface""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_2495 ; sc:license "MIT" ; sc:name "SSIPe" ; sc:url "https://zhanglab.ccmb.med.umich.edu/SSIPe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0821, edam:topic_3293 ; sc:citation , "pmcid:PMC6827312", "pubmed:31501245" ; sc:description "A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16) | a GUI to Simplify the Generation of Sequence Similarity Networks | SSNpipe is a Python program, and independent all-inclusive executable binary files for most popular operating systems are freely available in release page | Please be aware that SSNpipe and all python Tkinter applications are unable to run on MacOS Mojave 10.14.6, due to an unidentified bug in the MacOS system. This issue should be patched in the soon to be released MacOS Catalina 10.15, click here for more information)" ; sc:license "GPL-3.0" ; sc:name "SSNpipe" ; sc:url "https://github.com/ahvdk/SSNpipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3318, edam:topic_3382 ; sc:citation , "pubmed:31634148" ; sc:description "Scaled Simplex Representation for Subspace Clustering." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3659 ; sc:name "SSRSC" ; sc:url "https://github.com/csjunxu/SSRSC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3336, edam:topic_3474, edam:topic_3542 ; sc:citation ; sc:description """Secondary Structure based End-to-End Learning model for Protein-Ligand Interaction Prediction. Abstract Computational prediction of bioactivity has become a critical aspect of modern drug discovery as it mitigates the cost, time, and resources required to find and screen new compounds. Deep Neural Networks (DNN) have recently shown excellent performance in modeling Protein-Ligand Interaction (PLI). However, DNNs are only effective when physically sound descriptions of ligands and proteins are fed into the network for further processing. Furthermore, previous research has not incorporated the secondary structure of the protein in a meaningful manner. In this work, we utilize secondary structure information of the protein which is extracted as the curvature and torsion of the backbone of protein to predict PLI. https://github.com/ekraka/SSnet""" ; sc:featureList edam:operation_2423 ; sc:name "SSnet" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/ekraka/SSnet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3489 ; sc:citation , "pubmed:31880560" ; sc:description """Subjective Evaluation of the Spectral Temporal SIMilarity (ST-SIM) Measure for Vibrotactile Quality Assessment. Recent standardization efforts for Tactile Internet (TI) and haptic codecs have paved the route for delivering tactile experiences in synchrony with audio and visual interaction components. Since humans are the ultimate consumers of tactile interactions, it is utmost important to develop objective quality assessment measures that are in close agreements with human perception. In this work, we present the results of a large-scale subjective study of a recently proposed objective quality assessment approach for vibrotactile signals called ST-SIM (Spectral Temporal SIMilarity). ST-SIM encompasses two components: perceptual spectral and temporal similarity measures. Two subjective experiments were conducted to validate ST-SIM, and elicited subjective ratings are used to create a VibroTactile Quality Assessment (VTQA) database.""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "ST-SIM" ; sc:url "https://www.raniahassen.com/Research/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444 ; sc:description "2D and 3D constrained Total Variation using the Split Bregman formulation" ; sc:featureList edam:operation_3359 ; sc:isAccessibleForFree true ; sc:name "HGGM-LIM Split-Bregman-ST-Total-Variation-MRI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/55211-hggm-lim-split-bregman-st-total-variation-mri" ; biotools:primaryContact "Juan Felipe Pérez Juste Abascal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3398 ; sc:citation , "pubmed:31789313" ; sc:description """Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. Changes in blood flow velocity and distribution are vital in maintaining tissue and organ perfusion in response to varying cellular needs. Further, appearance of defects in microcirculation can be a primary indicator in the development of multiple pathologies. Advances in optical imaging have made intravital microscopy (IVM) a practical approach, permitting imaging at the cellular and subcellular level in live animals at high-speed over time. Yet, despite the importance of maintaining adequate tissue perfusion, spatial and temporal variability in capillary flow is seldom documented. In the standard approach, a small number of capillary segments are chosen for imaging over a limited time. To comprehensively quantify capillary flow in an unbiased way we developed Spatial Temporal Analysis of Fieldwise Flow (STAFF), a macro for FIJI open-source image analysis software""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:name "STAFF" ; sc:softwareHelp ; sc:url "https://github.com/icbm-iupui/STAFF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0605, edam:topic_0654, edam:topic_3173, edam:topic_3518 ; sc:citation ; sc:description """New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches. Simple Tool for Analysis of Replication Timing with R. Visit our website : https://thomasdenecker.github.io/START-R/. We use Docker to develop and manage START-R. We invite you to verify that the following requirements are correctly satisfied before trying to bootstrap the application:""" ; sc:featureList edam:operation_3192 ; sc:license "BSD-3-Clause" ; sc:name "START-R" ; sc:url "https://github.com/thomasdenecker/START-R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3395 ; sc:citation , "pmcid:PMC6708268", "pubmed:31433284" ; sc:description "An Open Source Tool for Disease Modeling | The Eclipse Foundation - home to a global community, the Eclipse IDE, Jakarta EE and over 350 open source projects, including runtimes, tools and frameworks | The Spatiotemporal Epidemiological Modeler (STEM) Project | Some Eclipse Foundation pages use cookies to better serve you when you return to the site. You can set your browser to notify you before you receive a cookie or turn off cookies. If you do so, however, some areas of some sites may not function properly. To read Eclipse Foundation Privacy Policy click here | The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases" ; sc:featureList edam:operation_2426 ; sc:name "STEM" ; sc:url "http://www.eclipse.org/stem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885 ; sc:citation , "pubmed:30132900" ; sc:description "Probabilistic genotyping software that combines biological modelling and mathematical processes to interpret a wide range of complex DNA profiles." ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3629 ; sc:isAccessibleForFree false ; sc:license "Other" ; sc:name "STRmix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.strmix.com/" ; biotools:primaryContact "Vic Meles" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC6851049", "pubmed:31781551" ; sc:description """A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity. codes for the membrane transporter paper. codes for membrane transporter paper:. model_training_*.py are codes for parameter tuning in a server""" ; sc:featureList edam:operation_2871, edam:operation_2929, edam:operation_3454 ; sc:name "STS-NLSP" ; sc:url "https://github.com/dqwei-lab/STS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3382, edam:topic_3518 ; sc:citation ; sc:description "Tool for analysis and visualization of spatial transcriptomics datasets." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ST viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/SpatialTranscriptomicsResearch/st_viewer" ; biotools:primaryContact "Jose Fernandez Navarro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3305, edam:topic_3489 ; sc:citation ; sc:description """accurate and ultrafast genomic profiling with exact sequence matches. Ultrafast sequence typing and gene detection from NGS raw reads. See the full documentation at: https://sting.readthedocs.io/""" ; sc:featureList edam:operation_3211, edam:operation_3227, edam:operation_3472, edam:operation_3482, edam:operation_3840 ; sc:name "STing" ; sc:url "https://github.com/jordanlab/STing" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3603 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140 ; sc:citation , "pubmed:30373828" ; sc:description "Visualize the human surface proteome (surfaceome) and load your own expression data to inspect and uncover cellular phenotypes and new surfaceome markers." ; sc:featureList edam:operation_2489, edam:operation_2942 ; sc:name "SURFY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://wlab.ethz.ch/surfaceome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3302, edam:topic_3305, edam:topic_3500 ; sc:citation , "pubmed:31765613" ; sc:description """Risk-based surveillance for meat-borne parasites. There is a plethora of meat-borne hazards - including parasites - for which there may be a need for surveillance. However, veterinary services worldwide need to decide how to use their scarce resources and prioritise among the perceived hazards. Moreover, to remain competitive, food business operators - irrespective of whether they are farmers or abattoir operators - are preoccupied with maintaining a profit and minimizing costs. Still, customers and trade partners expect that meat products placed on the market are safe to consume and should not bear any risks of causing disease. Risk-based surveillance systems may offer a solution to this challenge by applying risk analysis principles; first to set priorities, and secondly to allocate resources effectively and efficiently.""" ; sc:name "SURVTOOLS" ; sc:url "https://survtools.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation , "pmcid:PMC6541270", "pubmed:31141524" ; sc:description "StrUctural Susceptibility PrEdiCTion on BDQ." ; sc:featureList edam:operation_0331, edam:operation_0478, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SUSPECT-BDQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/suspect_bdq/" ; biotools:primaryContact "David B. Ascher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2640, edam:topic_3300, edam:topic_3382 ; sc:citation , "pubmed:31577949" ; sc:description """Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Spatial Variance Components Analysis (SVCA). NB: If you are already a limix user, we recommend you install svca_limix and svca in a dedicated conda environment so there is no interference between your limix versions""" ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "SVCA" ; sc:url "https://github.com/damienArnol/svca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc:description """Genotyping structural variations with long reads. SVJedi : Genotyping structural variations with long read data. SVJedi is a structural variation (SV) genotyper for long read data. Based on a representation of the different alleles, it estimates the genotype of each variant in a given individual sample based on allele-specific alignment counts. SVJedi takes as input a variant file (VCF), a reference genome (fasta) and a long read file (fasta/fastq) and outputs the initial variant file with an additional column containing genotyping information (VCF)""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:license "AGPL-3.0" ; sc:name "SVJedi" ; sc:url "https://github.com/llecompte/SVJedi.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3175, edam:topic_3512 ; sc:citation ; sc:description "Impact prediction tool for structural variation." ; sc:featureList edam:operation_0484, edam:operation_3436, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SVScore" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lganel/SVScore" ; biotools:primaryContact "Ira M. Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3175, edam:topic_3500 ; sc:citation ; sc:description """SVants – A long-read based method for structural variation detection in bacterial genomes. Config file input files and parameters. Output from LastalAlignToGenome.sh. git clone https://github.com/EpiBlake/SVants.git""" ; sc:featureList edam:operation_0525, edam:operation_3198, edam:operation_3228 ; sc:license "GPL-3.0" ; sc:name "SVants" ; sc:url "https://github.com/EpiBlake/SVants" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0196, edam:topic_3170, edam:topic_3303 ; sc:citation , "pmcid:PMC6868818", "pubmed:31747936" ; sc:description "Genome-wide Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants using the long-fragment information from the 10x Genomics platform." ; sc:featureList edam:operation_0524, edam:operation_2429, edam:operation_3192, edam:operation_3216, edam:operation_3227 ; sc:license "MIT" ; sc:name "SVs" ; sc:url "https://github.com/grocsvs/grocsvs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight." ; sc:featureList edam:operation_3431, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SW-Tandem" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Logic09/SW-Tandem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3316 ; sc:citation , "pubmed:31734873" ; sc:description """Counting Kmers for Biological Sequences at Large Scale. This is a distributed kmer counting tools for TB-PB sequencing dataset""" ; sc:featureList edam:operation_0524, edam:operation_3472, edam:operation_3695 ; sc:name "SWAPCounter" ; sc:url "https://github.com/mengjintao/SWAPCounter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3520, edam:topic_3673 ; sc:citation , "pmcid:PMC6743289", "pubmed:31523183" ; sc:description "An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis | Introduction: As the number of the MS/MS spectra increases rapidly, the excessive computation time taken by MS/MS spectra data analysis has become a critical concern in computational biology. In this work, we designed and implemented SWPepNovo, an efficient de novo peptide sequencing tool for large-scale MS/MS spectra data analysis using a novel peptide-spectrum matches (PSMs) algorithm. To achieve the high performance, we designed an improved scoring algorithm to reduce the time complexity and eliminate the data dependence to enable all possible locality and vectorizations. Performance is also tuned by pre-fetching, double buffering mechanism, and an optimized memory access scheme, to achieve an optimum performance and best utilization of various computing resources within neo-heterogeneous many-core architecture" ; sc:featureList edam:operation_3202, edam:operation_3644, edam:operation_3646 ; sc:name "SWPepNovo" ; sc:url "https://github.com/ChuangLi99/SWPepNovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0593, edam:topic_3047 ; sc:citation , "pmcid:PMC6895709", "pubmed:31711608" ; sc:description """Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. A software for single particle tracking which includes intensity ratiometric measurements and analysis. Unpack the zip file to a folder of your choice. follow the instructions in the manual in order to get started""" ; sc:featureList edam:operation_0337, edam:operation_3457, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "SWiFi" ; sc:url "https://github.com/barakgilboa/SWiFi-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3500 ; sc:description "Database containing 4.373 video, 18.212 still images and 7.771 labels concerning sampled that were prepared and stored from 1910 at the “Stazione Zoologica Anton Dohrn di Napoli (SZN)”. Moreover, the digitised version of 38 documents (totalling 8406 pages) with important information about taxonomy, ecology and phylogenetic is also included." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SZN Zoological Collection Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://szn.i.hosei.ac.jp/HTML/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:37819886" ; sc:description "Sage is a proteomics database search engine to match tandem mass spectra to peptides. Sage also performs retention time prediction, quantificaiton and FDR control." ; sc:featureList edam:operation_2428, edam:operation_3631, edam:operation_3633 ; sc:license "MIT" ; sc:name "Sage" ; sc:softwareHelp ; sc:url "https://github.com/lazear/sage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6720087", "pubmed:31477007" ; sc:description "a tool for analyzing putative transcription factor binding sites in salmonid genomes | SalMotifDB: cis-regulatory motif database for salmonids | We're getting there, it's worth the wait" ; sc:featureList edam:operation_0441, edam:operation_0445, edam:operation_3439 ; sc:name "SalMotifDB" ; sc:url "https://salmobase.org/apps/SalMotifDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3407 ; sc:citation , "pmcid:PMC6727554", "pubmed:31488049" ; sc:description "> MEDIUM CONFIDENCE! | a novel method for selecting parameters for gene functional annotation routines | Novel strategy for selecting best parameters for gene functional annotation routines in merlin | readme instructions updated · 81b3a5a9" ; sc:featureList edam:operation_0495, edam:operation_1812, edam:operation_2422 ; sc:name "SamPler" ; sc:url "https://gitlab.bio.di.uminho.pt/merlin-sysbio/merlin-sampler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6499250", "pubmed:30252043" ; sc:description "Modular and versatile package for the quantitative analysis of high-throughput proteomics experiments." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SanXoT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cnic.es/wiki/proteomica/index.php/SanXoT_software_package" ; biotools:primaryContact "E. Bonzon-Kulichenko", "Jesús María Vázquez Cobos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3676 ; sc:citation ; sc:description "Genome-wide copy number variants (CNV) calling from off-target reads." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SavvyCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rdemolgen/SavvySuite" ; biotools:primaryContact "Matthew N. Wakeling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3489 ; sc:citation ; sc:description "ScType is a tool for fully-automated cell type identification from single-cell RNA-seq data. ScType provides a complete pipeline for single-cell RNA-seq data analysis (including data processing, normalization and clustering) and cell-type annotation." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3680 ; sc:name "ScType" ; sc:url "http://session.asuscomm.com:8080/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Accurate reference-based transcript assembler." ; sc:featureList edam:operation_0264, edam:operation_3258, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Scallop-LR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Kingsford-Group/scallop" ; biotools:primaryContact "Carl Kingsford" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0204, edam:topic_0602, edam:topic_3308 ; sc:description "Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data" ; sc:featureList edam:operation_2437, edam:operation_3792 ; sc:license "AGPL-3.0" ; sc:name "Scan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/zhangjunpeng411/Scan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0160, edam:topic_0166, edam:topic_0622 ; sc:citation , "pubmed:31711930" ; sc:description """Mapping the RNA structural landscape of viral genomes. ScanFold is an RNA sequence scanning pipeline which attempts to identify potentially functional RNA secondary structures. This is done by first scanning a single input sequence to identify regions which generate negative thermodynamic z-scores (a hallmark of functional RNA sequences), and subsequently identifying the specific base pairs which we…. Welcome to the ScanFold web server. Using the ScanFold web server you can identify regions of an RNA sequence which generate unusually stable secondary structures (one of the hallmarks of a functional RNA)""" ; sc:featureList edam:operation_0238, edam:operation_0502, edam:operation_2441 ; sc:name "ScanFold" ; sc:url "https://mosslabtools.bb.iastate.edu/scanfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation" ; sc:featureList edam:operation_3963 ; sc:name "ScanITD" ; sc:url "https://github.com/ylab-hi/ScanITD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description "A pipeline for recovery of unaligned reads utilising similarity with aligned reads | Rescue potential false negative unmapped reads in alignment tools | Manuscript available now on bioRxiv: https://www.biorxiv.org/content/early/2018/06/13/345876 | python3 usage: scavenger.py [options] -G/--genome_file -i/--input -at/--aligner_tool " ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3798 ; sc:license "MIT" ; sc:name "Scavenger" ; sc:url "https://github.com/VCCRI/Scavenger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3489 ; sc:citation , "pmcid:PMC5832410", "pubmed:29424689" ; sc:description """Sci-Hub provides access to nearly all scholarly literature. Source code and data analyses for the Sci-Hub Coverage Study. Analyses for the Sci-Hub Coverage Study. Manuscript for the Sci-Hub Coverage Study. Manuscript source for the Sci-Hub Coverage Study. Data for the Sci-Hub Stats Browser. removing barriers in the way of science. Din bedste informationskilde om sci hub. This project investigates the coverage of scholarly literature in the Sci-Hub and LibGen scimag repositories. It's based on using DOIs to uniquely identify articles. For more information, see the corresponding study:. This is the manuscript source for the study titled Sci-Hub provides access to nearly all scholarly literature. Sci-Hub is a pirate website that provides access to full texts from the scholarly literature, including paywalled articles. The first pirate website in the world to open mass and public access to tens of millions research papers""" ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_3431 ; sc:name "Sci-Hub" ; sc:url "https://github.com/greenelab/scihub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3305, edam:topic_3810 ; sc:citation , "pmcid:PMC6529016", "pubmed:31071088" ; sc:description "Modeling framework for studying population-scale family trees that combines techniques from the animal and plant breeding literature and from human genetics literature." ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sci-LMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TalShor/SciLMM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description """A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data. MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we developed SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results. Based on the SciApps workflow platform, we generated new components to support the complete cycle of the MaizeCODE data management""" ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3454 ; sc:name "SciApps" ; sc:url "https://sciapps.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3293, edam:topic_3297 ; sc:citation , "pmcid:PMC6702558", "pubmed:31528018" ; sc:description "Sequence analysis of the cytochrome c oxidase subunit 1 gene of Sarcoptes scabiei isolated from goats and rabbits in East Java, Indonesia | Software for the Molecular Biologist | Welcome to the Sci Ed Software website" ; sc:featureList edam:operation_0308, edam:operation_3200, edam:operation_3891 ; sc:name "Scientific Educational" ; sc:url "http://www.scied.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_2229 ; sc:citation ; sc:description "Accurate and Efficient Cell Lineage Tree Inference from Noisy Single Cell Data | Cell tree inference and genotype calling from noisy single cell data | ScisTree is a computer program for inferring cell tree and calling genotypes from uncertain single cell genotype data. 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Hou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1475 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1756 ; sc:encodingFormat edam:format_2077 ; sc:name "Protein residue" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "Annotation of secondary structure elements in proteins." ; sc:featureList edam:operation_0226 ; sc:name "SecStrAnnotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webchem.ncbr.muni.cz/API/SecStr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3794 ; sc:citation ; sc:description "Accurate tool for somatic structural variation and virus integration detection." ; sc:featureList edam:operation_0452, edam:operation_3227, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Seeksv" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/qiukunlong/seeksv" ; biotools:primaryContact "Bo Liao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071, edam:topic_3474 ; sc:citation , "pubmed:30923381" ; sc:description "PyTorch-based deep learning library for sequence data." ; sc:featureList edam:operation_3278, edam:operation_3279 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Selene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.3.1" ; sc:url "https://selene.flatironinstitute.org/" ; biotools:primaryContact "Troyanskaya Laborator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3321, edam:topic_3474 ; sc:citation ; sc:description "Computational predictor of the mutations generated by repair of CRISPR-Cas9-induced double-strand breaks (command line version of FORECasT)." ; sc:featureList edam:operation_2238, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SelfTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/felicityallen/SelfTarget" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3295 ; sc:citation , "pmcid:PMC6612869", "pubmed:31510653" ; sc:description "discovery of differential chromatin interactions via a self-similarity measure | SELFISH (Discovery of Differential Chromatin Interactions via a Self-Similarity Measure) is a tool for finding differential chromatin interactions between two Hi-C contact maps. 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A Python implementation of Selfish is available at Ay-lab" ; sc:featureList edam:operation_0272, edam:operation_3192, edam:operation_3501 ; sc:name "Selfish" ; sc:url "https://github.com/ucrbioinfo/Selfish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3300, edam:topic_3360 ; sc:citation , "pubmed:31675495" ; sc:description "SeneQuest contains information on gene-to-senescence associations is crucial for increasing our understanding of the molecular mechanisms driving senescence." ; sc:name "SeneQuest" ; sc:url "http://Senequest.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3810 ; sc:citation , "pmcid:PMC6710408", "pubmed:31481971" ; sc:description "Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy | As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important" ; sc:featureList edam:operation_3227 ; sc:name "Sentieon DNASeq" ; sc:url "https://github.com/ncsa/Sentieon_DNASeq_Benchmarking" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3050, edam:topic_3837 ; sc:citation , "pmcid:PMC6802221", "pubmed:31628336" ; sc:description "Radar vision in the mapping of forest biodiversity from space." ; sc:featureList edam:operation_2429, edam:operation_2940, edam:operation_3435 ; sc:name "Sentinel-1" ; sc:url "https://github.com/So-YeonBae/Sentinel1-Biodiversity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3810 ; sc:citation ; sc:description "A Generic Practice for Generating Dual-pol Covariance Matrix Elements in SNAP S-1 Toolbox." ; sc:license "GPL-3.0" ; sc:name "Sentinel-1 SLC" ; sc:url "https://github.com/mrslab-iitb/sentinel-1-SLC-preprocessing-polarimetry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0199 ; sc:citation ; sc:description "Web-based feature extraction tool which computes protein and DNA sequence driven features. It can calculate 252 protein- based and 42 DNA- based descriptors." ; sc:featureList edam:operation_0250, edam:operation_0267, edam:operation_0455 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Seq2Feature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.iitm.ac.in/bioinfo/SBFE/index.html" ; biotools:primaryContact "Prof. Michael Gromiha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "a python tool to evaluate genomic prediction in complex scenarios | SeqBreed.py is a python3 software to simulate populations under (genomic) selection. It inherits most of funcionality from SBVB (Perez-Enciso et al., 2017, https://github.com/miguelperezenciso/sbvb1) and pSBVB (Zingaretti et al. 2018, https://github.com/lauzingaretti/pSBVB) softwares but code has been completely rewritten. It is now much more user friendly and adds numerous new features such as easy selection implementation (BLUP, GBLUP, SSTEP), plots (PCA, GWAS).." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3891 ; sc:name "SeqBreed" ; sc:url "https://github.com/miguelperezenciso/SeqBreed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0160, edam:topic_0623, edam:topic_3168 ; sc:citation , "pubmed:31878100" ; sc:description "Graph Theory-Based Sequence Descriptors as Remote Homology Predictors." ; sc:featureList edam:operation_0524, edam:operation_3092, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "SeqDivA" ; sc:url "https://github.com/eancedeg/SeqDivA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation , "pubmed:31540993" ; sc:description "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using \"-m a\" (allele mode)" ; sc:featureList edam:operation_3182, edam:operation_3211, edam:operation_3482 ; sc:license "GPL-2.0" ; sc:name "SeqSero2" ; sc:url "http://denglab.info/SeqSero2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3673 ; sc:citation , "pmcid:PMC6602489", "pubmed:31045209" ; sc:description "Web server for the extraction of DNA or protein sequences from next-generation sequencing data." ; sc:featureList edam:operation_0433, edam:operation_3216, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SeqTailor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shiva.rockefeller.edu/SeqTailor/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_0623, edam:topic_3474 ; sc:citation , "pmcid:PMC6918593", "pubmed:31847804" ; sc:description """Modeling aspects of the language of life through transfer-learning protein sequences. Modelling the Language of Life - Deep Learning Protein Sequences. Repository for the paper Modeling aspects of the language of life through transfer-learning protein sequences. Holds pre-trained SeqVec model for creating embeddings for amino acid sequences. Also, contains checkpoint for fine-tuning""" ; sc:featureList edam:operation_0267, edam:operation_0337, edam:operation_0477, edam:operation_2489, edam:operation_3904 ; sc:license "MIT" ; sc:name "SeqVec" ; sc:url "https://github.com/Rostlab/SeqVec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3382 ; sc:citation , "pubmed:31368484" ; sc:description "making graph genomes intuitive to commuters | displays multiple genomic sequences in the form of a tube map | A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a \"tube map\"-like visualization of sequence graphs which have been created with vg | Link to working demo: https://vgteam.github.io/sequenceTubeMap/ | Run Sequence Tube Maps On Your Own | If you are using vg and want visualize the graphs it generates, the online version is limited to small file sizes. For visualizing bigger data sets you can run Sequence Tube Maps on your own. You can either run Tube Maps completely on your local (Linux) machine or use your local browser to access Tube Maps running on any other (Linux) machine you have access to" ; sc:license "MIT" ; sc:name "Sequence tube maps" ; sc:url "https://vgteam.github.io/sequenceTubeMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "The Sequencing Initiative Suomi (SISu) search engine offers a way to search for data on sequence variants in Finns. It provides valuable summary data for researchers and clinicians as well as other people having an interest in genetics in Finland. With SISu, you can examine the attributes and appearance of different variants in Finnish cohorts and see their aggregate distribution in Finland visualized on a map." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Sequencing Initiative Suomi (SISu)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.sisuproject.fi/" ; biotools:primaryContact "Risto Kajanne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3305, edam:topic_3418 ; sc:citation ; sc:description "Determining the serotype composition of mixed samples of pneumococcus using whole genome sequencing | Pneumococcal serotype quantification using NGS reads | SeroCall can identify and quantitate the capsular serotypes in Illumina whole-genome sequencing samples of S. pneumoniae, calculating abundances of each serotype in mixed cultures. The software is written in Python (compatible with Python 2 or 3), and is freely available under an open source GPLv3 license" ; sc:featureList edam:operation_3798, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SeroCall" ; sc:url "https://github.com/knightjimr/serocall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description "an open source tool to infer epidemiological and immunological dynamics from serological data | Inference framework for serological data | serosolver is a modelling and inference package that uses a dynamic model to infer antibody dynamics and infection histories from cross-sectional or longitudinal serological data. The model infers individual-level infection histories, historical attack rates, and patterns of antibody dynamics by accounting for cross-reactive antibody responses and measurement error" ; sc:license "GPL-3.0" ; sc:name "Serosolver" ; sc:url "https://github.com/seroanalytics/serosolver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Evaluation of Cell Type Deconvolution R Packages on Single Cell RNA-seq Data." ; sc:featureList edam:operation_3435, edam:operation_3629, edam:operation_3659 ; sc:name "Seurat SingleR" ; sc:url "https://github.com/qianhuiSenn/scRNA_cell_deconv_benchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315 ; sc:citation ; sc:description "Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci | [posMatrix,retVals]=ShNeigh(heatmapMatrix,method_type)" ; sc:name "ShNeigh" ; sc:url "https://github.com/fangzhen-li/ShNeigh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_3474 ; sc:citation , "pmcid:PMC6612843", "pubmed:31510707" ; sc:description "RNA SHAPE prediction using graph kernel | SHApe simulation with graph KERnels | import shaker.rna_tools.rna_io as rio" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2441 ; sc:name "ShaKer" ; sc:url "https://github.com/BackofenLab/ShaKer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6366102", "pubmed:30727942" ; sc:description "Platform-agnostic data harmonizer for gene expression data." ; sc:featureList edam:operation_0313, edam:operation_0533, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Shambhala" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/oncobox-admin/harmony" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , ; sc:description "Fast tool for mapping-free gene separation of reads, using Bloom filter." ; sc:featureList edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Shark" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/AlgoLab/shark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0632 ; sc:citation , "pmcid:PMC6933856", "pubmed:31730280" ; sc:description "Shift-T is a server for an automated Variable-Temperature NMR Data Analysis." ; sc:featureList edam:operation_0461, edam:operation_2476, edam:operation_3215 ; sc:license "MIT" ; sc:name "Shift-T" ; sc:url "http://meieringlab.uwaterloo.ca/shiftt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3297 ; sc:description "App developed in Shiny and usable in R environment that allows to visualize, explore, filter and extract data from FoodMicrobionet." ; sc:name "ShinyFMBN" ; sc:softwareVersion "1.1" ; sc:url "https://data.mendeley.com/datasets/8fwwjpm79y/1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3500 ; sc:citation , "pubmed:31882993" ; sc:description "ShinyGO is a graphical enrichment tool for animals and plants." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3083 ; sc:name "ShinyGO" ; sc:url "http://bioinformatics.sdstate.edu/go/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3581 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391, edam:topic_3473 ; sc:citation ; sc:description "A software framework for performing benchmarks of machine-learning classification algorithms" ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ShinyLearner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/srp33/ShinyLearner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:name "Experimental measurement" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3934 ; sc:citation , "pubmed:32049322" ; sc:description "Precise, high-performance FlowSOM-style cytometry data analysis in a browser, in an R Shiny app." ; sc:featureList edam:operation_0313, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ShinySOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.com/exaexa/ShinySOM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC6834530", "pubmed:31736735" ; sc:description "ShuTu is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining." ; sc:featureList edam:operation_1812, edam:operation_3450, edam:operation_3799 ; sc:name "ShuTu" ; sc:url "http://personal.psu.edu/dzj2/ShuTu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0625 ; sc:citation , "pmcid:PMC6836738", "pubmed:31628257" ; sc:description """Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data. Accumulation and selection of somatic mutations in a Darwinian framework result in intra-tumor heterogeneity (ITH) that poses significant challenges to the diagnosis and clinical therapy of cancer. Identification of the tumor cell populations (clones) and reconstruction of their evolutionary relationship can elucidate this heterogeneity. Recently developed single-cell DNA sequencing (SCS) technologies promise to resolve ITH to a single-cell level. However, technical errors in SCS data sets, including false-positives (FP) and false-negatives (FN) due to allelic dropout, and cell doublets, significantly complicate these tasks. Here, we propose a nonparametric Bayesian method that reconstructs the clonal populations as clusters of single cells, genotypes of each clone, and the evolutionary relationship between the clones""" ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3432 ; sc:name "SiCloneFit" ; sc:url "https://bitbucket.org/hamimzafar/siclonefit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3474 ; sc:citation , "pubmed:31789550" ; sc:description """A general response process theory for situational judgment tests. Situational judgment tests (SJTs) have emerged as a staple of assessment methodologies for organizational practitioners and researchers. Despite their prevalence, many questions regarding how to interpret respondent choices or how variations in item construction and instruction influence the nature of observed responses remain. Existing conceptual and empirical efforts to explore these questions have largely been rooted in reflexive psychometric measurement models that describe participant responses as indicative of (usually multiple) latent constructs. However, some have suggested that a key to better understanding SJT responses lies in unpacking the judgment and decision-making processes employed by respondents and the psychological and contextual factors that shape how those processes play out. To this end, the present article advances an integrative and generalizable process-oriented theory of SJT responding""" ; sc:name "SiRJ" ; sc:url "https://grandjam.shinyapps.io/sirj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Sierra is an R package designed for detecting differential transcript usage analysis from polyA-enriched single cell RNASeq data. Sierra identifies coordinates of read pileups (i.e. peaks) and performs UMI counting, followed by differential usage analysis between defined cell populations. Please read vignette for a demonstration on how to use this software""" ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3891 ; sc:name "Sierra" ; sc:url "https://github.com/VCCRI/Sierra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2830, edam:topic_3379 ; sc:citation ; sc:description "Web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials." ; sc:featureList edam:operation_0560 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SieveSifter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sieve.fredhutch.org/viz" ; biotools:primaryContact "Andrew Fiore-Gartland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0749, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:31697324" ; sc:description "scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies." ; sc:featureList edam:operation_0277, edam:operation_2428, edam:operation_3439 ; sc:name "SigHotSpotter" ; sc:url "https://SigHotSpotter.lcsb.uni.lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3068, edam:topic_3676 ; sc:citation ; sc:description "Tool for visualizing and exploring patterns of small mutational events." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "SigProfilerMatrixGenerator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AlexandrovLab/SigProfilerMatrixGenerator" ; biotools:primaryContact "Erik Bergstrom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0621, edam:topic_3474, edam:topic_3510 ; sc:citation , "pmcid:PMC6923836", "pubmed:31861981" ; sc:description """signal peptide recognition based on semantic segmentation. A signal peptide predictor based on deep learning. For CPU: pip3 install -r requirement.cpu.txt. For GPU (suggest): pip3 install -r requirement.gpu.txt""" ; sc:featureList edam:operation_0277, edam:operation_0418, edam:operation_3439 ; sc:name "SigUNet" ; sc:url "https://github.com/mbilab/SigUNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3277, edam:topic_3308 ; sc:citation , "pmcid:PMC6823428", "pubmed:31672983" ; sc:description """integrated 'omics knowledgebase for mammalian cellular signaling pathways. A multi-omics knowledgebase for cellular signaling pathways. Welcome to the Signaling Pathways Project. The Signaling Pathways Project is a multi-omics knowledgemine based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench relevant to cellular signaling pathways. Learn more ». 1555 datasets found. Use the filter to narrow the listings. Transcriptomic Cistromics (ChIP-Seq)""" ; sc:featureList edam:operation_0306, edam:operation_0440, edam:operation_0533, edam:operation_3359, edam:operation_3439 ; sc:name "Signaling Pathways Project" ; sc:softwareHelp ; sc:url "https://www.signalingpathways.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6720940", "pubmed:31477009" ; sc:description "package for cancer mutational signatures | SigsPack R/Bioconductor package for mutational signature estimation | SigsPack provides estimations of a sample's exposure to mutational processes described by a set of known mutational signatures (for example from COSMIC). The exposure stability is quantified by bootstrapping the mutational catalogue" ; sc:featureList edam:operation_0337, edam:operation_3202, edam:operation_3435 ; sc:name "SigsPack" ; sc:url "https://github.com/bihealth/SigsPack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3382 ; sc:citation ; sc:description "Automated Spatially Targeted Optical Micro Proteomics (autoSTOMP) to determine protein complexity of subcellular structures | Automate what you see on a computer monitor | What is it? For what is it? Get it? Use it? Get help? Contribute? | Latest stable version: 2.0.0 —— Nightly builds: 2.1.0-SNAPSHOT | Both left the project at Sikuli-X-1.0rc3 during 2012, when I decided to take over development and support and name it SikuliX | SikuliX automates anything you see on the screen of your desktop computer running Windows, Mac or some Linux/Unix. It uses image recognition powered by OpenCV to identify GUI components. This is handy in cases when there is no easy access to a GUI's internals or the source code of the application or web page you want to act on" ; sc:featureList edam:operation_3501 ; sc:name "SikuliX" ; sc:url "http://sikulix.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3343 ; sc:citation , "pubmed:31066547" ; sc:description "SiliS-PTOXRA (DRY-in Silico Screening & Prediction of Toxic Hazard and Risk Assessment) for the prediction of toxicological endpoints." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SiliS-PTOXRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tomocomd.com/apps/ptoxra" ; biotools:primaryContact "César R. García-Jacas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3855 ; sc:citation ; sc:description "An open-source Simulink library for developing closed-loop brain signal interfaces in animals and humans | Simulink Brain Signal Interface (SimBSI) | SimBSI is an open-source graphical environment for the rapid prototyping of animal and human brain-computer interfaces (BCIs). SimBSI is designed as a library on top of the graphical programming environment of Simulink with three goals in mind:" ; sc:featureList edam:operation_0337, edam:operation_3891 ; sc:name "SimBSI" ; sc:softwareHelp ; sc:url "https://bitbucket.org/neatlabs/simbsi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3173, edam:topic_3308, edam:topic_3315 ; sc:citation ; sc:description """Bayesian Linear Mixed Models for Motif Activity Analysis. Simulate gene expression data where gene expression is determined by a linear inlfuential factor, such as motifs.""" ; sc:featureList edam:operation_2426, edam:operation_2495, edam:operation_3659 ; sc:license "MIT" ; sc:name "SimGEXPwMotifs" ; sc:url "https://github.com/Sim19/SimGEXPwMotifs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Software tool enabling confident phosphosite assignment." ; sc:featureList edam:operation_3501, edam:operation_3627, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SimPhospho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/simphospho/" ; biotools:primaryContact "Garry L Corthals", "Veronika Suni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3168 ; sc:citation , "pubmed:31764964" ; sc:description """an R package to simulate genetic sequence data for pedigrees. Simulate Genetic Sequence Data for Pedigrees. Methods to simulate genetic sequence data for pedigrees, with functionality to simulate genetic heterogeneity among pedigrees. Christina Nieuwoudt, Angela Brooks-Wilson, and Jinko Graham (2019) """ ; sc:featureList edam:operation_3196, edam:operation_3562 ; sc:license "GPL-2.0" ; sc:name "SimRVSequences" ; sc:url "https://cran.r-project.org/web/packages/SimRVSequences/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6916212", "pubmed:31842741" ; sc:description """alternative splicing-aware simulation of biological sequence evolution. To add a sequence you need to click the "Add sequence" button is the top left corner of the main application screen. Sequences must be in the arc-annotated format: first line starts with > and following is the sequence header. Next line is the RNA Sequence and then the secondary structure inforamtion. You can add multitude sequences at the same time. The sequences will be added to the list in the side menu. To delete sequences, you can click on those you want deleted and click the "Delete selected" button to remove them. If you want to clear the whole list, the button "Delete all" will do it. The buttons "Select All" and "Unselect All" are used to make this easier when working with multiple sequences""" ; sc:featureList edam:operation_0232, edam:operation_0491, edam:operation_2499 ; sc:name "SimSpliceEvol" ; sc:url "https://github.com/UdeS-CoBIUS/SimSpliceEvol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:31446517" ; sc:description "> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'vessel pathlines', 'vessel', 'FCNN', 'vessel pathline' | Accelerating cardiovascular model building with convolutional neural networks | The only fully opensource software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis | Blood velocity distribution in CABG simulation | Blood velocity in coronary aneurism | SimVascular components svModel, svMesh, svPre, and svPost are provided under the full BSD license subject to the terms below: | Copyright © 1998-2007 Stanford University, Charles Taylor, Nathan Wilson, Ken Wang. See SimVascular Acknowledgements file for additional contributors to the source code" ; sc:name "SimVascular" ; sc:url "http://simvascular.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3512 ; sc:citation , "pubmed:31504187" ; sc:description "fast and resource frugal de novo comparative metagenomics | Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets | This github directory stores Simka and SimkaMin software. This readme focuses on Simka features. All information about SimkaMin is located in the simkaMin directory" ; sc:featureList edam:operation_0476, edam:operation_3472, edam:operation_3644 ; sc:license "AGPL-3.0" ; sc:name "SimkaMin" ; sc:url "https://github.com/GATB/simka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6917719", "pubmed:31848434" ; sc:description "An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces." ; sc:featureList edam:operation_3562 ; sc:name "SimpactCyan" ; sc:url "https://simpactcyan.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130 ; sc:citation , "pubmed:31394001" ; sc:description "A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions | Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time" ; sc:name "SimpleDSFviewer" ; sc:url "https://github.com/hscsun/SimpleDSFviewer-5.0.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634 ; sc:citation , "pmcid:PMC6602488", "pubmed:31114901" ; sc:description "Interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database." ; sc:featureList edam:operation_3197, edam:operation_3436, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Simple ClinVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://simple-clinvar.broadinstitute.org/" ; biotools:primaryContact "Dennis Lal", "Eduardo Pérez-Palma", "Marie Gramm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC6715530", "pubmed:31377170" ; sc:description "> HOMEPAGE MISSING! | A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species | Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by searching for combinations of genes that have previously been implicated as being cell-type specific, an approach that is not quantitative and does not explicitly take advantage of other single-cell RNA-seq studies. Here, we describe our tool, SingleCellNet, which addresses these issues and enables the classification of query single-cell RNA-seq data in comparison to reference single-cell RNA-seq data. SingleCellNet compares favorably to other methods in sensitivity and specificity, and it is able to classify across platforms and species" ; sc:featureList edam:operation_3800 ; sc:name "SingleCellNet" ; sc:url "https://github.com/pcahan1/singleCellNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Inference of intercellular networks from single-cell transcriptomics." ; sc:featureList edam:operation_3083, edam:operation_3659 ; sc:name "SingleCellSignalR" ; sc:url "https://github.com/SCA-IRCM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC6677298", "pubmed:31374080" ; sc:description "Linked Data Services platform for decentralized knowledge base | LodView is a powerful RDF viewer, IRI dereferencer and opensource SPARQL navigator | It is a long established fact that a reader will be distracted by the readable content of a page when looking at its layout. The point of using Lorem Ipsum is that it has a more-or-less normal distribution of letters, as opposed to using 'Content here, content here', making it look like readable English | Lorem Ipsum is simply dummy text of the printing and typesetting industry" ; sc:featureList edam:operation_2422, edam:operation_3559, edam:operation_3760 ; sc:name "SinoPedia" ; sc:url "http://sinopedia.library.sh.cn/sparql" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3303, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc:description """A single-sample circadian biomarker that performs across populations and platforms. SkinPhaser is a Shiny app of predicing the circadian phase using expression values of 12 biomarker genes from human epidermis samples""" ; sc:featureList edam:operation_0269, edam:operation_2495, edam:operation_3454 ; sc:name "SkinPhaser" ; sc:url "https://github.com/gangwug/SkinPhaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC6504038", "pubmed:31063501" ; sc:description "Automated sleep stage scoring with sequence to sequence deep learning approach." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SleepEEGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SajadMo/SleepEEGNet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3512, edam:topic_3534 ; sc:citation , "pubmed:31494246" ; sc:description "A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome | Free Bootstrap 4 Pingendo Aquamarine template for unique events" ; sc:featureList edam:operation_3096, edam:operation_3901, edam:operation_3902 ; sc:name "SliceIt" ; sc:url "http://sliceit.soic.iupui.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31519740" ; sc:description "> MEDIUM CONFIDENCE! | Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ | scripts used in the Smart-3SEQ paper" ; sc:featureList edam:operation_0308, edam:operation_2495, edam:operation_3233 ; sc:name "Smart-3SEQ" ; sc:url "https://github.com/jwfoley/Smart-3SEQ_paper_scripts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3360, edam:topic_3421, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC6854692", "pubmed:31754347" ; sc:description "Two predictive precision medicine tools for hepatocellular carcinoma." ; sc:featureList edam:operation_0531, edam:operation_3503, edam:operation_3659 ; sc:name "Smart Cancer Predictive System" ; sc:url "https://zhangzhiqiao2.shinyapps.io/Smart_cancer_predictive_system_HCC_2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3298, edam:topic_3337 ; sc:citation , "pubmed:31591642" ; sc:description """Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data. Soft Windowing on Linear Regression. The main function in the package utilizes a windowing function in the form of an exponential weighting function to linear models. The bandwidth and sharpness of the window are controlled by two parameters. Then, a series of tests are used to identify the right parameters of the window (see Hamed Haselimashhadi et al (2019) )""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3659 ; sc:license "LGPL-2.0" ; sc:name "SmoothWin" ; sc:url "http://CRAN.R-project.org/package=SmoothWin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3315 ; sc:citation ; sc:description "Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3472 ; sc:license "Apache-2.0" ; sc:name "Smudgeplots" ; sc:url "https://github.com/KamilSJaron/smudgeplot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC6879379", "pubmed:31777414" ; sc:description """A Case Study in Deploying Weak Supervision at Industrial Scale. Programmatically Building and Managing Training Data. Build Training Sets Programmatically. Labeling and managing training datasets by hand is one of the biggest bottlenecks in machine learning. In Snorkel, write heuristic functions to do this programmatically instead!""" ; sc:name "Snorkel DryBell" ; sc:url "http://snorkel.stanford.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3068, edam:topic_3168 ; sc:citation ; sc:description "Web-server framework to explore and visualize large genomic variation data in lab and its applications to wheat and its progenitors." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SnpHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://guoweilong.github.io/SnpHub/" ; biotools:primaryContact "Weilong Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3855 ; sc:citation , "pmcid:PMC6411228", "pubmed:30811390" ; sc:description "Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://vatlab.github.io/sos-docs/" ; biotools:primaryContact "B. Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050, edam:topic_3810 ; sc:citation , "pmcid:PMC6530169", "pubmed:31117932" ; sc:description "Identification and resolution of plant taxonomic names." ; sc:featureList edam:operation_0495, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Solr-Plant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcbi.brown.edu/solrplant" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0091, edam:topic_0797 ; sc:author ; sc:citation , "pubmed:30032301" ; sc:description "SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_2423, edam:operation_3209 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SonicParanoid" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.9" ; sc:url "http://iwasakilab.bs.s.u-tokyo.ac.jp/sonicparanoid/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6834292", "pubmed:31652275" ; sc:description """A graphical model approach to identify primary genes in perturbed biological pathways. Topological gene-set analysis has emerged as a powerful means for omic data interpretation. Although numerous methods for identifying dysregulated genes have been proposed, few of them aim to distinguish genes that are the real source of perturbation from those that merely respond to the signal dysregulation. Here, we propose a new method, called SourceSet, able to distinguish between the primary and the secondary dysregulation within a Gaussian graphical model context. The proposed method compares gene expression profiles in the control and in the perturbed condition and detects the differences in both the mean and the covariance parameters with a series of likelihood ratio tests.""" ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3562 ; sc:name "SourceSet" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/SourceSet/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation ; sc:description """The South Green platform is a local network of scientists gathering Bioinformatics skills based on the Agropolis campus that hosts research institutes such as CIRAD, IRD, INRA, SupAgro, Alliance of Bioversity international and CIAT. Based on this strong local community in the field of agriculture, food, biodiversity and environment, this network of national and international scope, develops bioinformatics applications and resources dedicated to genetics and genomics of tropical and Mediterranean plants. South Green relies on the computer technical platforms of its partner institutes.""" ; sc:name "SouthGreen platform" ; sc:softwareHelp , , ; sc:url "https://southgreen.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3810 ; sc:description "A Galaxy instance focused on agriculture, food, biodiversity and environment, from the Agropolis campus in France." ; sc:name "SouthGreen Galaxy" ; sc:softwareHelp ; sc:url "http://galaxy.southgreen.fr/galaxy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_1929 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3308, edam:topic_3810 ; sc:citation , ; sc:description "The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers)." ; sc:featureList edam:operation_0338, edam:operation_2403, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "South Green Genome Hubs" ; sc:softwareHelp ; sc:url "https://www.southgreen.fr/genomehubs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6747016", "pubmed:31549018" ; sc:description "Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data | SoyCSN (Soybean Context Specific Network) - | SoyCSN (Soybean Context Specific Network) | SoyCSN computes and visualizes any of the 14 soybean context specific networks both at the expression and interactome level. Users can compare the gene-gene relationship differences at different confidence levels across all the soybean tissues" ; sc:featureList edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:name "SoyCSN" ; sc:url "http://soykb.org/SoyCSN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "A Soybean mine instance with genomic data from the Legume Information Systems (LIS) multi-species chado database and genetic data pulled from Soybase" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "SoyMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.10" ; sc:url "https://mines.legumeinfo.org/soymine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation , "pubmed:31550555" ; sc:description "> HOMEPAGE MISSING! | Towards a fast and reliable clustering for potentially divergent biological sequences | This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed package was also intensively evaluated on simulated and real genomic and protein data sets. The clustering results were compared to the most known traditional tools, such as UCLUST, CD-HIT and DNACLUST" ; sc:name "SpCLUST" ; sc:url "https://github.com/johnymatar/SpCLUST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """integrating tissue morphology and spatial gene expression to predict disease cells. SpaCell has been developed for analysing spatial transcriptomics (ST) data, which include imaging data of tissue sections and RNA expression data across the tissue sections. The ST data add a novel spatial dimension to the traditional gene expression data from dissociated cells. SpaCell is desinged to integrates the two histopathological imaging and sequencing fields, with the ultimate aim to discover novel biology and to improve histopathological diagnosis in a quantitative and automated way""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3799 ; sc:license "MIT" ; sc:name "SpaCell" ; sc:url "https://github.com/BiomedicalMachineLearning/SpaCell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Apache Spark based Read Clustering tool to cluster a large number of DNA/RNA sequences generated from next-generation sequence technologies, including Illumina and PacBio." ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SpaRC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/berkeleylab/jgi-sparc/" ; biotools:primaryContact "Zhong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6598954", "pubmed:31093725" ; sc:description "Encouraging durable memory using spaced testing in pediatric radiology." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Spaced Radiology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.spacedradiology.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Spaniel Spatial Transcriptomics Analysis." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Spaniel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/RachelQueen1/Spaniel" ; biotools:primaryContact "Rachel Queen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2830, edam:topic_3315, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc:description "Apache Spark is a unified analytics engine for big data processing, with built-in modules for streaming, SQL, machine learning and graph processing. Melanoma expression analysis with Big Data technologies." ; sc:featureList edam:operation_0252, edam:operation_2495, edam:operation_3659 ; sc:name "Spark" ; sc:url "http://spark.apache.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3316 ; sc:citation , "pmcid:PMC6894754", "pubmed:31805063" ; sc:description """Production-quality memory-efficient Apache Spark based genome analysis framework. SparkGA2 is an Apache Spark based scalable implementation of the best practice DNA analysis pipeline by Broad Institute, which is an improvement over the similar SparkGA1 (https://github.com/HamidMushtaq/SparkGA1.git)""" ; sc:featureList edam:operation_0487, edam:operation_2409, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SparkGA2" ; sc:url "https://github.com/HamidMushtaq/SparkGA2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31713629" ; sc:description """a database for spatially resolved transcriptomes. Welcome to SpatialDB! click thumbnails to quickly browse the spatial gene expression profiles. Spatially resolved transcriptomics providing gene expression profiles with positional information is key to tissue function and fundamental to disease pathology""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3501 ; sc:name "SpatialDB" ; sc:url "https://www.spatialomics.org/SpatialDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description """A new approach to estimating pairwise sequence alignments. SimpleFastaParser from Bio.SeqIO.FastaIO. To create filtered datasets run Bacterial_pipeline_part1.py and Bacterial_pipeline_part2.py""" ; sc:featureList edam:operation_0491, edam:operation_3198, edam:operation_3695 ; sc:name "Spectral Jaccard Similarity" ; sc:url "https://github.com/TavorB/spectral_jaccard_similarity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304 ; sc:citation ; sc:description """SpikeInterface is an unified framework for spike sorting. Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3802 ; sc:name "SpikeInterface" ; sc:url "http://github.com/SpikeInterface" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3406 ; sc:citation ; sc:description "A software tool for quantitative analysis of nanoscale spine morphology | Abstract Super-resolution microscopy provides diffraction-unlimited optical access to the intricate morphology of neurons in living brain tissue, resolving their finest structural details, which are critical for neuronal function. However, as existing image analysis software tools have been developed for diffraction-limited images, they are generally not well suited for quantifying nanoscale structures like dendritic spines. We present SpineJ, a semi-automatic ImageJ plugin that is specifically designed for this purpose. SpineJ comes with an intuitive and user-friendly graphical user interface, facilitating fast, accurate, and unbiased analysis of spine morphology" ; sc:featureList edam:operation_3450, edam:operation_3799 ; sc:name "SpineJ" ; sc:url "https://github.com/flevet/SpineJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3320, edam:topic_3474 ; sc:citation , "pmcid:PMC6933889", "pubmed:31881982" ; sc:description """ab initio prediction of splice sites using convolutional neural network. This is the source code for SpliceFinder""" ; sc:featureList edam:operation_0232, edam:operation_0433, edam:operation_3439 ; sc:name "SpliceFinder" ; sc:url "https://gitlab.deepomics.org/wangruohan/SpliceFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3577 ; sc:citation , "pubmed:31617569" ; sc:description """a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data. RNAseq pipeline for alternative splicing junctions. SpliceLauncher is a pipeline tool to study the alternative splicing. It works in three steps:. SpliceLauncher comes with a ready to use config.cfg file. It contains the paths of software and files used by SpliceLauncher. The INSTALL mode of SpliceLauncher updates this config.cfg file. If you define the path to GFF (v3) file and path to the FASTA genome, the INSTALL mode will extract all necessary information from this GFF and indexing the STAR genome. This informations are stored in a BED file that contains the exon coordinates, in a sjdb file that contains the intron coordinates and a text file that contains the details of transcript structures. You need to define where these files will saving by the -O, --output argument""" ; sc:featureList edam:operation_2499, edam:operation_3225, edam:operation_3800 ; sc:license "MIT" ; sc:name "SpliceLauncher" ; sc:url "https://github.com/raphaelleman/SpliceLauncher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6507234", "pubmed:31068132" ; sc:description "Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpliceV" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/flemingtonlab/SpliceV" ; biotools:primaryContact "Erik Flemington" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3474 ; sc:citation , "pubmed:29580738" ; sc:description "SpliceVec: Distributed feature representations for splice junction prediction" ; sc:featureList edam:operation_0337, edam:operation_2990 ; sc:name "SpliceVec-g" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/aaiitggrp/SpliceVec-g" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:31783254" ; sc:description """Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks. SpliceVisuL: Visualization of Bidirectional Long Short-term Memory Networks for Splice Junction Prediction""" ; sc:featureList edam:operation_2990, edam:operation_3083 ; sc:name "SpliceVisuL" ; sc:url "https://github.com/aaiitggrp/SpliceVisuL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Integrative, scalable tool for the discovery of splice-altering variants." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Spliceogen" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/VCCRI/Spliceogen" ; biotools:primaryContact "Steve Monger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3174 ; sc:citation , "pmcid:PMC6765119", "pubmed:31361894" ; sc:description "> MEDIUM CONFIDENCE! | Genome-wide epistasis and co-selection study using mutual information | SpydrPick is a command line tool for performing 'direct coupling analysis' of aligned categorical datasets. It constructs a coupling graph based on thresholded node-pair Mutual Information (MI) scoring, followed by pruning of edges that represent indirect couplings using the ARACNE algorithm | Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure | Home: https://github.com/santeripuranen/SpydrPick | License: GNU Affero General Public License" ; sc:featureList edam:operation_0484, edam:operation_3227, edam:operation_3461 ; sc:name "SpydrPick" ; sc:url "https://anaconda.org/bioconda/spydrpick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3293, edam:topic_3382 ; sc:citation ; sc:description "Software tool that automatically generates interactive web-based two-dimensional graphical representations of raw DNA sequences." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Squiggle" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Lab41/squiggle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC6700779", "pubmed:31426747" ; sc:description "A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction | This is our model of MBD pulldown alignments generated from SssI-treated DNA proposed in the publication entitled \"A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction\". Please read through the instructions in the README before using the software. Test files are provided in the \"source\" folder. Links to the indexes of CpGs in hg18 and the corresponding yi Λ file, generated from that list using our experimental presets and summed on 10bp windows, are also given" ; sc:featureList edam:operation_0417, edam:operation_0430, edam:operation_3186 ; sc:name "SssI" ; sc:url "http://bioserv.mps.ohio-state.edu/SssICalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:30649230" ; sc:description "R Package for Stacking with Applications to Scenarios Involving Sequential Addition of Samples and Features." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sstack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://cran.r-project.org/web/packages/Sstack/index.html" ; biotools:primaryContact "Kevin Matlock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3474 ; sc:citation , "pubmed:31683069" ; sc:description "A stacking based prediction of protein-carbohydrate binding sites from sequence." ; sc:featureList edam:operation_2575 ; sc:name "StackCBPred" ; sc:url "https://bmll.cs.uno.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3304 ; sc:citation , "pmcid:PMC6643891", "pubmed:31040111" ; sc:description "Interscholastic Network To Generate LexA Enhancer Trap Lines in Drosophila." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StanEx1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stanex.stanford.edu/about/" ; biotools:primaryContact "Lutfi Huq", "Seung K. Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3277, edam:topic_3489 ; sc:citation ; sc:description "Staphopia is a database focusing on the genomes of the bacterial pathogen Staphylococcus aureus. Life-threatening Methicillin-resistant S. aureus (MRSA) infections strike across our society, both in the community and hospital settings. In recent years whole genome shotgun sequencing of clinical isolates has become common. As of August 2017 there were over 44,000 publicly available S. aureus sequencing projects in EBI's ENA database. Staphopia aims to provide rapid analysis of these whole-genome datasets as well as useful S. aureus specific results, such as genotype, antibiotic resistance and virulence gene profiles." ; sc:featureList edam:operation_3211, edam:operation_3431, edam:operation_3482, edam:operation_3840 ; sc:license "MIT" ; sc:name "Staphopia" ; sc:url "http://staphopia.emory.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3293 ; sc:citation , , "pmcid:PMC4137710", "pubmed:24899668", "pubmed:30298398" ; sc:description "Extendable software package for Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates." ; sc:featureList edam:operation_0323, edam:operation_0503 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "StatAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://statalign.github.io/" ; biotools:primaryContact "Adam Novak", "Joe Herman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "Stereological and Automated Analysis Platform for Assessing Histological Labelling in Cleared Tissue Specimens." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StereoMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://imagej.net/StereoMate" ; biotools:primaryContact "David L. Bennett", "Steven J. West" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0166, edam:topic_3169, edam:topic_3179, edam:topic_3794 ; sc:citation ; sc:description """Evaluation and Classification of Peak Profiles for Sequencing Data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets""" ; sc:featureList edam:operation_2495, edam:operation_2575, edam:operation_3215, edam:operation_3222, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "StoatyDive" ; sc:url "https://anaconda.org/bioconda/stoatydive" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pubmed:31418766" ; sc:description "A phylogenetic tool to construct pathogen transmission networks | Welcome to the StrainHub Repo - Files and Data - StrainHub Online: | Strainhub is designed as a web-based software to generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata. The software maps the metadata onto the tree and performs a parsimony ancestry reconstruction step to create links between the associated metadata and enable the construction of the network. Users also have the option to skip the StrainHub ancestry reconstruction step by generating a maximum clade credibility tree (MCC) through BEAST phylogeography | Generate disease transmission networks and associated metrics from a combination of a phylogenetic tree and associated metadata" ; sc:featureList edam:operation_0545, edam:operation_0555, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "StrainHub" ; sc:url "http://strainhub.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3308, edam:topic_3360, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6923958", "pubmed:31856731" ; sc:description """a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. Stress predicting framework with microarray data based on CMCL and logical correlation model. Stress Predictor based on Machine Learning. python learn.py dataset/dataset_learn_v2_005.limma.csv dataset/dataset_learn_v2_005.label.csv --reduce_updown --save output/model_v2 --save_csv output/model_v2 --epoch_count 1000 --batch_size 0. --reduce_updown Use this parameter if dataset is separated into up and down column""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3196, edam:operation_3565 ; sc:name "StressGenePred" ; sc:url "https://github.com/bhi-kimlab/StressGenePred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3300, edam:topic_3304, edam:topic_3334 ; sc:citation ; sc:description "This is a tool for analysis of video data of mice engaged in string-pulling. It analyses Phenotyping motor behavior of mice for sensory, whole-body and bimanual skilled hand function." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "String-pulling" ; sc:url "https://github.com/samsoon-inayat/string_pulling_mouse_matlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885 ; sc:citation , "pmcid:PMC6694510", "pubmed:31412777" ; sc:description "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Genotyping low-coverage whole-genome sequencing intercross pedigrees from outbred founders' | Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders | Whole-genome genotyping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing | Carlborg's Lab (Yanjun Zan, Thibaut Payen, Örjan Carlborg) - BMC - Uppsala University | Experimental intercrosses of divergent lines are useful to map loci (quantitative trait loci; QTL) contributing to phenotypic variation using the recombinant founder mosaic genotypes in the F2 generation | git clone https://github.com/CarlborgGenomics/Stripes" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "Stripes" ; sc:url "https://github.com/CarlborgGenomics/Stripes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pubmed:26615437" ; sc:description "Program for alignment of structures of DNA-protein complexes." ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "StructAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mouse.genebee.msu.ru/tools/StructAlign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0196 ; sc:citation ; sc:description "Tool for 3D protein structure profiling." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0482 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "StructureProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.zbh.uni-hamburg.de/forschung/amd/software/structureprofiler.html" ; biotools:primaryContact "Matthias Rarey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "a pipeline for building custom databases for common metagenome profilers | Ley Lab MetaGenome Profiler DataBase generator | de la Cuesta-Zuluaga, Jacobo, Ruth E. Ley, and Nicholas D. Youngblut. 2019. “Struo: A Pipeline for Building Custom Databases for Common Metagenome Profilers.” bioRxiv. https://doi.org/10.1101/774372" ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3460 ; sc:name "Struo" ; sc:url "https://github.com/leylabmpi/Struo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3379 ; sc:citation , "pmcid:PMC6904404", "pubmed:31823031" ; sc:description "StudyPortal combines the free sources ClinicalTrials.gov, PubMed, OpenStreetMap and Geonames.org to provide you an integrated search for visualization of suitable clinical studies and scientific articles that match your search criteria." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "StudyPortal" ; sc:url "https://studyportal.uni-muenster.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3314, edam:topic_3448 ; sc:citation , "pubmed:31508962" ; sc:description "A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces | SuAVE: Surface Assessment Via grid Evaluation" ; sc:featureList edam:operation_0387, edam:operation_1816 ; sc:name "SuAVE" ; sc:url "http://www.biomatsite.net/suave-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3336 ; sc:citation ; sc:description "RDKit-based overlap measure that combines volumetric shape and pharmacophoric features to give a combined overlap score similar to OpenEye's Tversky Combo and Malhotra and Karanicolas' COS measure." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SuCOS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/susanhleung/SuCOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0621, edam:topic_0634, edam:topic_2229, edam:topic_3407 ; sc:citation , "pubmed:31603468" ; sc:description """predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. MOTIVATION:Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder, and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. RESULTS:We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction""" ; sc:featureList edam:operation_0253, edam:operation_2489, edam:operation_3092 ; sc:name "SubMito-XGBoost" ; sc:url "https://github.com/QUST-AIBBDRC/SubMito-XGBoost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC6518800", "pubmed:31088372" ; sc:description "Random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Subdyquency" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/weiba/Subdyquency" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_3314 ; sc:citation , "pmcid:PMC6320881", "pubmed:30563078" ; sc:description "Intuitive and fast interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences or quality images." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SugarSketcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glycoproteome.expasy.org/sugarsketcher/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0622, edam:topic_3810 ; sc:author ; sc:citation ; sc:description "The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources." ; sc:featureList edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Sugarcane Genome Hub" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sugarcane-genome.cirad.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3068, edam:topic_3174, edam:topic_3293 ; sc:citation , "pmcid:PMC9825549", "pubmed:36318251" ; sc:description "SulfAtlas describes the family and sub-families of structurally-related sulfatases. Sub-families are created based on phylogenetic analyses and essentially correspond to different substrate specificities" ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "SulfAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sulfatlas.sb-roscoff.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:30510236" ; sc:description "Software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SumHer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dougspeed.com/sumher/" ; biotools:primaryContact "Doug Speed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:31142576" ; sc:description "An R package for summarizing multiple enrichment analysis results." ; sc:featureList edam:operation_2497, edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Sumer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bzhanglab/sumer" ; biotools:primaryContact "Zhiao Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "Tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SummaryAUC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lsncibb/SummaryAUC" ; biotools:primaryContact "Jianxin Shi", "Lei Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3474, edam:topic_3794 ; sc:citation , "pubmed:31545722" ; sc:description "Image Super-Resolution as a Defense Against Adversarial Attacks | super-resolution-adversarial-defense | We use wavelet denoising and image super resolution as pre-processing steps to defend images against adversarial attacks. If you find our work useful in your research or publication, please cite our work:" ; sc:featureList edam:operation_3629 ; sc:name "Super-Resolution" ; sc:url "https://github.com/aamir-mustafa/super-resolution-adversarial-defense" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6798642", "pubmed:31681583" ; sc:description """Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Super CRF toolbox for training an conditional random field in combination with super pixel annotations""" ; sc:name "SuperCRF" ; sc:url "https://github.com/Henrik86/SuperCRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6770523", "pubmed:31480377" ; sc:description "A Super-Clustering Approach for Fully Automated Single Particle Picking in Cryo-EM | A Super Clustering Approach for Single Particle Picking in cryo-EM Images" ; sc:featureList edam:operation_3432, edam:operation_3458 ; sc:name "SuperCryoEMPicker" ; sc:url "https://github.com/jianlin-cheng/SuperCryoEMPicker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:31116387" ; sc:description "Random Forest and Gaussian Mixture predictor of high confidence genotypes in single cell data." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SureTypeSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/puko818/SureTypeSC" ; biotools:primaryContact "Ivan Vogel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6509810", "pubmed:31072374" ; sc:description "Pipeline for high-throughput extraction of cell contours from 3D image stacks." ; sc:featureList edam:operation_3446, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CECILL-C" ; sc:name "SurfCut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sverger/SurfCut" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3399, edam:topic_3421 ; sc:citation , "pmcid:PMC6143968" ; sc:description "P01.152 Evaluation of Factor V Leiden variant as risk a factor for venous thromboembolism in glioblastoma patients | The Swedish Frequency resource for genomics (SweFreq) is a website developed to make genomic datasets more findable and accessible in order to promote collaboration, new research and increase public benefit. You can contact swefreq@scilifelab.se if you want to find out more about this resource and how it could benefit you and your research | {{ mainCtrl.msg.level }}! {{ mainCtrl.msg.msg }}" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:name "SweGen" ; sc:url "https://swegen-exac.nbis.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621, edam:topic_0622, edam:topic_3293 ; sc:citation , "pmcid:PMC6812468", "pubmed:31648300" ; sc:description """A fast, memory-efficient, multiple genome orthology classifier. A high performance tool to identify orthologs and paralogs across genomes. SwiftOrtho is orthology analysis tool which identifies orthologs, paralogs and co-orthologs for genomes. It is a graph-based approach""" ; sc:featureList edam:operation_0327, edam:operation_0544, edam:operation_2421, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SwiftOrtho" ; sc:url "https://github.com/Rinoahu/SwiftOrtho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6765120", "pubmed:31372651" ; sc:description "> LOW CONFIDENCE! | Nonparametric expression analysis using inferential replicate counts | R scripts used in the Swish paper" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3800 ; sc:name "Swish" ; sc:url "https://github.com/azhu513/swishPaper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3676 ; sc:citation , "pubmed:30565316" ; sc:description "System for Quality-Assured Data Analysis (SyQADA) - workflow management system that seeks to improve reproducibility in as simple a framework as feasible." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SyQADA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://scheetlabsoftware.org/syqada/" ; biotools:primaryContact "Paul Scheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC6913012", "pubmed:31842948" ; sc:description """SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:name "SyRI" ; sc:url "https://schneebergerlab.github.io/syri/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation , ; sc:description """Symbolic computing in Python. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select domain specific submodules. The supplementary materials provide additional examples and further outline details of the architecture and features of SymPy. SymPy is an open source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become the standard symbolic library for the scientific Python ecosystem.""" ; sc:name "SymPy" ; sc:url "https://www.sympy.org/en/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3398, edam:topic_3895 ; sc:citation , "pmcid:PMC6690502", "pubmed:31423466" ; sc:description "evaluation of free management platforms for synthetic biology designs | Web application enabling users and software to browse, upload, and share synthetic biology designs | Dumps all sequences from SynBioHub instances as FASTA | A parts repository for synthetic biology | SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources" ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:name "SynBioHub" ; sc:url "https://synbiohub.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31596456" ; sc:description """An Automatic Tool to Quantify Synapses from Microscopy Images. A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images. SynQuant is a Fiji plugin that automatically quantify synapses from fluorescence microscopy images. Try SynQuant Now!. SynQuant performs better than peer unsupervised methods [5-8] for all the three data sets we tested (3D in-vivo [2], array tomography [3], neuron-astrocyte coculture [4])""" ; sc:featureList edam:operation_3435, edam:operation_3450, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SynQuant" ; sc:url "https://github.com/yu-lab-vt/SynQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Specific tools for pre-processing datas in order to use them in SynTView." ; sc:name "SynTViewTools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31728519" ; sc:description """SyntDB: defining orthologues of human long noncoding RNAs across primates. SyntDB - the database of human long non-coding RNAs conserved across primates. Comprehensive collection of long noncoding RNAs (lncRNAs) and their evolutionary relationships in twelve primate species, including human""" ; sc:featureList edam:operation_2422 ; sc:name "SyntDB" ; sc:url "http://syntdb.amu.edu.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0102, edam:topic_0749, edam:topic_0797 ; sc:citation , "pmcid:PMC6892358", "pubmed:31776723" ; sc:description """The JAX Synteny Browser for mouse-human comparative genomics. An interactive web-based conserved synteny browser application. The Jackson Laboratory Synteny Browser. An interactive web-based conserved synteny browser application, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genomes based on the biological attributes of the features. The current implementation for the browser supports the reference genomes of the laboratory mouse and human. Show true orientation of comparison genome relative to reference Always show gene symbols Show anchors. Reference species (outer ring) Mus musculus Homo sapiens""" ; sc:featureList edam:operation_3194, edam:operation_3208, edam:operation_3209 ; sc:license "CC-BY-4.0" ; sc:name "Synteny Browser" ; sc:url "http://syntenybrowser.jax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0749, edam:topic_3295, edam:topic_3512 ; sc:citation ; sc:description """Improved target gene prediction. Abstract Motivation Identifying the genes regulated by a given transcription factor (its “target genes”) is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TF’s binding site and the expression of the gene across a set of tissues. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene. Results We present the T-Gene algorithm, which overcomes these limitations. T-Gene can be used to predict which genes are most likely to be regulated by a TF, and which of the TF’s binding sites are most likely involved in regulating particular genes.""" ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3463 ; sc:name "T-Gene" ; sc:url "http://meme-suite.org/tools/tgene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3379, edam:topic_3473 ; sc:citation , ; sc:description """Automated data extraction software for medical summary using text mining (T-Library). Library project of Physician’s empirical knowledge. Automatic extraction of medical information from medical record. Yamada T, Kondo Y, Momosaki R. 2019. Automated data extraction software for medical summary using text mining (T-Library) PeerJ Preprints 7:e27685v1 https://doi.org/10.7287/peerj.preprints.27685v1""" ; sc:featureList edam:operation_0306 ; sc:name "T-Library" ; sc:url "http://www.picoron.com/tlibrary/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6613037", "pubmed:31510645" ; sc:description "Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis | temporal multi-task sparse canonical correlation analysis | T-MTSCCA: temporal multi-task SCCA model for longitudinal brain imagign genetics" ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "T-MTSCCA" ; sc:url "https://github.com/dulei323/TMTSCCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3168 ; sc:citation , "pubmed:31580402" ; sc:description """an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Release 3: Maria Bogaerts maria.bogaerts@ibe.upf-csic.es, Josefa Gonzalez josefa.gonzalez@ibe.upf-csic.es. T-lex is a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data. Problems during installation? Try our DOCKER file.""" ; sc:featureList edam:operation_3196, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "T-lex3" ; sc:url "https://github.com/GonzalezLab/T-lex3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3047, edam:topic_3170, edam:topic_3489 ; sc:citation , "pubmed:31624839" ; sc:description """user friendly database of tRNA sequences and structures. Discover the best tRNA database available!. There is simplified list of what you can do:. Search by sequence, structure and other properties. See available and generated models""" ; sc:featureList edam:operation_0337, edam:operation_0464, edam:operation_2421, edam:operation_2422 ; sc:name "T-psi-C" ; sc:url "http://tpsic.igcz.poznan.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3390, edam:topic_3418 ; sc:citation , "pmcid:PMC6701161", "pubmed:31389338" ; sc:description "> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'mDAD', 'T1DToolkit.org' | Designing Online and Mobile Diabetes Education for Fathers of Children With Type 1 Diabetes | T1D Toolkit – Manage Diabetes Better | Research QuestionBlog Post FeedbackTech Support | This field is for validation purposes and should be left unchanged" ; sc:name "T1D" ; sc:url "http://T1DToolkit.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "T1TAdb is a database of Type I Toxin-Antitoxin systems." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0346, edam:operation_2488 ; sc:name "T1TAdb" ; sc:url "https://d-lab.arna.cnrs.fr/t1tadb" ; biotools:primaryContact "Fabien Darfeuille", "Nicolas J. Tourasse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6873396", "pubmed:31757212" ; sc:description "TACITuS is a portal, which deals with data pre-processing, selection and, eventually, integration of transcriptomic data coming from diverse sources, such as ArrayExpress." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3435 ; sc:name "TACITuS" ; sc:url "https://tacitus.app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3512, edam:topic_3673 ; sc:citation , "pmcid:PMC6933632", "pubmed:31881832" ; sc:description """A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. TAD-Lactuca is a tool to predict Topologically Associating Domains(TAD) boundary using histone marks information. It was written in Python language, using Random Forests(RF) and Multilayer Perception(MLP)""" ; sc:featureList edam:operation_0303, edam:operation_0438, edam:operation_2404 ; sc:name "TAD-Lactuca" ; sc:url "https://github.com/LoopGan/TAD-Lactuca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC6612822", "pubmed:31510701" ; sc:description "phylogenetic augmentation of microbiome samples enhances phenotype classification | TADA is a new data augmentation technique for classifying phenotypes based on the microbiome. Our algorithm, TADA, uses available data and a statistical generative model to create new samples augmenting existing ones, addressing issues of low-sample-size. In generating new samples, TADA takes into account phylogenetic relationships between microbial species. Adding these synthetic samples to the training set improves the accuracy of downstream classification, especially when the training data have an unbalanced representation of classes" ; sc:name "TADA" ; sc:url "https://github.com/tada-alg/TADA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3512, edam:topic_3517 ; sc:citation , "pubmed:31045203" ; sc:description "Genome-wide supervised learning of non-coding loci associated to complex phenotypes." ; sc:featureList edam:operation_0488, edam:operation_3232, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAGOOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/aitgon/tagoos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3557, edam:topic_3697 ; sc:citation , "pmcid:PMC6292648", "pubmed:30507938" ; sc:description "Tool for analysis of the morphology of microbial colonies." ; sc:featureList edam:operation_0417, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TAMMiCol" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HaydenTronnolone/TAMMiCol" ; biotools:primaryContact "H. Tronnolone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3512, edam:topic_3534 ; sc:citation ; sc:description "Tool for alternative polyadenylation site analysis." ; sc:featureList edam:operation_2575, edam:operation_3798, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAPAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/arefeen/TAPAS" ; biotools:primaryContact "Tao Jiang", "Xinshu Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6549370", "pubmed:31164077" ; sc:description "Pipeline for TARgeted VIRal strain reconstruction from metagenomic data." ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TAR-VIR" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/chjiao/TAR-VIR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:description "BLAST service for the entire “TARA OCEANS” collection, an international project to which many researchers of the institute cooperated. It includes assembled sequences of prokaryotic and eukaryotic fractions." ; sc:featureList edam:operation_0346 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TARA BLAST Service" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.szn.it/tara-oceans-data-blast-service/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3895 ; sc:citation , "pubmed:31053031" ; sc:description "Package for Calibrated Flow Cytometry Analysis." ; sc:featureList edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TASBE Flow Analytics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tasbe.github.io/" ; biotools:primaryContact "Jacob Beal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0821, edam:topic_3297, edam:topic_3474 ; sc:citation ; sc:description """An in-silico method for predicting the thermal activity for xylanases from GH10 and GH11 families. a multi-step method for the classification of xylanases from glycoside hydrolases families 10 and 11 based on their optimum temperature of activity. TAXyl: An in-silico method for predicting the optimum temperature of activity for xylanases from GH10 and GH11 families. Xylanases are involved in lignocellulosic biomass degradation and the enzyme optimum temperature is an essential factor to be considered for choosing an appropriate biocatalyst for specific usage""" ; sc:featureList edam:operation_0474, edam:operation_1777, edam:operation_3092 ; sc:license "MIT" ; sc:name "TAXyl" ; sc:url "https://github.com/mehdiforoozandeh/TAXyl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3063, edam:topic_3324, edam:topic_3384 ; sc:citation , , "pubmed:31838261" ; sc:description """Prediction of multiple drug resistant pulmonary tuberculosis against drug sensitive pulmonary tuberculosis by CT nodular consolidation sign. International partnership for clinical informatics. and advanced research in tuberculosis. Leveraging clinical, genomic, and imaging data.""" ; sc:name "TB Portals" ; sc:url "https://tbportals.niaid.nih.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC6752186", "pubmed:31576231" ; sc:description "Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma." ; sc:featureList edam:operation_0531, edam:operation_3503, edam:operation_3659 ; sc:name "TCGA-LGG" ; sc:url "https://portal.gdc.cancer.gov/projects/TCGA-LGG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3293 ; sc:citation , "pmcid:PMC6756559", "pubmed:31509525" ; sc:description "> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'tree-child', 'BTC' | Generation of Binary Tree-Child phylogenetic networks | Supplementary files for \"Generation of Tree-Child phylogenetic networks\" | If you have pipenv installed, the requirements can be installed by executing pipenv install. Notice however that graphviz must be installed previously (only needed to run the Jupyter notebook). Once installed, the jupyter notebooks can be run with pipenv run jupyter-notebook, and the scripts with pipenv run python script.py | The jupyter notebook can also be run without installing anything:" ; sc:featureList edam:operation_0552, edam:operation_0555, edam:operation_3478 ; sc:name "TCGenerators" ; sc:url "https://github.com/bielcardona/TCGenerators" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0202, edam:topic_0749, edam:topic_3068, edam:topic_3407 ; sc:citation , "pmcid:PMC6874874", "pubmed:31781261" ; sc:description "A Network Pharmacology Approach for Uncovering the Osteogenic Mechanisms of Psoralea corylifolia Linn." ; sc:featureList edam:operation_2436, edam:operation_2489 ; sc:name "TCMSP" ; sc:url "https://old.tcmsp-e.com/tcmsp.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description "T Cell Relation Extraction (TCRE) - Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TCRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hammerlab/t-cell-relation-extraction" ; biotools:primaryContact "Eric Czech" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "The TCRex web tool provides a user-friendly interface to predict the recognition of pathogenic & cancer epitopes by human T cell receptors (TCRs). It can predict TCR–epitope binding based on TCR beta chain information from full repertoire data files from standard files (Immunoseq, MiXCR, etc), and calculates appropriate statistics." ; sc:featureList edam:operation_0252, edam:operation_2403, edam:operation_2995, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "TCRex" ; sc:softwareHelp ; sc:softwareVersion "v0.2.1" ; sc:url "https://tcrex.biodatamining.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0804, edam:topic_2275 ; sc:citation , "pmcid:PMC6787230", "pubmed:31601838" ; sc:description """Structural modelling of TCR-pMHC class I complexes. Structural modeling tool of TCR-pMHC class I complexes. TCRpMHCmodels predicts the three-dimensional structure of TCR-pMHC class I complexes using comparative modelling. Upon submission, this tool automatically selects the best templates and provides within minutes a complete three-dimensional model. The input must include all protein chains from the TCR-pMHC complex (the TCR alpha chain, the TCR beta chain, the peptide chain and the MHC chain), separated by a fasta header. The tool will automatically detect the chain types""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3899 ; sc:name "TCRpMHCmodels" ; sc:url "http://www.cbs.dtu.dk/services/TCRpMHCmodels/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC6612886", "pubmed:31510643" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:TCSM' | Modeling clinical and molecular covariates of mutational process activity in cancer | Tumor Covariate Signature Model (TCSM) | This repository contains the code for reproducing the results on real data from the paper Modeling Clinical and Molecular Covariates of Mutational Process Activity in Cancer, which implements the Tumor Covariate Signature Model (TCSM)" ; sc:featureList edam:operation_0239, edam:operation_3557 ; sc:license "MIT" ; sc:name "TCSM" ; sc:url "https://github.com/lrgr/tcsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6889579", "pubmed:31795943" ; sc:description "A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations." ; sc:name "TCSRWRLD" ; sc:url "http://www.cuilab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "analysis of single and comparative transcriptomes | Download TCW package: www.agcol.arizona.edu/software/tcw or from this site | Transcriptome Computational Workbench | AGCoL : TCW Home : Doc Index : singleTCW Guide : DE Guide : multiTCW Guide : Tour | Description: For single-transcriptome (singleTCW) - similarity search against annotation databases, GO annotation, ORF finding and differential analysis. For multi-transcriptome (multiTCW) - compute similar pairs, provide statistics for pairs, compute clusters, provide statistics for clusters. Both singleTCW and multiTCW provide graphical interfaces for extensive query and display of the results | TCW provides analysis and query for sequences (transcriptome, proteome), and comparison of species sequences. TCW uses Java, mySQL, optionally R, and various External packages. It has been tested on Linux and Mac" ; sc:featureList edam:operation_0224, edam:operation_0436, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "TCW" ; sc:url "https://github.com/csoderlund/TCW" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Multiple sequence alignment program. The main characteristic is that it will allow you to combine results obtained with several alignment methods." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/tcoffee_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Cedric Notredame" ; sc:citation , ; sc:description "Multiple sequence alignment that combines several alignment methods." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CRG", "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/tcoffee/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0622 ; sc:citation , "pmcid:PMC3125728", "pubmed:21558174" ; sc:description "A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "T-Coffee (SIB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.vital-it.ch/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6663192", "pubmed:31410373" ; sc:description "> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Betti', 'resting-state' | Exact topological inference of the resting-state brain networks in twins | Exact Topological Inference (ETI) for Brain Networks | The data/codes presented here is published in [4,5,6]. Using the data, we will show how to construct Betti plots from weighted brain graphs, where the weights are Pearson correlations. Then show how to perform the exact topological inference and obtain the p-value on the Betti plots. The Betti plots are the basic data visualization technique in persistent homology but statistical inference procedure has been lacking in the field [1,2,3]. New exact topological inference framework is developed for determining statistical significance of Betti plots | The codes have been tested with MacBook Pro with MATLAB 2016" ; sc:featureList edam:operation_3216, edam:operation_3562 ; sc:name "TDA" ; sc:url "http://www.stat.wisc.edu/~mchung/TDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC6690219", "pubmed:31428129" ; sc:description "> HOMEPAGE MISSING! | A Software to Identify Complete and Truncated T-DNA Insertions | Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3196 ; sc:name "TDNAscan" ; sc:url "https://github.com/noble-research-institute/TDNAscan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3752 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc:description "TDimpute is a novel transfer learning-based neural network to impute missing gene expression data from DNA methylation data. In the tool, the pan-cancer dataset from TCGA was utilized for training a general model for all cancers, which was then fine-tuned on the target cancer dataset for imputation." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "TDimpute" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://github.com/sysu-yanglab/TDimpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3673 ; sc:description "TE-Tracker is a program for detecting germline transposition events through whole-genome resequencing." ; sc:name "TE-Tracker" ; sc:url "http://www.genoscope.cns.fr/externe/tetracker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3305 ; sc:citation , "pmcid:PMC6860463", "pubmed:31705406" ; sc:description """A Verification Checklist to Reduce Errors in Models and Improve Their Credibility. This is the model verification repository. An application example is uploaded on the repository. This example will be updated further and with other elaborated examples. The TECH-VER checklist consists of five domains: (1) input calculations; (2) event-state (patient flow) calculations; (3) result calculations; (4) uncertainty analysis calculations; and (5) other overall checks (e.g. validity or interface). In health economic literature, checklists or best practice recommendations on model validation credibility always declare verification of the programmed model as a fundamental step, such as ‘is the model implemented correctly and does the implementation accurately represent the conceptual model?’ However, to date, little operational guidance for the model verification process has been given""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3435 ; sc:name "TECH-VER" ; sc:url "https://www.imta.nl/techver" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_1957 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736 ; sc:citation ; sc:description "Graph-based computational method for decomposing protein structures into closed loops." ; sc:featureList edam:operation_0246 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "TEF" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::TEF" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203 ; sc:citation , "pubmed:31095490" ; sc:description "Prediction of essential proteins by integrating network topology, subcellular localization information, gene expression profile and GO annotation data." ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TEGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wzhangwhu/TEGS" ; biotools:primaryContact "Wei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3399 ; sc:citation ; sc:description "TEMPO (TEmporal Modeling of Pathway Outliers) - method for modeling and detecting gene sets with disruption of some temporal pattern of expression." ; sc:featureList edam:operation_2436, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TEMPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcb.cs.tufts.edu/tempo/" ; biotools:primaryContact "Christopher Pietras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC6899341", "pubmed:31824778" ; sc:description "TEffectR is an R package for studying the potential effects of transposable elements on gene expression with linear regression model." ; sc:featureList edam:operation_2495, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "TEffectR" ; sc:url "https://github.com/karakulahg/TEffectR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199 ; sc:citation , "pubmed:31381222" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'maizeTE_variation' | Transposable elements contribute to dynamic genome content in maize | Structural transposable element (TE) annotation of multiple maize genomes | TEs along a region of the genome: | We reconstruct the history of TEs nesting into each other. For example, the blue TE on the left inserted first, and then was disrupted by the insertion of green and yellow TEs" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3216 ; sc:name "TEs" ; sc:url "https://mcstitzer.github.io/maize_TEs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0736, edam:topic_0749, edam:topic_0780, edam:topic_3293 ; sc:citation ; sc:description """lineage-level classification of transposable elements using conserved protein domains. Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH""" ; sc:featureList edam:operation_3478 ; sc:name "TEsorter" ; sc:url "https://github.com/zhangrengang/TEsorter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:31665425" ; sc:description """an expanded motif database for DNA shape features of transcription factor binding sites. Responsive Bootstrap 4 Admin & Dashboard Template. TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs). These structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. The DNA shape features were predicted using our recently published high-throughput method (Zhou et al. NAR 2013) and visualized in the form of heat maps. Users can download these DNA shape feature data and perform further analysis, for example, to identify which DNA shape feature(s) at which position(s) in the target DNA contribute to the DNA binding specificity of a TF. Users can also compare DNA shape profiles, both qualitatively and quantitatively, between two TF datasets from the database, or between a set of uploaded sequences and a TF from the database""" ; sc:featureList edam:operation_0337, edam:operation_0445, edam:operation_3092, edam:operation_3891, edam:operation_3894 ; sc:name "TFBSshape" ; sc:url "https://tfbsshape.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pubmed:31746988" ; sc:description """Constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. It seems like you are using Internet Explorer, which is not supported yet. Please switch to Chrome , Firefox , or Safari""" ; sc:featureList edam:operation_0463, edam:operation_3083, edam:operation_3792 ; sc:name "TFmiR2" ; sc:url "http://service.bioinformatik.uni-saarland.de/tfmir2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3512, edam:topic_3674 ; sc:citation , "pubmed:31754708" ; sc:description "TFregulomeR comprises of a comprehensive compendium of transcription factor binding sites (TFBSs) derived from the MethMotif and GTRD, as well as the ready-to-use functionality in R language facilitating data access, integration and analysis. The binding motifs predicted in-silico from MethMotif and GTRD describe cell specific transcription factor (TF) binding propensities, while the DNA methylation profiles from MethMotif portray a second epigenetic dimension in TF binding events. The whole toolbox allows a better understanding of the TF binding propensities in a cell-specific manner." ; sc:featureList edam:operation_0268, edam:operation_0445, edam:operation_3222, edam:operation_3900, edam:operation_3903 ; sc:name "TFregulomeR" ; sc:url "https://github.com/benoukraflab/TFregulomeR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0749, edam:topic_3168 ; sc:citation ; sc:description "TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads." ; sc:featureList edam:operation_0525, edam:operation_3183, edam:operation_3198, edam:operation_3216 ; sc:name "TGS-GapCloser" ; sc:url "https://github.com/BGI-Qingdao/TGS-GapCloser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "Rapid Reconstruction of Time-varying Gene Regulatory Networks with Limited Main Memory | Abstract Reconstruction of time-varying gene regulatory networks underlying a time-series gene expression data is a fundamental challenge in the computational systems biology. The challenge increases multi-fold if the target networks need to be constructed for hundreds to thousands of genes. There have been constant efforts to design an algorithm that can perform the reconstruction task correctly as well as can scale efficiently (with respect to both time and memory) to such a large number of genes. However, the existing algorithms either do not offer time-efficiency, or they offer it at other costs memory-inefficiency or imposition of a constraint, known as the ‘smoothly time-varying assumption’" ; sc:featureList edam:operation_0277, edam:operation_1781, edam:operation_3439 ; sc:name "TGS-Lite" ; sc:url "https://github.com/sap01/TGS-Lite-supplem/blob/master/README.md" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3067 ; sc:citation , "pmcid:PMC6697955", "pubmed:31419946" ; sc:description "Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries | *: Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human body parts are crucial for building medical text mining applications. To achieve this, we establish a mapping system consisting of a Wikipedia-based scoring algorithm and a named entity normalization method (NEN). The mapping system makes full use of information available on Wikipedia, which is a comprehensive Internet medical knowledge base" ; sc:featureList edam:operation_2429, edam:operation_3280, edam:operation_3432 ; sc:name "THBP" ; sc:url "https://github.com/xuyanbuaa/THBP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3055 ; sc:citation , , ; sc:description "Testing Haplotype Effects In Association Studies" ; sc:license "GPL-3.0" ; sc:name "THESIAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.1" ; sc:url "https://github.com/daissi/thesias" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0605, edam:topic_0625, edam:topic_3676 ; sc:citation , "pmcid:PMC6795695", "pubmed:31649706" ; sc:description """Bioinformatics pipeline for the analysis of TILLinG mutants in conjunction with the new optimised reference sequence for tetraploid wheat. This tool consists of TILLING populations developed in tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and John Innes Centre.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227, edam:operation_3229, edam:operation_3431 ; sc:name "TILLinG" ; sc:url "http://wheat-tilling.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0821, edam:topic_3314 ; sc:citation , "pubmed:31568581" ; sc:description """A Code for Modeling and Generating Electric Fields-Features and Applications to Enzymatic Reactivity. TITAN (elecTric fIeld generaTion And maNipulation) is being developed by:""" ; sc:featureList edam:operation_0386, edam:operation_2476 ; sc:name "TITAN" ; sc:url "https://titan-code.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0593, edam:topic_0634 ; sc:citation ; sc:description "Computational tool to assess titin’s role as a disease gene." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TITINdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://fraternalilab.kcl.ac.uk/TITINdb/" ; biotools:primaryContact "Franca Fraternali" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3379, edam:topic_3421 ; sc:citation , "pmcid:PMC6676499", "pubmed:31404154" ; sc:description "The use of patient-specific equipoise to support shared decision-making for clinical care and enrollment into clinical trials | Total Knee Replacement (TKR) Decision Support | TMC Total Knee Replacement (TKR) Math Equipoise | Welcome to the Knee Arthritis Treatment Tool" ; sc:featureList edam:operation_3557, edam:operation_3659 ; sc:name "TKR" ; sc:url "http://medicalequipoise.com/tkrclinician" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3300 ; sc:citation , "pmcid:PMC6649004", "pubmed:31459527" ; sc:description "Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion | TM-IMC: Text Mining and Induce Matrix Completion for GPCR function prediction | TM-IMC is an algorithm for automated annotation of Gene Ontology (GO) term for G protein-coupled receptors (GPCRs) using features derived from text mining and induced matrix completion of GPCR-GO associatation matrix" ; sc:featureList edam:operation_0267, edam:operation_0306, edam:operation_0480 ; sc:name "TM-IMC" ; sc:url "https://zhanglab.ccmb.med.umich.edu/TM-IMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:31676507" ; sc:description "A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments." ; sc:featureList edam:operation_3196, edam:operation_3200, edam:operation_3435, edam:operation_3800 ; sc:name "TM3 seq" ; sc:url "https://lufpa.github.io/TM3Seq-Pipeline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pubmed:31504188" ; sc:description "Phylogenetic Tree-based Microbiome Association Test | Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals" ; sc:featureList edam:operation_0325, edam:operation_0499, edam:operation_3478 ; sc:name "TMAT" ; sc:url "http://healthstat.snu.ac.kr/software/tmat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3176, edam:topic_3368 ; sc:citation , "pubmed:31490686" ; sc:description "> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'iBIOMES', 'Lite', 'iBIOMES Lite', 'nucleosome' | TMB Library of Nucleosome Simulations | Nucleosomes are the fundamental building blocks of chromatin, the biomaterial that houses the genome in all higher organisms. A nucleosome consists of 145-147 base pairs of DNA wrapped 1.7 times around eight histones. Given a four-letter code (A, C, G, T), there are approximately 4147 or 1088 oligonucleotides that can form a nucleosome. Comparative, rather than comprehensive, studies are required. Here we introduce the TMB Library of nucleosome simulations and present a meta-analysis of over 20 μs of all atom molecular dynamics simulations representing 518 different realizations of the nucleosome. The TMB Library serves as a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES Lite as a tool for managing a laboratory's simulation library" ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_2476 ; sc:name "TMB" ; sc:url "http://dna.engr.latech.edu/~tmbshare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0602, edam:topic_0736, edam:topic_0820 ; sc:citation , "pubmed:31682836" ; sc:description "A Web Tool for Predicting Stability of Transmembrane α-Helix Association." ; sc:featureList edam:operation_0279, edam:operation_2415, edam:operation_3767 ; sc:name "TMPfold" ; sc:url "https://opm.phar.umich.edu/tmpfold_server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC6727351", "pubmed:31484546" ; sc:description "improving reference-free cell composition estimation by cross-cell type differential analysis | Tools for the analysis of heterogeneous tissues | This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. improve variable selection in reference-free deconvolution | DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, GeneExpression, GeneTarget, MethylationArray, Microarray, Software" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3629 ; sc:license "GPL-2.0" ; sc:name "TOAST" ; sc:url "https://bioconductor.org/packages/TOAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation." ; sc:featureList edam:operation_0337, edam:operation_0445, edam:operation_3222 ; sc:license "MIT" ; sc:name "TOBIAS" ; sc:softwareHelp ; sc:url "https://github.com/loosolab/TOBIAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0749, edam:topic_3300, edam:topic_3489 ; sc:citation , "pmcid:PMC6890663", "pubmed:31796752" ; sc:description """database of traits of fish to promote advances in fish aquaculture. toff-project – Database of Traits OF Fish. TOFF (i.e. Traits OF Fish) is a curated database focusing on functional trait information for fish that aims at bringing together behavioral, morphological, phenological, and physiological traits coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. We ultimately aim to provide an inclusive and accessible data resource to facilitate advances in fish research""" ; sc:featureList edam:operation_3435, edam:operation_3907 ; sc:name "TOFF" ; sc:url "http://toff-project.univ-lorraine.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3384, edam:topic_3452 ; sc:citation , "pmcid:PMC3493036", "pubmed:23127075" ; sc:description "Proton Monte Carlo platform for research and clinical applications." ; sc:featureList edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "TOPAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.topasmc.org/home" ; biotools:primaryContact "Joseph Perl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3314, edam:topic_3318 ; sc:citation , "pmcid:PMC6377808", "pubmed:30609382" ; sc:description "Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology." ; sc:isAccessibleForFree true ; sc:name "TOPAS-nBio" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://gray.mgh.harvard.edu/software/258-topas-nbio" ; biotools:primaryContact "Joost Verburg", "Thomas Bortfeld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31804057" ; sc:description """Dose-Response Metabolomics to Understand Biochemical Mechanisms and Off-Target Drug Effects with the TOXcms Software. Job opportunities are available""" ; sc:featureList edam:operation_0490, edam:operation_3435, edam:operation_3891 ; sc:name "TOXcms" ; sc:url "http://pattilab.wustl.edu/software/toxcms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "Therapeutic Peptide Design DataBase." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TP-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dyn.life.nthu.edu.tw/design" ; biotools:primaryContact "Chung-Yu Lan", "Hua-Wen Fu", "Lee-Wei Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3050 ; sc:citation , "pubmed:31471976" ; sc:description "measuring functional diversity across scales based on TPD with R | Methods for Measuring Functional Diversity Based on Trait Probability Density | Tools to calculate trait probability density functions (TPD) at any scale (e.g. populations, species, communities). TPD functions are used to compute several indices of functional diversity, as well as its partition across scales. These indices constitute a unified framework that incorporates the underlying probabilistic nature of trait distributions into uni- or multidimensional functional trait-based studies. See Carmona et al. (2016) for further information" ; sc:license "GPL-3.0" ; sc:name "TPD" ; sc:url "https://CRAN.R-project.org/package=TPD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pubmed:31099386" ; sc:description "Tumor Purity Estimation from SNVs." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TPES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/l0ka/tpes.git" ; biotools:primaryContact "Alessio Locallo", "Francesca Demichelis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Software to quantify mRNA abundance of genomic features." ; sc:featureList edam:operation_1812, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TPMCalculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ncbi/TPMCalculator" ; biotools:primaryContact "David Landsman", "Leonardo Mariño-Ramírez", "Lorinc Pongor", "Roberto Vera Alvarez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0820, edam:topic_3172, edam:topic_3474 ; sc:citation , , , "pmcid:PMC6956793", "pmcid:PMC7703753", "pubmed:31165141", "pubmed:31702773", "pubmed:34477909" ; sc:description "TPOT stands for Tree-based Pipeline Optimization Tool. Consider TPOT your Data Science Assistant. TPOT is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "TPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EpistasisLab/tpot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:20013374", "pubmed:20101611", "pubmed:21082435", "pubmed:25631240" ; sc:description "Institute for Systems Biology \"Trans-Proteomic Pipeline\"" ; sc:name "Trans-Proteomic Pipeline (TPP)" ; sc:url "http://tools.proteomecenter.org/software.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "a scalable workflow for predicting cancer of unknown primary based on next-generation transcriptome profiling | Cancer of unknown primary site (CUP) accounts for 5% of all cancer diagnoses. These patients may benefit from more precise treatment when primary cancer site was identified. Advances in high-throughput sequencing have enabled cost-effective sequencing the transcriptome for clinical application. Here, we present a free, scalable and extendable software for CUP predication called TRANSCUP, which enables (1) raw data processing, (2) read mapping, (3) quality report, (4) gene expression quantification, (5) random forest machine learning model building for cancer type clas-sification. TRANSCUP achieved high accuracy, sensitivity and specificity for tumor type classifica-tion based on external RNA-seq datasets. It has potential for broad clinical application for solving the CUP problem" ; sc:featureList edam:operation_2495, edam:operation_3800 ; sc:license "MIT" ; sc:name "TRANSCUP" ; sc:url "https://github.com/plsysu/TRANSCUP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6908688", "pubmed:31831861" ; sc:description "TRANSNAP is a web database providing comprehensive information on Japanese pear transcriptome." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3672 ; sc:name "TRANSNAP" ; sc:url "http://plantomics.mind.meiji.ac.jp/nashi/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830 ; sc:citation ; sc:description "Software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing." ; sc:featureList edam:operation_0230 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TRAPeS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/YosefLab/TRAPeS" ; biotools:primaryContact "Shaked Afik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3393, edam:topic_3855 ; sc:citation ; sc:description """The TRAX Light-Rail Train Air Quality Observation Project. - Department of Atmospheric Sciences. Department of Atmospheric Sciences. College of Mines and Earth Sciences. Monitoring Air Quality Along UTA TRAX Lines.""" ; sc:featureList edam:operation_2428, edam:operation_3799 ; sc:name "TRAX" ; sc:url "http://utahaq.chpc.utah.edu/aq/cgi-bin/mobile_data.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31145698" ; sc:description "Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data." ; sc:featureList edam:operation_3215, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TRC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/dhyeonyu/software" ; biotools:primaryContact "Donghyeon Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation , "pmcid:PMC7525938", "pubmed:32993478" ; sc:description "T-cell Receptor/Immunoglobulin Profiler (TRIP)" ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "tripr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/TRIP" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3673 ; sc:citation ; sc:description "Chromosome-scale sequence assembly of Triticeae genomes with open-source tools." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TRITEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tritexassembly.bitbucket.io" ; biotools:primaryContact "Martin Mascher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3557 ; sc:citation ; sc:description "Web-tool for prediction of protein–protein Interactions in human Transcriptional Regulation." ; sc:featureList edam:operation_2492, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TRI_tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.vin.bg.ac.rs/180/tools/tfpred.php" ; biotools:primaryContact "Nevena Veljkovic", "Vladimir Perovic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "Tool for visualizing and analyzing cancer hallmarks in signaling networks." ; sc:featureList edam:operation_2497, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "EPL-1.0" ; sc:name "TROVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/trove2017/Trove" ; biotools:primaryContact "Huey Eng Chua", "Sourav S. Bhowmick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3047 ; sc:citation , "pubmed:31765328" ; sc:description """Mapping spatio-temporal dynamics of single biomolecules in living cells. TRamWAy helps analyzing single molecule dynamics. It infers the diffusivity, drift, force and potential energy across space and time""" ; sc:featureList edam:operation_2429, edam:operation_3436 ; sc:name "TRamWAy" ; sc:url "http://github.com/DecBayComp/TRamWAy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0736, edam:topic_3512 ; sc:citation ; sc:description "Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "TSDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://shenlab.sols.unlv.edu/shenlab/software/TSD/transcript_display.html" ; biotools:primaryContact "Kenneth Watanabe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3337, edam:topic_3517 ; sc:citation , "pubmed:31680168" ; sc:description """a trait-tissue association map for human complex traits and diseases. deTSDB, deTS, TSEA, tissue-specificity. TSEA-DB provides a comprehensive reference for trait-associated tissues. A systematic tissue-specific enrichment analysis (TSEA) has been conducted using deTS to infer tissues in which trait-associated genes are enriched. Two reference tissue panels are collected: the GTEx v7 panel (47 tissues) and the ENCODE panel (44 tissues). A total of 5019 GWAS summary statistics data sets for human complex traits and diseases (435 + 161 GWAS data sets from the non-UKBB panel and 4423 data sets from the UKBB panel) have been analyzed for their causal tissues. Content 1. 1. Collection and processing of GWAS summary statistics for complex traits and diseases. The Multi-Trait Collection (MTC) traits were previously reported in the work by Liu et al., 2019""" ; sc:featureList edam:operation_2428, edam:operation_2436, edam:operation_3196, edam:operation_3232, edam:operation_3431 ; sc:name "TSEA-DB" ; sc:url "https://bioinfo.uth.edu/TSEADB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """Translational Bioinformatics Tool Suite For Network Analysis And Mining. An R software for Gene Co-Expression Analysis. Gene co-expression network (GCN) mining aims to mine gene modules with highly correlated expression profiles across sample cohorts. It may help to reveal latent molecular interactions, identify novel gene functions, pathways and drug targets, as well as providing disease mechanistic insights on for biological researchers. TSUNAMI is developed to allow biological researchers with no programing background to perform GCN mining themselves. Users can get access to our online service from http://spore.ph.iu.edu:3838/zhihuan/TSUNAMI/""" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3557, edam:operation_3766 ; sc:name "TSUNAMI" ; sc:url "https://github.com/huangzhii/TSUNAMI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0804, edam:topic_2640 ; sc:citation , "pubmed:31437642" ; sc:description "A computational tool for the specific prediction of tumor T cell antigens | Nowadays, cancer is considered a global pandemic and millions of people die every year because this disease remains a challenge for the world scientific community. Even with the efforts made to combat it, there is a growing need to discover and design new drugs and vaccines. Among these alternatives, antitumor peptides are a promising therapeutic solution to reduce the incidence of deaths caused by cancer. In the present study, we developed TTAgP, an accurate bioinformatic tool that uses the random forest algorithm for antitumor peptide predictions, which are presented in the context of MHC class I. The predictive model of TTAgP was trained and validated based on several features of 922 peptides" ; sc:featureList edam:operation_0252, edam:operation_3631 ; sc:name "TTAgP" ; sc:url "https://github.com/reumandc/tsvr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3068 ; sc:citation ; sc:description """A FIJI Macro for quantifying pattern in extracellular matrix. Welcome to The Worklfow Of Matrix BioLogy Informatics (TWOMBLI). Twombli is a Fiji plugin. To get started download the TWOMBLI folder to your computer. Your browser does not support the video tag""" ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3799 ; sc:name "TWOMBLI" ; sc:url "https://github.com/wershofe/TWOMBLI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "In the TXG-MAPr, users can analyze dose- and time-response curves, compound correlation plots and functional annotation of the WGCNA modules to derive mechanistic information of the toxicity. In addition, we included the prediction of transcription factor activities, as well as physical interactions between downstream proteins encoded by the transcriptome, which might be useful in analyzing the perturbations triggered by exposure with toxic compounds. Users can investigate module perturbation of the TG-GATEs compounds by looking at the module eigengene scores (EGS)" ; sc:featureList edam:operation_2945 ; sc:name "TXG-MAPr" ; sc:url "https://txg-mapr.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2275, edam:topic_3385, edam:topic_3452 ; sc:citation , "pubmed:31768058" ; sc:description """In situ structure determination at nanometer resolution using TYGRESS. TYGRESS:Tomography-Guided 3D Reconstruction of Subcellular Structures. Tomography-Guided 3D Reconstruction of Subcellular Structures (TYGRESS) is a hybrid method, which combines the advantageous features of both cryo-electron tomography and single particle cryo-EM to achieve higher resolution than before of complex subcellular structures within their native environment. Back to UT Southwestern Back to UTSW Labs""" ; sc:featureList edam:operation_0478, edam:operation_3458 ; sc:name "TYGRESS" ; sc:url "https://www.utsouthwestern.edu/labs/nicastro/tygress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_3301 ; sc:citation , "pmcid:PMC6522516", "pubmed:31097708" ; sc:description "Automated high-throughput platform for state-of-the-art genome-based taxonomy." ; sc:featureList edam:operation_0544, edam:operation_3431, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TYGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tygs.dsmz.de" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0637, edam:topic_2885, edam:topic_3174 ; sc:citation , "pmcid:PMC6805505", "pubmed:31638897" ; sc:description """A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms. The "tranucleotide-derived Z-value Manhattan Distance” (TZMD) approach profiles genomic composition with high resolution, which can distinguish bacteria at even strain level""" ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3435 ; sc:name "TZMD" ; sc:url "https://github.com/Yizhuangzhou/TZMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Targeted Bisulfite Sequencing Analysis Pipeline A pipeline to analyze the data obtained from targeted bisulfite sequencing through the ion-torrent platform. TaBSAP is a pipeline to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step and enables a researcher to analyze the methylation levels of their samples straight away. It's main features are: -Bisulfite mapping and methylation calling in one single step -Supports single-end read alignments -Alignment seed length, number of mismatches etc. are adjustable -The output gives heatmap with categories.""" ; sc:featureList edam:operation_3186, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TaBSAP" ; sc:softwareVersion "1.0.0", "1.0.1", "1.0.2" ; sc:url "https://github.com/pradyumnasagar/TaBSAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_3512 ; sc:citation , "pubmed:30456524" ; sc:description "Web platform for taxonomic profile-based fungal gene prediction." ; sc:featureList edam:operation_0476, edam:operation_3460, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TaF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://taf.genome-report.com/" ; biotools:primaryContact "Theragen Etex Bio Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3489 ; sc:citation , "pubmed:31846397" ; sc:description """open-source mobile software for distributed studies of hearing. TabSINT is an open source platform for administering tablet based hearing-related exams, as well as general-purpose questionnaires. It is meant to be flexible, easy-to-use, and useful for administrators who manage studies of all sizes. Open source platform for hearing assessments,and general purpose questionnaires""" ; sc:name "TabSINT" ; sc:url "http://tabsint.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:31410856" ; sc:description "A Tool to Analyze the Binding Affinity | Taba: Tool to Analyze Binding Affinity | Taba is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. You can use a higher version as well" ; sc:featureList edam:operation_0482, edam:operation_2950 ; sc:name "Taba" ; sc:url "https://github.com/azevedolab/taba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC6447449", "pubmed:30936560" ; sc:description "Computational tool that reveals vast protein modification landscapes from large tandem mass spectrometry datasets." ; sc:featureList edam:operation_0417, edam:operation_3645, edam:operation_3649 ; sc:name "TagGraph" ; sc:url "http://kronos.stanford.edu/TAG_GRAPH/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0780 ; sc:citation ; sc:description "Tool for predicting conserved microRNA targets and target mimics in plants." ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TarHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://tarhunter.genetics.ac.cn/" ; biotools:primaryContact "Xuan Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3518, edam:topic_3519 ; sc:citation , "pubmed:31851778" ; sc:description """Long noncoding RNA ZFAS1 promotes tumorigenesis and metastasis in nasopharyngeal carcinoma by sponging miR-892b to up-regulate LPAR1 expression. Search for predicted microRNA targets in mammals. 1. Select a species Human Mouse Rat Chimpanzee Rhesus Cow Dog Opossum Chicken Frog. 2. Enter a human gene symbol (e.g. "Hmga2"). TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer , 7mer , and 6mer sites that match the seed region of each miRNA.""" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3223 ; sc:name "TargetScanHuman" ; sc:url "http://www.targetscan.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3336 ; sc:citation ; sc:description "Connecting genetics and drug discovery | This is the Target Gene Notebook source-code repository | to build TGN backend against git repository:" ; sc:featureList edam:operation_3196 ; sc:license "MIT" ; sc:name "Target Gene Notebook" ; sc:url "http://tgn.broadinstitute.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6905110", "pubmed:31857821" ; sc:description """in-field counting of wheat spikes with context-augmented local regression networks. This is the repository for TasselNetv2, presented in:""" ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3799 ; sc:name "TasselNetv2" ; sc:url "https://tinyurl.com/TasselNetv2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0781, edam:topic_3520 ; sc:citation ; sc:description "An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples." ; sc:featureList edam:operation_3460, edam:operation_3649, edam:operation_3767 ; sc:name "TaxIt" ; sc:url "https://gitlab.com/rki_bioinformatics/TaxIt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0140, edam:topic_2229, edam:topic_3520 ; sc:citation , "pmcid:PMC6902019", "pubmed:31849937" ; sc:description """An Atlas of the Subcellular Proteome of Human T Cells. This is a curated an in-depth subcellular proteomic map of primary human CD4+ T cells, divided into cytosolic, nuclear and membrane fractions generated by an optimized fractionation and HiRIEF-LC-MS MS workflow for limited amounts of primary cells. The subcellular proteome of T cells was mapped under steady state conditions, as well as upon 15 min and 1 h of T cell receptor (TCR) stimulation, respectively. We quantified the subcellular distribution of 6,572 proteins and identified a subset of 237 potentially translocating proteins, including both well-known examples and novel ones. Microscopic validation confirmed the localization of selected proteins with previously known and unknown localization, respectively.""" ; sc:featureList edam:operation_2428, edam:operation_2489, edam:operation_3630 ; sc:name "TcellSubC" ; sc:url "https://tcellatlas.kaust.edu.sa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3519 ; sc:citation , "pmcid:PMC6715295", "pubmed:31425522" ; sc:description "Deconvolving the effects of pervasive and autonomous transcription of transposable elements | TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data | #About TeXP is a pipeline for quantifying abundances of Transposable Elements transcripts from RNA-Seq data. TeXP is based on the assumption that RNA-seq reads overlapping Transposable Elements is a composition of pervasive transcription signal and autonomous transcription of Transposable Elements" ; sc:featureList edam:operation_0372, edam:operation_3233, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "TeXP" ; sc:url "https://github.com/gersteinlab/texp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0769, edam:topic_2258, edam:topic_2840, edam:topic_3474 ; sc:citation , "pubmed:31612715" ; sc:description "A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows." ; sc:featureList edam:operation_0337, edam:operation_3695 ; sc:license "CC-BY-4.0" ; sc:name "TeachOpenCADD-KNIME" ; sc:url "https://hub.knime.com/volkamerlab/space/TeachOpenCADD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC3436826", "pubmed:22962446" ; sc:description "Telescope is an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. It allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Moreover, output files are rendered in HTML in real time, allowing the use of markdown and rich-text features. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted." ; sc:featureList edam:operation_0310 ; sc:name "Telescope" ; sc:url "https://github.com/Mangul-Lab-USC/telescope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6786656", "pubmed:31568525" ; sc:description """Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq. It can be used for Statistical Performance of TE Quantification Methods. All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.""" ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3198, edam:operation_3800, edam:operation_3891 ; sc:license "MIT" ; sc:name "Telescope" ; sc:softwareHelp ; sc:url "https://github.com/mlbendall/telescope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6540518", "pubmed:31138115" ; sc:description "In silico estimation of telomere content and composition from cancer genomes." ; sc:featureList edam:operation_3435, edam:operation_3798, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TelomereHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html" ; biotools:primaryContact "Lina Sieverling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3315 ; sc:citation , "pubmed:30957838" ; sc:description "Package to study genetic variation in tera-scale genotypes as it performs PCA of large-scale datasets." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TeraPCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aritra90/TeraPCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3512, edam:topic_3542 ; sc:citation , "pubmed:31732725" ; sc:description """Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. This repository contains data and materials linked to the Terminome-Seq project. The preprint of the manuscript is 2019_Terminome-Seq.pdf or it can be downloaded from the Bioarxiv website here https://www.biorxiv.org/content/10.1101/621938v2""" ; sc:featureList edam:operation_2441, edam:operation_2488, edam:operation_3902 ; sc:name "Terminome-seq" ; sc:url "https://github.com/BenoitCastandet/Terminome_Seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3316, edam:topic_3810 ; sc:citation , "pmcid:PMC6764783", "pubmed:31565027" ; sc:description "Terra Populus' Architecture for Integrated Big Geospatial Services | Boundaries are missing for the selected sample geography. Please select a different sample geography" ; sc:name "Terra" ; sc:url "https://data.terrapop.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:31392327" ; sc:description "a set theoretical utility for exploring sequence variant data | Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data | Tersect is a command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data. The tool generates index files based on provided variant data (VCF files) which can then be used to rapidly execute flexible set theoretical queries and output the resulting lists of variants in selected regions" ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3798 ; sc:license "MIT" ; sc:name "Tersect" ; sc:url "https://github.com/tomkurowski/tersect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2269 ; sc:citation , "pmcid:PMC6663104", "pubmed:31360055" ; sc:description "A Set of Stata Commands for Confirmatory Tetrad Analysis | This respository contains three Stata commands for conducting Confirmatory Tetrad Analysis (CTA). In addition, the repository is set up so that the commands can be installed within Stata. Simply type \"net install tetrad, from(https://github.com/sbauldry/tetrad/raw/master) replace\" without the quotes in Stata's command window. These commands are introduced in Bauldry and Bollen (2016)" ; sc:name "Tetrad" ; sc:url "https://github.com/sbauldry/tetrad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC6836478", "pubmed:31699079" ; sc:description """a web-based prediction tool for discriminating thalassemia trait and iron deficiency anemia. ThalPred: Development of Decision Model for Discriminating Thalassemia Trait and Iron Deficiency Anemia""" ; sc:name "ThalPred" ; sc:url "http://codes.bio/thalpred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ThaleMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "4.3.1-20210109" ; sc:url "https://bar.utoronto.ca/thalemine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3063, edam:topic_3071 ; sc:citation ; sc:description "Web-based data management tool for health and medical research." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "The Ark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sphinx.org.au/the-ark/" ; biotools:primaryContact "Adrian Bickerstaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3307, edam:topic_3318 ; sc:citation , "pubmed:31117786" ; sc:description "Theoretical Reims-Tomsk Spectral data." ; sc:featureList edam:operation_0386, edam:operation_0476, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TheoReTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://theorets.univ-reims.fr" ; biotools:primaryContact "Andrei Nikitin", "Michael Rey", "Vladimir G. Tyuterev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pubmed:31555805" ; sc:description "the Therapeutic Structural Antibody Database | The Structural Antibody Database | (Therapeutic Structural Antibody Database) | Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link] | SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]" ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:name "Thera-SAbDab" ; sc:url "http://opig.stats.ox.ac.uk/webapps/therasabdab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:31078672" ; sc:description "High-throughput analysis software for non-invasive thermal assessment of laboratory mic." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ThermoLabAnimal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ThermoLabAnimal/ThermoLabAnimal_FreeVersion" ; biotools:primaryContact "Paulo Aguiar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC6752863", "pubmed:31483777" ; sc:description "Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction | This is a TensorFlow implementation accompanying our paper. This codebase is based on Shreshthgandhi's Tensorflow implementation of the cdeepbind model. The framework of model training and testing have beed adopted with minor changes. Other code files have been modified and re-structured with changes specific to our model. And the folder, scripts/RNAsubopt is a copy of RNAsubopt from the ViennaRNA project | We used two datasets to evaluate our model. The following datsets were used for training our models | You can download the datasets from the corresponding website. After that, you should prepare the data used in the training code according to the steps below. We use the CLIP-seq dataset as an example | BTW, The ThermoNet implementation is available at invitro bin deepbind_model utils_update.py" ; sc:featureList edam:operation_0278, edam:operation_3901, edam:operation_3902 ; sc:name "ThermoNet" ; sc:url "https://github.com/suyufeng/ThermoNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML" ; sc:featureList edam:operation_3215, edam:operation_3434, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ThermoRawFileParser" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/compomics/ThermoRawFileParser" ; biotools:primaryContact "Computational Omics and Systems Biology Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3520 ; sc:citation , "pubmed:31363206" ; sc:description "quantifying phosphopeptide positional isomers | The human phosphorylation regulatory network represents a complex signaling cascade where proteins can be phosphorylated at multiple sites resulting in different functional states. Here we present Thesaurus, a hybrid search engine that detects, localizes, and quantifies novel positional isomers using site-specific fragment ions directly from data independent acquisition mass spectrometry experiments. This software works for several PTMs in addition to phosphorylation. Check out our paper describing Thesaurus and what it can do at Nature Methods (Searle et al, 2019)!" ; sc:featureList edam:operation_0417, edam:operation_3216, edam:operation_3629 ; sc:name "Thesaurus" ; sc:url "http://bitbucket.org/searleb/thesaurus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "Tool for determining the threshold in short RNA-seq datasets." ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Threshold-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cm.jefferson.edu/threshold-seq/" ; biotools:primaryContact "Isidore Rigoutsos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Software for scalable execution of portable pipelines on the cloud." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tibanna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/4dn-dcic/tibanna" ; biotools:primaryContact "Burak H. Alver", "Peter J. Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6612900", "pubmed:31510677" ; sc:description "efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain | TideHunter is an efficient and sensitive tandem repeat detection and consensus calling tool which is designed for tandemly repeated long-read sequence (INC-seq, R2C2, NanoAmpli-Seq)" ; sc:featureList edam:operation_3192, edam:operation_3195, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "TideHunter" ; sc:url "https://github.com/yangao07/TideHunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3277, edam:topic_3678 ; sc:citation , "pmcid:PMC6833352", "pubmed:31709289" ; sc:description "Time-energy measured data on modern multicore systems running shared-memory applications." ; sc:name "Time-energy" ; sc:url "https://github.com/dloghin/multicores-time-energy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3168, edam:topic_3386 ; sc:citation , "pubmed:31523773" ; sc:description "Scripts for analyzing transposon sequencing data used by the Whiteley lab | Custom scripts for analyzing (parsing, mapping, and tallying) Tn-seq reads and determining differentially abundant transposon insertion mutants | The scripts contained herein can be used to automatically analyze high-throughput (Illumina) sequencing reads derived from transposon-genome junctions" ; sc:featureList edam:operation_1812, edam:operation_3192, edam:operation_3461 ; sc:name "Tn-seq" ; sc:url "https://github.com/WhiteleyLab/Tn-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0637 ; sc:citation , "pmcid:PMC6323299", "pubmed:30624651" ; sc:description "Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TogoGenome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://togogenome.org/" ; biotools:primaryContact "Keita Urashima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0637, edam:topic_3489 ; sc:citation , "pmcid:PMC6323299", "pubmed:30624651" ; sc:description "Generic Web framework for rendering an information block." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TogoStanza" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://togostanza.org/" ; biotools:primaryContact "Keita Urashima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Genome browser for tomato (cultivar Heinz 1706 version 2.50) that includes RNAseq tags, EST and Tentative Consensus sequences to investigate the functional and structural annotation of the tomato genome." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Tomato Genome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/cgi-bin/gb2/gbrowse/SL250/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Tool for selecting high-quality top-down proteomics mass spectra." ; sc:featureList edam:operation_3627, edam:operation_3637, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Top-Down Garbage Collector" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://patternlabforproteomics.org/tdgc/" ; biotools:primaryContact "Diogo B. Lima", "Julia Chamot-Rooke", "Paulo C. Carvalho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6858545", "pubmed:31591578" ; sc:description "A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3458 ; sc:license "GPL-3.0" ; sc:name "Topaz" ; sc:url "http://topaz.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models." ; sc:featureList edam:operation_0302, edam:operation_3458, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "Topaz-Denoise" ; sc:url "https://github.com/tbepler/topaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6437914", "pubmed:30922379" ; sc:description "R package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "Topconfects" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/topconfects.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3308 ; sc:citation , "pubmed:31874858" ; sc:description """a graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology. Topological-tumour-graphs""" ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3659 ; sc:name "Topological Tumor Graphs" ; sc:url "https://github.com/Henrik86/Topological-tumour-graphs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A post sequencing QC tool for Oxford Nanopore sequencers." ; sc:featureList edam:operation_3218 ; sc:name "ToulligQC" ; sc:url "https://github.com/GenomicParisCentre/toulligQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3343 ; sc:citation , "pmcid:PMC6792352", "pubmed:31566444" ; sc:description "> LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'agonist', 'RXR' | Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library | Concentration 5-30% of expected value" ; sc:featureList edam:operation_3642 ; sc:name "Tox21" ; sc:url "https://tripod.nih.gov/tox21/samples" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382 ; sc:citation , "pubmed:31874186" ; sc:description "A method for merging multiple independent neuronal traces." ; sc:featureList edam:operation_3552 ; sc:name "TraceMontage" ; sc:url "https://www.cai-lab.org/tracemontage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3421 ; sc:citation ; sc:description "Track-Control is an automatic video-based real-time closed-loop behavioral control toolbox." ; sc:name "Track-Control" ; sc:url "https://github.com/GuangWei-Zhang/TraCon-Toolbox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3071 ; sc:citation ; sc:description "TrackFind is a FAIR genomic tracks search and curation engine. It supports crawling of the TrackHub Registry and other data portals to fetch track metadata. Crawled metadata can be accessed through hierarchical browsing or by search queries, both through a web-based user interface and as a RESTful API. TrackFind supports advanced SQL-based search queries that can be easily built in the user interface, and the search results can be browsed and exported in JSON or GSuite format. The RESTful API allows downstream tools and scripts to easily integrate TrackFind search, currently demonstrated by the GSuite HyperBrowser and EPICO." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TrackFind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://trackfind.elixir.no/" ; biotools:primaryContact "Dmytro Titov", "Eivind Hovig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3377 ; sc:citation ; sc:description "Genome-wide tool for preliminary assessment of therapeutic target druggability." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TractaViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/NeilPearson-Lilly/TractaViewer" ; biotools:primaryContact "Neil Pearson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation , , "pubmed:32447016" ; sc:description "A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity | Files needed to build a Singularity container to run the TractoFlow pipeline | Singularity related files for TractoFlow | The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram" ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TractoFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/scilus/tractoflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "Machine learning tool for microscopy pixel classification." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Trainable Weka Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2.33" ; sc:url "https://imagej.net/Trainable_Weka_Segmentation" ; biotools:primaryContact "Ignacio Arganda-Carreras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. The second version of NanoSim (v2.0.0) uses minimap2 as default aligner to align long genomic ONT reads to reference genome. It leads to much faster alignment step and reduces the overall runtime of NanoSim. We also utilize HTSeq, a python package, to read SAM alignment files efficiently.""" ; sc:featureList edam:operation_0335, edam:operation_3185, edam:operation_3198, edam:operation_3258 ; sc:name "Trans-NanoSim" ; sc:url "https://github.com/bcgsc/NanoSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3512, edam:topic_3673 ; sc:description "TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks." ; sc:featureList edam:operation_0436, edam:operation_0524, edam:operation_3644 ; sc:name "TransDecoder" ; sc:url "https://github.com/TransDecoder/TransDecoder/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6480747", "pubmed:31014374" ; sc:description "De novo transcriptome assembler that uses line graph iteration." ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "TransLiG" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/transcriptomeassembly/files/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC6827441", "pubmed:31695967" ; sc:description """a novel machine learning approach for eukaryotic promoter prediction. Approach for prediction of eukaryotic transcription start sites. A deep learning approach for precise prediction of eukaryotic transcription start sites. Our approach offers significant improvement over existing promoter prediction methods. We provide the full basis for the comparison and encourage users to freely access our computational method to facilitate and streamline their own analyses. ./data/ contains some data files. TSS_MSU.txt was used for TSS sequence taking. Rice genome can be downloaded from MSU rice experiment official page""" ; sc:featureList edam:operation_0440, edam:operation_3196, edam:operation_3659, edam:operation_3663 ; sc:license "GPL-2.0" ; sc:name "TransPrise" ; sc:url "https://github.com/StepanAbstro/TransPrise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation ; sc:description "Software for the prediction of orthologs between two species, based on transcripts sequence similarities. A procedure to extend BLAST alignments and to define orthologs based on the “Bidirectional Best Hit” approach was implemented." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Transcriptologs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/LucaAmbrosino/Transcriptologs.git" ; biotools:primaryContact "Luca Ambrosino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """Fast and Reliable Tool for QSAR. Transformer CNN for QSAR/QSPR modelling. The repository contains the source code for a new Transformer-CNN method described in our paper http://arxiv.org/abs/1911.06603. First, we trained the Transformer model on SMILES canonicalization task, e.g., given an arbitrary SMILES, the model converts it to a canonical one. Second, we use the internal representation of the Transformer (the output of the encoding stack with shape (BATCH, LENGTH, EMBEDDING)) as SMILES embeddings and build upon them CharNN model (Convolution and HighWay as it is done in DeepChem). The resulting model works both in classification and regression settings""" ; sc:featureList edam:operation_3659 ; sc:name "Transformer-CNN" ; sc:url "https://github.com/bigchem/transformer-cnn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pubmed:31835003" ; sc:description "A Computational Theory for the Discretized Entorhinal Cortex." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "Transition Scale-Spaces" ; sc:url "https://github.com/rochus/transitionscalespace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3314, edam:topic_3512 ; sc:citation , "pubmed:31557893" ; sc:description "A Code for Computing Kinetic and Related Parameters in Chemical Transformations and Transport Phenomena | Recent advances in phenomenological descriptions of the kinetics of rate processes (Aquilanti et al., 2010, 2017, 2018) motivated this code based on detailed formulations given in previous works | Theoretical and Computational Chemistry" ; sc:featureList edam:operation_0334, edam:operation_0337, edam:operation_3891 ; sc:name "Transitivity" ; sc:url "http://www.vhcsgroup.com/transitivity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC6510757", "pubmed:31076573" ; sc:description "Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models." ; sc:featureList edam:operation_0427 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Transposons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AlexShein/transposons/" ; biotools:primaryContact "Maria Poptsova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation "pubmed:31797618" ; sc:description "Tree-Weighting for Multi-Study Ensemble Learners." ; sc:name "Tree-Weighting" ; sc:url "https://github.com/m-ramchandran/tree-weighting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6705769", "pubmed:31437182" ; sc:description "Clustering biological sequences using phylogenetic trees | Efficient phylogenetic clustering of viral sequences | TreeCluster is a tool that, given a tree T (Newick format) and a distance threshold t, finds the minimum number of clusters of the leaves of T such that some user-specified constraint is met in each cluster. The user can also specify a branch support threshold s such that no pair of leaves in any cluster can be connected by branches with support less than or equal to s. Note that all leaves given a cluster of -1 are singletons, meaning they did not cluster with any other leaves (i.e., each leaf with a cluster of -1 is in its own cluster)" ; sc:featureList edam:operation_0546, edam:operation_0557, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "TreeCluster" ; sc:url "https://github.com/niemasd/TreeCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3293 ; sc:citation , "pubmed:31114853" ; sc:description "R package that performs analyses of expression evolution from RNA-seq data, including optimized input formatting, normalization and pair-wise distance evaluation, expression character tree inference and preliminary phylogenetic network analysis." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TreeExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/hr1912/TreeExp" ; biotools:primaryContact "Hang Ruan", "Xun Gu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3168, edam:topic_3301, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. Computational Biology Research Laboratory. TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts. TreeFix-TP is designed for scenarios where multiple strain ... Our websites may use cookies to personalize and enhance your experience. By continuing without changing your cookie settings, you agree to this collection. For more information, please see our University Websites Privacy Notice . TreeFix-TP is a program for reconstructing highly accurate transmission phylogenies, i.e., phylogenies depicting the evolutionary relationships between infectious disease strains (viral or bacterial) transmitted between different hosts""" ; sc:featureList edam:operation_0540, edam:operation_0547, edam:operation_3478 ; sc:name "TreeFix-TP" ; sc:url "https://compbio.engr.uconn.edu/software/treefix-tp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3512 ; sc:citation , "pmcid:PMC6612878", "pubmed:31510668" ; sc:description "a new method for improving the scalability of species tree estimation methods | TreeMerge is a tool for scaling phylogengy estimation methods to large datasets. TreeMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). TreeMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2019)" ; sc:featureList edam:operation_0544, edam:operation_0547, edam:operation_0555 ; sc:name "TreeMerge" ; sc:url "http://github.com/ekmolloy/treemerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_3293 ; sc:citation ; sc:description "Treerecs is an open-source (species- and gene-) tree reconciliation software distributed under the GNU AGPL licence." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0492 ; sc:license "AGPL-3.0" ; sc:name "Treerecs" ; sc:url "https://project.inria.fr/treerecs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3500 ; sc:citation , "pubmed:31418539" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'TreeshrewDB v2.0' | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome | Symbol Accession number Full gene name |  Fan Y, Yu D et al., 2014. Tree shrew database (TreeshrewDB): a knowledge base for Chinese tree shrew genome biology. Scientific Reports, 4: 7145 | 2019-09-05 Upgrading, some functions are not available" ; sc:featureList edam:operation_0484, edam:operation_0525, edam:operation_3216 ; sc:name "TreeshrewDB" ; sc:url "http://www.treeshrewdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659 ; sc:citation ; sc:description "Software tool to prioritize important genes in pathways and their non-coding regulators." ; sc:featureList edam:operation_0533, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TriPOINT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.uconn.edu/ajt06004/TriPOINT" ; biotools:primaryContact "Asa Thibodeau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31070854" ; sc:description "Efficient pipeline for mitochondrial assembly from transcriptomic reads in nonmodel species." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Trimitomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bplese/Trimitomics" ; biotools:primaryContact "Ana Riesgo", "Bruna Plese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3489 ; sc:citation , "pmcid:PMC6829499", "pubmed:31688940" ; sc:description """A tool for interactive visualization and comparison of genetic maps. Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases. It facilitates development of biological websites by providing tools to integrate and display biological data using the generic database schema, Chado, together with Drupal, a popular website creation and content management system. Tripal MapViewer is a new interactive tool for visualizing genetic map data. Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and heritable phenotypic markers. It also provides graphical comparison of maps sharing the same markers as well as dot plot and correspondence matrices""" ; sc:featureList edam:operation_0282, edam:operation_0490, edam:operation_2421 ; sc:name "Tripal MapViewer" ; sc:url "https://gitlab.com/mainlabwsu/tripal_map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3810 ; sc:description "TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis." ; sc:name "TropGeneDB" ; sc:url "http://tropgenedb.cirad.fr/tropgene/JSP/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3173, edam:topic_3512 ; sc:citation ; sc:description "Toolkit for rapidly simulating ChIP-seq data using statistical models of the experimental steps." ; sc:featureList edam:operation_3222, edam:operation_3798, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Tulip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gymreklab/Tulip" ; biotools:primaryContact "An Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_3673 ; sc:citation , "pubmed:31125057" ; sc:description "Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs." ; sc:featureList edam:operation_3196, edam:operation_3233 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TumorCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yongzhuang/TumorCNV" ; biotools:primaryContact "Yongzhuang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6710255", "pubmed:31451757" ; sc:description "Construction of complete Tupaia belangeri transcriptome database by whole-genome and comprehensive RNA sequencing | Tupaia belangeri (Family Tupaia, Genus Tupaia) | Tupaia ( Tupaia belangeri ) is a small mammal belonging to the family Tupaiidae, which consists of four genera and 19 extant species. The members of the genus Tupaia , which are colloquially referred to as the tree shrews, were first recorded in a sketch by William Ellis on a voyage with Captain Cook in 1780. Tree shrews are similar in appearance to squirrels, and their body weight ranges between 120-200 g. The natural habitat of the tree shrews consists of the tropical rainforests in South East Asia, where they feed on fruits, insects, and small vertebrates" ; sc:featureList edam:operation_2495, edam:operation_3216, edam:operation_3501 ; sc:name "TupaiaBase" ; sc:url "http://tupaiabase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Protein MD Setup tutorial using BioExcel Building Blocks - a Jupyter Notebook tutorial." ; sc:name "Tutorial: MD Setup" ; sc:url "https://github.com/bioexcel/biobb_wf_md_setup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3399, edam:topic_3697 ; sc:citation , "pubmed:31526404" ; sc:description "The UK Adult Twin Registry Update | If you would like access to data or samples from the Department Of Twin Research & Genetic Epidemiology or are interested in proposing a collaboration with us, please first follow the link DTR Policy Document for data access which will give you the necessary background information | You will then need to complete a “Data Access Proposal Form” (links below) and email the completed form to the Data Access Manager Victoria Vazquez or fax to +44 (0)20 7188 6718 for consideration by the Department of Twin Research Executive Committee | No attempt should be made to link or combine the data provided under this agreement to other information or archived data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, unless specific permission to do so has been received from the TwinsUK TREC | The proposal should specify the data and or samples required clearly" ; sc:name "TwinsUK" ; sc:url "http://twinsuk.ac.uk/resources-for-researchers/access-our-data/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3295, edam:topic_3673 ; sc:citation ; sc:description """a tool to genotype mobile element insertions from whole genome resequencing data. Genotyping of segregating mobile elements insertions. This pipeline is developped by Jainy Thomas (University of Utah) and Clement Goubert (Cornell University). Elaborated with the collaboration of Jeffrey M. Kidd (University of Michigan). TypeTE is a pipeline dedicated to genotype segregating Mobile Element Insertion (MEI) previously scored with a MEI detection tool such as MELT (Mobile Element Locator Tool, Gardner et al., 2017). Please adress all you questions and comments using the "issue" tab of the repository""" ; sc:featureList edam:operation_3183, edam:operation_3196, edam:operation_3227 ; sc:name "TypeTE" ; sc:url "https://github.com/clemgoub/TypeTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3517 ; sc:citation , "pubmed:31400194" ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:U-PASS' | unified power analysis and forensics for qualitative traits in genetic association studies | GWAS power calculator / generic power calculations for large scale association tests. Built with R Shiny | U-PASS: a Unified Power Analysis of Association Studies" ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "U-PASS" ; sc:url "https://github.com/Pill-GZ/U-PASS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3512 ; sc:citation ; sc:description "Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "UALCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ualcan.path.uab.edu/analysis.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Suite" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071 ; sc:description """Unified Biological Dictionaries (UniBioDicts) is a set of software packages that unite many of the most important biological controlled vocabularies, database vocabularies, and ontologies, under a common query-interface. These packages can access these disparate biological resources, and map their vocabulary data onto a common representation consisting of terms (which biocurators prefer to use), a unique identifier (which computers can reason with), and various descriptive metadata. This cross-resource infrastructure is essential for an efficient, modernized biocuration process, as it directly enables the autocomplete-based curation of particularly context-rich annotations, that combine terminology from across biological niches.""" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "UniBioDicts" ; sc:url "https://github.com/UniBioDicts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Utilities for handling sequences and assemblies from the UCSC Genome Browser project." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "UCSC Genome Browser Utilities" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hgdownload.cse.ucsc.edu/downloads.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3305, edam:topic_3412, edam:topic_3421 ; sc:citation , "pmcid:PMC6773358", "pubmed:31575580" ; sc:description "The Upper Gastrointestinal Cancer Registry (UGICR) is a clinical quality registry, that collects information about the diagnosis, treatment and outcomes of individuals with upper gastrointestinal cancer. The registry is managed by the Cancer Research Program part of Public Health and Preventive Medicine , Monash University." ; sc:featureList edam:operation_3454 ; sc:name "UGICR" ; sc:url "https://ugicr.org.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC6508075", "pubmed:31080962" ; sc:description "> MEDIUM CONFIDENCE! | A Model Based Tool to Detect Tandem Repeats | ULTRA Locates Tandemly Repetitive Areas | To contribute to ULTRA development, you want to be on the develop branch, which is where we are currently integrating feature branches. For more information, see the ULTRA wiki" ; sc:featureList edam:operation_0368, edam:operation_0452 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ULTRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TravisWheelerLab/ULTRA" ; biotools:primaryContact "Daniel Olson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3120, edam:topic_3168 ; sc:citation ; sc:description "a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries | UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries" ; sc:featureList edam:operation_0232, edam:operation_3225, edam:operation_3227 ; sc:license "MIT" ; sc:name "UMI-VarCal" ; sc:url "https://gitlab.com/vincent-sater/umi-varcal-master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC6550413", "pubmed:31120875" ; sc:description "Efficient algorithms to discover alterations with complementary functional association in cancer." ; sc:featureList edam:operation_3219, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "UNCOVER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/VandinLab/UNCOVER" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description "Method and associated software for discovering somatic mutations using the integration of DNA and RNA sequencing." ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UNCeqR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://lbc.unc.edu/~mwilkers/unceqr_dist/" ; biotools:primaryContact "Matt Wilkerson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6923391", "pubmed:31857624" ; sc:description """An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. A unified environment for DNN-based automated segmentation of neuronal EM images. Check the following pages after installation. Click the link "main.exe" in [UNI-EM] to launch the control panel. Urakubo, H., Bullmann, T., Kubota, Y., Oba, S., Ishii, S., UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images. Scientific Reports 9, 19413 (2019) doi:10.1038/s41598-019-55431-0""" ; sc:license "GPL-3.0" ; sc:name "UNI-EM" ; sc:url "https://github.com/urakubo/UNI-EM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_3518 ; sc:citation , "pmcid:PMC6694573", "pubmed:31412768" ; sc:description "a web tool for the integration and visualization of biomolecular networks for protein function prediction | In order to execute an experiment, you must first create an experiment design | {{ experiment.name }}-{{ experiment.newid }}" ; sc:featureList edam:operation_1777, edam:operation_3083, edam:operation_3439 ; sc:name "UNIPred-Web" ; sc:url "http://unipred.di.unimi.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3337, edam:topic_3384 ; sc:citation , "pubmed:31134468" ; sc:description "Big data analytics research data platform to improve care of patients with cardiomyopathies using routine electronic health records and standardized biobanking." ; sc:featureList edam:operation_0306, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "UNRAVEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.unravelrdp.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:31841402" ; sc:description """Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation. Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018. UNet++: A Nested U-Net Architecture for Medical Image Segmentation. UNet++ is a new general purpose image segmentation architecture for more accurate image segmentation. UNet++ consists of U-Nets of varying depths whose decoders are densely connected at the same resolution via the redesigned skip pathways, which aim to address two key challenges of the U-Net: 1) unknown depth of the optimal architecture and 2) the unnecessarily restrictive design of skip connections""" ; sc:featureList edam:operation_0479, edam:operation_3436 ; sc:license "MIT" ; sc:name "UNet++" ; sc:url "https://github.com/MrGiovanni/UNetPlusPlus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31369377" ; sc:description "Unsupervised Online Video Object Segmentation With Motion Property Understanding | Tao Zhuo, Zhiyong Cheng, Peng Zhang, Yongkang Wong, and Mohan Kankanhalli | Results on DAVIS-2016 TrainVal Dataset (50 videos)" ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:name "UOVOS" ; sc:url "https://www.github.com/visiontao/uovos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:description "A Convolution Neural Network (CNN) model to classify publications with accession annotations according to UniProtKB categories" ; sc:featureList edam:operation_3927 ; sc:name "UPCLASS" ; sc:url "http://goldorak.hesge.ch/bioexpclass/upclass/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0637, edam:topic_0821, edam:topic_3293 ; sc:citation , "pmcid:PMC6902001", "pubmed:31820805" ; sc:description """an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific peroxygenases (UPOs) present in the fungal kingdom. The fungal UPOs in this database are obtained by searching against all the fungal genomes present in the Ensembl database. This server uses profile hidden Markov models (HMMs) for homology search and incorporates clustering algorithms to group the most similar sequences""" ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_2995, edam:operation_3092, edam:operation_3431 ; sc:name "UPObase" ; sc:url "http://upobase.bioinformaticsreview.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC6829132", "pubmed:31690598" ; sc:description "Expression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early Undergraduates." ; sc:featureList edam:operation_2421, edam:operation_3463 ; sc:name "URCFG" ; sc:url "http://www.urcfg.ucla.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31689538" ; sc:description """Sample sizes and population differences in brain template construction. Caucasian and Chinese Brain templates [US200 CN200]""" ; sc:featureList edam:operation_3435 ; sc:name "US200 CN200" ; sc:url "https://www.nitrc.org/projects/us200_cn200/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3335, edam:topic_3379 ; sc:citation , "pmcid:PMC6717797", "pubmed:31496866" ; sc:description "Clinical and pharmacological application of multiscale multiphysics heart simulator, UT-Heart | Cardiotoxicity Hazard Map/ECG Data Base NEW | The world’s leading technologies open the new door for:" ; sc:featureList edam:operation_2426 ; sc:name "UT-Heart" ; sc:url "http://ut-heart.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6434621", "pubmed:30909881" ; sc:description "User-friendly Transcriptome Analysis Pipeline.(UTAP) is open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyse transcriptome sequence data." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "UTAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://utap.readthedocs.io/en/latest/index.html" ; biotools:primaryContact "Refael Kohen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6886508", "pubmed:31744903" ; sc:description """The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting. The UTRome.org database is intended as a comprehensive resource for 3'UTR biology in C. elegans . The database provides detailed information on 3'UTR structures and alternative polyadenylation for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar ) as well as new annotations generated by others. 3'UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of 3'UTRs we are building a 3'UTR database for C. elegans .""" ; sc:featureList edam:operation_0428, edam:operation_0463, edam:operation_3792 ; sc:name "UTRome" ; sc:url "http://www.UTRome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301 ; sc:author ; sc:citation ; sc:description "The Unified Variant Pipeline (UVP) is used to identify variants and assign lineage from Mycobacterium tuberculosis sequence data." ; sc:featureList edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UVP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.6.0", "2.7.0" ; sc:url "https://github.com/CPTR-ReSeqTB/UVP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:31435647" ; sc:description "visualization and enhanced analysis of circular RNAs via back and canonical forward splicing | An R-shiny app that provides backsplice and canonical splicing analysis for both circRNA and parental transcripts | An R package that provides analysis and visualisation of canonical and backsplice junctions. Takes output provided by the STAR aligner as well as CIRI2 and circExplorer2 output and enables circRNA downstream analysis | Ularcirc manuscript now available through Nucleic Acids Research | Author and maintainer: David Humphreys (d.humphreys at victorchang dot edu dot au) | Ularcirc can annotate circRNA with overlapping gene information. This is obtained from available bioconductor databases. Use the following command to identify what databases to download:" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Ularcirc" ; sc:url "https://github.com/VCCRI/Ularcirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description """Geothematic open data in Umbria region. Carta di pericolosità sismica locale dell’Umbria. Benvenuti nel Portale Open Data dell' Umbria. I dati della Pubblica Amministrazione umbra a disposizione dei cittadini. www.regione.umbria.it leggi di più. La cartografia di pericolosità sismica vettoriale della Regione Umbria è stata ultimata nel 2013 utilizzando tutti gli originali d'autore delle carte di pericolosità sismica locale realizzate alla scala 1:10.000, riviste ed omogeneizzate""" ; sc:featureList edam:operation_3891 ; sc:name "Umbria" ; sc:url "http://dati.umbria.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0605, edam:topic_3306, edam:topic_3474, edam:topic_3895 ; sc:citation , "pubmed:31636460" ; sc:description """Unified rational protein engineering with sequence-based deep representation learning. UniRep model, usage, and examples. UniRep, a mLSTM "babbler" deep representation learner for protein engineering informatics. Analysis and figure code from Alley et al. 2019. git clone https://github.com/churchlab/UniRep-analysis.git. First clone or fork this repository and navigate to the repository's top directory (cd UniRep). We recommend using our docker environments. Install docker to get started""" ; sc:featureList edam:operation_0476, edam:operation_1777, edam:operation_3630 ; sc:name "UniRep" ; sc:url "https://github.com/churchlab/UniRep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3068, edam:topic_3316, edam:topic_3473 ; sc:description """Top ‱ cited papers from PUBMED. Unicorn Papers are based on an equal contribution (EC) citation model in which the total number of citations had been divided by the number of the authors. Currently, the list contains 3405 papers with ECcit ≥ 847.0 (updated monthly since 2020). ‱ - permyriad, literally meaning "for (every) myriad (ten thousand)\"""" ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-2.5" ; sc:name "Unicorn Papers" ; sc:softwareHelp ; sc:url "http://unicornpapers.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_0637, edam:topic_3071 ; sc:citation , "pubmed:31843688" ; sc:description """Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Retrieving Information of Proteins from Uniprot. Connect to Uniprot to retrieve information about proteins using their accession number such information could be name or taxonomy information. UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProtknowledgebase). M. Soudy, A. Anwar, E.A. Ahmed, et al., UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase), Journal of Proteomics (2019), https://doi.org/10.1016/j.jprot.2019.103613""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "UniprotR" ; sc:url "https://cran.r-project.org/web/packages/UniprotR/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:31436473" ; sc:description "Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola | Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola" ; sc:featureList edam:operation_0308 ; sc:name "Uniqprimer" ; sc:url "https://github.com/SouthGreenPlatform/Uniqprimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0176, edam:topic_0602, edam:topic_0821 ; sc:citation , "pmcid:PMC6933841", "pubmed:31710727" ; sc:description """Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS. Implementation of a visualization prototype for molecular structures and networks using the Unity3D game engine. Implementation of numerous graphical methods as spheres, particle systems, bond, etc.""" ; sc:featureList edam:operation_0337, edam:operation_0409, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "UnityMol-APBS" ; sc:url "https://sourceforge.net/projects/unitymol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0622, edam:topic_0623, edam:topic_0781 ; sc:citation ; sc:description "Classification and annotation of viral sequences based on RefSeq annotation." ; sc:featureList edam:operation_0361, edam:operation_0363, edam:operation_0447, edam:operation_3431 ; sc:name "VADR" ; sc:url "https://github.com/nawrockie/vadr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC6735694", "pubmed:31494667" ; sc:description "High-throughput variant antigen profiling in African trypanosomes of livestock | Variant Antigen Profiling for Trypanosoma congolense and Trypanosoma vivax | Trypanosomes are important human and veterinary parasites that cause potentially lethal blood infections and a chronic wasting disease (African trypanosomiasis). These organisms use antigenic variation to evade the host immune response, for which their genomes contain many hundreds of variable antigen genes. Making sense of this hypervariable repertoire is a major challenge in genome analysis and a bottleneck in vaccine development | the VAPPER code for the first time, please type:" ; sc:featureList edam:operation_2939, edam:operation_3227, edam:operation_3891 ; sc:name "VAPPER" ; sc:url "https://github.com/PGB-LIV/VAPPER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3375, edam:topic_3577 ; sc:citation , "pubmed:31495872" ; sc:description "Search for Drug Transporter Entries: | Examples: P-glycoprotein 1 ; BCRP ; OATP1B1 ; Oxaliplatin ; Lung cancer .. | Search Drug Transporter by Transporter Name: | J. Y. Yin, W. Sun, F. C. Li, J. J. Hong, X. X. Li, Y. Zhou, Y. J. Lu, M. Z. Liu, X. Zhang, N. Chen, X. P. Jin, J. Xue, S. Zeng * , L. S. Yu * & F. Zhu * . VARIDT 1.0: Variability of Drug Transporter Database. Nucleic Acids Research . doi: 10.1093/nar/gkz779 (2020). PMID: 31495872" ; sc:featureList edam:operation_2495, edam:operation_3202 ; sc:name "VARIDT" ; sc:url "http://varidt.idrblab.net/ttd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6842140", "pubmed:31703556" ; sc:description """sampling complementary RNA reads from the sequence read archive. VARUS: Drawing Diverse Samples from RNA-Seq Libraries. VARUS was originally written by Willy Bruhn as a Bachelors' thesis supervised by Mario Stanke. This repository is a copy of https://github.com/WillyBruhn/VARUS made in November 2018 and contains many bugfixes, an incremental intron database feature and an extension for using HISAT al alternative alignment program""" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3258, edam:operation_3431 ; sc:name "VARUS" ; sc:url "https://github.com/Gaius-Augustus/VARUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_2814, edam:topic_2828 ; sc:citation , "pmcid:PMC6933850", "pubmed:31724231" ; sc:description "VASE is a web-tool for visualizing alignments on a protein structure. It allows you to enter the ID of a protein structure in PDB format for which VASE will generate an interface. VASE will show a set of homologous sequences, aligned to the sequence of your structure, along with entropy/variability data and a 3D interface. Here's an example: 1CRN." ; sc:featureList edam:operation_0292, edam:operation_0295, edam:operation_0319, edam:operation_0570, edam:operation_2488 ; sc:name "VASE" ; sc:url "https://github.com/cmbi/vase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:31425086" ; sc:description "A Visual Analytics Toolkit for Social Spambot Labeling | Visual Analytics Toolkit for Social Spambots Labeling | The server is currently busy. Please wait. | Thank you for your participation | You have completed all the sessions | Label as Spambot Label as Genuine | Please express your opinion about VASSL:" ; sc:featureList edam:operation_3891 ; sc:name "VASSL" ; sc:url "https://vassl.new-dimension.co" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation , "pubmed:31442673" ; sc:description "A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data | In this article, we introduce the variant call format-diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators" ; sc:featureList edam:operation_3225, edam:operation_3227 ; sc:name "VCF-DART" ; sc:url "https://github.com/sirselim/diagnostics_exome_reporting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3168, edam:topic_3473 ; sc:citation , "pmcid:PMC6625089", "pubmed:31127704" ; sc:description "A web-based visualization tool for high-throughput variant data mining and management." ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VCF-Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://diseasegps.sjtu.edu.cn/VCF-Server?lan=eng" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0625, edam:topic_2885 ; sc:citation ; sc:description """a one-click client-side software to construct population phylogeny from genome-wide SNPs. VCF2PopTree is a client-side software written in Javascript and it runs. purely within the user’s computer/browser. VCF2PopTree is compatible""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3196 ; sc:license "MIT" ; sc:name "VCF2PopTree" ; sc:url "https://github.com/sansubs/vcf2pop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "SNP/Indel Variant Calling Pipeline and data management tool used for analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer’s Disease Sequencing Project." ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VCPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.niagads.org/resources/tools-and-software/vcpa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3452 ; sc:citation , "pmcid:PMC6890217", "pubmed:31794595" ; sc:description "Use of three points to determine the accuracy of guided implantation." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "VDING" ; sc:url "https://github.com/coolleafly/VDING" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_0804 ; sc:citation , "pubmed:31602484" ; sc:description """an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers easy searching of genotype and haplotype data inferred from AIRR-seq datasets. From these data we can explore the variability of the genomic loci of the Ig and TR encoding genes across populations""" ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_2421, edam:operation_3196 ; sc:name "VDJbase" ; sc:url "https://www.vdjbase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0160, edam:topic_0219, edam:topic_2830 ; sc:citation , "pubmed:31588507" ; sc:description "VDJdb is a database extension, new analysis infrastructure and a T-cell receptor motif compendium." ; sc:featureList edam:operation_0224, edam:operation_0238, edam:operation_0416 ; sc:name "VDJdb" ; sc:url "https://vdjdb.cdr3.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3474, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:31873730" ; sc:description """a Variant Filtering tool based on Ensemble methods. Variant Ensemble Filter, an ensemble based filter for VCF files. VEF is designed for filtering variants of single non-cancerous samples. This bash script calls example script vef_clf.py and vef_apl.py located in the example/ directory to train and apply the filter, respectively. After running test.sh, there will be 2 filter models in example/data with the .clf extension, along with 2 filtered VCF files with the .vef.vcf extension""" ; sc:featureList edam:operation_3227, edam:operation_3359, edam:operation_3675, edam:operation_3695 ; sc:license "MIT" ; sc:name "VEF" ; sc:url "http://github.com/ChuanyiZ/vef" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3500 ; sc:citation , "pmcid:PMC6753167", "pubmed:31572120" ; sc:description """An Open-Source Matlab-Based Toolbox for the Collection and Analysis of Electromyography Combined With Transcranial Magnetic Stimulation. The combination of electromyography (EMG) and transcranial magnetic stimulation (TMS) offers a powerful non-invasive approach for investigating corticospinal excitability in both humans and animals. Acquiring and analyzing the data produced with this combination of tools requires overcoming multiple technical hurdles. Due in part to these technical hurdles, the field lacks standard routines for EMG data collection and analysis. This poses a problem for study replication and direct comparisons. Although software toolboxes already exist that perform either online EMG data visualization or offline analysis, there currently are no openly available toolboxes that flexibly perform both and also interface directly with peripheral EMG and TMS equipment""" ; sc:featureList edam:operation_0337 ; sc:name "VETA" ; sc:url "https://github.com/greenhouselab/Veta/tree/master/data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203 ; sc:author ; sc:description """Performs intersectional genetics-related operations to find VEnCodes using databases provided by the FANTOM5 consortium, namely the CAGE enhancer and transcription start site (TSS) databases. For more information on the VEnCode technology, please refer to Macedo and Gontijo, bioRxiv 2019""" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "VEnCode" ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/AndreMacedo88/VEnCode" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC6886159", "pubmed:31787090" ; sc:description "Virtual Grid Engine (VGE) is a kind of middleware for running bioinformatics software pipelines on large-scale supercomputers which do not support any grid engine survices. VGE employs master-worker model. It first reserves processors and/or cores by running the job which is parallelized by MPI, then asign divided small tasks onto its worker processes. VGE is written in python." ; sc:featureList edam:operation_3359 ; sc:name "VGE" ; sc:url "https://github.com/SatoshiITO/VGE" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3620 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3489 ; sc:author , "Bryan Brancotte" ; sc:citation ; sc:contributor ; sc:description """The Viral Host Range database represents a unique resource for the community to rapidly find, document analyze and disseminate data related to the range of hosts that a virus can infect. Over the years, countless host range experiments have been performed in many laboratories. However, these data are not readily available to the community and are therefore underexploited. The VHRdb is an online resource that centralizes experimental data related to the host range of viruses. While it originates from bacteriophages and bacteria interaction studies, its design is compatible with viruses infecting all living forms. Users can browse publicly available data to find which host is infected by a virus, and vice versa. Users can also upload their own data while keeping it private or making it public, analyze results across independent sets of data, generate and visualize outputs. Data implemented in the VHRdb are linked to users and, if available, to publications and sequence identifiers.""" ; sc:featureList edam:operation_3436 ; sc:license "MIT" ; sc:name "Viral Host Range database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://viralhostrangedb.pasteur.cloud/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation , ; sc:description """Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. Virus Identification By iteRative ANnoTation. Discovery Environment Applications List. Created by upendra_35, last modified on Nov 04, 2019. If you find VIBRANT useful please consider citing our preprint on bioRxiv:. Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387. VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies. The QuickStart tutorial provides an introduction to basic DE functionality and navigation. Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions""" ; sc:featureList edam:operation_0362, edam:operation_3192, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "VIBRANT" ; sc:url "https://wiki.cyverse.org/wiki/display/DEapps/VIBRANT-1.0.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC6708137", "pubmed:31443733" ; sc:description "a computational tool for assessing clinical impacts of somatic variants | A Computational Tool for Assessing Clinical Impacts of Somatic Variants Following the AMP-ASCO-CAP 2017 Guidelines | Variant Interpretation for Cancer (VIC) | Clinical Interpretations of Variants in Cancer | java -jar target/VIC-1.0-jar-with-dependencies.jar [-b ] [-d ] [-h] [-input_type ] [-i ] [-cancer_type ] [-convert2annovar ] [-l ] [-skip_annovar] [-o ] [-annotate_variation ] [-table_annovar ] [-s ] [-otherinfo ] [-db ]" ; sc:featureList edam:operation_1812, edam:operation_3225, edam:operation_3227 ; sc:name "VIC" ; sc:url "https://github.com/HGLab/VIC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3421 ; sc:citation ; sc:description "A precision virtual crossmatch decision support system for interpretation of ambiguous molecular HLA typing data | VICTOR: VIrtual CrossmaTch for mOleculaR typing data | This prototype tool computes virtual crossmatch using the candidate’s unacceptable antigens including high resolution alleles and molecular HLA typing of the donor | Web services interface information for Transplanttoolbox" ; sc:featureList edam:operation_0416, edam:operation_3196, edam:operation_3891 ; sc:name "VICTOR" ; sc:url "http://www.transplanttoolbox.org/victor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3308, edam:topic_3379, edam:topic_3400 ; sc:citation , "pmcid:PMC6927110", "pubmed:31865910" ; sc:description """ontology classification and study of vaccine responses given various experimental and analytical conditions. VIO: Vaccine Investigation Ontology. Statistics of Vaccine Investigation Ontology. IRI: https://raw.githubusercontent.com/vaccineontology/VIO/master/src/ontology/vio.owl. VIO and its usage in studying Yellow Fever vaccine-induced host response were presented in the VDOS-2018 workshop: https://sites.google.com/site/vdosworkshop/VDOS-2018. Note: This version of statistics metrics does not include any instance data yet. This feature will be added in the future""" ; sc:featureList edam:operation_0560, edam:operation_3431, edam:operation_3435, edam:operation_3501 ; sc:name "VIO" ; sc:url "http://www.ontobee.org/ontology/VIO" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3752 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654, edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3520 ; sc:citation "pubmed:17545182" ; sc:description "VIPER is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT tag approach. The software allows one to display the data as a two-dimensional plot of spectrum number (i.e. elution time) vs. mass. It can read MS data from several file formats: .PEK, .CSV (Decon2LS format), .mzXML, and .mzData." ; sc:featureList edam:operation_3203, edam:operation_3432, edam:operation_3627, edam:operation_3628, edam:operation_3694, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "VIPER LC-MS" ; sc:url "https://omics.pnl.gov/software/viper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:31598702" ; sc:description """a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resource, UTHealth, SBMI, Zhongming Zhao""" ; sc:featureList edam:operation_0238, edam:operation_0440, edam:operation_0463 ; sc:name "VISDB" ; sc:url "https://bioinfo.uth.edu/VISDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc:description "Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells | ValIdated Systematic IntegratiON of hematopoietic epigenomes | The VISION project aims to harvest truly valuable information from the flood of epigenomic data on hematopoietic cells as" ; sc:featureList edam:operation_0441, edam:operation_3557 ; sc:name "VISION" ; sc:url "http://usevision.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence features metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3175, edam:topic_3511 ; sc:author ; sc:citation , "pubmed:31589307" ; sc:description "Haplotype-aware structural variants simulator for short, long and linked reads" ; sc:featureList edam:operation_2426, edam:operation_2928, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "VISOR" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/davidebolo1993/VISOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC6697931", "pubmed:31419935" ; sc:description "a Variant-Information Search Tool for precision oncology | The Variant Information Search Tool developed @ WBI" ; sc:featureList edam:operation_2421, edam:operation_3280 ; sc:name "VIST" ; sc:url "https://vist.informatik.hu-berlin.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3489, edam:topic_3892 ; sc:citation , "pubmed:31682440" ; sc:description """VMD Plugin to Browse, Discover, and Install VMD Extensions. In this page, you can find all the possible alternatives to install the VMD Store extension. 1. Install VMD Store through VMD Tk Console This installation process can be used ... Biomolecular SIMulations Research Group""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3436 ; sc:name "VMD Store" ; sc:url "https://biosim.pt/how-to-install-vmd-store/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3697 ; sc:citation ; sc:description "Virtual Metabolic Human (VMH) database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data." ; sc:featureList edam:operation_3501, edam:operation_3660, edam:operation_3715 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VMH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vmh.life" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3416, edam:topic_3452 ; sc:citation , "pubmed:31840849" ; sc:description "Vascular Network Analysis (VNA) is a novel analysis protocol based on freely available or commonly used software to generate vascular data from μCT scans." ; sc:featureList edam:operation_2428, edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "VNA" ; sc:url "http://github.com/McBrideGagyiLab/VNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pubmed:31791122" ; sc:description """Untargeted Metabolomics Feature Clustering Approach for Clinical Breath Gas Chromatography. Metabolic profiling of breath analysis involves processing, alignment, scaling and clustering of thousands of features ex-tracted from Gas Chromatography Mass spectrometry (GC-MS) data from hundreds of participants. The multi-step data processing is complicated, operator error-prone and time-consuming. Automated algorithmic clustering methods that are able to cluster features in a fast and reliable way are necessary. These accelerate metabolic profiling and discovery plat-forms for next generation medical diagnostic tools. Our unsupervised clustering technique, VOCCluster, prototyped in Py-thon, handles features of deconvolved GC-MS breath data. VOCCluster was created from a heuristic ontology based on the observation of experts undertaking data processing with a suite of software packages.""" ; sc:featureList edam:operation_3432, edam:operation_3801, edam:operation_3803 ; sc:name "VOCCluster" ; sc:url "https://github.com/Yaser218/Untargeted-Metabolomics-Clustering/tree/master/VOCCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3400, edam:topic_3697 ; sc:citation , "pmcid:PMC6701114", "pubmed:31429723" ; sc:description "visual analysis of disease-associated microbiome-immune system interplay | Visualization of Linear Regression Elements | Visualization of linear regression elements comparing microbiome and immune system readouts" ; sc:featureList edam:operation_1812, edam:operation_3501, edam:operation_3659 ; sc:name "VOLARE" ; sc:url "http://aasix.cytoanalytics.com/volare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154 ; sc:citation , "pmcid:PMC6602475", "pubmed:31114895" ; sc:description "VOLPES (Visualization Of PhysicochEmical Sequence properties) - interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences." ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VOLPES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://volpes.univie.ac.at" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6509870", "pubmed:31074382" ; sc:description "Variational projection for accurate clustering of single-cell transcriptomic data." ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ShengquanChen/VPAC" ; biotools:primaryContact "Rui Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , "pubmed:31765830" ; sc:description """A Customizable Variant Prioritization Ordering Tool for Annotated Variants. VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. VPOT provides various functions for the purpose of speeding up variant discovery""" ; sc:featureList edam:operation_3226, edam:operation_3461, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "VPOT" ; sc:url "https://github.com/VCCRI/VPOT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3292, edam:topic_3315, edam:topic_3332 ; sc:citation ; sc:description """Exploring Drugbank in Virtual Reality Chemical Space. VRTK is a toolkit to rapidly build VR solutions. VRTK is a collection of useful, reusable solutions to common problems found when building for virtual reality. VRTK aims to help productivity by speeding up the creation process from prototyping ideas to building complete solutions""" ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:name "VRTK" ; sc:url "http://www.vrtk.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0611, edam:topic_3170 ; sc:citation , "pubmed:31374129" ; sc:description "Transcriptional profiling aligned with in situ expression image analysis reveals mosaically-expressed molecular markers for GABA neuron sub-groups in the ventral tegmental area | VTA Expression Data Extractor" ; sc:featureList edam:operation_3192, edam:operation_3501 ; sc:name "VTA" ; sc:url "https://gitlab.com/mlinitaur/vta-expression-data-extractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3384, edam:topic_3399, edam:topic_3577 ; sc:citation , "pmcid:PMC6857688", "pubmed:31730697" ; sc:description """Deep learning for clustering of multivariate clinical patient trajectories with missing values. Deep learning for clustering of multivariate short time series with potentially many missing values. This repository contains code for a new method for clustering multivariate short time series with potentially many missing values (published here), a setting commonly encountered in the analysis of longitudinal clinical data, but generally still poorly addressed in the literature. Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values". Supporting code for the manuscript "Deep learning for clustering of multivariate clinical patient trajectories with missing values\"""" ; sc:featureList edam:operation_1812, edam:operation_3432, edam:operation_3557 ; sc:license "LGPL-2.1" ; sc:name "VaDER" ; sc:url "https://github.com/johanndejong/VaDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3277 ; sc:citation , "pubmed:31751680" ; sc:description """Allele Min-Set Cover Software. To facilitate reference-material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and preselection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of reference samples from the 1000 Genomes Project to cover 237 variants considered putatively pathogenic (of which 12 were classified as pathogenic or likely pathogenic) in the original 56 medically actionable genes recommended by the American College of Medical Genetics and Genomics (ACMG). The number of samples, number of alleles, and processing time were measured in subsets of the 237 target alleles.""" ; sc:name "VarCover" ; sc:url "https://github.com/erscott/varcover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3325 ; sc:description "VarFish is an easy-to-use web-based database system designed for empowering geneticists in the analysis of clinical and whole exome sequencing variant data sets for individuals and families. It provides a set of tools for supporting the full workflow from (i) variant data quality control, (ii) variant filtration and (iii) efficient assessment of variants based on visual alignment inspection and annotation data such as functional and frequency annotation." ; sc:license "MIT" ; sc:name "VarFish" ; sc:url "https://github.com/bihealth/varfish-server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:31834354" ; sc:description "VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones." ; sc:featureList edam:operation_0484, edam:operation_2422, edam:operation_3675 ; sc:license "MIT" ; sc:name "VarGen" ; sc:url "https://github.com/MCorentin/VarGen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533 ; sc:citation , "pmcid:PMC6291943", "pubmed:30541431" ; sc:description "VarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses." ; sc:isAccessibleForFree true ; sc:name "VarGenius" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/frankMusacchia/VarGenius" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0166, edam:topic_0654 ; sc:citation ; sc:description "Tool for mapping a list of chromosome coordinates, and their variants, to the corresponding protein residues in the canonical UniProt protein sequence." ; sc:featureList edam:operation_0321, edam:operation_2422, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VarMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/DisaStr/GetPage.pl?varmap=TRUE" ; biotools:primaryContact "James Stephenson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pubmed:30192923" ; sc:description "Package for variable selection in model-based clustering of mixed-data with missing values." ; sc:featureList edam:operation_3432, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VarSelLCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "2.1.3" ; sc:url "https://CRAN.R-project.org/package=VarSelLCM/" ; biotools:primaryContact "Mohammed Sedki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3325, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC6792253", "pubmed:31615419" ; sc:description """prioritizing clinically reported variants with binary classification algorithms. VarSight is a collection of scripts used to test the application of classification algorithms for identifying variants that will be returned on a clinical report. VarSight relies on Codicem to perform common clinical pipeline pre-processing, namely variant annotation and filtering. In addition to data available in Codicem, it also uses gene rankings that are based on Human Phenotype Ontology (HPO) terms using both a built in calculation (cosine score) and the external tool PyxisMap. The classifiers in VarSight ingest a total of 95 features that are run through a feature selection process to get the top 20 features. Those 20 features are used to test both classification of reported variants and prioritization of reported variants in a larger filtered list. Results from the latest version of VarSight tests are available in the folder labeled "paper\"""" ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "VarSight" ; sc:url "https://github.com/HudsonAlpha/VarSight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0634, edam:topic_2814, edam:topic_3120 ; sc:citation , "pmcid:PMC6933866", "pubmed:31606900" ; sc:description """Disease variants and protein structure. Disease Variants and Structure""" ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_2488, edam:operation_3227 ; sc:name "VarSite" ; sc:url "https://www.ebi.ac.uk/thornton-srv/databases/VarSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description """heuristic-free alignment for assessing linear and graph read aligners. Vargas computes optimal alignments of short reads to a directed acyclic graph (DAG). After building a graph, reads are aligned using a SIMD-vectorized version of the Smith-Waterman dynamic programming algorithm, with 16 -- 64 reads per vector depending on the instruction set""" ; sc:featureList edam:operation_0495, edam:operation_2422, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:license "MIT" ; sc:name "Vargas" ; sc:url "https://github.com/langmead-lab/vargas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2885, edam:topic_3320 ; sc:citation ; sc:description "Benchmark database suite comprising variation datasets for testing and training methods for variation effect prediction." ; sc:featureList edam:operation_0331, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VariBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://structure.bmc.lu.se/VariBench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_3068, edam:topic_3168, edam:topic_3298 ; sc:citation , "pubmed:31705629" ; sc:description """A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. VariCarta is a curated, web-based database housing ASD-linked genes created from the meta-analysis of -omic sequencing literature. VariCarta is a database of human DNA genetic variants found in individuals diagnosed with Autism Spectrum Disorder (ASD) and reported in peer-reviewed scientific literature.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3436 ; sc:name "VariCarta" ; sc:url "http://varicarta.msl.ubc.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3174 ; sc:citation , "pmcid:PMC6612864", "pubmed:31510647" ; sc:description "Building large updatable colored de Bruijn graphs via merging | VARI-merge is a pair of tools (vari-merge and color-merge) capable of merging the succinct colored de Bruijn graphs produced by VARI. The VARI-merge branch includes all of VARI | Cosmo is a fast, low-memory DNA assembler that uses a succinct de Bruijn graph | VARI is an extension to Cosmo and supports offline construction of succinct colored de Bruijn graphs. It can be found in the VARi branch, however all the components are also in this branch. You should use this branch for the VARI tools because it includes an important bugfix: Palendromes are not duplicated during the revcomp generation phase of succinct de Bruijn graph construction" ; sc:featureList edam:operation_0524, edam:operation_3211, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "VariMerge" ; sc:url "https://github.com/cosmo-team/cosmo/tree/VARI-merge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3577 ; sc:citation ; sc:description "A Large-Scale Genomic Variant Search Index." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3211, edam:operation_3226, edam:operation_3227 ; sc:name "VariantStore" ; sc:url "https://github.com/Kingsford-Group/variantstore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203 ; sc:citation , "pmcid:PMC5765404", "pubmed:28967166" ; sc:description """VariantValidator is a user-friendly software tool designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Sequence Variant Nomenclature. VariantValidator ensures that users are guided through the intricacies of the HGVS nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately inter-converts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF) VariantValidator interfaces with the hgvs package to parse, format, and manipulate biological sequence variants. See https://github.com/biocommons/hgvs/ for details of the hgvs package VariantValidator is a highly functional platform enabling high-throughput and embeddable utilisation of functionality of https://variantvalidator.org/""" ; sc:featureList edam:operation_1812, edam:operation_3227 ; sc:license "AGPL-3.0" ; sc:name "VariantValidator" ; sc:url "http://variantvalidator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3325 ; sc:author "Sofia Papadomitriou" ; sc:citation , ; sc:description """VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. A variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). VarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. VarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel. You can use it through the online tool ORVAL: https://orval.ibsquare.be.""" ; sc:featureList edam:operation_2423, edam:operation_3197, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Variant Combination Pathogenicity Predictor (VarCoPP) 2.0" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Interuniversity Institute of Bioinformatics in Brussels" ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://varcopp.ibsquare.be" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3676 ; sc:citation , "pubmed:31086968" ; sc:description "Variant Score Ranker (VSR) - web application for intuitive missense variant prioritization." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Variant Score Ranker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://vsranker.broadinstitute.org" ; biotools:primaryContact "Dennis Lal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation , "pmcid:PMC6624979", "pubmed:31300006" ; sc:description "Variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Variational Bayes approach (GEMINI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sellerslab/gemini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3168, edam:topic_3303 ; sc:citation ; sc:description """a complete and efficient tool to support NGS data analysis. High precision on genetic analysis""" ; sc:featureList edam:operation_2428, edam:operation_3197 ; sc:name "Varstation" ; sc:url "http://varstation.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3489 ; sc:citation , "pmcid:PMC6776151", "pubmed:31598083" ; sc:description """Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. a DNA marker database for vegetables""" ; sc:featureList edam:operation_0415, edam:operation_3196, edam:operation_3432 ; sc:name "VegMarks" ; sc:url "https://vegmarks.nivot.affrc.go.jp/resource/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6941187", "pubmed:31881980" ; sc:description """venn diagram based network propagation analysis framework for comparing multiple biological experiments. Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee and Sun Kim. Handles I/O between front-end & back-end. Currently, Venn-diaNet uses String DB""" ; sc:featureList edam:operation_2495, edam:operation_2497, edam:operation_3501 ; sc:name "Venn-diaNet" ; sc:url "http://biohealth.snu.ac.kr/software/venndianet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "R package for the analysis of nucleic acids structural data, with an emphasis in complex RNA structures." ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VeriNA3d" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mmb.irbbarcelona.org/gitlab/dgallego/veriNA3d" ; biotools:primaryContact "Modesto Orozco", "Pablo D. Dans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC6685253", "pubmed:31406507" ; sc:description "a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity | The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study" ; sc:featureList edam:operation_2942, edam:operation_3436, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "ViSEAGO" ; sc:url "https://bioconductor.org/packages/ViSEAGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description """An innovative visualization R package to ensure behavioral raw data reliability and transparency. Background In recent years, the scientific community encouraged the use of raw data graphs to improve the reliability and transparency of the results presented in papers. However, methods to visualize raw data are limited to one variable per graph and or only small samples. In behavioral science as in many other fields, multiple variables need to be plotted together to allow insights of the behavior or the process observations. In this paper, we present ViSiElse, an R-package offering a new approach in raw data visualization. Methods. ViSiElse was developed with the open-source software R to provide a solution for the complete visualization of the raw time data. Results. ViSiElse grants a global overview of a process by combining the visualization of multiple actions timestamps for all participants in a single graph. Individuals and or group behavior can easily be assessed""" ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:name "ViSiElse" ; sc:url "https://cran.csiro.au/web/packages/ViSiElse/ViSiElse.pdf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC6658840", "pubmed:31372596" ; sc:description "Accelerating structure-function mapping using the ViVa webtool to mine natural variation | If Autoforward does not work, follow this link to go to Clay's ViVa website.." ; sc:featureList edam:operation_3196 ; sc:name "ViVa" ; sc:url "http://plantsynbiolab.bse.vt.edu/ViVa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "VICTOR is an interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering outputs." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "VICTOR" ; sc:url "http://bib.fleming.gr:3838/VICTOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_3474 ; sc:citation , "pubmed:31583641" ; sc:description """Vienna Graph Clustering. The graph clustering framework VieClus -- Vienna Graph Clustering. The main project page of to open source framework VieClus -- Vienna Graph Clustering. This is the release of our memetic algorithm, VieClus (Vienna Graph Clustering), to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. In our experimental evaluation, we show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration in a small amount of time. In fact, for most of the small instances, we can improve the old benchmark result in less than a minute. Moreover, while the previous best result for different instances has been computed by a variety of solvers, our algorithm can now be used as a single tool to compute the result. VieClus - Vienna Graph Clustering is a memetic algorithm""" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "VieClus" ; sc:softwareHelp ; sc:url "http://vieclus.taa.univie.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:31580400" ; sc:description """A C ++ Variant Integration Kit for Next Generation Sequencing Association Analysis. Documentation for VikNGS — VikNGS 0.0.1 documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_3196, edam:operation_3436, edam:operation_3791 ; sc:name "VikNGS" ; sc:url "https://vikngsdocs.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC6829986", "pubmed:31684876" ; sc:description "The method is essentially an EM algorithm." ; sc:featureList edam:operation_0487, edam:operation_3216, edam:operation_3432, edam:operation_3798 ; sc:name "VirBin" ; sc:url "https://github.com/chjiao/VirBin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6764358", "pubmed:31579606" ; sc:description """a Fiji macro for automated assessment of viral plaque statistics. Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user's needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "ViralPlaque" ; sc:url "https://sourceforge.net/projects/viralplaque/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6909514", "pubmed:31836005" ; sc:description "Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference." ; sc:featureList edam:operation_3196, edam:operation_3200, edam:operation_3226 ; sc:name "Vireo" ; sc:url "https://github.com/single-cell-genetics/vireo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229 ; sc:citation , "pubmed:31373613" ; sc:description "> HOMEPAGE MISSING! | a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data | MOTIVATION:The immune system has diverse types of cells that are differentiated or activated via various signaling pathways and transcriptional regulation upon challenging conditions. Immunophenotyping by flow and mass cytometry are the major approaches for identifying key signaling molecules and transcription factors directing the transition between the functional states of immune cells. However, few proteins can be evaluated by flow cytometry in a single experiment, preventing researchers from obtaining a comprehensive picture of the molecular programs involved in immune cell differentiation. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled unbiased genome-wide quantification of gene expression in individual cells on a large scale, providing a new and versatile analytical pipeline for studying immune cell differentiation" ; sc:featureList edam:operation_2495 ; sc:name "VirtualCytometry" ; sc:url "https://www.grnpedia.org/cytometry/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:31504195" ; sc:description "a stand-alone program for visualizing and analyzing statistical features of biological sequences | For Microsoft Windows platform, just download the VisFeature-win32-x64.zip package from https://github.com/wangjun1996/VisFeature/releases. Unpack it to your favorite location and then open VisFeature.exe | We have tested these codes on Windows10-64bit platform and Ubuntu 16.04.5 LTS platform. There is no guarantee that these codes can be compiled and executed on other platforms without modifications" ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "VisFeature" ; sc:url "https://github.com/wangjun1996/VisFeature" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2333, edam:format_3751 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "A framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "VisR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.4" ; sc:url "https://visrsoftware.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC6698994", "pubmed:31452600" ; sc:description "Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS | Single test file Multiple test files | If you use VisioProt-MS for your research please cite: | Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux; VisioProt-MS: interactive 2D maps from intact protein mass spectrometry, Bioinformatics, bty680, https://doi.org/10.1093/bioinformatics/bty680 | You are in test mode. Click on a button to select a single test file or multiple test files. Uncheck to exit and upload your own data" ; sc:featureList edam:operation_3629, edam:operation_3633 ; sc:name "VisioProt-MS" ; sc:url "https://masstools.ipbs.fr/mstools/visioprot-ms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3512 ; sc:citation ; sc:description "Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains." ; sc:featureList edam:operation_3202, edam:operation_3798 ; sc:name "VizGVar" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://vizport.io/vizgvar/" ; biotools:primaryContact "Allan Orozco-Solano", "Antonio Solano-Román" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_0798 ; sc:citation , "pubmed:31589313" ; sc:description "Web-Assisted Symbolic Plasmid Synteny Server." ; sc:featureList edam:operation_0578, edam:operation_2421 ; sc:name "WASPS" ; sc:url "https://archaea.i2bc.paris-saclay.fr/wasps/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_2275 ; sc:citation ; sc:description "Tool for improving the design of drugs based on protein-water interactions." ; sc:featureList edam:operation_0482, edam:operation_2415, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "WATCLUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://watclust.wordpress.com/" ; biotools:primaryContact "Adrian G. Turjanski", "Marcelo A. Marti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3372 ; sc:author "Marc Chakiachvili" ; sc:citation ; sc:description "WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances." ; sc:featureList edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "WAVES" ; sc:operatingSystem "Linux" ; sc:provider "LIRMM" ; sc:softwareHelp , ; sc:softwareVersion "1.6" ; sc:url "http://www.atgc-montpellier.fr/waves/" ; biotools:primaryContact "Vincent Lefort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:description "This code is implementation of an algorithm to segment the nucleus of white blood cells (WBCs)" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "An Efficient Technique for White Blood Cells Nuclei Automatic Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36634-an-efficient-technique-for-white-blood-cells-nuclei-automatic-segmentation" ; biotools:primaryContact "Mostafa M. A. Mohamed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6757419", "pubmed:31547811" ; sc:description "weighted bipartite network projection for microRNA-disease association prediction | BACKGROUND:Recently, numerous biological experiments have indicated that microRNAs (miRNAs) play critical roles in exploring the pathogenesis of various human diseases. Since traditional experimental methods for miRNA-disease associations detection are costly and time-consuming, it becomes urgent to design efficient and robust computational techniques for identifying undiscovered interactions. METHODS:In this paper, we proposed a computation framework named weighted bipartite network projection for miRNA-disease association prediction (WBNPMD). In this method, transfer weights were constructed by combining the known miRNA and disease similarities, and the initial information was properly configured. Then the two-step bipartite network algorithm was implemented to infer potential miRNA-disease associations" ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "WBNPMD" ; sc:url "https://github.com/Dicrop/WBNPMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2815, edam:topic_3673 ; sc:citation ; sc:description "Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3644 ; sc:license "AGPL-3.0" ; sc:name "WENGAN" ; sc:url "https://github.com/adigenova/wengan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6375192", "pubmed:30760221" ; sc:description "Pipeline for detecting whole genome duplication events using the genome or transcriptome annotations." ; sc:featureList edam:operation_3258 ; sc:isAccessibleForFree true ; sc:name "WGDdetector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yongzhiyang2012/WGDdetector" ; biotools:primaryContact "Yongzhi Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3534 ; sc:author ; sc:citation ; sc:description "WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein." ; sc:name "WHISCY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://bianca.science.uu.nl/whiscy/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3168 ; sc:citation , "pubmed:31860070" ; sc:description """A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. A cost-effective approach to diploid assembly for single samples and trios. It includes the following steps: construct sequence graph from illumina, align long reads to the graph and partition these long reads to two haplotypes.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3454, edam:operation_3644 ; sc:license "MIT" ; sc:name "WHdenovo" ; sc:url "https://github.com/shilpagarg/WHdenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:31057068" ; sc:description "Fast and Memory Efficient Approach for Mapping NGS Reads to a Reference Genome." ; sc:featureList edam:operation_3198, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "WIT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.algorithm-skg.com/wit/home.html" ; biotools:primaryContact "Sanjeev Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0637, edam:topic_0659, edam:topic_3050, edam:topic_3697 ; sc:citation ; sc:description """A Tool for Within-Taxon Operational Taxonomic Unit Diversity Analysis. A Tool for Within-Taxon Operational Taxonomic Unit (OTU) Diversity. Please copy the OTU Table and the rep_set.fna file into the same directory of witod.py and util directory""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "WITOD" ; sc:url "https://github.com/johncava/WITOD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3399 ; sc:citation , "pmcid:PMC6707408", "pubmed:31463184" ; sc:description "a multi-dimensional program organised around World Pneumonia Day | There are limited examples of population-based approaches that engage a broad range of stakeholders for prevention of pneumonia. In 2010, a multi-dimensional public-private partnership was established around World Pneumonia Day (WPD) in Seoul, Korea and included the following components: a) formation of an expert advisory group, b) creation of educational materials tailored for lay persons, c) creation of a dedicated WPD internet website in the local language, d) organisation of a WPD venue in central Seoul, e) creation of video and social networking messages for wide distribution, and f) engagement of parents, health-care professionals, public health agencies and policymakers" ; sc:name "WPD" ; sc:url "http://www.wpdk.ivi.int/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_0749, edam:topic_0780, edam:topic_3512 ; sc:citation , "pubmed:31693067" ; sc:description """Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server. If you use WPMIAS, please cite this article: Yuhan Fei, Yiyang Mao, Chengji Shen, Rui Wang, Hongsheng Zhang, Ji Huang, "WPMIAS: Whole-degradome-based Plant MicroRNA-Target Interaction Analysis Server", Bioinformatics, 2019, in press. DOI:10.1093/bioinformatics/btz820""" ; sc:featureList edam:operation_0463, edam:operation_3454, edam:operation_3792 ; sc:name "WPMIAS" ; sc:url "https://cbi.njau.edu.cn/WPMIAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description """A Python Package for the Design of Materials for Harnessing Heat. Pioneering the design of materials to harness heat. WPTherml stands for William Paterson University's tool for Thermal Energy and Radiation management with Multi Layer nanostructures. Project maintained by FoleyLab Hosted on GitHub Pages — Theme by mattgraham. WPTherml stands for William Paterson University’s tool for Thermal Energy and Radiation management with Multi Layer nanostructures.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "WPTherml" ; sc:url "https://github.com/FoleyLab/wptherml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736 ; sc:citation , "pmcid:PMC6929547", "pubmed:31874617" ; sc:description """Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion. 2D-wavelet-for-protein-structural-classes-prediction We constructed a prediction model based on wavelet denoising using different feature expression methods. A new fusion idea, first fuse and then denoise, is proposed in this article. Two types of pseudo amino acid compositions are utilized to distill feature vectors. Then, a two-dimensional (2-D) wavelet denoising algorithm is used to remove the redundant information from two extracted feature vectors. The two feature vectors based on parallel 2-D wavelet denoising are fused, which is known as PWD-FU-PseAAC. The project includes three original datasets, source code for two-dimensional wavelet denoising and source code for feature vector prediction""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0474 ; sc:name "Wang-xiaoheng" ; sc:url "https://github.com/Xiaoheng-Wang12/Wang-xiaoheng/tree/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3314, edam:topic_3372 ; sc:citation , "pubmed:31658458" ; sc:description "Wannier90 is a tool for obtaining maximally localized wannier functions from DFT calculations." ; sc:featureList edam:operation_0337 ; sc:name "Wannier90" ; sc:url "http://aiida-wannier90.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3306, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC6858868", "pubmed:31591575" ; sc:description """Real-time cryo-electron microscopy data preprocessing with Warp. If you just want to use Warp, all tutorials and binaries can be found at http://www.warpem.com. Continue reading this README only if you're interested in compiling Warp from source""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3458 ; sc:license "GPL-3.0" ; sc:name "Warp" ; sc:url "http://github.com/cramerlab/warp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:31838514" ; sc:description "WebAnno is a general purpose web-based annotation tool for a wide range of linguistic annotations including various layers of morphological, syntactical, and semantic annotations.Additionaly, custom annotation layers can be defined, allowing WebAnno to be used also for non-linguistic annotation tasks." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3778 ; sc:name "WebAnno" ; sc:url "http://webanno.github.io/webanno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3375, edam:topic_3534 ; sc:citation ; sc:description "Cleavage sites analysis tool for natural and unnatural substrates from diverse data source." ; sc:featureList edam:operation_3216, edam:operation_3501, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "WebMetabase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webmetabase.com:8182/WebMetabaseBioinformatics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_3172, edam:topic_3473, edam:topic_3474, edam:topic_3489 ; sc:author "Miguel Rocha", "Sara Cardoso", "Telma Afonso" ; sc:citation ; sc:contributor "Marcelo Maraschin" ; sc:description "WebSpecmine is a web-based application designed to perform the analysis of metabolomics data based on spectroscopic and chromatographic techniques (NMR, Infrared, UV-visible, and Raman, and LC/GC-MS)) and compound concentrations." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "WebSpecmine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webspecmine.bio.di.uminho.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275 ; sc:citation ; sc:description """An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser. 1 Abstract Molecular docking is a computational technique for predicting how a small molecule might bind a macromolecular target. Among docking programs, AutoDock Vina is particularly popular. Like many docking programs, Vina requires users to download install an executable file and to run that file from a Unix- or DOS-like command-line interface. Choosing proper configuration parameters and analyzing Vina output is also sometimes challenging. These issues are particularly problematic for students and novice researchers. We have created Webina, a new version of Vina, to address these challenges. Webina is a JavaScript WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage. The docking calculations take place on the user’s own computer rather than a remote server""" ; sc:featureList edam:operation_0478, edam:operation_3454 ; sc:name "Webina" ; sc:url "http://durrantlab.com/webina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC6558888", "pubmed:31185910" ; sc:description "Web application for the analysis of fluorescent reporter gene data." ; sc:featureList edam:operation_1812, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "WellInverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://team.inria.fr/ibis/wellinverter/" ; biotools:primaryContact "Hidde de Jong", "Johannes Geiselmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3512, edam:topic_3810, edam:topic_3912 ; sc:citation , "pmcid:PMC6836449", "pubmed:31694550" ; sc:description """a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BACKGROUND:CRISPR Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION:We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat""" ; sc:featureList edam:operation_0440, edam:operation_3096 ; sc:name "WheatCRISPR" ; sc:url "https://crispr.bioinfo.nrc.ca/WheatCrispr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation ; sc:description """This project aims at building an International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-access web based system to access to the available data resources and bioinformatics tools. The web portal indexes and makes findable any kind of data from wheat related species. The WheatIS search is an implementation of DataDiscovery.""" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3625, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "WheatIS" ; sc:softwareHelp , , , ; sc:url "https://urgi.versailles.inrae.fr/wheatis/" ; biotools:primaryContact "Support service" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Wheat IWGSC RefSeq v1.0" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "WheatMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://urgi.versailles.inra.fr/WheatMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318 ; sc:citation , "pmcid:PMC6773861", "pubmed:31575870" ; sc:description """Time series of heat demand and heat pump efficiency for energy system modeling. This repository contains scripts that compile heat demand and COP time series for European countries.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:license "MIT" ; sc:name "When2Heat" ; sc:url "https://github.com/oruhnau/when2heat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation ; sc:description "Whisper is a tool for an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement." ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "Whisper 2" ; sc:url "https://github.com/refresh-bio/whisper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "Automatic white blood cells detector using differential evolution (DE)" ; sc:featureList edam:operation_2429, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "White blood cells detection using differential evolution (DE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47111-white-blood-cells-detection-using-differential-evolution-de" ; biotools:primaryContact "Erik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC6780109", "pubmed:31438611" ; sc:description "Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data | large scale GC-MS data preprocessing workflow | WiPP - A Workflow for improved Peak Picking - Quick Start Guide | WiPP is an open source large scale GC-MS data preprocessing workflow built in Python 3 that uses machine learning to optimise, automate and combine the peak detection process of commonly used peak picking algorithms" ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3629 ; sc:license "MIT" ; sc:name "WiPP" ; sc:url "https://github.com/bihealth/WiPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC6838453", "pubmed:31720321" ; sc:description """An indoor multi-camera multi-space dataset with contextual information and annotations for people detection and tracking. Nowadays, camera networks are part of our every-day life environments, consequently, they represent a massive source of information for monitoring human activities and to propose new services to the building users. To perform human activity monitoring, people must be detected and the analysis has to be done according to the information relative to the environment and the context. Available multi-camera datasets furnish videos with few (or none) information of the environment where the network was deployed. The proposed dataset provides multi-camera multi-space video sets along with the complete contextual information of the environment. The dataset regroups 11 video sets (composed of 62 single videos) recorded using 6 indoor cameras deployed on multiple spaces""" ; sc:featureList edam:operation_3359 ; sc:name "WiseNET" ; sc:url "https://wisenet.checksem.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3293, edam:topic_3500 ; sc:citation ; sc:description "Complete genome assembly of the Wolbachia endosymbiont of the horn fly Haematobia irritans irritans." ; sc:featureList edam:operation_0525, edam:operation_3431, edam:operation_3840 ; sc:name "Wolbachia" ; sc:url "https://github.com/gerthmicha/wolbachia-mlst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0602, edam:topic_0654 ; sc:citation "pubmed:21473782" ; sc:description "To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. This Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network." ; sc:featureList edam:operation_2436, edam:operation_2497, edam:operation_3432, edam:operation_3501 ; sc:name "WordCloud Cytoscape Plugin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://baderlab.org/Software/WordCloudPlugin" ; biotools:primaryContact "Layla Oesper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3405 ; sc:citation , "pmcid:PMC6531084", "pubmed:31096452" ; sc:description "Interactive web-based platform presenting global cancer statistics , which can be used for cancer research." ; sc:featureList edam:operation_2429, edam:operation_2942 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "World Cancer Map" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://worldmap.csmu-liawyp.tw" ; biotools:primaryContact "Yung-Po Liaw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2830, edam:topic_3512 ; sc:citation , "pubmed:31552661" ; sc:description "Immunostainings in Nervous System Development of the Nematode C. elegans | Embryo series courtesy of Einhard Schierenberg | WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes. Wormbook also contains: WormMethods, a collection of protocols for nematode researchers; WormHistory, personal perspectives on C. elegans research; and the Worm Breeder's Gazette, an informal, non-refereed, biannual newsletter for the interchange of ideas and information related to C. elegans and other nematodes. Additional chapters can be found in GENETICS" ; sc:name "WormBook" ; sc:url "http://www.wormbook.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3382 ; sc:citation , "pmcid:PMC6925079", "pubmed:31728898" ; sc:description """open-source robotics platform for survival and behavior analysis in C. elegans. WormBot, C. elegans lifespan robotic image aquisition platform. Homepage UW Pathology Seattle, Washington, USA. WormBot is an open hardware and open software robotic microscopy screening platform designed for C. elegans behavior and survival analysis. This site contains links and information for building the WormBot, an open hardware project designed for automatted survival analysis in the nematode C. elegans. The WormBot is an extremely simple and inexpensive robotics platform that captures timelapse images and realtime movies of nematodes in standard tissue culture plates""" ; sc:featureList edam:operation_3503 ; sc:name "WormBot" ; sc:url "http://wormbot.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Intermine data mining platform for C. elegans and related nematodes" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "WormMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "273" ; sc:url "http://intermine.wormbase.org/tools/wormmine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation ; sc:description "an interactive platform for systems genetics in Caenorhabditis elegans | eQTL visualization and investigation | All eQTL patterns for a single trait" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232 ; sc:name "WormQTL2" ; sc:url "http://www.bioinformatics.nl/WormQTL2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3489 ; sc:citation , "pubmed:31094692" ; sc:description "Massive XML-based biological data management platform." ; sc:featureList edam:operation_0224, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "X2H" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lyotvincent/X2H" ; biotools:primaryContact "Jian Liu", "Lei Zhang", "Qiuru Liu", "Shuhui Su", "Yongzhuang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31400221" ; sc:description "Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data | Wiki for programs and pipelines for sequencing data analysis | 3. XAEM: step by step instruction and explanation | Annotation reference: XAEM requires a fasta file of transcript sequences and a gtf file of transcript annotation. XAEM supports all kinds of reference and annotation for any species. In the XAEM paper, we use the UCSC hg19 annotation:" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3800 ; sc:name "XAEM" ; sc:url "https://github.com/WenjiangDeng/XAEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0659 ; sc:citation , "pubmed:31698618" ; sc:description """Inferring the three-dimensional structures of the X-chromosome during X-inactivation. 3D cubic lattice, 3D structure of the X-chromosome, Xist lncRNA, X-chromosome inactivation. 3D-XCI is a lattice-based 3D modeling tool for generating accurate and stable high-resolution 3D chromosome structures based on population Hi-C data""" ; sc:name "XCI" ; sc:url "http://dna.cs.miami.edu/3D-XCI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , , "pubmed:33091000" ; sc:description "An algorithm for extracting ion chromatograms." ; sc:featureList edam:operation_3203, edam:operation_3636 ; sc:name "XFlow" ; sc:url "https://github.com/optimusmoose/jsms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295 ; sc:citation , "pubmed:31392406" ; sc:description "> HOMEPAGE MISSING! | an eXtreme Gradient Boosting based method for identifying pseudouridine sites | As one of the most popular post-transcriptional modifications, pseudouridine (Ψ) participates in a series of biological processes. Therefore, the efficient detection of pseudouridine sites is very important in revealing its functions in biological processes. Although experimental techniques have been proposed for identifying Ψ sites at single-base resolution, they are still labor intensive and expensive. Recently, to fill the experimental method's gap, computational methods have been proposed for identifying Ψ sites. However, their performances are still unsatisfactory. In this paper, we proposed an eXtreme Gradient Boosting (xgboost)-based method, called XG-PseU, to identify Ψ sites based on the optimal features obtained using the forward feature selection together with increment feature selection method" ; sc:name "XG-PseU" ; sc:url "http://www.bioml.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2828, edam:topic_3448 ; sc:citation , "pmcid:PMC6718201", "pubmed:31475914" ; sc:description "extended gradient descent algorithm for lattice finding | Directory Algorithm documentation | Directory precomputedSamplePoints" ; sc:license "LGPL-3.0" ; sc:name "XGANDALF" ; sc:url "https://stash.desy.de/users/gevorkov/repos/xgandalf/browse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6933652", "pubmed:31881847" ; sc:description "Putative biomarkers for predicting tumor sample purity based on gene expression data." ; sc:featureList edam:operation_2454, edam:operation_3463, edam:operation_3659 ; sc:license "Apache-2.0" ; sc:name "XGBoost" ; sc:url "https://cran.r-project.org/web/packages/xgboost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "XIBD (X chromosome Identity by Descent) performs pairwise identity by descent (IBD) mapping on the autosomes and the X chromosome." ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "XIBD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.wehi.edu.au/software/XIBD/" ; biotools:primaryContact "Lyndal Henden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0593, edam:topic_3678 ; sc:citation , "pubmed:31748843" ; sc:description """multi-dimensional NMR analysis software. Xipp (pronounced zip) is an NMR analysis software package created and supported by Dr. Daniel S. Garrett in the lab of Dr. G. Marius Clore. This software package is designed to study labeled proteins and nucleotides and is a complete re-write and extension of the PIPP package using Java. Xipp uses the same file format for Peak-Pick files and assignment tables as was used in PIPP. In addition many of the keyboard and mouse commands are the same as used by PIPP. The primary differences between PIPP and Xipp is that Xipp allows multiple NMR experiments to be viewed and overlayed at same and has built-in ability to aid in backbone assignment. The most important difference is that PIPP is no longer supported while Xipp is actively supported""" ; sc:featureList edam:operation_0320, edam:operation_3214, edam:operation_3695 ; sc:name "XIPP" ; sc:url "https://spin.niddk.nih.gov/dgarrett/Xipp/xipp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3678 ; sc:citation , ; sc:description "XL-mHG is a Semiparametric Test for Enrichment in Ranked Lists." ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "XL-mHG" ; sc:url "https://github.com/flo-compbio/xlmhg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3337, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description """Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. WM tract atlases for the human (HCP and UK Biobank) and Macaque brain and connectivity blueprint atlases for the human (HCP) and macaque brain. Reference: Warrington S, Bryant KL, Khrapitchev AA, Sallet J, Charquero-Ballester M, Douaud G, Jbabdi S, Mars RB*, Sotiropoulos SN* (in prep.) XTRACT - Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain. XTRACT - a command-line tool for automated tractography. XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to define a set of masks in standard space (e.g. MNI152)""" ; sc:featureList edam:operation_3435 ; sc:name "XTRACT" ; sc:url "http://www.fmrib.ox.ac.uk/fsl/XTRACT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3786 ; sc:name "Query script" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Search and retrieve integrated Xenopus tropicalis and Xenopus laevis data" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2422, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "XenMine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "b BETA bUpdated on:Sep-02-2015" ; sc:url "http://www.xenmine.org/xenmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2640, edam:topic_3170, edam:topic_3304, edam:topic_3673 ; sc:citation ; sc:description """Cloud-based BAM cleansing tool for RNA and DNA from Xenograft. A cloud-based tool for mouse read cleansing in xenograft samples. XenoCP is a tool for cleansing mouse reads in xenograft BAMs. XenoCP can be easily incorporated into any workflow, as it takes a BAM file as input and efficiently cleans up the mouse contamination. The output is a clean human BAM file that could be used for downstream genomic analysis. St. Jude Children's Research Hospital - Pediatric Cancer Genomic Data Portal. Your web browser (Chrome 68) is out of date. Update your browser for more security, speed and the best experience on this site. Update browser Ignore""" ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "XenoCP" ; sc:url "https://pecan.stjude.cloud/permalink/xenocp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31142512" ; sc:description "Integrative pharmacogenomics analysis of patient-derived xenografts." ; sc:featureList edam:operation_0533, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Xeva" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bhklab/Xeva" ; biotools:primaryContact "Benjamin Haibe-Kains" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2259, edam:topic_3382 ; sc:citation , "pmcid:PMC6842926", "pubmed:31749833" ; sc:description """A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images. XitoSBML - the spatial SBML plugin for ImageJ. XitoSBML: Spatial SBML Plugin for ImageJ. XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images. XitoSBML is not just a converter, but also a spatial model editor so that users can add molecules(species), reactions, and advection/diffusion coefficients to the converted Spatial SBML model""" ; sc:featureList edam:operation_2426, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "XitoSBML" ; sc:url "https://github.com/spatialsimulator/XitoSBML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0780, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material." ; sc:featureList edam:operation_3472, edam:operation_3840 ; sc:name "Xylella" ; sc:url "https://github.com/lfaino/xylella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC6873394", "pubmed:31757199" ; sc:description """Better quality score compression through sequence-based quality smoothing. YALFF (Yet Another Lossy FASTQ Filter) is a smoother for FASTQ files which uses an FM-Index to store the k-mer database. The compressed index greatly reduces the amount of memory required compared to other tools such as QUARTZ. This is because the dictionary of k-mers can be linearized into contigs""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3211, edam:operation_3472 ; sc:license "MIT" ; sc:name "YALFF" ; sc:url "https://github.com/yhhshb/yalff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6670153", "pubmed:31366376" ; sc:description "Identification of a novel long non-coding RNA within RUNX1 intron 5 | This site uses cookies. By continuing to browse the site you are agreeing to our use of cookies. Find out more here . {{alert.msg}}" ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_2495 ; sc:name "YAPP" ; sc:url "http://www.bioinformatics.org/yapp/cgi-bin/yapp.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pmcid:PMC6693274", "pubmed:31409274" ; sc:description "Fast and interpretable segment-based alternative splicing and gene expression analysis | Transcript Segment Library Construction for RNA-Seq Quantification | Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3800 ; sc:name "Yanagi" ; sc:url "https://github.com/HCBravoLab/yanagi" . a sc:SoftwareApplication ; 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sc:softwareHelp ; sc:url "https://biokinet.belozersky.msu.ru/yosshiserver/" ; biotools:primaryContact "Dmitry Suplatov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_2830 ; sc:citation , "pmcid:PMC6602444", "pubmed:31106372" ; sc:description "Antibody high-density alignment visualization and analysis platform with an integrated database." ; sc:featureList edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Yvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.icb.ufmg.br/yvis/" ; biotools:primaryContact , "Liza F Felicori" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2840, edam:topic_3304 ; 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Version 1.4" ; sc:featureList edam:operation_3799 ; sc:name "Zirmi" ; sc:url "https://github.com/ADParedes/Zirmi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation , "pubmed:31566657" ; sc:description "A phylogenetic simulator of trees, genomes and sequences that accounts for dead linages | Evolution simulator with extinct lineages | Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages | Zombi is a flexible platform of genome evolution which can be of great interest to those who want to test different evolutionary hypotheses under simulations and need to use a fast and easy-to-use tool to generate species trees, gene trees or sequences. Zombi's output is especially simple and easy to read, understand and parse" ; sc:featureList edam:operation_0325, edam:operation_0544, edam:operation_3478 ; sc:name "Zombi" ; sc:url "https://github.com/AADavin/ZOMBI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3452 ; sc:citation , "pubmed:30710911" ; sc:description "R package for modelling the scattering properties of weak scattering targets using the distorted wave Born approximation." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ZooScatR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AustralianAntarcticDivision/ZooScatR" ; biotools:primaryContact "Australian Antarctic Division" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2828, edam:topic_3489 ; sc:citation , "pubmed:31738502" ; sc:description """Large-Scale Structural Refinement and Screening of Zirconium Metal-Organic Frameworks for H2S/CH4 Separation. You can find more than 182 experimentally synthesized guest-free and disorder-free Zirconium-based metal-organic frameworks (Zr-MOFs), which contain no less than 10 coordinated Zr6O8 inner cores. These structures are optimized by a combination of periodic density functional theory (DFT) and molecular mechanics method, and are given in cif format""" ; sc:featureList edam:operation_2422 ; sc:name "Zr-MOFs" ; sc:url "https://mofs-genomics.github.io/Zr-MOFs-Database" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:26476781" ; sc:description "Python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery." ; sc:featureList edam:operation_2436 ; sc:name "A-DaGO-Fun" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://web.cbio.uct.ac.za/ITGOM/adagofun/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:29329522" ; sc:description "A web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. 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sc:name "a-o-tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Julia-F-S/a-o-tool" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3444 ; sc:citation , "pubmed:35878599" ; sc:description "A pipeline to automatically process and analyze simultaneously acquired EEG-fMRI data for sleep research" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "A-PASS" ; sc:url "https://github.com/guangyuanzou/A-PASS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0123, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC8925138", "pubmed:35296230" ; sc:description "Protein structure modeling using MSA transformer" ; 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Applied to a whole SNP dataset, the tool gives as output a list of SNP-sets associated with the disease and, for each SNP-set, the list of significant SNPs." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "ABACUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://sysbiobig.dei.unipd.it/?q=Software#ABACUS" ; biotools:primaryContact "Barbara Di Camillo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830 ; sc:citation , "pmcid:PMC9710585", "pubmed:36699363" ; sc:description "Approach to predicting antibody-antigen complex structures from sequence." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:name "AbAdapt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sysimm.org/abadapt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3304 ; sc:citation , "pmcid:PMC5048072", "pubmed:27354695" ; sc:description "The package is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function 'aba_enrich' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. 'aba_enrich' interfaces the ontology enrichment software FUNC to perform the statistical analyses." ; sc:featureList edam:operation_2436 ; sc:license "GPL-2.0" ; sc:name "ABAEnrichment" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ABAEnrichment.html" ; biotools:primaryContact "Steffi Grote" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2830, edam:topic_3474, edam:topic_3930 ; sc:citation , "pmcid:PMC9813736", "pubmed:36618397" ; sc:description "A deep learning method for predicting antibody-antigen interactions based on sequence information." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AbAgIntPre" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.zzdlab.com/AbAgIntPre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC10320167", "pubmed:37207341" ; sc:description "A comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires." ; sc:featureList edam:operation_0292, edam:operation_0416, edam:operation_0553 ; sc:isAccessibleForFree true ; sc:name "Abalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cao.labshare.cn/abalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3293, edam:topic_3308 ; sc:citation , "pmcid:PMC6778792", "pubmed:31413154" ; sc:description "The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species." ; sc:featureList edam:operation_3192, edam:operation_3216 ; sc:name "abalonedb" ; sc:url "http://abalonedb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3751 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_3751 ; sc:name "Resource metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3617 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2269, edam:topic_3518 ; sc:citation ; sc:description "An R package which functions provide an automated pipeline to perform expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis. A GUI interface is also provided." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2409, edam:operation_2428, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "ABarray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ABarray.html" ; biotools:primaryContact "Yongming Andrew Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3895 ; sc:citation ; sc:description "Abasy (Across-bacteria systems) Atlas contains the most comprehensive collection of reconstructed and meta-curated bacterial gene regulatory networks having enough quality to allow system-level analyses." ; sc:featureList edam:operation_0438, edam:operation_1781, edam:operation_2437, edam:operation_3431 ; sc:name "Abasy Atlas" ; sc:url "https://abasy.ccg.unam.mx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "abawaca (A Binning Algorithm Without A Cool Acronym) is a binning program that can take advantage of different types of information such as differential coverage and DNA signature." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "abawaca" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CK7/abawaca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:18818729" ; sc:description "Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ABBA" ; sc:operatingSystem "Linux" ; sc:url "http://www.biofacebook.com/?p=250" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation "pubmed:25995231" ; sc:description "Computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs." ; sc:featureList edam:operation_0445 ; sc:name "ABC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mlupien/ABC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0736, edam:topic_0769, edam:topic_3300 ; sc:citation ; sc:description """A containerized web server for the identification and topology prediction of ABC proteins. ABC-Finder i.e., A Docker-based package for the identification of ABC proteins in all organisms, and downstream analysis and visualization of the topology of ABC proteins using an interactive web browser.""" ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "ABC-finder" ; sc:url "http://abc-finder.osdd.jnu.ac.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7379852", "pubmed:32765587" ; sc:description "A web application for analysis of breast cancer GWAS variants." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3431, edam:operation_3661 ; sc:name "ABC-GWAS" ; sc:url "http://education.knoweng.org/abc-gwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3179 ; sc:citation , "pmcid:PMC8896320", "pubmed:35240993" ; sc:description "abc4pwm is a software tool for clustering of pwms, classficiation of pwms to their DNA binding Domain, motif search, and other supportive modules." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3192, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "abc4pwm" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://omer0191.github.io/abc4pwm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3277, edam:topic_3697 ; sc:citation , "pmcid:PMC10767846", "pubmed:37994699" ; sc:description "The atlas of biosynthetic gene clusters in the human microbiome." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "ABC-HuMi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ccb.uni-saarland.de/abc_humi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3400, edam:topic_3408 ; sc:citation , "pubmed:35920330" ; sc:description "ABC portal provides web-based interactive analysis modules, especially a comprehensive cell-cell communication analysis and disease-related gene signature analysis." ; sc:license "Not licensed" ; sc:name "ABC portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://abc.sklehabc.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC3597143", "pubmed:23357921" ; sc:contributor ; sc:description "Providides pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5 - 30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans)." ; sc:featureList edam:operation_2422 ; sc:license "Not licensed" ; sc:name "AbCD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yunliweb.its.unc.edu/AbCD.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3360 ; sc:citation , "pmcid:PMC6722159", "pubmed:31501752" ; sc:description "An Alzheimer's Disease Biomarker Comprehensive Database for Humans. It includes the information for all the genetic parameters like mitochondrial genes, polymorphic genes (SNP's), transcription factors, proteins, miRNAs, Associative pathway, and AD brain images." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:name "Alzheimers Disease Biomarker Comprehensive Database (ABCD)" ; sc:url "http://www.bioinfoindia.org/abcd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workbench" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0780, edam:topic_3390, edam:topic_3810 ; sc:citation ; sc:description "The Aliment to Bodily Condition knowledgebase (ABCkb) is a database connecting plants and human health." ; sc:featureList edam:operation_1812, edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "Aliment to Bodily Condition knowledgebase (ABCkb)" ; sc:url "https://github.com/atrautm1/ABCkb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:33057581" ; sc:description """An automatic data mining tool based on a consistent voting method with a user-friendly graphical interface. In order to extract useful information from a huge amount of biological data nowadays, simple and convenient tools are urgently needed for data analysis and modeling. In this paper, an automatic data mining tool, termed as ABCModeller (Automatic Binary Classification Modeller), with a user-friendly graphical interface was developed here, which includes automated functions as data preprocessing, significant feature extraction, classification modeling, model evaluation and prediction. In order to enhance the generalization ability of the final model, a consistent voting method was built here in this tool with the utilization of three popular machine-learning algorithms, as artificial neural network, support vector machine and random forest.""" ; sc:featureList edam:operation_3436, edam:operation_3936, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "ABCModeller" ; sc:url "http://lishuyan.lzu.edu.cn/ABCModeller.rar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3361 ; sc:citation , "pubmed:34460364" ; sc:description "Adaptive Bezier-Curve Network for Real-time End-to-end Text Spotting." ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "ABCNet" ; sc:softwareVersion "V.2" ; sc:url "https://git.io/AdelaiDet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3400, edam:topic_3948, edam:topic_3966 ; sc:citation , "pmcid:PMC9581038", "pubmed:36303781" ; sc:description "AbCPE web server implements a multi-label classification algorithm that predicts antibody class(es) for epitopes. This data driven machine learning based algorithm offers prediction of epitopes potentially recognised by an individual or multiple classes of antibodies viz. IgG, IgE, IgA and IgM (excluding IgD)." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480, edam:operation_3891 ; sc:license "Other" ; sc:name "AbCPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.unipune.ac.in/AbCPE/Home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_3400 ; sc:citation "pubmed:16894596" ; sc:description "Server to predict linear B cell epitope regions in an antigen sequence, using an artificial neural network. This server will assist in locating epitope regions that are useful in selecting synthetic vaccine candidates, disease diagonosis and also in allergy research." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "ABCpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/abcpred/" ; biotools:primaryContact "Gajendra P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:34609711" ; sc:description "ABCpred is a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors." ; sc:isAccessibleForFree true ; sc:name "ABCpred" ; sc:url "http://codes.bio/abcpred/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description "Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein." ; sc:featureList edam:operation_0321, edam:operation_3482, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "ABCRpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webs.iiitd.edu.in/raghava/abcrpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3315, edam:topic_3407 ; sc:citation , "pubmed:35657711" ; sc:description "ABCstats is an R package for metabolomics data transformation. Adaptive Box-Cox (ABC) transformation improves the data normality for statistical analysis." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ABCstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HuanLab/ABCstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0196, edam:topic_0623, edam:topic_0736, edam:topic_0821 ; sc:citation , "pmcid:PMC7737780", "pubmed:33040418" ; sc:description "The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes." ; sc:featureList edam:operation_0249, edam:operation_0310, edam:operation_0479, edam:operation_2488 ; sc:name "AbDesign" ; sc:url "https://github.com/Fleishman-Lab/AbDesign_for_enzymes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_2830, edam:topic_3297 ; sc:citation ; sc:description "Integrated online application for identification of optimal immunizing peptides for antibody production using peptide-based strategy." ; sc:featureList edam:operation_0252 ; sc:name "AbDesigner3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sysbio.chula.ac.th/AbDesigner3D/" ; biotools:primaryContact "Trairak Pisitkun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3168, edam:topic_3374 ; sc:citation ; sc:description "AbDiver is a tool to explore the natural antibody landscape to aid therapeutic design." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "AbDiver" ; sc:softwareHelp ; sc:url "http://research.naturalantibody.com/abdiver" ; 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sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:36063052" ; sc:description "ABEILLE (ABerrant Expression Identification empLoying machine LEarning from sequencing data) is a variational autoencoder (VAE) based method for the identification of AGEs from the analysis of RNA-seq data without the need of replicates or a control group." ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ABEILLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jlabory.shinyapps.io/ABEILLE-main/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2830, edam:topic_3382 ; sc:citation , "pubmed:37188806" ; 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625 ; sc:description "abi2link is designed to create linkage files out of ABI genotype and phenotype files." ; sc:featureList edam:operation_0335 ; sc:name "abi2link" ; sc:url "http://www.imbs-luebeck.de/imbs/node/40" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "abi2xml is a command line utility to convert an abi trace file to an xml file. 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A mechanistic model of methane emission from animal slurry with a focus on microbial groups." ; sc:featureList edam:operation_0417, edam:operation_2426, edam:operation_3633 ; sc:name "ABM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sashahafner/ABM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2640 ; sc:citation "pubmed:22935054" ; sc:description "Employing agent-based model (ABM) tool to simulate brain tumor growth that includes an EGFR signaling pathway together with a related cell-cycle pathway, angiogenesis and tyrosine kinase inhibitors (TKIs) treatment. The users can apply this tool to predict the responses of brain cancer to TKIs, and to reveal the dual role of angiogenesis during TKI treatment." ; sc:featureList edam:operation_2426, edam:operation_3660 ; sc:name "ABM-TKI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/agentbasedtumormodeling/home" ; biotools:primaryContact "Xiaoqiang Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0102 ; sc:citation "pubmed:21169377" ; sc:description "Portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping." ; sc:featureList edam:operation_2423, edam:operation_2478, edam:operation_2520 ; sc:name "ABMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hkbic.cuhk.edu.hk/software/abmapper" ; biotools:primaryContact "Hong Kong Bioinformatics Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0610, edam:topic_3500, edam:topic_3679 ; sc:citation ; sc:description """abmR is an R package for agent-based model analysis of large-scale movements across taxa. 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The software calculates numerous event-specific metrics for each scored event." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ABOSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zenodo.org/record/6962129" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_2830 ; sc:citation , "pmcid:PMC10239192", "pubmed:37270525" ; sc:description "Web application for documentation and analysis of substitutants." ; sc:featureList edam:operation_0314, edam:operation_2940, edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ABPEPserver" ; sc:url "https://rhpc.nki.nl/sites/shiny/ABPEP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0769 ; sc:citation ; sc:description "abPOA can perform multiple sequence alignment (MSA) on a set of input sequences and generate a consensus sequence by applying the heaviest bundling algorithm to the final alignment graph." ; sc:featureList edam:operation_0310, edam:operation_0492, edam:operation_0496 ; sc:license "MIT" ; sc:name "abPOA" ; sc:url "https://github.com/yangao07/abPOA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:24907369" ; sc:description "Realigner for next generation sequencing data. 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The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. 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sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3374 ; sc:description "Perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files." ; sc:isAccessibleForFree true ; sc:name "Absolute and Comparison Analysis for Affymetrix Data" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/7331-absolute-and-comparison-analysis-for-affymetrix-data" ; biotools:primaryContact "Abram Jujunashvili" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3519, edam:topic_3674 ; sc:citation , "pmcid:PMC9846423", "pubmed:36629453" ; sc:description "Automated R tool to efficiently analyse region-specific CpG methylation from bisulfite sequencing PCR." ; sc:featureList edam:operation_3185, edam:operation_3186, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ABSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ABSP-methylation-tool/ABSP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2032 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3617 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170 ; sc:citation , "pmcid:PMC4973090", "pubmed:27488180" ; sc:description "An R package which provides RNA-Seq analysis based on modelling absolute expression differences." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2426, edam:operation_2495, edam:operation_3223 ; 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Generates BLAST hits against each of the reference genomes, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.""" ; sc:featureList edam:operation_0224, edam:operation_0323, edam:operation_0492, edam:operation_0552, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ACES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TNTurnerLab/ACES" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:name "Gene ID (NCBI)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2292 ; sc:name "GenBank accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2803 ; sc:name "Clone ID (RefSeq)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2704 ; sc:name "Clone ID (IMAGE)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3512 ; sc:citation , "pmcid:PMC3272079", "pubmed:20064451" ; sc:description "A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace)." ; sc:featureList edam:operation_0224 ; sc:name "AceView genes database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NCBI" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3056 ; sc:citation "pubmed:23379678" ; sc:description "The Ancestral Recombination Graph tool is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it." ; sc:featureList edam:operation_2478 ; sc:name "ACG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://arup.utah.edu/acg/" ; biotools:primaryContact "Brendan O'Fallon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3175, edam:topic_3518 ; sc:citation ; sc:description "This tool includes functions for reading aCGH data from image analysis output files and clone information files or creating S3 objects for storing these data. It also incudes basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects." ; sc:featureList edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "aCGH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/aCGH.html" ; biotools:primaryContact "Peter Dimitrov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_0166 ; sc:citation , "pmcid:PMC10320090", "pubmed:37158246" ; sc:description "Application for fast calculation of partial atomic charges of structures from the Alphafold database." ; sc:featureList edam:operation_0474, edam:operation_0478, edam:operation_3431, edam:operation_3893 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "aCharges" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://alphacharges.ncbr.muni.cz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:14962935" ; sc:description "The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. 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Three functions include Attention mechanism threshold, Contour equalization, and Lung segmentation (ACL)." ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:license "Not licensed" ; sc:name "ACL" ; sc:url "https://github.com/Lqs-github/ACL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_0798, edam:topic_3053, edam:topic_3957 ; sc:citation "pubmed:19933762" ; sc:description "This database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). 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It does not rely on a specific array technology (although the array should be a \"tiling\" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is fast and can be applied on whole-genome tiling array experiments easily with enough memory." ; sc:featureList edam:operation_3501 ; sc:license "GPL-2.0" ; sc:name "ACME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ACME.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_2275 ; sc:citation "pubmed:26017195" ; sc:description "The Ambivalent Covariance Models are stochastic homology search tools that support more than one consensus secondary RNA structures." ; sc:featureList edam:operation_0475 ; sc:name "aCMs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv2.cebitec.uni-bielefeld.de/acms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0202, edam:topic_0602, edam:topic_0780, edam:topic_2640 ; sc:citation , "pmcid:PMC8419280", "pubmed:34497528" ; sc:description """The Database for Elucidating the Relationships Between Natural Products, Compounds, Molecular Mechanisms, and Cancer Types. ACNPD is an online tool that provides users with a quick search of the pharmacological mechanisms of natural anti-cancer products. The database contains 10 common cancer types, XXX compounds, XXX pharmacological mechanisms, involving PI3K/Akt, PI3K/Akt/mTOR, Wnt/ β-catenin and other signaling pathways. The web interface allows users to query related queries in a variety of ways.""" ; sc:featureList edam:operation_0306, edam:operation_2421 ; sc:name "ACNPD" ; sc:url "http://www.acnpd-fu.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3474, edam:topic_3673 ; sc:citation ; sc:description "ACO is a lossless quality scores compression algorithm based on adaptive coding order and this software can be used for both encoding and decoding." ; sc:featureList edam:operation_1812, edam:operation_3435, edam:operation_3802 ; sc:license "MIT" ; sc:name "ACO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Yoniming/code" ; biotools:primaryContact "Niu Yi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; 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sc:description "ACovPepDB is a comprehensive peptides database of anti-coronavirus peptides, which contains 518 enrties with 214 unique ACovPs manually extracted from research articles and public databases." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ACovPepDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/ACovPepDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC8279753", "pubmed:34276801" ; sc:description "Improving the Prediction of Anticancer Peptides Using Data Augmentation." ; sc:featureList edam:operation_3435, edam:operation_3935 ; sc:name "ACP-DA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/chenxgscuec/ACPDA" . a sc:SoftwareApplication ; 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sc:featureList edam:operation_3631, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "ACP-MLC" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Nicole-DH/ACP-MLC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640 ; sc:citation , "pubmed:36326080" ; sc:description "A prediction model of anticancer peptides based on feature extraction." ; sc:featureList edam:operation_3631, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "ACP_MS" ; sc:url "https://github.com/Zhoucaimao1998/Zc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC9763336", "pubmed:36535969" ; sc:description "ACPred-BMF server is used for anticancer peptide (ACP) prediction." ; 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Find your mutation or gene of interest. You are viewing an updated version (2021) of the ActiveDriverDB. To view the previous version please visit activedriverdb.org/v2020. cystic fibrosis mutations in CFTR. 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The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters for different population structures, genetic models, selection strategies, and mating designs. 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AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available." ; sc:featureList edam:operation_0232, edam:operation_3192, edam:operation_3237 ; sc:name "AdapterRemoval" ; sc:softwareVersion "v2.3.2" ; sc:url "https://github.com/MikkelSchubert/adapterremoval" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3168, edam:topic_3518 ; sc:description "Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when operating in high-dimensional settings (). The utilities provided here extend the use of this general methodology to many common data analytic challenges that arise in modern computational and genomic biology." ; sc:featureList edam:operation_2424, edam:operation_3223, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "adaptest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/adaptest.html" ; biotools:primaryContact "Weixin Cai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation "pubmed:18497299" ; sc:description "Software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity." ; sc:featureList edam:operation_3478 ; sc:name "AdaptML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://almlab.mit.edu/adaptml.html" ; biotools:primaryContact "Eric Alm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3295, edam:topic_3320, edam:topic_3334, edam:topic_3512 ; sc:citation , "pmcid:PMC7979890", "pubmed:33741983" ; sc:description "ADAS-viewer (Visualization of Alzheimer's Disease Alternative Splicing) is a web-based application for integrative analysis of multi-omics data in Alzheimer's disease." ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_3196 ; sc:name "ADAS-viewer" ; sc:softwareHelp , ; sc:url "http://genomics.chpc.utah.edu/AD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3125 ; sc:citation ; sc:description "The database of Allelic Dosage-corrected Allele-Specific human Transcription factor binding sites provides a genomic map of allele-specific binding at hundreds thousands single-nucleotide polymorphisms constructed by meta-analysis of thousands of ChIP-Seq experiments." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "ADASTRA" ; sc:softwareHelp ; sc:softwareVersion "5.1.2" ; sc:url "https://adastra.autosome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3071 ; sc:citation , "pmcid:PMC6017986", "pubmed:29951204" ; sc:description "Web Tool for Navigating and Plotting SomaLogic ADAT Files." ; sc:featureList edam:operation_2495, edam:operation_2939 ; sc:license "Apache-2.0" ; sc:name "ADAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://foocheung.shinyapps.io/adat/" ; biotools:primaryContact "Foo Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3379, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC7744022", "pubmed:33344750" ; sc:description "ADataViewer is an interactive web application for identify cohort data sets that are suitable for their research in regards to the Alzheimer's disease data landscape." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3435 ; sc:name "ADataViewer" ; sc:url "https://adata.scai.fraunhofer.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3068, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:34146104" ; sc:description "A Novel Data-Adaptive Robust Method for Identifying Tissue Specificity Scores." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AdaTiSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mwgrassgreen/AdaTiSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_2830, edam:topic_3170 ; sc:citation , "pmcid:PMC8604336", "pubmed:34752449" ; sc:description "ADC is an efficient method to identify highly interrelated genes across datasets." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3891 ; sc:name "ADC" ; sc:url "https://github.com/zhanglabtools/ADC" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3336, edam:topic_3379 ; sc:citation , "pmcid:PMC10768060", "pubmed:37831118" ; sc:description "ADCdb: The database of antibody-drug conjugates." ; sc:featureList edam:operation_0224, edam:operation_0480, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "ADCdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/adcdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3047, edam:topic_3292, edam:topic_3336, edam:topic_3369, edam:topic_3376 ; sc:citation ; sc:description "Addgene is an nonprofit online database for plasmids and plasmid associated information." ; sc:name "Addgene" ; sc:url "https://www.addgene.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2840, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9227411", "pubmed:35745053" ; sc:description "AddictedChem is a base of controlled substances and a platform for predicting NPS." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3216, edam:operation_3929, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AddictedChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://design.rxnfinder.org/addictedchem/prediction/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0203, edam:topic_3295, edam:topic_3419 ; sc:citation , "pmcid:PMC8113760", "pubmed:34025933" ; sc:description "AddictGene is an integrated knowledge base for differentially expressed genes associated with psychostimulants," ; sc:featureList edam:operation_2422, edam:operation_3223, edam:operation_3431, edam:operation_3672 ; sc:name "AddictGene" ; sc:softwareHelp ; sc:url "http://159.226.67.237/sun/addictgedb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8496238", "pubmed:34544122" ; sc:description """AddTag is a two-step approach with supporting software package that facilitates CRISPR/Cas-mediated precision genome editing. CRISPR Cas-induced genome editing is a powerful tool for genetic engineering, however, targeting constraints limit which loci are editable with this method. Since the length of a DNA sequence impacts the likelihood it overlaps a unique target site, precision editing of small genomic features with CRISPR Cas remains an obstacle. We introduce a two-step genome editing strategy that virtually eliminates CRISPR Cas targeting constraints and facilitates precision genome editing of elements as short as a single base-pair at virtually any locus in any organism that supports CRISPR Cas-induced genome editing. Our two-step approach first replaces the locus of interest with an "AddTag" sequence, which is subsequently replaced with any engineered sequence, and thus circumvents the need for direct overlap with a unique CRISPR Cas target site.""" ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "AddTag" ; sc:url "https://github.com/tdseher/addtag-project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33401309" ; sc:description "ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0463, edam:operation_2441, edam:operation_3223 ; sc:name "ADeditome" ; sc:url "https://ccsm.uth.edu/ADeditome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3948 ; sc:citation , "pmcid:PMC8344678", "pubmed:34254996" ; sc:description "An integrated platform of age-dependent expression and immune profiles across human tissues." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3800 ; sc:name "ADEIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://geneyun.net/ADEIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3473 ; sc:citation , "pubmed:33074804" ; sc:description "AdelaiDet is an open source toolbox for multiple instance-level recognition tasks on top of Detectron2. All instance-level recognition works from our group are open-sourced here." ; sc:featureList edam:operation_3359, edam:operation_3436 ; sc:name "AdelaiDet" ; sc:url "http://git.io/AdelaiDet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0654, edam:topic_3303 ; sc:citation , "pmcid:PMC7470936", "pubmed:32692355" ; sc:description "Adenita is a 3D visualization and modeling toolkit for the in silico design of static and dynamic DNA nanostructures. Based on a multiscale data model, it visualizes DNA-based structures on different abstraction levels and enable users to load and create DNA origami structures and combine them with proteins." ; sc:featureList edam:operation_0570, edam:operation_2442, edam:operation_3216 ; sc:license "BSD-3-Clause" ; sc:name "Adenita" ; sc:url "https://github.com/edellano/Adenita-SAMSON-Edition-Linux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation ; sc:description "Adenosiland represents the first attempt of an integrated bioinformatics and chemoinformatics web-resource dedicated to adenosine receptors. This informatics platform provides a wide-ranging of structure based and ligand based query functions to facilitate the exploration of adenosine receptor structures from primary sequences to three-dimensional architectures. Here, we present an overview of Adenosiland platform describing the most valuable searching tools and their functionalities." ; sc:featureList edam:operation_2406 ; sc:name "Adenosiland" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:url "http://mms.dsfarm.unipd.it/Adenosiland/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:author "Nicole Mentenich" ; sc:citation , "pubmed:32529631" ; sc:description "AdEPro (Animation of Adverse Event Profiles) is an app that (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "Animation of Adverse Event Profiles (AdEPro)" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=adepro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_3378, edam:topic_3379 ; sc:citation , "pmcid:PMC7660953", "pubmed:33215076" ; sc:description "ADEPT is a tool for a high-sensitivity natural language processing (NLP) pipeline for detecting potential adverse drug events (ADEs) with easily interpretable output for high-efficiency human review and adjudication of true ADEs." ; sc:featureList edam:operation_3778 ; sc:license "Apache-2.0" ; sc:name "Adverse drug event presentation and tracking (ADEPT)" ; sc:url "https://github.com/hms-dbmi/adept" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_0166, edam:topic_2275, edam:topic_3382 ; sc:citation "pubmed:23609539" ; sc:description "Adepth web server provides both depth and height representation of an atom in a macromolecule; it is capable of computing isosurfaces for atomic depths and presenting graphical view of marcomolecular shape at some distance away from the surface." ; sc:featureList edam:operation_0387, edam:operation_0478, edam:operation_2950 ; sc:name "Adepth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodev.cea.fr/adepth" ; biotools:primaryContact "Adepth coordinator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:21121022" ; sc:description "Software package for peptide identification using two different types of MS/MS spectra." ; sc:featureList edam:operation_3631 ; sc:name "ADEPTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cs.uwaterloo.ca/~l22he/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1147 ; sc:name "GEO accession number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:name "Pathway or network report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , "pmcid:PMC8223391", "pubmed:34167460" ; sc:description "ADEx: Autoimmune Diseases Explorer is a comprehensive and centralized database for exploring omics data in Autoimmune Diseases. The database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases." ; sc:featureList edam:operation_0313, edam:operation_0571, edam:operation_2495, edam:operation_3431, edam:operation_3436, edam:operation_3501, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "ADEx: Autoimmune Diseases Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://adex.genyo.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168, edam:topic_3320 ; sc:citation , "pubmed:32246828" ; sc:description "ADFinder is an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software would facilitate research of programmed DNA eliminations and all down-stream analyses." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_3196 ; sc:name "ADFinder" ; sc:url "https://github.com/weibozheng/ADFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0203, edam:topic_3277, edam:topic_3518 ; sc:citation "pubmed:16837524", "pubmed:21624890" ; sc:description "ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information." ; sc:featureList edam:operation_2436, edam:operation_2495, edam:operation_3223, edam:operation_3762 ; sc:name "ADGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.btool.org/ADGO2" ; biotools:primaryContact "ADGO Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_0128, edam:topic_3474, edam:topic_3957 ; sc:citation , "pmcid:PMC9576568", "pubmed:36267921" ; sc:description "An attention-based deep hybrid model for protein-protein interaction prediction." ; sc:featureList edam:operation_0267, edam:operation_2492, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ADH-PPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opendfki.de/PPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0637, edam:topic_3303, edam:topic_3375 ; sc:citation , , "pubmed:31438176" ; sc:description "Computation of adherence to medications from Electronic Healthcare Data." ; sc:featureList edam:operation_0224, edam:operation_0337 ; sc:name "AdhereR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://cran.r-project.org/web/packages/AdhereR/index.html" ; biotools:primaryContact "Dan Dediu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in", "Script" ; sc:applicationSubCategory edam:topic_0153, edam:topic_2229, edam:topic_3382, edam:topic_3407 ; sc:citation , "pmcid:PMC9635306", "pubmed:35947507" ; sc:description "A simple toolbox of two ImageJ plugins for quantifying adipocyte morphology and function in tissues and in vitro." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AdipoQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hansenjn/AdipoQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "A scalable tool to visualize the adjacency matrix with values on the edges, direction, and the sum of value as the node size." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Adjacency-Matrix-Visualizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/73772-adjacency-matrix-visualizer" ; biotools:primaryContact "Chaohan Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3418, edam:topic_3474 ; sc:citation , "pmcid:PMC7402217", "pubmed:32185818" ; sc:description "Adjusted-ADJUST is a script for the automatic identification of artifacts in electroencephalograph (EEG) data." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Adjusted-ADJUST" ; sc:url "https://github.com/ChildDevLab/MADE-EEG-preprocessing-pipeline/tree/master/adjusted_adjust_scripts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444 ; sc:description "ALC is a dynamic fMRI connectivity toolbox for single-subject validation." ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Adjusted Local Connectivity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/61814-adjusted-local-connectivity" ; biotools:primaryContact "Mangor Pedersen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3653 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3653 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3520, edam:topic_3572 ; sc:description "A tool for adjusting mass spectrometry peaks in PKL file. 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3379 ; sc:citation , "pubmed:34176369" ; sc:description "Validating ADME QSAR Models Using Marketed Drugs." ; sc:featureList edam:operation_0409, edam:operation_2428, edam:operation_3799 ; sc:name "ADME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://opendata.ncats.nih.gov/adme/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_0654, edam:topic_3295 ; sc:citation , "pubmed:35617175" ; sc:description "A manually curated database for the differential methylation in Alzheimer's disease." ; sc:featureList edam:operation_2421 ; sc:license "Not licensed" ; sc:name "ADmeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biobdlab.cn/ADmeth" . a sc:SoftwareApplication ; 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Becker's Robot Swarm Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3974 ; sc:citation , "pmcid:PMC10371492", "pubmed:37471595" ; sc:description "AGHmatrix software is an R-package to build relationship matrices using pedigree (A matrix) and/or molecular markers (G matrix) with the possibility to build a combined matrix of Pedigree corrected by Molecular (H matrix). 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The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data." ; sc:featureList edam:operation_2429, edam:operation_3196 ; sc:name "AgileGenotyper" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130204" ; sc:url "http://dna.leeds.ac.uk/agile/AgileGenotyper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "AgilePairedEndReadsCombiner reads a matching pair of fasta or fastq files created from a paired end sequence run which used PCR products as the library template and combines the data to produce a single read file contain data equivalent to the whole PCR product." ; sc:featureList edam:operation_0335 ; sc:name "AgilePairedEndReadsCombiner" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20140923" ; sc:url "http://dna.leeds.ac.uk/agile/AgilePairedEndReadsCombiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3056, edam:topic_3676 ; sc:citation "pubmed:24307375" ; sc:description "Enables the rapid filtering, screening and sorting of indel variants derived from an exome sequencing experiment to allow the rapid detection of possible deleterious variants." ; sc:featureList edam:operation_3197 ; sc:name "AgilePindelFilter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/agile/AgilePindelFilter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "AgileQualityFilter performs a number of pre-alignment tasks on sequence data from an Illumina GA-II clonal sequencer. The primary function of AgileQualityFilter is to remove low quality sequence data before alignment to a reference sequence." ; sc:featureList edam:operation_0335, edam:operation_2428, edam:operation_2928 ; sc:name "AgileQualityFilter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20121127" ; sc:url "http://dna.leeds.ac.uk/agile/AgileQualityFilter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "This script normalises a set of gene expression data files against a predefined reference data set. The normalisation uses LOESS regression. The major assumption is that the actual data and the reference set have a similar epxression frequency distribution. 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Deep learning model (Temporal conv net, using dilated conv layers) detects post-translational modified peptides based on their ms/ms spectrum." ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3755, edam:operation_3860 ; sc:license "MIT" ; sc:name "AHLF" ; sc:url "http://gitlab.com/dacs-hpi/ahlf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3301, edam:topic_3339, edam:topic_3340 ; sc:citation "pubmed:12824404" ; sc:description "This tool offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2421, edam:operation_3431 ; sc:name "AHMII" ; sc:url "http://www.wdcm.org/AHMII/ahmii.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "AhNGE is a Database for Arachis hypogaea nodule developmental gene expression." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_2422, edam:operation_3672 ; sc:name "AhNGE" ; sc:url "http://nipgr.ac.in/AhNGE/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2814, edam:topic_3534 ; sc:citation , "pmcid:PMC9750100", "pubmed:36282546" ; sc:description "Webserver & command-line tool for search and alignment of APO (unbound) protein structures from HOLO (bound) forms and vice versa. Features: customizable search of Apo-Holo pairs in the PDB, alignment to the query structure, batch mode for fast parallel dataset processing, visualization via Molstar and PyMol, public documented REST-API." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AHoJ: Apo Holo Protein Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.4.7" ; sc:url "http://apoholo.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3376 ; sc:citation , "pmcid:PMC4383949", "pubmed:25392419" ; sc:description "Manually curated database of experimentally validated Antihypertensive peptides (AHTPs) with comprehensive information that includes: sequence, inhibitory concentration (IC50), log value of inhibitory concentration (pIC50) and toxicity." ; sc:featureList edam:operation_0226, edam:operation_2409 ; sc:name "AHTPDB" ; sc:softwareHelp , ; sc:url "https://webs.iiitd.edu.in/raghava/ahtpdb/" ; biotools:primaryContact "DR. Gajendra P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation "pubmed:26538599" ; sc:description "AHTpin is an in silico method developed to predict and design efficient antihypertensive peptides." ; sc:featureList edam:operation_2415 ; sc:name "AHTpin" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ahtpin/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3335, edam:topic_3474 ; sc:citation , "pubmed:35474167" ; sc:description "Accurate prediction of anti-hypertensive peptides based on convolutional neural network and gated recurrent unit" ; sc:featureList edam:operation_0267, edam:operation_0433, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AHTPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ahtps.zhanglab.site/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:33719168" ; sc:description """A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion. cloud_download Download test images. To run the AI-biopsy framework please follow these steps:. process and result folders from ML training (Not included in this repository). Pre-trained Models of CNN architectures should be downloaded from the "Pre-trained Models" part of https://github.com/wenwei202/terngrad/tree/master/slim#pre-trained-models and be located in your machine (e.g. GitHub_AI-biopsy/scripts/slim/run/checkpoint). The files for pre-trained models are available under the column named "Checkpoint". For accurate results, we recommend the use of axial images with a visible prostate gland. Also, 7 slices per patient are used in voting system to measure the accuracy of the trained model for individual patients. ||| CORRECT NAME OF TOOL COULD ALSO BE 'h4AI-biopsy'""" ; sc:featureList edam:operation_3443 ; sc:license "MIT" ; sc:name "AI-biopsy" ; sc:url "https://ai-biopsy.eipm-research.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation ; sc:description "AI-CT-COVID-19 is a collaborative online AI engine for precise CT-based COVID-19 diagnosis using federated learning to provide people worldwide an effective AI model for precise CT-COVID diagnosis." ; sc:name "AI-CT-COVID-19" ; sc:url "http://www.ai-ct-covid.team/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC7671397", "pubmed:33575629" ; sc:description "AI-Driver (AI-based driver classifier) is an ensemble method for predicting the driver status of somatic missense mutations based on 23 pathogenicity features. AI-Driver is an ensemble method for identifying driver mutations in personal cancer genomes." ; sc:featureList edam:operation_0331, edam:operation_3227 ; sc:name "AI-Driver" ; sc:url "http://aidriver.maolab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3373, edam:topic_3474 ; sc:citation ; sc:description "AI4AMP is a sequence-based antimicrobial peptides (AMP) predictor based on PC6 protein encoding method and deep learning." ; sc:featureList edam:operation_2492, edam:operation_3927 ; sc:name "AI4AMP" ; sc:url "http://symbiosis.iis.sinica.edu.tw/PC_6/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3393, edam:topic_3940 ; sc:citation , "pubmed:34273560" ; sc:description "A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis." ; sc:featureList edam:operation_0337, edam:operation_3218, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:name "AIAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Zhang-lab/ATAC-seq_QC_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation "pubmed:20047774" ; sc:description "Lightweight, non-intrusive MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output." ; sc:featureList edam:operation_2409 ; sc:name "AIBench" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.aibench.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_0196, edam:topic_0736 ; sc:citation , , "pmcid:PMC4086082", "pmcid:PMC4481839", "pubmed:24831546", "pubmed:25701568" ; sc:description "AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. 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AIDD explores editome by mapping both ADAR and APOBEC editing sites on a global and local level and produces publication ready visualization of ADAR editing landscapes." ; sc:featureList edam:operation_3096, edam:operation_3680, edam:operation_3891 ; sc:name "AIDD" ; sc:url "https://github.com/RNAdetective/AIDD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8501087", "pubmed:34625565" ; sc:description "AIDE (Annotation-effIcient Deep lEarning) is a deep learning framework for automatic medical image segmentation with imperfect datasets, including those having limited annotations, lacking target domain annotations, and containing noisy annotations. Automatic segmentation of medical images plays an essential role in both scientific research and medical care. Deep learning approaches have presented encouraging performances, but existing high-performance methods typically rely on very large training datasets with high-quality manual annotations, which are normally difficult or even impossible to obtain in many clinical applications." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:license "LGPL-2.1" ; sc:name "AIDE" ; sc:url "https://github.com/lich0031/AIDE" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382, edam:topic_3421, edam:topic_3474, edam:topic_3934 ; sc:citation ; sc:description "AIDeveloper is a software tool that allows you to train, evaluate and apply deep neural nets for image classification within a graphical user-interface (GUI)." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3802 ; sc:license "BSD-3-Clause" ; sc:name "AIDeveloper" ; sc:url "https://github.com/maikherbig/AIDeveloper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3400 ; sc:citation ; sc:description "AIdrug2cov is a network representation learning-based methodology to discover drug mechanism and anti-inflammatory response for patients with COVID-19." ; sc:name "AIdrug2cov" ; sc:url "https://github.com/pengsl-lab/AIdrug2cov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3375, edam:topic_3474 ; sc:citation ; sc:description "Artificial Intelligence-based Web-App for Virtual Screening of Inhibitors against SARS-COV-2." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:name "AIDrugApp" ; sc:url "https://sars-covid-app.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3324, edam:topic_3412, edam:topic_3577 ; sc:citation , "pmcid:PMC10229817", "pubmed:37266419" ; sc:description "An easy-to-use AIHF-nomogram to predict advanced liver fibrosis in patients with autoimmune hepatitis." ; sc:featureList edam:operation_2428, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "AIHF-nomogram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ndth-zzy.shinyapps.io/AIHF-nomogram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3332, edam:topic_3473, edam:topic_3524 ; sc:citation , , "pmcid:PMC7479590", "pubmed:32901044" ; sc:description "Sophisticated framework designed from scratch to be a flexible and scalable infrastructure for computational science. Being able to store the full data provenance of each simulation, and based on a tailored database solution built for efficient data mining implementations, AiiDA gives the user the ability to interact seamlessly with any number of HPC machines and codes thanks to its flexible plugin interface, together with a powerful workflow engine for the automation of simulations." ; sc:featureList edam:operation_3762 ; sc:license "MIT" ; sc:name "AiiDA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.aiida.net/" ; biotools:primaryContact "Andrius Merkys" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3299, edam:topic_3332, edam:topic_3336, edam:topic_3371 ; sc:citation , "pmcid:PMC7267738", "pubmed:32498019" ; sc:description "AILDE (Auto In Silico Ligand Directing Evolution) server is developed according to the CSO (Computational Substitution Optimization) protocol, which was designed to automatically perform computational substitution, energy minimization, and binding affinity evaluation. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead." ; sc:featureList edam:operation_0531, edam:operation_3216, edam:operation_3938 ; sc:name "AILDE" ; sc:softwareHelp ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/AILDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation "pubmed:15376910" ; sc:description "The Automatic Image Processing for Microarrays tool is designed for uncalibrated microarray gridding and quantitative image analysis. Uncalibrated microarray image analysis supports integration of expression data from different sources and can improve reproducibility." ; sc:featureList edam:operation_0571, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AIM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/aim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC8820645", "pubmed:35081109" ; sc:description "Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments." ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "AIME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tianwei-yu/AIME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_0821, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC8385923", "pubmed:34368837" ; sc:description "A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe." ; sc:featureList edam:operation_0478, edam:operation_3937, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AIMEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SIAT-code/AIMEE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3315, edam:topic_3512, edam:topic_3519 ; sc:citation ; sc:description "A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk." ; sc:featureList edam:operation_3799, edam:operation_3927 ; sc:name "aiMeRA" ; sc:softwareHelp ; sc:url "https://github.com/bioinfo-ircm/aiMeRA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3169, edam:topic_3512 ; sc:citation ; sc:description "AIModules enables you to find transcription factor binding sites (TFBSs) and modules on DNA using own matrices or the JASPAR 2022 database." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0337, edam:operation_0445 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "AIModules" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-wuerz.de/aimodules/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_2640 ; sc:citation ; sc:description "This package contains the necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). 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It can handle protein families with tens of thousand of sequences and is particularly suitable for evolutionary coupling analysis, preparing the computation of protein 3D structures and detection of functionally constrained interactions." ; sc:featureList edam:operation_0492, edam:operation_0564, edam:operation_2479 ; sc:license "MIT" ; sc:name "AlignmentViewer" ; sc:url "http://alignmentviewer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description """A Python package for parsing complex features from high-throughput long-read sequencing. Align sequences and then parse features. alignparse documentation — alignparse 0.1.2 documentation. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features. For each read that passes the filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses. alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features""" ; sc:featureList edam:operation_1812, edam:operation_3198, edam:operation_3695 ; sc:name "alignparse" ; sc:url "https://jbloomlab.github.io/alignparse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_2814 ; sc:citation ; sc:description "Viewing protein secondary structure predictions within large multiple sequence alignments. The module is part of the ANTHEPROT package." ; sc:featureList edam:operation_0570 ; sc:name "ALIGNSEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://antheprot-pbil.ibcp.fr/" ; biotools:primaryContact "Gilbert Deleage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269 ; sc:citation , "pmcid:PMC5081975", "pubmed:27784265" ; sc:description "AlignStat is a web-tool and R package for statistical comparison of alternative multiple sequence alignments." ; sc:featureList edam:operation_2451 ; sc:license "Other" ; sc:name "AlignStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.2" ; sc:url "http://alignstat.science.latrobe.edu.au/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "LC-MS alignment algorithm based on Wasserstein distance." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Alignstein" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/grzsko/Alignstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "ALION is a sequence alignment tool. 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Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass""" ; sc:featureList edam:operation_0525, edam:operation_2429, edam:operation_2495 ; sc:name "alkaligrass" ; sc:url "http://xhhuanglab.cn/data/alkaligrass.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1088 ; sc:name "Article ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1086 ; sc:name "Compound identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "Chemicals prioritization for topics of interest using gene-related PubMed abstracts." ; sc:featureList edam:operation_0305 ; sc:name "Alkemio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm.uni-mainz.de/medlineranker" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3321 ; sc:citation "pubmed:22833229" ; sc:description "Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect." ; sc:featureList edam:operation_2406, edam:operation_2423, edam:operation_3630 ; sc:name "ALL-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pappso.inra.fr/bioinfo/all_p/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3676 ; sc:citation ; sc:description "All2 is a tool for filtering variants from all2all comparison of multiple clones or single cells. There are no variant allele frequency and mutation spectrum plots for structural variant mode and the format of the output files will be slightly different from the SNV/INDEL analyses." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "All2" ; sc:url "https://github.com/abyzovlab/All2" ; biotools:primaryContact "Alexej Abyzov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_3316 ; sc:citation , "pmcid:PMC7542712", "pubmed:33028201" ; sc:description "AllCoPol is a collection of tools for the analysis of polyploids, which allow to infer ancestral allele combinations as well as corresponding subgenome phylogenies." ; sc:featureList edam:operation_3432, edam:operation_3478, edam:operation_3840 ; sc:license "MIT" ; sc:name "AllCoPol" ; sc:url "https://github.com/AGOberprieler/allcopol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0749 ; sc:citation ; sc:description "It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome." ; sc:featureList edam:operation_0238 ; sc:name "Allegro" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://acgt.cs.tau.ac.il/allegro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_2830, edam:topic_3056, edam:topic_3305 ; sc:citation "pubmed:21062830" ; sc:description "The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms." ; sc:featureList edam:operation_0487, edam:operation_0542, edam:operation_3196, edam:operation_3221, edam:operation_3227 ; sc:name "Allele frequency net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.allelefrequencies.net" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:22925629" ; sc:description "R package to simulate small populations. Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period." ; sc:featureList edam:operation_2426 ; sc:name "AlleleRetain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/alleleretain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC8212829", "pubmed:34178449" ; sc:description "AlleleShift is an R package to predict and visualize population-level changes in allele frequencies in response to climate change." ; sc:featureList edam:operation_0337, edam:operation_0554, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlleleShift" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RoelandKindt/AlleleShift" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_2830 ; sc:citation , "pubmed:31677971" ; sc:description "A Bayesian Inference of Allelic Inclusion Rates in the Human T Cell Receptor Repertoire." ; sc:featureList edam:operation_3658 ; sc:name "allelic inclusion" ; sc:url "https://github.com/JasonACarter/Allelic_inclusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC4465016", "pubmed:26066318" ; sc:contributor ; sc:description "Provides a framework for allelic specific expression investigation using RNA-seq data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "AllelicImbalance" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AllelicImbalance.html" ; biotools:primaryContact "Jesper R Gadin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3304, edam:topic_3382, edam:topic_3444, edam:topic_3512 ; sc:citation , "pmcid:PMC3531093", "pubmed:23193282" ; sc:description "The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3223 ; sc:name "Allen Brain Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.brain-map.org" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Integration of gene expression data, connectivity data and neuroanatomical information for the adult and developing brain in mouse, human and non-human primate." ; sc:featureList edam:operation_2495 ; sc:name "Allen Brain Atlas-API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://help.brain-map.org/display/api/RESTful+Model+Access+%28RMA%29" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3173 ; sc:citation , "pmcid:PMC7076970", "pubmed:32183716" ; sc:description "A comprehensive gene set function enrichment tool for both model and non-model species. This is a tool designed for functional genomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets, or differential epigenomic modification gene sets etc) are continuously generated. AllEnricher incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3501, edam:operation_3928 ; sc:license "MIT" ; sc:name "AllEnricher" ; sc:url "https://github.com/zd105/AllEnricher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0601, edam:topic_0804, edam:topic_3400 ; sc:citation , "pmcid:PMC9252832", "pubmed:35640594" ; sc:description "A web server for predicting protein allergenicity potential." ; sc:featureList edam:operation_0252, edam:operation_0474, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AllerCatPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://allercatpro.bii.a-star.edu.sg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3400, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:36244612" ; sc:description "A novel web app for prediction of protein allergenicity." ; sc:featureList edam:operation_0252, edam:operation_0491 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ALLERDET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://allerdet.frangam.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3510 ; sc:citation "pubmed:24403538" ; sc:description "Fast and accurate sequence-based allergen prediction tool that models protein sequences as text documents and employs support vector machine in text classification for allergen prediction." ; sc:featureList edam:operation_2479 ; sc:name "Allerdictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://allerdictor.vbi.vt.edu/" ; biotools:primaryContact "Ha Dang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3307 ; sc:citation "pubmed:24167156" ; sc:description "Bioinformatics tool for allergenicity prediction based on a novel descriptor fingerprint approach." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "AllergenFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ddg-pharmfac.net/AllergenFP/" ; biotools:primaryContact "Drug Design Group" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pubmed:19671381" ; sc:description "A platform for allergen knowledge." ; sc:featureList edam:operation_0224 ; sc:name "Allergome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.allergome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775 ; sc:citation "pubmed:24878803" ; sc:description "Server for in silico prediction of allergens based on the main physicochemical properties of proteins." ; sc:featureList edam:operation_2479 ; sc:name "AllerTOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ddg-pharmfac.net/AllerTOP/" ; biotools:primaryContact "Drug Design Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC7291640", "pubmed:32532211" ; sc:description "AllesTM is an integrated tool to predict almost all structural features of transmembrane proteins that can be extracted from atomic coordinate data. It blends several machine learning algorithms: random forests and gradient boosting machines, convolutional neural networks in their original form as well as those enhanced by dilated convolutions and residual connections, and, finally, long short-term memory architectures." ; sc:featureList edam:operation_0249, edam:operation_0269, edam:operation_0303, edam:operation_0474, edam:operation_2241 ; sc:license "MIT" ; sc:name "AllesTM" ; sc:url "https://github.com/phngs/allestm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:31383970" ; sc:description "Genome scaffolding based on HiC data in heterozygous and high ploidy genomes" ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "allhic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tanghaibao/allhic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_3068, edam:topic_3489, edam:topic_3571 ; sc:citation , "pmcid:PMC6893393", "pubmed:31796553" ; sc:description "A modern data ecosystem for model organism databases." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "Alliance Genome Resources" ; sc:url "http://www.alliancegenome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:23615333" ; sc:description "The Allelic imbalance meter tool offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "MPL-1.1" ; sc:name "Allim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://code.google.com/p/allim/" ; biotools:primaryContact "Christian Schlötterer", "Ram Vinay Pandey", "Susanne U. Franssen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3336 ; sc:citation ; sc:description "Identifies potential endogenous or exogenous allosteric modulators as well as their characterization in human allosterome. Automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator–protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082 ; sc:citation "pubmed:23842804" ; sc:description "Tool for the prediction of allosteric sites in proteins." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "Allosite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mdl.shsmu.edu.cn/AST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:18340039" ; sc:description "De novo assembly of whole-genome shotgun microreads." ; sc:featureList edam:operation_0310, edam:operation_0524 ; sc:name "ALLPATHS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.broadinstitute.org/computational-rd/computational-research-and-development" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199 ; sc:citation , "pmcid:PMC3029755", "pubmed:21187386" ; sc:description "Short read assembler that works on both small and large (mammalian size) genomes." ; sc:featureList edam:operation_0310, edam:operation_3197 ; sc:license "MIT" ; sc:name "Allpaths-LG" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://www.broadinstitute.org/computational-rd/computational-research-and-development" ; biotools:primaryContact "David B. Jaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3418 ; sc:citation ; sc:description "RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia." ; sc:featureList edam:operation_0314, edam:operation_3225, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ALLSorts" ; sc:softwareHelp ; sc:url "https://github.com/Oshlack/AllSorts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:24676684" ; sc:description "This modelling environment provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations." ; sc:featureList edam:operation_0477 ; sc:name "ALMOST" ; sc:operatingSystem "Linux" ; sc:url "http://www-mvsoftware.ch.cam.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3393, edam:topic_3572 ; sc:citation , "pmcid:PMC5167069", "pubmed:27559158" ; sc:description "Simplifying quality control of high-throughput sequencing data." ; sc:featureList edam:operation_3218 ; sc:name "AlmostSignificant" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/bartongroup/AlmostSignificant" ; biotools:primaryContact "Joe Ward" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3512 ; sc:citation , "pmcid:PMC8386716", "pubmed:34447886" ; sc:description "Aln2tbl is a Python script for building a mitochondrial features table from a assembly alignment in fasta format. The sequencing, annotation and analysis of complete mitochondrial genomes is an important research tool in phylogeny and evolution. Starting with the primary sequence, genes features are generally annotated automatically to obtain preliminary annotations in the form of a feature table. Further manual curation in a graphic alignment editor is nevertheless necessary to revise annotations. As such, the automatically generated feature table is invalidated and has to be modified manually before submission to data banks." ; sc:featureList edam:operation_0310, edam:operation_0361, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "Aln2tbl" ; sc:url "https://github.com/IMEDEA/mitogenomics" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0780, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "AlnC is an extensive database of long non-coding RNAs in Angiosperms." ; sc:featureList edam:operation_0278, edam:operation_0436, edam:operation_2421, edam:operation_3431 ; sc:name "AlnC" ; sc:url "http://nipgr.ac.in/AlnC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "alntools processes next-generation sequencing read alignments into a sparse compressed incidence matrix (aka Equivalence Classes) and stores it in a pre-defined binary format for efficient downstream analyses and storage. 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These groups of amino acids can form a reduced alphabet for building sequence motifs (eMOTIFs) or for detecting correlations between columns of amino acids (MCSeq)." ; sc:featureList edam:operation_2479 ; sc:name "Alphabet" ; sc:operatingSystem "Linux" ; sc:url "http://motif.stanford.edu/distributions/alphabet/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_2258 ; sc:description "AlphaCharges is a web server for the calculation of partial atomic charges on protein structures, created by AlphaFold." ; sc:featureList edam:operation_0474, edam:operation_3431, edam:operation_3893 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AlphaCharges" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://alphacharges.ncbr.muni.cz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:22540033" ; sc:description "Package for simulating genomic selection or GWAS data, that drops simulated haplotypes through a pedigree using MaCS. 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These sequences will be formed by characters of a finite alphabet." ; sc:featureList edam:operation_0492 ; sc:name "AlphaMALIG" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.1" ; sc:url "http://alggen.lsi.upc.es/recerca/align/alphamalig/intro-alphamalig.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge." ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlphaMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MannLabs/alphamap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3307, edam:topic_3796 ; sc:citation "pubmed:24872425" ; sc:description "Simple software package for simulating data in multi-parent populations." ; sc:featureList edam:operation_2426 ; sc:name "AlphaMPSim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/hickeyjohn/workstuff/alphampsim" ; biotools:primaryContact "John Hickey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "R implementation of the method for partitioning genetic trends. Partition/Decomposition of Breeding Values by Paths of Information." ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:license "GPL-2.0" ; sc:name "AlphaPart" ; sc:url "http://CRAN.R-project.org/package=AlphaPart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "Framework for MS-based proteomics." ; sc:featureList edam:operation_3630, edam:operation_3631, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlphaPept" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MannLabs/alphapept" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9700817", "pubmed:36433986" ; sc:description "A modular deep learning framework to predict peptide properties for proteomics." ; sc:featureList edam:operation_0417, edam:operation_3629, edam:operation_3631, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AlphaPeptDeep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MannLabs/alphapeptdeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121 ; sc:citation "pubmed:14997542" ; sc:description "This server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure." ; sc:featureList edam:operation_0267, edam:operation_0492 ; sc:name "AlphaPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/alphapred/" ; biotools:primaryContact "Dr. G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3047, edam:topic_3957 ; sc:citation , "pmcid:PMC9805587", "pubmed:36413069" ; sc:description "A Python package for protein-protein interaction screens using AlphaFold-Multimer." ; sc:featureList edam:operation_0474, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AlphaPulldown" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.embl-hamburg.de/AlphaPulldown" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment." ; sc:featureList edam:operation_2426, edam:operation_3196 ; sc:license "MIT" ; sc:name "AlphaSimR" ; sc:softwareHelp ; sc:url "https://alphagenes.roslin.ed.ac.uk/wp/software-2/alphasimr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation , "pmcid:PMC7093224", "pubmed:31995373" ; sc:description "AlphaSpace2 is a surface topographical mapping tool." ; sc:featureList edam:operation_2429, edam:operation_2464, edam:operation_2492 ; sc:name "AlphaSpace2" ; sc:softwareHelp ; sc:url "http://www.nyu.edu/projects/yzhang/AlphaSpace2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC8526765", "pubmed:34543758" ; sc:description """Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization. High-resolution MS-based proteomics generates large amounts of data, even in the standard LC-tandem MS configuration. Adding an ion mobility dimension vastly increases the acquired data volume, challenging both analytical processing pipelines and especially data exploration by scientists. This has necessitated data aggregation, effectively discarding much of the information present in these rich datasets. Taking trapped ion mobility spectrometry (TIMS) on a quadrupole TOF (Q-TOF) platform as an example, we developed an efficient indexing scheme that represents all data points as detector arrival times on scales of minutes (LC), milliseconds (TIMS), and microseconds (TOF). 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This method provides alignment-free and spatial-temporal analysis of multi-FASTA data through the implementation of a C toolkit that is highly flexible and with characteristics covering large-scale data, namely extensive collections of genomes/proteomes. This toolkit is ideal for scenarios entangling the presence of multiple sequences from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence(s) in (multi-) FASTA format.""" ; sc:featureList edam:operation_2403 ; sc:funder ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AltaiR" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/cobilab/altair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:20513647" ; sc:description "AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions)." ; sc:featureList edam:operation_0276, edam:operation_0303, edam:operation_2495, edam:operation_2499, edam:operation_3223 ; sc:name "AltAnalyze" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.altanalyze.org" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2060 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203 ; sc:citation , "pmcid:PMC514699", "pubmed:15310390" ; sc:description "Convenience data structures and functions to handle cdfenvs." ; sc:featureList edam:operation_0527 ; sc:license "GPL-2.0" ; sc:name "altcdfenvs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/altcdfenvs.html" ; biotools:primaryContact "Laurent Gautier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:20439312" ; sc:description "ALTER is a program-oriented web tool for the conversion between DNA and protein alignments." ; sc:featureList edam:operation_0260, edam:operation_2479 ; sc:name "ALTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sing.ei.uvigo.es/ALTER/" ; biotools:primaryContact "ALTER Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602 ; sc:citation ; sc:description "Cross-platform and standalone tool for analyzing gene expression datasets to highlight significantly rewired pathways across case-vs-control conditions. The Tool is designed to analyze human gene expression datasets (with Entrez ID)." ; sc:featureList edam:operation_2497 ; sc:name "Altered Pathway Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://bioinfo.icgeb.res.in/APA/" ; biotools:primaryContact "Abhinav Kaushik", "Dinesh Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3120, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:15292448" ; sc:description "The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_0526, edam:operation_2499 ; sc:name "Alternative Splicing Gallery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://statgen.ncsu.edu/asg/" ; biotools:primaryContact "Jeremy Leipzig", "Steffen Heber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749, edam:topic_3170 ; sc:citation ; sc:description "Method incorporating alternate reference haplotypes to generate gene- and haplotype-level estimates of transcript abundance for any genomic region where such information is available." ; sc:featureList edam:operation_0487, edam:operation_3680 ; sc:name "AltHapAlignR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jknightlab/AltHapAlignR" ; biotools:primaryContact "Julian C Knight", "Peter Humburg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2275, edam:topic_2814, edam:topic_2828, edam:topic_3474 ; sc:citation , "pmcid:PMC6938380", "pubmed:31846452" ; sc:description """Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. altMOD is a MODELLER (https://salilab.org/modeller/) [1] plugin for improved 3D homology model building. Right now, it allows to incorporate in the program's objective function terms for interatomic distances statistical potentials, such as DOPE [2] and DFIRE [3]. The effect of adding statistical potentials in the objective function of MODELLER is described in Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling" (Janson et al., 2019). In a benchmark with 225 single-template homology models, we found that the inclusion of DOPE in the objective function of MODELLER brings an average improvement of 1.3% and 2.0% in GDT-HA [4] and lDDT [5] and a large improvement of -29.8% in MolProbity scores [6]""" ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3454 ; sc:name "altMOD" ; sc:url "https://github.com/pymodproject/altmod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC4756442", "pubmed:26883204" ; sc:description "Altools is a software package that allows the precise detection of polymorphisms and structural variations." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "Altools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/altools/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3360, edam:topic_3500, edam:topic_3518 ; sc:citation , "pubmed:35303580" ; sc:description "AltWOA is a novel feature selection algorithm where Altruistic property of candidate whales are embedded to the Whale Optimization Algorithm (WOA)." ; sc:featureList edam:operation_0314, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AltWOA" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/Rohit-Kundu/AltWOA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0769, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC9655980", "pubmed:36361669" ; sc:description "Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood-Brain Barrier Permeability" ; sc:featureList edam:operation_2428, edam:operation_3799, edam:operation_4009 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Alvascience" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.alvascience.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC9759058", "pubmed:36528564" ; sc:description "A web browser-based tool to analyze lung intravital microscopy." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3937 ; sc:license "Other" ; sc:name "Alveolus Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/uic-evl/AlveolusAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_2640, edam:topic_3307 ; sc:citation "pubmed:26417198" ; sc:description "Fast bam file viewer from the National Cancer Informatics Program." ; sc:featureList edam:operation_3208 ; sc:name "Alview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbiit.nci.nih.gov/ncip" ; biotools:primaryContact "Richard P. Finney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3300, edam:topic_3315 ; sc:citation ; sc:description """Interactive, visual simulation of a spatio-temporal model of gas exchange in the human alveolus. In interdisciplinary fields such as systems biology, close collaboration between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to penetrate the model in its dependencies in order to correctly interpret the results in the physiological context. When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging. We promote interactive, visual simulations as an engaging way to communicate theoretical models in physiology and to thereby advance our understanding of the process of interest""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3435 ; sc:name "Alvin" ; sc:url "https://ge.gitlab-pages.informatik.uni-wuerzburg.de/Dev/alveolus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3382 ; sc:citation , "pmcid:PMC7967992", "pubmed:33726674" ; sc:description "Alvis is a tool for contig and read ALignment VISualisation and chimera detection. It produces LaTeX and SVG alignment diagrams from a number of common alignment formats." ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_0450, edam:operation_1812, edam:operation_3198 ; sc:name "Alvis" ; sc:softwareHelp ; sc:url "https://github.com/SR-Martin/alvis" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC7580783", "pubmed:32603655" ; sc:description "Selective Neuronal Vulnerability in Alzheimer's Disease." ; sc:featureList edam:operation_2436, edam:operation_3450, edam:operation_3799 ; sc:name "Selective Neuronal Vulnerability Alzheimer Disease" ; sc:url "http://alz.princeton.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:35619290" ; sc:description "A tool to discriminate disease-causing and neutral mutations in Alzheimer's disease." ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Alz-disc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/alzdisc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3170 ; sc:citation , "pubmed:35040932" ; sc:description "AlzCode is a web resource that developed pipeline to evaluate the association of genes with AD. The association of genes with AD are validated by multiple lines of functional genomic evidence with statistical approaches." ; sc:featureList edam:operation_1781, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "AlzCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.alzcode.xyz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0202, edam:topic_0602, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc:description "A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer’s Therapeutic Discovery. A Network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3925 ; sc:name "AlzGPS" ; sc:url "https://alzgps.lerner.ccf.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC8742670", "pubmed:35035265" ; sc:description "AM-UNet: Automated Mini 3D End-to-End U-NetBased Network For Brain Claustrum Segmentation." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AM-UNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AhmedAlbishri/AM-UNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0634, edam:topic_3407, edam:topic_3941 ; sc:citation , "pmcid:PMC8317061", "pubmed:34335304" ; sc:description "A Comprehensive Database for Association Between Microbiota and Disease." ; sc:featureList edam:operation_2421, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "Amadis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gift2disease.net/GIFTED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3379 ; sc:citation , "pubmed:34406360" ; sc:description "An R package for Meta-analysis of metabolomics non-integral data." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Amanida" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mariallr/amanida" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC4734057", "pubmed:26835189" ; sc:description "AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics." ; sc:featureList edam:operation_2478, edam:operation_2479 ; sc:license "GPL-3.0" ; sc:name "AMAS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/marekborowiec/AMAS" ; biotools:primaryContact "Marek L. Borowiec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3520 ; sc:citation "pubmed:21800894" ; sc:description "Series of tools written in C++ that allows you to segment your mass spectrometry imaging dataset into regions with similar molecular signatures. The software allows for user input at each step of the process and returns the regions as well as the associated molecular signatures. It is composed of two dynamic libraries and a series of executables using the libraries as a base." ; sc:featureList edam:operation_2406, edam:operation_3214, edam:operation_3443 ; sc:name "AMASS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bix.ucsd.edu/AMASS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324, edam:topic_3337, edam:topic_3575 ; sc:citation ; sc:description "Automated tool for antimicrobial resistance surveillance system (AMASS) was developed as an offline, open-access and easy-to-use application that allows a hospital to perform data analysis independently and generate isolate-based and sample-based surveillance reports stratified by infection origin from routinely collected electronic databases. The application was built in R, which is a free software environment." ; sc:featureList edam:operation_3431 ; sc:name "AMASS" ; sc:url "http://www.amass.website" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workbench" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3315, edam:topic_3697 ; sc:citation , "pmcid:PMC8759573", "pubmed:35047812" ; sc:description "Adaptive and powerful microbiome multivariate association analysis via feature selection." ; sc:featureList edam:operation_0324, edam:operation_3435, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AMAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kzb193/AMAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3315 ; sc:citation ; sc:description "Augments the Cytoscape network readers by adding the ability to read in an adjacency matrix." ; sc:featureList edam:operation_2409 ; sc:name "aMatReader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.3" ; sc:url "http://www.cgl.ucsf.edu/cytoscape/utilities3/amatreader.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_2269, edam:topic_3676 ; sc:citation ; sc:description "A web tool to query data for a set of 5k variants that were predicted with high pathogenic probability" ; sc:featureList edam:operation_0307, edam:operation_3225, edam:operation_3461 ; sc:name "AmazonForest" ; sc:url "https://www2.lghm.ufpa.br/amazonforest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3577 ; sc:citation ; sc:description "An R-package for interactive alteration annotations for molecular tumor boards." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3695 ; sc:name "AMBAR" ; sc:url "http://sysbio.uni-ulm.de/?Software:Ambar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3307 ; sc:citation , , "pmcid:PMC1989667", "pubmed:16200636" ; sc:description "The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos." ; sc:featureList edam:operation_2426 ; sc:name "AMBER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ambermd.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation , "pmcid:PMC5479118", "pubmed:28636905" ; sc:description "An automated workflow tool for Kepler to perform AMBER GPU molecular dynamics simulations." ; sc:featureList edam:operation_2476 ; sc:license "LGPL-2.0" ; sc:name "AmberGPUMDSimulation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation" ; biotools:primaryContact "Rommie E. Amaro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0209, edam:topic_2275 ; sc:citation , "pmcid:PMC10135445", "pubmed:37189382" ; sc:description "A scripting tool for running amber MD in an easy way." ; sc:featureList edam:operation_0482, edam:operation_2476, edam:operation_3893, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AmberMDrun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/9527567/AmberMDrun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2275 ; sc:citation "pubmed:16200636" ; sc:description "Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models." ; sc:featureList edam:operation_2476 ; sc:name "AmberTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ambermd.org/#AmberTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3172 ; sc:citation "pubmed:23531303" ; sc:description "The Active Modules for Bipartite Networks is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. It does not require predefined pathways and gives highly specific predictions of affected areas of metabolism." ; sc:featureList edam:operation_3660 ; sc:name "AMBIENT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ambient-bio/?source=navbar" ; biotools:primaryContact "William Bryant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2258, edam:topic_3314 ; sc:citation , "pubmed:34342942" ; sc:description "Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation." ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_3502 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "Ambit-SLN" ; sc:url "http://ambit.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_2258, edam:topic_2814, edam:topic_3172 ; sc:citation ; sc:description "Software module for reaction representation, reaction search and structure transformation." ; sc:featureList edam:operation_2497 ; sc:license "Apache-2.0" ; sc:name "Ambit-SMIRKS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ambit.sourceforge.net/smirks/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769, edam:topic_3168, edam:topic_3518 ; sc:citation , "pmcid:PMC9252723", "pubmed:35639514" ; sc:description "Aquaculture Molecular Breeding Platform (AMBP): a web server and standalone version for genotype imputation and genetic analysis in aquaculture" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AMBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mgb.qnlm.ac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3293 ; sc:citation , "pubmed:34951625" ; sc:description "Accurate mutation clustering from single-cell sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMC" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/qasimyu/amc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3500, edam:topic_3520 ; sc:citation , "pmcid:PMC10609207", "pubmed:37887413" ; sc:description """Metabolite concentrations in animal tissues and convenient comparison of quantitative metabolomic data.""" ; sc:featureList edam:operation_3431, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Animal Metabolite Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://amdb.online" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2275, edam:topic_3382 ; sc:citation , "pmcid:PMC7493944", "pubmed:32938494" ; sc:description "A versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4." ; sc:featureList edam:operation_0337, edam:operation_0482 ; sc:name "AMDock" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/Valdes-Tresanco-MS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3064, edam:topic_3382 ; sc:citation , "pubmed:37427934" ; sc:description """Automatic Midline Extraction and Background Subtraction of Ratiometric Fluorescence Time-Lapses of Polarized Single Cells. AMEBaS is a new computer program that has been developed to automate the study of cells with polarity and is based in pollen tube growth and ion dynamics data. This program uses a three-step process to analyze fluorescent markers in cells with polarity.""" ; sc:featureList edam:operation_3446, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "AMEBaS" ; sc:url "https://github.com/badain/amebas.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation , "pmcid:PMC18254954", "pubmed:18254954" ; sc:description "The Annotation, Mapping, Expression and Network (AMEN) software is a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. 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Banga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "The GO Consortium GO browser and search engine." ; sc:featureList edam:operation_0224, edam:operation_2451, edam:operation_2495, edam:operation_3559 ; sc:name "AmiGO 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://amigo.geneontology.org/amigo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0621, edam:topic_0654 ; sc:citation , "pubmed:35385068" ; sc:description "AMIGOS III is a plugin to PyMOL for pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids." ; sc:featureList edam:operation_0249, edam:operation_0570, edam:operation_1812, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "AMIGOS III" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pylelab/AMIGOSIII. a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3070, edam:topic_3344 ; sc:description "Analysis of amino acid conservation using conservation index" ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Amino acid conservation.zip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47155-amino-acid-conservation-zip" ; biotools:primaryContact "Guangdi Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3342, edam:topic_3376, edam:topic_3382, edam:topic_3383, edam:topic_3679 ; sc:citation ; sc:description "AMIS (A Mouse Imaging Server) is a still growing webserver providing imaging information about the distribution of certain GPCRs in mice." ; sc:name "AMIS" ; sc:url "https://amis.docking.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3577 ; sc:citation , "pmcid:PMC7176885", "pubmed:32150667" ; sc:description "a web‐based prognostic model to predict the prognosis of Acute myeloid leukaemia patients. Using log-rank test and univariate COX regression analysis as well as LASSO-COX, AML patients were divided into high-risk and low-risk groups based on AML risk score (AMLRS) which was constituted by 10 survival-related genes." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3659, edam:operation_3891 ; sc:name "AMLRS" ; sc:url "https://tcgi.shinyapps.io/amlrs_nomogram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC7001226", "pubmed:32019565" ; sc:description "AMLVaran, the AML Variant Analyzer is a web-based software platform for variant analysis on targeted NGS data, addressing the requirements of a clinical setting." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "AMLVaran" ; sc:url "https://amlvaran.uni-muenster.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:citation , "pubmed:35394910" ; sc:description "Adaptive Multilinear Meshes (AMMs) is a new framework to represent piecewise multilinear volumetric data using mixed-precision adaptive meshes." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "AMM" ; sc:url "https://github.com/llnl/amm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:citation ; sc:description "Tool which helps enable adaptive management by codifying knowledge in the form of models generated from numerous analyses and data sets. Facilitates this process by storing all models and data sets in a single object that can be updated and saved, thus tracking changes in knowledge through time. A shiny application called AM Model Manager (modelMgr()) enables the use of these functions via a GUI." ; sc:featureList edam:operation_2409 ; sc:name "AMModels" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/AMModels/index.html" ; biotools:primaryContact "Jon Katz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3816 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3816 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154 ; sc:citation "pubmed:18925937", "pubmed:28486703" ; sc:description "Automatic Molecular Mechanics Optimization for in silico Screening 2. Efficient computational refinement of protein–small organic molecule complexes. Employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes." ; sc:featureList edam:operation_0322 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "AMMOS" ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php" ; biotools:primaryContact "Maria A. Miteva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0219, edam:topic_0780, edam:topic_3303, edam:topic_3375 ; sc:citation , "pmcid:PMC10172712", "pubmed:37120901" ; sc:description "Curated database of Indian anti-tubercular medicinal plants." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "AMMPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ammpdb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3293, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:20974635" ; sc:description "It is a new functional genomic databases serving the amoebozoa research communities. It contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. Importantly it utilizes the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2422 ; sc:name "AmoebaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://AmoebaDB.org" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174 ; sc:citation "pubmed:24974201" ; sc:description "Database engine for comparing metagenomic data at massive scale. It first obtains the sequence signature of metagenomes and organizes them as points in high dimensional space." ; sc:featureList edam:operation_0310, edam:operation_2478 ; sc:name "Amordad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/amordad/" ; biotools:primaryContact "Andrew Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:15383210" ; sc:description "AMOS is a Modular, Open-Source whole genome assembler." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3180, edam:operation_3184 ; sc:name "AMOS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://amos.sourceforge.net/" ; biotools:primaryContact "AMOS team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. This tool aims to search active modules in multi-layer WGCN using a continuous optimization approach." ; sc:featureList edam:operation_2425 ; sc:license "GPL-2.0" ; sc:name "AMOUNTAIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AMOUNTAIN.html" ; biotools:primaryContact "Dong Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_3301, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9793967", "pubmed:36461699" ; sc:description "Prediction of antimicrobial peptide function based on a BERT model." ; sc:featureList edam:operation_2995, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMP-BERT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/GIST-CSBL/AMP-BERT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3063, edam:topic_3474 ; sc:citation , "pubmed:32750857" ; sc:description "AMPZero is a predictor designed for predicting the effectiveness of a peptide sequence against various microbial species. The predictor takes the peptide sequence and any N/C-termini modifications together with the genomic sequence of a microbial species to generate targeted predictions." ; sc:featureList edam:operation_3482, edam:operation_3631, edam:operation_3938 ; sc:name "AMP0" ; sc:url "http://ampzero.pythonanywhere.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3301, edam:topic_3474 ; sc:citation , "pmcid:PMC9487607", "pubmed:35988923" ; sc:description "Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data." ; sc:featureList edam:operation_3431, edam:operation_3461, edam:operation_3968 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AMPBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://BioGenies.info/AMPBenchmark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3168, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9511757", "pubmed:36163001" ; sc:description "A tool for hemolytic activity prediction of antimicrobial peptides using transfer learning." ; sc:featureList edam:operation_2995, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AMPDeep" ; sc:url "https://github.com/milad73s/AMPDeep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2332 ; sc:name "Experiment report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2332 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Suite", "Web service" ; sc:applicationSubCategory edam:topic_3336 ; sc:citation ; sc:description "Annotated collection of normalized data describing antimicrobial peptides, their sources, their 3D structures, and their target organisms. It enables users to perform quick queries and allows the entire peptide community to contribute to the repository." ; sc:featureList edam:operation_0224, edam:operation_2424, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Antimicrobial Peptide Database (AMPed)" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://amped.uri.edu/" ; biotools:primaryContact "Lenore M Martin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_0780 ; sc:citation , "pubmed:33135060" ; sc:description "AmPEPpy is a Python application that implements a random forest classifier for predicting antimicrobial peptide sequences using the distribution descriptor set from the global protein sequence descriptors. amPEPpy has improved portability, increased accuracy relative to similar methods, and includes utilities for easily training and optimizing random forest classifiers on novel training data." ; sc:featureList edam:operation_3631 ; sc:license "GPL-3.0" ; sc:name "amPEPpy" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/tlawrence3/amPEPpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0621 ; sc:citation , "pubmed:37236434" ; sc:description "A computational model to identify antimicrobial peptides and their functions based on sequence-derived information." ; sc:featureList edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "AMPFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/abcair/AMPFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Automated Phylogenomic Inference Pipeline for bacterial sequences. From a given a set of protein sequences, it automatically identifies 31 phylogenetic marker genes. It then generates high-quality multiple sequence alignments for these genes and make tree-based phylotype assignments." ; sc:featureList edam:operation_2478 ; sc:license "CC-BY-4.0" ; sc:name "AMPHORA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://phylogenomics.me/software/amphora/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:24144838" ; sc:description "Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data and genomic data." ; sc:featureList edam:operation_0525, edam:operation_2478 ; sc:name "AmphoraNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pitgroup.org/amphoranet/" ; biotools:primaryContact "PIT Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0194, edam:topic_3174 ; sc:citation "pubmed:25296554" ; sc:description "Visualize outputs generated by the metagenomic and genomic analysis tool AMPHORA2 or its webserver implementation AmphoraNet." ; sc:featureList edam:operation_3184, edam:operation_3208 ; sc:name "AmphoraVizu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pitgroup.org/amphoravizu/" ; biotools:primaryContact "PIT Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "An R package for fast genome-wide prediction of antimicrobial peptides. It is fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs." ; sc:name "ampir" ; sc:url "https://github.com/legana/ampir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2275, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC7189366", "pubmed:32243153" ; sc:description """AMPL is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery. The ATOM Modeling PipeLine (AMPL) extends the functionality of DeepChem and supports an array of machine learning and molecular featurization tools. AMPL is an end-to-end data-driven modeling pipeline to generate machine learning models that can predict key safety and pharmacokinetic-relevant parameters. AMPL has been benchmarked on a large collection of pharmaceutical datasets covering a wide range of parameters.""" ; sc:featureList edam:operation_3359, edam:operation_3799, edam:operation_3938 ; sc:license "MIT" ; sc:name "AMPL" ; sc:url "https://github.com/ATOMconsortium/AMPL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation ; sc:description "A program for Molecular Replacement with search ensembles generated from uncoventional models." ; sc:featureList edam:operation_3454 ; sc:name "Ample" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ccp4.ac.uk/ample/" ; biotools:primaryContact "D. J. Rigden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3519 ; sc:citation ; sc:description "It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems." ; sc:featureList edam:operation_2928, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "amplican" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/amplican.html" ; biotools:primaryContact "Eivind Valen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , ; sc:description "AmpliconDesign is an interactive webserver for the design, documentation and analysis of targeted bisulfite sequencing studies." ; sc:featureList edam:operation_0308, edam:operation_3186, edam:operation_3192, edam:operation_3206, edam:operation_3207 ; sc:license "GPL-3.0" ; sc:name "AmpliconDesign" ; sc:url "https://amplicondesign.dkfz.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal." ; sc:featureList edam:operation_0450 ; sc:name "AmpliconNoise" ; sc:url "https://code.google.com/archive/p/ampliconnoise/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC8788131", "pubmed:35078402" ; sc:description "AMPlify is an attentive deep learning model for antimicrobial peptide prediction." ; sc:featureList edam:operation_3192, edam:operation_3461, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "AMPlify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/AMPlify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description """Automated methylation analysis of amplicons from bisulfite flowgram sequencing. The Roche 454 GS Junior sequencing platform allows locus-specific DNA methylation analysis using deep bisulfite amplicon sequencing. However, bisulfite-converted DNA reads may contain long T homopolymers, and the main sources of errors on pyrosequencing platforms are homopolymer over- and undercalls. Furthermore, existing tools do not always meet the analysis requirements for complex assay designs with multiple regions of interest (ROIs) from multiple samples. We have developed the amplikyzer software package to address the above challenges. It directly aligns the intensity sequences from standard flowgram files (SFF format) to given amplicon reference sequences, without converting to nucleotide FASTA format first, avoiding information loss by rounding flow intensities, and taking special measures to correctly process long homopolymers""" ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3198, edam:operation_3204 ; sc:name "amplikyzer" ; sc:url "https://bitbucket.org/svenrahmann/amplikyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description "Tool to process and analyze targeted NGS data." ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "amplimap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/koelling/amplimap" ; biotools:primaryContact "Nils Koelling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3656, edam:topic_3674 ; sc:citation , "pmcid:PMC5123276", "pubmed:27884103" ; sc:description "Pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons." ; sc:featureList edam:operation_3186, edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "ampliMethProfiler" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/amplimethprofiler/" ; biotools:primaryContact "Giovanni Scala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_3168, edam:topic_3519 ; sc:citation ; sc:description "The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "ampliQueso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ampliQueso.html" ; biotools:primaryContact "Michal Okoniewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "Ampred server predicts the Antimicrobial activity of given sequence. The activity may be antifungal, antiviral and antibacterial .This server works based on Multidimensional signatures of antimicrobial peptides" ; sc:featureList edam:operation_2479 ; sc:name "Ampred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/Antimicrobial/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3307 ; sc:citation "pubmed:2314284" ; sc:description "Suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. It also implements flexible pattern matching and database scanning options, and includes functions for running randomisations to estimate the significance of sequence similarities." ; sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "AMPS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/software.html#msa" ; biotools:primaryContact "The Barton Group" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation ; sc:description "NMR protein structure refinement. Amber (acronym to Assisted Model Building with Energy Refinement) is a suite of programs 1N3L that allow users to perform molecular dynamics (MD) simulations on biological systems. This web portal makes available the entire functionality of AMBER, in particular (but not only) using NMR-derived information as restraints for MD." ; sc:featureList edam:operation_0320, edam:operation_2476 ; sc:name "AMPS-NMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CERM" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://py-enmr.cerm.unifi.it/access/index" ; biotools:primaryContact "Antonio Rosato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3679 ; sc:citation ; sc:description "Matlab functions for analysis of patterns in (functions of) parameter values of the Add-my-Pet collection." ; sc:featureList edam:operation_2409, edam:operation_3460 ; sc:name "AmPtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/AmPtool.html" ; biotools:primaryContact "Starrlight Augustine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_3746 ; sc:name "Biodiversity data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050 ; sc:citation ; sc:description "ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "ampvis" ; sc:softwareHelp ; sc:url "https://github.com/MadsAlbertsen/ampvis2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data" ; sc:featureList edam:operation_3482 ; sc:name "AMR-meta" ; sc:url "https://github.com/smarini/AMR-meta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324 ; sc:description """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms""" ; sc:featureList edam:operation_3482 ; sc:name "AMRFinderPlus" ; sc:softwareVersion "3.11.14", "3.11.17", "3.11.18", "3.11.20", "3.11.26" ; sc:url "https://github.com/ncbi/amr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3324 ; sc:citation , "pmcid:PMC7994358", "pubmed:33776956" ; sc:description "AMRmap is a interactive web platform for the monitoring of antibiotic resistance in Russia, which contains a set of tools for the analysis and visualization of data on the susceptibility of microorganisms to antimicrobial agents." ; sc:featureList edam:operation_0337, edam:operation_3482, edam:operation_3659 ; sc:name "AMRmap" ; sc:url "https://amrmap.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0601 ; sc:citation , "pmcid:PMC3397139", "pubmed:20423529", "pubmed:22555647" ; sc:description "Predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences." ; sc:featureList edam:operation_2479, edam:operation_3645 ; sc:name "AMS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "4.0-1.5" ; sc:url "https://code.google.com/p/automotifserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3500 ; sc:citation , "pmcid:PMC6362447", "pubmed:30766677" ; sc:description "Animal movement tools (amt) for managing tracking data and conducting habitat selection analyses." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "amt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.6" ; sc:url "https://cran.r-project.org/package=amt" ; biotools:primaryContact "Johannes Signer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3409, edam:topic_3452 ; sc:citation , "pmcid:PMC8316401", "pubmed:34217953" ; sc:description "Asymmetric multi-task attention network for prostate bed segmentation in computed tomography images." ; sc:featureList edam:operation_3443, edam:operation_3927 ; sc:license "MIT" ; sc:name "AMTA-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/superxuang/amta-net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3385, edam:topic_3569 ; sc:citation , "pmcid:PMC5167257", "pubmed:27992448" ; sc:description "Automated multi-peak tracking kymography (AMTraK) is a software tool that uses peak information and distance minimization to track and automatically quantify kymographs." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "AMTraK" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.iiserpune.ac.in/~cathale/SupplementaryMaterial/Amtrak.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC8408950", "pubmed:34465366" ; sc:description """AMULET: ATAC-seq MULtiplet Estimation Tool which is a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Running AMULET consists of two parts: 1) Identifying all loci with >2 uniquely aligning reads for each cell, and 2) detecting multiplets that have more loci with >2 reads than expected. The bash shell script combines both of these steps, but they can be run independently as well. The latter (multiplet detection) may be useful for running multiplet detection using q-values different from the default.""" ; sc:featureList edam:operation_3198, edam:operation_3802, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "AMULET" ; sc:url "https://ucarlab.github.io/AMULET/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "AMVOC (Analysis of Mouse VOcal Communication) A deep, unsupervised method for rapid detection, analysis, and classification of ultrasonic vocalizations." ; sc:featureList edam:operation_2422, edam:operation_3432, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AMVOC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tyiannak/amvoc/tree/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0154, edam:topic_0219, edam:topic_0634 ; sc:citation , "pubmed:36243982" ; sc:description "AmyloGraph is a database of interactions between amyloid proteins and its functionalities are also accessible in an R package." ; sc:featureList edam:operation_3431, edam:operation_3436, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AmyloGraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://AmyloGraph.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121 ; sc:citation "pubmed:19589171" ; sc:description "Consensus prediction method for identifying possible amyloidogenic regions in protein sequences." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "AMYLPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://aias.biol.uoa.gr/AMYLPRED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , "pmcid:PMC3542318", "pubmed:23326595" ; sc:contributor ; sc:description "A Consensus Method for Amyloid Propensity Prediction." ; sc:featureList edam:operation_2423 ; sc:name "AMYL-PRED 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://aias.biol.uoa.gr/AMYLPRED2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1093 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1332 ; sc:name "Sequence set (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation ; sc:description "An online database dedicated to amyloid precursor families and to their amino acid sequence signatures." ; sc:featureList edam:operation_0224, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "AMYPdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://amypdb.genouest.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC9095707", "pubmed:35546347" ; sc:description "AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning." ; sc:featureList edam:operation_3092, edam:operation_3436, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AMYPred-FRL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/AMYPred-FRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654 ; sc:citation "pubmed:16538282" ; sc:description "Software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others." ; sc:featureList edam:operation_0436, edam:operation_2478, edam:operation_3658 ; sc:name "ANACONDA" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/software/anaconda/" ; biotools:primaryContact "José Luis Oliveira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3175, edam:topic_3676 ; sc:citation ; sc:description "An automated pipeline for somatic copy number variation detection and annotation from tumor exome sequencing data." ; sc:featureList edam:operation_3233 ; sc:name "Anaconda" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://mcg.ustc.edu.cn/bsc/ANACONDA/" ; biotools:primaryContact "Xiaohua Jiang", "Yuanwei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "Analysis and Forecast COVID-19 Patients Worldwide using Regression." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "Analysis and Forecast COVID-19 Patients Worldwide" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75430-analysis-and-forecast-covid-19-patients-worldwide" ; biotools:primaryContact "Akhilesh Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Analysis of the trajectory of close contacts in the spread of new coronary pneumonia( COVID19)" ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:name "Analysis of the trajectory of COVID19 close contacts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75211-analysis-of-the-trajectory-of-covid19-close-contacts" ; biotools:primaryContact "hangjun ji" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3372 ; sc:citation ; sc:description "Modular system that enables sharing of customizable R analyses via the web." ; sc:featureList edam:operation_3431 ; sc:license "Artistic-2.0" ; sc:name "AnalysisPageServer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnalysisPageServer.html" ; biotools:primaryContact "Brad Friedman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602 ; sc:citation ; sc:description "This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. 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Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_3169, edam:topic_3512 ; sc:citation ; sc:description "ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to use these GRNs to identify the key transcription factors in cell fate determination." ; sc:featureList edam:operation_0445, edam:operation_2437, edam:operation_3222 ; sc:license "MIT" ; sc:name "ANANSE" ; sc:softwareHelp ; sc:url "https://github.com/vanheeringen-lab/ANANSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3168 ; sc:citation , "pubmed:27502218" ; sc:contributor ; sc:description "The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls." ; sc:featureList edam:operation_3431 ; sc:license "BSD-4-Clause" ; sc:name "Anaquin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Anaquin.html" ; biotools:primaryContact "Ted Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2814 ; sc:citation "pubmed:26424857" ; sc:description "Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "ANARCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3174, edam:topic_3297 ; sc:citation , "pubmed:31178894" ; sc:description "ANASTASIA (Automated Nucleotide Animoacid Sequences Translational plAtform for Synthetic Interpretation and Analysis) is a metagenomics analysis platform and repository." ; sc:featureList edam:operation_0292, edam:operation_0346, edam:operation_0361, edam:operation_0524, edam:operation_1777, edam:operation_2422, edam:operation_3218, edam:operation_3460 ; sc:name "ANASTASIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://motherbox.chemeng.ntua.gr/anastasia_dev/" ; biotools:primaryContact "Aristotelis Chatziioannou", "Eleftherios Pilalis", "Olga Papadodima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2259, edam:topic_3474 ; sc:citation , "pmcid:PMC8555137", "pubmed:34706638" ; sc:description """ANAT (Advanced Network Analysis Tool) is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart out the molecular pathways that underlie these systems. ANAT (Advanced Network Analysis Tool) , is an all-in-one resource that provides access to up-to-date large-scale physical association data in several organisms, advanced algorithms for network reconstruction, and a number of tools for exploring and evaluating the obtained network models. It is a plug-in for Cytoscape.""" ; sc:featureList edam:operation_0276, edam:operation_3925, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ANAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cs.tau.ac.il/~bnet/ANAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444 ; sc:description "Matlab functions for flexible plotting of intracranial or fMRI data on 3D brain models" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Anatomical data visualization toolfbox for fMRI ECoG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71634-anatomical-data-visualization-toolfbox-for-fmri-ecog" ; biotools:primaryContact "Edden M. Gerber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:35768752" ; sc:description "A medical image segmentation software supporting user interventions and user-defined funtion extention" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AnatomySketch" ; sc:url "https://github.com/DlutMedimgGroup/AnatomySketch-Software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation , "pmcid:PMC5961460", "pubmed:29742397" ; sc:description "A python package with modules to measure anharmonicity in the form of higher-order statistics and its variation as a function of time, output a storyboard representation of the simulations to identify key anharmonic conformational events, and identify putative anharmonic conformational substates and visualization of transitions between these substates." ; sc:featureList edam:operation_2476 ; sc:license "BSD-3-Clause" ; sc:name "ANCA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://csb.pitt.edu/anca/index.html" ; biotools:primaryContact "S. Chakra Chennubhotla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2814, edam:topic_3794 ; sc:citation , "pmcid:PMC7711068", "pubmed:33330622" ; sc:description "A web server for amino acid networks construction and analysis." ; sc:featureList edam:operation_0321, edam:operation_0570, edam:operation_3927 ; sc:name "ANCA" ; sc:url "http://sysbio.suda.edu.cn/anca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome." ; sc:featureList edam:operation_3432 ; sc:name "AncesHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2009" ; sc:url "http://www.imperial.ac.uk/people/l.coin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3307, edam:topic_3510 ; sc:citation "pubmed:9071022" ; sc:description "Software which infer ancestral amino acid sequences from a set of homologous amino acid sequences whose phylogenetic relationships are known." ; sc:featureList edam:operation_0253, edam:operation_0540 ; sc:name "Ancestor" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.personal.psu.edu/nxm2/ancestor2.htm" ; biotools:primaryContact "Laboratory of Masatoshi Nei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293 ; sc:citation ; sc:description "AncestralClust is a tool to cluster divergent sequences. A neighbor-joining phylogenetic tree is built from a random number of user-specified initial sequences, the tree is split into initial clusters based on the longest branch lengths, each initial cluster is aligned with a multiple sequence alignment and the ancestral sequence from each cluster is inferred by the root node after being midpoint rooted. The rest of the sequences are assigned to the clusters based on their closest genetic distance to the ancestral sequence (or saved for a future iteration if the distance is greater than the average distance between clusters). The process reiterates until all sequences are assigned to a cluster." ; sc:featureList edam:operation_0291, edam:operation_0326, edam:operation_0491, edam:operation_3478, edam:operation_3745 ; sc:license "GPL-3.0" ; sc:name "AncestralClust" ; sc:url "https://github.com/lpipes/ancestralclust" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3524 ; sc:citation "pubmed:26072510" ; sc:description "Algorithm that infers the clonal evolution and tumor composition, including mixing fractions of a tumor from multi-sample DNA sequence data." ; sc:featureList edam:operation_0415, edam:operation_2476 ; sc:name "AncesTree" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://compbio.cs.brown.edu/projects/ancestree/" ; biotools:primaryContact "Raphael Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_3056, edam:topic_3796 ; sc:citation ; sc:description "Ancestry_HMM-S (AHMMS) is a program designed to infer adaptive introgression from population genomic data." ; sc:featureList edam:operation_0296, edam:operation_0487, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "Ancestry_HMM-S" ; sc:url "https://github.com/jesvedberg/Ancestry_HMM-S/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0610, edam:topic_3053 ; sc:citation ; sc:description "Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3198 ; sc:name "ancestryinfer" ; sc:url "https://github.com/Schumerlab/ancestryinfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3053 ; sc:citation ; sc:description "ANCESTRYMAP finds skews in ancestry that are potentially associated with disease genes in recently mixed populations. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations. It is most advantageous to apply this approach to populations that have descended from a recent mix of two ancestral groups that have been geographically isolated." ; sc:featureList edam:operation_2429 ; sc:name "ANCESTRYMAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:26508762" ; sc:description "Algebraic graph-based method to identify the most significant sub-network underlying ethnic difference in complex diseases risk in a recently admixed population." ; sc:featureList edam:operation_2478, edam:operation_2497 ; sc:name "ancGWAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://web.cbio.uct.ac.za/~emile/software.html" ; biotools:primaryContact "Emile Chimusa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Post-processing tools for de novo assemblies." ; sc:featureList edam:operation_3180, edam:operation_3183 ; sc:name "ANCHOR" ; sc:operatingSystem "Linux" ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/anchor" ; biotools:primaryContact "Rod Docking" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2333 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3320 ; sc:citation ; sc:description "A python package to find unimodal, bimodal, and multimodal features in any data that is normalized between 0 and 1, for example alternative splicing or other percent-based units." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "anchor (Expedition suite)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YeoLab/anchor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3464, edam:format_3475 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3464, edam:format_3475 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_3534, edam:topic_3538 ; sc:citation ; sc:description "Prediction of protein binding regions in disordered proteins" ; sc:featureList edam:operation_2464, edam:operation_3904 ; sc:name "ANCHOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2" ; sc:url "https://iupred3.elte.hu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Anchored DIALIGN is a WWW server for multiple alignment of protein and nucleic acid sequences using DIALIGN with user-defined anchor points.Alignments can be created either fully automatically or by using a list of user-defined constraints. By specifying such anchor points, the user can force the program to align selected segments of the sequences to each other. The remaining parts of the sequences are then aligned automatically, respecting the constraints imposed by the selected anchor points." ; sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "Anchored DIALIGN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.2.2" ; sc:url "http://dialign.gobics.de/anchor/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3174, edam:topic_3697, edam:topic_3943 ; sc:citation , "pmcid:PMC7838265", "pubmed:33500403" ; sc:description "AncientMetagenomeDir is a community curated resource of metadata of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples" ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "AncientMetagenomeDir" ; sc:softwareHelp ; sc:softwareVersion "20.09", "20.09.1", "20.12", "21.03", "21.06", "21.09" ; sc:url "https://spaam-community.github.io/AncientMetagenomeDir" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:description "Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment." ; sc:featureList edam:operation_3200 ; sc:name "ANCOMBC" ; sc:url "https://github.com/FrederickHuangLin/ANCOMBC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:25627242" ; sc:description "Webserver/tool for evaluation coordinate and ordinal correlations between genomic tracks and/or expression or protein binding profiles." ; sc:featureList edam:operation_2238 ; sc:name "AnCorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ancorr.eimb.ru" ; biotools:primaryContact "Galina Kravatskaya", "Vladimir Chechetkin", "Youri Kravatsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC7488989", "pubmed:32921303" ; sc:description """A web-based module of ANDSystem for the search of knowledge in the scientific literature. The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3280, edam:operation_3925 ; sc:name "ANDDigest" ; sc:url "https://anddigest.sysbio.ru/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168, edam:topic_3277 ; sc:citation ; sc:description "The fundamental data structure underlying, is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment. They include the root mean square deviation plot and the computation of base conversion frequencies, variation, inter-sample clustering and visualization, threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values." ; sc:featureList edam:operation_0230, edam:operation_0292, edam:operation_0492, edam:operation_2423, edam:operation_2424, edam:operation_3202, edam:operation_3429, edam:operation_3432, edam:operation_3434 ; sc:name "ANDES" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20120225" ; sc:url "http://andestools.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0870 ; sc:encodingFormat edam:format_1423 ; sc:name "Sequence distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:author "Fabian Klötzl" ; sc:citation ; sc:contributor "Bernhard Haubold", "Peter Pfaffelhuber" ; sc:description "andi estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes." ; sc:featureList edam:operation_0289 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "andi" ; sc:operatingSystem "Linux" ; sc:provider "Max Planck Institute for Evolutionary Biology", "evolbio.mpg.de" ; sc:softwareHelp ; sc:softwareVersion "0.11" ; sc:url "https://github.com/EvolBioInf/andi" ; biotools:primaryContact "Fabian Klötzl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0736 ; sc:citation "pubmed:11911710" ; sc:description "Web tool that helps to assign structural domains to protein sequences and to classify them according to SCOP." ; sc:featureList edam:operation_0474, edam:operation_2479, edam:operation_2996 ; sc:name "AnDom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.html" ; biotools:primaryContact "Dominik Schaack & Steffen Schmidt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:12824331", "pubmed:14696385" ; sc:description "This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF)." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_2406, edam:operation_2415, edam:operation_2487 ; sc:name "Andrej Sali Lab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://salilab.org/our_resources.shtml" ; biotools:primaryContact "Andrej Sali" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Tool, developed for the reconstruction of molecular genetic networks. It is based on an automated text- and data- mining techniques." ; sc:featureList edam:operation_3660 ; sc:name "ANDSystem" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://pbiosoft.com/en/andsystem" ; biotools:primaryContact "Vladimir A Ivanisenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3416, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:33507353" ; sc:description "Anduin is a freely available research tool to segment vertebrae in a CT scan, uploaded as NIFTI data. It allows to calculate trabecular vBMD, download the segmentation as NIFTI, and vertebral centroid coordinates as JSON files." ; sc:featureList edam:operation_3799 ; sc:license "CC-BY-SA-4.0" ; sc:name "anduin" ; sc:url "https://anduin.bonescreen.de" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3263, edam:topic_3344 ; sc:citation , "pmcid:PMC8444998", "pubmed:34541525" ; sc:description "A free online citizen science platform." ; sc:featureList edam:operation_3283, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Anecdata" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.anecdata.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3382 ; sc:citation , "pubmed:32856793" ; sc:description """A Simple Web-Based Platform to Build Stakeholder Understanding of Groundwater Behavior. This package models simple aquifer and well configurations.""" ; sc:featureList edam:operation_2426 ; sc:name "anem" ; sc:url "http://gopalpenny.shinyapps.io/anem-app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3168 ; sc:citation , "pmcid:PMC4888588", "pubmed:27246460" ; sc:description "This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data." ; sc:featureList edam:operation_3233 ; sc:license "Artistic-2.0" ; sc:name "AneuFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AneuFinder.html" ; biotools:primaryContact , "Aaron Taudt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3390, edam:topic_3794 ; sc:citation ; sc:description "Detection of Cerebral Aneurysm using Modified Hough Circle Transform" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Aneurysm detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63729-jm61288-aneurysm_detection" ; biotools:primaryContact "Jubin Mitra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3308, edam:topic_3335 ; sc:citation , "pubmed:34626395" ; sc:description "anexVis is a transcriptome tool to visualize organ/tissue-specific glycosaminoglycan biosynthetic and catabolic pathways in human health and diseases. anexVis allows one to analyze a large number of genes that are related to biosynthetic and catabolic pathways of all glycosaminoglycans, such as heparan sulfate, chondroitin sulfate, keratan sulfate, and hyaluronic acid, in parallel across various human tissues organs. Such visual analyses have not been accessible to the broad research community despite the accumulation of a large amount of RNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_3463, edam:operation_3926 ; sc:name "anexVis" ; sc:url "https://anexvis.chpc.utah.edu/" ; biotools:primaryContact "Balagurunathan Kuberan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion." ; sc:featureList edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "ANF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ANF.html" ; biotools:primaryContact "Tianle Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3325, edam:topic_3676 ; sc:citation ; sc:description """An open-source computational platform for the analysis of sequencing data for rare genetic diseases. Anfisa is a Variant Analysis and Curation Tool. Its purpose is to bring together Genetic Research and Clinical settings and provide a medical geneticist with access to research Genome.""" ; sc:featureList edam:operation_3197 ; sc:license "Apache-2.0" ; sc:name "AnFiSA" ; sc:url "https://github.com/ForomePlatform/AnFiSA#public-demo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "Database of Streptocarpus rexii transcriptome." ; sc:featureList edam:operation_0310, edam:operation_0361, edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "Angeldust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:url "http://www.beaconlab.it/angeldust" ; biotools:primaryContact "David Horner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8433338", "pubmed:34508124" ; sc:description "A fully automatic method to segment the vessels would eliminate potential subjectivity and provide a quantitative and systematic measurement of diameter reduction. Here, we have designed a convolutional neural network, AngioNet, for vessel segmentation in X-ray angiography images" ; sc:featureList edam:operation_3443, edam:operation_3695, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AngioNet" ; sc:url "https://github.com/kritiyer/AngioNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3307, edam:topic_3382 ; sc:citation "pubmed:15822812" ; sc:description "Automated image analysis tool for quantification of angiogenesis. It is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. It provides quantitative and repeatable measurements of the lengths and sizes of tubule complexes as well as the numbers of junctions (branching points) in the tubule complexes." ; sc:featureList edam:operation_2426, edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:name "AngioQuant" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.tut.fi/sgn/csb/angioquant/" ; biotools:primaryContact "Antti Niemistö" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:16960968" ; sc:description "Program for predicting coding sequences from low quality cDNA. To achieve error-tolerant prediction, it uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences." ; sc:featureList edam:operation_0436 ; sc:name "ANGLE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cbrc3.cbrc.jp/~shimizu/index.php?Kana%20Shimizu%27s%20web%20site#t11a427e" ; biotools:primaryContact "Kana Shimizu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_2814 ; sc:citation , "pmcid:PMC5860525", "pubmed:28035031" ; sc:description "Method of determining the orientation of an α-helix relative to a defined axis in a rotationally symmetric protein structure such as a membrane protein channel." ; sc:featureList edam:operation_0250, edam:operation_0474 ; sc:name "AnglerFish" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://anglerfish.cryst.bbk.ac.uk/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_3016, edam:format_3462 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330, edam:format_3008 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3056 ; sc:citation ; sc:description "Software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data." ; sc:featureList edam:operation_2238, edam:operation_2403, edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "ANGSD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp , ; sc:softwareVersion "0.901" ; sc:url "http://www.popgen.dk/angsd" ; biotools:primaryContact "Anders Albrechtsen", "Thorfinn Korneliussen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3056, edam:topic_3168 ; sc:citation , "pubmed:27480660" ; sc:description "ANGSD-wrapper is a utility developed to aid in the analysis of next generation sequencing data." ; sc:featureList edam:operation_2403, edam:operation_3196 ; sc:name "angsd-wrapper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mojaveazure/angsd-wrapper" ; biotools:primaryContact "Paul Hoffman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3382, edam:topic_3383 ; sc:citation ; sc:description "Quantification of fibrous spatial point patterns from single-molecule localization microscopy data." ; sc:featureList edam:operation_3443 ; sc:name "Angular-Ripleys-K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RubyPeters/Angular-Ripleys-K" ; biotools:primaryContact "Dylan Owen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:34259329" ; sc:description "Artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom." ; sc:name "AniAMPpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aniamppred.anvil.app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation , "pubmed:32986825" ; sc:description "Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3' untranslated regions and thereby influencing a series of biological processes. 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However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human." ; sc:featureList edam:operation_0428, edam:operation_2421, edam:operation_2495 ; sc:name "Animal-APAdb" ; sc:url "http://gong_lab.hzau.edu.cn/Animal-APAdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation , "pubmed:34551433" ; sc:description "A comprehensive animal enhancer RNA database." ; sc:featureList edam:operation_2421, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "Animal-eRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gong_lab.hzau.edu.cn/Animal-eRNAdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3500, edam:topic_3810 ; sc:citation , "pubmed:36300636" ; sc:description "A SNP database for multiple animals." ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196, edam:operation_3557, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Animal-SNPAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_0625, edam:topic_2885, edam:topic_3500 ; sc:citation , "pmcid:PMC8728226", "pubmed:34850103" ; sc:description "The Animal QTLdb and CorrDB are unique resources for livestock animal genetics and genomics research which have been used extensively by the international livestock genome research community." ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Animal QTLdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.animalgenome.org/QTLdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3512, edam:topic_3679 ; sc:citation "pubmed:22080564" ; sc:description "Comprehensive TF database; identified and classified all the genome-wide TFs in 50 sequenced animal genomes. 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LaZerte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0610, edam:topic_3299, edam:topic_3407, edam:topic_3500 ; sc:citation , "pmcid:PMC9163144", "pubmed:35654905" ; sc:description "AnimalTraits is a curated database containing body mass, metabolic rate and brain size measurements across a wide range of terrestrial animal taxa." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3695, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "AnimalTraits" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://animaltraits.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Anipose is an open-source toolkit for robust, markerless 3D tracking of animal behavior from multiple camera views. 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ImageJ macro language was used to encode the complete NMJ-morph workflow into seven navigation windows that generate robust data for 19 individual pre- post-synaptic variables""" ; sc:featureList edam:operation_3435 ; sc:license "CC-BY-4.0" ; sc:name "aNMJ-morph" ; sc:url "https://datashare.ed.ac.uk/handle/10283/3421" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2717 ; sc:encodingFormat edam:format_2031 ; sc:name "Oligonucleotide probe annotation" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Functions for handling data from BioConductor Affymetrix annotation data packages. 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Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047 ; sc:citation ; sc:description "AnnapuRNA is a knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method." ; sc:featureList edam:operation_0478, edam:operation_2489, edam:operation_3893 ; sc:license "GPL-3.0" ; sc:name "AnnapuRNA" ; sc:url "https://github.com/filipspl/AnnapuRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation ; sc:description """From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray.\"""" ; sc:license "BSD-3-Clause" ; sc:name "anndata" ; sc:softwareHelp ; sc:url "https://github.com/scverse/anndata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3473 ; sc:citation , "pmcid:PMC7939269", "pubmed:33684153" ; sc:description "Anne O’Tate is a value-added PubMed search engine for analysis and text mining." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3802 ; sc:name "Anne O Tate" ; sc:url "http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775 ; sc:citation "pubmed:19389726" ; sc:description "ANNIE integrates over twenty protein function prediction tools in a single website. 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Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl." ; sc:featureList edam:operation_0361 ; sc:license "GPL-2.0" ; sc:name "annmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/annmap.html" ; biotools:primaryContact "Chris Wirth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation ; sc:description "Annotation browsing 2.0." ; sc:featureList edam:operation_0524, edam:operation_3208, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Anno-J" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dandelion.liveholonics.com/dart/annoj.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0114, edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description """an R Package to annotate and prioritize putative oncogenic RNA fusions. Filter and prioritize fusion calls. Using annoFuse, users can filter out fusions known to be artifactual and retained high-quality fusion calls using support of at least one junction read and remove false calls if there is disproportionate spanning fragment support of more than 10 reads compared to the junction read count. For prioritization, users can capture known as well as putative driver fusions reported in TCGA, or fusions containing gene partners that are known oncogenes, tumor suppressor genes, or COSMIC genes. Finally, users can also determine recurrent fusions across the cohort and recurrently-fused genes within each histology. By providing a standardized filtering and annotation method from multiple callers (STAR-Fusion and Arriba) users are able to merge, filter and prioritize putative oncogenic fusions across the PBTA""" ; sc:featureList edam:operation_2436, edam:operation_3695 ; sc:name "annoFuse" ; sc:url "https://github.com/d3b-center/annoFuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:25701574" ; sc:description "Pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission" ; sc:featureList edam:operation_0361, edam:operation_3258 ; sc:name "Annocript" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/frankMusacchia/Annocript" ; biotools:primaryContact "Frank Musacchia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0749 ; sc:citation , "pmcid:PMC7203733", "pubmed:31930398" ; sc:description "AnnoGen is a toolkit for annotating three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy, and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_2422 ; sc:license "MIT" ; sc:name "AnnoGen" ; sc:url "https://github.com/shengqh/annogen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640 ; sc:description "Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest." ; sc:featureList edam:operation_2421 ; sc:name "Annokey" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bjpop.github.io/annokey/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2815 ; sc:citation , "pmcid:PMC5112684", "pubmed:27852242" ; sc:description "A web server for systematically annotating novel human lncRNAs." ; sc:featureList edam:operation_0361 ; sc:name "AnnoLnc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://annolnc.cbi.pku.edu.cn/index.jsp" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_2885, edam:topic_3794 ; sc:citation , "pmcid:PMC7319567", "pubmed:32406920" ; sc:description "AnnoLnc2 is a web server for integratively annotating novel human and mouse lncRNAs" ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3661 ; sc:name "AnnoLnc2" ; sc:softwareHelp ; sc:url "http://annolnc.gao-lab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "AnnoMiner is a web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators." ; sc:featureList edam:operation_0362, edam:operation_3222, edam:operation_3223, edam:operation_3501, edam:operation_3672 ; sc:name "AnnoMiner" ; sc:softwareHelp ; sc:url "http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0621, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Automatic preparation of annotated DNA sequences for bulk submissions to ENA." ; sc:featureList edam:operation_0260, edam:operation_0361, edam:operation_3200, edam:operation_3431 ; sc:license "BSD-2-Clause" ; sc:name "annonex2embl" ; sc:url "https://github.com/michaelgruenstaeudl/annonex2embl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0602, edam:topic_0621, edam:topic_3053 ; sc:citation , "pmcid:PMC9252745", "pubmed:35640593" ; sc:description "The Annotation Query (AnnoQ) is an integrated functional annotation platform for large-scale genetic variant annotation." ; sc:featureList edam:operation_0224, edam:operation_0361, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "AnnoQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://annoq.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_0659, edam:topic_0769, edam:topic_0780 ; sc:citation , "pmcid:PMC8825457", "pubmed:34792587" ; sc:description "AnnoSINE is a SINE annotation tool for plant genomes. The program is designed to generate high-quality non-redundant SINE libraries for genome annotation. 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bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_1920, edam:format_2332 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Using R enviroments for annotation." ; sc:featureList edam:operation_0361, edam:operation_2421 ; sc:license "Artistic-2.0" ; sc:name "annotate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/annotate.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9724561", "pubmed:36472574" ; sc:description "annotate_my_genomes is a pipeline that aims to annotate genome-guided transcriptome assemblies from StringTie, coming from long read RNA-Seq alignments in vertebrate genomes (i.e. PacBio technology)" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "annotate_my_genomes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cfarkas/annotate_my_genomes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3169 ; sc:citation , ; sc:description "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution." ; sc:featureList edam:operation_3222 ; sc:name "annotategenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotategenes/annotateGenes/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622 ; sc:citation , "pmcid:PMC4015944", "pubmed:24564446" ; sc:description "Web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations." ; sc:featureList edam:operation_0362 ; sc:name "AnnotateGenomicRegions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cru.genomics.iit.it/AnnotateGenomicRegions/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here." ; sc:featureList edam:operation_0226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "annotatemyids" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fannotatemyids%2Fannotatemyids%2F3.12.0%2Bgalaxy1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169 ; sc:citation , ; sc:description "This tool annotates peaks with genomic feature (promoter, enhancer, exon, intron, etc.) and creates a .png file with distribution." ; sc:featureList edam:operation_0362 ; sc:name "annotatepeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/annotatepeaks/annotatePeaks/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3621 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1920 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3366 ; sc:citation ; sc:description "Provides user interface and database connection code for annotation data packages using SQLite data storage." ; sc:featureList edam:operation_0361, edam:operation_2421 ; sc:license "Artistic-2.0" ; sc:name "AnnotationDbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0219 ; sc:description "It provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages." ; sc:featureList edam:operation_0226 ; sc:license "Artistic-2.0" ; sc:name "AnnotationFilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/AnnotationFilter.html" ; biotools:primaryContact "Bioconductor Maintainer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2031, edam:format_2195 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2031, edam:format_2195 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3621 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3366, edam:topic_3489 ; sc:citation ; sc:description "Provides code for generating Annotation packages and their databases. 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The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. 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It can work on Windows, Linux and Mac platform.""" ; sc:featureList edam:operation_0337, edam:operation_0428, edam:operation_3800 ; sc:name "APA-Scan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/compbiolabucf/APA-Scan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web API", "Web application", "Web service", "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0202, edam:topic_2258, edam:topic_3071, edam:topic_3473 ; sc:author "Apache Taverna community" ; sc:citation ; sc:description "Open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation." ; sc:featureList edam:operation_0224, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Apache Taverna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Apache Software Foundation", "cs.manchester.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "3" ; sc:url "http://taverna.incubator.apache.org/" ; biotools:primaryContact "Apache Taverna community", "Apache Taverna mailing lists" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Trino is a distributed SQL query engine designed to query large data sets distributed over one or more heterogeneous data sources. Trino is a tool designed to efficiently query vast amounts of data using distributed queries. If you work with terabytes or petabytes of data, you are likely using tools that interact with Hadoop and HDFS. Trino was designed as an alternative to tools that query HDFS using pipelines of MapReduce jobs, such as Hive or Pig, but Trino is not limited to accessing HDFS. Trino can be and has been extended to operate over different kinds of data sources, including traditional relational databases and other data sources such as Cassandra. Trino was designed to handle data warehousing and analytics: data analysis, aggregating large amounts of data and producing reports. These workloads are often classified as Online Analytical Processing (OLAP).""" ; sc:featureList edam:operation_0224 ; sc:license "Apache-2.0" ; sc:name "Apache Trino" ; sc:softwareHelp , ; sc:softwareVersion "Release 406 (25 Jan 2023)" ; sc:url "https://trino.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description """Web-based notebook that enables data-driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more.""" ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Apache Zeppelin" ; sc:softwareHelp ; sc:softwareVersion "0.10.1" ; sc:url "https://zeppelin.apache.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3583 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10234309", "pubmed:37117035" ; sc:description "Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ." ; sc:featureList edam:operation_0428, edam:operation_3435, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APAIQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://anaconda.org/joshuachou/apaiq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7320624", "pubmed:32321166" ; sc:description "A R bioinformatics package for analysis of alternative polyadenylation isoforms. Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data." ; sc:featureList edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "APAlyzer" ; sc:url "https://bioconductor.org/packages/release/bioc/html/APAlyzer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0820, edam:topic_3314, edam:topic_3382 ; sc:citation , "pubmed:34085265" ; sc:description "Open source software tool for fast and light-weight data analysis and data conversion from platereaders and images to formats of more powerful analysis software such as MATLAB, GraphPad Prism and SBToolbox2 (IQMTools)." ; sc:featureList edam:operation_0269, edam:operation_2995, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Aparecium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gpcr.ut.ee/aparecium.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC9411867", "pubmed:36035147" ; sc:description "A web-based platform for alternative polyadenylation analyses in hematological cancers." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APAview" ; sc:url "https://github.com/Wu-xjtu/APAview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2275, edam:topic_3318 ; sc:citation , "pubmed:33052694" ; sc:description "Atom Pair-Based Scoring function (APBScore) is a physical-based scoring function, which includes pairwise van der Waals (VDW), electrostatic interaction, and hydrogen bond energies between the receptor and ligand." ; sc:featureList edam:operation_0387, edam:operation_0394, edam:operation_3938 ; sc:license "GPL-3.0" ; sc:name "APBScore" ; sc:url "https://github.com/BaoJingxiao/APBScore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2640, edam:topic_3301 ; sc:citation , "pmcid:PMC7332564", "pubmed:32339223" ; sc:description "A R package and Shiny app for covariate adjusted principal coordinates analysis." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "aPCoA" ; sc:url "https://biostatistics.mdanderson.org/shinyapps/aPCoA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_2814, edam:topic_3520 ; sc:citation ; sc:description "Functions to estimate a bipartite graph of protein complex membership using AP-MS data." ; sc:featureList edam:operation_0320 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "apComplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/apComplex.html" ; biotools:primaryContact "Denise Scholtens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0769 ; sc:citation , , "pmcid:PMC7304703", "pmcid:PMC8041394", "pubmed:33720735" ; sc:description "APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints." ; sc:featureList edam:operation_3501, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "APE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.7" ; sc:url "https://github.com/sanctuuary/APE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_2885, edam:topic_3125, edam:topic_3168 ; sc:citation , "pmcid:PMC9580900", "pubmed:36304290" ; sc:description "A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_0365, edam:operation_0564, edam:operation_0578 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ApE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jorgensen.biology.utah.edu/wayned/ape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520, edam:topic_3524 ; sc:citation "pubmed:20836568" ; sc:description "Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC." ; sc:featureList edam:operation_2426, edam:operation_3627 ; sc:name "APECS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://trac.nbic.nl/apecs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "It provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "apeglm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/apeglm.html" ; biotools:primaryContact "Anqi Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3175, edam:topic_3512 ; sc:citation ; sc:description """Aperture is a new alignment-free SV caller designed for cfDNA dataset. Aperture applies a unique strategy of k-mer based searching, fast breakpoint detection using binary labels and candidates clustering to detect SVs and viral integrations in high sensitivity, especially when junctions span repetitive regions, followed by a barcode based filter to ensure specificity. Aperture takes paired-end reads in fastq format as inputs and reports all SVs and viral integrations in VCF 4.2 format.""" ; sc:featureList edam:operation_3192, edam:operation_3228, edam:operation_3472, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "Aperture" ; sc:url "https://github.com/liuhc8/Aperture" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0121, edam:topic_3474 ; sc:citation ; sc:description "Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool." ; sc:featureList edam:operation_2423, edam:operation_3630, edam:operation_3637 ; sc:name "APEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "http://sourceforge.net/projects/apexqpt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3365 ; sc:citation , "pmcid:PMC5215480", "pubmed:27417145" ; sc:description "apex is an R package that can be used for phylogenetic studies. It implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data." ; sc:featureList edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "apex" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "https://cran.r-project.org/web/packages/apex/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3293 ; sc:citation , "pubmed:30840059" ; sc:description "R package designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis." ; sc:featureList edam:operation_0296, edam:operation_0499, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "aphid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.3" ; sc:url "https://cran.r-project.org/package=aphid" ; biotools:primaryContact "Shaun Wilkinson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "An aphid genome database." ; sc:featureList edam:operation_0258 ; sc:isAccessibleForFree true ; sc:name "AphidBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:url "http://aphidbase.com/" ; biotools:primaryContact "BIPAA platform" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Automated Pipeline for Infants Continuous EEG (APICE) is a fully automated, flexible, and modular. Artifacts are detected using multiple algorithms and adaptive thresholds, making it suitable to different age groups and testing procedures without redefining parameters" ; sc:featureList edam:operation_3435 ; sc:name "APICE" ; sc:url "https://github.com/neurokidslab/eeg_preprocessing" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "APICURON is an open resource that tracks and credits the work of biocurators across multiple participating knowledgebases. Biocuration is essential to extract knowledge from research data and make it available in a structured and standardized way to the scientific community. However, processing biological data - mainly from literature - requires a huge effort which is difficult to quantify and acknowledge. APICURON collects biocuration events from third party resources and aggregates this information, spotlighting biocurator contributions. APICURON promotes biocurator engagement implementing gamification concepts like badges, medals and leaderboards and at the same time provides a monitoring service for registered resources. APICURON adopts a data model that is flexible enough to represent and track the majority of biocuration activities." ; sc:featureList edam:operation_3436 ; sc:name "APICURON" ; sc:softwareHelp ; sc:url "http://apicuron.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:encodingFormat edam:format_1963 ; sc:name "Protein name (UniProt)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , , "pmcid:PMC4987915", "pmcid:PMC6354026", "pubmed:27131791", "pubmed:30715274" ; sc:description """APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. APID also includes a data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions reliability of the "edges") and a mapping of the functional environment of the proteins (functional annotations of the "nodes").""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "APID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:url "http://apid.dep.usal.es" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:encodingFormat edam:format_1963 ; sc:name "Protein name (UniProt)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:author ; sc:citation , , "pmcid:PMC4987915", "pmcid:PMC6354026", "pubmed:27131791", "pubmed:30715274" ; sc:description """APID Interactomes provides a comprehensive collection of protein interactomes for more than 500 organisms based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Construction of the interactomes is done with a methodological approach to report quality levels and coverage over the proteomes for each organism included. APID unifies PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. APID also includes a data visualization web-tool that allows the construction of sub-interactomes using query lists of proteins of interest and the visual exploration of the corresponding networks, including an interactive selection of the properties of the interactions reliability of the "edges") and a mapping of the functional environment of the proteins (functional annotations of the "nodes").""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "APID Interactomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:url "http://apid.dep.usal.es" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC6929291", "pubmed:31870282" ; sc:description """Antimicrobial peptide identification using multi-scale convolutional network. BACKGROUND:Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem. RESULTS:In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. To further improve the performance, we also incorporated additional information into the designed model and proposed a fusion model""" ; sc:featureList edam:operation_3092, edam:operation_3631, edam:operation_3695 ; sc:name "APIN" ; sc:url "https://github.com/zhanglabNKU/APIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2640, edam:topic_3336, edam:topic_3542 ; sc:citation , "pmcid:PMC9734560", "pubmed:36494486" ; sc:description "A database of apoptosis-inducing anticancer peptides." ; sc:featureList edam:operation_0250, edam:operation_0267, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ApInAPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinf.modares.ac.ir/software/ApInAPDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "APIR: flexible and powerful FDR-control framework for aggregating peptides identified by multiple database search algorithms from mass spectrometry data." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3436, edam:operation_3631 ; sc:name "APIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yiling0210/APIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3071, edam:topic_3382 ; sc:citation ; sc:description """Collection of wing images for conservation of honey bees (Apis mellifera) biodiversity in Europe. We provide 26,481 forewing images of honey bee workers. They represent 1,725 samples from 13 European countries. The shape of the wings was described using the coordinates for 19 landmarks at wing veins’ intersections. The whole dataset, including the wing images, landmark coordinates, geographic coordinates of sampling locations, and other data, is available on the Zenodo website under a Public Domain licence.""" ; sc:featureList edam:operation_2238 ; sc:license "CC0-1.0" ; sc:name "Apis-wings-EU" ; sc:url "https://zenodo.org/record/7244070" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3796 ; sc:citation "pubmed:16877866" ; sc:description "The Association in the Presence of Linkage tool provides a novel test for association in the presence of linkage using general pedigree data." ; sc:featureList edam:operation_0324 ; sc:name "APL" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://hihg.med.miami.edu/software-download/apl-version-1.1" ; biotools:primaryContact "John P. Hussman Institute for Human Genomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0820, edam:topic_2229 ; sc:citation , "pubmed:36752505" ; sc:description "APL@VORO is a software designed to aid in analyzing membrane simulations made with GROMACS." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2476 ; sc:license "Other" ; sc:name "APL_voro" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://aplvoro.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC7431853", "pubmed:32807888" ; sc:description """The R package apLCMS is designed for the processing of LC/MS based metabolomics data. It starts with a group of LC/MS files in the same folder, and generates a table with features in the rows and intensities in the columns. There are two major routes of data analysis. The first, which we call unsupervised analysis, doesn't use existing knowledge. It detects peaks de novo from the data based on the data itself. The second, which we call hybrid analysis, combines de novo peak detection with existing knowledge. The existing knowledge can come from two sources - known metabolites and historically detected features from the same machinery.""" ; sc:featureList edam:operation_3215, edam:operation_3435, edam:operation_3799 ; sc:name "apLCMS" ; sc:url "https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3714 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3651 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts MaxQuant APL (Andromeda peak lists) to MGF." ; sc:featureList edam:operation_0335 ; sc:name "APLToMGFConverter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.wehi.edu.au/people/andrew-webb/1298/apl-mgf-converter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation "pubmed:26861916" ; sc:description "ApoCanD: Database of Human Apoptotic Proteins in the context of cancer" ; sc:featureList edam:operation_2945 ; sc:name "apocand" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/apocand/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3538 ; sc:citation , "pmcid:PMC7773485", "pubmed:33381830" ; sc:description "APOD (Accurate Predictor Of Disordered flexible linkers) is an accurate sequence-based predictor of disordered flexible linkers. It utilizes both local- and protein-level inputs that quantify propensity for disorder, sequence composition, sequence conservation and selected putative structural properties." ; sc:featureList edam:operation_0267, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "APOD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yanglab.nankai.edu.cn/APOD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0659, edam:topic_3172, edam:topic_3308 ; sc:citation ; sc:description "Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) is a platform where users can upload and map multiple types of 'omics' data such as genomics, transcriptomics, proteomics, metabolomics, etc. in human cellular interaction networks. User can filter the interactions (protein-protein, gene regulatory, etc.) based on the status of the omics data. This filtered network of interaction can be used to identify topologically important nodes (TINs), namely hubs, central nodes and bottleneck nodes." ; sc:featureList edam:operation_0276, edam:operation_0533, edam:operation_1781, edam:operation_3660, edam:operation_3925 ; sc:name "APODHIN" ; sc:url "http://www.hpppi.iicb.res.in/APODHIN/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_0602, edam:topic_0622, edam:topic_3512 ; sc:citation "pubmed:12537571" ; sc:description "Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_3096 ; sc:name "Apollo Genome Annotation and Curation Tool" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://apollo.berkeleybop.org" ; biotools:primaryContact "Apollo team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pubmed:32167530" ; sc:description "Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size." ; sc:featureList edam:operation_0232, edam:operation_0310, edam:operation_3198, edam:operation_3359, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "Apollo" ; sc:url "https://github.com/CMU-SAFARI/Apollo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0176 ; sc:citation , "pmcid:PMC10185404", "pubmed:37115636" ; sc:description "Predicting allosteric pockets in protein biological assemblages." ; sc:featureList edam:operation_2476, edam:operation_3897, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://apop.bb.iastate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC7820372", "pubmed:33490085" ; sc:description "ApoPred is a tool for odentification of apolipoproteins and their subfamilies with multifarious features." ; sc:featureList edam:operation_1777, edam:operation_3936, edam:operation_3937 ; sc:name "ApoPred" ; sc:url "http://tang-biolab.com/server/ApoPred/service.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:description "Tool to automate the process of creating standalone, model-exploration apps for SimBiology model" ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "App Builder for SimBiology Models" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43832-app-builder-for-simbiology-models" ; biotools:primaryContact "Fulden Buyukozturk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6396488", "pubmed:30819089" ; sc:description "R package for accurate SNP-based parentage analysis in the absence of guiding information." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "apparent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://cran.r-project.org/package=apparent" ; biotools:primaryContact "Arthur Melo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3416 ; sc:citation , "pmcid:PMC7780701", "pubmed:33424481" ; sc:description "APPECO (Applying Evidence with Confidence) is a tool that aims to help you find and use the best evidence for the rehabilitation of patients with Multiple Sclerosis." ; sc:featureList edam:operation_2422 ; sc:name "APPECO" ; sc:url "http://www.appeco.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0203, edam:topic_2640 ; sc:citation "pubmed:25091586" ; sc:description "Web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. It provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients." ; sc:featureList edam:operation_0415, edam:operation_2478 ; sc:name "APPEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.appex.kr/appex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3360 ; sc:citation , "pubmed:37159410" ; sc:description "Web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "AppIndels" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://AppIndels.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3047, edam:topic_3957 ; sc:citation , "pmcid:PMC9639416", "pubmed:36353604" ; sc:description "An R package for building and computational analysis of protein-protein interaction networks." ; sc:featureList edam:operation_2949, edam:operation_3359, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "APPINetwork" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://forgemia.inra.fr/GNet/appinetwork" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3293 ; sc:citation , ; sc:description "Set of tools to analyse promoter sequences on a genome-wide scale." ; sc:featureList edam:operation_0253 ; sc:license "GPL-3.0" ; sc:name "APPLES" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cyverseuk.org/applications/warwick/analysis-of-plant-promoter-linked-elements/" ; biotools:primaryContact "Eran Tauber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293 ; sc:citation , "pubmed:31545363" ; sc:description "Scalable Distance-based Phylogenetic Placement with or without Alignments | distance based phylogenetic placement | APPLES stands for Accurate Phylogenetic Placement with LEast Squares and addresses the problem of phylogenetic placement of DNA and protein sequences into an already existing reference tree. APPLES is a command-line tool and it can run on Linux, Mac OSX, and Windows" ; sc:featureList edam:operation_0545, edam:operation_0547, edam:operation_3478 ; sc:license "MIT" ; sc:name "APPLES" ; sc:url "http://github.com/balabanmetin/apples" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3474 ; sc:citation ; sc:description "The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED)." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "APPLESEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mhpuglia/APPLESEED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3320, edam:topic_3512 ; sc:author "Jose Rodriguez" ; sc:citation , , , , "pmcid:PMC8728124", "pubmed:23161672", "pubmed:25990727", "pubmed:34755885" ; sc:contributor "ISCIII" ; sc:description "Annotates variants with biological data such as protein structural information, functionally important residues, conservation of functional domains and evidence of cross-species conservation." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_3672 ; sc:funder "ISCIII" ; sc:name "APPRIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BU_CNIO", "CNIO", "INB" ; sc:softwareHelp , ; sc:softwareVersion "2022_07.v47" ; sc:url "https://appris.bioinfo.cnio.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_2275, edam:topic_3534 ; sc:citation "pubmed:21557747" ; sc:description "Computational tool that predicts the interaction of a PPR (pentatricopeptide repeat) with its RNA binding site." ; sc:featureList edam:operation_0245, edam:operation_0420 ; sc:name "aPPRove" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cs.colostate.edu/~approve/" ; biotools:primaryContact "Thomas Harrison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:citation ; sc:description "ApproximantCoefficientsSIR is a MATLAB tool that computes the the coefficients of an approximate analytic solution to the SIR epidemic model." ; sc:isAccessibleForFree true ; sc:name "ApproximantCoefficientsSIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75131-approximantcoefficientssir" ; biotools:primaryContact "Nathaniel Barlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176 ; sc:citation ; sc:description "APPTEST is an innovative new method for the automatic prediction of peptide tertiary structures." ; sc:featureList edam:operation_0471, edam:operation_0474, edam:operation_2476, edam:operation_3454, edam:operation_4009 ; sc:name "APPTEST" ; sc:url "https://research.timmons.eu/apptest" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC7961182", "pubmed:33748796" ; sc:description "Appyters are standalone applications for generating jupyter notebooks, the appyter catalog features many bioinformatics related appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications. Appyters present to users an entry form enabling them to upload their data and set various parameters for a multitude of data analysis workflows." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2436, edam:operation_3891, edam:operation_3935 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "Appyters" ; sc:url "https://appyters.maayanlab.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_3474 ; sc:citation , "pubmed:32821925" ; sc:description "aPRBind is a convolutional neural network (CNN)-based ab-initio method for RNA-binding residue prediction. aPRBind is trained with sequence features and structural ones (particularly including residue dynamics information and residue-nucleotide propensity developed by us) that are extracted from the predicted structures by I-TASSER" ; sc:featureList edam:operation_0476, edam:operation_3901, edam:operation_3902 ; sc:name "aPRBind" ; sc:url "https://github.com/ChunhuaLiLab/aPRbind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0659 ; sc:citation , "pmcid:PMC5499795", "pubmed:28334975" ; sc:description "Integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins." ; sc:featureList edam:operation_1777 ; sc:name "APRICOT" ; sc:url "https://pypi.org/project/bio-apricot/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3316, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC7746519", "pubmed:32777825" ; sc:description """APRICOT (Advanced Platform for Reproducible Infrastructures in the Cloud via Open Tools) is an open-source extension to support customised virtual infrastructure deployment and usage from Jupyter notebooks. Scientific publications are meant to exchange knowledge among researchers but the inability to properly reproduce computational experiments limits the quality of scientific research. Furthermore, bibliography shows that irreproducible preclinical research exceeds 50%, which produces a huge waste of resources on nonprofitable research at Life Sciences field. As a consequence, scientific reproducibility is being fostered to promote Open Science through open databases and software tools that are typically deployed on existing computational resources. However, some computational experiments require complex virtual infrastructures, such as elastic clusters of PCs, that can be dynamically provided from multiple clouds""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "APRICOT" ; sc:url "https://github.com/grycap/apricot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3050 ; sc:citation , "pubmed:36029248" ; sc:description "Apscale is a metabarcoding pipeline that handles the most common tasks in metabarcoding pipelines like paired-end merging, primer trimming, quality filtering, otu clustering and denoising as well as an otu filtering step." ; sc:featureList edam:operation_0232, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "APSCALE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DominikBuchner/apscale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description "This search engine recommends PubMed articles relevant to a given article. It automatically extracts keywords from the title and abstract indexed in PubMed to generate recommendations. The database contains all PubMed records, providing up to 60 recommendations per searched article. Researchers were invited to annotate degrees of relevance for provided recommendations. All evaluations received will be curated into a benchmark dataset to be made available for free download and redistribution." ; sc:featureList edam:operation_0305 ; sc:isAccessibleForFree true ; sc:name "Article-based PubMed Search Engine (APSE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pubmed.ict.griffith.edu.au/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allow to predict the secondary structure of protein's from their amino acid sequence" ; sc:featureList edam:operation_2945 ; sc:name "apssp" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/apssp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3542 ; sc:description "APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence." ; sc:featureList edam:operation_0267, edam:operation_0271, edam:operation_2423, edam:operation_2479, edam:operation_2488 ; sc:name "APSSP2" ; sc:url "https://webs.iiitd.edu.in/raghava/apssp2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3003 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1317, edam:topic_3295 ; sc:citation ; sc:description "A tool for designing primers and identifying accurate normalization controls for ATAC-qPCR." ; sc:featureList edam:operation_2419, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "ATAC Primer Tool (APT)" ; sc:softwareHelp ; sc:url "https://github.com/ChangLab/ATACPrimerTool" ; biotools:primaryContact "Howard Y Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3374 ; sc:citation , "pubmed:29986050" ; sc:description "Design RNA complexes that hybridize via sticky bridges." ; sc:featureList edam:operation_0310 ; sc:name "AptaBlocks" ; sc:url "https://github.com/wyjhxq/AptaBlocks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071, edam:topic_3316 ; sc:citation ; sc:description "Allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets." ; sc:featureList edam:operation_3432 ; sc:name "AptaCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#aptatools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0654 ; sc:citation , "pmcid:PMC9805580", "pubmed:36440922" ; sc:description "AptaMat is a simple script which aims to measure differences between DNA or RNA secondary structures. The method is based on the comparison of the matrices representing the two secondary structures to analyze, assimilable to dotplots." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_0502, edam:operation_2488, edam:operation_2518 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AptaMat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GEC-git/AptaMat.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3511 ; sc:citation "pubmed:26395772" ; sc:description "Computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information." ; sc:featureList edam:operation_0415, edam:operation_2441 ; sc:name "APTANI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://aptani.unimore.it/" ; biotools:primaryContact "Silvio Bicciato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7955126", "pubmed:33712618" ; sc:description "Aptardi (Alternative Polyadenylation Trascriptome Analysis from RNA sequencing and DNA sequencing Information) predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence." ; sc:featureList edam:operation_0314, edam:operation_0428, edam:operation_3192, edam:operation_3258, edam:operation_3800 ; sc:license "MIT" ; sc:name "aptardi" ; sc:url "https://github.com/luskry/aptardi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_3299 ; sc:citation , "pubmed:31999328" ; sc:description "A method for optimized de novo motif discovery of RNA aptamers via HTS-SELEX." ; sc:featureList edam:operation_0238, edam:operation_0278 ; sc:name "AptCompare" ; sc:url "https://bitbucket.org/shiehk/aptcompare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3393 ; sc:citation , "pubmed:33715568" ; sc:description "The Automated Phonetic Transcription (APT) Comparison Tool (APTct) is an online tool that facilitates the comparison of phonetic transcriptions for a variety of clinical and research purposes." ; sc:featureList edam:operation_3096, edam:operation_3799 ; sc:name "APTct" ; sc:url "https://aptct.auburn.edu" ; biotools:primaryContact "Dallin J. Bailey" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1856 ; sc:name "PDB insertion code" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0153, edam:topic_0154, edam:topic_0601 ; sc:citation , "pmcid:PMC10503417", "pubmed:37596782" ; sc:description "A web server that identifies weak molecular interactions in protein structures." ; sc:featureList edam:operation_0417, edam:operation_0477, edam:operation_1839 ; sc:isAccessibleForFree true ; sc:name "AQcalc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aqcalcbiocomputing.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "The AQMM was developed to perform absolute quantification of multiple metagenomes and it's parallel metatranscriptome. In order to use this algorithm, the experiment should be designed with both metagenome and metatranscriptome data. From the initial stage, the molecular experimental data should be recorded to help on estimating the overall DNA or RNA of a unit (ml/gram) of the sample. 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Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data. Induced chromatin interactions anchored with protein contacts will be readily differentiated using AQuA-HiChIP, but with normalizing by total interactive paired-end tags (PETs), differential interaction frequencies may produce false positives or false negatives.""" ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3799 ; sc:name "AQuA-HiChIP" ; sc:url "https://github.com/GryderArt/AQuA-HiChIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3361, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc:description "AQUA (Advanced QUery Architecture for the SPARC Portal) is an application that aims at improving the search capabilities of the SPARC Portal." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AQUA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SPARC-FAIR-Codeathon/aqua" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC9342733", "pubmed:35913974" ; sc:description "A tool to assist aquaculture production design based on abiotic requirements of animal species." ; sc:featureList edam:operation_3960 ; sc:license "Not licensed" ; sc:name "AquaDesign" ; sc:url "https://github.com/GregoireButruille/AquaDesign" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:encodingFormat edam:format_1963 ; sc:name "Sequence accession (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1869 ; sc:encodingFormat edam:format_2330 ; sc:name "Organism identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1063 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0893 ; sc:encodingFormat edam:format_3464 ; sc:name "Sequence-structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3510 ; sc:author "Andrea Schafferhans", "Christian Stolte", "Kenneth S Sabir", "Seán I O'Donoghue" ; sc:citation ; sc:contributor "Alexander von Humboldt Foundation", "Benjamin Wellmann", "Burkhard Rost", "CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform", "Fabian A Buske", "Julian Heinrich", "Manfred Roos", "Maria Kalemanov", "Nelson Perdigão", "Vivian Ho" ; sc:description "Simplifying the generation of insight from protein structures through structure visualisation, annotated with protein features; loads sequence-to-structure alignments from the PSSH2 database, sequence features from UniProt and Interpro and user defined features on demand from JSON files; there is also a WebAPI (see ...)." ; sc:featureList edam:operation_0338, edam:operation_0339, edam:operation_0474, edam:operation_0564, edam:operation_0570 ; sc:funder "Alexander von Humboldt Foundation", "CSIRO's OCE Science Leader program and its Computational and Simulation Sciences platform" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Aquaria" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Department for Bioinformatics and Computational Biology, Technische Universität München", "Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney", "Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney", "RostLab", "School of Molecular Bioscience, The University of Sydney" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://aquaria.ws" ; biotools:primaryContact "Andrea Schafferhans", "Seán O'Donoghue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC8209617", "pubmed:34151028" ; sc:description "Open-source laboratory software for design, execution and data management. Build reproducible experimental workflows, manage samples, store data, and share know-how." ; sc:featureList edam:operation_2409, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Aquarium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.aquarium.bio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3500 ; sc:citation ; sc:description """Expanding our understanding of the trade in aquatic marine wildlife. Marine Aquarium Biodiversity and Trade Flow. Aquariumtradedata.org is a commitment to understanding the diversity and magnitude of the marine aquarium trade by illuminating and evaluating the global shipping pathways of the trade. You will be logged off in seconds due to inactivity. Click here to continue using this web page. Clownfish, or anemonefish (family Pomacentridae), are some of the most iconic fish species on tropical coral reefs, where they live symbiotically with giant sea anemones. Read more about the global trade of clownfish by RET TALBOT""" ; sc:featureList edam:operation_2422, edam:operation_3436 ; sc:name "aquarium trade date data" ; sc:url "https://www.aquariumtradedata.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2828 ; sc:citation "pubmed:21665925" ; sc:description "AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models." ; sc:featureList edam:operation_3453 ; sc:name "AquaSAXS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lorentz.dynstr.pasteur.fr/aquasaxs.php" ; biotools:primaryContact "Poitevin F." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_3263, edam:topic_3308 ; sc:citation , "pubmed:36243967" ; sc:description "A spatial omics database and analysis platform." ; sc:featureList edam:operation_0247, edam:operation_0314, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Aquila" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://aquila.cheunglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384 ; sc:citation ; sc:description "Novel automatic muscle artifact reduction method for ictal EEG interpretation." ; sc:featureList edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "AR2" ; sc:url "https://github.com/shennanw/AR2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation "pubmed:15094041" ; sc:description "Predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2492, edam:operation_3439 ; sc:name "Ar_NHPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ar_nhpred" ; biotools:primaryContact "Dr. G. P. S. Raghava" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_3345 ; sc:author ; sc:contributor "Maciej Szymanski" ; sc:description "An automatic pipeline for exploration of SRA datasets with sequences as a query" ; sc:featureList edam:operation_0253, edam:operation_0292, edam:operation_0338, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ARA (Automated Record Analysis)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "https://github.com/maurya-anand/ARA" ; biotools:primaryContact "Wojciech Karlowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3518 ; sc:citation "pubmed:17684564" ; sc:description "An \"\"Electronic Fluorescent Pictograph\"\" browser for exploring and analyzing large-scale biological data sets (using example of Arabidopsis). Explores microarray and other data for hypothesis generation. eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets." ; sc:featureList edam:operation_3429 ; sc:name "Arabidopsis eFP Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bar.utoronto.ca/efp_arabidopsis/cgi-bin/efpWeb.cgi" ; biotools:primaryContact "Nicholas Provart" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780 ; sc:citation ; sc:description "Integrated network of Arabidopsis growth regulators." ; sc:featureList edam:operation_3562 ; sc:name "Arabidopsis growth regulators network" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/supplementary_data/ehsab/gene_prioritization/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:11779843" ; sc:description "Program for assembling data from whole genome shotgun sequencing experiments." ; sc:featureList edam:operation_0310 ; sc:name "Arachne" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.broadinstitute.org/computational-rd/computational-research-and-development" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3626 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3334 ; sc:citation ; sc:description "A simulation environment with simple user interface for analyzing neural and neuroglial networks organisation, optimisation and execution." ; sc:featureList edam:operation_2497, edam:operation_3562, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ARACHNE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/LeonidSavtchenko/Arachne" ; biotools:primaryContact "Leonid Savtchenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0154, edam:topic_3500 ; sc:citation "pubmed:19674480", "pubmed:21036864" ; sc:description "ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface." ; sc:featureList edam:operation_0245, edam:operation_0346, edam:operation_3092 ; sc:name "ArachnoServer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.arachnoserver.org" ; biotools:primaryContact "ArachnoServer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis." ; sc:featureList edam:operation_2945, edam:operation_3629 ; sc:name "ARACNE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE?" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0780, edam:topic_3298, edam:topic_3382 ; sc:citation , , "pmcid:PMC7721323", "pubmed:33037149" ; sc:description "ARADEEPOPSIS is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ARADEEPOPSIS" ; sc:softwareHelp ; sc:softwareVersion "1.0", "1.1", "1.2", "1.2.1", "1.3", "1.3.1" ; sc:url "https://github.com/Gregor-Mendel-Institute/aradeepopsis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659 ; sc:citation , "pmcid:PMC373265", "pubmed:14704338" ; sc:description "ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes" ; sc:featureList edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "aragorn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ansikte.se/ARAGORN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3050 ; sc:citation ; sc:description "arakno is an R package for effective spider nomenclature, distribution and trait data retrieval from online resources. Online open databases are increasing in number, usefulness, and ease of use. There are currently two main global databases exclusive for spiders, the World Spider Catalogue (WSC) and the World Spider Trait (WST) database. Both are regularly used by thousands of researchers. Computational tools that allow effective processing of large data are now part of the workflow of any researcher and R is becoming a de facto standard for data manipulation, analysis, and presentation. Here we present an R package, arakno , that allows interface with the two databases. Implemented tools include checking species names against nomenclature of the WSC, obtaining and mapping data on distribution of species from both WST and the Global Biodiversity Information Facility (GBIF), and downloading trait data from the WST." ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "arakno" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=arakno" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1895 ; sc:name "Locus ID (AGI)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_0820 ; sc:citation , "pmcid:PMC166783", "pubmed:12529511" ; sc:description "Plant membrane proteins." ; sc:featureList edam:operation_0224 ; sc:name "ARAMEMNON database of plant membrane proteins" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Botanical Institute University of Cologne" ; sc:softwareHelp ; sc:url "http://aramemnon.botanik.uni-koeln.de/" ; biotools:primaryContact "Rainer Schwacke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0196, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:34013348" ; sc:description "Accurate long-Reads Assembly correction Method for Indel errorS (ARAMIS) is a NGS long-reads indels correction pipeline that combines several correction software in just one step using accurate short reads. As a proof OF concept, six organisms were selected based on their different GC content, size and genome complexity, and their PacBio-assembled genomes were corrected thoroughly by this pipeline." ; sc:featureList edam:operation_0452, edam:operation_0524, edam:operation_0525, edam:operation_3195 ; sc:name "ARAMIS" ; sc:url "https://github.com/genomics-ngsCBMSO/ARAMIS.git" ; biotools:primaryContact "B Aguado" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:31642487" ; sc:description "A major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. AraPheno is a public database collection of Arabidopsis thaliana phenotypes." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3283, edam:operation_3431, edam:operation_3557 ; sc:license "MIT" ; sc:name "AraPheno" ; sc:softwareHelp , , , ; sc:url "https://arapheno.1001genomes.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625 ; sc:citation , "pubmed:27862469" ; sc:description "Resource for Arabidopsis thaliana genomics. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services" ; sc:featureList edam:operation_0224, edam:operation_0227 ; sc:license "Not licensed" ; sc:name "Araport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.araport.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3360, edam:topic_3517 ; sc:author ; sc:citation ; sc:description """AraQTL is the A.thaliana workbench and database for eQTL analysis. It allows easy access to the data of all published Arabidopsis thaliana genetical genomics experiments.""" ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_3232 ; sc:name "AraQTL" ; sc:softwareVersion "1.0" ; sc:url "https://www.bioinformatics.nl/AraQTL" ; biotools:primaryContact "Basten L. Snoek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0769 ; sc:citation , "pmcid:PMC10027432", "pubmed:36752514" ; sc:description "A graph-based modular reasoning tool for translational biomedicine." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "ARAX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://arax.rtx.ai" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , ; sc:description "The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria" ; sc:featureList edam:operation_0259, edam:operation_0260, edam:operation_0278, edam:operation_0287, edam:operation_0289, edam:operation_0291, edam:operation_0294, edam:operation_0326, edam:operation_0346, edam:operation_0349, edam:operation_0368, edam:operation_0371, edam:operation_0492, edam:operation_0496, edam:operation_0558, edam:operation_0567, edam:operation_3080, edam:operation_3081 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "ARB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "6.0.6" ; sc:url "http://arb-home.de" ; biotools:primaryContact "ARB Users Mailing List" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "ARBic is an All-Round Biclustering Algorithm for Analyzing Gene Expression Data. Identifying significant biclusters of genes with specific expression patterns is an effective approach to reveal functionally correlated genes in gene expression data. However, existing algorithms are limited to finding either broad or narrow biclusters but both due to failure of balancing between effectiveness and efficiency. ARBic can accurately identify any meaningful biclusters of shape no matter broad or narrow in a large scale gene expression data matrix, even when the values in the biclusters to be identified have the same distribution as that the background data has. ARBic is developed by integrating column-based and row-based strategies into biclustering procedure. The column-based strategy borrowed from ReBic, a recently published biclustering tool, prefers to narrow bicluters." ; sc:featureList edam:operation_3463, edam:operation_3501 ; sc:license "MIT" ; sc:name "ARBic" ; sc:url "https://github.com/holyzews/ARBic" ; biotools:primaryContact "Guojun Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , ; sc:description "ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads. It is used for merging and scaffolding an existing genome assembly. It takes a position sorted read alignment file in the bam/sam format with 10X Chromium barcodes in the BX tag, and if additionally provided with the genome fasta file used for mapping, it will sort and merge the provided contigs into scaffolds. A key functionality is the possibility to resolve links between contigs by overlap-layout-consensus (OLC) instead of indiscriminately inserting a gap between them." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "ARBitR" ; sc:url "https://github.com/markhilt/ARBitR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:24990605" ; sc:description "Pipeline for automated retrieval of all sequences for a specified gene from GenBank." ; sc:featureList edam:operation_0349, edam:operation_2422 ; sc:name "ARBitrator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.jzehrlab.com/nifh" ; biotools:primaryContact "Jonathan P. Zehr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pubmed:30445495" ; sc:description """efficient and scalable inference of gene regulatory networks. Usage Example — arboreto 0.1.5 documentation. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_2437 ; sc:license "BSD-3-Clause" ; sc:name "Arboreto" ; sc:softwareHelp ; sc:softwareVersion "0.1.5" ; sc:url "http://arboreto.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:23640720" ; sc:description "Scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories." ; sc:featureList edam:operation_0324, edam:operation_2495 ; sc:name "Arboretum" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pages.discovery.wisc.edu/~sroy/arboretum/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "ARC is a pipeline which facilitates iterative, reference guided de novo assemblies." ; sc:featureList edam:operation_0310 ; sc:name "ARC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.4-beta" ; sc:url "http://ibest.github.io/ARC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3068, edam:topic_3318, edam:topic_3393 ; sc:citation , "pmcid:PMC7921781", "pubmed:33665184" ; sc:description "Academic Resources Platform for COVID-19 The Academic Resources for COVID-19 (ARC) is an online platform to match equipment, consumables, reagents and other critical resources needed by Swiss diagnostic laboratories involved in combating the Sars-CoV-2 virus with Swiss academic groups who are able and willing to provide them." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3799 ; sc:name "ARC" ; sc:url "http://arc.epfl.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.It is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation. It translates text-based descriptions of biological networks into standardized diagrams. Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations." ; sc:featureList edam:operation_0337 ; sc:name "Arcadia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0rc2" ; sc:url "http://arcadiapathways.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2305 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1775 ; sc:citation , "pmcid:PMC2373754", "pubmed:12441387" ; sc:description "Ab initio predictions of enzyme class (if any) from sequence." ; sc:featureList edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ArchaeaFun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/ArchaeaFun/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3293, edam:topic_3299, edam:topic_3678 ; sc:citation "pubmed:19860910" ; sc:description "Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees." ; sc:featureList edam:operation_0324, edam:operation_0326, edam:operation_0558 ; sc:name "Archaeopteryx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://en.bio-soft.net/tree/ATV.html" ; biotools:primaryContact "Tan Jie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3510 ; sc:citation "pubmed:25150734" ; sc:description "Tool able to decode protein sequence motifs that have a potential to form amyloids." ; sc:featureList edam:operation_2479, edam:operation_3092 ; sc:name "ArchCandy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.montp.cnrs.fr/?r=ArchCandy" ; biotools:primaryContact "Andrey V. Kajava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0166 ; sc:author ; sc:citation , "pmcid:PMC3964960", "pubmed:24265221" ; sc:description "Structural classification of loops extracted from known protein structures." ; sc:featureList edam:operation_2475 ; sc:name "ArchDB14" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "upf.edu" ; sc:softwareHelp ; sc:url "http://sbi.imim.es/archdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0780 ; sc:citation ; sc:description "Plant Root System Architecture Analysis Using DART and RSML Files." ; sc:featureList edam:operation_2990 ; sc:license "GPL-2.0" ; sc:name "archiDART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.3" ; sc:url "https://archidart.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_2275 ; sc:citation "pubmed:22809339" ; sc:description "This tool detects architectures of all-β and α/β-classes" ; sc:featureList edam:operation_0319 ; sc:name "ArchiP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip" ; biotools:primaryContact "Evgeniy Aksianov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0621, edam:topic_0821, edam:topic_3407 ; sc:citation ; sc:description "Architect is a tool for producing high-quality metabolic models through improved enzyme annotation. Architect is a pipeline for automatic metabolic model reconstruction. Given the protein sequences of an organism, enzyme annotation is first performed through ensemble approaches (that is, combining predictions from individual enzyme annotation tools), followed by gap-filling." ; sc:featureList edam:operation_3092, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Architect" ; sc:url "https://github.com/ParkinsonLab/Architect" ; biotools:primaryContact "John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0166, edam:topic_0623 ; sc:citation "pubmed:15229886" ; sc:description "This tool performs a structural classification of kinase loops with information of functional residues to find relationships between structure and function of classified kinase-loops." ; sc:featureList edam:operation_2479 ; sc:name "ArchKI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.uab.es/cgi-bin/archki/loops.pl?class=all&set=ArchKI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16844985" ; sc:description "ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop." ; sc:featureList edam:operation_0224, edam:operation_0474, edam:operation_0477, edam:operation_0481 ; sc:name "ArchPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinsilico.org/ARCHPRED/" ; biotools:primaryContact "biosilico Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3308, edam:topic_3512, edam:topic_3940 ; sc:citation ; sc:description "ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available. Maybe licensed under GPL>=2." ; sc:featureList edam:operation_3196, edam:operation_3222, edam:operation_3436, edam:operation_3891 ; sc:license "MIT" ; sc:name "ArchR" ; sc:url "http://www.ArchRProject.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "ArchSchema is a java program that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB." ; sc:featureList edam:operation_2479 ; sc:name "ArchSchema" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "http://www.ebi.ac.uk/Tools/archschema/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "Scaffolding genome assemblies using 10X Genomics Chromium data or stLFR linked reads" ; sc:featureList edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "ARCS" ; sc:softwareVersion "1.2.4" ; sc:url "https://github.com/bcgsc/ARCS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3307, edam:topic_3678 ; sc:citation "pubmed:18986374" ; sc:description "Toolkit of Perl modules aimed at bioinformatics, genomics, and gerontology, partly based on the BioPerl package, which aim is to allow the comparative genomics of aging. It is a collection of data-mining tools, algorithms, parsers, wrappers, spiders and web applications, etc." ; sc:featureList edam:operation_2476, edam:operation_2478 ; sc:name "ARCT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genomics.senescence.info/software/perl.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "ARD2 (Alpha-rod Repeat Detector) is an application for the identification of alpha-rod repeats, also defined as alpha-solenoids (HEAT, Armadillo among others) in protein sequences using a neural network." ; sc:featureList edam:operation_2479 ; sc:name "ARD2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm-01.zdv.uni-mainz.de/~fournier/ard2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_3534 ; sc:author "G.Launay" ; sc:citation , ; sc:contributor "J.Martin", "R.Lavery" ; sc:description "Analysis of surfaces of protein structures." ; sc:featureList edam:operation_0478, edam:operation_2423 ; sc:name "arDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CNRS", "UCBL", "ibcp.fr" ; sc:softwareHelp ; sc:softwareVersion "0.9" ; sc:url "http://ardock.ibcp.fr" ; biotools:primaryContact "Guillaume Launay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3305 ; sc:citation ; sc:description "AREAdata is a worldwide climate dataset averaged across spatial units at different scales through time. It is a PearseLab data resource where you can download daily estimates of climate/environmental data which have been averaged across different levels of spatial units. Additionally, we include data on population density and estimates from future climate forecasting models at the same spatial levels." ; sc:featureList edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "AREAdata" ; sc:url "https://pearselab.github.io/areadata/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation "pubmed:22035330" ; sc:description "AREM: Aligning Short Reads from ChIP-sequencing by Expectation Maximisation" ; sc:featureList edam:operation_3198, edam:operation_3222 ; sc:name "AREM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jakebiesinger/AREM" ; biotools:primaryContact "Xiaohui Xie" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_1476 ; sc:name "RNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pubmed:37479079" ; sc:description "Arena is a stand-alone program used for the full-atomic reconstruction of RNA structures from coarse-grained models." ; sc:featureList edam:operation_0295, edam:operation_0321, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Arena" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanggroup.org/Arena/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation "pubmed:19040715", "pubmed:22439608" ; sc:description "visualization of multi-layered networks in 3D" ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Arena3D" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://arena3d.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:33885790" ; sc:description "Arena3Dweb is the first, fully interactive and dependency-free, web application which allows the visualization of multi-layered graphs in 3D space. 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The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs as well as related publications." ; sc:featureList edam:operation_0224, edam:operation_0339, edam:operation_0349, edam:operation_0570, edam:operation_0573 ; sc:isAccessibleForFree true ; sc:name "AREsite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bioinf.uni-leipzig.de" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://rna.tbi.univie.ac.at/AREsite" ; biotools:primaryContact "Jörg Fallmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3382 ; sc:citation , "pmcid:PMC8004990", "pubmed:33806863" ; sc:description """ARETT (Augmented Reality Eye Tracking Toolkit for Head Mounted Displays) is a toolkit for Unity 3D which contains scripts for acquiring eye tracking data on the Microsoft HoloLens 2. 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ARGEOS will allow you to carry out a systematic search for transcriptomes, collecting all the unique datasets from the most popular databases. With the web tool, you can conveniently select publicly available datasets for data reanalysis! All you need is to compose a query that will be searched. ARGEOS will let you carry out a systematic search for transcriptomes, methylation data, CHIP-seq experiments, and many others. Handy output format minimizes the need for additional information." ; sc:featureList edam:operation_2421 ; sc:name "ARGEOS" ; sc:url "http://www.ar-geos.org" ; biotools:primaryContact "Dmitry V. Chistyakov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0219, edam:topic_0602, edam:topic_0623 ; sc:citation , "pubmed:32058567" ; sc:description "ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3482 ; sc:name "ARGminer" ; sc:url "https://bench.cs.vt.edu/argminer/#/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0621, edam:topic_0749, edam:topic_3125 ; sc:citation "pubmed:15980502" ; sc:description "Tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes." ; sc:featureList edam:operation_0239, edam:operation_0438, edam:operation_2454, edam:operation_3198 ; sc:name "ARGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/" ; biotools:primaryContact "Nikolay A. Kolchanov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC7641515", "pubmed:33154995" ; sc:description "Argonaut is a web-based utility which facilitates collaborative exploration of Condition/Control-type mass spectrometry experiments. Spreadsheets of quantitative values can be uploaded and organized in a way that best describes your specific experimental setup. Brief statistical analysis is conducted on uploaded data to calculate the significance of molecular perturbations for each condition. 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Flexible ligand docking is possible with ArgusLab, where the ligand is described as a torsion tree and grids are constructed that overlay the binding site. Ligand’s root node is placed on a search point in the binding site and a set of diverse and energetically favorable rotations is created." ; sc:featureList edam:operation_2421, edam:operation_2430, edam:operation_3432 ; sc:name "ArgusLab" ; sc:operatingSystem "Windows" ; sc:softwareVersion "4.0.1" ; sc:url "http://www.arguslab.com/arguslab.com/ArgusLab.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3516 ; sc:citation , "pmcid:PMC4751548", "pubmed:26684930" ; sc:description "An R Package for Analysis of Illumina Genotyping Arrays." ; sc:featureList edam:operation_3196 ; sc:name "argyle" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/andrewparkermorgan/argyle" ; biotools:primaryContact "Andrew P. 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sc:isAccessibleForFree true ; sc:name "AromTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hewg2008/AromTool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3299 ; sc:citation , "pubmed:34117635" ; sc:description "An R package for geometric morphometric methods and virtual anthropology applications." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Arothron" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=34117635" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0092, edam:topic_0602, edam:topic_2828 ; sc:citation ; sc:description "A program for building macromolecular models from crystallograpgic data. It builds proteins, RNA/DNA, seqondary structure, side chains, loops, solvent and ligands" ; sc:featureList edam:operation_0297, edam:operation_0570, edam:operation_2406, edam:operation_2481, edam:operation_3445 ; sc:isAccessibleForFree true ; sc:name "ARP wARP" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.embl-hamburg.de/ARP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2814 ; sc:citation , "pmcid:PMC5282402", "pubmed:27964945" ; sc:description "A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures." ; sc:featureList edam:operation_0248 ; sc:name "Arpeggio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://structure.bioc.cam.ac.uk/arpeggio/" ; biotools:primaryContact "Jubb HC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description """ARPEGGIO is a snakemake workflow that analyzes whole genome bisulfite sequencing (WGBS) data coming from (allo)polyploid species. The workflow includes all basic steps in WGBS data analysis (trimming, quality check and alignment), a read sorting tool specific for allopolyploids, the most comprehensive statistical tool for Differential Methylation (DM) analysis and a set of downstream analyses to obtain a list of genes showing differential methylation. This folder provides the ARPEGGIO config file and the metadata file used to run the analyses of the Mimulus dataset. 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Species specific probe sets were designed by adapting a previously reported maskless array synthesis strategy." ; sc:featureList edam:operation_0571 ; sc:name "Array Design" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://compbio.med.wayne.edu/software/primerDesign/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. 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To overcome such difficulty, a novel model-based clustering method is developed." ; sc:featureList edam:operation_2495, edam:operation_3432 ; sc:name "ArrayCluster" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.ism.ac.jp/~higuchi/arraycluster.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0203 ; sc:citation "pubmed:21071405" ; sc:description "Public repository of functional genomics data supporting publications. 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It significantly predicts expression levels with higher fidelity than technical replicates of the same RNA pool, demonstrating its utility in the integration of data sets from different platforms." ; sc:featureList edam:operation_2495 ; sc:name "aRrayLasso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/adam-sam-brown/aRrayLasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_2885, edam:topic_3516 ; sc:citation "pubmed:25336502" ; sc:description "Tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms." ; sc:featureList edam:operation_0484, edam:operation_3196 ; sc:name "ArrayMaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cw2014/ArrayMaker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2259, edam:topic_2640, edam:topic_3175 ; sc:citation ; sc:description """A curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides an entry point for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. The arrayMap resource represents the part of the Progenetix project for which direct access to source data (i.e. probe-specific genomic array read-outs) has been available during data curation.""" ; sc:featureList edam:operation_0362, edam:operation_3233, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "arrayMap" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://arraymap.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "ArrayMiner® is a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. 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Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3179, edam:topic_3365, edam:topic_3518 ; sc:citation "pubmed:15215429" ; sc:description "ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. 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Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases." ; sc:featureList edam:operation_0313 ; sc:license "GPL-2.0" ; sc:name "ArrayTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ArrayTools.html" ; biotools:primaryContact "Arthur Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0208, edam:topic_2840, edam:topic_3518 ; sc:citation "pubmed:14630514" ; sc:description "This tool provides an integrated solution for managing, analyzing, and interpreting microarray gene expression data. 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ARTEM doesn’t rely on sequence similarity, annotated interactions, or backbone topology. Instead, ARTEM assumes at least one residue-residue match has a close-to-zero RMSD in the ideal superposition. Then, ARTEM tries all N*M single-residue matches and derives a subset of mutually closest residues as the matches for each of the single-residue-based superpositions. Finally, ARTEM returns the superpositions ordered by their size, letting the user choose the best one based on any specific requirements. 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It takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region)." ; sc:featureList edam:operation_2403 ; sc:name "ARTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:20460509" ; sc:description "Adaptive Rank Truncated Product is an R package for analyzing pre-defined genetic pathway based on a genetic association study." ; sc:featureList edam:operation_2497 ; sc:name "ARTP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://dceg.cancer.gov/tools/analysis/artp" ; biotools:primaryContact "Division of Cancer Epidemiology and Genetics (DCEG), NCI", "Han Zhang", "Kai Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2885 ; sc:citation "pubmed:16204124", "pubmed:16845038" ; sc:description "ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_2422, edam:operation_3196 ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/ARTS/" ; biotools:primaryContact "ARTS team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3293, edam:topic_3336 ; sc:citation , "pmcid:PMC8728217", "pubmed:34718689" ; sc:description "ARTS-DB is an online repository of precomputed results of Antibiotic Resistant Target Seeker (ARTS), a rapid genome mining tool for the exploration of antibiotics with interesting and novel targets. ARTS-DB supports two main searching functionalities." ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3482 ; sc:name "ARTS-DB" ; sc:softwareHelp ; sc:url "https://arts-db.ziemertlab.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0780 ; sc:citation , "pmcid:PMC5570205", "pubmed:28472505" ; sc:description "Antibiotic Resistant Target Seeker. Specific and efficient genome mining for antibiotics with interesting and novel targets. Automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. It integrates target directed genome mining methods, antibiotic gene cluster predictions and ‘essential gene screening’ to provide an interactive page for rapid identification of known and putative targets in BGCs." ; sc:featureList edam:operation_0224, edam:operation_3482 ; sc:license "GPL-3.0" ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "https://arts.ziemertlab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8329541", "pubmed:34330087" ; sc:description "ARTS is a fully automated biomarker that outputs a score linked to the likelihood a person suffers from arteriolosclerosis based on brain MRI data (3D T1w, T2w FLAIR, DTI data) and basic demographic information (age at MRI, sex). The higher the ARTS score, the higher the likelihood of arteriolosclerosis." ; sc:featureList edam:operation_2238, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "ARTS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://www.nitrc.org/projects/arts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0781, edam:topic_2830, edam:topic_3948, edam:topic_3966 ; sc:author "ICMR-National Institute of Virology" ; sc:citation ; sc:description "ArVirInd is a knowledge-base of Arbo-Viral proteins from India and its neighbourhood. his is a annotated database, which acts as a repository of Protein sequences for arbo-viruses along with antigenic information. Users can search for protein sequences by virus / protein name or by country of origin (India and countries of the Indian subcontinent: Nepal, Bhutan, Bangladesh, SriLanka, Pakistan) and year of collection (that is, the year of outbreak which defines the origin of the strain)." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "ArVirInd" ; sc:url "http://www.arvirind.co.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3342, edam:topic_3473 ; sc:citation , ; sc:contributor ; sc:description """ARX is a comprehensive open source software for anonymizing sensitive personal data. It supports a wide variety of (1) privacy and risk models, (2) methods for transforming data and (3) methods for analyzing the usefulness of output data. The software has been used in a variety of contexts, including commercial big data analytics platforms, research projects, clinical trial data sharing and for training purposes. ARX is able to handle large datasets on commodity hardware and it features an intuitive cross-platform graphical user interface.""" ; sc:featureList edam:operation_3283 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ARX Data Anonymization Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://arx.deidentifier.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3320, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC9726986", "pubmed:36473963" ; sc:description "A pan-cancer database of alternative splicing for molecular classification of cancer." ; sc:featureList edam:operation_0264, edam:operation_3463, edam:operation_3659 ; sc:license "Not licensed" ; sc:name "AS-CMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.pmrc.re.kr/ASCMC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "AS-Quant generates the expression level of alternative splicing among two different biological conditions." ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_0433 ; sc:name "AS-Quant" ; sc:softwareHelp ; sc:url "https://github.com/CompbioLabUCF/AS-Quant" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_2814 ; sc:citation , "pubmed:12824330", "pubmed:15980437" ; sc:description "This system consists of servers for protein structure analysis and modelling." ; sc:featureList edam:operation_0302, edam:operation_0477, edam:operation_2406, edam:operation_2480, edam:operation_2481 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "AS2TS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteinmodel.org/" ; biotools:primaryContact "Adam Zemla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3517 ; sc:citation ; sc:description "Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs." ; sc:featureList edam:operation_3197 ; sc:license "Artistic-2.0" ; sc:name "ASAFE" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASAFE.html" ; biotools:primaryContact "Qian Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "Galaxy-based framework to analyze microbiota data." ; sc:featureList edam:operation_0564, edam:operation_2403 ; sc:license "Apache-2.0" ; sc:name "ASaiM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ASaiM" ; biotools:primaryContact "Bérénice Batut" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0204 ; sc:citation ; sc:description "A framework for promoter analysis based on a fast search engine using enhanced suffix arrays. The framework includes several statistics for calculating over-representation of motifs in a set of promoters from co-regulated genes compared to a background set." ; sc:featureList edam:operation_0445 ; sc:license "GPL-3.0" ; sc:name "ASAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://asap.binf.ku.dk/Asap/Home.html" ; biotools:primaryContact "Troels T. Marstrand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_2269, edam:topic_3168, edam:topic_3293 ; sc:citation , "pubmed:33058550" ; sc:description """ASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments. ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.""" ; sc:featureList edam:operation_0310, edam:operation_3200, edam:operation_3359, edam:operation_3478 ; sc:name "ASAP" ; sc:softwareHelp , ; sc:url "https://bioinfo.mnhn.fr/abi/public/asap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0634, edam:topic_0769, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC7205315", "pubmed:32339164" ; sc:description "Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning (ASAP-SML) is a pipeline to identify distinguishing features in targeting antibody set when compared to a reference non-targeting set. The pipeline first extracts germline, CDR canonical structure, isoelectric point and frequent positional motifs features from sequences and creates an antibody feature fingerprint. Machine-learning and statistical significance testing are applied to antibody sequences and feature fingerprints to identify distinguishing feature values and combinations thereof. When applied to an MMP-targeting set, ASAP identifies salient features and recommends features to use when designing novel MPP-targeting antibody sequences." ; sc:featureList edam:operation_2238, edam:operation_2404, edam:operation_3937 ; sc:license "MIT" ; sc:name "ASAP-SML" ; sc:url "https://github.com/HassounLab/ASAP-SML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "Automated Single-cell Analysis Pipeline." ; sc:featureList edam:operation_0564, edam:operation_3680 ; sc:name "ASAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/DeplanckeLab/ASAP" ; biotools:primaryContact "Bart Deplancke" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3655, edam:format_3747 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3655, edam:format_3747 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments." ; sc:featureList edam:operation_0314, edam:operation_3630, edam:operation_3632, edam:operation_3635, edam:operation_3638, edam:operation_3658, edam:operation_3705, edam:operation_3741 ; sc:name "ASAPRatio" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/ASAPRatio.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "ASAS (Analysis and Simulation of Atomic Spectra) software is a tool to be used in studies involving atomic spectroscopy." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "ASAS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "Beta 1.0" ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX-D-16-00062" ; biotools:primaryContact "Jhonatha Ricardo dos Santos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pubmed:12354655" ; sc:description "Discriminates aa substitutions with high and low probabilities of occurrence." ; sc:featureList edam:operation_2451 ; sc:name "ASaturA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/ASaturA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3168, edam:topic_3308 ; sc:citation "pubmed:21080965" ; sc:description "Empirical Bayes method to detect differential expression based on sequencing technology." ; sc:featureList edam:operation_2238, edam:operation_3695, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "ASC" ; sc:softwareHelp ; sc:url "http://www.stat.brown.edu/Zwu/research.aspx" ; biotools:primaryContact "Bethany D Jenkins", "LeAnn P Whitney", "Mak A Saito", "Melissa Mercier", "Sonya T Dyhrman", "Tatiana A Rynearson", "Zhijin Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Asc-Seurat is an Analytical single-cell Seurat-based web application." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3890 ; sc:license "GPL-3.0" ; sc:name "Asc-Seurat" ; sc:softwareHelp ; sc:url "https://github.com/KirstLab/asc_seurat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0736, edam:topic_0749, edam:topic_2828 ; sc:citation , "pubmed:36794725" ; sc:description "A website to calculate advanced structural characteristics of G-quadruplexes.ssr (X3DNA.ORG)" ; sc:featureList edam:operation_0249, edam:operation_0320, edam:operation_3216, edam:operation_3454 ; sc:license "Not licensed" ; sc:name "ASC-G4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tiny.cc/ASC-G4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_2885, edam:topic_3421, edam:topic_3519 ; sc:citation , "pmcid:PMC7188954", "pubmed:32391349" ; sc:description "AScall is a web tool providing automatic processing of allele specific real-time PCR experiments: variation conducted real-time whereis each allele is detected by independent reaction separated into individual wells. The positive outcome of the reaction for a particular allele is judged by the increase in the fluorescent signal." ; sc:featureList edam:operation_0308, edam:operation_0337, edam:operation_0484, edam:operation_3196 ; sc:license "MIT" ; sc:name "AScall" ; sc:url "http://shtest.evrogen.net/AScall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:33508309" ; sc:description "aScan is a software tool for the determination of allele-specific-expression at the single individual level from matched RNA-Seq and genomic data." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "aScan" ; sc:url "https://github.com/Federico77z/aScan/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2640, edam:topic_3320 ; sc:citation , "pmcid:PMC9825479", "pubmed:36318242" ; sc:description "A comprehensive knowledgebase of alternative splicing in human cancers." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-3.0" ; sc:name "ASCancer Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/ascancer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC10562615", "pubmed:37822561" ; sc:description "Positional feature annotation and protein structure-based representation of single amino acid variations." ; sc:featureList edam:operation_0331 ; sc:isAccessibleForFree true ; sc:name "ASCARIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huggingface.co/spaces/HUBioDataLab/ASCARIS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_2333 ; sc:name "Raw microarray data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3574 ; sc:citation ; sc:description "Tool for accurate dissection of genome-wide allele-specific copy number in tumors. It accounts for normal cell admixture and tumor aneuploidy in the analysis of SNP array data from cancer samples. It allows analysis of Illumina and Affymetrix SNP array data of tumor samples (with or without matching germline samples)." ; sc:featureList edam:operation_3208, edam:operation_3233 ; sc:name "ASCAT" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "UiO" ; sc:softwareHelp , ; sc:softwareVersion "2.4" ; sc:url "https://www.crick.ac.uk/peter-van-loo/software/ASCAT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , , "pmcid:PMC6735844", "pubmed:31505654" ; sc:description "scRNA-seq analysis toolkit (R package) for quality control, normalization, dimensionality reduction, clustering and differential expression." ; sc:featureList edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ascend" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/IMB-Computational-Genomics-Lab/ascend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3067, edam:topic_3306, edam:topic_3379 ; sc:citation , "pmcid:PMC8423288", "pubmed:34492004" ; sc:description "ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds). A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves." ; sc:featureList edam:operation_2426, edam:operation_2428, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASCENT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wmglab-duke/ascent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3398 ; sc:citation , "pmcid:PMC9617685", "pubmed:36325307" ; sc:description "Automated Selection of Changepoints using Empirical P-values and Trimming (ASCEPT), to select an optimal set of changepoints in mobile health data" ; sc:featureList edam:operation_3192, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ASCEPT" ; sc:url "https://github.com/matthewquinn1/changepointSelect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description "ASCoVPred is a machine learning-based platform for quantitative prediction of anti-SARS-CoV-2 activity and human cell toxicity of molecules. ASCoVPred is a collection of compounds descriptors / fingerprints (FPs) calculator tool (PaDEL v2.21) and different machine learning (ML) algorithms (implemented in Weka v3.8.2) that are used to build the ML-based quantitative structure-activity relationship (QSAR) prediction models. These QSAR models can be used for ML-assisted prediction of anti-SARS-CoV-2 activity and human cell toxicity of compounds." ; sc:featureList edam:operation_3799 ; sc:name "ASCoVPred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://14.139.62.220/ascovpred/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0154, edam:topic_0209, edam:topic_0634 ; sc:citation "pubmed:21051350" ; sc:description "AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area." ; sc:featureList edam:operation_0224, edam:operation_0250, edam:operation_2414 ; sc:name "ASD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mdl.shsmu.edu.cn/ASD/" ; biotools:primaryContact "ASD Support", "Jian Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3474 ; sc:citation , "pmcid:PMC10311404", "pubmed:37387128" ; sc:description "Genome-wide scans for selective sweeps using convolutional neural networks." ; sc:featureList edam:operation_0451, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "ASDEC" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/pephco/ASDEC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3407, edam:topic_3512 ; sc:citation , "pmcid:PMC7591752", "pubmed:33173536" ; sc:description "ASDmiR is a step-wise method to uncover miRNA regulation related to autism spectrum disorder. MiRNAs (miRNAs) are involved in nervous system developmental, and have potential to cause ASD. However, the miRNA regulation mechanism in ASD is largely unclear. In this work, we present a novel framework, ASDmiR, to identify miRNA-target networks and modules, miRNA sponge networks and modules for uncovering the pathogenesis of ASD, as well as conduct enrichment analysis." ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_2436, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "ASDmiR" ; sc:url "https://github.com/chenchenxiong/ASDmiR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation , "pubmed:36449588" ; sc:description "Semi-supervised medical image segmentation using adversarial consistency learning and dynamic convolution network." ; sc:featureList edam:operation_3927 ; sc:license "Not licensed" ; sc:name "ASE-Net" ; sc:url "https://github.com/SUST-reynole/ASE-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "R package to predict lysine sites that can be acetylated by a specific KAT-family." ; sc:featureList edam:operation_0417 ; sc:license "GPL-3.0" ; sc:name "ASEB" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASEB.html" ; biotools:primaryContact "Likun Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3168, edam:topic_3320 ; sc:citation "pubmed:15980562" ; sc:description "Tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs." ; sc:featureList edam:operation_0264, edam:operation_2499 ; sc:name "ASePCR" ; sc:url "http://genome.ewha.ac.kr/ASePCR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3170, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "Animal Sex Reversal database." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0544, edam:operation_3223 ; sc:name "ASER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://aser.ihb.ac.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3168, edam:topic_3305, edam:topic_3810 ; sc:citation , "pmcid:PMC6935939", "pubmed:31694969" ; sc:description """Rapid Sequence-Based Characterization of African Swine Fever Virus by Use of the Oxford Nanopore MinION Sequence Sensing Device and a Companion Analysis Software Tool. https://www.ncbi.nlm.nih.gov/pubmed/?term=31694969. O'Donnell VK, Grau FR, Mayr GA, Sturgill Samayoa, Dodd KA, Barrette RW., RAPID SEQUENCE-BASED CHARACTERIZATION OF AFRICAN SWINE FEVER VIRUS USING THE OXFORD NANOPORE MINION SEQUENCE SENSING DEVICE AND A COMPANION ANALYSIS SOFTWARE TOOL. J Clin Microbiol. 2019 Nov 6. pii: JCM.01104-19. doi: 10.1128/JCM.01104-19. Foreign Animal Disease Diagnostic Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Plum Island Animal Disease Center, New York.""" ; sc:featureList edam:operation_0310, edam:operation_3185, edam:operation_3200, edam:operation_3211 ; sc:license "MIT" ; sc:name "ASF-FAST" ; sc:url "https://github.com/rwbarrette/ASFV_MinION_RapidAssembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0160, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:34133282" ; sc:description "Protein Fold Recognition based on Evolutionary Features with Variable Parameters using Full Connected Neural Network." ; sc:featureList edam:operation_0303, edam:operation_3936, edam:operation_3937 ; sc:name "ASFold-DNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bioinformatics-Laboratory/project/tree/master/ASFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description "A web server for the development of customized scoring functions in the field of protein docking." ; sc:featureList edam:operation_3891, edam:operation_3899, edam:operation_3938 ; sc:name "ASFP" ; sc:softwareHelp ; sc:url "http://cadd.zju.edu.cn/asfp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0199, edam:topic_3056, edam:topic_3796 ; sc:citation , "pmcid:PMC7159030", "pubmed:32294195" ; sc:description "The African Swine Fever Virus Database (ASFVdb) is an integrative resource for genomic and proteomic analyses of African swine fever virus." ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3208 ; sc:name "ASFVdb" ; sc:url "http://asfvdb.popgenetics.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC9945835", "pubmed:36813801" ; sc:description "Using scRNA-seq data, Asgard repurposes drugs and predicts personalized drug combinations to address the cellular heterogeneity of patients." ; sc:featureList edam:operation_3223, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ASGARD" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/lanagarmire/ASGARD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation ; sc:description "The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA)." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "ASGSCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASGSCA.html" ; biotools:primaryContact "Hela Romdhani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3169, edam:topic_3940 ; sc:citation , ; sc:description "A method for allele-specific modeling of diploid Hi-C data (chromatin contacts and structures) using hierarchical Bayesian modeling." ; sc:featureList edam:operation_0487, edam:operation_3435, edam:operation_3557 ; sc:name "ASHIC" ; sc:url "https://github.com/wmalab/ASHIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pubmed:33792647" ; sc:description "Automated Selection of High quality Libraries for the Extensive analYsis of Strandseq data (ASHLEYS) is an automated quality control for single-cell Strand-seq data." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_0487, edam:operation_2428 ; sc:license "MIT" ; sc:name "ASHLEYS" ; sc:url "http://github.com/friendsofstrandseq/ashleys-qc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0623, edam:topic_0659 ; sc:citation "pubmed:11751222", "pubmed:11847076", "pubmed:15130931", "pubmed:15980557" ; sc:description "Server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_1781, edam:operation_2495, edam:operation_3659 ; sc:name "ASIAN" ; sc:url "http://eureka.cbrc.jp/asian/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3172 ; sc:citation ; sc:description "Automatic Statistical Identification in Complex Spectra quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty." ; sc:featureList edam:operation_3214, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "ASICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASICS.html" ; biotools:primaryContact "Gaëlle Lefort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:18480122" ; sc:description "Design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs." ; sc:featureList edam:operation_0267, edam:operation_0465, edam:operation_2008 ; sc:name "AsiDesigner" ; sc:url "http://sysbio.kribb.re.kr/AsiDesigner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33647976" ; sc:description "ASimulatoR is a tool for splice-aware RNA-Seq data simulation." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "ASimulatoR" ; sc:url "https://github.com/biomedbigdata/ASimulatoR" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2305 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2376 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3751 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2376, edam:format_3751 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3366 ; sc:author "Olivier Filangi" ; sc:description "AskOmics is a visual SPARQL query interface supporting both intuitive data integration and querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL" ; sc:featureList edam:operation_0224, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Askomics" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/askomics" ; biotools:primaryContact "Anthony Bretaudeau", "Olivier Dameron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3170, edam:topic_3320, edam:topic_3500 ; sc:citation , "pmcid:PMC6993437", "pubmed:32000661" ; sc:description """A database for alternative splicing atlas in livestock animals. The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa), chickens (Gallus gallus) and horses (Equus Caballus).""" ; sc:featureList edam:operation_0264, edam:operation_2421, edam:operation_3799 ; sc:name "ASlive" ; sc:url "http://ASlive.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3300, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:37000299" ; sc:description "Novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "ASLncR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/aslncr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "ASLPrep is a robust preprocessing pipeline for Arterial Spin Labeling data. ASLPrep is a Arterial Spin Labeling (ASL) data preprocessing and Cerebral Blood FLow (CBF) computation pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "ASLPrep" ; sc:softwareHelp ; sc:url "https://pennlinc.github.io/aslprep_paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3401, edam:topic_3444 ; sc:citation , "pmcid:PMC6690842", "pubmed:31406952" ; sc:description "Imaging Clinically Relevant Pain States Using Arterial Spin Labeling | The Center for Functional Neuroimaging at the University of Pennsylvania provides unification for currently distributed medical center efforts in physiological and clinical brain imaging and advance the general interests of the brain imaging community through targeted methods development, symposia and colloquia, handling of regulatory issues, and fund-raising efforts | Updated manual, ASL MoCo code, and asl_perf_subtract.m. Major new features include: | asl_perf_subtract.m has been updated with new parameters (T1b, T2wm, Rwm-blood) from the latest literature. CBF quantification for PASL using voxelwise M0 value has been updated. Please see the document therein for the details | Made a new version for SPM12. Major new features include: | 1) wraper functors for most of the processing steps," ; sc:featureList edam:operation_3799 ; sc:name "ASLtbx" ; sc:softwareHelp ; sc:url "https://cfn.upenn.edu/~zewang/ASLtbx.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Cconverts the Celera ASM assembly format to the Consed ACE or the CAF file format." ; sc:featureList edam:operation_0310, edam:operation_0335 ; sc:name "asm2ace" ; sc:operatingSystem "Linux" ; sc:softwareVersion "0.6" ; sc:url "http://sourceforge.net/projects/asm2ace/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_0634, edam:topic_3172, edam:topic_3360 ; sc:citation , "pmcid:PMC10218045", "pubmed:37239321" ; sc:description "Integrative method for identifying key biomarkers from multi-omics data." ; sc:featureList edam:operation_0314, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "asmbPLS-DA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RunzhiZ/asmbPLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC8728259", "pubmed:34664666" ; sc:description "Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and differential DNA methylation in diverse organisms." ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:name "ASMdb" ; sc:url "http://www.dna-asmdb.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3300, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:36939943" ; sc:description "Machine learning framework for prediction of abiotic stress-specific miRNAs in plants." ; sc:featureList edam:operation_0463, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "ASmiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/asmir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_2815, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:15215376" ; sc:description "Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes." ; sc:featureList edam:operation_0310, edam:operation_0477, edam:operation_0526, edam:operation_2499 ; sc:name "ASmodeler" ; sc:url "http://genome.ewha.ac.kr/ECgene/ASmodeler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3516 ; sc:citation , "pmcid:PMC4690232", "pubmed:26705468" ; sc:description "Software for discovery, genotyping and characterization of structural variants." ; sc:featureList edam:operation_3202 ; sc:name "AsmVar" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinformatics-centre.github.io/AsmVar/" ; biotools:primaryContact "Shujia Huang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "An ASP-based method for finding attractors in genetic regulatory networks." ; sc:featureList edam:operation_1781 ; sc:name "ASP-G" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:name "Mathematical model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2585 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:citation ; sc:description "A toolkit for constructing statistical models for biological processes. 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Johnson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "An Emboss tool that searches for a sequence assembly and returns the data in one of the EMBOSS assembly formats." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "assemblyget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://www.bioinformatics.nl/cgi-bin/emboss/assemblyget" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3173, edam:topic_3372 ; sc:citation "pubmed:21601686" ; sc:description "Software tool for computing the robotic commands for 2ab assembly. It takes as input a list of composite parts described in terms of their basic part composition." ; sc:featureList edam:operation_0310 ; sc:name "assemblyManager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://andersonlab.qb3.berkeley.edu/#/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "This series of scripts calculates various metrics on an input FASTA file. Typically this is most useful on either denovo genomic or transcriptomic data." ; sc:featureList edam:operation_0310 ; sc:name "assemblystats" ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0102, edam:topic_3053, edam:topic_3168, edam:topic_3169, edam:topic_3170 ; sc:citation "pubmed:21838806" ; sc:description "Software of allele specific study of next generation sequencing data, with emphasis on RNA-seq and ChIP-seq data." ; sc:featureList edam:operation_2429 ; sc:name "asSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bios.unc.edu/~weisun/software/asSeq.htm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_2330 ; sc:name "Genotype/phenotype report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885 ; sc:citation ; sc:description "An R package for subset-based analysis of heterogeneous traits and subtypes." ; sc:featureList edam:operation_2238, edam:operation_3194 ; sc:license "GPL-2.0" ; sc:name "ASSET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ASSET.html" ; biotools:primaryContact "William Wheeler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2013, edam:format_2058 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013, edam:format_2058 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269 ; sc:citation ; sc:description "Tool to evaluate the pathway deregulation/activation status in patient samples. It employs a Bayesian factor analysis approach to adapt predetermined pathway signatures derived from knowledge-based literatures or from perturbation experiments to the cell-/tissue-specific pathway signatures. 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It is a user-friendly computational pipeline for the search of coevolution between hundreds and even thousands of proteins." ; sc:featureList edam:operation_2421, edam:operation_2464, edam:operation_2492 ; sc:name "AutoCoEv" ; sc:url "https://github.com/mattilalab/autocoev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3297 ; sc:citation , "pmcid:PMC9036508", "pubmed:35468739" ; sc:description "AutoCoV, a deep learning method with multiple loss object, that can track the early spread of COVID-19 in terms of spatial and temporal patterns until the disease is fully spread over the world in July 2020." ; sc:featureList edam:operation_3432, edam:operation_3472, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "AutoCoV" ; sc:url "https://github.com/smaster7/AutoCoV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0654 ; sc:citation ; sc:description "AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in sequence traces. 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It enables to prepare, explore, and share interactive 3D and immersive VR structural walkthroughs directly in a web browser" ; sc:featureList edam:operation_0297, edam:operation_0570, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Autodesk Molecule Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://moleculeviewer.lifesciences.autodesk.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_0654, edam:topic_2885 ; sc:citation , "pubmed:15335214" ; sc:description "AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). 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AutoFAIR a semi-automated tool to assess a resource according to the Findability, Accessibility, Interoperability and Reusability (FAIR) criteria. 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sc:description "This program reads in ultrasound videos and automates the process of measuring muscle architecture." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Automated Measurement of Muscle Architecture from Ultrasound Images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "5.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43863-automated-measurement-of-muscle-architecture-from-ultrasound-images" ; biotools:primaryContact "Benjamin Infantolino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3382 ; sc:description "Automatic objective neuronal spike detection for electrophys. measurements." ; sc:featureList edam:operation_3450 ; sc:isAccessibleForFree true ; sc:name "Automatic objective neuronal spike detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; 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Web server allows you to unravel the reaction mechanisms (with intermediates and transition states) of your system, just providing an equilibrium structure (reactant)" ; sc:featureList edam:operation_0244, edam:operation_0334, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "AutoMeKin" ; sc:operatingSystem "Linux" ; sc:url "https://rxnkin.usc.es/amk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC9290317", "pubmed:35833885" ; sc:description "Automated Retinal Vascular Morphology Quantification via a Deep Learning Pipeline." ; sc:featureList edam:operation_2428, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "AutoMorph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rmaphoh/AutoMorph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3473, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9047440", "pubmed:35412809" ; sc:description "An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3215 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "automRm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.gwdg.de/joerg.buescher/automrm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3307, edam:topic_3569 ; sc:citation "pubmed:21317138" ; sc:description "Mathematica package for analyzing time-series of oscillatory signals, particularly those originating from biological/chemical systems." ; sc:featureList edam:operation_2426 ; sc:name "Autoosc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://babylone.ulb.ac.be/autoosc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3318, edam:topic_3365 ; sc:citation ; sc:description "The paper-based microfluidic device design software." ; sc:featureList edam:operation_0337 ; sc:name "AutoPAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MaceLab/AutoPAD" ; biotools:primaryContact "MaceLab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0602, edam:topic_0659, edam:topic_0749 ; sc:citation , "pubmed:37589496" ; sc:description "High-resolution data source for the analysis of autophagy and its regulation." ; sc:featureList edam:operation_1781, edam:operation_2421, edam:operation_2422, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "AutophagyNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://autophagynet.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:description "An automatic pipeline for phylogenetic analysis." ; sc:featureList edam:operation_0323 ; sc:name "Autophylo" ; sc:operatingSystem "Linux" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://code.google.com/p/autophylo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC10365084", "pubmed:37492662" ; sc:description "Framework for simple experimentation with radiomics features. 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sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MartinFXP/B-NEM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """The bio2byte tools server (b2btools) offers the following single protein sequence based predictions: - Backbone and sidechain dynamics (DynaMine) - Helix, sheet, coil and polyproline-II propensity - Early folding propensity (EFoldMine) - Disorder (DisoMine) - Beta-sheet aggregation (Agmata) In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA""" ; sc:featureList edam:operation_0267, edam:operation_3092, edam:operation_3904 ; sc:name "b2bTools" ; sc:url "https://www.bio2byte.be/b2btools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3047, edam:topic_3332, edam:topic_3374 ; sc:citation , "pmcid:PMC8556334", "pubmed:34716354" ; sc:description "Blood-Brain Barrier Database (B3DB) is a curated diverse molecular database of blood-brain barrier permeability with chemical descriptors." ; sc:featureList edam:operation_3431, edam:operation_3659, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "B3DB" ; sc:url "https://github.com/theochem/B3DB" ; biotools:primaryContact "Paul W. Ayers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3304, edam:topic_3334, edam:topic_3374, edam:topic_3930 ; sc:citation , "pubmed:34269889" ; sc:description "B3Pdb: a database of blood-brain barrier-penetrating peptides." ; sc:featureList edam:operation_0224, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "B3Pdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/b3pdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0804, edam:topic_3304, edam:topic_3374, edam:topic_3474 ; sc:citation ; sc:description "In silico tool for predicting and designing Blood-Brain Barrier Penetrating Peptides." ; sc:featureList edam:operation_3631 ; sc:name "B3pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/b3pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3292 ; sc:citation ; sc:description "A tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families." ; sc:featureList edam:operation_2990 ; sc:name "The B6 Database (B6DB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PARMA" ; sc:softwareHelp ; sc:url "http://bioinformatics.unipr.it/B6db" ; biotools:primaryContact "Riccardo Percudani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0611, edam:topic_3315 ; sc:citation , "pubmed:31486672" ; sc:description "A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software | Structural learning of Bayesian networks (BNs) from observational data has gained increasing applied use and attention from various scientific and industrial areas. The mathematical theory of BNs and their optimization is well developed. Although there are several open-source BN learners in the public domain, none of them are able to handle both small and large feature space data and recover network structures with acceptable accuracy. bAIcis® is a novel BN learning and simulation software from BERG. It was developed with the goal of learning BNs from \"Big Data\" in health care, often exceeding hundreds of thousands features when research is conducted in genomics or multi-omics. 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It provide curated database for transfer elements search and annotation." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3482 ; sc:name "BacAnt" ; sc:softwareHelp ; sc:url "http://bacant.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3524 ; sc:citation ; sc:description "Modeling framework for cellular communities in their environments. Can be used for simulation of organisms living in communities. Each organism is represented individually and genome scale metabolic models determine the uptake and release of compounds. Biological processes such as movement, diffusion, chemotaxis and kinetics are available along with data analysis techniques." ; sc:featureList edam:operation_3660 ; sc:name "BacArena" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cran.r-project.org/web/packages/BacArena/index.html" ; biotools:primaryContact "Johannes Zimmermann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "A Comprehensive and Interactive Web-Resource to Discern Antibiotic Resistance Gene Diversity in –Omics Datasets." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "BacARscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteininformatics.org/mkumar/bacarscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3379 ; sc:citation , "pmcid:PMC7033354", "pubmed:32095660" ; sc:description "An online platform for clinical back-averaging. 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BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers several possibilities to query detailed strain information. 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BacDiveR helps you investigate this data offline, and semi-automatically in R." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BacDiveR: A Programmatic Interface For BacDive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , ; sc:softwareVersion "0.7.0" ; sc:url "https://tibhannover.github.io/BacDiveR/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0623, edam:topic_0821, edam:topic_3301 ; sc:citation , "pmcid:PMC7283322", "pubmed:32518231" ; sc:description "BacEffluxPred is a SVM based 2-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins and their sub-families." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "BacEffluxPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteininformatics.org/mkumar/baceffluxpred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0621, edam:topic_0780 ; sc:citation , "pubmed:16873501" ; sc:description "Predictor for the subcellular localization of proteins in eukaryotes." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:name "BaCelLo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/bacello" ; biotools:primaryContact , "Andrea Pierleoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "This server allows to use the BACHSCORE tool with the aim of discriminating the best model of a protein (the native state or a structure very similar to it) among a large set of alternative conformations." ; sc:featureList edam:operation_2406 ; sc:license "GPL-3.0" ; sc:name "BACH Bayesian Analysis Conformation Hunt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://bachserver.pd.infn.it/" ; biotools:primaryContact "Antonio Trovato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_3174, edam:topic_3300, edam:topic_3944 ; sc:citation , "pubmed:32702093" ; sc:description "AciDB is a database of about 600 manually curated acidophilic organisms, their genomic information and associated metadata." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2940 ; sc:license "MIT" ; sc:name "bAciDB" ; sc:url "http://AciDB.cl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3308, edam:topic_3794 ; sc:citation "pubmed:26227145" ; sc:description "Tool to identify the presence of common RNA background in a PAR-CLIP dataset." ; sc:featureList edam:operation_2495 ; sc:name "BackCLIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/phrh/BackCLIP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Back-translate a protein sequence to ambiguous nucleotide sequence." ; sc:featureList edam:operation_0371 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "backtranambig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/backtranambig.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Back-translate a protein sequence to ambiguous nucleotide sequence. It reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid." ; sc:featureList edam:operation_0371 ; sc:name "backtranambig (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/st/emboss_backtranambig/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Back-translate a protein sequence to a nucleotide sequence." ; sc:featureList edam:operation_0371 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "backtranseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/backtranseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3489 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Back-translate a protein sequence to a nucleotide sequence, using codon frequency.It reads a protein sequence and writes the nucleic acid sequence it is most likely to have come from." ; sc:featureList edam:operation_0371 ; sc:name "backtranseq (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/st/emboss_backtranseq/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0622, edam:topic_0634, edam:topic_0654 ; sc:citation "pubmed:22135301" ; sc:description "An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes." ; sc:featureList edam:operation_0487, edam:operation_0523, edam:operation_0578, edam:operation_2429, edam:operation_2871 ; sc:name "BacMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bacmap.wishartlab.com/" ; biotools:primaryContact "Feedback form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3574, edam:topic_3912 ; sc:description "A set of tools used in production and exploration of bacterial artificial chromosome restriction maps based on the information on the cloneDB server." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "bacmapping" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/Ewinden/bacmapping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3372, edam:topic_3391 ; sc:citation , "pubmed:32966562" ; sc:description "Bacnet is a Java based platform for fast development of ‘personalized’ multiomics website. Bacnet is easy to import, modify and deploy on web server." ; sc:featureList edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "Bacnet" ; sc:url "https://github.com/becavin-lab/bacnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3293 ; sc:citation "pubmed:24076250" ; sc:description "BAse COmposition CAlculator is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions." ; sc:featureList edam:operation_2089 ; sc:name "BaCoCa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://annelida.de/research/bioinformatics/software/index.html" ; biotools:primaryContact "Torsten H. Struck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_2640, edam:topic_3053 ; sc:citation "pubmed:21498400" ; sc:description "Bayesian Analysis of COpy number Mixtures is a statistically-principled in silico approach to accurately estimate genomic deletions and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We have developed a cross-platform and open source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues and other relevant processing steps. We also provide an R interface, bacomR." ; sc:featureList edam:operation_3658 ; sc:name "BACOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://code.google.com/p/bacom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC5273857", "pubmed:28129774" ; sc:description "This tool can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies by constructing an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores." ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "bacon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/bacon.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_0769, edam:topic_3299 ; sc:citation ; sc:description "The BACPHLIP software is designed to test whether a given phage genome is likely to be either temperate (lysogenic) or virulent (lytic). 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Cluster HMMs are available for downloading." ; sc:featureList edam:operation_0297, edam:operation_1777, edam:operation_2421, edam:operation_2489, edam:operation_2492, edam:operation_3439, edam:operation_3459 ; sc:isAccessibleForFree true ; sc:name "BAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp , ; sc:softwareVersion "3.0" ; sc:url "https://bar.biocomp.unibo.it/bar3/" ; biotools:primaryContact "Giuseppe Profiti" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123, edam:topic_0623, edam:topic_3307 ; sc:citation "pubmed:21622657" ; sc:description """BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB. This is a legacy version, please refer to https://bio.tools/bar for the latest release.""" ; sc:featureList edam:operation_0297, edam:operation_1777, edam:operation_2489, edam:operation_3459 ; sc:isAccessibleForFree true ; sc:name "BAR-PLUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://bar.biocomp.unibo.it/bar2.0/" ; biotools:primaryContact "Giuseppe Profiti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_2229, edam:topic_3168, edam:topic_3912 ; sc:citation , "pubmed:34031609" ; sc:description "The BAR-Seq web application, an online, freely available and easy-to-use software that allows performing clonal tracking analyses on raw sequencing data without any computational resources or advanced bioinformatic skills. BAR-Seq pipeline is a strategy for clonal tracking of cells harboring homology-directed targeted integration of a barcoding cassette.BAR-Seq can be applied to most editing strategies." ; sc:featureList edam:operation_3096, edam:operation_3695, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "BAR-Seq" ; sc:softwareHelp ; sc:url "http://www.bioinfotiget.it/barseq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "A freely available catalogue describing expertise and molecular analysis resources available at centers and companies in Sweden for analysis of biobanked samples." ; sc:featureList edam:operation_2421 ; sc:name "BARC" ; sc:provider "bils.se" ; sc:url "http://barcdb.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3293 ; sc:citation "pubmed:7882153" ; sc:description "Encodes a multiple alignment according to the method developed by Véronique Barriel (C.R.Acad.Sci.III 317(7):693-701).From a an existing alignment (which will not be changed) BARCOD builds a character matrix suitable for use in phylogeny recontstruction programs. The method allows to encode each insertion/deletion event as one single event (whatever the number of nucleotides involved), while retaining any indel common to two or more taxa as a possibly shared character." ; sc:featureList edam:operation_0492 ; sc:name "BARCOD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://wwwabi.snv.jussieu.fr/public/Barcod/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3168, edam:topic_3345 ; sc:description "The program generates barcodes for sequences suitable for Illumina sequencing." ; sc:featureList edam:operation_0231, edam:operation_0364, edam:operation_2403, edam:operation_3200 ; sc:name "Barcode generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comailab.genomecenter.ucdavis.edu/index.php/Barcode_generator" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3452, edam:topic_3511 ; sc:citation ; sc:description "A tool to generate unique, orthogonal genetic tags for qPCR detection. barCoder is a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes and appropriate spacer sequences." ; sc:featureList edam:operation_0308, edam:operation_3200, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "barCoder" ; sc:url "https://github.com/ECBCgit/Barcoder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3421, edam:topic_3500 ; sc:citation ; sc:description "barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data from cellular barcoding experiments." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:license "CC0-1.0" ; sc:name "barcodetrackR" ; sc:url "https://dunbarlabNIH.github.io/barcodetrackR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "It is a web tool for selecting an optimal set of barcode sequences. User must provide a set of candidate barcodes from which the defined number of barcodes is selected." ; sc:featureList edam:operation_2425 ; sc:name "BARCOSEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ekhidna2.biocenter.helsinki.fi/barcosel/" ; biotools:primaryContact "Panu Somervuo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation "pubmed:19874596" ; sc:description "Design of barcoded primers, for multiplexed high-throughput sequencing." ; sc:featureList edam:operation_0227, edam:operation_2409, edam:operation_3200, edam:operation_3237 ; sc:license "GPL-3.0" ; sc:name "Barcrawl Bartab" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.phyloware.com/Phyloware/XSTK.html" ; biotools:primaryContact "Daniel N. Frank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description "The bardensr (barcode dexmixing through non-negative spatial regression) package is a collection of tools for modeling linearly multiplexed observations. There is some true signal we are interested in, but our observations are some noisy linear mixture of those signals." ; sc:featureList edam:operation_2495, edam:operation_3443, edam:operation_3659 ; sc:license "MIT" ; sc:name "BarDensr" ; sc:softwareHelp ; sc:url "https://github.com/jacksonloper/bardensr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3379 ; sc:citation , "pmcid:PMC7272289", "pubmed:32246534" ; sc:description "BAREB, a BAyesian REpulsive Biclustering model, that can simultaneously cluster the Periodontal diseases (PD) patients and their tooth sites after taking the patient- and site-level covariates into consideration. BAREB uses the determinantal point process (DPP) prior to induce diversity among different biclusters to facilitate parsimony and interpretability." ; sc:featureList edam:operation_3432, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "BAREB" ; sc:url "https://cran.r-project.org/package=BAREB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3170, edam:topic_3308, edam:topic_3512, edam:topic_3934 ; sc:citation , "pmcid:PMC8756634", "pubmed:35021985" ; sc:description "The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data." ; sc:featureList edam:operation_2422, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "baredSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lldelisle/baredSC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3810 ; sc:citation , "pmcid:PMC10064564", "pubmed:37003963" ; sc:description "Integrative gene expression database for barley." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "BarleyExpDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://barleyexp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0780, edam:topic_3053, edam:topic_3174 ; sc:citation , "pmcid:PMC7040090", "pubmed:32133024" ; sc:description "BarleyNet is a co-functional gene network with a companion web server for network-assisted systems genetics analysis of cultivated barley. It is a Bayesian statistics-based combination of a wide range of biological data, including the genomic information of the latest IBSC_v2 genome and barley-specific gene expression profiles. It is able to prioritize novel genes for biological trait of interest or infer functions of unannotated barley genes by combining prior knowledge from forward- or reverse-genetics studies of user with the information included in BarleyNet via three in silico gene/function prioritization algorithms implemented in BarleyNet web server." ; sc:featureList edam:operation_2495, edam:operation_3663, edam:operation_3927 ; sc:name "BarleyNet" ; sc:url "https://www.inetbio.org/barleynet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_2885, edam:topic_3071, edam:topic_3500 ; sc:citation , "pmcid:PMC7698660", "pubmed:33247932" ; sc:description "BarleyVarDB is a comprehensive genomic variation database for Barley." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_3196, edam:operation_3227, edam:operation_3431 ; sc:name "BarleyVarDB" ; sc:url "http://146.118.64.11/BarleyVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation ; sc:description "Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale." ; sc:featureList edam:operation_2441 ; sc:name "BARNACLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "0.21" ; sc:url "http://sourceforge.net/projects/barnacle-rna/" ; biotools:primaryContact "Thomas Hamelryck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:22244497" ; sc:description "Barracuda is a high-speed sequence aligner based on BWA and uses the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:license "MIT" ; sc:name "BarraCUDA" ; sc:operatingSystem "Linux" ; sc:url "http://seqbarracuda.sourceforge.net/" ; biotools:primaryContact "Klus P." . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_1975 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622 ; sc:author "Torsten Seemann" ; sc:description "Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S)." ; sc:featureList edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "Barrnap" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Melbourne, Australia", "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/tseemann/barrnap" ; biotools:primaryContact "Australia", "Torsten Seemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "BARS is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines." ; sc:featureList edam:operation_3659 ; sc:name "BARS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "Transcription factor prediction tool with query gene sets or epigenomic profiles." ; sc:featureList edam:operation_0438 ; sc:name "BART" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://faculty.virginia.edu/zanglab/bart/" ; biotools:primaryContact "Chongzhi Zang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3169, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc:description "BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analysis for Regulation of Transcription) to make the prediction." ; sc:featureList edam:operation_0444, edam:operation_2495, edam:operation_3223 ; sc:name "BART Cancer" ; sc:url "https://zanglab.github.io/bartcancer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3179, edam:topic_3940 ; sc:citation ; sc:description "BART3D is a computational method for inferring transcriptional regulators (TRs) associated with genome-wide differential chromatin interactions (DCIs) detected by comparing two Hi-C maps. And Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data." ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "BART3D" ; sc:url "https://github.com/zanglab/bart3d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_0654 ; sc:citation ; sc:description "Fast and accurate clustering algorithm to count barcode reads." ; sc:featureList edam:operation_0291, edam:operation_3200 ; sc:name "Bartender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://github.com/LaoZZZZZ/bartender-1.1" ; biotools:primaryContact "Sasha Levy", "Song Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation ; sc:description "This web server is to perform Binding Analysis for Regulation of Transcription (BART) is a bioinformatics tool for predicting functional factors (including transcription factors and chromatin regulators) that bind at cis-regulatory regions to regulate gene expression in human or mouse, taking a query gene list or a ChIP-seq dataset as input." ; sc:featureList edam:operation_0441, edam:operation_2422, edam:operation_2436 ; sc:name "BARTweb" ; sc:url "http://bartweb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC8962164", "pubmed:35346022" ; sc:description "A software tools for barcoded single-cell genomics" ; sc:featureList edam:operation_3200, edam:operation_3431, edam:operation_3629, edam:operation_3799, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "BarWare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AllenInstitute/BarWare-pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382, edam:topic_3421 ; sc:citation , "pubmed:32568756" ; sc:description "Breast Aesthetic Scale Calculator (BAS-Calc) is a platform for calculating Breast Aesthetic Scale (BAS) score, which is a quick and simple objective assessment of results in cosmetic breast surgery" ; sc:name "BAS-Calc" ; sc:operatingSystem "Mac" ; sc:url "https://www.breastsymmetry.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3168 ; sc:citation , "pmcid:PMC7808871", "pubmed:33412762" ; sc:description "BaSDAS (Barcode-Seq Data Analysis System) is a GUI-based pooled knockout screening data analysis system to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information" ; sc:featureList edam:operation_0337, edam:operation_3928 ; sc:name "BaSDAS" ; sc:url "http://barcode.appex.kr/barcode/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "A comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis." ; sc:featureList edam:operation_0224 ; sc:name "BASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://base.thep.lu.se" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0804, edam:topic_3168, edam:topic_3304 ; sc:citation ; sc:description "An easy-to-use software for complete data analysis in single cell immunoglobulin cloning." ; sc:license "GPL-3.0" ; sc:name "BASE" ; sc:url "https://github.com/automatedSequencing/BASE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0769, edam:topic_3053 ; sc:citation ; sc:description "BASE is a workflow to integrate non-ubiquitous genes in comparative genomics analyses for selection. It is used to built to ease the inference and interpretation of selection regimes in the context of comparative genomics. While the majority of these analyses are restricted to ortholog groups of ubiquitous genes - i.e. genes which are present in all the species considered - BASE allows to integrate ortholog groups of non-ubiquitous genes - i.e. genes which are not present in all the species considered." ; sc:featureList edam:operation_2422, edam:operation_3907 ; sc:name "BASE" ; sc:url "http://github.com/for-giobbe/BASE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "Base Pad is a windows based base sequence editor. Search, complement, XNA to amino acid,amino acid to XNA,3 to1 & 1to 3 letter code, invert, find ORF,statistics of bps,2bp palindromes" ; sc:featureList edam:operation_2421 ; sc:name "Base Pad" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://www.bioinformatics.org/groups/?group_id=493" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "This package provides tools to work with Illumina bcl2Fastq software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "basecallQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/basecallQC.html" ; biotools:primaryContact "Thomas Carroll" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3743 ; sc:name "Ordination plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0621, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC9936955", "pubmed:36818730" ; sc:description "Lightweight detection of sequences in raw MinION data. BaseLess reduces your MinION sequencing device to a simple species detector. As a trade-off, it runs on inexpensive computational hardware like single-board computers. 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Vallejos", "Nils Eling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3168 ; sc:citation ; sc:description "Basic peak calling on STARR-seq data." ; sc:featureList edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "BasicSTARRseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BasicSTARRseq.html" ; biotools:primaryContact "Annika Buerger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_0769, edam:topic_3125, edam:topic_3398 ; sc:citation , "pmcid:PMC9664905", "pubmed:36381610" ; sc:description "Basicsynbio is an open-source Python package to help facilitate BASIC DNA Assembly workflows." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_1812, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "basicsynbio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://basicsynbio.web.app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "Probabilistic model of the conformational space of amino acid side chains in proteins. 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Specifically, few programs enable high-throughput peak assessment of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) data acquired in either selected or multiple reaction monitoring (SRM and MRM) modes. It is a Gaussian naïve Bayes classifier for targeted lipidomics, that annotates peak identities according to eight features related to retention time, intensity, and peak shape. 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Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included." ; sc:featureList edam:operation_2403 ; sc:name "BATS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.math.unipa.it/~raffaele/BATS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3334, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:36045507" ; sc:description "Boston ASL Template and Simulator (BATS) offers high-quality, high-resolution perfusion-weighted and quantitative perfusion templates accompanied by ATT and different anatomical contrasts readily available in the Montreal Neurological Institute space." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "BATS" ; sc:url "http://github.com/manueltaso/batsasltemplate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC8185956", "pubmed:34113262" ; sc:description "Streamlining Bayesian Calibration With Artificial Neural Network Metamodeling." ; sc:featureList edam:operation_2238, edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BayCANN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hjalal/BayCANN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2269, edam:topic_3170, edam:topic_3316 ; sc:citation , "pmcid:PMC8104932", "pubmed:33772539" ; sc:description "Bayesian analysis of allele-specific expression (BayesASE) is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating Allelic imbalance (AI) and formally comparing levels of AI between conditions." ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "BayesASE" ; sc:url "https://github.com/McIntyre-Lab/BayesASE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:15842491" ; sc:description "Program that estimates recent migration rates between populations using MCMC." ; sc:featureList edam:operation_3658 ; sc:name "BayesAssNM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.rannala.org/?page_id=245" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:19661376" ; sc:description "Bayesian basecaller" ; sc:featureList edam:operation_3185 ; sc:license "GPL-3.0" ; sc:name "BayesCall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bayescall.sourceforge.net/" ; biotools:primaryContact "Wei-Chun Kao", "Yun S. Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:21352386" ; sc:description "BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model." ; sc:featureList edam:operation_3658 ; sc:name "BayeScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cmpg.unibe.ch/software/bayescan/" ; biotools:primaryContact "Matthieu Foll" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:citation , "pmcid:PMC8715862", "pubmed:34975350" ; sc:description "An R Package for Bayesian Trial Design Using Historical Control Data." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BayesCTDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://CRAN.R-project.org/package=BayesCTDesign" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2769 ; sc:encodingFormat edam:format_2306 ; sc:name "Transcript ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_0749, edam:topic_3308 ; sc:citation ; sc:description "Bayesian method for doing transcriptome assembly from RNA-seq data." ; sc:featureList edam:operation_0310, edam:operation_3258, edam:operation_3563 ; sc:license "MIT" ; sc:name "Bayesembler" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioinformatics-centre.github.io/bayesembler/" ; biotools:primaryContact "Jonas Andreas Sibbesen", "Lasse Maretty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "This software tool is used for accessing the performance of different epidemiological models (including both growth and compartmental models) in a Bayesian framework." ; sc:isAccessibleForFree true ; sc:name "BayesEpiModels" ; sc:softwareHelp ; sc:url "https://github.com/liqiwei2000/BayesEpiModels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "We develop this web app to help local people assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. 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Here the morphological clones are defined as trees similar (and not the same) at the tree-level structure with varying fine-scale structural detail." ; sc:featureList edam:operation_2426 ; sc:license "MIT" ; sc:name "BayesForest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/inuritdino/BayesForest/wiki" ; biotools:primaryContact "Ilya Potapov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:15012769" ; sc:description "Bayesian estimation of the coancestry coefficient FST" ; sc:featureList edam:operation_3658 ; sc:name "BAYESFST" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.reading.ac.uk/Statistics/genetics/software.html" ; biotools:primaryContact "D.J. Balding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:35709752" ; sc:description "BayeshERG : A Bayesian Graph Neural Network for predicting hERG blockers." ; sc:featureList edam:operation_0478, edam:operation_0479, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "BayeshERG" ; sc:url "https://github.com/GIST-CSBL/BayeshERG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3344 ; sc:description "3D reconstruction algorithm for electron cryo-microscopy." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "A Bayesian Adaptive Basis Algorithm for Single Particle Reconstruction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36040-a-bayesian-adaptive-basis-algorithm-for-single-particle-reconstruction" ; biotools:primaryContact "Alp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3053 ; sc:citation ; sc:description "A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. 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It can be customized to different kind of biological applications, e.g. microarray, ChIP-chip, ditag, CAGE data analysis by integrating appropriately chosen features and functionalities." ; sc:featureList edam:operation_0238 ; sc:name "BayesMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bayesmd.binf.ku.dk/" ; biotools:primaryContact "Anders Krogh", "Man-Hung Eric Tang", "Ole Winther" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:16646800" ; sc:description "R package for Mendelian risk prediction. 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Its core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers." ; sc:featureList edam:operation_2425, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "BEclear" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BEclear.html" ; biotools:primaryContact "Markus Merl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2815, edam:topic_3304 ; sc:citation ; sc:description "Interpreting DNA methylation findings from blood in the context of brain." ; sc:featureList edam:operation_3204 ; sc:name "BECon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://redgar598.shinyapps.io/BECon/" ; biotools:primaryContact "M S Kobor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3345 ; sc:citation ; sc:description "Biological Entity Dictionary. Get and explore mapping between identifiers of biological entities. 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Barrett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP)." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "bed to protein map" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Convert bedGraph to bigWig file." ; sc:featureList edam:operation_0335 ; sc:name "bedGraphToBigWig" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.encodeproject.org/software/bedgraphtobigwig/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0160 ; sc:citation ; sc:description "BEDOPS is an open-source command-line toolkit that performs efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. 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The end coordinate is computed by inspecting the CIGAR string. 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sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v2.10.0" ; sc:url "https://github.com/arq5x/bedtools6" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Create a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file. Example usage would be to cull a BAM file from an exome capture experiment to include on the \"on-target\" alignments." ; sc:featureList edam:operation_0292 ; sc:name "bedtools_intersectbed_bam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools5" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , , ; sc:description "Merge multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files." ; sc:featureList edam:operation_0232 ; sc:name "bedtools_mergebedgraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools7" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Identify common intervals among multiple, sorted BED files." ; sc:featureList edam:operation_0415 ; sc:name "bedtools_multiintersectbed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/arq5x/bedtools8" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3174, edam:topic_3372 ; sc:citation , "pmcid:PMC6941791", "pubmed:31903447" ; sc:description "BedtoolsR is an R package that provides a convenient wrapper for bedtools functions allowing for the documentation and use of them from within the R programming environment, using standard R data types. It uses the version of bedtools installed on your system, rather than its own version, such that you should be able to use it interchangeably from the command line or within R. It also includes additional functionality including the ability to provide either file paths or R objects as inputs and outputs. 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It is capable of installing sequence databanks, such as: Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl, Fasta and Silva, as well as any files using these formats. In addition, BeeDeeM can install major biological classifications (ontologies), such as NCBI Taxonomy, Gene Ontology, Enzyme and Intepro. BeeDeeM can be used from the command-line or from a graphical user interface. It is cluster ready: use of a job scheduler (e.g. PBS, SLURM), smooth use of cluster structures (e.g. data downloading from Internet-connected nodes vs. data processing on network-isolated nodes). 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Raghava", "Harpreet Kaur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:11934756" ; sc:description "Beta Turn predictions in proteins" ; sc:featureList edam:operation_2945 ; sc:name "betatpred3" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/betatpred3/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:15145798" ; sc:description "This software predicts the beta turns and their types in a protein from its amino acid sequence." ; sc:featureList edam:operation_0267 ; sc:name "Betaturns" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/betaturns/" ; biotools:primaryContact "Dr. G.P.S. Raghava", "Harpreet Kaur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3173, edam:topic_3295, edam:topic_3308 ; sc:description "A deep learning framework based on the variational autoencoder (VAE) to impute missing values in transcriptome and methylome data analysis." ; sc:featureList edam:operation_3557 ; sc:license "BSD-3-Clause" ; sc:name "betaVAEImputation" ; sc:url "https://github.com/gevaertlab/BetaVAEImputation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:24677176" ; sc:description "This software recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area." ; sc:featureList edam:operation_0245 ; sc:name "BetaVoid" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://voronoi.hanyang.ac.kr/software.htm#BetaVoidWin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:name "Structural profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3542 ; sc:author ; sc:citation , , , "pubmed:23297037" ; sc:description "A software package for the analysis of TransMembrane β-barrel proteins." ; sc:featureList edam:operation_0267, edam:operation_0269 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BetAware" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/betaware" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3464 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0820 ; sc:citation , "pubmed:33972021" ; sc:description "BetAware-Deep is web server for predicting the topology of TransMembrane Beta-Barrel (TMBB) proteins in Gram-negative bacteria." ; sc:featureList edam:operation_0269 ; sc:isAccessibleForFree true ; sc:name "BetAware-Deep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/betaware2/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC7875426", "pubmed:33513136" ; sc:description "Bootstrap Elastic net regression from Time Series (BETS) is a statistical framework based on Granger causality for the recovery of a directed gene network from transcriptional time-series data. BETS uses elastic net regression and stability selection from bootstrapped samples to infer causal relationships among genes. BETS is highly parallelized, enabling efficient analysis of large transcriptional data sets." ; sc:featureList edam:operation_3659, edam:operation_3672, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "BETS" ; sc:url "https://github.com/lujonathanh/BETS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0219, edam:topic_3308 ; sc:citation "pubmed:22568790" ; sc:description "An easy to use tool designed primarily to augment Agilent’s transcriptome-wide rabbit, Oryctolagus cuniculus, gene expression microarray." ; sc:featureList edam:operation_2495 ; sc:name "Better Bunny" ; sc:softwareHelp ; sc:url "http://cptweb.cpt.wayne.edu/BB/" ; biotools:primaryContact "Alan Dombkowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC7877041", "pubmed:33568049" ; sc:description "BetweenNet is a computational approach that integrates genomic data with a protein-protein interaction network to identify cancer driver genes. BetweenNet utilizes a measure based on betweenness centrality on patient specific networks to identify the so-called outlier genes that correspond to dysregulated genes for each patient. 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Includes examples for visualizing RNA-sequencing datasets and differentially expressed genes | Big multivariate data plotted interactively | bigPint: Make BIG data pint-sized | Welcome to the bigPint package website! If you are a new user, please begin by reading from the Get Started tab at the top of this website. There are ten short vignette articles in that tab, and we recommend reading them in order. These short vignette articles consist of reproducible code that provide: | Alternatives to data metrics object | Clustering, DataImport, DifferentialExpression, GeneExpression, MultipleComparison, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, Software, Transcription, Visualization" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "bigPint" ; sc:url "https://lindsayrutter.github.io/bigPint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "BiG-SLiCE is a Python-based tool to perform a large-scale (>> 1 million) clustering analysis of Biosynthetic Gene Cluster data." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BiG_SLiCE" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/medema-group/bigslice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pmcid:PMC8247109", "pubmed:34193046" ; sc:description "BiGAN-lncRNA-disease-associations-prediction based on bidirectional generative adversarial network." ; sc:featureList edam:operation_3891, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "BiGAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TomasYang001/BiGAN-lncRNA-disease-associations-prediction.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3334, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "Toolbox for integration of BigBrain 3D histology with multimodal neuroimaging." ; sc:featureList edam:operation_2429, edam:operation_3435 ; sc:name "BigBrainWarp" ; sc:softwareHelp ; sc:url "https://github.com/caseypaquola/BigBrainWarp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3673, edam:topic_3676 ; sc:citation "pubmed:26323715" ; sc:description "Tool to run the Burrows-Wheeler Aligner-BWA on a Hadoop cluster. 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Metabolic networks and estimated fluxes can be visualized with hypergraphs." ; sc:featureList edam:operation_3660 ; sc:name "BiGGR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BiGGR.html" ; biotools:primaryContact "Anand K. Gavai", "Hannes Hettling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC9926792", "pubmed:36782330" ; sc:description "R package of performing biobank-scale gene-based association test via knockoffs." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BIGKnock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Iuliana-Ionita-Laza/BIGKnock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3336 ; sc:author , "Maxim Nazarov" ; sc:citation , "pubmed:34608741" ; sc:description "BIGL R-package which allows for a quick screening of drug combinations. Combination therapies are increasingly adopted as the standard of care for various diseases to improve treatment response, minimise the development of resistance and or minimise adverse events. 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BigMatrix protects against segfaults by monitoring and restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames." ; sc:featureList edam:operation_2425 ; sc:license "Artistic-2.0" ; sc:name "bigmemoryExtras" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/bigmemoryExtras.html" ; biotools:primaryContact "Peter M. Haverty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:author "Lisandro Dalcin" ; sc:citation , "pubmed:33301409" ; sc:description "BigMPI4py is a Python module that wraps mpi4py, supporting object sizes beyond this boundary. BigMPI4py automatically determines the optimal object distribution strategy, and uses vectorized methods, achieving higher parallelization efficiency. BigMPI4py facilitates the implementation of Python for Big Data applications in multicore workstations and High Performance Computer systems. We use BigMPI4py to speed-up the search for germ line specific de novo DNA methylated unmethylated motifs from the 59 whole genome bisulfite sequencing DNA methylation samples from 27 human tissues of the ENCODE project." ; sc:license "GPL-3.0" ; sc:name "BigMPI4py" ; sc:softwareHelp ; sc:url "https://gitlab.com/alexmascension/bigmpi4py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Workbench" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0654, edam:topic_3524 ; sc:author "Adam Hospital", "Cesare Cugnasco", "Laia Codó", "Pau Andrio" ; sc:citation ; sc:description "Comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations." ; sc:featureList edam:operation_2421, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "BigNASim" ; sc:operatingSystem "Linux" ; sc:provider "Barcelona Supercomputing Center", "Institute of Research In Biomedicine - Barcelona", "Technic University of Catalonia", "University of Barcelona" ; sc:softwareHelp , ; sc:url "http://mmb.irbbarcelona.org/BIGNASim/" ; biotools:primaryContact "Adam Hospital" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3305, edam:topic_3318, edam:topic_3390, edam:topic_3418 ; sc:citation , , "pubmed:33019308", "pubmed:33019311" ; sc:description "A public health decision support system for measuring obesogenic behaviors of children in relation to their local environment. Inferring the Spatial Distribution of Physical Activity in Children Population from Characteristics of the Environment. Children and adolescents with obesity have a higher risk of developing various diseases later on, compared to children without obesity. The reasons why some children become obese are complex, and behaviour, the living environment, and public health policies all play a role. BigO collects and analyses anonymous data on children's behavioural patterns and their living environment. With advanced analytics BigO extracts data-driven evidence on which local factors are involved, and how these factors influence childhood obesity in Europe." ; sc:featureList edam:operation_0531, edam:operation_3283, edam:operation_3436 ; sc:name "BigO" ; sc:url "http://bigoprogram.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:22289480" ; sc:description "Quality assessment package for next-genomics sequencing data." ; sc:featureList edam:operation_3218 ; sc:name "BIGpre" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/bigpre/" ; biotools:primaryContact "Tong Zhang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3468, edam:format_3548, edam:format_3549, edam:format_3550, edam:format_3551 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3546 ; sc:encodingFormat edam:format_2330, edam:format_3468, edam:format_3548, edam:format_3549, edam:format_3550, edam:format_3551 ; sc:name "Image metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3468, edam:format_3548, edam:format_3549, edam:format_3550, edam:format_3551 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3546 ; sc:encodingFormat edam:format_2330, edam:format_3468, edam:format_3548, edam:format_3549, edam:format_3550, edam:format_3551 ; sc:name "Image metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3384 ; sc:author "Erwin Vast" ; sc:citation ; sc:contributor "NRG Lab, Washington University School of Medicine" ; sc:description "Imaging platform based on the open source XNAT software. It is used for sharing de-identified medical imaging data, and for data exchange in collaborative research projects. The data is served in a standardized way, with proper access control." ; sc:featureList edam:operation_3431, edam:operation_3443 ; sc:name "BIGR XNAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Erasmus MC" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bigr-xnat.erasmusmc.nl" ; biotools:primaryContact "Stefan Klein" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "The Next Generation Sequencing (NGS) raw data are stored in FASTA and FASTQ text-based file formats. Common operations on FASTA/Q files include searching, filtering, sampling, deduplication and sorting, among others. We can find several tools in the literature for FASTA/Q file manipulation but none of them are well fitted for large files of tens of GB (likely TBs in the near future) since mostly they are based on sequential processing. The exception is seqkit that allows some routines to use a few threads but, in any case, the scalability is very limited. To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize the commands included in seqkit. In this way, in most cases it is from tens to hundreds of times faster than other state-of-the-art tools such as seqkit, samtools and pyfastx." ; sc:featureList edam:operation_0233, edam:operation_0371, edam:operation_0372, edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "BigSeqKit" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/citiususc/BigSeqKit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0654, edam:topic_2885 ; sc:citation ; sc:description "Analysis of massive SNP arrays." ; sc:featureList edam:operation_0484 ; sc:name "bigsnpr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://privefl.github.io/bigsnpr/" ; biotools:primaryContact "Florian Privé", "Michael G B Blum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3569, edam:topic_3570 ; sc:citation ; sc:description "Fast statistical analysis of large-scale data encoded as matrices." ; sc:featureList edam:operation_2238 ; sc:name "bigstatsr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://privefl.github.io/bigstatsr/" ; biotools:primaryContact "Florian Privé", "Michael G B Blum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3517 ; sc:citation , "pmcid:PMC6995189", "pubmed:32005132" ; sc:description "BigTop is a 3D reality tool for GWAS visualization. It demonstrates some of the potential of virtual reality for scientific visualization by providing an easy way for scientists and science enthusiasts to become immersed in their data. 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It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. 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Genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests." ; sc:featureList edam:operation_2238, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "BIMBAM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.haplotype.org/bimbam.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc:description "Efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements." ; sc:featureList edam:operation_3197 ; sc:name "biMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.helsinki.fi/~mjxpirin/download.html" ; biotools:primaryContact "Matti Pirinen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pubmed:35998480" ; sc:description "A novel Bioinformatic Inference and Multiscale Modeling (BIMM) method that can discovers hub genes of TGFβ, MYC, and SMAD3 varied underlie DEX treatment" ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3928 ; sc:license "Not licensed" ; sc:name "BIMM" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/chenm19/BIMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3071, edam:topic_3810 ; sc:citation , "pmcid:PMC8378516", "pubmed:34415997" ; sc:description "The Breeding Information Management System (BIMS). 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Hogue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3071 ; sc:citation "pubmed:26026136" ; sc:description "This package implements functions for multi-class discriminant analysis using binary predictors, for corresponding variable selection, and for dichotomizing continuous data." ; sc:featureList edam:operation_2945 ; sc:name "binda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://strimmerlab.org/software/binda/" ; biotools:primaryContact "Korbinian Strimmer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2580 ; sc:name "BindingDB Monomer ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; 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sc:provider "Skaggs School of Pharmacy and Pharmaceutical Sciences" ; sc:softwareHelp ; sc:url "http://www.bindingdb.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0749, edam:topic_2275 ; sc:citation ; sc:description "BINDKIN (effect of point mutations on the BINDing affinity of protein KINase:ligand complexes) benchmark, contains a of available wild type and mutant kinase:ligand complexes." ; sc:featureList edam:operation_0331, edam:operation_0337, edam:operation_0477 ; sc:license "Apache-2.0" ; sc:name "BINDKIN" ; sc:url "https://github.com/CSB-KaracaLab/BINDKIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0654, edam:topic_3474, edam:topic_3511 ; 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Previous methods such as Seurat, Liger, Harmony did not work on this case unless match feature empricallcy. For example, integration of scRNA-seq and scATAC-seq data requires to calculate the gene/promoter activity by counting peaks in gene body, which always loses information. 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Bader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0654, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:27198220" ; sc:description "Automatic server to predict DNA and RNA binding proteins given the three dimensional structure of the protein." ; sc:featureList edam:operation_2575 ; sc:name "BindUP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bindup.technion.ac.il/" ; biotools:primaryContact "Yael Mandel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC9667820", "pubmed:36190332" ; sc:description "A web server for ligand binding residue and pocket prediction from protein structures." ; sc:featureList edam:operation_0272, edam:operation_0474, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "BindWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/BindWeb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc:description """BingleSeq is a user-friendly R package for Bulk and Single-cell RNA-Seq data analyses. To begin DE analysis of Bulk RNA-Seq data, first a count table with a specific format (shown above) must be loaded. BingleSeq allows some flexibility in terms of the ‘separator’ used. Once a count table is loaded, it is displayed to allow the user to check whether it was loaded appropriately. A metadata table is also required in a specific format (shown above).""" ; sc:featureList edam:operation_2939, edam:operation_3501, edam:operation_3680, edam:operation_3891 ; sc:license "MIT" ; sc:name "BingleSeq" ; sc:url "https://github.com/dbdimitrov/BingleSeq/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2338 ; sc:name "Ontology identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2338 ; sc:encodingFormat edam:format_1964 ; sc:name "Ontology identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation ; sc:description "A tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network." ; sc:featureList edam:operation_3501 ; sc:name "BiNGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "3.0.2" ; sc:url "http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html" ; biotools:primaryContact "Steven Maere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_2885 ; sc:citation , "pmcid:PMC8933389", "pubmed:35437391" ; sc:description "BinMat offers users of fragment analysis methods an efficient and easy-to-use platform to process their binary data matrices, by means of either a graphical user interface or an R package." ; sc:featureList edam:operation_0337, edam:operation_0543, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BinMat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://clarkevansteenderen.shinyapps.io/BINMAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3301, edam:topic_3837 ; sc:author "Harihara Muralidharan", "Nidhi Shah" ; sc:citation , "pmcid:PMC7945042", "pubmed:33717033" ; sc:description "Binnacle estimates coverage for graph scaffolds and integrates with existing metagenome binning tools. Binnacle accurately computes coverage of graph scaffolds and seamlessly integrates with leading binning methods such as MetaBAT2, MaxBin 2.0, and CONCOCT. Using graph scaffolds, as opposed to contigs (most common approach) for binning improves the contiguity and quality of metagenomic bins and can captures a broader set of the accessory elements of the reconstructed genomes." ; sc:featureList edam:operation_0479, edam:operation_0523, edam:operation_2495, edam:operation_3216, edam:operation_3798 ; sc:name "Binnacle" ; sc:url "https://github.com/marbl/binnacle" ; biotools:primaryContact "Mihai Pop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610 ; sc:citation , "pmcid:PMC6802074", "pubmed:31641444" ; sc:description """Analysis of interval-grouped data in weed science. Nonparametric Estimation for Interval-Grouped Data. Kernel density and distribution estimation for interval-grouped data (Reyes, Francisco-Fernandez and Cao 2016, 2017) , , (Gonzalez-Andujar, Francisco-Fernandez, Cao, Reyes, Urbano, Forcella and Bastida 2016) and nonparametric estimation of seedling emergence indices (Cao, Francisco-Fernandez, Anand, Bastida and Gonzalez-Andujar 2011) """ ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "binnednp" ; sc:url "https://cran.r-project.org/package=binnednp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3360, edam:topic_3520 ; sc:citation , "pmcid:PMC9345815", "pubmed:35917032" ; sc:description "A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data." ; sc:featureList edam:operation_3215, edam:operation_3436, edam:operation_3704 ; sc:license "GPL-3.0" ; sc:name "binneR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aberhrml.github.io/binneR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Scripts required to calculate tetramer frequencies and create input files for ESOM" ; sc:featureList edam:operation_0291 ; sc:license "Other" ; sc:name "Binning" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/tetramerFreqs/Binning" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3697 ; sc:description "Improving genome bins through the combination of different binning programs" ; sc:featureList edam:operation_0291, edam:operation_3798 ; sc:name "Binning_refiner" ; sc:url "https://github.com/songweizhi/Binning_refiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation , "pmcid:PMC4520292", "pubmed:26306093" ; sc:description "BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "BINoculars" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/id03/binoculars" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3077 ; sc:citation ; sc:description "Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. It provides the user with a complete interface for the analysis of biological networks in Cytoscape environment." ; sc:featureList edam:operation_0224 ; sc:license "LGPL-2.0" ; sc:name "BiNoM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://binom.curie.fr/" ; biotools:primaryContact "Andrei Zinovyev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2269, edam:topic_3360 ; sc:citation , "pmcid:PMC7456085", "pubmed:32859146" ; sc:description "The binomialRF package is an R package that provides a feature selection algorithm to be used in randomForest classifiers. Treating each tree as a quasi binomial stochastic process in a random forest, binomialRF determines a feature’s importance by how often they are selected in practice vs. as expected by random chance. Given that trees are co-dependent as they subsample the same data, a theoretical adjustment is made using a generalization of the binomial distribution that adds a parameter to model correlation/association between trials." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3936 ; sc:name "binomialRF" ; sc:url "https://github.com/SamirRachidZaim/binomialRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3047, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC7217866", "pubmed:32398743" ; sc:description """An R workflow for detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP. Accurate drug resistance detection is key for guiding effective tuberculosis treatment. While genotypic resistance can be rapidly detected by molecular methods, their application is challenged by mixed mycobacterial populations comprising both susceptible and resistant cells (heteroresistance). For this, next-generation sequencing (NGS) based approaches promise the determination of variants even at low frequencies. However, accurate methods for a valid detection of low-frequency variants in NGS data are currently lacking. To tackle this problem, we developed the variant detection tool binoSNP which allows the determination of low-frequency single nucleotide polymorphisms (SNPs) in NGS datasets from Mycobacterium tuberculosis complex (MTBC) strains.""" ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "binoSNP" ; sc:url "http://www.github.com/ngs-fzb/binoSNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:26894997" ; sc:description "Novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems." ; sc:featureList edam:operation_3258 ; sc:name "BinPacker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/transcriptomeassembly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3127, edam:topic_3168, edam:topic_3169 ; sc:citation ; sc:description "Peak detection method for ChIP-sequencing data with biological replicates." ; sc:featureList edam:operation_3222 ; sc:license "GPL-2.0" ; sc:name "BinQuasi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/BinQuasi/index.html" ; biotools:primaryContact "Emily Goren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation" ; sc:featureList edam:operation_0291 ; sc:license "GPL-3.0" ; sc:name "BinSanity" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/edgraham/BinSanity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3303, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC7053013", "pubmed:31925435" ; sc:description "A system to find answers to questions from biomedical texts. The system is configured by a configuration file." ; sc:featureList edam:operation_0495, edam:operation_2421, edam:operation_2422 ; sc:name "Bio-AnswerFinder" ; sc:url "https://github.com/scicrunch/bio-answerfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Parse CIGAR strings and translate coordinates to/from reference/query." ; sc:featureList edam:operation_2409 ; sc:name "Bio-Cigar" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/MullinsLab/Bio-Cigar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170, edam:topic_3372 ; sc:citation ; sc:description "Virtualization containers for single-step execution of NGS pipelines." ; sc:featureList edam:operation_3763 ; sc:license "MIT" ; sc:name "Bio-Docklets" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BCIL/BioDocklets" ; biotools:primaryContact "Konstantinos Krampis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3305, edam:topic_3324, edam:topic_3421 ; sc:citation , "pmcid:PMC9931203", "pubmed:36812589" ; sc:description "Large-Scale Application of Named Entity Recognition to Biomedicine and Epidemiology." ; sc:featureList edam:operation_1812, edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Bio-Epidemiology-NER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/Bio-Epidemiology-NER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070 ; sc:description "Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information)." ; sc:featureList edam:operation_0335 ; sc:name "Bio-Formats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5.0.8" ; sc:url "http://www.openmicroscopy.org/site/products/bio-formats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_2275, edam:topic_3306, edam:topic_3336 ; sc:citation , "pmcid:PMC8059640", "pubmed:33898512" ; sc:description "Biophysical approach for GPCRs Automated Template Selection (Bio-GATS) is a tool for automated GPCR template selection through a biophysical approach for homology modeling." ; sc:featureList edam:operation_0269, edam:operation_0477, edam:operation_2421, edam:operation_2995, edam:operation_3938 ; sc:name "Bio-GATS" ; sc:url "https://github.com/amara86/Bio-GATS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3316 ; sc:citation "pubmed:19796405" ; sc:description "Service platform for interdisciplinary work on biological application domains. It uses the jETI (Java Electronic Tool Integration Platform) service integration technology for remote tool integration and the jABC framework as a graphical workflow modeling tool." ; sc:featureList edam:operation_3760 ; sc:name "Bio-jETI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ls5-www.cs.tu-dortmund.de/projects/biojeti/about.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2229, edam:topic_3306, edam:topic_3315 ; sc:citation ; sc:description """BIO-LGCA is a cellular automaton modelling class for analyzing collective cell migration. To overcome drawbacks of classical on-lattice models, we introduce a novel on-lattice, agent-based modelling class for collective cell migration, which we call biological lattice-gas cellular automaton (BIO-LGCA). The BIO-LGCA is characterised by synchronous time updates and the explicit consideration of individual cell velocities.""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3446 ; sc:name "BIO-LGCA" ; sc:url "https://github.com/sisyga/BIO-LGCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "The first tool for integrating methodologically diverse OD (Ortholog detection) methods." ; sc:featureList edam:operation_2403, edam:operation_2423, edam:operation_3429, edam:operation_3432 ; sc:name "bio-MOSAIC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pythonhosted.org/bio-MOSAIC/" ; biotools:primaryContact "Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:25819670" ; sc:description "A Ruby binding to the SAMtools library.Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format." ; sc:featureList edam:operation_2928 ; sc:name "Bio-samtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/helios/bioruby-samtools" ; biotools:primaryContact "Raoul J.P. Bonnal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …)." ; sc:featureList edam:operation_2421 ; sc:name "Bio-SeCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.deib.polimi.it/bio-seco/seco/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0218 ; sc:citation , "pmcid:PMC9458692", "pubmed:36097541" ; sc:description "Bio-SODA is a question answering system over domain knowledge graphs, such as scientific datasets, where training data (in the form of questions and corresponding SPARQL queries) is rare or unavailable." ; sc:featureList edam:operation_0224 ; sc:license "Apache-2.0" ; sc:name "Bio-SODA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/anazhaw/Bio-SODA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3077, edam:topic_3344 ; sc:citation , "pmcid:PMC5210639", "pubmed:27924016" ; sc:description "Bioscience query tool discovery system." ; sc:featureList edam:operation_0305 ; sc:license "GPL-3.0" ; sc:name "Bio-TDS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biotds.org/" ; biotools:primaryContact "Etienne Gnimpieba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0798, edam:topic_3168 ; sc:citation "pubmed:26794317" ; sc:description "This software contains a set of tools to analyse the output from Transposon Directed Insertion Sequencing (TraDIS)  analyses." ; sc:featureList edam:operation_2403 ; sc:name "Bio-Tradis" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sanger-pathogens/Bio-Tradis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Bio2Midi converts the text of a DNA or protein sequence to a MIDI file, which you may immediately audition, or import into any MIDI sequencer for further compositional processing." ; sc:featureList edam:operation_2409 ; sc:name "Bio2MIDI" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://algoart.com/bio2midi.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0821, edam:topic_3407 ; sc:citation , "pubmed:32108855" ; sc:description "Bio2Rxn is as a web-based tool to provide putative enzymatic reaction predictions for uncharacterized protein sequences. Bio2Rxn adopts a consensus strategy by incorporating six types of enzyme prediction tools." ; sc:featureList edam:operation_2489 ; sc:name "Bio2Rxn" ; sc:url "http://design.rxnfinder.org/bio2rxn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0091, edam:topic_0623 ; sc:citation , "pmcid:PMC7737766", "pubmed:32734663" ; sc:description "Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data." ; sc:featureList edam:operation_2406, edam:operation_2476, edam:operation_2939, edam:operation_3192, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "Bio3D" ; sc:softwareHelp , ; sc:url "http://thegrantlab.org/bio3d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2814, edam:topic_3168, edam:topic_3382 ; sc:citation , "pubmed:32006275" ; sc:description "Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. This application facilitates the identification of protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations, and the quantitative comparison of their predicted structural dynamics." ; sc:featureList edam:operation_2406, edam:operation_2476, edam:operation_2939, edam:operation_3891 ; sc:name "Bio3D-Web" ; sc:url "https://bitbucket.org/Grantlab/bio3d-web" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_3382 ; sc:citation , "pmcid:PMC6875409", "pubmed:31772845" ; sc:description """From command-line bioinformatics to bioGUI. bioGUI provides install modules for bioinformatic software for users and allows developers to script a GUI for their applications. bioGUI: a universal GUI for CLI applications. Tools for bioGUI (e.g. CWL Parser/argparse2biogui/...). With bioGUI developers can easily build a graphical-user-interface (GUI) for their command-line only application. Such a GUI then enables many more people to use their software. Especially in biology, the domain experts are often computer novices and have difficulties using tools written for them by bioinformaticiens/computer scientists. bioGUI documentation — bioGUI documentation. An python argparse-extension which first supplies two useful argparse-type extensions and second provides means to convert the python argparse parser into a bioGUI template. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "bioGUI" ; sc:softwareHelp ; sc:url "https://github.com/mjoppich/bioGUI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0654, edam:topic_2269, edam:topic_2885 ; sc:description "Bio C# contains classes for handling fasta IO, Blast-search (using an own algorithm), local and global alignments, quality sequence IO, statistics (Mann-Whitney, Poisson Distribution), distribution of features along chromosomes, SNP-identification, gene expression statistics, 454-sequence handling, microsatellite search and basic sequence statistics" ; sc:featureList edam:operation_2421 ; sc:name "Bio C" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://www.kofler.or.at/bioinformatics/biosharp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_2640, edam:topic_3308 ; sc:citation , "pmcid:PMC9972522", "pubmed:36852877" ; sc:description "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data" ; sc:featureList edam:operation_0276, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "bio_contrast_subgraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tlancian/bio_cs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2840, edam:topic_3068, edam:topic_3172, edam:topic_3314 ; sc:citation ; sc:description "The MOSAIC bioacc application is a turn-key web tool providing bioaccumulation metrics (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3454 ; sc:name "bioacc" ; sc:url "https://mosaic.univ-lyon1.fr/bioacc" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:35876792" ; sc:description "Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioADAPT-MRC" ; sc:url "https://github.com/mmahbub/BioADAPT-MRC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_3315, edam:topic_3382, edam:topic_3892 ; sc:citation , "pmcid:PMC7710046", "pubmed:33206646" ; sc:description "BioAFMviewer is an interactive interface for simulated atomic force microscopy scanning of biomolecular structures and dynamics" ; sc:featureList edam:operation_0337, edam:operation_0477, edam:operation_2476, edam:operation_3431 ; sc:name "BioAFMviewer" ; sc:operatingSystem "Windows" ; sc:url "http://www.bioafmviewer.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3305, edam:topic_3360, edam:topic_3379, edam:topic_3390 ; sc:citation ; sc:description "A toolkit for quantification of biological age from blood-chemistry and organ-function-test data." ; sc:featureList edam:operation_2940, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioAge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/dayoonkwon/BioAge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_3500, edam:topic_3673 ; sc:citation ; sc:description "Bioinformatics Aider (BioAider) is a visualization analysis tool for efficient and convenient in gene annotation and mutation screening on multiple genome-sequencing data." ; sc:featureList edam:operation_0331, edam:operation_0451, edam:operation_3227 ; sc:name "BioAider" ; sc:url "https://github.com/ZhijianZhou01/BioAider" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0218 ; sc:citation , "pmcid:PMC9022356", "pubmed:35448946" ; sc:description "Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT." ; sc:featureList edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "BioALBERT" ; sc:url "https://github.com/usmaann/BioALBERT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2182, edam:format_2572, edam:format_3016 ; sc:name "File name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2330 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Bioinformatics file javascript-based reformatter. Something like awk for VCF, BAM, SAM, FASTQ or FASTA." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BioAlcidae" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/BioAlcidae" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3173, edam:topic_3308 ; sc:citation "pubmed:27401965", "pubmed:27987167" ; sc:description "User-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) reseacher in mind, but a couple of them can be useful to the wider research community." ; sc:featureList edam:operation_0314, edam:operation_2464, edam:operation_3463, edam:operation_3501 ; sc:name "Bio-Analytic Resource (BAR)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bar.utoronto.ca/welcome.htm" ; biotools:primaryContact "Nicholas J. Provart" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1566 ; sc:encodingFormat edam:format_2054 ; sc:name "Protein-ligand interaction report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1566 ; sc:encodingFormat edam:format_2054 ; sc:name "Protein-ligand interaction report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3473 ; sc:citation , "pmcid:PMC5330305", "pubmed:27367556" ; sc:description "Computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data." ; sc:featureList edam:operation_2949 ; sc:license "Artistic-2.0" ; sc:name "bioassayR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/bioassayR.html" ; biotools:primaryContact "Tyler Backman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3474, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC9294424", "pubmed:35753697" ; sc:description "Automated feature engineering and metalearning to predict noncoding RNAs in bacteria." ; sc:featureList edam:operation_3096, edam:operation_3799, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "BioAutoML" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Bonidia/BioAutoML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_2269, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Meta’omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures." ; sc:featureList edam:operation_3194 ; sc:name "bioBakery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/biobakery/biobakery/wiki/Home" ; biotools:primaryContact "Curtis Huttenhower" . a sc:SoftwareApplication ; 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sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Biobase.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0160, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:15905283", "pubmed:17537825" ; sc:description "Server for feature extraction and Bayesian network modeling of biological sequence data." ; sc:featureList edam:operation_2497, edam:operation_3562, edam:operation_3660 ; sc:name "BioBayesNet" ; sc:url "http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3842 ; sc:name "Molecular simulation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3314 ; sc:author , , , , "Pau Andrio" ; sc:citation , , "pmcid:PMC6736963", "pubmed:31506435" ; sc:contributor , ; sc:description "Biobb (BioExcel building blocks) are Python building blocks wrapping popular computational biomolecular tools." ; sc:featureList edam:operation_0224, edam:operation_2423, edam:operation_2426, edam:operation_2480, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BioExcel Building Blocks (BioBB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioExcel Center of Excellence for Computational Biomolecular Research" ; sc:softwareHelp , , , , , , , , , , , ; sc:softwareVersion "1.0.0 2019.4", "2.0.0 2020.1", "3.0.0 2020.2", "3.0.1 2020.3", "3.5.0 2020.4", "3.5.1 2021.1", "3.6.0 2021.2", "3.7.0 2021.3", "Alpha" ; 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While it was specifically developed to investigate rare variant burden in traditional genetic trait studies, it can be used to apply multiple levels of burden testing and is useful for exploring the natural distribution of rare variants in ancestral populations." ; sc:featureList edam:operation_3197 ; sc:license "Other" ; sc:name "BioBin" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.0.0 - 2.2.1", "2.3.0" ; sc:url "http://ritchielab.psu.edu/software/biobin-download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:22536962" ; sc:description "Open source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials." ; sc:featureList edam:operation_0570 ; sc:name "BioBlender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioblender.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0196, edam:topic_2275 ; sc:citation , "pmcid:PMC8796382", "pubmed:34791029" ; sc:description "Biobox provides a collection of data structures and methods for loading, manipulating and analyzing atomistic and pseudoatomistic structures." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_2476, edam:operation_3891, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Biobox" ; sc:softwareHelp ; sc:url "https://github.com/degiacom/biobox" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3365 ; sc:citation ; sc:description "This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in BioConductor, and converting them to tidy data. 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It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation." ; sc:featureList edam:operation_2422 ; sc:name "BioSamples" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Identifiers.org" ; sc:softwareHelp ; sc:url "https://www.ebi.ac.uk/biosamples/" ; biotools:primaryContact "Query email" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description "BioSANS is a free software for systems biology which is currently being developed in Academia Sinica Institute of Chemistry." ; sc:featureList edam:operation_0244, edam:operation_2426, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BioSANS" ; sc:url "https://github.com/efajiculay/SysBioSoft/tree/main/BioSANS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:url "http://emboss.open-bio.org/rel/rel6/apps/biosed.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "This service provides operations to (i) obtain synonyms for protein names from a number of sources (ii) provide uniprot identifiers for the input." ; sc:featureList edam:operation_2422 ; sc:name "BioSemantics Suite" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://biosemantics.org/index.php/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:31504851" ; sc:description "an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches | BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches | : Home : Server : Tutorial : Document : Download : Citation : Contact us : | Established in 2017, the platform BioSeq-Analysis (1) is for the first time proposed to analyze various biological sequences at sequence-level based on machine learning approaches, which can do the following main steps automatically: feature extraction, predictor construction, and performance evaluation. 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BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). 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Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "BIOSMILE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bws.iis.sinica.edu.tw/BWS/" ; biotools:primaryContact "BIOSMILE Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3292 ; sc:citation "pubmed:25859612" ; sc:description "BiDesigned and developed as an enhancement to BioSM. It is, on average, 8 times faster than BioSM without compromising the quality of the predictions made. 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Pagès" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2814, edam:topic_3070, edam:topic_3344 ; sc:description "A basic matlab toolkit for analysis protein structure" ; sc:featureList edam:operation_1812, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "bioStructureM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/66466-yuan-yu-biostructurem" ; biotools:primaryContact "Yuan-Yu Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3678 ; sc:citation ; sc:description "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication." ; sc:name "BioStudies" ; sc:softwareHelp ; sc:url "https://www.ebi.ac.uk/biostudies/" ; biotools:primaryContact "Ugis Sarkans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Management of patients information and the analysis of peptide profiles from mass spectrometry." ; sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "GPL-1.0" ; sc:name "BioSunMS" ; sc:softwareHelp ; sc:url "http://biosunms.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2814, edam:topic_3077 ; sc:citation , "pmcid:PMC3924234", "pubmed:24330655" ; sc:description "A web tool for the superimposition of biomolecules and assemblies with rotational symmetry." ; sc:featureList edam:operation_0250 ; sc:license "GPL-3.0" ; sc:name "BioSuper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwww-ablab.ucsd.edu/biosuper/" ; biotools:primaryContact "Ruben Abagyan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2275, edam:topic_3168 ; sc:citation ; sc:description "Contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures." ; sc:featureList edam:operation_0571, edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "biosvd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/biosvd.html" ; biotools:primaryContact "Anneleen Daemen", "Matthew Brauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0204, edam:topic_0602, edam:topic_0625, edam:topic_2229 ; sc:citation ; sc:description "BioSWITCH iis a command-line program using the BioPAX standardised language to “switch on” static regulatory networks so that they can be executed in GINML to predict cellular behaviour. Using a previously published haematopoiesis gene network, we show that BioSWITCH successfully and faithfully automates the network de-coding and re-coding into an executable logical network. BioSWITCH also supports the integration of a BioPAX model into an existing GINML graph." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3196, edam:operation_3431, edam:operation_3928 ; sc:license "MIT" ; sc:name "BioSWITCH" ; sc:url "https://github.com/CBigOxf/BioSWITCH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3070 ; sc:citation ; sc:description "Syntax highlighting for computational biology to bring you intuitively close to your data. BioSyntax supports .sam, .flagstat, .vcf, .fasta, .fastq, .faidx, .clustal, .pdb, .gtf, .bed files & more." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "bioSyntax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1-beta4" ; sc:url "https://biosyntax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_3912 ; sc:description "biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads" ; sc:featureList edam:operation_0310 ; sc:name "biosyntheticSPAdes" ; sc:url "http://cab.spbu.ru/software/spades" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3407, edam:topic_3489 ; sc:citation "pubmed:19854944" ; sc:description "Database that centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other type." ; sc:featureList edam:operation_0224, edam:operation_3282, edam:operation_3431, edam:operation_3625, edam:operation_3660 ; sc:name "BioSystems" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/biosystems" ; biotools:primaryContact "Lewis Y. Geer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC9096447", "pubmed:35571058" ; sc:description "BioTAGME framework which combinesTAGME annotation framework based on Wikipedia corpus, with DT-Hybrid methodology." ; sc:featureList edam:operation_0306, edam:operation_3778, edam:operation_3927 ; sc:license "Proprietary" ; sc:name "BioTAGME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biotagme.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:21938637" ; sc:description "Interactive tool for building, visualizing, and simulating genetic regulatory networks. It is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time." ; sc:featureList edam:operation_3562 ; sc:name "BioTapestry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biotapestry.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3308, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC9495986", "pubmed:36138825" ; sc:description "A user friendly tool to perform transcript expression analysis" ; sc:featureList edam:operation_0571, edam:operation_1812, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "bioTEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CMA-Lab/bioTEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3297, edam:topic_3303 ; sc:citation , "pubmed:37083961" ; sc:description "Interactive guide of commercial lectins for glycobiology and biomedical research applications." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "BiotechLec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.unilectin.eu/biotechlec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0218, edam:topic_3473 ; sc:citation ; sc:description "The biotext library offers resources to support text mining strategy using bioinformatics tool." ; sc:featureList edam:operation_0306, edam:operation_3435, edam:operation_3960 ; sc:name "Biotext" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://pypi.org/project/biotext/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:25100685" ; sc:description "Implements an enhanced version of the TextQuest algorithm, providing a user friendly web-based interface. BTQ collects abstracts from Medline literature and OMIM databases matching a user query. Identification of relevant terms enables the representation of text records in a Vector Space Model and the calculation of pairwise document similarities. Employing suitable clustering algorithms, results are transformed into clusters of records along with their corresponding terms." ; sc:featureList edam:operation_3279 ; sc:name "BioTextQuest+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.med.uoc.gr/biotextquest" ; biotools:primaryContact "IOANNIS ILIOPOULOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description """BioTherapi : Bioinformatics for Therapeutic Peptides and Proteins. This include all the relevant information about the use of Peptides/Proteins in drug and synthesis of new peptides. It also cover problems, in their formulation, synthesis and delivery process.""" ; sc:featureList edam:operation_2945 ; sc:name "BioTherapi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/biotherapi/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite", "Workbench" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3303 ; sc:citation ; sc:description "BioThings is a toolkit for building high-performance data APIs in biomedical research. BioThings SDK provides a Python-based toolkit to build high-performance data APIs (or web services) from a single data source or multiple data sources. It has the particular focus on building data APIs for biomedical-related entities, a.k.a \"BioThings\" (such as genes, genetic variants, drugs, chemicals, diseases, etc.).." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BioThings" ; sc:softwareHelp ; sc:url "https://biothings.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3360, edam:topic_3452 ; sc:citation , "pubmed:35640613" ; sc:description "BioTIP: an R-package for Characterization of Biological Tipping Points." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3463 ; sc:license "Not licensed" ; sc:name "BioTIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xyang2uchicago/BioTIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0091, edam:topic_3307, edam:topic_3372 ; sc:citation ; sc:description "A comprehensive library for computational molecular biology" ; sc:license "BSD-3-Clause" ; sc:name "Biotite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.29.0" ; sc:url "https://www.biotite-python.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "This package facilitates the discovery of biomarkers from biological sequencing data based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of parameters defined via causal inference whose estimators admit asymptotically linear representations." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "biotmle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/biotmle.html" ; biotools:primaryContact "Nima Hejazi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_3572 ; sc:author ; sc:description "A rule-based checker for the bio.tools database." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "biotools-linter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://biotools-linter.biodata.ceitec.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0769, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "BioTracs is a transversal framework for computational workflow standardization and traceability. The BioTracs project aims at providing an open community-driven analytics platform. It is an effort for standardizing the implementation and traceability of analytics workflows in bioinformatics." ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:name "BioTracs" ; sc:url "https://bioaster.github.io/biotracs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0798 ; sc:citation , "pmcid:PMC4896371", "pubmed:26794317" ; sc:description "The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "biotradis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sanger-pathogens/Bio-Tradis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC9252798", "pubmed:35536252" ; sc:description "BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction." ; sc:featureList edam:operation_0417, edam:operation_3803, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "BioTransformer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.1.0" ; sc:url "https://biotransformer.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602, edam:topic_2259, edam:topic_3391 ; sc:citation , , ; sc:description """BioTranslator performs semantic interpretation of genomic data, using pathway analysis and gene prioritization approaches The tool is available at: http://www.biotranslator.gr:8080/ http://motherbox.chemeng.ntua.gr/anastasia_dev/""" ; sc:featureList edam:operation_0533, edam:operation_1781, edam:operation_2238, edam:operation_2436, edam:operation_3083, edam:operation_3223, edam:operation_3352, edam:operation_3559 ; sc:name "BioTranslator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biotranslator.gr:8080/" ; biotools:primaryContact "Aristotelis Chatziioannou", "Eleftherios Pilalis", "Olga Papadodima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_2259, edam:topic_3070 ; sc:citation "pubmed:22161332" ; sc:description "Open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data." ; sc:featureList edam:operation_2426 ; sc:name "BioUML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biouml.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3344 ; sc:citation , "pmcid:PMC8756089", "pubmed:34636886" ; sc:description "BioVAE is a pre-trained latent variable language model for biomedical text mining. Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BioVAE" ; sc:url "https://github.com/aistairc/BioVAE" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3464 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:name "Ontology" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3070 ; sc:description "JSON payloads and ontologies become widely adopted in the life science community, validation of ontologies described in JSON documents becomes ever more important. ELIXIR biovalidator is a custom extension to existing JSON Schema syntax to include ontology validation and an implementation based on the Ajv javascript library" ; sc:featureList edam:operation_2428 ; sc:name "biovalidator" ; sc:url "https://github.com/elixir-europe/biovalidator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_0797, edam:topic_3307 ; sc:citation , "pmcid:PMC2584113", "pubmed:18925949" ; sc:description "BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.biovenn.nl." ; sc:featureList edam:operation_0337, edam:operation_2424, edam:operation_3282 ; sc:name "BioVenn" ; sc:softwareVersion "1.0" ; sc:url "https://www.biovenn.nl" ; biotools:primaryContact "Tim Hulsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602 ; sc:citation "pubmed:12824406", "pubmed:14757037", "pubmed:15919725", "pubmed:15980482" ; sc:description "System that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information." ; sc:featureList edam:operation_3455, edam:operation_3625 ; sc:name "Bioverse" ; sc:url "http://bioverse.compbio.washington.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3372 ; sc:citation , "pmcid:PMC9233186", "pubmed:35782729" ; sc:description "A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BioVisReport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://biovis.report/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0780, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "BioViz Connect is a web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3208, edam:operation_3680 ; sc:name "BioViz Connect" ; sc:url "https://bioviz.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0780, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC9580933", "pubmed:36304269" ; sc:description "BioViz Connect, a middleware Web application that links CyVerse science gateway resources to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the user’s personal computer." ; sc:featureList edam:operation_3208 ; sc:name "BioViz Connect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioviz.org/connect.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "This package is designed to provide a set of utilities, color schemes and conventions for genomic data. 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The tool accepts DNA or protein sequences, given in FASTA-format, and performs a Blast homology search against UniProtKB databases. Matching sequences with similar annotations are merged into families of similar descriptions, which are, in turn, further unified, based on assigned GO-profiles retrieved from GOA, into sets of functionally equivalent sequences. As a result, a reliable description will be obtained." ; sc:featureList edam:operation_1777, edam:operation_2422, edam:operation_3092, edam:operation_3672 ; sc:name "BLANNOTATOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ekhidna.biocenter.helsinki.fi/poxo/blannotator" ; biotools:primaryContact "BLANNOTATOR Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2830, edam:topic_3305, edam:topic_3575, edam:topic_3673 ; sc:citation , ; sc:description "The blantyreESBL R package is a repository for data generated as part of a study into carriage of resistant bacteria in Blantyre, Malawi" ; sc:featureList edam:operation_0323, edam:operation_0337, edam:operation_3431, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "blantyreESBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.5281/zenodo.5554082" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:22988817" ; sc:description "Software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error." ; sc:featureList edam:operation_0495, edam:operation_2429 ; sc:name "Blasr" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/PacificBiosciences/blasr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1966, edam:format_2330, edam:format_2333, edam:format_3331, edam:format_3464, edam:format_3475, edam:format_3752, edam:format_3836 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091 ; sc:citation , , , , "pmcid:PMC2447716", "pmcid:PMC3692093", "pmcid:PMC5013910", "pubmed:18440982", "pubmed:2231712", "pubmed:23609542", "pubmed:27256311" ; sc:description "A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:isAccessibleForFree true ; sc:name "BLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://blast.ncbi.nlm.nih.gov/Blast.cgi" ; biotools:primaryContact "BLAST Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Patrick Durand" ; sc:citation ; sc:description "A tool capable of filtering NCBI BLAST results with user-defined constraints." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BLAST-Filter-Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "plealog.com" ; sc:softwareHelp , ; sc:softwareVersion "5.0.0" ; sc:url "https://github.com/pgdurand/BLAST-Filter-Tool" ; biotools:primaryContact "Patrick Durand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3372 ; sc:citation , "pmcid:PMC8066848", "pubmed:33902722" ; sc:description "BLAST-QC is a tool for automated analysis of BLAST results. It is a quality control filter and parser for NCBI BLAST XML results." ; sc:featureList edam:operation_0495, edam:operation_1812, edam:operation_2421 ; sc:license "MIT" ; sc:name "BLAST-QC" ; sc:url "https://github.com/torkian/blast-QC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3673 ; sc:citation , "pmcid:PMC7199347", "pubmed:32366294" ; sc:description "Blast2Fish is a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. It is a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data." ; sc:featureList edam:operation_0524, edam:operation_2421, edam:operation_2422, edam:operation_2436, edam:operation_3644 ; sc:name "Blast2Fish" ; sc:url "http://blast2fish.ntou.edu.tw" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , , "pmcid:PMC2425479", "pubmed:16081474", "pubmed:18445632" ; sc:description "Bioinformatics platform for high-quality functional annotation and analysis of genomic datasets. It allows analyzing and visualizing newly sequenced genomes by combining state-of-the-art methodologies, standard resources and algorithms. It allows to gain biological insights fast and easy even for completely novel genomes. Perform out-of-the-box the entire workflow of functional annotation of your transcriptomic datasets including its analysis and biological interpretation." ; sc:featureList edam:operation_3672 ; sc:name "Blast2GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.blast2go.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_3168 ; sc:citation "pubmed:12824420" ; sc:description "Tool to retrieve protein sequences using similarity (BLAST) and keyword searches." ; sc:featureList edam:operation_0346 ; sc:name "BLAST2SRS" ; sc:url "http://blast2srs.embl.de/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Sequence similarity search program." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "BLAST API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=54653532" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080 ; sc:citation , , ; sc:description "Returns the list best hits from a list of BLAST results." ; sc:featureList edam:operation_0491 ; sc:name "blast_best_score" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/pgp_tools/blast_best_score/0.0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0781, edam:topic_3324 ; sc:description "BLAST database focused on the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "BLAST Betacoronavirus Database" ; sc:url "https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&DATABASE=genomic/Viruses/Betacoronavirus" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation , , "pmcid:PMC2803857", "pubmed:20003500" ; sc:description "Find regions of sequence similarity and alignments between a query sequence and database sequences." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "BLAST (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "NCBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:description "BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs" ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "BLAST (SIB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/blast/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_0797, edam:topic_3293 ; sc:author "Patrick Durand" ; sc:description "Tool that aims at displaying in a graphical way results from the NCBI BLAST software." ; sc:featureList edam:operation_0491, edam:operation_0567, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "BLAST Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Plealog" ; sc:softwareHelp ; sc:softwareVersion "5.5.2" ; sc:url "https://github.com/pgdurand/BlastViewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Uses NCBI Blast to align nucleotide sequences that have large indels or are difficult to align globally. It selects the most representative sequence from the input sequences and then extracts the blast query anchored multiple alignment. Alternatively, the user can choose which sequence to use as an anchor. It also outputs a matrix representing regions of homology along the sequences." ; sc:featureList edam:operation_0492 ; sc:name "BlastAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://evolve.zoo.ox.ac.uk/Evolve/Blastalign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_2885 ; sc:citation , ; sc:description "BlastFrost is a highly efficient method for querying 100,000s of genome assemblies. BlastFrost builds on the recently developed Bifrost, which generates a dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants." ; sc:featureList edam:operation_0224, edam:operation_0524, edam:operation_0525, edam:operation_3196, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "BlastFrost" ; sc:url "https://github.com/nluhmann/BlastFrost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3316 ; sc:description "New tool for computing intensive approximate pattern matching in a sequence graph or a de-Bruijn graph. Given an oriented graph and a set of  query sequences, it detects paths in the graph on which query sequences align at most at the given edit distance." ; sc:featureList edam:operation_0292 ; sc:name "BlastGraph" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/GuillaumeHolley/BlastGraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0081, edam:topic_3489 ; sc:citation , "pubmed:31650686" ; sc:description """BlastGUI is A Python-Based Cross-Platform Local BLAST Visualization Software. Users can build databases and perform sequence filtering and sequence alignment through a graphical user interface. The operation visualization, automatic sequence filtering, and cross-platform use can significantly facilitate the analysis of biological data and the mining of biological information.""" ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "BlastGUI" ; sc:url "https://github.com/byemaxx/BlastGUI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3174 ; sc:citation , "pubmed:26585406" ; sc:description "BlastKOALA (KEGG Orthology And Links Annotation) is a KEGG Web service for annotating genomes and understanding organisms." ; sc:featureList edam:operation_0362, edam:operation_0533 ; sc:isAccessibleForFree true ; sc:name "BlastKOALA" ; sc:softwareHelp ; sc:url "https://www.kegg.jp/blastkoala/" ; biotools:primaryContact "Minoru Kanehisa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:17483516" ; sc:description "Modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences." ; sc:featureList edam:operation_0346 ; sc:name "BLASTO" ; sc:url "http://oxytricha.princeton.edu/BlastO/index.html" ; biotools:primaryContact "Laura F. Landweber" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Recursive psi-blast against the ProDom database." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "blastprodom" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://prodom.prabi.fr/prodom/current/documentation/blastProDom.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3345 ; sc:citation ; sc:description "A new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. We have shown that this approach has better sensitivity and specifity than other softwares with comparable computational cost." ; sc:featureList edam:operation_0338 ; sc:name "BlastR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.2" ; sc:url "http://www.tcoffee.org/Projects/blastr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Convert BlastXML results into GFF3 format." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "blastxml to gapped gff3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3/1.1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:11932250" ; sc:description "Fast, accurate spliced alignment of DNA sequences." ; sc:featureList edam:operation_0292 ; sc:name "BLAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.ucsc.edu/cgi-bin/hgBlat?command=start" ; biotools:primaryContact "Mirror and source code questions", "Server and website access problems", "Website and data questions" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC10077662", "pubmed:37024980" ; sc:description "Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE." ; sc:featureList edam:operation_0314, edam:operation_3185, edam:operation_3200, edam:operation_3799, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BLAZE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shimlab/BLAZE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196 ; sc:citation , "pmcid:PMC9853099", "pubmed:36685727" ; sc:description "A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis." ; sc:featureList edam:operation_0292, edam:operation_0524, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BLEND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CMU-SAFARI/BLEND" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24451628" ; sc:description "BLoom-filter-based Error correction Solution for high-throughput Sequencing reads is a novel algorithm that produces accurate correction results with much less memory compared with previous solutions." ; sc:featureList edam:operation_3195 ; sc:name "BLESS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/bless-ec/wiki/Home/" ; biotools:primaryContact "Anand Ramachandran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0157, edam:topic_0196, edam:topic_0621, edam:topic_3912 ; sc:citation ; sc:description "Basic Long-read Enabled Toolkit for Interspersed DNA Elimination Studies (BleTIES) is a tool for prediction and targeted assembly of internally eliminated sequences (IESs) in ciliate genomes, using single-molecule long read sequencing. The design and name of the software was inspired by ParTIES." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3096, edam:operation_3198 ; sc:license "MIT" ; sc:name "BleTIES" ; sc:url "https://github.com/Swart-lab/bleties" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3474 ; sc:citation , "pmcid:PMC8961055", "pubmed:35382539" ; sc:description "A Python package for integrating BioLector microcultivation devices in the Design-Build-Test-Learn cycle." ; sc:featureList edam:operation_1812, edam:operation_3799, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "bletl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JuBiotech/bletl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3308 ; sc:citation , "pubmed:33821954" ; sc:description "Blight is an associative data structure, similar to a hashtable, able to index a kmer set. It associates each kmer with a unique identifier and can identify alien kmers (kmer absent from the index) associated with the identifier -1. The kmer identifiers are in[0, N[ where N is the number of kmer in the index. Hence, one can see Blight as a Minimal Perfect Hash Function (MPHF) that handle alien kmers." ; sc:featureList edam:operation_0224, edam:operation_0524, edam:operation_3472 ; sc:license "AGPL-3.0" ; sc:name "BLight" ; sc:url "http://github.com/Malfoy/BLight" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "Includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level, methods for data summarization and t-test performance." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "blima" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/blima.html" ; biotools:primaryContact "Vojtech Kulvait" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199 ; sc:citation "pmcid:PMC3072818", "pubmed:21479081" ; sc:description "BLIMP: Software for Best Linear IMPutation" ; sc:featureList edam:operation_3557 ; sc:license "Not licensed" ; sc:name "BLIMP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://stephenslab.uchicago.edu/software_pages/blimp/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_2275 ; sc:citation ; sc:description """Server for performing blind docking calculations. Unique approach where user only inputs ligand and protein, and where the whole protein surface area is processed in order to find potential ligand interaction spots. 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Both single and paired ends are supported." ; sc:featureList edam:operation_2429, edam:operation_3186 ; sc:license "GPL-3.0" ; sc:name "BRAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://brat.nlplab.org/" ; biotools:primaryContact "Goran Topić", "Pontus Stenetorp", "Sampo Pyysalo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3305, edam:topic_3360, edam:topic_3375 ; sc:citation , "pmcid:PMC7730379", "pubmed:33291237" ; sc:description "The Biomarker Reliability Assessment Tool (BRAT) was developed to help researchers set targets to improve exposure assessment in studies of chemicals with a short half-life. The BRAT software uses a simple pharmacokinetic model to simulate exposure, internal levels, and resulting urinary levels in individuals from a population based on user-specified inputs (e.g., biological half-life, within- and between-person variability in exposure). 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It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction. Second, BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. Finally, BraTS Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion" ; sc:featureList edam:operation_3283, edam:operation_3435, edam:operation_3443 ; sc:license "AGPL-3.0" ; sc:name "BraTS Toolkit" ; sc:url "https://neuronflow.github.io/BraTS-Toolkit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3168, edam:topic_3300, edam:topic_3335 ; sc:citation , "pubmed:37734217" ; sc:description "Open-source software for automated electrocardiographic and vectorcardiographic analysis." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "BRAVEHEART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/BIVectors/BRAVEHEART" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3334, edam:topic_3444 ; sc:citation , "pmcid:PMC4993811", "pubmed:27601990" ; sc:description "BRAVIZ is a software tool that integrates interactive visualization with real-time statistical analyses, facilitating access to multi-facetted neuroscience data and automating many cumbersome and error-prone tasks required to explore such data." ; sc:featureList edam:operation_3443 ; sc:license "LGPL-2.0" ; sc:name "BRAVIZ" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://diego0020.github.io/braviz/" ; biotools:primaryContact "Diego A. 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It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). 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To take the correlation between two data sources into consideration, we further develop BREMSC, which uses random effects to incorporate the two data sources. 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It contains fragments from 7290 proteins from the Astral40 set, fragmented in lengths ranging from 4 to 14 amino acids and clustered against 6 different distance thresholds on similarity of the protein backbone. 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Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "xxxxxxxxxxx" ; sc:name "brovo" ; sc:url "http://xx.xx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3361, edam:topic_3678 ; sc:citation "pubmed:21947531" ; sc:description "This software estimates the incubation time and the docking ratio of nanoparticles to a target spot. 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sc:citation ; sc:description "A BrowserViz subclassing example, xy plotting in the browser using d3." ; sc:featureList edam:operation_0490, edam:operation_0564 ; sc:license "GPL-2.0" ; sc:name "BrowserVizDemo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BrowserVizDemo.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "BRS-nonint (Balanced Random Sampling of Non-interactions) is a method of sampling non-interactions randomly from the complement graph of protein-protein interactions, while the degree of each protein in the ‘positive’ dataset (interactions) equals to that in the ‘negative’ dataset (non-interactions)." ; sc:featureList edam:operation_2479 ; sc:name "BRS-nonint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.leeds.ac.uk/BRS-nonint/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3168, edam:topic_3500, edam:topic_3512 ; sc:citation ; sc:description "BrumiR is a toolkit for de novo discovery of microRNAs from sRNA-seq data using a de Bruijn graph." ; sc:featureList edam:operation_0463, edam:operation_0524, edam:operation_3792 ; sc:license "MIT" ; sc:name "BrumiR" ; sc:url "https://github.com/camoragaq/BrumiR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154 ; sc:citation , "pubmed:36111859" ; sc:description "Drug-Protein Interaction Prediction by Correcting the Effect of Incomplete Information in Heterogeneous Information." ; sc:featureList edam:operation_2929, edam:operation_3094 ; sc:license "Not licensed" ; sc:name "BRWCP" ; sc:url "https://github.com/lyfdomain/BRWCP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0102, edam:topic_3168, edam:topic_3674 ; sc:citation , "pmcid:PMC3840619", "pubmed:24206606" ; sc:description "A versatile aligning pipeline for bisulfite sequencing data." ; sc:featureList edam:operation_3186 ; sc:license "MIT" ; sc:name "BS-Seeker2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2/" ; biotools:primaryContact "Weilong Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_2885 ; sc:citation "pubmed:26319221" ; sc:description "An ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling." ; sc:featureList edam:operation_0484 ; sc:name "BS-SNPer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/hellbelly/BS-Snper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "Bisulfite Sequencing Virus integration Finder." ; sc:featureList edam:operation_3461 ; sc:license "LGPL-3.0" ; sc:name "BS-virus-finder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/BGI-SZ/BSVF" ; biotools:primaryContact "Bolund Christian N S Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; 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sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC9788957", "pubmed:36513410" ; sc:description "A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BSATOS" ; sc:url "https://github.com/maypoleflyn/BSATOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation ; sc:description "BiSuflite Bolt (BSBolt) is a fast and scalable bisulfite sequencing processing platform. 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Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. 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Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3517 ; sc:citation , "pubmed:35333298" ; sc:description "A single-cell RNAseq differential expression analysis approach in case-control study" ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "BSDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/mqzhanglab/BSDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:description "Quality control package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing." ; sc:featureList edam:operation_3218 ; sc:name "BSeQC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "https://github.com/hutuqiu/bseqc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "The Blazing Signature Filter is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. 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Payne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC8374653", "pubmed:34430326" ; sc:description "A template for parallelization of iterative numerical algorithms on cluster computing systems." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "BSF-skeleton" ; sc:url "https://github.com/leonid-sokolinsky/BSF-skeleton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3534 ; sc:citation "pubmed:22759425" ; sc:description "Tool for predicting the binding sites for the given proteins. It is implemented in Java." ; sc:featureList edam:operation_2479 ; sc:name "BsFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/guofeics/bsfinder" ; biotools:primaryContact "Lusheng Wang, Professor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1919, edam:format_2330 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation ; sc:description "Infrastructure shared by all the Biostrings-based genome data packages." ; sc:featureList edam:operation_0368, edam:operation_1812, edam:operation_2403 ; sc:license "Artistic-2.0" ; sc:name "BSgenome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BSgenome.html" ; biotools:primaryContact "H. 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Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it also adaptible in the sense that one can direct the alignment based on known biases within the data set. 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Describe Image Patterns in Natural Structures. A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure. The facility to obtain high quality digital images creates the opportunity to measure natural variables using image analyses. Bwimage is an R package to analyze patterns in black and white images from natural structures. A computational tool to describe patterns from black and white images""" ; sc:featureList edam:operation_0320, edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "bwimage" ; sc:url "https://cran.r-project.org/web/packages/bwimage/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091 ; sc:description "Illustrates the Burrows-Wheeler Matrix (BWM) Transform." ; sc:featureList edam:operation_3211, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "Burrows-Wheeler Matrix (BWM) Transform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29126-burrows-wheeler-matrix-bwm-transform" ; biotools:primaryContact "Michael Chan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:18227115" ; sc:description "BWT-SW is a local alignment tool for searching nucleotide sequences. It performs the same function as BLASTn, the BLAST program for finding regions of local similarity between nucleotide sequences. While BLAST is an approximation of the Smith-Waterman local alignment algorithm and may miss significant alignments, BWT-SW finds all local alignments." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "BWT-SW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mruffalo/bwt-sw" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3511 ; sc:description "Command-line utility for bigWig files. BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth)." ; sc:featureList edam:operation_0335 ; sc:name "bwtool 1.0 gamma" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/CRG-Barcelona/bwtool/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Tools for manipulating biological data, particularly multiple sequence alignments." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "bx-python" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bxlab/bx-python" ; biotools:primaryContact "Taylor Lab at Johns Hopkins University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36739821" ; sc:description "Learning to reconstruct 3D spinal structures from bi-planar X-ray images." ; sc:featureList edam:operation_3436, edam:operation_3443 ; sc:license "Not licensed" ; sc:name "BX2S-Net" ; sc:url "https://github.com/NBU-CVMI/bx2s-net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation , "pubmed:32678892" ; sc:description "BYASE is a Python package that uses Bayesian inference to identify gene-level and isoform-level ASE (Allele-specific expression) in polyploid (diploid or higher) organisms from single-end or paired-end RNA-seq data." ; sc:featureList edam:operation_3223, edam:operation_3454, edam:operation_3661 ; sc:license "GPL-3.0" ; sc:name "BYASE" ; sc:url "https://github.com/ncjllld/byase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623 ; sc:citation "pubmed:22080550" ; sc:description "Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences." ; sc:featureList edam:operation_0224, edam:operation_0361, edam:operation_2436, edam:operation_2479 ; sc:name "BYKdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bykdb.ibcp.fr/BYKdb/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3293 ; sc:citation "pubmed:16551582" ; sc:description "Implementation of a new method for inferring branch lengths and site-specific substitution rates from nucleotide sequences. It makes use of the Bayesian Markov Chain Monte Carlo method and of the uniformization (randomization) technique to calculate sequence substitution probabilities in complicated DNA substitution models such as general time reversible model (GTR)." ; sc:featureList edam:operation_0550 ; sc:name "BYPASSR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cmt.ua.ac.be/lcovaci/lucian/ligia/bypassr.html" ; biotools:primaryContact "Ligia M. Mateiu MD PhD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0218, edam:topic_0622 ; sc:citation ; sc:description "Variant annotation & filtering for any size data." ; sc:featureList edam:operation_0362, edam:operation_3197 ; sc:name "Bystro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bystro.io/" ; biotools:primaryContact "Suppoer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_2533 ; sc:citation "pubmed:26338660" ; sc:description "Web-tool that allows to compute mutation rates from fluctuation assays." ; sc:featureList edam:operation_3799 ; sc:name "bz-rates" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/bzrates" ; biotools:primaryContact "Alexandre Gillet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3518 ; sc:citation ; sc:description "BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:name "BZScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2" ; sc:url "http://tagc.univ-mrs.fr/welcome/spip.php?rubrique7" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3334, edam:topic_3337, edam:topic_3384 ; sc:citation , "pubmed:34003431" ; sc:description "C-BIG Repository is an open science resource that promotes scientific research and discovery in neurological diseases and accelerates the development of new treatments." ; sc:featureList edam:operation_3283, edam:operation_3436 ; sc:name "C-BIG" ; sc:url "https://cbigr-open.loris.ca" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33684532" ; sc:description "c-CSN is a script for single-cell RNA sequencing data analysis by conditional cell-specific network." ; sc:featureList edam:operation_3927, edam:operation_3935 ; sc:name "c-CSN" ; sc:url "https://github.com/LinLi-0909/c-CSN" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0219 ; sc:citation "pubmed:26454276" ; sc:description "Software to detect remote/distant homologues from protein sequence databases. It is based on HMMs(Hidden Markov Models) for identifying the deep evolutionary relationships of protein sequences." ; sc:featureList edam:operation_2479 ; sc:name "C-HMM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/RSLabNCBS/C-HMM" ; biotools:primaryContact "Swati Kaushik, PhD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC7037582", "pubmed:32123556" ; sc:description "C-RNNCrispr is a framework for CRISPR/Cas9 single guide RNA (sgRNA) on-target activity prediction using convolutional and recurrent neural networks." ; sc:featureList edam:operation_3096, edam:operation_3659, edam:operation_3927 ; sc:name "C-RNNCrispr" ; sc:url "https://github.com/Peppags/C-RNNCrispr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3170 ; sc:citation ; sc:description "Webapp written using Vue and d3.js for epigenetic data visualization by biologists." ; sc:featureList edam:operation_3208 ; sc:license "MIT" ; sc:name "C-state" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ccmb.res.in/rakeshmishra/c-state/" ; biotools:primaryContact "Divya Tej Sowpati", "Rakesh K Mishra", "Surabhi Srivastava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3303 ; sc:citation ; sc:description "A System for Predicting Mortality of Patients with COVID-19 Pneumonia at the Time They Require Mechanical Ventilation." ; sc:featureList edam:operation_0252, edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "C-TIME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phoenixmed.arizona.edu/ctime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3307, edam:topic_3569 ; sc:citation "pubmed:24862384" ; sc:description "Co-target-Co-function Analyzer, is a Perl-based, versatile and user-friendly web tool with online instructions. Based on the hypergeometric analysis, this novel tool can determine whether given pairs of miRNAs are co-functionally enriched." ; sc:featureList edam:operation_3792 ; sc:name "C2Analyzer" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/c2analyzer/" ; biotools:primaryContact "Arindam Deb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3452 ; sc:citation , "pubmed:37328716" ; sc:description "Non-rigid point cloud registration for middle ear diagnostics with endoscopic optical coherence tomography." ; sc:name "C2P-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/nct_tso_public/c2p-net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_2830 ; sc:citation ; sc:description "A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence | cAb-Rep is a database of curated antibody repertoires. It currently includes 306 B cell repertoires collected from 121 human individuals, including healthy, vaccinated, and autoimmune disease donors. The database has a total of 267.9 and 72.9 million curated full-length V(D)J heavy and light chain transcripts respectively, which were generated using illumina sequencing technology in previous studies. We removed redundancy and sequencing errors in the raw datasets, and annotated each transcript including gene origin, antibody isotype, mutations, post-translational modification, and other characteristics" ; sc:featureList edam:operation_3431, edam:operation_3797 ; sc:name "cAb-Rep" ; sc:url "https://cab-rep.c2b2.columbia.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3360, edam:topic_3676 ; sc:citation , , "pmcid:PMC3956037", "pmcid:PMC4160307", "pubmed:22588877", "pubmed:23550210" ; sc:description "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets." ; sc:name "cBioPortal" ; sc:url "http://www.cBioportal.org/index.do" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pubmed:31504161" ; sc:description "Accurate loop calling for 3D genomic data with cLoops | Accurate and flexible loops calling tool for 3D genomic data | cLoops: loop-calling for ChIA-PET, Hi-C, HiChIP and Trac-looping | Chromosome conformation capture (3C) derived high-throughput sequencing methods such as ChIA-PET,HiChIP and Hi-C provide genome-wide view of chromatin organization. Fine scale loops formed by interactions of regulatory elements spanning hundreds kilobases can be detected from these data. Here we introduce cLoops ('see loops'),a common loops calling tool for ChIA-PET, HiChIP and high-resolution Hi-C data. Paired-end tags (PETs) are first classified as self-ligation and inter-ligation clusters using an optimized unsupervisied clustering algorithm. The significances of the inter-ligation clusters are then estimated using permutated local background" ; sc:featureList edam:operation_3501 ; sc:license "MIT" ; sc:name "cLoops" ; sc:softwareHelp ; sc:url "https://github.com/YaqiangCao/cLoops" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3517 ; sc:citation , "pubmed:31070705" ; sc:description "Identification of disease-associated loci using machine learning for genotype and network data integration." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CPL-1.0" ; sc:name "cNMTF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://lgl15.github.io/cnmtf_web/index.html" ; biotools:primaryContact "Luis G. Leal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050 ; sc:citation ; sc:description "R Tools for Estimating Climate from Vegetation." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "cRacle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.github.com/rsh249/cRacle" ; biotools:primaryContact "R. Harbert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640 ; sc:citation , "pmcid:PMC6410695", "pubmed:30867986" ; sc:description "R package for accessing microRNA and transcription factor-gene expression correlations in cancer." ; sc:featureList edam:operation_0463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cRegulome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=cRegulome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3295, edam:topic_3517 ; sc:citation , "pmcid:PMC9767941", "pubmed:36539420" ; sc:description "C-GWAS is a powerful method for combining GWAS summary statistics of multiple potentially related traits and detect SNPs with multi-trait effects." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3435, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "C-GWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Fun-Gene/CGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474, edam:topic_3954 ; sc:citation , "pubmed:33136540" ; sc:description "CA-Net is a Comprehensive Attention Comvolutional Neural Networks for Explainable Medical Image Segmentation." ; sc:featureList edam:operation_3925 ; sc:name "CA-Net" ; sc:url "https://github.com/HiLab-git/CA-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3324, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36403354" ; sc:description "a novel end-to-end fully convolutional network, named Class-Aware Attention Network (CAA-Net), for automatically diagnosing infectious keratitis (normal, viral keratitis, fungal keratitis, and bacterial keratitis) using corneal photographs" ; sc:license "Not licensed" ; sc:name "CAA-Net" ; sc:url "https://github.com/SWF-hao/CAA-Net_Pytorch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0130, edam:topic_2814 ; sc:citation "pubmed:26502070" ; sc:description "Contact area-based alignment is a flexible protein structure alignment method based on the residue-residue contact area." ; sc:featureList edam:operation_0295 ; sc:name "CAB-align" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html" ; biotools:primaryContact "Mayuko Takeda-Shitaka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3303, edam:topic_3395 ; sc:citation , "pubmed:32845335" ; sc:description "CABEAN is a Software Tool for the Control of Asynchronous Boolean Networks. Combining the two categories, there are six different control strategies. CABEAN provides the following methods to solve the six source-target control problems:." ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_2428 ; sc:name "CABEAN" ; sc:url "https://satoss.uni.lu/software/CABEAN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2269 ; sc:citation "pubmed:26846964" ; sc:description "A Cytoscape 3.2.0 app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness." ; sc:featureList edam:operation_1781, edam:operation_3439 ; sc:name "CABERNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bimib.disco.unimib.it/index.php/CABERNET" ; biotools:primaryContact "marco antoniotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0199, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC9196194", "pubmed:35711759" ; sc:description "A Web Application for the Bioinformatic Analysis of Bacterial Genomes." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3227, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CABGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aureus.procc.fiocruz.br/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32915731" ; sc:description "CABNet is a category Attention Block for Imbalanced Diabetic Retinopathy Grading" ; sc:featureList edam:operation_3436 ; sc:license "MIT" ; sc:name "CABNet" ; sc:url "https://github.com/he2016012996/CABnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:18952627" ; sc:description "Celera Assembler is scientific software for DNA research." ; sc:featureList edam:operation_0310 ; sc:name "CABOG" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://wgs-assembler.sourceforge.net/" ; biotools:primaryContact "J. Miller" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2380 ; sc:name "CABRI accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2597 ; sc:name "CABRI catalogue name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2330 ; sc:name "Cell line report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3339, edam:topic_3340 ; sc:author "Brendan Vaughan", "Domenico Marra", "Francesca Piersigilli" ; sc:citation ; sc:contributor "Beatrice Dutertre", "Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)", "Francois Guissart", "Gerrit Stegehuis", "Herbert Milch", "Louis Jones", "Louis Rechaussat", "Manfred Kracht" ; sc:description "Common Access to Biological Resources and Information - A collection of European Biological Resource Centre catalogues." ; sc:featureList edam:operation_0224 ; sc:funder "Common Access to Biological Resources and Information (CABRI), EU 5th FP (1996-1999)" ; sc:isAccessibleForFree true ; sc:name "CABRI" ; sc:operatingSystem "Linux" ; sc:provider "USMI" ; sc:softwareHelp ; sc:url "http://www.cabri.org/" ; biotools:primaryContact "Paolo Romano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:23658222" ; sc:description "Efficient procedure for the simulation of structure flexibility of folded globular proteins." ; sc:featureList edam:operation_2406 ; sc:name "CABS-flex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biocomp.chem.uw.edu.pl/CABSflex" ; biotools:primaryContact "Andrzej Koliński", "Laboratory of Theory of Biopolymers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:23748950" ; sc:description "CABS-fold is a web server for the de novo and consensus-based prediction of protein structure. 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bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate server cache file for DAS servers or for the DAS registry." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cachedas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cachedas.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate server cache file for Dbfetch/WSDbfetch data sources." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cachedbfetch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cachedbfetch.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate server cache file for EB-eye search domains." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cacheebeyesearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cacheebeyesearch.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate server cache file for an Ensembl server." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cacheensembl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cacheensembl.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Script" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3489 ; sc:citation , "pmcid:PMC9283915", "pubmed:35845039" ; sc:description "CACHET-CADB is 259 days long contextualised single-channel ECG arrhythmia database from 24 patients recording under a free-living ambulatory setting" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CACHET-CADB" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/cph-cachet/cachet-ecg-db" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:36100346" ; sc:description "Classification of anticancer peptides via deep neural network and skip-gram-based word embedding model." ; sc:license "Not licensed" ; sc:name "cACP-DeepGram" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/shahidakbarcs/cACP-DeepGram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_3293 ; sc:author "Benedict Paten" ; sc:citation , , , "pmcid:PMC3166836", "pmcid:PMC7673649", "pubmed:21385048", "pubmed:21665927", "pubmed:33177663" ; sc:description "Cactus is a reference-free whole-genome multiple alignment program." ; sc:featureList edam:operation_0492, edam:operation_3182 ; sc:name "Cactus" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "https://github.com/ComparativeGenomicsToolkit/cactus" ; biotools:primaryContact "Benedict Paten", "David Haussler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3676 ; sc:citation , "pmcid:PMC7988935", "pubmed:33761980" ; sc:description "CACTUS is a tool for integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells." ; sc:featureList edam:operation_2429, edam:operation_3196, edam:operation_3227, edam:operation_3432, edam:operation_3891 ; sc:name "CACTUS" ; sc:url "https://github.com/LUMC/CACTUS" ; biotools:primaryContact "Ewa Szczurek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC9133807", "pubmed:35646870" ; sc:description "Cancer Antigens Database (CAD) designed to facilitate users to perform a complete exploration of cancer antigens online." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3695 ; sc:license "Not licensed" ; sc:name "CAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cad.bio-it.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3510, edam:topic_3511 ; sc:citation , , "pubmed:22933340", "pubmed:32006279" ; sc:description "New evaluation function quantifying differences between physical contacts in a model and the reference structure." ; sc:featureList edam:operation_2424 ; sc:name "CAD-score" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.lt/software/cad-score" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3068 ; sc:citation ; sc:description """CADA (Case Annotations and Disease Dnnotations) is a phenotype-driven gene prioritization tool for rare syndromes. The tool utilizes both disease-level annotations from Human Phenotype Ontology (HPO) and clinical cases-level annotations to construct a gene-phenotype association network. Later, by applying network representation learning method on the network, disease-causing genes are prioritized by a link prediction task. gene prioritization from case annotations and disorder annotations. Web site created using create-react-app. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/genetalk (GENE-TALK.DE)""" ; sc:featureList edam:operation_2454, edam:operation_3359, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "CADA" ; sc:softwareHelp ; sc:url "https://cada.gene-talk.de/webservice/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation "pubmed:26304587" ; sc:description "The purpose of this software, Comparing Alignment results of user Data Based on the relative reliability and advantage of Uniquely aligned REads, is to evaluate spliced aligner performance on user’s RNA-Seq data by comparing a pair of alignment results obtained either from two different aligners with the similar parameter set or from two different parameter sets with the same aligner." ; sc:featureList edam:operation_2928 ; sc:name "CADBURE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cadbure.sourceforge.net/" ; biotools:primaryContact "Praveen K. Raj Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2269, edam:topic_3063, edam:topic_3325, edam:topic_3574 ; sc:citation , , , "pmcid:PMC3992975", "pmcid:PMC6323892", "pmcid:PMC7901104", "pubmed:24487276", "pubmed:30371827", "pubmed:33618777" ; sc:description "Combined Annotation Dependent Depletion (CADD) - tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome." ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CADD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cadd.gs.washington.edu/" ; biotools:primaryContact "CADD support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3336, edam:topic_3373, edam:topic_3577 ; sc:citation , "pmcid:PMC9252786", "pubmed:35580047" ; sc:description "Cancer Driver Drug Interaction Explorer (CADDIE) It provides an interface for a variety of CADDIEs functionalities, giving the user the possibility to execute tasks on CADDIE programmatically without using the website." ; sc:featureList edam:operation_3925, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CADDIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://exbio.wzw.tum.de/caddie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2885, edam:topic_3053, edam:topic_3678 ; sc:citation "pubmed:21045063" ; sc:description "Comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others." ; sc:featureList edam:operation_0484, edam:operation_3501, edam:operation_3661, edam:operation_3672 ; sc:name "CADgene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.life.hust.edu.cn/CADgene/browseGene.php?GeneID=5728" ; biotools:primaryContact "Qing Kenneth Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0654, edam:topic_2275 ; sc:citation "pubmed:19531737" ; sc:description "This software simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs." ; sc:featureList edam:operation_2442 ; sc:name "Cadnano" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cadnano.org/" ; biotools:primaryContact "Shawn Douglas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_2815 ; sc:citation "pubmed:22080563" ; sc:description "Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available." ; sc:featureList edam:operation_0337, edam:operation_3194, edam:operation_3208, edam:operation_3209, edam:operation_3216 ; sc:name "CADRE Genomes Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cadre-genomes.org.uk/index.html" ; biotools:primaryContact "Jane Mabey Gilsenan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC8680165", "pubmed:34915921" ; sc:description "Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures." ; sc:featureList edam:operation_3436, edam:operation_3891, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CaDRReS-Sc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CSB5/CaDRReS-Sc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:author ; sc:citation , "pubmed:34028849" ; sc:description "Category encoding (CAEN) method is proposed to select feature genes for bulk and single-cell RNA-seq data classification. This novel method encodes categories by employing the rank of sequence samples for each gene in each class. Correlation coefficients are considered for gene and class with the rank of sample and a new rank of category. The highest gene correlation coefficients are considered feature genes, which are the most effective for classifying bulk and single-cell RNA-seq dataset." ; sc:featureList edam:operation_2995, edam:operation_3463, edam:operation_3936 ; sc:license "GPL-2.0" ; sc:name "CAEN" ; sc:url "https://bioconductor.org/packages/devel/bioc/html/CAEN.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3055, edam:topic_3517 ; sc:citation , "pmcid:PMC10767927", "pubmed:37855690" ; sc:description "CaeNDR, the Caenorhabditis Natural Diversity Resource. CaeNDR enables quantitative genetics and genomics studies across three Caenorhabditis species. The platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CarNDR provides interative tools to explore natural variation and enable GWAS mappings." ; sc:featureList edam:operation_0282, edam:operation_0361, edam:operation_3196, edam:operation_3227, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "CaeNDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://caendr.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3315 ; sc:description "Computes the entropy for Cellular Automata" ; sc:isAccessibleForFree true ; sc:name "CAentropy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/40281-caentropy-m" ; biotools:primaryContact "Ehsan Tahami" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097, edam:topic_0821 ; sc:citation ; sc:description "Capillary Automated Footprinting Analysis algorithms. The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping (‘footprinting’)." ; sc:featureList edam:operation_2481 ; sc:name "CAFA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.41" ; sc:url "https://simtk.org/home/cafa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3321, edam:topic_3518 ; sc:citation ; sc:description "Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "CAFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CAFE.html" ; biotools:primaryContact "Sander Bollen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0798, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:33393985" ; sc:description """A software suite for analysis of paired-sample transposon insertion sequencing data. 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A comprehensive resource on enhancer information for TCGA cancer types. CancerEnD Genome-wide association studies have successfully identified thousands of genomic loci potentially associated with hundreds of complex traits in the past decade.""" ; sc:featureList edam:operation_2421, edam:operation_3503 ; sc:name "CancerEnD" ; sc:url "https://webs.iiitd.edu.in/raghava/cancerend/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "One stop portal for cancer resources" ; sc:featureList edam:operation_2945 ; sc:name "canceres" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/canceres/db.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2640, edam:topic_3301 ; sc:citation , "pmcid:PMC7692641", "pubmed:33142753" ; sc:description """CancerGram identifies anticancer peptides using random forests and n-gram encoding. Antimicrobial peptides (AMPs) constitute a diverse group of bioactive molecules that provide multicellular organisms with protection against microorganisms, and microorganisms with weaponry for competition. Some AMPs can target cancer cells; thus, they are called anticancer peptides (ACPs). Due to their small size, positive charge, hydrophobicity and amphipathicity, AMPs and ACPs interact with negatively charged components of biological membranes. AMPs preferentially permeabilize microbial membranes, but ACPs additionally target mitochondrial and plasma membranes of cancer cells.""" ; sc:name "CancerGram" ; sc:url "http://biongram.biotech.uni.wroc.pl/CancerGram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_2815, edam:topic_3379 ; sc:citation , "pmcid:PMC10308937", "pubmed:37255431" ; sc:description "Human endogenous retrovirus (HERV) expression database for human cancer accelerates studies of the retrovirome and predictions for HERV-based therapies." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "CancerHERVdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://erikstricker.shinyapps.io/cancerHERVdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Class-I HLA alleles Database" ; sc:featureList edam:operation_2945 ; sc:name "cancerhla1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancerhla1/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2640, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:33010176" ; sc:description """CancerImmunityQTL is a database to systematically evaluate the impact of genetic variants on immune infiltration in human cancer. Tumor-infiltrating immune cells, as the component of tumor microenvironment, could influence tumor progress, prognosis and response to therapy profoundly. Genetic variants are considered as crucial factors that affect immune response. So far, tumor-infiltrating immune cells can be quantified from RNA sequencing data of human tumors using bioinformatics approaches based on immune-specific marker genes or expression signature. Therefore, we systematically explored the effects of single nucleotide polymorphisms (SNPs) on tumor-infiltrating immune cells, and identified immunity quantitative trait loci (immunQTLs) across 33 cancer types from TCGA.""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3799 ; sc:name "CancerImmunityQTL" ; sc:url "http://www.cancerimmunityqtl-hust.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "This package provides an R interface for running mathematical models of tumor progression. It has the underlying models implemented in C++ and the output and analysis features implemented in R." ; sc:featureList edam:operation_2426 ; sc:license "GPL-2.0" ; sc:name "CancerInSilico" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CancerInSilico.html" ; biotools:primaryContact "Elana J. Fertig", "Thomas D. Sherman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3068, edam:topic_3360 ; sc:citation , "pmcid:PMC7061090", "pubmed:32147717" ; sc:description "CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting and analyzing data." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2495, edam:operation_3431 ; sc:name "CancerLivER" ; sc:url "https://webs.iiitd.edu.in/raghava/cancerliver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc:description "CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus (GEO) and ArrayExpress." ; sc:featureList edam:operation_2436, edam:operation_2939, edam:operation_3659, edam:operation_3792, edam:operation_3891 ; sc:name "CancerMIRNome" ; sc:url "http://bioinfo.jialab-ucr.org/CancerMIRNome" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3273 ; sc:encodingFormat edam:format_2330 ; sc:name "Sample ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver and passenger genes, and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "CancerMutationAnalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CancerMutationAnalysis.html" ; biotools:primaryContact "Simina M. Boca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0601, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC9569343", "pubmed:36243772" ; sc:description "Cancermuts is a package for the automtic retrieval and annotation of cancer mutations." ; sc:featureList edam:operation_0417, edam:operation_2422, edam:operation_3226, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Cancermuts" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.github.com/ELELAB/cancermuts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3173, edam:topic_3360, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC9195411", "pubmed:35698059" ; sc:description "A VAE based deep learning approach to cancer tissue of origin classification." ; sc:featureList edam:operation_3935 ; sc:license "Not licensed" ; sc:name "CancerNet" ; sc:url "https://www.cancer.gov/tcga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC9119687", "pubmed:35601606" ; sc:description "A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines" ; sc:featureList edam:operation_3223, edam:operation_3927, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CancerOmicsNet" ; sc:url "https://github.com/pulimeng/CancerOmicsNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description "Comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains." ; sc:featureList edam:operation_3225 ; sc:name "Cancerouspdomains" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cancerouspdomains.ir/" ; biotools:primaryContact "Zahra Razaghi-Moghadam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC5431423", "pubmed:28473704" ; sc:description "CancerPDF is a manually curated database of cancer-associated peptides found in different human bodyfluids (e.g., serum, urine, plasma and saliva)." ; sc:featureList edam:operation_2945 ; sc:name "CancerPDF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancerpdf/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_2640 ; sc:citation , "pmcid:PMC4384006", "pubmed:25270878" ; sc:description "A repository of experimentally verified anticancer peptides (ACPs) and anticancer proteins. Data were manually collected from published research articles, patents and from other databases." ; sc:featureList edam:operation_0224 ; sc:name "CancerPPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancerppd/" ; biotools:primaryContact "Gajendra P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "CancerPred is a web-server specially trained for predicting the Cancerlectins. Lectins are important biomolecules and play important functions in many processes e.g cell to cell recognition, host-pathogen interactions etc. In the same way Cancerlectins are those lectins which are known to play roles in cancer metastasis and tumor progress, oncogenesis etc. CancerPred is mainly designed for distinguishing Cancerlectins from Non-cancer lectins." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "CancerPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancer_pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_2640, edam:topic_3520 ; sc:citation , "pmcid:PMC10767844", "pubmed:37823596" ; sc:description "Resource to functionally decipher the proteome landscape in cancer." ; sc:featureList edam:operation_0417, edam:operation_2436, edam:operation_3223, edam:operation_3630 ; sc:isAccessibleForFree true ; sc:name "CancerProteome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/CancerProteome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_0218, edam:topic_0602, edam:topic_3303 ; sc:citation "pubmed:20952398" ; sc:description "CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine." ; sc:featureList edam:operation_0306, edam:operation_0314, edam:operation_2436, edam:operation_2495, edam:operation_3223 ; sc:name "CancerResource" ; sc:url "http://bioinformatics.charite.de/cancerresource/" ; biotools:primaryContact "Bjoern Gohlke", "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC8728207", "pubmed:34643725" ; sc:description "Database of single-cell expression map across various human cancers." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "CancerSCEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/cancerscem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC8117642", "pubmed:33980137" ; sc:description "CancerSiamese is a tool for one-shot learning for predicting primary and metastatic tumor types unseen during model training." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3927 ; sc:license "MIT" ; sc:name "CancerSiamese" ; sc:url "https://github.com/MMostavi/CancerSiamese" ; biotools:primaryContact , "Yidong Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6987109", "pubmed:31992766" ; sc:description "CANCERSIGN is a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes." ; sc:featureList edam:operation_0367, edam:operation_3629, edam:operation_3799, edam:operation_3891 ; sc:name "CANCERSIGN" ; sc:url "https://github.com/bcb-sut/CANCERSIGN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "CancerSP is a web bench developed for analyzing genomics data and for predicting Early and Late stage of cancer using genomics data." ; sc:featureList edam:operation_2945 ; sc:name "CancerSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancersp/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2640 ; sc:citation ; sc:description "This tool integrates the current common computational biology methods for cancer subtypes identification and provides a standarized framework for cancer subtypes analysis based on genomic datasets." ; sc:featureList edam:operation_0253 ; sc:license "GPL-2.0" ; sc:name "CancerSubtypes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CancerSubtypes.html" ; biotools:primaryContact "Taosheng Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description """In silico Platform for designing genome-based Personalized immunotherapy or Vaccine against Cancer.""" ; sc:featureList edam:operation_2945 ; sc:name "cancertope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancertope/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7179925", "pubmed:32324757" ; sc:description "CancerTSP is a web-bench designed for stage prediction of Papillary Thyroid Carcinoma (PTC) using RNA expression data (derived from RNA-seq experiments in the form of RNA-Seq FPKM values). Primarily Early v/s Late stage prediction module predicts stage of PTC tissue sample. Further Cancer v/s Normal prediction module predicts whether tissue sample is cancerous or normal. Analysis module allows the user to analyze data regarding expression of an RNA transcript in Early or Late stage of PTC." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3435 ; sc:name "CancerTSP" ; sc:url "http://webs.iiitd.edu.in/raghava/cancertsp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "CancerUBM is a web bench developed for analyzing proteomics data and for predicting cancer status of a urine sample from its proteomics data." ; sc:featureList edam:operation_2945 ; sc:name "cancerubm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/cancerubm/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3379, edam:topic_3474, edam:topic_3966 ; sc:citation , "pmcid:PMC9364268", "pubmed:35967400" ; sc:description "A library of peptide-based cancer vaccines and their clinical attributes, named CancerVaccine" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0560 ; sc:license "Not licensed" ; sc:name "CancerVaccine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://peptidecancervaccine.weebly.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2640, edam:topic_3379, edam:topic_3512 ; sc:citation ; sc:description "CancerVar is a web server for improved evidence-based clinical interpretation for cancer somatic mutations. CancerVar is a bioinformatics software tool for clinical interpretation of somatic variants." ; sc:featureList edam:operation_0224, edam:operation_3226, edam:operation_3227 ; sc:name "CancerVar" ; sc:url "http://cancervar.wglab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall p-value will be returned for each test. Plotting functions are also available." ; sc:featureList edam:operation_0324 ; sc:license "Artistic-2.0" ; sc:name "CAnD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CAnD.html" ; biotools:primaryContact "Caitlin McHugh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3572 ; sc:citation , "pmcid:PMC8524992", "pubmed:34663427" ; sc:description "CanDI - A global cancer data integrator." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CanDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GilbertLabUCSF/CanDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_2885, edam:topic_3500, edam:topic_3517 ; sc:citation ; sc:description "CandiHap is a user-friendly local software, that can fast preselect candidate causal SNPs from Sanger or next-generation sequencing data, and report results in table and exquisite vector-graphs within a minute. Investigators can use CandiHap to specify a gene or linkage sites based on GWAS and explore favourable haplotypes of candidate genes for target traits." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:name "CandiHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xukaili/CandiHap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:32871004" ; sc:description "Causal Network of Diseases (CaNDis) is a web server for the exploration of a human causal interaction network, which we expanded with data on diseases and FDA-approved drugs, on the basis of which we constructed a disease–disease network in which the links represent the similarity between diseases." ; sc:featureList edam:operation_3094, edam:operation_3925 ; sc:name "CaNDis" ; sc:url "http://candis.ijs.si" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_2885 ; sc:citation "pubmed:26779212" ; sc:description "New pipeline to automatically identify the candidate polymorphic SSRs for a given species or genus based on their assembled sequences." ; sc:featureList edam:operation_3202 ; sc:name "CandiSSR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.plantkingdomgdb.com/CandiSSR/index.html" ; biotools:primaryContact "Li-Zhi Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0209, edam:topic_0601, edam:topic_2275 ; sc:citation , "pubmed:32069042" ; sc:description "CANDOCK (Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials) is a novel docking algorithm, that utilizes a hierarchical approach to reconstruct ligands from an atomic grid using graph theory and generalized statistical potential functions to sample biologically relevant ligand conformations. Our algorithm accounts for protein flexibility, solvent, metal ions, and cofactor interactions in the binding pocket that are traditionally ignored by current methods." ; sc:featureList edam:operation_0244, edam:operation_3893, edam:operation_3899, edam:operation_3938 ; sc:license "GPL-3.0" ; sc:name "CANDOCK" ; sc:url "https://github.com/chopralab/candock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_2269, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:33876217" ; sc:description "Cancer-Driving Site Profiling DataBase (CanDriS) is a platform to comprehensively proflie the cancer-driving sites at the pan-cancer and tumor-type level for the somatic mutations collected from The Cancer Genome Atlas (TCGA PanCanAtlas project) and International Cancer Genome Consortium (ICGC) (ICGC Release 25) by an in-house method CanDriS." ; sc:featureList edam:operation_2454, edam:operation_3092 ; sc:name "CanDriS" ; sc:url "http://biopharm.zju.edu.cn/candrisdb/" ; biotools:primaryContact "Xun Gu", "Zhan Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3318, edam:topic_3382 ; sc:citation ; sc:description "CandyCodes is a simple universally unique edible identifiers for confirming the authenticity of pharmaceuticals." ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:license "MIT" ; sc:name "CandyCodes" ; sc:url "https://github.com/groverlab/candycodes" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC4710974", "pubmed:26758513" ; sc:description "Application for Comprehensive automated Analysis of Next-generation sequencing Experiments." ; sc:featureList edam:operation_3223, edam:operation_3680 ; sc:name "CANEapp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app" ; biotools:primaryContact "Dmitry Velmeshev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0108, edam:topic_0602, edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC3572035", "pubmed:23418540" ; sc:description "Query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. It stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information." ; sc:featureList edam:operation_0224, edam:operation_2497 ; sc:name "canEvolve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.canevolve.org/AnalysisResults/AnalysisResults.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:20180949" ; sc:description "CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3237 ; sc:name "CANGS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://i122server.vu-wien.ac.at/CANGS1.1/" ; biotools:primaryContact "Schlötterer C." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3403, edam:topic_3474 ; sc:citation , "pmcid:PMC9913129", "pubmed:36765528" ; sc:description "Machine Learning-Based Mortality Prediction Model for Critically Ill Cancer Patients Admitted to the Intensive Care Unit (CanICU)." ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CanICU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yonsei-cancer-center.shinyapps.io/CanICU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_2640, edam:topic_3360, edam:topic_3400 ; sc:citation , "pmcid:PMC8288037", "pubmed:34345532" ; sc:description "Database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "CanImmunother" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biomedical-web.com/cancerit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2815, edam:topic_2885, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC10457218", "pubmed:37351774" ; sc:description "Functional tool useful for comparative analyses of human and canine mitochondrial genomes." ; sc:featureList edam:operation_0267, edam:operation_0464, edam:operation_0484 ; sc:isAccessibleForFree true ; sc:name "Canis MitoSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://canismitosnp.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3308, edam:topic_3320, edam:topic_3676 ; sc:citation , "pmcid:PMC10571338", "pubmed:37828501" ; sc:description """Database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). CanISO enables to facilitate expression-based analysis at gene- and transcript isoform-level in each sample, in a group (normal or tumor), and between both conditions. Since GTEx data in human is included into CanISO database, comparison function can also be supported between samples of dogs and humans.""" ; sc:featureList edam:operation_0264, edam:operation_0487, edam:operation_2421, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "CanISO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.kobic.re.kr/caniso/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10133402", "pubmed:37123454" ; sc:description "Database to study the functional impact of isoform switching events in diseases." ; sc:featureList edam:operation_0264, edam:operation_3435, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CanIsoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.caniso.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_2640, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC9825769", "pubmed:36477791" ; sc:description "A database for genome-wide DNA methylation annotation in cancers." ; sc:featureList edam:operation_0314, edam:operation_3207, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CanMethdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://meth.liclab.net/CanMethdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_3068, edam:topic_3303 ; sc:citation , "pmcid:PMC8087868", "pubmed:33942873" ; sc:description "CANNUSE is a database containing the traditional uses of Cannabis." ; sc:featureList edam:operation_0553, edam:operation_2421, edam:operation_3501 ; sc:name "CANNUSE" ; sc:url "http://cannusedb.csic.es" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6668299", "pubmed:31396192" ; sc:description "A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis | The Molecular Bioinformatics Center provides an integrated approach to the use of gene and protein sequence information, molecular structures, and related resources, in molecular biology | (A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis) | Step 1: Upload genome contig files | YY Liu, JW Lin and CC Chen (2019) cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis . Front. Microbiol. 10 :1687. doi: 10.3389/fmicb.2019.01687" ; sc:featureList edam:operation_0323, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "cano-wgMLST_BacCompare" ; sc:url "http://baccompare.imst.nsysu.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33230292" ; sc:description "CANOPUS is a tool for predicting compound classes directly from MS/MS. 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The canopy creation process is then repeated perpetually(canopy walk) from the previously created centroid until the distance between previous centroid is small enough. All points from the last canopy are then marked, and will not become seed points again. The above will be repeated for all possible seed points." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "canopy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/HeyHo/mgs-canopy-algorithm/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0199, edam:topic_3168 ; sc:citation "pubmed:17234753", "pubmed:17537827" ; sc:description "Combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations." ; sc:featureList edam:operation_0331, edam:operation_0408, edam:operation_0478 ; sc:name "CanPredict" ; sc:url "http://www.cgl.ucsf.edu/Research/genentech/canpredict/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3474 ; sc:description "CanProSite is developed in IIT Madras from Protein Bioinformatics Lab. It is useful for the identification of disease prone sites in lung cancer using deep neural network" ; sc:name "CanProSite" ; sc:url "https://web.iitm.ac.in/bioinfo2/CanProSite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2640, edam:topic_3053 ; sc:citation , , "pmcid:PMC7059924", "pubmed:32142536", "pubmed:33335023" ; sc:description "The CanRisk tool is a web interface to BOADICEA, the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm, risk prediction model used to calculate future breast and ovarian cancer risks in women. This is the first comprehensive model that allows for reliable breast cancer risk prediction in unaffected women on the basis of mutation screening information for rare (high risk and moderate risk) breast cancer genetic susceptibility variants, common cancer genetic susceptibility variants (using polygenic risk scores), explicit family history, personal lifestyle, hormonal and reproductive risk factors, and mammographic density." ; sc:featureList edam:operation_3283 ; sc:name "CanRisk" ; sc:url "http://CanRisk.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2640, edam:topic_3336 ; sc:citation "pubmed:22013161" ; sc:description "canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. 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Using genetic programming the prior network is adapted to match the desired behavior as specified in the experimental results.""" ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CANTATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sysbio-bioinf/Cantata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "De-novo assembly tool for long read chemistry like Nanopore data and PacBio data." ; sc:featureList edam:operation_0524 ; sc:name "CANU" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/marbl/canu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC5200944", "pubmed:28105316" ; sc:description "Variant level frequency data from cancer germline sequencing studies." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3227, edam:operation_3229 ; sc:license "MIT" ; sc:name "CanVar" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://canvar.icr.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3676 ; sc:citation ; sc:description "CanVaS is a Greek cancer patient genetic variation resource." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3283 ; sc:name "CanVaS" ; sc:url "http://ithaka.rrp.demokritos.gr/CanVaS/genes" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1915 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_1915 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3316, edam:topic_3391 ; sc:description "Complexity Analysis Viral Sequences" ; sc:featureList edam:operation_2945, edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CANVAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/jorgeMFS/canvas" ; biotools:primaryContact "Jorge Miguel Ferreira da Silva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0128, edam:topic_0769 ; sc:citation , "pubmed:34432510" ; sc:description "CANVS is an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. The elucidation of a protein's interaction association network is important for defining its biological function. Mass spectrometry-based proteomic approaches have emerged as powerful tools for identifying protein-protein interactions (PPIs) and protein-protein associations (PPAs). However, interactome association experiments are difficult to interpret, considering the complexity and abundance of data that are generated. Although tools have been developed to identify protein interactions associations quantitatively, there is still a pressing need for easy-to-use tools that allow users to contextualize their results. To address this, we developed CANVS, a computational pipeline that cleans, analyzes, and visualizes mass spectrometry-based interactome association data" ; sc:featureList edam:operation_2949, edam:operation_3799, edam:operation_3925 ; sc:name "CANVS" ; sc:url "https://sourceforge.net/projects/canvs/files/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2640 ; sc:citation ; sc:description "Package that provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout." ; sc:featureList edam:operation_3208 ; sc:license "GPL-2.0" ; sc:name "caOmicsV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/caOmicsV.html" ; biotools:primaryContact "Henry Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "CaosDB is a software toolbox for data management. Its focus lies on managing data in dynamic environments of research and development where changes are too frequent or projects are too small to bear the great cost of implementing a traditional specialized and but inflexible data management system. The research data management system (RDMS) CaosDB uses a semantic data model that allows to grow and change in those dynamic environments!" ; sc:name "CaosDB" ; sc:url "https://caosdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation "pubmed:10508846" ; sc:description "Web-based contig assembly." ; sc:featureList edam:operation_0310, edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:name "CAP3 Sequence Assembly Program" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosrv.cab.unina.it/webcap3/" ; biotools:primaryContact "X. Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3068, edam:topic_3169 ; sc:citation ; sc:description "Software package for the analysis of Capture-C data." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "capC-MAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/cbrackley/capC-MAP" ; biotools:primaryContact "Chris A. Brackley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:24931987" ; sc:description "An extension of DSD  that takes in to account a measure of interaction confidence while also incorporating directed pathway data." ; sc:featureList edam:operation_3439 ; sc:name "capDSD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dsd.cs.tufts.edu/capdsd/" ; biotools:primaryContact "Ben Hescott" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_3053 ; sc:citation , "pmcid:PMC3808451", "pubmed:24204223" ; sc:description "Combine complementary information across multiple related phenotypes to infer directed epistatic interactions between genetic markers. This analysis can be applied to a variety of engineered and natural populations." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "CAPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/cape/" ; biotools:primaryContact "Anna L. Tyler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_3297 ; sc:citation ; sc:description "CapiPy (Computer Assistance for Protein Immobilisation – Python) is a small collection of 4 main packages to retrieve useful information for the immobilisation of a query protein. Information from each module, specially the Blast and modeller is preferentially used by the others. In case no such information is given, the user will have to input the necessary information." ; sc:featureList edam:operation_0477, edam:operation_2421, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "CapiPy" ; sc:url "https://github.com/drou0302/CapiPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3518 ; sc:citation "pubmed:17476945" ; sc:description "Novel approach for clustering samples (treatments, patients, condition etc) by using annotational information about the genes. The algorithm searches all pre-defined gene classes for classes that exhibit a strong clustering of the samples. These are then used to split the samples in two groups until no significant splits can be found. The result is visualized as a tree with gene classes as nodes and groups of samples as leaves." ; sc:featureList edam:operation_0291 ; sc:name "CAPIU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.mpimp-golm.mpg.de/research-projects-publications/tools-services/capiu" ; biotools:primaryContact "Henning Redestig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3077, edam:topic_3318 ; sc:citation , "pmcid:PMC7899353", "pubmed:33617576" ; sc:description "capl is an R package for use with data collected using the Canadian Assessment of Physical Literacy. The package contains functions that will calculate CAPL scores and interpretations from raw data." ; sc:featureList edam:operation_0337 ; sc:name "capl" ; sc:url "http://www.github.com/barnzilla/capl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:24447569" ; sc:description "The software calculates probabilities that each RNA base position is located within each secondary structural context for long RNA sequences." ; sc:featureList edam:operation_2439 ; sc:name "CapR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/fukunagatsu/software/capr" ; biotools:primaryContact "Tsukasa Fukunaga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0154, edam:topic_0749, edam:topic_2885, edam:topic_3945 ; sc:citation , "pmcid:PMC7690079", "pubmed:33243176" ; sc:description "Bioinformatics Tool for Comparative Analyses of Proteins In Bacteria (CAPRIB) is a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. 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The tool is fully browsable and searchable and is regularly updated." ; sc:featureList edam:operation_0245, edam:operation_0250, edam:operation_0360, edam:operation_2996 ; sc:name "CAPS-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home" ; biotools:primaryContact "Narcis Fernandez-Fuentes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3379, edam:topic_3524 ; sc:citation ; sc:description "Simulation of targeted sequencing. Given a genome sequence and a set of probes, it simulates the fragmentation, the dynamics of probe hybridization and the sequencing of the captured fragments on Illumina and PacBio sequencing platforms. The simulated data can be used for evaluating the performance of the analysis pipeline, as well as the efficiency of the probe design." ; sc:featureList edam:operation_0550 ; sc:license "BSD-2-Clause" ; sc:name "CapSim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Devika1/capsim" ; biotools:primaryContact "Lachlan J M Coin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC7285745", "pubmed:32517646" ; sc:description "CapsNet-SSP is a multilane capsule network for predicting human saliva-secretory proteins. Compared with disease biomarkers in blood and urine, biomarkers in saliva have distinct advantages, as they can be examined with convenient clinical tests and through noninvasive sample collection." ; sc:featureList edam:operation_3092, edam:operation_3767, edam:operation_3927 ; sc:name "CapsNet-SSP" ; sc:url "http://www.csbg-jlu.info/CapsNet-SSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0601, edam:topic_3295 ; sc:citation , "pmcid:PMC9735261", "pubmed:36544479" ; sc:description "Capsule network-based prediction of lysine crotonylation sites in human non-histone proteins." ; sc:featureList edam:operation_0239, edam:operation_3092, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CapsNh-Kcr" ; sc:url "https://github.com/Jhabindra-bioinfo/CapsNh-Kcr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0659, edam:topic_3542 ; sc:citation , "pmcid:PMC8120853", "pubmed:33985444" ; sc:description "Capsule-LPI is a LncRNA-protein interaction predicting tool based on a capsule network." ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_3094, edam:operation_3901 ; sc:name "Capsule-LPI" ; sc:softwareHelp ; sc:url "http://csbg-jlu.site/lpc/predict" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_3293, edam:topic_3794, edam:topic_3944 ; sc:citation , "pmcid:PMC9158481", "pubmed:35664339" ; sc:description "An interactive web tool to provide taxonomic context for a given phylogenetic tree." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CAPT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ghattab/CAPT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0601, edam:topic_0634, edam:topic_3300, edam:topic_3474 ; sc:citation , "pubmed:34806952" ; sc:description "Captor is a tool for O-glycosylation site prediction in Homo sapiens. It works by combining properties and sequence features with support vector machine." ; sc:featureList edam:operation_0253, edam:operation_0417, edam:operation_3645 ; sc:name "Captor" ; sc:url "https://github.com/YanZhu06/Captor/" ; biotools:primaryContact "Cangzhi Jia", "Jia Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0202, edam:topic_0625, edam:topic_3382, edam:topic_3676 ; sc:citation ; sc:description "CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems." ; sc:featureList edam:operation_0337, edam:operation_3280, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "CaPTure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LieberInstitute/CaPTure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3940 ; sc:citation ; sc:description "CaptureCompendium is a comprehensive toolkit for 3C analysis." ; sc:featureList edam:operation_0337, edam:operation_0365, edam:operation_3198 ; sc:name "CaptureCompendium" ; sc:url "http://userweb.molbiol.ox.ac.uk/public/telenius/CaptureCompendium/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3382, edam:topic_3518 ; sc:citation "pubmed:15381628", "pubmed:16845053" ; sc:description "Tool for storing, analyzing and visualizing CGH-array data." ; sc:featureList edam:operation_3197, edam:operation_3211, edam:operation_3233, edam:operation_3443 ; sc:name "CAPweb" ; sc:url "http://bioinfo.curie.fr/CAPweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Capybara is a R tool to measure cell identity and fate transitions. 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sc:applicationSubCategory edam:topic_3068, edam:topic_3170, edam:topic_3421, edam:topic_3422 ; sc:citation , "pmcid:PMC9714541", "pubmed:36466852" ; sc:description "Interactive web server for comprehensive analysis of renal allograft rejection in immune microenvironment." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3659 ; sc:license "Other" ; sc:name "CARARIME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cararime.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0203, edam:topic_3292, edam:topic_3489, edam:topic_3518 ; sc:citation , "pubmed:35352122" ; sc:description "Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART) is a software tool for glycan microarray experimental design, data storage, processing, presentation and reporting." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CarbArrayART" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://glycosciences.med.ic.ac.uk/carbarrayart.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Carbohydrate epitope prediction server" ; sc:featureList edam:operation_2945 ; sc:name "CARBOTOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/carbotope/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_2814 ; sc:citation "pubmed:22038416" ; sc:description "Novel tool that applies support vector machine (SVM) for identifying carboxylation sites on glutamate residue." ; sc:featureList edam:operation_2479 ; sc:name "Carboxylator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/Carboxylator/" ; biotools:primaryContact "Tzong-Yi Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3474, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:34035047" ; sc:description "CarDEC (Count adapted regularized Deep Embedded Clustering) is a joint deep learning computational tool that is useful for analyses of single-cell RNA-seq data." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3463 ; sc:license "MIT" ; sc:name "CarDEC" ; sc:url "https://github.com/jlakkis/CarDEC" ; biotools:primaryContact "Justin Lakkis", "Mingyao Li", "Xiangjie Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3316 ; sc:citation , "pubmed:32203388" ; sc:description "This R package contains a Bayesian method to infer clonal structure for a population of cells using single-cell RNA-seq data (and possibly other data modalities)." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3629, edam:operation_3933 ; sc:name "cardelino" ; sc:url "https://github.com/single-cell-genetics/cardelino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3335, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:33196972" ; sc:description "CardIAc is an open-source application designed as an alternative to commercial software for left ventricle myocardial strain quantification in short-axis cardiac magnetic resonance images. CardIAc was developed as a 3D Slicer extension for an easy installation and usability. The source code is available opon request to the corresponding author." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:license "BSD-Source-Code" ; sc:name "CardIAc" ; sc:url "http://www.cardiacatlas.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Software for semi-automatic segmentation of cardiac ischemia tissues from histological images." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Cardiac Ischemia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/66902-cardiac-ischemia" ; biotools:primaryContact "Jiri Chmelik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "CardIAP web app, an automated method for the identification of spatio-temporal patterns in a calcium fluorescence imaging sequence. 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Bemis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3474, edam:topic_3574, edam:topic_3676 ; sc:citation , ; sc:description "CardioBoost is a disease-specific machine learning classifier to predict the pathogenicity of rare (gnomAD Allele Frequency <=0.1%) missense variant in genes associated with cardiomyopathies and arrhythmias that outperforms existing genome-wide prediction tools." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3461 ; sc:name "CardioBoost" ; sc:url "https://www.cardiodb.org/cardioboost/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3063, edam:topic_3315, edam:topic_3335 ; sc:citation ; sc:description "CardioPy is an open-source heart rate variability toolkit for single-lead EKG. 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The input of a set of RNA sequences are not required to be previously aligned." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_0502, edam:operation_2439 ; sc:name "CARNAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.lifl.fr/carnac" ; biotools:primaryContact "Carnac team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3337, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC10526726", "pubmed:37352650" ; sc:description "Creating connectomes for different atlases when raw data is not available." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "CAROT" ; sc:url "http://carotproject.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3365 ; sc:citation "pubmed:26508755" ; sc:description "CaRpools is an R package for exploratory data analysis of pooled CRISPR/Cas9 screens." ; sc:featureList edam:operation_2945 ; sc:name "CaRpools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/boutroslab/caRpools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3518 ; sc:citation "pubmed:1470435", "pubmed:15215383" ; sc:description "Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. 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Haverty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:description "CARROT is a tool for relationship inference that leverages linkage disequilibrium to differentiate between rotated relationships, such as (first-, second-, etc) uncle-niece." ; sc:featureList edam:operation_2990, edam:operation_3625 ; sc:name "CARROT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://carrot.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3293 ; sc:citation , "pmcid:PMC9450951", "pubmed:36069936" ; sc:description "CarrotOmics is an integrated web-based relational database, developed to house and integrate genomic, genetic and breeding data for carrot and related species. 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It solves marker ordering problems and can also join maps (genetic or radiated hybrid) on various pedigrees: backcross, RI (ri self, ri sib), F2 intercross, phase known outbreds, haploid and diploid radiation hybrids up to now." ; sc:featureList edam:operation_2429 ; sc:name "CarthaGene 1.3 beta" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://forgemia.inra.fr/thomas.schiex/carthagene" ; biotools:primaryContact "Patrick Chabrier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2229, edam:topic_2830, edam:topic_3315 ; sc:citation ; sc:description "CARTmath is a mathematical model of CAR-T immunotherapy in preclinical models. 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It can predict an organism's uptake and secretion capabilities without requiring gap-filling, although gap-filling is also supported. Additionally, CarveMe allows the generation of microbial community models by merging single species models. The tool offers advanced features such as manual adjustment of blasting options, an orthology-based search using eggNOG-mapper (kegg-bigg branch), the ability to provide a custom media library for gap-filling, and the generation of models compatible with various SBML formats. Furthermore, CarveMe supports ensemble modeling, which helps explore how different alternative solutions can lead to diverse network structures and predict various phenotypes. During the model carving process, users can select from provided templates or create their own customized universe model to suit their specific needs." ; sc:featureList edam:operation_3217, edam:operation_3436, edam:operation_3660, edam:operation_3663 ; sc:funder "European Union's Horizon 2020" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CarveMe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "NTNU" ; sc:softwareHelp , , ; sc:softwareVersion "1.0.0", "1.1.0", "1.2.0", "1.3.0", "1.4.0 - 1.4.1", "1.5.0 - 1.5.2" ; sc:url "https://github.com/cdanielmachado/carveme" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0622, edam:topic_0654 ; sc:citation ; sc:description "Application for viewing gene expression data in a whole-genome context. It has been used to “draw” microarray data onto a set of chromosomes so that changes in DNA copy number can identify regions of chromosome loss or duplication within the genome of tumor cells (Nat Genet. 1999 Sep;23(1):41-6)." ; sc:featureList edam:operation_3501 ; sc:name "Caryoscope" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "0.4.0" ; sc:url "http://www.stanford.edu/group/sherlocklab/software.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3678 ; sc:citation "pubmed:9355862" ; sc:description "It is a software for simulating radiogenic aberrations in detail.This software simulates chromosomal rearrangements produced by ionizing radiation during the G0/G1 phase of the cell cycle. It gives a cell-by-cell record of simulated rearrangements, much as in an actual experiment." ; sc:featureList edam:operation_2423 ; sc:name "CAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://radiobiology.math.berkeley.edu/CAS/index.html" ; biotools:primaryContact "Ray Sachs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_3053 ; sc:citation "pubmed:26358729" ; sc:description "This software provides all possible RGEN targets in the given input sequence (e.g. exon), with the useful information including potential off-target numbers within 2nt mismatches and optional 3nt bulge via Cas-OFFinder, and out-of-frame scores via Microhomology-predictor." ; sc:featureList edam:operation_0231 ; sc:name "Cas-Designer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rgenome.net/cas-designer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN)." ; sc:featureList edam:operation_3938 ; sc:name "Cas-OFFinder" ; sc:url "https://github.com/snugel/cas-offinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description "Context-aware seeds (CAS) is a seeding framework for finding finding all valid mappings but uses fewer (and longer) seeds, which reduces seed frequencies and increases efficiency of seed-and-extend NGS read mappers. CAS achieves this improvement by attaching a confidence radius to each seed in the reference genome." ; sc:featureList edam:operation_3096, edam:operation_3198, edam:operation_3211 ; sc:name "CAS" ; sc:url "https://github.com/Kingsford-Group/CAS_code" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2840, edam:topic_3068, edam:topic_3314 ; sc:citation , "pmcid:PMC9199008", "pubmed:35559614" ; sc:description "CAS Common Chemistry is an open web resource that provides access to reliable chemical substance information for the scientific community." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "CAS Common Chemistry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://commonchemistry.cas.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3383 ; sc:citation , "pmcid:PMC5671565", "pubmed:28849545" ; sc:description "Cell Annotation Software was designed for neuroscience research by researchers specializing in an image processing domain." ; sc:featureList edam:operation_3443 ; sc:name "CAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://home.agh.edu.pl/~pioro/cas/" ; biotools:primaryContact "Karolina Nurzynska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3320, edam:topic_3324, edam:topic_3512 ; sc:citation , "pmcid:PMC9583055", "pubmed:36266726" ; sc:description "A database resource for the COVID-19 Alternative Splicing Atlas." ; sc:featureList edam:operation_0264, edam:operation_3800, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CASA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.splicedb.net/casa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_3678 ; sc:citation ; sc:description "Interactive survival analysis and visualization. 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In addition. It contains a Cas type predictive model used to assign each gene located in the region defined by a cassette’s boundaries a Cas label from a set of pre-defined Cas types. 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With a user input of region or gene of interest, it will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study. It also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization." ; sc:featureList edam:operation_0224, edam:operation_0484, edam:operation_3196, edam:operation_3233 ; sc:name "CaSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cistrome.dfci.harvard.edu/CaSNP/" ; biotools:primaryContact "X. Shirley Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8889671", "pubmed:35236300" ; sc:description "CASowary is a command line machine learning tool written in Python 3.6.8 for predicting the efficacy of sgRNAs for CRISPR Cas13 and other transcript targeting systems." ; sc:featureList edam:operation_3096, edam:operation_3222, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CASowary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Janga-Lab/CASowary" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3383 ; sc:citation "pubmed:12504751" ; sc:description "Image analysis tool in comet assay. It has been developed to work with either color, or gray-scale images of fluorescence-stained comets saved in TIF format. In its present version it does not control a video or CCD camera. Comets stained with silver (dark cells on white background) must be converted into negative images in order to be analysed correctly." ; sc:featureList edam:operation_3443 ; sc:name "CASP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://casplab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3524 ; sc:citation "pubmed:9239508" ; sc:description "Computerized Affected Sibling Pair Analyzer and Reporter, main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing." ; sc:featureList edam:operation_0283 ; sc:name "CASPAR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html" ; biotools:primaryContact "Richa Agarwala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , "pmcid:PMC4005600", "pubmed:24795787" ; sc:description "Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision." ; sc:featureList edam:operation_2499 ; sc:license "GPL-2.0" ; sc:name "casper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/casper.html" ; biotools:primaryContact "David Rossell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3168 ; sc:citation , "pmcid:PMC4168710", "pubmed:25252785" ; sc:description "Context-aware scheme for paired-end reads from high-throughput amplicon sequencing." ; sc:featureList edam:operation_3198 ; sc:name "CASPER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://best.snu.ac.kr/casper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC9464881", "pubmed:36147659" ; sc:description "A method to identify chromatin topological associated domains based on spatial density cluster." ; sc:featureList edam:operation_2937, edam:operation_3432, edam:operation_3435 ; sc:license "Other" ; sc:name "CASPIAN" ; sc:url "https://gitee.com/ghaiyan/caspian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_1317, edam:topic_2275, edam:topic_2828 ; sc:citation "pubmed:15215460" ; sc:description "Web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model." ; sc:featureList edam:operation_0321, edam:operation_0322, edam:operation_0477, edam:operation_3455 ; sc:name "CaspR" ; sc:url "http://igs-server.cnrs-mrs.fr/Caspr/index.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31681950" ; sc:description "An analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long noncoding RNAs." ; sc:featureList edam:operation_2422 ; sc:name "CASPR" ; sc:url "https://judithbergada.github.io/CASPR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0621, edam:topic_3474, edam:topic_3912 ; sc:citation , "pmcid:PMC8327967", "pubmed:34395100" ; sc:description "Web service for identifying Cas proteins." ; sc:featureList edam:operation_0436, edam:operation_1777, edam:operation_3096, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CASPredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation , "pmcid:PMC7575051", "pubmed:32403123" ; sc:description "CaSQ converts CellDesigner models to Boolean models encoded in SBML-Qual" ; sc:featureList edam:operation_2429, edam:operation_2476, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "CaSQ" ; sc:url "https://github.com/soli/casq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3524 ; sc:citation ; sc:description "Software package for simulating and sampling protein sequences with an explicit genotype-to-phenotype map." ; sc:featureList edam:operation_2426 ; sc:name "CASS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://liberles.cst.temple.edu/Software/CASS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_2259 ; sc:citation "pubmed:26656005" ; sc:description "cluster assignment by islands of sites, is a tool to predict secondary metabolite (SM) gene clusters around a given anchor (or backbone) gene." ; sc:featureList edam:operation_2423 ; sc:name "CASSIS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sbi.hki-jena.de/cassis/" ; biotools:primaryContact "Dr. Ekaterina Shelest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3169, edam:topic_3365 ; sc:citation ; sc:description "An integrated system that supports all steps of computational ChIP-seq data analysis and supersedes the laborious application of several single command line tools. It provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection) to various follow-up analyses." ; sc:featureList edam:operation_2429, edam:operation_2497 ; sc:name "CASSys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.zbh.uni-hamburg.de/en/research/application-oriented-bioinformatics/researchprojects/cassys.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC7953362", "pubmed:33717762" ; sc:description "CAST-HSROC is a web application for calculating the summary points of diagnostic test accuracy from the hierarchical summary Receiver Operating Characteristic model." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:name "CAST-HSROC" ; sc:url "https://youkiti.shinyapps.io/CAST-HSROC/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3169 ; sc:citation , "pubmed:35294034" ; sc:description "An application to visualize circadian and heat stress-responsive genes in plants." ; sc:featureList edam:operation_0314, edam:operation_0531, edam:operation_3925 ; sc:license "Not licensed" ; sc:name "CAST-R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nagellab.shinyapps.io/CASTR-v1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "Cell Adhesion Supervised Training and Learning Environment (CASTLE) is a series of ImageJ plugins. CASTLE combines effective techniques for phase-contrast image processing with statistical analysis and machine learning algorithms to interpret the results." ; sc:featureList edam:operation_2939, edam:operation_3443, edam:operation_3891 ; sc:license "MIT" ; sc:name "CASTLE" ; sc:url "https://gitlab.bham.ac.uk/spillf-leukocytes-image-analysis/castle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3375, edam:topic_3407 ; sc:citation ; sc:description "CASTLE (Computational Analysis of SynThetic LEthals) is a collection of synthetic lethal data for various pathogenic organisms, generated computationally. Here, you can find synthetic lethal genes and reactions for more than 70 organisms." ; sc:featureList edam:operation_0224, edam:operation_3660 ; sc:name "CASTLE" ; sc:url "https://ramanlab.github.io/CASTLE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2640, edam:topic_3324 ; sc:citation , "pmcid:PMC10311336", "pubmed:37387151" ; sc:description "Phylogenomic branch length estimation using quartets." ; sc:featureList edam:operation_0547, edam:operation_3942, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CASTLES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ytabatabaee/CASTLES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_3945 ; sc:citation , "pmcid:PMC10259028", "pubmed:37308829" ; sc:description "Systems-level sequence evolution simulator." ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_3481 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CastNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/carlosj-rr/CastNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_3293 ; sc:citation ; sc:description "Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters." ; sc:featureList edam:operation_0324 ; sc:license "GPL-2.0" ; sc:name "castor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.3" ; sc:url "https://cran.r-project.org/web/packages/castor/index.html" ; biotools:primaryContact "Stilianos Louca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:12824325", "pubmed:16844972", "pubmed:9741840", "pubmed:9741841", "pubmed:9761470" ; sc:description "Locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins." ; sc:featureList edam:operation_0320, edam:operation_0387, edam:operation_2406, edam:operation_2575 ; sc:name "CASTp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sts.bioe.uic.edu/castp/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602 ; sc:description "a tool for pathway analysis of proteomic and phosphoproteomic datasets" ; sc:featureList edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "CausalPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/PathwayAndDataAnalysis/causalpath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3444 ; sc:citation , "pubmed:36194719" ; sc:description "A Cross-Slice Attention Transformer Model for Prostate Zonal Segmentation in MRI." ; sc:name "CAT-Net" ; sc:url "https://github.com/aL3x-O-o-Hung/CAT-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC6805573", "pubmed:31640809" ; sc:description "Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs." ; sc:featureList edam:operation_0310, edam:operation_0436, edam:operation_3460 ; sc:license "MIT" ; sc:name "CAT and BAT" ; sc:softwareHelp ; sc:url "https://github.com/dutilh/CAT" ; biotools:primaryContact "Bas E. Dutilh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script", "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769 ; sc:citation , "pubmed:36314636" ; sc:description "CAT is a collection of tools designed for the construction of various chemical compounds." ; sc:featureList edam:operation_3216, edam:operation_3907 ; sc:license "LGPL-3.0" ; sc:name "CAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nlesc-nano/CAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_2885, edam:topic_3295, edam:topic_3940 ; sc:citation ; sc:description "CATA (The chromatin accessibility of cancer database) is a comprehensive Cancer ATAC-seq database that aim to provided a large number of available resources on cancer ATAC-seq datas. The database was annotated with potential functions of ATAC-Peak in the cancer." ; sc:featureList edam:operation_3196, edam:operation_3222, edam:operation_3661 ; sc:name "CATA" ; sc:url "http://bio.licpathway.net/cata/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3314, edam:topic_3318, edam:topic_3489 ; sc:citation , , "pmcid:PMC6538711", "pubmed:31138816" ; sc:description "A web-platform for sharing data and software for computational catalysis research." ; sc:featureList edam:operation_0320, edam:operation_0387 ; sc:name "Catalysis-hub.org" ; sc:url "https://www.catalysis-hub.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "Mass cytometry uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. Cytometry dATa anALYSis Tools is designed to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation." ; sc:featureList edam:operation_3214, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "CATALYST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CATALYST.html" ; biotools:primaryContact "Helena L. Crowell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0736, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:23680785" ; sc:description "Provides the ability to find structural matches to a user-specified catalytic site among all Protein Data Bank (PDB) proteins. The web server can also examine a user-specified protein to identify structural matches to a library of catalytic sites." ; sc:featureList edam:operation_0245, edam:operation_0477, edam:operation_2487, edam:operation_2575, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Catalytic Site Identification" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://catsid.llnl.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0130, edam:topic_0154, edam:topic_0176, edam:topic_3297 ; sc:citation , "pmcid:PMC9252799", "pubmed:35544315" ; sc:description "A user-friendly, web-based modelling tool to design and manipulate proteins, DNA and DNA nanostructures. State-of-the-art features from standalone tools for modelling, manipulation, and visualization of complex molecular systems" ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_0477, edam:operation_2476, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Catana" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://catana.ait.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2259, edam:topic_3474 ; sc:citation "pubmed:23650495" ; sc:description "Combining dATa Across species using Positive-Unlabeled Learning Techniques, is a supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network." ; sc:featureList edam:operation_0253 ; sc:name "Catapult" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.marcottelab.org/index.php/Catapult" ; biotools:primaryContact "Edward Marcotte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0625, edam:topic_0780, edam:topic_3407 ; sc:citation , "pmcid:PMC6986263", "pubmed:32038539" ; sc:description "CATAStrophy is a classification method for describing lifestyles/trophic characteristics of filamentous plant pathogens using carbohydrate-active enzymes (CAZymes). The name CATAStrophy is a backronym portmanteau hybrid where \"CATAS\" means CAZyme Assisted Training And Sorting." ; sc:featureList edam:operation_2939, edam:operation_3802, edam:operation_3891, edam:operation_3929 ; sc:license "BSD-3-Clause" ; sc:name "CATAStrophy" ; sc:url "https://github.com/ccdmb/catastrophy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179 ; sc:citation ; sc:description "A tool for exploring patterns in ChIP profiling data." ; sc:featureList edam:operation_0292, edam:operation_3432 ; sc:name "CATCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://catch.cmbi.ru.nl" ; biotools:primaryContact "Fiona Nielsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3056, edam:topic_3174 ; sc:citation "pubmed:21121040" ; sc:description "Estimate ecological diversity with both parametric and non-parametric estimators." ; sc:featureList edam:operation_2238, edam:operation_2423, edam:operation_3221 ; sc:name "CatchAll" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.northeastern.edu/catchall/" ; biotools:primaryContact "John Bunge" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2388 ; sc:name "TAIR accession (At gene)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2388 ; sc:name "TAIR accession (At gene)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2388 ; sc:name "TAIR accession (At gene)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2388 ; sc:name "TAIR accession (At gene)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0780 ; sc:citation , "pmcid:PMC2238931", "pubmed:17940091" ; sc:description "This database contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples)." ; sc:featureList edam:operation_0224 ; sc:name "Complete Arabidopsis transcriptome database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Unité de Recherche en Génomique Végétale" ; sc:softwareHelp ; sc:url "http://urgv.evry.inra.fr/CATdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3299, edam:topic_3316 ; sc:citation ; sc:description "A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data." ; sc:featureList edam:operation_0436, edam:operation_3096, edam:operation_3197, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CATE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/theLongLab/CATE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203 ; sc:citation ; sc:description "A collection of tools for performing categoric analysis." ; sc:featureList edam:operation_2238 ; sc:license "Artistic-2.0" ; sc:name "Category" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Category.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3547 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3047 ; sc:citation , "pmcid:PMC4010757", "pubmed:24808906" ; sc:description "Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested)." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "categoryCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/categoryCompare.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:21097779" ; sc:description "CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This classification procedure uses a combination of automated and manual techniques which include computational algorithms, empirical and statistical evidence, literature review and expert analysis." ; sc:featureList edam:operation_0303, edam:operation_0320, edam:operation_2415 ; sc:name "CATH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cathdb.info/" ; biotools:primaryContact "I. Sillitoe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3382, edam:topic_3673 ; sc:citation , "pmcid:PMC9710666", "pubmed:36699387" ; sc:description "Cluster analysis tool for healthcare-associated infections." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CATHAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cathai.fordelab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation , "pmcid:PMC6668108", "pubmed:31362714" ; sc:description "HIV drug resistance prediction with weighted categorical kernel functions | BACKGROUND:Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. Predicting drug resistance to previously unobserved variants is therefore very important for an optimum medical treatment. In this paper, we propose the use of weighted categorical kernel functions to predict drug resistance from virus sequence data. These kernel functions are very simple to implement and are able to take into account HIV data particularities, such as allele mixtures, and to weigh the different importance of each protein residue, as it is known that not all positions contribute equally to the resistance." ; sc:featureList edam:operation_3482, edam:operation_3891 ; sc:name "catkern" ; sc:url "https://bitbucket.org/elies_ramon/catkern" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2269 ; sc:citation , "pubmed:33315262" ; sc:description "CATKINAS is a Catalytic MicroKinetic Analysis Software, which is aimed for the Mechanism Auto-analysis and Catalyst Screening." ; sc:featureList edam:operation_3799, edam:operation_3927 ; sc:name "CATKINAS" ; sc:url "https://www.catkinas.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3315, edam:topic_3534 ; sc:citation , "pmcid:PMC7022172", "pubmed:31980525" ; sc:description """Considering protease-as-substrate interactions in proteolytic networks. Enzymes are catalysts in biochemical reactions that, by definition, increase rates of reactions without being altered or destroyed. However, when that enzyme is a protease, a subclass of enzymes that hydrolyze other proteins, and that protease is in a multiprotease system, protease-as-substrate dynamics must be included, challenging assumptions of enzyme inertness, shifting kinetic predictions of that system. Protease-on-protease inactivating hydrolysis can alter predicted protease concentrations used to determine pharmaceutical dosing strategies""" ; sc:featureList edam:operation_2426, edam:operation_3896, edam:operation_3927 ; sc:name "catKLS" ; sc:url "https://plattlab.shinyapps.io/catKLS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3361, edam:topic_3474 ; sc:citation , "pubmed:36462902" ; sc:description "Cross-event attention-based time-aware network for medical event prediction" ; sc:featureList edam:operation_3927 ; sc:license "Not licensed" ; sc:name "CATNet" ; sc:url "https://github.com/sherry6247/CATNet.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3336, edam:topic_3373, edam:topic_3474 ; sc:citation , "pmcid:PMC7437923", "pubmed:32764756" ; sc:description """A machine learning and network framework to discover new indications for small molecules. CATNIP = Creating A Translational Network for Indication Prediction. The CATNIP repurposing network can be searched either by specifying one or more drugs or diseases. The probability of CATNIP prediction that two drugs will share an indication is 0.95 by default, but can be changed by the user.""" ; sc:featureList edam:operation_0337, edam:operation_3927, edam:operation_3938 ; sc:license "MIT" ; sc:name "CATNIP" ; sc:url "http://www.github.com/coryandar/CATNIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC4961376", "pubmed:27459605" ; sc:description "CATO (Clone Alignment Tool) allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "CATO" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/cato-clone-alignment-tool/" ; biotools:primaryContact "Peter LaPan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "CATO is a modular software package for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging data and resting-state functional MRI data." ; sc:featureList edam:operation_2429 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dutchconnectomelab.nl/CATO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "Aan algorithm to estimate the binding propensity of protein-RNA pairs. 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This interface takes advantage of the VSM framework (https://github.com/vsmjs/) to generate customized VSM-templates for the annotation of specific causal statements. 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sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_1476, edam:format_2330 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:author , "Antonin Pavelka", "Petr Benes", "Petr Medek", "Vilem Sustr" ; sc:citation ; sc:contributor , , , , , , "Brno City Municipality", "Czech Science Foundation", "European Community", "European Regional Development Fund", "Eva Sebestova", "Grant Agency of the Czech Academy of Sciences", "Jiri Sochor", "Ministry of Education of the Czech Republic", "South Moravian Region" ; sc:description "A tool for identification and analysis of tunnels and channels in static and dynamic protein structures." ; sc:featureList edam:operation_0250 ; sc:funder "Brno City Municipality", "Czech Science Foundation", "European Community", "European Regional Development Fund", "Grant Agency of the Czech Academy of Sciences", "Ministry of Education of the Czech Republic", "South Moravian Region" ; 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biotools:primaryContact "CAVER team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1476 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_1476, edam:format_1957 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_2814 ; sc:author , , "Jan Plhak" ; sc:citation , ; sc:contributor , , , , , "Brno City Municipality", "Czech Science Foundation", "European Commission", "Ondrej Vavra" ; sc:description "Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3336 ; sc:citation ; sc:description "Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. 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As an emerging technique with steadily improving resolution, solid-state NMR spectroscopy has the unique capability in revealing the molecular structure and dynamics of insoluble complex carbohydrates. We developed and implemented CCMRD, Complex Carbohydrates Magnetic Resonance Database, a solid-state NMR database for complex carbohydrates. Currently, it holds more than 400 solid-state NMR spectra and expects rapid expansion. 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Single-cell genomics represents an ideal platform to enable the identification and comparison of normal and diseased transcriptional cell populations. We created cellHarmony, an integrated solution for the unsupervised analysis, classification, and comparison of cell types from diverse single-cell RNA-Seq datasets. cellHarmony efficiently and accurately matches single-cell transcriptomes using a community-clustering and alignment strategy to compute differences in cell-type specific gene expression over potentially dozens of cell populations" ; sc:name "cellHarmony" ; sc:softwareHelp ; sc:url "https://github.com/AltAnalyze/cellHarmony-Align" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3395 ; sc:citation , "pmcid:PMC9362878", "pubmed:35967929" ; sc:description "Cell Layers is an interactive Sankey tool for the quantitative investigation of gene expression, coexpression, biological processes, and cluster integrity across clustering resolutions." ; sc:featureList edam:operation_0313, edam:operation_2844, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cell Layers" ; sc:softwareHelp , ; sc:url "https://github.com/apblair/CellLayers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2229, edam:topic_3292, edam:topic_3407 ; sc:citation "pubmed:17038347" ; sc:description "Cell++ is a novel stochastic simulation environment which is capable of modelling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signalling." ; sc:featureList edam:operation_2426, edam:operation_3446, edam:operation_3562, edam:operation_3660 ; sc:name "Cell pp" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/cellpp/" ; biotools:primaryContact "C. Sanford" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pubmed:36161321" ; sc:description "A curated repository of cell types with multifaceted characterization." ; sc:featureList edam:operation_0314, edam:operation_3432 ; sc:license "CC-BY-3.0" ; sc:name "Cell Taxonomy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/celltaxonomy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_3326 ; sc:name "Resource metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2032 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3064 ; sc:citation ; sc:description "A method for comparing expression dynamics within and between single-cell differentiation trajectories." ; sc:featureList edam:operation_0314, edam:operation_3223, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "cellAlign" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/shenorrLab/cellAlign" ; biotools:primaryContact "Ayelet Alpert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3308 ; sc:citation , "pmcid:PMC10477937", "pubmed:37610325" ; sc:description "CellAnn is a web application for predicting cell types of single-cell clusters based on published reference datasets. CellAnn provides a comprehensive scRNA-seq reference database and users can easily find the relevant reference datasets in their analysis." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CellAnn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cellann.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2229, edam:topic_3308, edam:topic_3382 ; sc:citation ; sc:description "Cellar is a interactive single cell data annotation tool." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3501 ; sc:name "Cellar" ; sc:url "https://data.test.hubmapconsortium.org/app/cellar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation ; sc:description "RESTful Web Services for retrieving relevant biological information." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "CellBase" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "cipf.es", "http://bioinfo.cipf.es" ; sc:softwareHelp ; sc:url "http://docs.bioinfo.cipf.es/projects/cellbase/wiki" ; biotools:primaryContact "babelomics@cipf.es (Francisco García)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3489 ; sc:description "This package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated." ; sc:featureList edam:operation_0224, edam:operation_0226, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "cellbaseR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/cellbaseR.html" ; biotools:primaryContact "Mohammed OE Abdallah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0749, edam:topic_2640, edam:topic_2830 ; sc:citation , "pmcid:PMC8421219", "pubmed:34331449" ; sc:description "CellCall is a toolkit to infer intercellular communication networks and internal regulatory signals by integrating intracellular and intercellular signaling." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "CellCall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ShellyCoder/cellcall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3474, edam:topic_3940 ; sc:citation , "pmcid:PMC10070275", "pubmed:37012226" ; sc:description "Supervised cell type identification for single-cell ATAC-seq data." ; sc:featureList edam:operation_0313, edam:operation_0417, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cellcano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://marvinquiet.github.io/Cellcano/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description "CellChat is a R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data" ; sc:featureList edam:operation_0244, edam:operation_0533, edam:operation_3799 ; sc:name "CellChat" ; sc:url "https://github.com/sqjin/CellChat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_3168, edam:topic_3299 ; sc:citation , "pmcid:PMC7182211", "pubmed:32027371" ; sc:description "CellCoal simulates the somatic evolution of single-cells. CellCoal generates a coalescent genealogy for a sample of somatic cells - no recombination - obtained from a growing population, together with a another cell as outgroup, introduces mutations along this genealogy, and produces single-cell diploid genotypes (single-nuclotide variants or SNVs)." ; sc:featureList edam:operation_2426, edam:operation_3196, edam:operation_3227 ; sc:name "CellCoal" ; sc:softwareHelp ; sc:url "https://github.com/dapogon/cellcoal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315 ; sc:citation ; sc:description "The Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing one of the major hurdles with computational research. In addition, this platform allows scientists to simulate and analyze the models in real-time on the web, including the ability to simulate loss/gain of function and test what-if scenarios in real time." ; sc:featureList edam:operation_2426 ; sc:name "CellCollective" ; sc:url "https://cellcollective.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0634, edam:topic_3170 ; sc:citation , "pmcid:PMC10767892", "pubmed:37850657" ; sc:description "Atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "CellCommuNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.inbirg.com/cellcommunet/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:name "Protein name (UniProt)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_2229 ; sc:citation ; sc:description "A collection of genes and proteins involved in human and yeast cell cycle." ; sc:featureList edam:operation_0224 ; sc:name "Cell cycle database (CellCycleDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CNR-ITB" ; sc:softwareHelp ; sc:url "http://www.itb.cnr.it/cellcycle/index.html" ; biotools:primaryContact "Roberta Alfieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3489 ; sc:citation ; sc:description "A unified repository for scRNA-seq data and visual exploration." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "CellDepot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://celldepot.bxgenomics.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2640, edam:topic_2830, edam:topic_3308 ; sc:citation , "pmcid:PMC9581332", "pubmed:36275810" ; sc:description "A RShiny application and R package for the visualization and analysis of single-cell lineage tracing data." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3200 ; sc:license "CC-BY-SA-4.0" ; sc:name "CellDestiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://perie-team.shinyapps.io/CellDestiny/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC9487655", "pubmed:35998893" ; sc:description "Inferring Perturbation Responses in Temporally-Sampled Single Cell Data." ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CellDrift" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KANG-BIOINFO/CellDrift" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0208, edam:topic_2229, edam:topic_2640, edam:topic_3173 ; sc:citation , "pubmed:32437684" ; sc:description "CELLector is an R package and R Shiny application allowing researchers to select the most relevant cancer cell lines in a patient-genomic-guided fashion." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3795 ; sc:license "GPL-3.0" ; sc:name "CELLector" ; sc:softwareHelp ; sc:url "https://ot-cellector.shinyapps.io/CELLector_App/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:description """Cellenics® is an open source, cloud-based analytics tool for single cell RNA sequencing data. It allows you to explore and analyze single cell datasets without the need to develop bioinformatics skills. Cellenics® has a user-friendly interface with a clear workflow. Offers a variety of pre-loaded publication-ready plots. Cellenics® software was developed by © 2020-2022 President and Fellows of Harvard College. Biomage is an open source software company that provided services to Harvard Medical School for the design and development of Cellenics®.""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "Cellenics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://scp.biomage.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC10257576", "pubmed:37261846" ; sc:description "Scalable and interactive visual analytics app for exploring multimodal single-cell data." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cellenium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bayer-Group/cellenium" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3300, edam:topic_3304 ; sc:citation ; sc:description "CellExplorer is a graphical user interface (GUI) and standardized pipeline for exploring and characterizing single cells acquired with extracellular electrodes." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3802 ; sc:license "BSD-3-Clause" ; sc:name "CellExplorer" ; sc:softwareHelp ; sc:url "http://CellExplorer.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2330 ; sc:name "Cell line report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3277 ; sc:citation ; sc:description "This package provides functionalities for the fitting of cell population growth models on experimental OD curves." ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:license "Artistic-2.0" ; sc:name "cellGrowth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/cellGrowth.html" ; biotools:primaryContact "Julien Gagneur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3308 ; sc:citation , "pubmed:35394016" ; sc:description "An R package designed to demultiplex cell hashing data" ; sc:featureList edam:operation_0314, edam:operation_3200, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cellhashR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BimberLab/cellhashR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3523 ; sc:citation , "pmcid:PMC3036618", "pubmed:21251254" ; sc:description "This package analyzes high-throughput assays performed in microtitre plate formats. The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview of the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries." ; sc:featureList edam:operation_1812, edam:operation_2428, edam:operation_2495, edam:operation_3435 ; sc:license "Artistic-2.0" ; sc:name "cellHTS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/cellHTS2.html" ; biotools:primaryContact "Joseph Barry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3382, edam:topic_3385, edam:topic_3452, edam:topic_3500 ; sc:citation , "pmcid:PMC3531121", "pubmed:23203874" ; sc:description "This Image Library is a repository for images and movies of cells from a variety of organisms. It demonstrates cellular architecture and functions with high quality images, videos, and animations. This comprehensive and easily accessible Library is designed as a public resource first and foremost for research, and secondarily as a tool for education. The long-term goal is the construction of a library of images that will serve as primary data for research." ; sc:featureList edam:operation_3443, edam:operation_3446, edam:operation_3552, edam:operation_3553 ; sc:name "The Cell: An Image Library" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cellimagelibrary.org/" ; biotools:primaryContact "David Orloff, Manager of the Library" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154 ; sc:citation , "pmcid:PMC7929259", "pubmed:33471060" ; sc:description "Cellinker is a platform of ligand-receptor interactions for intercellular communication analysis." ; sc:featureList edam:operation_0224, edam:operation_0571, edam:operation_2421, edam:operation_2422 ; sc:name "Cellinker" ; sc:url "http://www.rna-society.org/cellinker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3572 ; sc:citation ; sc:description "A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets." ; sc:featureList edam:operation_3218 ; sc:license "GPL-2.0" ; sc:name "cellity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/cellity.html" ; biotools:primaryContact "Tomislav Ilicic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2229, edam:topic_3068, edam:topic_3170 ; sc:citation ; sc:description "CellKb Immune is a manually curated database of mammalian immune marker gene sets optimized for rapid cell type identification. CellKb Immune is a subset of the CellKb database containing immune cell types from mouse. Marker gene sets of all hematopoietic cell types are manually collected from scientific literature and annotated with cell, tissue and disease ontologies. Read more about the data collection process here." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3778 ; sc:name "CellKb Immune" ; sc:url "https://www.cellkb.com/immune" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation ; sc:description "Visualize protein-protein interaction (PPI) networks in the context of subcellular localization." ; sc:featureList edam:operation_0337, edam:operation_3553 ; sc:license "GPL-3.0" ; sc:name "CellMap" ; sc:url "https://github.com/sacdallago/cellmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC5043525", "pubmed:27687735" ; sc:description "Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. 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The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. 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New version available! Please, check our updated tutorial. Updates include:. Raw count/UMI data can be provided as input. 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This kit is mainly developed and operated by Synthetic Platform of BGI-Research, for a detailed list of authors, see authors.md. 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It's implemented in Python with a command line interface that adheres to UNIX pipeline philosophy. Chanjo leverages Sambamba to annotate coverage and completeness for a general BED-file. The output can then easily to loaded into a SQL database that enables investigation of coverage across regions and samples. 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ABC can then be used for the interactive visualization of the alignment." ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_0495, edam:operation_0496 ; sc:name "CHAOS DIALIGN WWW server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dialign.gobics.de/chaos-dialign-submission" ; biotools:primaryContact "Prof. Dr. Burkhard Morgenstern" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0659, edam:topic_0780, edam:topic_3293, edam:topic_3512 ; sc:citation , "pmcid:PMC9015123", "pubmed:35436292" ; sc:description "CHAPAO (Compressing Alignments using Hierarchical and Probabilistic Approach) is a novel reference-based technique for compressing MSA files." ; sc:featureList edam:operation_0492, edam:operation_3198, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CHAPAO" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/ashiq24/CHAPAO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053 ; sc:citation ; sc:description "Chaplin (Case-control haplotype inference package.) is a software program for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study." ; sc:featureList edam:operation_0487 ; sc:name "Chaplin" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.2.3" ; sc:url "http://genetics.emory.edu/labs/epstein/software/chaplin/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3053 ; sc:citation , "pmcid:PMC4000056", "pubmed:24650281" ; sc:description "Geometrical approach to identify differentially expressed genes." ; sc:featureList edam:operation_3223 ; sc:name "Characteristic Direction Method" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.maayanlab.net/CD/" ; biotools:primaryContact "Avi Ma'ayan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1502 ; sc:name "Amino acid index (chemical classes)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1523 ; sc:name "Protein charge plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw a protein charge plot." ; sc:featureList edam:operation_0405 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "charge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/charge.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "Identifies genomic duplications or deletions from gene expression data." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "CHARGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CHARGE.html" ; biotools:primaryContact "Benjamin Mayne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:35077535" ; sc:description "CharID (Chromatin Accessible Region Interaction Detector), a two-step model that combines neural network and ensemble learning to predict OCR-mediated loops." ; sc:featureList edam:operation_0445, edam:operation_0481, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:name "CharID" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/Yin-Shen/CharID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC3062148", "pubmed:20858772" ; sc:description "This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. 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To our knowledge, this is the first tool to de novo predict potential open chromatin regions from DNA sequence and assay data. The result of OCR (Open Chromatin Region) assay technologies such as DNase-seq and ATAC-seq represents the open state of a tissue at a given time and does not cover all the chromatin accessible information of this species. To predict the potential open regions of different tissues at different times in the whole sequence can help to understand gene transcription and regulation from a global perspective.""" ; sc:featureList edam:operation_0438, edam:operation_3216, edam:operation_3222, edam:operation_3644 ; sc:name "CharPlant" ; sc:url "https://github.com/Yin-Shen/CharPlant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0219, edam:topic_0821 ; sc:citation "pubmed:22140108" ; sc:description "Curated database of biochemically characterized proteins. The initial data set was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. 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CHARTS is a web application, and associated backened analysis pipeline, for exploring publicly available single-cell RNA-seq data from human tumors." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3436 ; sc:name "CHARTS" ; sc:url "http://charts.morgridge.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3316 ; sc:citation ; sc:description "Chaste (Cooper et al., 2020) is an open-source, general-purpose simulation package for modelling soft tissues and discrete cell populations that can be used with MPI. This tool allows using different modelling frameworks on a given problem, enabling users to select the most appropriate one for their research and to better understand the limitations of each one of them. Chaste has been used for a wide range of projects, such as intestinal (Dunn et al., 2013) or colonic crypt (Dunn et al., 2012) studies." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Chaste" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2021.1" ; sc:url "http://www.cs.ox.ac.uk/chaste/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3300, edam:topic_3315 ; sc:citation ; sc:description "The chaste_codegen module takes CellML models as input, via cellmlmanip to read and manipulate them, then uses templating to generate C++ code." ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "chaste_codegen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/chaste-codegen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC5860084", "pubmed:29036271" ; sc:description "Text mining approach to organize and evaluate scientific literature on cancer." ; sc:featureList edam:operation_0306 ; sc:name "CHAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://chat.lionproject.net/" ; biotools:primaryContact "Simon Baker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0166, edam:topic_0623, edam:topic_0736 ; sc:citation "pubmed:15980521" ; sc:description "Tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided." ; sc:featureList edam:operation_0245, edam:operation_0295, edam:operation_0448, edam:operation_0504 ; sc:name "CHC_FIND" ; sc:url "http://schubert.bio.uniroma1.it/CHC_FIND/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1106 ; sc:name "dbSNP ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1904 ; sc:name "Locus ID (EntrezGene)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3335 ; sc:citation , "pubmed:35961607" ; sc:description "A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations." ; sc:featureList edam:operation_0314, edam:operation_1812, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "CHDbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://chddb.fwgenetics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3335 ; sc:citation , "pmcid:PMC7327432", "pubmed:32608479" ; sc:description "CHDGKB (A knowledgebase of non-syndromic congenital heart disease genetic variations) is a manually curated database of genetic variations associated with non syndromic congenital heart disease. CHDGKB contains a comprehensive information of genetic variations for 370 subtypes of human congenital heart disease reported in PubMed from 1998, which would provide an exhaustive and summary of current status of non-syndromic CHD genetic research that can contribute to better interpret the human variants for illustrating NS-CHD causing variants." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3659 ; sc:name "CHDGKB" ; sc:url "http://www.sysbio.org.cn/CHDGKB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0769, edam:topic_3169, edam:topic_3179, edam:topic_3676 ; sc:citation , "pmcid:PMC9735260", "pubmed:36544470" ; sc:description "ChIP-exo Analysis Pipeline (ChEAP) that executes the one-step process, starting from trimming and aligning raw sequencing reads to visualization of ChIP-exo results." ; sc:featureList edam:operation_0238, edam:operation_0337, edam:operation_0389, edam:operation_3192, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ChEAP" ; sc:url "https://github.com/SBML-Kimlab/ChEAP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1174 ; sc:name "ChEBI ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:encodingFormat edam:format_2331 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3369 ; sc:citation ; sc:description "Dictionary of molecular entities focused on small chemical compounds. \"Molecular entity\" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms." ; sc:featureList edam:operation_0224 ; sc:name "ChEBI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI Databases" ; sc:softwareHelp , , ; sc:url "http://www.ebi.ac.uk/chebi/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1174 ; sc:name "ChEBI ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:encodingFormat edam:format_2331 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_2258 ; sc:citation ; sc:description "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. \"Molecular entity\" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." ; sc:featureList edam:operation_0224, edam:operation_2422 ; sc:name "ChEBI WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/chebi/webServices.do" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2828 ; sc:citation , "pmcid:PMC6944088", "pubmed:31921444" ; sc:description "checkCIF reports on the consistency and integrity of crystal structure determinations reported in CIF format." ; sc:featureList edam:operation_2428, edam:operation_3431, edam:operation_3454 ; sc:name "checkCIF" ; sc:url "https://checkcif.iucr.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3297 ; sc:description "A Microsoft Windows-based software application for checking biotechnology Sequence Listings for compliance with 37 Code of Federal Regulations (CFR) 1.821 – 1.825 for both ‘old rules’ (October 1990) and ‘new rules’ (July 1998)." ; sc:featureList edam:operation_0335 ; sc:name "Checker" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.4.6" ; sc:url "http://www.uspto.gov/patents-getting-started/patent-basics/types-patent-applications/utility-patent/checker-version-446" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0622, edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3572 ; sc:citation ; sc:description "CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes." ; sc:featureList edam:operation_0236, edam:operation_2238, edam:operation_2428, edam:operation_3180, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "CheckM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://ecogenomics.github.io/CheckM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2830, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:33905501" ; sc:description "CheckMyBlob is a machine learning system that detects and validates ligands in X-ray electron density maps. Upload your files or type a PDB code to try it out!." ; sc:featureList edam:operation_2428, edam:operation_3431, edam:operation_4009 ; sc:name "CheckMyBlob" ; sc:url "https://checkmyblob.bioreproducibility.org" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "Hugo Varet" ; sc:citation , "pubmed:30165585" ; sc:description "When sequencing several libraries simultaneously, the selection of compatible combinations of indexes is critical for ensuring that the sequencer will be able to decipher the short, sample-specific barcodes added to each fragment. However, researchers have few tools to help them choose optimal indexes. Here, we present checkMyIndex, an online R/Shiny application that facilitates the selection of the right indexes as a function of the experimental constraints." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "checkMyIndex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://checkmyindex.pasteur.fr" ; biotools:primaryContact "Hugo Varet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9248842", "pubmed:35775980" ; sc:description "CheckMySequence is a Python package for the automated detection of register-shift errors in cryo-EM models." ; sc:featureList edam:operation_0479, edam:operation_2428, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "checkMySequence" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/gchojnowski/checkmysequence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_2640, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc:description "CheckSumStats is an R package for the identification of errors and analytical issues in the results and metadata of genome-wide association studies (GWAS)" ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CheckSumStats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MRCIEU/CheckSumStats" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Report STOP codons and ORF statistics of a protein." ; sc:featureList edam:operation_0436 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "checktrans" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/checktrans.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes." ; sc:featureList edam:operation_0310, edam:operation_2428, edam:operation_3198 ; sc:name "CheckV" ; sc:url "http://bitbucket.org/berkeleylab/CheckV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0637, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description "CHEER is a hierarchical model, which can learn the species masking feature via deep learning classifier, for new RNA virus taxonomy classification." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3798 ; sc:name "CHEER" ; sc:url "https://github.com/KennthShang/CHEER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3382, edam:topic_3474, edam:topic_3934 ; sc:citation ; sc:description "Cheetah is a simple to use Python library to support the development of analysis workflows and real-time cybergenetic control platforms that combine microscopy imaging and environmental control. The toolkit relies on a U-Net convolutional neural network to perform cell segmentation and uses this with additional functions that can label, track and generate control signals based on this information." ; sc:featureList edam:operation_2495, edam:operation_3443, edam:operation_3553 ; sc:license "MIT" ; sc:name "Cheetah" ; sc:url "https://www.github.com/BiocomputeLab/cheetah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3520 ; sc:citation , "pubmed:34128979" ; sc:description "Web server to model protein complexes using tandem cross-linking mass spectrometry data." ; sc:featureList edam:operation_3643, edam:operation_3767, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "Cheetah-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.txms.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314 ; sc:description "Chem4Word makes it easier to insert and modify chemical information, such as labels, formulas, and 2D depictions, within Microsoft Word. Additionally, it enables the creation of inline “chemical zones,” the rendering of print-ready visual depictions of chemical structures, and the ability to store and expose chemical information in a semantically rich manner." ; sc:featureList edam:operation_0337 ; sc:name "Chem4Word 2.0.1.0" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "beta5" ; sc:url "http://chem4word.codeplex.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2258, edam:topic_3071, edam:topic_3371 ; sc:citation ; sc:description "The package provides a comprehensive collection of tools for processing files with chemical structures and associated data." ; sc:featureList edam:operation_2480 ; sc:license "GPL-3.0" ; sc:name "chemalot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/chemalot/chemalot/" ; biotools:primaryContact "Man-ling Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3343 ; sc:citation , , "pmcid:PMC5720369", "pubmed:28045544", "pubmed:33405340" ; sc:description "Chembench is a free portal that enables researchers to mine available chemical and biological data. Chembench can help researchers rationally design or select new compounds or compound libraries with significantly enhanced hit rates in screening experiments." ; sc:featureList edam:operation_3799, edam:operation_3938, edam:operation_4009 ; sc:name "Chembench" ; sc:url "https://chembench.mml.unc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2815, edam:topic_3336 ; sc:citation , "pmcid:PMC9513561", "pubmed:36164975" ; sc:description "An integrative platform to navigate the biology, structure and chemical inhibition of human proteins." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ChemBioPort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://chembioport.thesgc.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3373 ; sc:citation , "pmcid:PMC7178400", "pubmed:31913451" ; sc:description "ChemBioServer is an an advanced web server pipeline for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing." ; sc:featureList edam:operation_3432, edam:operation_3695, edam:operation_3938 ; sc:name "ChemBioServer 2.0" ; sc:url "http://chembioserver.vi-seem.eu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2646 ; sc:name "Compound ID (ChEMBL)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:encodingFormat edam:format_2331 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3369 ; sc:citation , , "pubmed:19194660" ; sc:contributor ; sc:description "Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature." ; sc:featureList edam:operation_2422 ; sc:name "ChEMBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Identifiers.org" ; sc:softwareHelp , ; sc:url "https://www.ebi.ac.uk/chembldb/" ; biotools:primaryContact "ChEMBL Help" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "BLAST search against biological molecules (e.g. mAbs) stored in ChEMBL database." ; sc:featureList edam:operation_0346 ; sc:name "ChEMBL API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/compound" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_2258 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "BLAST search against protein targets stored in ChEMBL database." ; sc:featureList edam:operation_0346 ; sc:name "ChEMBL BLAST Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/target" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3324 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "Search against small molecules stored in ChEMBL NTD database." ; sc:featureList edam:operation_0339 ; sc:name "ChEMBL NTD Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chemblntd/compound/structure_home" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "Search against small molecules stored in ChEMBL database." ; sc:featureList edam:operation_0339 ; sc:name "ChEMBL Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/compound" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2133 ; sc:name "Logical operator" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC2705353", "pubmed:19500393" ; sc:description "ChemChains is a logical network simulation and analysis suite." ; sc:featureList edam:operation_0244, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Chemchain" ; sc:softwareHelp ; sc:softwareVersion "1.20" ; sc:url "https://www.bioinformatics.org/chemchains/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "A logical network simulation and analysis suite. The driving force behind the development of this tool was to be able to study and visualize the complex dynamics of biological signal transduction networks. It considers the approach of using Boolean modeling technique. The most prominent feature of that is that it allows users to interact with the model in a continuous manner." ; sc:featureList edam:operation_2945, edam:operation_3562 ; sc:name "ChemChains" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22" ; sc:url "http://www.bioinformatics.org/chemchains/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3172, edam:topic_3292, edam:topic_3407, edam:topic_3955 ; sc:citation ; sc:description """Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks. Instructions for installation and explanation of the ChemChaste package may be found in ChemChaste_Documentation.pdf.""" ; sc:featureList edam:operation_0334, edam:operation_2426, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ChemChaste" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/OSS-Lab/ChemChaste" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0202, edam:topic_3524 ; sc:citation ; sc:description "Analyzing potential interaction effects of chemical mixtures." ; sc:featureList edam:operation_2497 ; sc:name "ChemDIS-Mixture" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cwtung.kmu.edu.tw/chemdis/mixture" ; biotools:primaryContact "Chun-Wei Tung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343, edam:topic_3520 ; sc:citation ; sc:description "Engine for metabolite annotation in mass spectrometry." ; sc:featureList edam:operation_0226, edam:operation_3214 ; sc:license "BSD-2-Clause" ; sc:name "ChemDistiller" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://bitbucket.org/iAnalytica/chemdistillerpython" ; biotools:primaryContact "Kirill A Veselkov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154 ; sc:description "Used for drawing accurate, chemically-aware structures for use in database queries, preparation of publication-quality graphics, and entry for modeling and other programs that require an electronic description of molecules and reactions." ; sc:featureList edam:operation_0224 ; sc:name "ChemDraw Ultra" ; sc:operatingSystem "Mac", "Windows" ; sc:url "http://www.cambridgesoft.com/software/overview.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2840, edam:topic_3314, edam:topic_3810 ; sc:citation , "pubmed:32402873" ; sc:description "ChemFate predicts daily chemical environmental concentrations for four classes of chemicals in nine environmental compartments (e.g., air, freshwater, coastal seawater, natural soil, urban soil, agricultural soil with and without applied biosolids). 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ChemFLuc is a public webserver which could be useful to flag FLuc inhibitors in large dataset." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3938 ; sc:name "ChemFLuc" ; sc:url "http://admet.scbdd.com/chemfluc/index/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336, edam:topic_3369, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:33201188" ; sc:description "ChemFLuo is a web-server for structure analysis and identification of fluorescent compounds. Fluorescent detection methods are indispensable tools for chemical biology. However, the undesirable effect induced by fluorescent compound interference has produced many false positive results, thus hampering the efficiency of drug development. In order to prescreen potential fluorescent interferences, we build a reliable prediction model based on a large data set. ChemFluo is a public webserver which could be useful to flag blue and green fluorescent compounds in large dataset." ; sc:featureList edam:operation_0303, edam:operation_2428, edam:operation_3938 ; sc:name "ChemFLuo" ; sc:url "http://admet.scbdd.com/chemfluo/index/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3292 ; sc:citation , "pubmed:36305829" ; sc:description "ChemFOnt (the Chemical Functional Ontology) is a hierarchical, OWL-compatible ontology describing the functions and actions of more than 341,000 biologically important chemicals." ; sc:featureList edam:operation_3435, edam:operation_3559, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "ChemFOnt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.chemfont.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2258, edam:topic_3068, edam:topic_3314 ; sc:citation , , "pmcid:PMC6896769" ; sc:description """Fast cheminformatics fingerprint search, at your fingertips. Chemfp is a set of command-line tools and a Python library for fingerprint generation and high-performance similarity search. There are two ways to try out chemfp. From the download page page you can request an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license""" ; sc:featureList edam:operation_0335, edam:operation_2421, edam:operation_3435 ; sc:name "chemfp" ; sc:url "http://www.chemfp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0625, edam:topic_3343, edam:topic_3974 ; sc:citation , "pmcid:PMC10085634", "pubmed:37014365" ; sc:description "A tool for chemical genomics analysis and phenotypic profiling." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3920 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "ChemGAPP" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/HannahMDoherty/ChemGAPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:33381797" ; sc:description "ChemGenerator is a web server for generating potential ligands for specific targets." ; sc:featureList edam:operation_3938, edam:operation_4009 ; sc:name "ChemGenerator" ; sc:url "http://smiles.tcmobile.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3332 ; sc:citation ; sc:description "A tool tuned for navigation in biologically relevant chemical space." ; sc:featureList edam:operation_2945 ; sc:name "ChemGPS-NP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://chemgps.bmc.uu.se/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:name "Molecular property (general)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation ; sc:description "Match either a single name of a chemical compound or a whole list of names against reference databases, even when the notations are different. This matching is solely done on the name (string) basis of chemical compounds without identifying the exact chemical structure of the molecule described." ; sc:featureList edam:operation_2422 ; sc:name "ChemHits" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "HITS" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://sabio.h-its.org/chemHits/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3047, edam:topic_3068, edam:topic_3369, edam:topic_3895 ; sc:citation , "pubmed:33970229" ; sc:description "ChemHub is a comprehensive database for selecting biosynthetic target molecules based on compound functions." ; sc:name "ChemHub" ; sc:url "http://www.rxnfinder.org/chemhub/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0203, edam:topic_1775, edam:topic_3474 ; sc:citation , "pubmed:36567619" ; sc:description "Grain protein function prediction based on self-attention mechanism and bidirectional LSTM." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Chemical-SA-BiLSTM" ; sc:url "https://github.com/HwaTong/Chemical-SA-BiLSTM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_3047 ; sc:citation , "pubmed:32440008" ; sc:description "The Chemical Checker (CC) is a resource that provides processed, harmonized and integrated bioactivity data on 800,000 small molecules. The CC divides data into five levels of increasing complexity, ranging from the chemical properties of compounds to their clinical outcomes. In between, it considers targets, off-targets, perturbed biological networks and several cell-based assays such as gene expression, growth inhibition and morphological profilings. In the CC, bioactivity data are expressed in a vector format, which naturally extends the notion of chemical similarity between compounds to similarities between bioactivity signatures of different kinds." ; sc:name "Chemical Checker" ; sc:url "https://chemicalchecker.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3071 ; sc:description "This service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier." ; sc:featureList edam:operation_2422 ; sc:name "NCI CADD Chemical Identifier Resolver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cactus.nci.nih.gov/chemical/structure/documentation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_0634, edam:topic_3300, edam:topic_3336 ; sc:citation , "pubmed:36268860" ; sc:description "An expert review-based public resource to empower chemical probe assessment, selection and use." ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Chemical Probes Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.chemicalprobes.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2258, edam:topic_2275, edam:topic_3343 ; sc:citation , "pmcid:PMC7268608" ; sc:description "ChemicalToolbox is a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model." ; sc:featureList edam:operation_0310, edam:operation_0482, edam:operation_2476 ; sc:name "ChemicalToolbox" ; sc:url "https://cheminformatics.usegalaxy.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3303, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC9930109", "pubmed:36728505" ; sc:description "Chemistry42 is a software platform for de novo small molecule design and optimization that integrates Artificial Intelligence (AI) techniques with computational and medicinal chemistry methodologies. Chemistry42 efficiently generates novel molecular structures with optimized properties validated in both in vitro and in vivo studies and is available through licensing or collaboration." ; sc:featureList edam:operation_0478, edam:operation_0479, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Chemistry42" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://chemistry42.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3077, edam:topic_3343, edam:topic_3373, edam:topic_3376 ; sc:citation ; sc:description "Webserver to easily browse, navigate and mine chemical space. The first version features more than 8000 approved, in development, and rejected drugs, as well as over 47 000 environmental chemicals." ; sc:featureList edam:operation_3660 ; sc:name "ChemMaps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.chemmaps.com/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0218, edam:topic_2258, edam:topic_3473 ; sc:citation "pubmed:21576229" ; sc:description "ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available." ; sc:featureList edam:operation_0360, edam:operation_2483, edam:operation_3432 ; sc:name "ChemMine Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://chemmine.ucr.edu" ; biotools:primaryContact "Thomas Girke" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_2330 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_2330 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation ; sc:description "This package provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. This package aims to make a subset of these utilities available from within R." ; sc:featureList edam:operation_0335, edam:operation_2425, edam:operation_2945, edam:operation_3429, edam:operation_3438 ; sc:name "ChemmineOB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ChemmineOB.html" ; biotools:primaryContact "Thomas Girke" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_2330 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_2330 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation , "pmcid:PMC2638865", "pubmed:18596077" ; sc:description "Cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_2421, edam:operation_2424, edam:operation_2425, edam:operation_2945, edam:operation_3429, edam:operation_3432, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ChemmineR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.26.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ChemmineR.html" ; biotools:primaryContact "Thomas Girke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:19491216" ; sc:description "A server to predict chemokines and their receptors." ; sc:featureList edam:operation_2945 ; sc:name "chemopred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/chemopred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3474, edam:topic_3678 ; sc:citation , "pmcid:PMC7161969", "pubmed:32298284" ; sc:description "ChemOS is a portable, modular and versatile software package, which supplies the structured layers indis-pensable for operating autonomous laboratories. Additionally, it enables remote control oflaboratories, provides access to distributed computing resources, and comprises state-of-the-art machine learning methods." ; sc:featureList edam:operation_3435 ; sc:license "Apache-2.0" ; sc:name "ChemOS" ; sc:url "https://github.com/aspuru-guzik-group/ChemOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0769, edam:topic_3314 ; sc:citation ; sc:description "Chemotion is a repository for chemistry research data that provides solutions for current challenges to store research data in a feasible manner, allowing the conservation of domain specific information in a machine readable format. A main advantage of the repository Chemotion is the comprehensive functionality, which offers options to collect, prepare and reuse data using discipline specific methods and data processing tools. For selected analytical data, automated procedures are implemented to facilitate the curation of the data. Chemotion provides functions to facilitate the publishing process of data and the citation of the deposited data" ; sc:featureList edam:operation_3283, edam:operation_3431, edam:operation_3946 ; sc:name "Chemotion" ; sc:url "http://chemotion-repository.net/home/welcome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2258, edam:topic_3332 ; sc:citation ; sc:description "Open Source electronic lab notebook for chemists in academia." ; sc:featureList edam:operation_0570, edam:operation_2480 ; sc:license "AGPL-3.0" ; sc:name "chemotion_ELN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ComPlat/chemotion_ELN" ; biotools:primaryContact "Stefan Bräse" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_1964 ; sc:name "Compound name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3345 ; sc:citation , "pmcid:PMC9825489", "pubmed:36200827" ; sc:description "Mapping between chemical perturbation and transcriptional response for non-cancer cells" ; sc:featureList edam:operation_2423, edam:operation_2426 ; sc:name "ChemPert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://chempert.uni.lu/" ; biotools:primaryContact "Antonio del Sol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8365825", "pubmed:34447555" ; sc:description "ChemPix: an offline, hand-drawn hydrocarbon structure recognition tool using deep learning." ; sc:featureList edam:operation_0337, edam:operation_3927, edam:operation_4009 ; sc:license "Apache-2.0" ; sc:name "ChemPix" ; sc:url "https://github.com/mtzgroup/ChemPixCH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0605, edam:topic_3314 ; sc:citation , "pmcid:PMC7955638", "pubmed:33712066" ; sc:description "ChemProps is a RESTful API enabled database for composite polymer name standardization." ; sc:featureList edam:operation_2421 ; sc:name "ChemProps" ; sc:url "https://materialsmine.org/nm#/ChemProps" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_1196 ; sc:name "Compound name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC3531079", "pubmed:23185041" ; sc:description "Ressource of annotated and predicted chemical-protein interactions." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ChemProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/ChemProt-2.0/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2275 ; sc:citation ; sc:description "This web server provides online access to realize a full workflow of building a Structure‑Activity/Property Relationship(SAR/SPR) model. It provides a browser-based pipelining which requires no programming skills." ; sc:featureList edam:operation_0322 ; sc:name "ChemSAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://chemsar.scbdd.com/" ; biotools:primaryContact "Dongsheng Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3047, edam:topic_3314, edam:topic_3473 ; sc:citation , "pmcid:PMC6907231" ; sc:description "ChemScanner, a software that can be used for the extraction of chemical information from ChemDraw binary (CDX) or ChemDraw XML-based (CDXML) files and to retrieve the ChemDraw scheme from DOC, DOCX or XML documents. This can facilitate the reuse of chemical information embedded into diverse documents used as standard storage and communication instrument in chemical sciences." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3907 ; sc:license "AGPL-3.0" ; sc:name "ChemScanner" ; sc:url "https://github.com/complat/chem_scanner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314, edam:topic_3382 ; sc:citation , "pubmed:32212690" ; sc:description "ChemSchematicResolver IS A Toolkit to Decode 2D Chemical Diagrams with Labels and R-Groups into Annotated Chemical Named Entities." ; sc:featureList edam:operation_0337, edam:operation_3280, edam:operation_3443 ; sc:license "MIT" ; sc:name "ChemSchematicResolver" ; sc:softwareHelp ; sc:url "http://www.chemschematicresolver.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3343, edam:topic_3382 ; sc:citation , "pmcid:PMC9710581", "pubmed:36700113" ; sc:description "Chemsearch is a cross-platform server application used to create, browse, and search a chemical compounds library." ; sc:featureList edam:operation_1812, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Chemsearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gem-net/chemsearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0593, edam:topic_3172, edam:topic_3371, edam:topic_3520 ; sc:citation ; sc:description "ChemSpectra is a web-based spectra editor for analytical data. This web service provides NMR/IR/MS processing for jcamp/RAW/mzML files." ; sc:featureList edam:operation_3096, edam:operation_3215, edam:operation_3629 ; sc:license "AGPL-3.0" ; sc:name "ChemSpectra" ; sc:url "https://eln.chemotion.net/chemspectra-editor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3071 ; sc:citation ; sc:description "Various search options for searching the ChemSpider database." ; sc:featureList edam:operation_2422 ; sc:name "ChemSpider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.chemspider.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3314 ; sc:description "ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads common chemical file formats using the Open Babel chemistry library. Spotlight can then index and search chemical data: molecular weights, formulas, SMILES, InChI, fingerprints, etc." ; sc:featureList edam:operation_2421 ; sc:name "ChemSpotlight" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://chemspotlight.openmolecules.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314, edam:topic_3315 ; sc:citation , "pubmed:31967474" ; sc:description "ChemStor is an open-source, automated computational system that can guarantee (mathematically verify a system is correct with respect to its specification), with regard to prescribed constraints, safe storage and disposal of chemicals used in academic, industrial, and domestic settings. ChemStor borrows concepts from formal methods - a branch of computer science capable of mathematically proving a specification or software is correct - to safely store or dispose of chemicals. If two or more chemicals can be combined in the same cabinet without forming possibly dangerous combinations of chemicals (while observing cabinet/shelf space constraints), then ChemStor determines that the storage configuration is safe." ; sc:name "ChemStor" ; sc:url "https://github.com/lilott8/BioScript" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "ChemT is an open-source software for building chemical compound libraries, based on a specific chemical template. The compound libraries generated can then be evaluated, using several Virtual Screening tools like molecular docking or QSAR modelling tools." ; sc:featureList edam:operation_0478 ; sc:name "ChemT" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "http://www.esa.ipb.pt/biochemcore/index.php/ds/c" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0218, edam:topic_0593, edam:topic_2258, edam:topic_3474 ; sc:citation ; sc:description "ChemTables is a dataset for semantic classificationon tables in chemical patents." ; sc:featureList edam:operation_0306 ; sc:license "Apache-2.0" ; sc:name "ChemTables" ; sc:url "https://github.com/zenanz/ChemTables" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_2258, edam:topic_3067, edam:topic_3292 ; sc:citation , "pmcid:PMC8991844", "pubmed:35415670" ; sc:description "A curated database of molecular tastants." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ChemTastesDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.5281/zenodo.5747393" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3047, edam:topic_3324, edam:topic_3379, edam:topic_3474 ; sc:citation , "pubmed:33822874" ; sc:description "ChemTB is a tool for identification of active molecules against Mycobacterium tuberculosis through machine learning." ; sc:featureList edam:operation_0303, edam:operation_3927, edam:operation_4009 ; sc:name "ChemTB" ; sc:url "http://cadd.zju.edu.cn/chemtb/" ; biotools:primaryContact , , "Dan Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description "ChemVox is an interactive Amazon Alexa skill that uses speech recognition to perform quantum chemistry calculations. This new application interfaces Alexa with cloud computing and returns the results through a capable device. ChemVox paves the way to making computational chemistry routinely accessible to the wider community." ; sc:name "ChemVox" ; sc:url "https://bitbucket.org/mtzcloud/chemvox_tutorial/src/master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9991053", "pubmed:36864626" ; sc:description "Improving annotation propagation on molecular networks through random walks." ; sc:featureList edam:operation_2421, edam:operation_3801, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ChemWalker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/computational-chemical-biology/ChemWalker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_3474 ; sc:description "CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions." ; sc:name "cherri" ; sc:url "https://github.com/BackofenLab/Cherri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_0602, edam:topic_0769 ; sc:citation , "pubmed:32926121" ; sc:description "CHEmical Shift Projection Analysis (CHESPA) and CHEmical Shift Covariance Analysis (CHESCA) can help reveal pathways of allosteric transitions in biological macromolecules by identifying changes in correlated Nuclear Magnetic Resonance (NMR) chemical shifts. CHESCA-SPARKY and CHESPA-SPARKY are plugins for the NMR analysis software NMRFAM-SPARKY" ; sc:featureList edam:operation_3925 ; sc:name "CHESCA-SPARKY and CHESPA-SPARKY" ; sc:url "https://sites.google.com/view/chescachespa-sparky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0593, edam:topic_3538, edam:topic_3542 ; sc:citation ; sc:description "CheSPI (Chemical shift Secondary structure Population Inference) is a tool for a simple and efficient method that provides unbiased and sensitive aggregate measures of local structure and disorder." ; sc:featureList edam:operation_0470, edam:operation_0570, edam:operation_2996, edam:operation_3904 ; sc:name "CheSPI" ; sc:url "https://st-protein.chem.au.dk/chespi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0622, edam:topic_3382, edam:topic_3673 ; sc:citation , "pubmed:33068420" ; sc:description "Chewie Nomenclature Server (chewie-NS) is a web server that allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potential confidentiality issues and the need to compare results." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3561, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "chewie-NS" ; sc:softwareHelp ; sc:url "https://github.com/B-UMMI/Chewie-NS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384 ; sc:citation , "pubmed:36288235" ; sc:description "Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays." ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CheXT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/VITA-Group/chext" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3293, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:33279606" ; sc:description "CHFinder is a tool to characterize genes coding for a key part of the jawed vertebrate adaptive immune system immunoglobulins." ; sc:featureList edam:operation_0324 ; sc:license "MIT" ; sc:name "CHfinder" ; sc:url "https://github.com/compimmuno/CHfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC7013921", "pubmed:32117445" ; sc:description "CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes." ; sc:featureList edam:operation_0306, edam:operation_3207, edam:operation_3919 ; sc:name "CHG" ; sc:url "http://www.bio-bigdata.com/CHG/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3176, edam:topic_3572, edam:topic_3656 ; sc:citation , "pmcid:PMC5224499", "pubmed:27625391" ; sc:description "Versatile and flexible pipeline for ChIA-PET data analysis." ; sc:featureList edam:operation_2478, edam:operation_3222 ; sc:name "ChIA-PET2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GuipengLi/ChIA-PET2" ; biotools:primaryContact "Guipeng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3169, edam:topic_3170, edam:topic_3179 ; sc:citation , "pmcid:PMC7439456", "pubmed:32832596" ; sc:description "ChIA-PIPE is a fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loop." ; sc:featureList edam:operation_0337, edam:operation_3222, edam:operation_3695 ; sc:name "ChIA-PIPE" ; sc:url "https://github.com/TheJacksonLaboratory/ChIA-PIPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3393 ; sc:description "Quality control pipeline for ChIP-seq data using a comprehensive set of quality control metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The framework allows assessing quality of samples with sharp or broad enrichment profiles, whereas previously proposed metrics were not taking this into account. It provides a reference compendium of quality control metrics and trained machine learning models for scoring samples." ; sc:featureList edam:operation_2428, edam:operation_3501 ; sc:license "GPL-2.0" ; sc:name "ChIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ChIC.html" ; biotools:primaryContact "Carmen Maria Livi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0602, edam:topic_2885 ; sc:citation ; sc:description "Robust detection of DNA looping interactions in Capture Hi-C data." ; sc:featureList edam:operation_3200 ; sc:name "CHiCAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://regulatorygenomicsgroup.org/chicago" ; biotools:primaryContact "Mikhail Spivakov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC4908757", "pubmed:27306882" ; sc:description "A pipeline for analysing Capture Hi-C data." ; sc:featureList edam:operation_2403 ; sc:license "Artistic-2.0" ; sc:name "Chicago" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Chicago.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_2885, edam:topic_3295 ; sc:author "Erle M. 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Orostica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0601, edam:topic_3169, edam:topic_3173, edam:topic_3940 ; sc:citation , "pmcid:PMC7658988", "pubmed:33177523" ; sc:description "ChromSCape is a user-friendly interactive Shiny/R application distributed as a Bioconductor package, that processes single-cell epigenomic data to assist the biological interpretation of chromatin landscapes within cell populations. 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Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms" ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "Cidane" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ccb.jhu.edu/software/cidane/" ; biotools:primaryContact "David Weese", "Gunnar W. Klau", "Knut Reinert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2814 ; sc:citation , "pmcid:PMC5232785", "pubmed:28076807" ; sc:description "Classification of Intrinsically Disordered Ensemble Regions." ; sc:featureList edam:operation_3092 ; sc:name "CIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pappulab.wustl.edu/CIDER/" ; biotools:primaryContact "Alex S. Holehouse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:33729787" ; sc:description "A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation." ; sc:featureList edam:operation_3646, edam:operation_3755, edam:operation_3767, edam:operation_3860 ; sc:name "CIDer-p" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dbwilburn/cider" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC8667531", "pubmed:34903266" ; sc:description "R package CIDER: Meta-Clustering for Single-Cell Data Integration and Evaluation" ; sc:featureList edam:operation_3223, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhiyhu/CIDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3305, edam:topic_3324, edam:topic_3966 ; sc:citation , "pmcid:PMC9585694", "pubmed:36271389" ; sc:description "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease." ; sc:featureList edam:operation_0416, edam:operation_3431, edam:operation_3559, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CIDO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ontobee.org/ontology/CIDO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0623, edam:topic_3293, edam:topic_3500 ; sc:citation "pubmed:21087991" ; sc:description "Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them." ; sc:featureList edam:operation_0308, edam:operation_0553, edam:operation_3208 ; sc:name "CiF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.fusariumdb.org/" ; biotools:primaryContact "David M. Geiser", "Kerry O'Donnell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC9119143", "pubmed:35051581" ; sc:description "A package for reading, writing, visualizing, and manipulating CIFTI files in R." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "ciftiTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mandymejia/ciftiTools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0637, edam:topic_3277, edam:topic_3500 ; sc:citation , "pmcid:PMC10211464", "pubmed:37221042" ; sc:description "Database and interactive platform for insect-associated trichomycete fungi." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "CIGAF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cigaf.eeb.utoronto.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3343, edam:topic_3360, edam:topic_3520 ; sc:citation , "pubmed:37469223" ; sc:description """An Ultrasensitive Chemical Isotope Labeling Assisted Pseudo-MRM Platform to Accelerate Exposomic Suspect Screening. Exposome is the future of next-generation environmental health to establish the association between environmental exposure and diseases. However, due to low concentrations of exposure chemicals, exposome has been hampered by lacking an effective analytical platform to characterize its composition. In this study, by combining the benefit of chemical isotope labeling and pseudo-multiple reaction monitoring (CIL-pseudo-MRM), we have developed one highly sensitive and high-throughput platform (CIL-ExPMRM) by isotope labeling urinary exposure biomarkers. Dansyl chloride (DnsCl), N< i>-methylphenylethylamine (MPEA), and their isotope-labeled forms were used to derivatize polar hydroxyl and carboxyl compounds, respectively ||| HOMEPAGE MISSING! ||| CORRECT NAME OF TOOL COULD ALSO BE 'MRM'""" ; sc:featureList edam:operation_3215, edam:operation_3633, edam:operation_3642 ; sc:isAccessibleForFree true ; sc:name "CIL-ExPMRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.exposomemrm.com/about" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3382 ; sc:citation , "pubmed:37598471" ; sc:description "A freely available open-source software for the analysis of mucociliary activity in respiratory cells." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3920 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Cilialyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/msdev87/Cilialyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_0780, edam:topic_2229 ; sc:citation , "pmcid:PMC10403755", "pubmed:37542408" ; sc:description "Integrated database for ciliopathy genes and ciliopathies." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CiliaMiner" ; sc:url "https://kaplanlab.shinyapps.io/ciliaminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0621, edam:topic_3063, edam:topic_3382, edam:topic_3390 ; sc:citation ; sc:description "CiliaQ is a simple, open-source ImageJ plugin for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images." ; sc:featureList edam:operation_3096, edam:operation_3443, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "CiliaQ" ; sc:url "https://github.com/hansenjn/CiliaQ" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3003 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3210 ; sc:encodingFormat edam:format_3003 ; sc:name "Genome index" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320 ; sc:author ; sc:contributor , , , , ; sc:description """This tool separates junction reads based on their linear or circular origin. Only non-ambiguous junction reads are used to compare the relative linear and circular transcript abundance. Together with the circ fraction (circ/(circ+lin)), a 95% confidence interval is provided.""" ; sc:featureList edam:operation_2441, edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "CiLiQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/OncoRNALab/CiLiQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3336, edam:topic_3376 ; sc:citation ; sc:description "Web-based tool for drug synergy analysis in small- and large-scale datasets." ; sc:featureList edam:operation_2497 ; sc:name "CImbinator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cimbinator.bioinfo.cnio.es/CombinationIndex" ; biotools:primaryContact "Miguel Vazquez", "Åsmund Flobak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3047, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC8981840", "pubmed:35379315" ; sc:description "CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds." ; sc:featureList edam:operation_0337, edam:operation_3935, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "CIME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/jku-vds-lab/cime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3295 ; sc:citation , "pmcid:PMC10332104", "pubmed:37430364" ; sc:description "CimpleG is a simple package to find single-CpG based signatures for use in classification and deconvolution." ; sc:featureList edam:operation_0417, edam:operation_0430, edam:operation_3557, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CimpleG" ; sc:url "http://costalab.github.io/CimpleG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3360, edam:topic_3474 ; sc:citation , "pubmed:31623474" ; sc:description """A speckle-tracking strain-based artificial neural network model to differentiate cardiomyopathy type. Click on the different areas to enter strain values.""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3659 ; sc:name "cimti" ; sc:url "https://cimti.usj.edu.lb/strain/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2258 ; sc:citation , "pubmed:33601989" ; sc:description "CIMtools is a ChemoInformatics Modeling tools distributive. It Include ISIDA Fragmentor python wrapper and RDtool atom-to-atom mapper python wrapper." ; sc:featureList edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "CIMtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cimm-kzn/CIMtools" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "The package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar. It calculates the chromosome instability index to quantitatively characterize genome-wide DNA copy number alterations. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses at the chromosome and cytoband level." ; sc:featureList edam:operation_3196, edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "CINdex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CINdex.html" ; biotools:primaryContact "Yuriy Gusev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pubmed:34524416" ; sc:description "Compressed indexes for fast retrieval of FASTQ files." ; sc:featureList edam:operation_2422, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CIndex" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/Hongweihuo-Lab/CIndex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2828, edam:topic_3520 ; sc:citation , "pubmed:34717419" ; sc:description "Real-time tools for analysis of dynamic diamond anvil cell experiment data." ; sc:featureList edam:operation_0337, edam:operation_3453, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Cinema Snap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cinemascience/cinema_snap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0654, edam:topic_2640, edam:topic_3068 ; sc:citation ; sc:description "An R package for chromosomal instability analysis." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CINmetrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/package=CINmetrics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3500 ; sc:citation , "pmcid:PMC9499239", "pubmed:36095011" ; sc:description "CINS combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie them." ; sc:featureList edam:operation_0276, edam:operation_0314, edam:operation_3094, edam:operation_3196, edam:operation_3891 ; sc:license "Not licensed" ; sc:name "CINS" ; sc:url "https://github.com/xiaoyeye/CINS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction." ; sc:featureList edam:operation_1781 ; sc:name "CIPHER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/c-guzman/cipher-workflow-platform" ; biotools:primaryContact "Carlos Guzman", "Iván D’Orso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308 ; sc:citation , "pubmed:32809944" ; sc:description "CIPHER-SC is the latest version of CIPHER, is a complete end-to-end prediction algorithm based on a context-aware network including single-cell data. CIPHER-SC is able to perform Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network with Single-Cell Data." ; sc:featureList edam:operation_2454 ; sc:name "CIPHER-SC" ; sc:url "http://github.com/YidingZhang117/CIPHER-SC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3518 ; sc:citation , "pmcid:PMC7227235", "pubmed:32414321" ; sc:description "Cluster Identity Predictor (CIPR) is a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments. CIPR provides a graphical user interface to quickly score gene expression profiles of unknown cell clusters against mouse or human references, or a custom dataset provided by the user. CIPR can be easily integrated into the current pipelines to facilitate scRNAseq data analysis. During the analysis of single cell RNA sequencing (scRNAseq) data, annotating the biological identity of cell clusters is an important step before downstream analyses and it remains technically challenging." ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3435, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "CIPR" ; sc:url "https://aekiz.shinyapps.io/CIPR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3307, edam:topic_3316, edam:topic_3372, edam:topic_3489 ; sc:citation , , "pmcid:PMC4362911", "pubmed:25861210" ; sc:description "Project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0499, edam:operation_0545 ; sc:name "CIPRes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phylo.org/" ; biotools:primaryContact "Mark A. Miller", "Terri Schwartz", "Wayne Pfeiffer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3384, edam:topic_3452 ; sc:citation , "pubmed:32750868" ; sc:description "CIR-Net is a method for Automatic Classification of Human Chromosome based on Inception-ResNet Architecture." ; sc:featureList edam:operation_3443 ; sc:license "MIT" ; sc:name "CIR-Net" ; sc:url "https://github.com/CloudDataLab/CIR-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0203 ; sc:citation , "pubmed:36113743" ; sc:description "A pseudo-Siamese framework for circRNA-RBP binding sites prediction integrating BiLSTM and soft attention mechanism." ; sc:featureList edam:operation_2575 ; sc:license "Not licensed" ; sc:name "circ-pSBLA" ; sc:url "https://github.com/gyj9811/circ-pSBLA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7602184", "pubmed:33066523" ; sc:description "circ2GO is a comprehensive database compiling and analyzing circular RNAs found in lung cancer cell lines providing the data in tables as well as visualizing it in transcript maps and in heatmaps. Importantly, we also provide easy-to-use online tools to find circular forms of genes associated with specific molecular functions, biological processes or cellular components or predict their targeted microRNAs. This resource will enable researchers to rapidly identify circular RNAs relevant for their specific research question." ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_2575, edam:operation_3192, edam:operation_3216 ; sc:name "circ2GO" ; sc:url "https://circ2GO.dkfz.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31373611" ; sc:description "A unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs | circMeta is a unified computational framework for circRNA analyses. circMeta mainly includes three function modules: (i) provide a comprehensive genomic feature annotation related to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements such as Alu and SINEs, competition score for forming circulation and RNA editing in back-spliced flanking introns (ii) develop a two-stage DE approach of circRNAs based on splicing junction reads (iii) develop a Bayesian hierarchical model for DE analysis of circRNAs based the ratio of circular reads to linear reads in spliced sites. circMeta mainly consists of four modules: circClass, circFeature, circJuncDE, circCLRDE | A unified computational framework for genomic feature annotation, differential expression analysis of circular RNAs" ; sc:featureList edam:operation_0441, edam:operation_2495, edam:operation_3501 ; sc:name "circMeta" ; sc:url "https://github.com/lichen-lab/circMeta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6773885", "pubmed:31608124" ; sc:description """Predicting circRNA-Disease Associations Based on Improved Collaboration Filtering Recommendation System With Multiple Data. March 31, 2018, the CircR2Disease has been updated. Circular RNAs (circRNAs) are widely expressed in diverse eukaryotic species and are characterized by covalently closed RNA loops through backsplicing events. They are known to function as miRNA sponges, regulators of alternative splicing, transcription factors and protein-coding templates for translation. To date, dysregulation of circRNAs have been associated with a group of diseases, i.e. various cancer. Here, CircR2Disease curated a database for experimentally supported associations between circRNAs and diseases, providing a platform for investigating mechanism of the disease-related circRNAs.""" ; sc:featureList edam:operation_2421, edam:operation_3435, edam:operation_3695 ; sc:name "circR2Disease" ; sc:url "http://bioinfo.snnu.edu.cn/CircR2Disease/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC6901070", "pubmed:31529043" ; sc:description "Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model | Contextual_Regression_for_CircRNA | Contextual Regression for CircRNA" ; sc:featureList edam:operation_0430, edam:operation_1812, edam:operation_3902 ; sc:license "GPL-3.0" ; sc:name "circRNA" ; sc:url "https://github.com/chl556/Contextual_Regression_for_CircRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31055837" ; sc:description "Pipeline for circRNA identification, transcript prediction, and abundance estimation." ; sc:featureList edam:operation_0264, edam:operation_0308, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "circRNAwrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/liaoscience/circRNAwrap" ; biotools:primaryContact "Yi Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0634, edam:topic_3320, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7100626", "pubmed:32219412" ; sc:description "circad is a comprehensive manually curated resource of circular RNA associated with diseases. Circular RNAs (circRNAs) are unique transcript isoforms characterised by back splicing of exon ends to form a covalently closed loop or circular conformation." ; sc:featureList edam:operation_0308, edam:operation_2421 ; sc:name "circad" ; sc:url "http://clingen.igib.res.in/circad/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_3391, edam:topic_3407 ; sc:citation , , "pmcid:PMC9252794", "pubmed:35657089" ; sc:description "Integrating circadian genomics, transcriptomics, proteomics and metabolomics." ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3436, edam:operation_3454 ; sc:name "CircadiOmics" ; sc:softwareHelp ; sc:url "http://circadiomics.ics.uci.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8513298", "pubmed:34645386" ; sc:description "A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data." ; sc:featureList edam:operation_1812, edam:operation_3198, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Circall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.meb.ki.se/sites/biostatwiki/circall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3308, edam:topic_3518, edam:topic_3678 ; sc:citation ; sc:description "Experimental Design and Power Calculation in Omics Circadian Rhythmicity Detection." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CircaPower" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/circaPower/circaPower" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7056934", "pubmed:32007626" ; sc:description "CircAST (CircRNAs with Alternative Spliced Transcripts) is a computational tool for circular RNA full-length assembly and quantification using RNA-Seq data with the back-spliced events detected by upstream circRNA identification tools, such as UROBORUS, CIRI2, or CIRCexplorer2." ; sc:featureList edam:operation_0264, edam:operation_0308, edam:operation_0310, edam:operation_3799 ; sc:name "CircAST" ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/xiaofengsong/CircAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7187532", "pubmed:32345360" ; sc:description "circAtlas is an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This database contains 1,007,087 highly reliable circRNAs, of which over 81.3% have been assembled into full-length sequences. We profile their expression pattern, conservation, and functional annotation. We describe a novel multiple conservation score, co-expression, and regulatory networks for circRNA annotation and prioritization." ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_2495 ; sc:name "circAtlas" ; sc:url "http://circatlas.biols.ac.cn/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation ; sc:description "Explore public circRNA datasets and download tools to discover circRNAs in RNA-seq data." ; sc:featureList edam:operation_2421 ; sc:name "circBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.circbase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0659, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9373444", "pubmed:35962324" ; sc:description "Python code for Predicting the Back-Splicing Sites for Circular RNA Formation by Cross-Validation and Convolutional Neural Networks" ; sc:featureList edam:operation_0253, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CircCNN" ; sc:url "https://github.com/szhh521/CircCNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC7057571", "pubmed:32138643" ; sc:description "CircDBG is an Algorithm of Circular RNA Detection by de Bruijn graph." ; sc:featureList edam:operation_0524, edam:operation_3198, edam:operation_3211 ; sc:name "CircDBG" ; sc:url "https://github.com/lxwgcool/CircDBG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC8299715", "pubmed:34296749" ; sc:description "An online transcriptome platform for human circRNA expressions in cancers." ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "circExp" ; sc:url "http://soft.bioinfo-minzhao.org/circexp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7056929", "pubmed:31904419" ; sc:description "CIRCexplorer3 is a CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression. It is a computational pipeline for Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq." ; sc:featureList edam:operation_0446, edam:operation_2495, edam:operation_3800 ; sc:name "CIRCexplorer3" ; sc:url "https://github.com/YangLab/CLEAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3175, edam:topic_3512 ; sc:citation , "pmcid:PMC9851293", "pubmed:36585787" ; sc:description "Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements. CircFusion is a new software tool to detect linear fusions and f-circRNAs from RNA-seq data, both in samples where the fusion breakpoint is known and in a discovery mode." ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_3198, edam:operation_3900 ; sc:isAccessibleForFree true ; sc:name "CircFusion" ; sc:url "https://github.com/annadalmolin/CircFusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC9513885", "pubmed:36167495" ; sc:description "An annotation algorithm circGPA that identifies prospective links between circRNAs and annotation terms. The algorithm is deterministic and based on generating polynomials." ; sc:featureList edam:operation_0463, edam:operation_2436, edam:operation_3799 ; sc:license "Not licensed" ; sc:name "circGPA" ; sc:url "https://github.com/petrrysavy/circgpa-paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3382, edam:topic_3940 ; sc:citation ; sc:description "circHiC is a Python library, built upon the widely used Matplotlib library, to display Hi-C-like data in circular strips together with the possibility to overlay genomic data (plots and heat maps). Tools are light and fast, aiming to facilitate the exploration and understanding of bacterial chromosome structuring data." ; sc:featureList edam:operation_0337 ; sc:license "BSD-3-Clause" ; sc:name "circHiC" ; sc:url "https://tree-timc.github.io/circhic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8308052", "pubmed:34356060" ; sc:description "An R Package to Explore Circular RNA Impact on Gene Expression and Pathways. The goal of circIMPACT is to detect the molecular pathways associated with the expression levels of certain circRNAs." ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_3223, edam:operation_3792, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "CircIMPACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AFBuratin/circIMPACT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_1930 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3047 ; sc:citation ; sc:description "A method for identifying genome-wide off-target cleavage sites of CRISPR–Cas9." ; sc:featureList edam:operation_0415, edam:operation_2403, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "CIRCLE-seq" ; sc:url "https://github.com/tsailabSJ/circleseq" ; biotools:primaryContact "Shengdar Q. Tsai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_2640, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC8728191", "pubmed:34792166" ; sc:description "An integrated resource and analysis platform for human eccDNAs." ; sc:featureList edam:operation_2437, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "CircleBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://circlebase.maolab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0769, edam:topic_2640, edam:topic_3940 ; sc:citation , "pmcid:PMC10202962", "pubmed:37217468" ; sc:description "Tool to identify extrachromosomal circular DNA from ATAC-Seq data." ; sc:featureList edam:operation_3096, edam:operation_3222, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "circlehunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/suda-huanglab/circlehunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7396586", "pubmed:32849764" ; sc:description "circLGB is a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing adenosine to inosine (A-to-I) deamination, A-to-I density and the internal ribosome entry site." ; sc:featureList edam:operation_0253, edam:operation_0463, edam:operation_3792 ; sc:name "circLGB" ; sc:url "https://github.com/Peppags/circLGB-circMRT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:author "Zuguang Gu" ; sc:citation , "pubmed:24930139" ; sc:description "Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3197 ; sc:name "circlize" ; sc:softwareHelp ; sc:softwareVersion "0.4.4" ; sc:url "https://CRAN.R-project.org/package=circlize" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0659 ; sc:citation ; sc:description "An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs." ; sc:featureList edam:operation_0282 ; sc:license "GPL-3.0" ; sc:name "circlncRNAnet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/smw1414/circlncRNAnet" ; biotools:primaryContact "Bertrand Chin-Ming Tan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3500, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC9074202", "pubmed:35524165" ; sc:description "CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions." ; sc:featureList edam:operation_0463, edam:operation_3216, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CircMiMi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://circmimi.genomics.sinica.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0634, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:34530446" ; sc:description "Database to integrate, analyze and visualize human disease-related circRNA transcriptome." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "circMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hpcc.siat.ac.cn/circmine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3360, edam:topic_3512, edam:topic_3794 ; sc:citation , "pubmed:32259207" ; sc:description "CircMiner is Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme. It is a sensitive and fast computational tool for detecting circular RNAs (circRNAs) from RNA-Seq data." ; sc:featureList edam:operation_3198, edam:operation_3472, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "CircMiner" ; sc:url "https://github.com/vpc-ccg/circminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC8728223", "pubmed:34850139" ; sc:description "CircNet 2.0 provides a practical and user-friendly platform on which researchers can explore novel cancer biomarkers and circRNAs related to the pathogenesis, diagnosis, and therapy of malignant and other diseases." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "CircNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://awi.cuhk.edu.cn/~CircNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC8769706", "pubmed:34698333" ; sc:description "CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3219, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CirComPara2" ; sc:url "https://github.com/egaffo/CirComPara2" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0797 ; sc:citation , ; sc:description "Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well." ; sc:featureList edam:operation_0337 ; sc:name "Circos" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://circos.ca/" ; biotools:primaryContact "Martin Krzywinski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "Circos visualization of whole-genome sequence variations stored in VCF files ." ; sc:featureList edam:operation_3208 ; sc:name "CircosVCF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ariel.ac.il/research/fbl/software" ; biotools:primaryContact "M. Salmon-Divon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3297, edam:topic_3512 ; sc:citation , "pmcid:PMC7081776", "pubmed:32211235" ; sc:description "CircParser is simple and fast pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumable host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using genome annotation file." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2421, edam:operation_2441, edam:operation_2454 ; sc:license "MIT" ; sc:name "CircParser" ; sc:url "https://github.com/SharkoTools/CircParser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3752 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC10143888", "pubmed:37111874" ; sc:description "Identification of Plant CircRNAs with a CNN-BiGRU-GLT Model." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:name "CircPCBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.circpcbl.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3500 ; sc:citation , "pubmed:33157302" ; sc:description "CircPlant is a tool for the exploration of plant circRNAs, their potential role as competing endogenous RNAs (ceRNAs), as well as function annotation. In addition to high efficiency and usability, CircPlant is confirmed to have robust high sensitivity and accuracy in detecting plant circRNAs, by analyzing simulated and real RNA-Seq datasets from Arabidopsis thaliana and Oryza sativa." ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "CircPlant" ; sc:url "http://bis.zju.edu.cn/circplant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0632, edam:topic_3170, edam:topic_3297, edam:topic_3519 ; sc:citation , "pmcid:PMC10197314", "pubmed:37208611" ; sc:description "Web-based platform for design of specific circular RNA primers." ; sc:featureList edam:operation_0308, edam:operation_0346, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "CircPrime" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://circprime.elgene.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3169, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC9580875", "pubmed:36304313" ; sc:description "Circr is a computational tool for the prediction of miRNA:circRNA associations. 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This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis. The pipeline used by circRNAprofiler is highly automated and customizable. Furthermore, circRNAprofiler includes additional functions for data visualization which facilitate the interpretation of the results." ; sc:featureList edam:operation_0463, edam:operation_3661, edam:operation_3792 ; sc:name "circRNAprofiler" ; sc:url "https://github.com/Aufiero/circRNAprofiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3308, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7798340", "pubmed:33430880" ; sc:description "A database for different circRNAs found in fluids." ; sc:featureList edam:operation_0315 ; sc:name "circRNAs" ; sc:url "https://mulongdu.shinyapps.io/circrnas_in_fluids/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation , "pubmed:32539144" ; sc:description "CIRCScan is machine learning framework used for predicting circRNAs expression in a cell/tissue specific manner by machine learning based on epigenetic features." ; sc:featureList edam:operation_0264, edam:operation_3435, edam:operation_3463 ; sc:license "GPL-2.0" ; sc:name "CIRCScan" ; sc:url "https://github.com/johnlcd/CIRCScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description "Software for computational circRNA analyses." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "circtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dieterich-lab/circtools" ; biotools:primaryContact "Christoph Dieterich", "Tobias Jakobi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "Fast simulation of Gaussian random fields via the Fast Fourier Transform" ; sc:featureList edam:operation_0244, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "Circulant Embedding method for generating stationary Gaussian field" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/38880-circulant-embedding-method-for-generating-stationary-gaussian-field" ; biotools:primaryContact "Zdravko Botev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3304 ; sc:description "Compute descriptive and inferential statistics for circular or directional data." ; sc:featureList edam:operation_0578 ; sc:isAccessibleForFree true ; sc:name "Circular Statistics Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.21.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/10676-circular-statistics-toolbox-directional-statistics" ; biotools:primaryContact "Philipp Berens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3511 ; sc:citation , "pmcid:PMC5440937", "pubmed:28532394" ; sc:description "Web application for creating circular sequence logos for DNA (or RNA) motifs. 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They could play as sponges for regulating microRNAs and RNA binding proteins. 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It is a protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors. 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "CISA has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools." ; sc:featureList edam:operation_0310 ; sc:name "CISA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20140304" ; sc:url "http://sb.nhri.org.tw/CISA/en/CISA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_0780, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC9434332", "pubmed:36061801" ; sc:description "CisCross web service that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana gene" ; sc:featureList edam:operation_0445, edam:operation_3215, edam:operation_3222, edam:operation_3501 ; sc:license "Not licensed" ; sc:name "CisCross" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://plamorph.sysbio.ru/ciscross/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3169, edam:topic_3179 ; sc:citation "pubmed:18978777" ; sc:description "An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis" ; sc:featureList edam:operation_0239, edam:operation_2238, edam:operation_2422 ; sc:name "CisGenome" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm" ; biotools:primaryContact "Admin", "Hongkai Ji", "Wing Hung Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3511 ; sc:citation , "pmcid:PMC4182448", "pubmed:25268582" ; sc:description "Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining." ; sc:featureList edam:operation_0438 ; sc:name "CisMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.ugr.es:9000/cisminer" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:15980500" ; sc:description "CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions." ; 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sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0749, edam:topic_3473 ; sc:citation "pubmed:16381958" ; sc:description "cisRED is a database system for genome-scale computational discovery of regulatory elements." ; sc:featureList edam:operation_0238, edam:operation_0438 ; sc:name "cisRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cisred.org/" ; biotools:primaryContact "Questions or comments" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:19995462" ; sc:description "Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2238 ; sc:name "CisRegTest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.moseslab.csb.utoronto.ca/alan/cis_reg_test.html" ; biotools:primaryContact "Alan Moses" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "CIST (Confidence Intervals for SAGE Tags )is a Windows program for the analysis of gene expression data generated using SAGE (Serial Analysis of Gene Expression)." ; sc:featureList edam:operation_2495 ; sc:name "CIST" ; sc:operatingSystem "Windows" ; sc:url "http://www.marksgeneticsoftware.net/CIST.HTM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1710 ; sc:encodingFormat edam:format_3547 ; sc:name "Structure image" ] ; 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sc:softwareVersion "4.010.83648" ; sc:url "https://bio.tools/clcbio_genomics_workbench" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_0659, edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3673 ; sc:citation "pubmed:19181860" ; sc:description "De novo and reference assembly SNP and small indel detection and annotation." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_0484, edam:operation_0524, edam:operation_0531, edam:operation_3180, edam:operation_3186, edam:operation_3198, edam:operation_3237, edam:operation_3662 ; sc:name "CLC Main Workbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.qiagenbioinformatics.com/products/clc-main-workbench/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "CLEAN is a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. 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Liu", "Sarah E. Calvo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0166, edam:topic_0736, edam:topic_1317 ; sc:citation "pubmed:21602266" ; sc:description "CLICK web server is a topology independent method of comparison of biomolecular 3D structures." ; sc:featureList edam:operation_2483, edam:operation_2487, edam:operation_2518 ; sc:name "CLICK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mspc.bii.a-star.edu.sg/click" ; biotools:primaryContact "Click Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_2229, edam:topic_3172, edam:topic_3382 ; sc:citation , "pubmed:33288959" ; sc:description "Click-ExM is a tool, which integrates click labeling into Expansion microscopy (ExM) to enable a ‘one-stop-shop’ method for nanoscale imaging of various types of biomolecule. By click labeling with biotin and staining with fluorescently labeled streptavidin, a large range of biomolecules can be imaged by the standard ExM procedure normally used for proteins." ; sc:featureList edam:operation_3435, edam:operation_3552, edam:operation_3715 ; sc:name "click-ExM" ; sc:url "https://github.com/Yujie-S/Click-ExM_data_process_and_example" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121, edam:topic_0209, edam:topic_2275, edam:topic_3318 ; sc:description "Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc." ; sc:featureList edam:operation_0478 ; sc:name "Click2Drug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.click2drug.org/" ; biotools:primaryContact "Vincent Zoete" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3383, edam:topic_3385, edam:topic_3474 ; sc:citation ; sc:description "CLIJx-Assistant is an intuitive user interface for building custom GPU-accelerated image processing workflows using CLIJ2 in Fiji. It visualizes workflows as image date flow graphs while building them. It suggests what to do next and generates scripts and human readable protocols to facilitate reproducible bio-image analysis." ; sc:featureList edam:operation_2409, edam:operation_3443, edam:operation_3799 ; sc:name "CLIJ-assistant" ; sc:url "https://clij.github.io/assistant/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2317 ; sc:name "Cell line name (exact)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2318 ; sc:name "Cell line name (truncated)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2320 ; sc:name "Cell line name (assonant)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2319 ; sc:name "Cell line name (no punctuation)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2331 ; sc:name "Cell line report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2331 ; sc:name "Cell line report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2331 ; sc:name "Cell line report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0963 ; sc:encodingFormat edam:format_2331 ; sc:name "Cell line report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation ; sc:description "Cell line integrated molecular authentication." ; sc:featureList edam:operation_0224 ; sc:name "CLIMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "IRCSS AOU San Martino IST" ; sc:softwareHelp ; sc:url "http://bioinformatics.hsanmartino.it/clima/" ; biotools:primaryContact "Paolo Romano" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1691 ; sc:name "Email address" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2892 ; sc:name "Cell type name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3340, edam:topic_3571 ; sc:author "Paolo Romano" ; sc:citation , "pmcid:PMC2686526", "pubmed:18927105" ; sc:contributor "Ottavia Aresu", "Paola Visconti" ; sc:description "Cell Line Integrated Molecular Authentication database and Identification tool. It represents a reference for validated molecular authentication of human cell lines independently from the platforms used." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "CLIMA 2" ; sc:operatingSystem "Linux" ; sc:provider "USMI" ; sc:softwareHelp ; sc:url "http://bioinformatics.hsanmartino.it/clima2/" ; biotools:primaryContact , "Barbara Parodi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0769 ; sc:citation , "pubmed:32629294" ; sc:description "CLIN-IK-LINKS is a web-based platform that enables users to create, modify and delete mappings as well as to define and execute workflows. The CLIN-IK-LINKS platform allows the composition and execution of clinical data transformation workflows to convert EHR data into EHR and/or semantic web standards." ; sc:name "CLIN-IK-LINKS" ; sc:url "http://keg.act.uji.es/demoCLINIKLINKS/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3337, edam:topic_3517, edam:topic_3676 ; sc:citation , "pmcid:PMC9590128", "pubmed:36274122" ; sc:description "CLIN_SKAT is a package within the R programming language to (i) first extract clinically relevant variants (rare and common), followed by (ii) gene-based association analysis by grouping the selected variants." ; sc:featureList edam:operation_0487, edam:operation_2436, edam:operation_3791, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "CLIN_SKAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ShihChingYu/CLIN_SKAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_0769, edam:topic_3050, edam:topic_3056 ; sc:citation , "pmcid:PMC8520269", "pubmed:34656096" ; sc:description "ClineHelpR is an R package for genomic cline outlier detection and visualization. ClineHelpR allows you to plot BGC (Bayesian Genomic Cline) output." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3799, edam:operation_3946 ; sc:license "GPL-3.0" ; sc:name "ClineHelpR" ; sc:softwareHelp ; sc:url "https://github.com/btmartin721/ClineHelpR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885, edam:topic_3050, edam:topic_3168 ; sc:citation ; sc:description "ClineHelpR is a R package that allows you to plot BGC (Bayesian Genomic Cline) output. After we ran BGC, we realized it wasn't easy to plot the BGC results, so we put together this package in the process of figuring it out." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196, edam:operation_3216, edam:operation_3436 ; sc:name "ClinePlotR" ; sc:url "http://github.com/btmartin721/ClinePlotR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3794 ; sc:citation , "pmcid:PMC7077056", "pubmed:32211391" ; sc:description """Candidate Cancer-Related lncRNA Prioritization via Integrating Multiple Biological Networks. Identification and characterization of lncRNAs in cancer with a view to their application in improving diagnosis and therapy remains a major challenge that requires new and innovative approaches. We have developed an integrative framework termed "CLING", aimed to prioritize candidate cancer-related lncRNAs based on their associations with known cancer lncRNAs. CLING focuses on joint optimization and prioritization of all candidates for each cancer type by integrating lncRNA topological properties and multiple lncRNA-centric networks. Validation analyses revealed that CLING is more effective than prioritization based on a single lncRNA network. Reliable AUC (Area Under Curve) scores were obtained across 10 cancer types, ranging from 0.85 to 0.94. Several novel lncRNAs predicted in the top 10 candidates for various cancer types have been confirmed by recent biological experiments""" ; sc:featureList edam:operation_2436, edam:operation_3927 ; sc:name "CLING" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/cling/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_3053, edam:topic_3577 ; sc:citation ; sc:description "ClinGen Variant Curation Interface is a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines." ; sc:featureList edam:operation_0224, edam:operation_3225 ; sc:name "ClinGen Variant Curation Interface" ; sc:url "https://curation.clinicalgenome.org" ; biotools:primaryContact "Helio Costa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC5228115", "pubmed:28081714" ; sc:description "The tool enables to assess the pathogenity of Mendelian germline sequence variants." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "OSL-3.0" ; sc:name "ClinGen Pathogenicity Calculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://calculator.clinicalgenome.org/site/cg-calculator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC8415107", "pubmed:34483871" ; sc:description """An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies. Clinica is command-line driven and written in Python. It uses the Nipype system for pipelining and combines widely-used software packages for neuroimaging data analysis (ANTs, FreeSurfer, FSL, MRtrix, PETPVC, SPM), machine learning (Scikit-learn) and the BIDS standard for data organization.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Clinica" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "http://www.clinica.run" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3421, edam:topic_3474, edam:topic_3794 ; sc:citation , "pubmed:36990584" ; sc:description "Trajectory forecasting of clinical events using Transformer and Generative Adversarial Networks." ; sc:featureList edam:operation_3891, edam:operation_3927, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "Clinical-GAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vigi30/Clinical-GAN" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:31437913" ; sc:description "Recurrent Deep Network Models for Clinical NLP Tasks | Sentence detection for clinical notes | Training and evaluation expects .labels/.txt file pairs where .labels is a file with lines of tokens in space separated format as shown below, and .txt is the plain text of the document | [segment] [start index] [end index] [tag] [is_identifier] [token text]" ; sc:license "Apache-2.0" ; sc:name "Clinical-sentences" ; sc:url "https://github.com/NLPIE/clinical-sentences" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3379, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC9846675", "pubmed:36451266" ; sc:description "Clinical-Longformer is a clinical knowledge enriched version of Longformer that was further pre-trained using MIMIC-III clinical notes." ; sc:featureList edam:operation_3096, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Clinical-Longformer" ; sc:url "https://github.com/luoyuanlab/Clinical-Longformer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3293, edam:topic_3379 ; sc:citation , "pmcid:PMC5324660", "pubmed:28008688" ; sc:description "Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification." ; sc:featureList edam:operation_2421 ; sc:name "Clinical NGS DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nishio470.wixsite.com/clinical-ngs-db" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3558 ; sc:name "Clinical trial report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3077 ; sc:citation ; sc:description "Easy access to results of publications and genetic or drug information in other databases that are relevant to a clinical trials." ; sc:featureList edam:operation_2422 ; sc:name "Clinical Trials Information Mediator" ; sc:provider "UDUS" ; sc:url "http://hhu3.at.xencon.de/ctim" ; biotools:primaryContact "Benjamin Braasch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3374, edam:topic_3379 ; sc:citation , "pmcid:PMC5359993", "pubmed:28400996" ; sc:description "Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis." ; sc:featureList edam:operation_2423 ; sc:license "GPL-3.0" ; sc:name "ClinicalLaboratory" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ClinicalLaboratory/Clinical-Laboratory" ; biotools:primaryContact "Christopher Naugler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description """Automatic generation of gene cluster comparison figures. Gene cluster comparison figure generator. A d3 chart for generating gene cluster comparison figures. clinker is a pipeline for easily generating publication-quality gene cluster comparison figures. Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file. clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.""" ; sc:featureList edam:operation_0291, edam:operation_0566, edam:operation_2938 ; sc:license "MIT" ; sc:name "clinker" ; sc:url "http://github.com/gamcil/clinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3379, edam:topic_3676 ; sc:citation , "pmcid:PMC4558641", "pubmed:26338694" ; sc:description "Tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories." ; sc:featureList edam:operation_3197, edam:operation_3359 ; sc:name "ClinLabGeneticist" ; sc:operatingSystem "Windows" ; sc:url "http://rongchenlab.org/software/clinlabgeneticist/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080 ; sc:description """The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus. The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result. Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.""" ; sc:featureList edam:operation_2478 ; sc:name "clinod" ; sc:url "https://www.compbio.dundee.ac.uk/www-nod/cli_help.jsp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1063 ; sc:encodingFormat edam:format_2330, edam:format_3016 ; sc:name "Sequence identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3063 ; sc:citation ; sc:description "Takes variants as input and queries NCBI eutilities to generate ClinVar Variation Report scoring metrics. The overall goal is to generate annotations of use for given batches of variants to inform clinical interpretation. The metrics include: Clinotator Raw Score, Average Clinical Assertion Age, Clinotator Predicted Significance and eclassification Recommendation." ; sc:featureList edam:operation_0226, edam:operation_0338, edam:operation_3225 ; sc:license "GPL-3.0" ; sc:name "Clinotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rbutleriii/Clinotator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3393 ; sc:citation , "pmcid:PMC4735967", "pubmed:26830926" ; sc:description "An integrated and user-friendly pipeline for quality control, filtering and trimming of Sanger and NGS sequencing data for hundred to thousands of samples/patients in a single run in clinical research." ; sc:featureList edam:operation_3218 ; sc:name "ClinQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/clinqc/" ; biotools:primaryContact "Ram Vinay Pandey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3325, edam:topic_3518, edam:topic_3673, edam:topic_3958 ; sc:citation , "pmcid:PMC7908648", "pubmed:33632298" ; sc:description "ClinSV is a tool for clinical grade structural and copy number variant detection from whole genome sequencing data." ; sc:featureList edam:operation_0492, edam:operation_3218, edam:operation_3226, edam:operation_3227, edam:operation_3228, edam:operation_3961 ; sc:name "ClinSV" ; sc:url "https://github.com/KCCG/ClinSV" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3996 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Python package for the analysis of trajectories in clinical data" ; sc:featureList edam:operation_0244, edam:operation_3890 ; sc:license "LGPL-2.1" ; sc:name "ClinTrajAn" ; sc:url "https://github.com/auranic/ClinTrajan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2815, edam:topic_3063, edam:topic_3325 ; sc:citation , , "pmcid:PMC3965032", "pmcid:PMC5753237", "pubmed:24234437", "pubmed:29165669" ; sc:description "A freely accessible, public archive of reports of relationships among medically important variants and phenotypes hosted by the NCBI. It integrates and cross-references data from multiple databases at NCBI. In addition to dbSNP and dbVar, it depends on MedGen to represent phenotype, Gene to represent genes, and on human RefSeqs to represent the location of sequence variation. Each record represents the submitter, the variation and the phenotype." ; sc:featureList edam:operation_0224, edam:operation_3197, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "ClinVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/clinvar/" ; biotools:primaryContact "Donna R. Maglott" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3168, edam:topic_3678, edam:topic_3794 ; sc:citation , , "pmcid:PMC3125793", "pmcid:PMC3458526", "pubmed:21665923", "pubmed:22641856" ; sc:description "CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics." ; sc:featureList edam:operation_0253, edam:operation_2238, edam:operation_3092, edam:operation_3202 ; sc:name "CLIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://clip.med.yale.edu/selection" ; biotools:primaryContact "Mohamed Uduman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3673, edam:topic_3676, edam:topic_3794 ; sc:citation ; sc:description "CliP is a tool for subclonal architecture reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model." ; sc:featureList edam:operation_0323, edam:operation_3196, edam:operation_3432 ; sc:license "AGPL-3.0" ; sc:name "CliP" ; sc:url "https://github.com/wwylab/CliP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "A new method and implementation named ClipCrop for detecting SVs with single-base resolution" ; sc:name "ClipCrop" ; sc:softwareHelp ; sc:url "https://github.com/shinout/clipcrop" ; biotools:primaryContact "Masao Nagasaki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations." ; sc:featureList edam:operation_2495, edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "clippda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/clippda.html" ; biotools:primaryContact "Stephen Nyangoma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC3592432", "pubmed:23002139" ; sc:description "This tool is for topological gene set analysis. It implements a two-step empirical approach based on the exploitation of graph decomposition into a junction tree to reconstruct the most relevant signal path." ; sc:featureList edam:operation_2497 ; sc:license "AGPL-3.0" ; sc:name "clipper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.6.2" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/clipper.html" ; biotools:primaryContact "Chiara Romualdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3169, edam:topic_3170, edam:topic_3520 ; sc:citation ; sc:description """p-value-free FDR control on high-throughput data from two conditions. 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It can also optionally plot:." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "clipplotr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ulelab/clipplotr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_0769, edam:topic_3169, edam:topic_3794 ; sc:citation , "pmcid:PMC10565428", "pubmed:37829674" ; sc:description """Nextflow pipeline for comprehensive CLIP data analysis. CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core clipseq" ; sc:url "https://nf-co.re/clipseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0749, edam:topic_3452, edam:topic_3520 ; sc:citation , "pubmed:33650866" ; sc:description "An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry." ; sc:featureList edam:operation_0366, edam:operation_0417, edam:operation_3629, edam:operation_3755, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "ClipsMS" ; sc:url "https://github.com/loolab2020/ClipsMS-Version-1.0.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC7850140", "pubmed:33554118" ; sc:description "ClipSV (Structural variation detection with clipped reads) is a tool for improving structural variation detection by read extension, spliced alignment and tree-based decision rules. 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The functional annotation could be also applied to short reads resulting from other type of experiments. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575, edam:operation_3222 ; sc:name "CLIPZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.clipz.unibas.ch" ; biotools:primaryContact "Mihaela Zavolan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0623, edam:topic_0820, edam:topic_2229, edam:topic_3293 ; sc:citation , "pmcid:PMC8893610", "pubmed:35239724" ; sc:description "“Cliquely” is a tool that discovers protein-protein interaction networks by identifying proteins that are functionally linked to each other." ; sc:featureList edam:operation_3094, edam:operation_3432, edam:operation_3900 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Cliquely" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/NoamAndRoy/Cliquely" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_0769, edam:topic_0821, edam:topic_3325, edam:topic_3520 ; sc:citation , "pmcid:PMC7423013", "pubmed:32802993" ; sc:description """A Comparative Effectiveness Study of Newborn Screening Methods for Four Lysosomal Storage Disorders. CLIR - Collaborative Laboratory Integrated Reports.""" ; sc:featureList edam:operation_3196, edam:operation_3767, edam:operation_3920 ; sc:name "CLIR" ; sc:url "https://clir.mayo.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:description "this work is to segment the cytoplasm and the nucleus of the CLL microscopic blood images" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Chronic Lemphocytic Leukemia Cell Segmentation Using Watershed and optimal Thresholding" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/39839-chronic-lemphocytic-leukemia-cell-segmentation-using-watershed-and-optimal-thresholding" ; biotools:primaryContact "Emad Mohammed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2269, edam:topic_2814 ; sc:citation , "pmcid:PMC6821021", "pubmed:31664895" ; sc:description """Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. Improving residue-residue contacts prediction. Welcome to use clmDCA for protein contact prediction. COLORS is more effcient than PSICOV, mfDCA and plmDCA.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0392, edam:operation_0474 ; sc:name "clmDCA" ; sc:url "http://protein.ict.ac.cn/clmDCA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "Contrastive Learning framework for Metagenome Binning (CLMB) is a framework for metagenomic binning. The basic idea of the CLMB module is that, since the noise of real dataset is hard to calculate, we add simulated noise to the data and force the training to be robustto them. By effectively tacking the noise in the metagenomics data using the contrastive deep learning framework, it is possible to group pairs of contigs that originate from the same type of bacterial together while dividing contigs from different species to different bins." ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3798, edam:operation_3935 ; sc:license "MIT" ; sc:name "CLMB" ; sc:url "https://github.com/zpf0117b/CLMB/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3386 ; sc:citation , "pmcid:PMC7351245", "pubmed:32655332" ; sc:description """An R Package for Linear Mixed Effects Models under Inequality Constraints. The R package CLME implements a linear mixed effects model where the regression coefficients are subject to linear order constraints. Inference is based on bootstrap methodology. Constrained Inference for Linear Mixed Effects Models. Estimation and inference for linear models where some or all of the fixed-effects coefficients are subject to order restrictions. This package uses the robust residual bootstrap methodology for inference, and can handle some structure in the residual variance matrix.""" ; sc:featureList edam:operation_3435, edam:operation_3658, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "CLME" ; sc:url "https://CRAN.R-project.org/package=CLME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0634 ; sc:citation , "pubmed:35997565" ; sc:description "A deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types." ; sc:featureList edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CLNN-loop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hwclnn.sdu.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3360, edam:topic_3678 ; sc:citation ; sc:description "clogitRV is tool for conditional logistic regression with a robust variance estimator." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "clogitRV" ; sc:url "https://github.com/sampsonj74/clogitRV" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3168, edam:topic_3360 ; sc:citation , "pmcid:PMC4091710", "pubmed:25010360" ; sc:description "This tool fits binomial distributions to counts obtained from NGS data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor." ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "Clomial" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Clomial.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0084, edam:topic_0194 ; sc:citation ; sc:description "ClonalFrameML is a maximum likelihood implementation of the Bayesian software ClonalFrame which was previously described by Didelot and Falush (2007). The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues" ; sc:featureList edam:operation_0539, edam:operation_2403, edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "ClonalFrameML" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/xavierdidelot/ClonalFrameML" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc:description "Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles." ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "Clonality" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Clonality.html" ; biotools:primaryContact "Irina Ostrovnaya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "ClonalOrigin is a tool for recombination detection in bacteria. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry." ; sc:featureList edam:operation_0451, edam:operation_2423 ; sc:name "ClonalOrigin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://code.google.com/p/clonalorigin/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2830, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC9972711", "pubmed:36849917" ; sc:description "Reconstructing the evolutionary history of a B cell lineage with minimum spanning tree and genotype abundances." ; sc:featureList edam:operation_0545, edam:operation_3192, edam:operation_3196, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ClonalTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/julibinho/ClonalTree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2640, edam:topic_3293 ; sc:citation ; sc:description "Examining the Spatial Clonal Architecture of Tumors." ; sc:featureList edam:operation_0247, edam:operation_0567, edam:operation_3478 ; sc:name "ClonArch" ; sc:url "https://github.com/elkebir-group/ClonArch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0749, edam:topic_3341, edam:topic_3382 ; sc:citation , "pubmed:32821900" ; sc:description """Automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. CLoNe - Clustering based on local density neighborhoods. CLoNe is a clustering algorithm with highly general applicability. Based on the Density Peaks algorithm from Rodriguez and Laio (Science, 2014), it improves on it by requiring a single parameter, 'pdc', that is intuitive and easy to use. 'pdc' can be incremeted if there are too many clusters, and decremented if there are not enough. Integer values between 1 and 10 are usually enough, with many values leading to the same results in most cases.""" ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_3432, edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "CLoNe" ; sc:url "http://www.epfl.ch/labs/lbm/resources" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102 ; sc:citation ; sc:description "Clone Mapper is an online suite of tools specifically adapted to the analysis pipeline typical for RNAi experiments with C. elegans." ; sc:featureList edam:operation_2429, edam:operation_2945 ; sc:name "Clone Mapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.lif.univ-mrs.fr/RNAiMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0804, edam:topic_3168 ; sc:citation , "pmcid:PMC5346239", "pubmed:28284194" ; sc:description "GUI for the sub-tasks of processing raw NGS data by wrapping available implementations of various algorithms." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "ClonoCalc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/ClonoSuite/clonocalc-plot" ; biotools:primaryContact "Anke Fähnrich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2830, edam:topic_3168 ; sc:citation , "pubmed:33325481" ; sc:description """a tool for identifying homologous immunoglobulin and T cell receptor sequences in large databases. ClonoMatch is an open source full-stack web service for an immunoglobulin Clonotype matching database. There are multiple steps for setting up ClonoMatch on your own system and it is recommended that the instructions for each step be read thoroughly before beginning. If you are familiar with the technologies involved these instructions will probably be straight forward, but there are a couple of steps that are custom to ClonoMatch and essential to getting the app working. ClonoMatch is webservice that allows users to input V3J clonotypes to search for similar B cell or T cell receptor sequences derived from adaptive immune repertoire sequencing (AIRR-seq). Single Clonotype Search Search Multiple Clonotypes From File.""" ; sc:featureList edam:operation_2421, edam:operation_3436, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "ClonoMatch" ; sc:url "https://github.com/crowelab/clonomatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804 ; sc:citation , "pubmed:23303508" ; sc:description "The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries." ; sc:featureList edam:operation_2403 ; sc:name "clonotypeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/clonotypeR.html" ; biotools:primaryContact "Charles Plessy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3315 ; sc:citation , "pmcid:PMC8754654", "pubmed:34928392" ; sc:description "cLoops2: full stack analysis tool for chromatin interactions." ; sc:featureList edam:operation_2939, edam:operation_3436, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "cLoops2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KejiZhaoLab/cLoops2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3384 ; sc:citation ; sc:description "A framework for closed-loop neurofeedback for real-time EEG decoding." ; sc:featureList edam:operation_3799 ; sc:name "ClosedLoop" ; sc:url "https://github.com/gretatuckute/ClosedLoop/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3334, edam:topic_3360, edam:topic_3384, edam:topic_3419 ; sc:citation ; sc:description """A platform for closed-loop intracranial stimulation in humans. Targeted interrogation of brain networks through invasive brain stimulation has become an increasingly important research tool as well as a therapeutic modality. The majority of work with this emerging capability has been focused on open-loop approaches. Closed-loop techniques, however, could improve neuromodulatory therapies and research investigations by optimizing stimulation approaches using neurally informed, personalized targets. Specifically, closed-loop direct electrical stimulation tests in humans performed during semi-chronic electrode implantation in patients with refractory epilepsy could help deepen our understanding of basic research questions as well as the mechanisms and treatment solutions for many neuropsychiatric diseases. However, implementing closed-loop systems is challenging""" ; sc:name "CLoSES" ; sc:url "https://github.com/Center-For-Neurotechnology/CLoSES-SEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0602, edam:topic_0634, edam:topic_3408 ; sc:citation "pubmed:20688969" ; sc:description "A curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases, mutation and links to external databases." ; sc:featureList edam:operation_0331, edam:operation_0367, edam:operation_0478, edam:operation_3202 ; sc:name "Clotbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.clotbase.bicnirrh.res.in/" ; biotools:primaryContact "ClotBase Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0202, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:33140820" ; sc:description """a web tool for the development of quantitative structure-activity relationship models in drug discovery. The Cloud 3D-QSAR Server is developed to help running 3D-QSAR jobs by submitting molecular structures and pKi values on web pages which is much more convenient than by command line. This server use Open3DQSAR as the QSAR software and Open Babel to process structure stuff.""" ; sc:featureList edam:operation_3625, edam:operation_3799, edam:operation_3938 ; sc:name "Cloud 3D-QSAR" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/cloud3dQSAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC6612831", "pubmed:31510642" ; sc:description "assembly of synthetic long reads using de Bruijn graphs | SPAdes Genome Assembler. Contribute to ablab/spades development by creating an account on GitHub | You can’t perform that action at this time | You signed in with another tab or window. 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Reload to refresh your session" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:name "cloudSPAdes" ; sc:url "http://cab.spbu.ru/software/spades/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation "pubmed:21645377" ; sc:description "Hadoop-based short read aligner" ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "CloudAligner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/cloudaligner/" ; biotools:primaryContact "Nguyen T" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_2885, edam:topic_3295, edam:topic_3316 ; sc:citation ; sc:description """an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation. Last updated: July 31, 2020. Please check our preprint on biorxiv and our published paper on Bioinformatics. Med Google Cloud Platform kan du oprette, implementere og skalere apps, websites og tjenester på den samme infrastruktur som Google. Fortsæt til Google Cloud Platform. Skriv den tekst, du hører eller ser. To be able use CloudASM, you need to create an account on https://cloud.google.com/ and set up how you want to be billed (e.g. with a credit card). As of January 2020, GCP offers $300 in credits for opening an account -- which is enough to test this pipeline.""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227, edam:operation_3919 ; sc:license "MIT" ; sc:name "CloudASM" ; sc:url "https://console.cloud.google.com/storage/browser/cloudasm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC8375622", "pubmed:34423340" ; sc:description "CloudBridge provides a consistent layer of abstraction over different Infrastructure-as-a-Service cloud providers, reducing or eliminating the need to write conditional code for each cloud." ; sc:featureList edam:operation_2475, edam:operation_3436, edam:operation_3762 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CloudBridge" ; sc:softwareHelp ; sc:url "https://github.com/gvlproject/cloudbridge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3577 ; sc:citation "pubmed:19357099" ; sc:description "CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes." ; sc:featureList edam:operation_3198 ; sc:name "CloudBurst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/cloudburst-bio/" ; biotools:primaryContact "Schatz MC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444, edam:topic_3452, edam:topic_3500 ; sc:citation , "pubmed:34253927" ; sc:description "CloudReg is a tool for cross-modal, nonlinear, image registration between arbitrary image volumes." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CloudReg" ; sc:url "https://cloudreg.neurodata.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC7672897", "pubmed:33203354" ; sc:description """a clustering-oriented de novo assembler for Illumina sequences. Clover is a clustering-oriented de novo assembler for Illumina sequences, which bases on the de Bruijn graph method and utilizes a novel k-mer clustering approach from the overlap-based concept to improve the robustness with respect to sequencing error especially using large k-mers.Clover achieves a superior assembly quality in terms of corrected N50 and E-size.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3472, edam:operation_3644 ; sc:name "Clover" ; sc:url "https://oz.nthu.edu.tw/~d9562563/src.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:35975958" ; sc:description "An Efficient DNA Clustering algorithm based on Tree Structure." ; sc:featureList edam:operation_2422, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Clover" ; sc:url "https://github.com/Guanjinqu/Clover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2828, edam:topic_3474 ; sc:citation , "pubmed:33381840" ; sc:description "CLPred is a tool for sequence-based protein crystallization predictor using bidirectional recurrent neural network with long short-term memory (BLSTM). BLSTM to capture the long-range interaction patterns between k-mers amino acids." ; sc:featureList edam:operation_0410 ; sc:name "CLPred" ; sc:url "https://github.com/xuanwenjing/CLPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:35294359" ; sc:description "Pruning Networks With Cross-Layer Ranking & k-Reciprocal Nearest Filters." ; sc:featureList edam:operation_3695 ; sc:license "Not licensed" ; sc:name "CLR-RNF" ; sc:url "https://github.com/lmbxmu/CLR-RNF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC7070946", "pubmed:32102294" ; sc:description """Continual Learning Benchmark for Remote Sensing Image Scene Classification. This is a database designed for the new task named Continual/Lifelong learning for remote sensing image scene classification. The existing remote sensing image scene classification datasets use static benchmarks and lack the standard to divide the datasets into several sequential learning training batches, which largely limits the development of Continual/Lifelong learning in remote sensing image scene classification. The proposed CLRS data set consists of 15,000 remote sensing images divided into 25 scene classes, namely, airport, bare-land, beach, bridge, commercial, desert, farmland, forest, golf-course, highway, industrial, meadow, mountain, overpass, park, parking, playground, port, railway, railway-station, residential, river, runway, stadium, and storage-tank. Each class has 600 images, and the image size is 256x256. The resolution of the images ranges from 0.26 m to 8.85 m.""" ; sc:featureList edam:operation_3359, edam:operation_3553 ; sc:name "CLRS" ; sc:url "https://github.com/lehaifeng/CLRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons." ; sc:featureList edam:operation_3196, edam:operation_3458 ; sc:license "GPL-3.0" ; sc:name "clst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/clst.html" ; biotools:primaryContact "Noah Hoffman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation ; sc:description "Tools for performing taxonomic assignment based on phylogeny using pplacer and clst." ; sc:featureList edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "clstutils" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/clstutils.html" ; biotools:primaryContact "Noah Hoffman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3168, edam:topic_3341, edam:topic_3511 ; sc:citation ; sc:description """a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries. Choose the library format of your file.""" ; sc:featureList edam:operation_0308, edam:operation_0335, edam:operation_0365 ; sc:name "CLUE" ; sc:url "http://www.crispr-clue.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3570 ; sc:citation , "pubmed:33532849" ; sc:description "CLUE (Constrained LUmping for differential Equations) is a tool for exact maximal reduction of kinetic models by constrained lumping of differential equations." ; sc:featureList edam:operation_3928, edam:operation_3935 ; sc:name "CLUE" ; sc:url "https://github.com/pogudingleb/CLUE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Clustering Markov Packager Across K- was developed in order to aid users analyse the results of STRUCTURE-like programs. The main pipeline offers a full pipeline for the summation and graphical representation of the results previously obtained by the user using a STRUCTURE-like program." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "CLUMPAK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://clumpak.tau.ac.il/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3398, edam:topic_3474, edam:topic_3954 ; sc:citation ; sc:description "Accurate Clustering-based Ensemble Method to Predict Motor Imagery Tasks from Multi-channel EEG Data." ; sc:isAccessibleForFree true ; sc:name "CluSem" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/MdOchiuddinMiah/MI-BCI_ML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_0736, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:14693807", "pubmed:15215358", "pubmed:16933295", "pubmed:20818657" ; sc:description "ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties." ; sc:featureList edam:operation_0250, edam:operation_0478, edam:operation_0482, edam:operation_2930, edam:operation_3432 ; sc:name "ClusPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cluspro.bu.edu/login.php" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0622, edam:topic_3697 ; sc:citation , "pmcid:PMC5910555", "pubmed:29678129" ; sc:description "For analyzing and comparing accessory genomic elements (AGEs) between genomes." ; sc:featureList edam:operation_3459 ; sc:license "GPL-3.0" ; sc:name "ClustAGE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/clustage/" ; biotools:primaryContact "Egon A. Ozer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , , , , "pmcid:PMC147148", "pmcid:PMC308517" ; sc:description """Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris. Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.""" ; sc:featureList edam:operation_0492 ; sc:funder "Science Foundation Ireland" ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "Clustal 2 (Clustal W, Clustal X)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0 - 2.1" ; sc:url "http://www.clustal.org/clustal2/" ; biotools:primaryContact "Clustal helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Finds the best global alignment for a set of input sequences (nucleic acid or protein)." ; sc:featureList edam:operation_0492 ; sc:name "Clustal WS (jabaws)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.compbio.dundee.ac.uk/jabaws/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , , "pmcid:PMC3261699", "pmcid:PMC5734385" ; sc:description "Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO." ; sc:featureList edam:operation_0492 ; sc:funder "Science Foundation Ireland" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Clustal Omega" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "1.0 - 1.2" ; sc:url "http://www.clustal.org/omega/" ; biotools:primaryContact "Clustal helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Des Higgins" ; sc:citation , ; sc:description "Multiple sequence alignment using guide trees and HMM profile-profile techniques." ; sc:featureList edam:operation_0492 ; sc:name "Clustal Omega (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University College Dublin" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/clustalo" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Align two or more protein sequences on the UniProt web site using ClustalOmega." ; sc:featureList edam:operation_0492 ; sc:name "ClustalO UniProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uniprot.org/align" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview." ; sc:featureList edam:operation_0492 ; sc:name "ClustalO WS (jabaws)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.compbio.dundee.ac.uk/jabaws" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , , , , "pmcid:PMC147148", "pmcid:PMC168907", "pmcid:PMC308517" ; sc:description "Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV)." ; sc:featureList edam:operation_0492 ; sc:name "Clustal 1.8 (Clustal W, Clustal X)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.8 - 1.83" ; sc:url "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/" ; biotools:primaryContact "Clustal helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Des Higgins" ; sc:citation , ; sc:description "General purpose global multiple sequence alignment program for DNA or proteins." ; sc:featureList edam:operation_0492 ; sc:name "ClustalW2 (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University College Dublin" ; sc:softwareHelp , , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/msa/clustalw2/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3293 ; sc:author "Des Higgins" ; sc:citation , ; sc:description "Phylogenetic tree generation from an alignment using neighbor-joining or UPGMA." ; sc:featureList edam:operation_0323 ; sc:name "ClustalW2 Phylogeny (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University College Dublin" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_1949, edam:format_1982, edam:format_1997 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation ; sc:description "ClustalW is a general purpose multiple sequence alignment program for DNA or proteins" ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "ClustalW (BioLib)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1." ; sc:url "https://biolib.com/bio-utils/clustalw/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "ClustalW is a general purpose multiple sequence alignment program for DNA or proteins" ; sc:featureList edam:operation_0492 ; sc:name "ClustalW (PBIL)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html" ; biotools:primaryContact "Gilbert Deleage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3321 ; sc:citation ; sc:description "This package implements several techniques for the comparison and visualisation of relationships between different clustering results. These relationships are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection: the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness." ; sc:featureList edam:operation_0291 ; sc:license "GPL-2.0" ; sc:name "clustComp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/clustComp.html" ; biotools:primaryContact "Aurora Torrente" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_2830 ; sc:citation ; sc:description "clusTCR is a Python interface for rapid clustering of large sets of CDR3 sequences. 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sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/clustering_resume/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "The ClusteringSuite is the software package that includes the cluster analysis tool." ; sc:featureList edam:operation_3432 ; sc:name "ClusteringSuite" ; sc:softwareHelp ; sc:url "https://github.com/bsc-performance-tools/clustering-suite" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; 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Hardcastle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:author "Paul Ka Po To" ; sc:citation , , "pubmed:34734728" ; sc:description "ClusterSheep is a GPU/CUDA-accelerated software tool for large-scale clustering of tandem mass spectra from shotgun proteomics." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "ClusterSheep" ; sc:url "https://github.com/kpto/ClusterSheep" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation ; sc:description "This package provides tools to assess if clusters have a separation different from random or permuted data. It investigates clusters of two or more groups by first, projecting all points onto a one dimensional line. 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CMM aims to achieve this goal by inferring all the information enclosed by dashed lines in the following figure." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3454, edam:operation_3557, edam:operation_3760 ; sc:license "MIT" ; sc:name "CMM" ; sc:url "https://github.com/HaohanWang/CMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3336, edam:topic_3375, edam:topic_3473 ; sc:citation , "pubmed:32986829" ; sc:description "CMNPD is the comprehensive marine natural products database based on manually curated data. CMNPD currently contains more than 31 000 chemical entities with various physicochemical and pharmacokinetic properties, standardized biological activity data, systematic taxonomy and geographical distribution of source organisms, and detailed literature citations. 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For this purpose, a database is queried in the background using protein/gene identifiers as input. The user can chose between different localization information by using an interactive table or linked bar charts with different categories. Cell environments can be explored in 3D in different navigation modes. Also, stereoscopic rendering is supported." ; sc:featureList edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CELLmicrocosmos 4 PathwayIntegration (CmPI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.2" ; sc:url "http://Cm4.CELLmicrocosmos.org" ; biotools:primaryContact "Bjorn Sommer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0797, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:11125067" ; sc:description "The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database." ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_3208 ; sc:name "CMR" ; sc:softwareHelp ; sc:url "http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC9469999", "pubmed:36099286" ; sc:description "CMRSegTools: an open-source application software designed for the segmentation and quantification of myocardial infarct lesion enabling full access to state-of-the-art segmentation methods and parameters, easy integration of new algorithms and standardised results sharing." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:license "CECILL-2.1" ; sc:name "CMRSegTools" ; sc:operatingSystem "Mac" ; sc:url "https://github.com/OpenCardiacMRISoftware/CMRSegTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3304, edam:topic_3334, edam:topic_3360, edam:topic_3500 ; sc:citation , "pmcid:PMC7228039", "pubmed:32413036" ; sc:description "The cms is an R package that uses tabular data from rat epilepsy studies and applies a composite measures scheme (via PCA) to select the most prominent features. Further, variables can be selected to perform cluster analysis on a subset in order to build a composite score. Finally, the cluster distribution is displayed for the subgroups and allows severity assessment between animal models." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3891 ; sc:name "CMS" ; sc:url "https://github.com/mytalbot/cms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0654 ; sc:citation , "pmcid:PMC5483318", "pubmed:28646874" ; sc:description "A heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment." ; sc:featureList edam:operation_0492 ; sc:name "CMSA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/wangvsa/CMSA" ; biotools:primaryContact "Ce Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_2640 ; sc:citation ; sc:description "Consensus molecular subtyping of colorectal cancer pre-clinical models." ; sc:featureList edam:operation_2995 ; sc:name "CMScaller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Lothelab/CMScaller" ; biotools:primaryContact "Lothe Lab" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2350 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2350 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3303 ; sc:description "Removes lower scoring overlaps from cmsearch results." ; sc:featureList edam:operation_2424, edam:operation_2928 ; sc:license "Freeware" ; sc:name "cmsearch-deoverlap" ; sc:url "https://github.com/EBI-Metagenomics/pipeline-v5/tree/master/tools/RNA_prediction/cmsearch-deoverlap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3068, edam:topic_3360, edam:topic_3379 ; sc:citation , "pmcid:PMC6944590", "pubmed:31930068" ; sc:description "CMTTdb (The Cancer Molecular-Targeted Therapy database) is an integrated database to store relevant information about molecular targeted agents as well as their combinatorial approaches in clinical trials and studies for cancer treatment. It contains the information from public available clinical trials to obtain the clinical agents, their corresponding targets, cancer subtypes, biomarkers, clinical features of the patients, as well as the treatment modalities (monotherapy or combinatorial therapies)" ; sc:featureList edam:operation_2422 ; sc:name "CMTTdb" ; sc:url "http://www.biosino.org/CMTTdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_3068, edam:topic_3168 ; sc:citation ; sc:description "An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping. It enables antiviral drug resistance genotyping, with Human Cytomegalovirus sequencing data." ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "cmvdrg" ; sc:url "https://github.com/ucl-pathgenomics/cmvdrg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_0154, edam:topic_2269, edam:topic_3678 ; sc:citation "pubmed:22669913" ; sc:description "Contact Map Web Viewer (CMWeb) is an online tool for studying basic properties of residue-residue contact formation and contact clusters. CMWeb can used to visualize contact maps, link contacts and display them in 3D or multiple sequence alignments, predict residue contacts, or calculate various contact statistics." ; sc:featureList edam:operation_0272, edam:operation_0392, edam:operation_0393, edam:operation_2429, edam:operation_2950 ; sc:name "CMWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://cmweb.enzim.hu" ; biotools:primaryContact "CMWeb support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0166, edam:topic_3168 ; sc:citation "pubmed:10838572", "pubmed:9270306" ; sc:description "Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment." ; sc:featureList edam:operation_0292, edam:operation_0294, edam:operation_0295 ; sc:name "Cn3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml" ; biotools:primaryContact "Stephen H. Bryant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pubmed:33423051" ; sc:description "CNA2Subpathway is an R package for identification of dysregulated subpathway driven by copy number alterations in cancer." ; sc:featureList edam:operation_0314, edam:operation_3927, edam:operation_3928, edam:operation_3961 ; sc:license "Apache-2.0" ; sc:name "CNA2Subpathway" ; sc:url "https://github.com/hanjunwei-lab/CNA2Subpathway" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC7419421", "pubmed:32850687" ; sc:description "CNA_origin is a Deep Learning Framework to Predict Tumor Tissue-of-Origin Based on Copy Number Alteration." ; sc:featureList edam:operation_2495, edam:operation_3937 ; sc:name "CNA_origin" ; sc:url "https://github.com/YingLianghnu/CNA_origin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3518 ; sc:citation , "pubmed:31901979" ; sc:description "CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-controlled situ synthesis of DNA microarrays, and is the highest density and widely used chip preparation technology. In addition, agilent aCGH (array-based Comparative Genomic Hybridization) platform also provides high performance, high resolution chip data. The raw array data were collected from GEO (Gene Expression Omnibus) and TCGA (The Cancer GenomeAtlas) databases. 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It performs a \"discrete\" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found." ; sc:featureList edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "CNAnorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CNAnorm.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:description "CNAnova is a stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data. It runs from the command line on the Linux platforms and is composed of several modules written in the R programming language." ; sc:featureList edam:operation_2495 ; sc:name "CNAnova" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.compbio.group.cam.ac.uk/software/cnanova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2640, edam:topic_2815, edam:topic_2885 ; sc:citation , "pmcid:PMC7010409", "pubmed:31939734" ; sc:description "CNApp is a user-friendly web tool that offers sample- and cohort-level association analyses, allowing a comprehensive and integrative exploration of CNAs with clinical and molecular variables. CNApp generates genome-wide profiles with tumor-purity correctiion, calculates CNA levels by computing broad, focal and global CNA scores (BCS, FCS and GCS, respectively), identifies CNAs associated with clinical features and molecular annotated variables and uses machine learning-based predictions to classify samples by using segmented data from either microarrays or next-generation sequencing. CNApp provides a unique scenario to comprehensively analyze CNAs and integrate them with molecular and clinical features." ; sc:featureList edam:operation_3233, edam:operation_3659, edam:operation_3799 ; sc:name "CNApp" ; sc:url "https://tools.idibaps.org/CNApp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC8826044", "pubmed:34878104" ; sc:description "An integrated environment for metabolic network analysis." ; sc:featureList edam:operation_3660, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "CNApy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cnapy-org/CNApy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3168, edam:topic_3277 ; sc:description "CNAseg is a novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses the Skellam distribution to compare read depth in tumour and control samples, which allows the use of smaller window sizes for copy number estimation and leads to greater sensitivity in pinpointing breakpoints for small CNAs." ; sc:featureList edam:operation_3233 ; sc:name "CNAseg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.compbio.group.cam.ac.uk/software/cnaseg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC10363024", "pubmed:37449891" ; sc:description "iCNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumours. CNAsim can be used to generate copy number profiles with noise patterns that mimic those of single-cell CNA detection algorithms, and to generate DNA-seq data for sampled cells." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CNAsim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/samsonweiner/CNAsim" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3475 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640 ; sc:citation ; sc:description "User-guided local and global copy-number segmentation for tumor sequencing data." ; sc:featureList edam:operation_3227, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CNAViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://elkebir-group.github.io/cnaviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3071 ; sc:citation ; sc:description "CNCDatabase(Cornell Non-Coding Cancer driver Database) provides a helpful resource for researchers to explore the pathological role of non-coding alterations and their associations with gene expression in human cancers. 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Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:36812693" ; sc:description "A multimodal deep-learning-based network for cranial nerves tract segmentation." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "CNTSeg" ; sc:url "https://github.com/IPIS-XieLei/CNTSeg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_3474, edam:topic_3518, edam:topic_3958 ; sc:citation , "pubmed:35240378" ; sc:description "A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database." ; sc:featureList edam:operation_3961 ; sc:name "CNV-ETLAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lmic.mgh.harvard.edu/CNV-ETLAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3474, edam:topic_3673, edam:topic_3958 ; sc:citation , "pmcid:PMC7671382", "pubmed:33575619" ; sc:description "CNV-JACG is a random forest based framework for assessing the accuracy of CNVs detected base on paired-end whole genome sequencing data." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3937, edam:operation_3961 ; sc:name "CNV-JACG" ; sc:url "https://github.com/sunnyzxh/CNV-JACG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "CNV-PG is an application written in Python, including two parts: CNV predicting (CNV-P) and CNV genotyping (CNV-G). For CNV-P, we trained on a subset of validated CNVs from different CNV callers separately to obtain the corresponding classifier used for the identification of true CNVs. For CNV-G, a genotyper, which is compatible with existing CNV callers and generating a uniform set of high-confidence genotypes." ; sc:featureList edam:operation_3196, edam:operation_3937 ; sc:name "CNV-PG" ; sc:url "https://github.com/wonderful1/CNV-PG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:19267900" ; sc:description "CNV-seq, a new method to detect copy number variation using high-throughput sequencing" ; sc:featureList edam:operation_3233 ; sc:name "CNV-seq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tiger.dbs.nus.edu.sg/cnv-seq/" ; biotools:primaryContact "Xie Chao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2332, edam:format_3003 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3953 ; sc:name "Pathway overrepresentation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3337, edam:topic_3958 ; sc:citation , "pmcid:PMC10174702", "pubmed:37104749" ; sc:description "The CNV-clinviewer is a user-friendly web-application for the interactive visualization, genomic exploration and standardized clinical significance interpretation of large copy-number variants (CNVs)." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "CNV-ClinViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cnv-ClinViewer.broadinstitute.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3673, edam:topic_3958 ; sc:citation , "pmcid:PMC8645205", "pubmed:34917425" ; sc:description "CNV-P: A machine-learning framework for filtering copy number variations." ; sc:featureList edam:operation_3359, edam:operation_3695, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CNV-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wonderful1/CNV-P" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3056, edam:topic_3175 ; sc:citation ; sc:description "Program for detecting the integrated copy number veriation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria. The result is a VCF format genotype file which can be used in GWAS/QLT research." ; sc:featureList edam:operation_3197, edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "CNVcaller" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://animal.nwsuaf.edu.cn/code/index.php/main/loadByGet?address%5b%5d=main/html/software.php&id=home" ; biotools:primaryContact "Yu Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation "pubmed:20805290" ; sc:description "CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage." ; sc:featureList edam:operation_2429, edam:operation_3196, edam:operation_3227, edam:operation_3233 ; sc:name "CNVer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.toronto.edu/CNVer/" ; biotools:primaryContact "CNVer support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3958 ; sc:author ; sc:citation , "pubmed:33983414" ; sc:description "CNVfilteR is an R/bioconductor package to identify false positives produced by germline NGS CNV detection tools." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3961 ; sc:license "Artistic-2.0" ; sc:name "CNVfilteR" ; sc:url "http://www.bioconductor.org/packages/CNVfilteR" ; biotools:primaryContact , , "Conxi Lázaro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "This package is intended to facilitate gene-set association with rare CNVs in case-control studies." ; sc:featureList edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "cnvGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/cnvGSA.html" ; biotools:primaryContact "Joseph Lugo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation ; sc:description "Joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association." ; sc:featureList edam:operation_3196 ; sc:name "cnvHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.033" ; sc:url "http://www.imperial.ac.uk/people/l.coin" ; biotools:primaryContact "LACHLAN COIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3316, edam:topic_3673, edam:topic_3676, edam:topic_3958 ; sc:citation , "pmcid:PMC8897915", "pubmed:35247967" ; sc:description "An open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage." ; sc:featureList edam:operation_3435, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CNVind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wkusmirek/CNVind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3676, edam:topic_3958 ; sc:citation , "pmcid:PMC8278790", "pubmed:34259866" ; sc:description "Multi-ethnic database for identifying copy number variations associated with cancer. View gene-centric CNV profile collected from healthy individuals and multiple cancer types." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3961 ; sc:name "CNVIntegrate" ; sc:url "http://cnvintegrate.cgm.ntu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation ; sc:description "CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data." ; sc:featureList edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "CNVkit" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "https://github.com/etal/cnvkit" ; biotools:primaryContact "Boris C. Bastian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2815, edam:topic_3053 ; sc:citation "pubmed:21324876" ; sc:description "CNV discovery and genotyping from read-depth analysis of personal genome sequencing." ; sc:featureList edam:operation_3196 ; sc:license "Other" ; sc:name "CNVnator" ; sc:softwareHelp ; sc:url "https://github.com/abyzovlab/CNVnator" ; biotools:primaryContact "Alexej Abyzov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3175, edam:topic_3676 ; sc:citation , "pmcid:PMC4147927", "pubmed:25161258" ; sc:description "Detecting intergenic copy number variation using off-target exome sequencing data." ; sc:featureList edam:operation_3233 ; sc:name "cnvOffSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/cnvoffseq/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level." ; sc:featureList edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "CNVPanelizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CNVPanelizer.html" ; biotools:primaryContact "Thomas Wolf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3673, edam:topic_3958 ; sc:citation ; sc:description "CNVpytor is a Python package for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing." ; sc:featureList edam:operation_0226, edam:operation_0337, edam:operation_0484, edam:operation_3196, edam:operation_3230, edam:operation_3961 ; sc:license "MIT" ; sc:name "CNVpytor" ; sc:url "https://github.com/abyzovlab/CNVpytor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description "This tool uses NGS data to measure human gene copy number for multiple samples, indentifying SNPs tagging copy number variants and detecting copy number polymorphic genomic regions." ; sc:featureList edam:operation_0484, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "CNVrd2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CNVrd2.html" ; biotools:primaryContact "Hoang Tan Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description "This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies." ; sc:featureList edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "CNVtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.68.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CNVtools.html" ; biotools:primaryContact "Chris Barnes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_3173, edam:topic_3325 ; sc:citation ; sc:description "CNVxplorer is a web server suited for the functional assessment of CNVs in a clinical diagnostic setting. CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs. It provides sequence constraint metrics, impact on regulatory elements and topologically associating domains, as well as expression patterns. Analyses offered cover (a) agreement with patient phenotypes; (b) visualizations of associations among genes, including those mediated by regulatory elements, and transcription factors; (c) enrichment on functional and pathway annotations; and (d) co-occurrence of terms across PubMed publications related to the query CNVs. 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sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "coda4microbiome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://malucalle.github.io/coda4microbiome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3512 ; sc:citation , "pmcid:PMC4379410", "pubmed:25577191" ; sc:description "A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation." ; sc:featureList edam:operation_0451 ; sc:name "CodABC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://code.google.com/archive/p/codabc/" ; biotools:primaryContact "Miguel Arenas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC9278500", "pubmed:35845844" ; sc:description "Codabench, a meta-benchmark platform that is open sourced and community driven for benchmarking algorithms or software agents versus datasets or tasks." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Codabench" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/codalab/codabench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3360, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:34498030" ; sc:description "CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CoDaCoRe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/egr95/R-codacore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_2269, edam:topic_3934 ; sc:citation ; sc:description "Compositional Data Analysis using Kernels (CODAK) is a tool for multivariate statistical learning methodology based on the kernel distance covariance framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "CODAK" ; sc:url "http://github.com/GhoshLab/CODAK/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3697 ; sc:citation , "pubmed:33106076" ; sc:description "Codaloss: direct interaction network inference for compositional data. One essential step in the analysis of microbiome compositional data is inferring the direct interaction network among microbial species. Here, we propose a novel loss function called codaloss for direct microbes interaction network estimation under the sparsity assumptions. We develop an alternating direction optimization algorithm to obtain sparse solution of codaloss as estimator. Compared to other state-of-the-art methods, our model makes less assumptions about the microbial networks and outperforms them in network inference." ; sc:featureList edam:operation_3799, edam:operation_3927 ; sc:name "codaloss" ; sc:url "https://github.com/xuebaliang/Codaloss" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1602 ; sc:name "Codon usage fraction difference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Codon usage table comparison." ; sc:featureList edam:operation_0285 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "codcmp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/codcmp.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Copy and reformat a codon usage table" ; sc:featureList edam:operation_0286, edam:operation_0335 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "codcopy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/codcopy.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0821, edam:topic_3125, edam:topic_3512 ; sc:citation , "pmcid:PMC9832946", "pubmed:36698765" ; sc:description "Tool to deoptimize the RNA or DNA sequences based on codon usage. Codon-pair deoptimization involves increasing the frequency of underrepresented codon pairs without changing codon usage or amino acid sequences." ; sc:featureList edam:operation_0284, edam:operation_0335, edam:operation_0489, edam:operation_2962 ; sc:isAccessibleForFree true ; sc:name "CoDe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/codeop/landing_page.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3050, edam:topic_3372, edam:topic_3810 ; sc:citation ; sc:description "CODECHECK is an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility." ; sc:featureList edam:operation_2428, edam:operation_3283, edam:operation_3431 ; sc:license "CC-BY-SA-4.0" ; sc:name "CODECHECK" ; sc:url "https://codecheck.org.uk/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0634, edam:topic_3168, edam:topic_3500, edam:topic_3511 ; sc:citation "pubmed:12824413" ; sc:description "COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences." ; sc:featureList edam:operation_0308, edam:operation_2419, edam:operation_3198, edam:operation_3237 ; sc:name "CODEHOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://blocks.fhcrc.org/codehop.html" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation , "pubmed:17344240" ; sc:description "This package facilitates reading, preprocessing and manipulating microarray data." ; sc:featureList edam:operation_2478 ; sc:license "GPL-2.0" ; sc:name "codelink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/codelink.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3474 ; sc:citation , "pubmed:34990838" ; sc:description "CODER embeddings excellently reflect semantic similarity and relatedness of medical concepts. One can use CODER for embedding-based medical term normalization or to provide features for machine learning. Similar to other pretrained language models, CODER can also be fine-tuned for specific tasks." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "CODER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GanjinZero/CODER" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3077 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Extract CDS, mRNA and translations from feature tables." ; sc:featureList edam:operation_0371, edam:operation_0372, edam:operation_0436 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "coderet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/coderet.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0621, edam:topic_3053, edam:topic_3174 ; sc:citation , "pmcid:PMC9825746", "pubmed:36511586" ; sc:description "Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement." ; sc:featureList edam:operation_0300, edam:operation_0361, edam:operation_0489 ; sc:license "BSD-3-Clause" ; sc:name "Codetta" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://github.com/kshulgina/codetta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation ; sc:description "A normalization and copy number variation calling procedure for whole exome DNA sequencing data. The tool relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model includes terms that specifically remove biases due to GC content, among others. It also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data." ; sc:featureList edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "CODEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CODEX.html" ; biotools:primaryContact "Yuchao Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3395 ; sc:citation , "pmcid:PMC4384009", "pubmed:25270877" ; sc:description "A next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities." ; sc:featureList edam:operation_2421 ; sc:name "CODEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://codex.stemcells.cam.ac.uk/" ; biotools:primaryContact "Bertie Gottgens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0621, edam:topic_2814 ; sc:citation , "pubmed:32750861" ; sc:description "CoDiFold is a de novo protein structure prediction by coupling contact with distance profile. In CoDiFold, contacts and distance profiles are organically combined into the Rosetta low-resolution energy function to improve the accuracy of energy function. As a result, the correlation between energy and root mean square deviation (RMSD) is improved." ; sc:featureList edam:operation_0475, edam:operation_0476, edam:operation_0477 ; sc:name "CoDiFold" ; sc:url "http://github.com/iobio-zjut/CoDiFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0610, edam:topic_0625, edam:topic_2640, edam:topic_3308 ; sc:citation , "pmcid:PMC7561188", "pubmed:33057419" ; sc:description "Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). CoDiNA categorizes links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks." ; sc:featureList edam:operation_3463, edam:operation_3766, edam:operation_3925 ; sc:license "GPL-2.0" ; sc:name "CoDiNA" ; sc:url "https://CRAN.R-project.org/package=CoDiNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3512 ; sc:description "Combined DNA Index System (CODIS) is a GUI tool for forensic paternity lawsuit." ; sc:isAccessibleForFree true ; sc:name "CODIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.28.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/24111-codis" ; biotools:primaryContact "Giuseppe Cardillo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0623, edam:topic_2229, edam:topic_2814, edam:topic_3071 ; sc:citation , "pubmed:36111870" ; sc:description "CoDNaS Quaternary is a high confidence database of conformational diversity in proteins that present a biologically relevant quaternary structure." ; sc:featureList edam:operation_0244, edam:operation_0570, edam:operation_2421, edam:operation_2422, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CoDNaS-Q" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ufq.unq.edu.ar/codnasq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0203, edam:topic_3047 ; sc:citation ; sc:description "CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RNA structure in its native ensemble. The conformers are taken from the wwPDB and include structures solved by X-Ray Diffraction, Nuclear Magnetic Resonance and cryo-Electron Microscopy. CoDNaS-RNA allows you to quantify the conformational diversity of a given RNA, compare the structures of selected conformers, retrieve site-specific interactions between RNA and bound polynucleotides or proteins, and get more data cross-referenced from external resources like RNAcentral." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3432 ; sc:name "CoDNaS-RNA" ; sc:url "http://ufq.unq.edu.ar/codnasrna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3293 ; sc:citation ; sc:description "Ranking codons and orthologs based on their phylogenetic signal." ; sc:featureList edam:operation_0285, edam:operation_2962, edam:operation_2964 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "codon congruence" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ridgelab/codon_congruence" ; biotools:primaryContact "Justin Miller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0621, edam:topic_3489, edam:topic_3678 ; sc:citation "pubmed:10592250" ; sc:description "Find GC content and frequency of codon usage for any organism that has a sequence in GenBank." ; sc:featureList edam:operation_0284, edam:operation_0285, edam:operation_0286, edam:operation_2964 ; sc:name "Codon Usage Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kazusa.or.jp/codon/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_2830 ; sc:citation , "pubmed:32705123" ; sc:description "CodonAdjust is a free software to optimize a codon nucleotide composition mimicking a certain amino acids profile (AA profile). CodonAdjust formulates the optimization of a codon nucleotide composition as a non-convex optimization problem which minimizes the squared error between the desired and the calculated AA profiles. We provide CodonAdjust with four different options, which have various customization in practical scenarios such as selecting or avoiding specific codons." ; sc:featureList edam:operation_0284, edam:operation_2962, edam:operation_3096 ; sc:license "GPL-3.0" ; sc:name "CodonAdjust" ; sc:url "https://github.com/tiffany-nguyen/CodonAdjust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622 ; sc:citation "pubmed:15222899", "pubmed:17537810" ; sc:description "CodonO is a method for measuring synonymous codon usage bias within and across genomes." ; sc:featureList edam:operation_0284, edam:operation_0286, edam:operation_2962, edam:operation_2963, edam:operation_2964 ; sc:name "CodonO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://digbio.missouri.edu/software/index.html" ; biotools:primaryContact "Ginger Han" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage" ; sc:featureList edam:operation_0236 ; sc:license "GPL-2.0" ; sc:name "CodonW" ; sc:softwareHelp ; sc:url "http://codonw.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC3651391", "pubmed:23621914" ; sc:description "Predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein." ; sc:featureList edam:operation_0331 ; sc:name "CoDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cib.cf.ocha.ac.jp/CoDP/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3325, edam:topic_3382, edam:topic_3399, edam:topic_3577 ; sc:citation , "pmcid:PMC6753183", "pubmed:31572203" ; sc:description """A Telemedicine Tool to Improve Awareness and Diagnosis for Patients With Congenital Dyserythropoietic Anemia. Algorithms and recommendations for diagnosis and management of congenital dyserythropoietic anemia (CDA). This website uses cookies to ensure you get the best experience on our website. Learn more. This is a web service dedicated to Congenital Dyseritropoyetic Anemias. Our aim is to provide information to patients and their families, but also to provide doctors with specific tools for this disease. Congenital Dyseritropoyetic Anemias. CoDysAn collaborates with various Associations.""" ; sc:featureList edam:operation_3920 ; sc:name "CoDysAn" ; sc:url "http://www.codysan.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0605, edam:topic_3325, edam:topic_3366, edam:topic_3372 ; sc:citation , "pmcid:PMC3554586", "pubmed:23244467" ; sc:description "Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integration connectors for different data sources along with ontology mapping techniques." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "COEUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/coeus/" ; biotools:primaryContact "Pedro Lopes", "Pedro Sernadela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3299 ; sc:citation ; sc:description "The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree." ; sc:featureList edam:operation_0547 ; sc:name "Coev-Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://coev.vital-it.ch/#/" ; biotools:primaryContact "Coev Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2259, edam:topic_3518 ; sc:description "Extracts the gene expression matrix from GEO DataSets (.CEL files) as a AffyBatch object. Additionally, can make the normalization process using two different methods (vsn and rma). 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Tatonetti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0632, edam:topic_0780, edam:topic_3500 ; sc:citation , , "pubmed:32406757" ; sc:description """an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation. Contextualization and Evaluation of COI-5P Barcode Data. Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. 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To address this need, we developed the COmposable Mammalian Elements of Transcription (COMET) an ensemble of TFs and promoters that enable the design and tuning of gene expression to an extent not previously possible. COMET currently comprises 44 activating and 12 inhibitory zinc-finger TFs and 83 cognate promoters, combined in a framework that readily accommodates new parts. This system can tune gene expression over three orders of magnitude, provides chemically inducible control of TF activity, and enables single-layer Boolean logic" ; sc:featureList edam:operation_0420, edam:operation_3891 ; sc:license "MIT" ; sc:name "COMET" ; sc:url "https://github.com/leonardlab/COMET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0623, edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation , "pmcid:PMC3125781", "pubmed:21622656" ; sc:description "CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data." ; sc:featureList edam:operation_0310, edam:operation_0314, edam:operation_0362 ; sc:name "CoMet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comet.gobics.de" ; biotools:primaryContact "CoMet Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3173, edam:topic_3517, edam:topic_3674 ; sc:citation , "pmcid:PMC4422463", "pubmed:25928765" ; sc:description "Visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns." ; sc:featureList edam:operation_3208 ; sc:name "coMET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epigen.kcl.ac.uk/comet/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623, edam:topic_0654, edam:topic_3174 ; sc:citation , "pmcid:PMC4401624", "pubmed:25884504" ; sc:description "Assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon)." ; sc:featureList edam:operation_2995 ; sc:license "GPL-2.0" ; sc:name "CoMeta" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jkawulok/cometa" ; biotools:primaryContact "Jolanta Kawulok" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC9385450", "pubmed:36016714" ; sc:description "CometAnalyser is an open-source deep-learning tool designed for the analysis of both fluorescent and silver-stained wide-field microscopy images. Once the comets are segmented and classified, several intensity/morphological features are automatically exported as a spreadsheet file." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "CometAnalyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/cometanalyser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3173, edam:topic_3301, edam:topic_3305, edam:topic_3674 ; sc:citation ; sc:description "A network-based methylome approach to investigate the multivariate nature of health and disease." ; sc:featureList edam:operation_3501, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "Comethyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/cemordaunt/comethyl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_2269, edam:topic_3172, edam:topic_3305 ; sc:citation , "pubmed:33889934" ; sc:description "COMETS Analytics is an online tool for analyzing and meta-analyzing metabolomics data in large research consortia." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3802 ; sc:name "COMETS Analytics" ; sc:url "https://www.comets-analytics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2815, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:23703208" ; sc:description "ComiR is a web tool for combinatorial microRNA (miRNA) target prediction. 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Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles." ; sc:featureList edam:operation_0224 ; sc:name "Comparative genometrics CG database" ; sc:provider "Université de Lausanne" ; sc:url "http://www2.unil.ch/comparativegenometrics/" ; biotools:primaryContact "Claude-Alain Roten" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3174 ; sc:description "This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples" ; sc:featureList edam:operation_2424 ; sc:name "Compare HUMAnN2 outputs" ; sc:url "https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; 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Badia - Barcelona Supercomputing Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3071, edam:topic_3343 ; sc:citation ; sc:description "Community data resource for environmental chemistry." ; sc:featureList edam:operation_0224 ; sc:name "CompTox Chemistry Dashboard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://comptox.epa.gov/dashboard" ; biotools:primaryContact "Antony J. 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sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/emboss_cons" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Creates a consensus from multiple alignments." ; sc:featureList edam:operation_0492, edam:operation_2479 ; sc:name "cons WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/cons.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation , "pubmed:34694364" ; sc:description "ConsAlifold, a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment." ; 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sc:name "consambig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/consambig.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1984 ; sc:name "Protein sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0821, edam:topic_3534 ; sc:citation , "pubmed:17519246" ; sc:description "An online WEB application that scores residue conservation a site on a Multiple Sequence Alignment based on Jensen-Shannon Divergence, introduced by Capra and Singh." ; sc:featureList edam:operation_0448, edam:operation_0492, edam:operation_3896, edam:operation_3897 ; 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sc:citation "pubmed:15215349" ; sc:description "The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling." ; sc:featureList edam:operation_0292, edam:operation_0295, edam:operation_0447, edam:operation_0477 ; sc:name "Consensus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stormo.wustl.edu/consensus/" ; biotools:primaryContact "Stormo Laboratory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6913255", "pubmed:31844586" ; sc:description """An R package for assessing consensus of multiple RNA-seq algorithms with RUV correction. RNA-seq analysis using multiple algorithms. This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. 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Add the phenotype to generated genotype data prepared with a genetic simulator. The output of cophesim can be used as a direct input for different genome wide association study tools." ; sc:featureList edam:operation_0226, edam:operation_2426 ; sc:license "MIT" ; sc:name "copheism" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.1" ; sc:url "https://bitbucket.org/izhbannikov/cophesim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation "pubmed:18928200" ; sc:description "Composition based Protein Identification" ; sc:featureList edam:operation_2945 ; sc:name "copid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/copid/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0798, edam:topic_3168, edam:topic_3305 ; sc:citation , "pmcid:PMC8325299", "pubmed:34332528" ; sc:description "COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids." ; sc:featureList edam:operation_0224, edam:operation_0578, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COPLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://castillo.dicom.unican.es/copla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2815, edam:topic_3500 ; sc:citation , "pmcid:PMC10209524", "pubmed:37171886" ; sc:description "Robust and scalable maximum exact match finding." ; sc:featureList edam:operation_2421, edam:operation_3435, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "copMEM2" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/wbieniec/copmem2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:36528813" ; sc:description "An ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants." ; sc:featureList edam:operation_0253, edam:operation_3663, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "COPPER" ; sc:url "https://github.com/yuanyuanbu/COPPER" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3466, edam:format_3508, edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910, edam:format_3547 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2330 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2331, edam:format_3508 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3466, edam:format_3508, edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2330 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author , "Patrick Wright" ; sc:citation , "pmcid:PMC4086077", "pubmed:24838564" ; sc:description "sRNA target prediction boosted by comparative information." ; sc:featureList edam:operation_0278 ; sc:isAccessibleForFree true ; sc:name "CopraRNA web server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "2.0.3.2" ; sc:url "http://rna.informatik.uni-freiburg.de/CopraRNA/" ; biotools:primaryContact , "Patrick Wright" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:19465386" ; sc:description "The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and domains may be compared in fold space." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_2415, edam:operation_2487 ; sc:name "COPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cops.services.came.sbg.ac.at/" ; biotools:primaryContact "TopSearch Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3172, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "CoPTR is a tool for accurate and robust inference of microbial growth dynamics from metagenomic sequencing." ; sc:featureList edam:operation_0525, edam:operation_2495, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "CoPTR" ; sc:softwareHelp ; sc:url "https://github.com/tyjo/coptr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_2815 ; sc:citation "pubmed:18442992" ; sc:description "Text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). It also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. Version 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It searches for indirect relations between genes, pathways, drugs and diseases." ; sc:featureList edam:operation_0306, edam:operation_3223 ; sc:name "CoPub" ; sc:url "http://www.copub.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3173, edam:topic_3940 ; sc:citation , "pmcid:PMC8514091", "pubmed:34644115" ; sc:description "Deconvoluting single-cell chromatin accessibility of genetic subclones in cancer." ; sc:featureList edam:operation_3196, edam:operation_3233, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Copy-scAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/spcdot/CopyscAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Network-based visual differential analysis. Clone a network view layout by mapping node column values." ; sc:featureList edam:operation_0277, edam:operation_0337, edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "copycatLayout" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://apps.cytoscape.org/apps/copycatLayout" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091 ; sc:author "Sarah Sandmann" ; sc:citation ; sc:description "CopyDetective is an algorithm for detection threshold aware CNV calling in matched whole-exome sequencing data. Software is available as an R shiny app." ; sc:featureList edam:operation_3233, edam:operation_3962, edam:operation_3963 ; sc:license "AGPL-3.0" ; sc:name "CopyDetective" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sandmanns/CopyDetective" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Disease report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC3582591", "pubmed:23442169" ; sc:description "Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results." ; sc:featureList edam:operation_2238, edam:operation_3233 ; sc:license "Artistic-2.0" ; sc:name "copynumber" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/copynumber.html" ; biotools:primaryContact "Gro Nilsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3301, edam:topic_3697, edam:topic_3941 ; sc:citation , "pmcid:PMC4021573", "pubmed:24708850" ; sc:description "Correct trait bias in microbial profiles" ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "copyrighter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fangly/AmpliCopyrighter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_3175, edam:topic_3574, edam:topic_3577 ; sc:citation "pubmed:21085617" ; sc:description "A computataional approuch for the inference of copy-number genotypes from personal genome sequencing data." ; sc:featureList edam:operation_2238, edam:operation_3197, edam:operation_3233 ; sc:name "CopySeq" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.embl.de/%7Ekorbel/CopySeq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC4396974", "pubmed:25887352" ; sc:description "This tool extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows extracting uniformly distributed copy number information, and it can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, this tool constitutes a widely applicable alternative to available copy number detection tools." ; sc:featureList edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "CopywriteR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CopywriteR.html" ; biotools:primaryContact "Thomas Kuilman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:description "An algorithm for ordering fingerprinted clones within contigs." ; sc:featureList edam:operation_2403, edam:operation_2944 ; sc:name "CORAL (Contig Ordering Algorithm)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/coral/" ; biotools:primaryContact "Kevin Teague" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Coral is a tool that can accurately bridge paired-end RNA-seq reads. The core of Coral is a optimization formulation that can capture the most reliable bridging path while also filter out false paths. An efficient dynamic programming algorithm is designed to calculate the top N optimum. Coral implements a consensus approach to select the best solution among the N candidates by taking into account the distribution of fragment length. Coral is modular, can be easily incorporated into existing RNA-seq analysis pipeline." ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3680, edam:operation_3800 ; sc:license "BSD-3-Clause" ; sc:name "Coral" ; sc:url "https://github.com/Shao-Group/coral" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3299, edam:topic_3360 ; sc:citation ; sc:description "Coral is a web-based visual analysis tool for creating and characterizing cohorts. Users can interactively create and refine cohorts, which can then be compared, characterized, and inspected down to the level of single items. Coral visualizes the evolution of cohorts and also provides intuitive access to prevalence information." ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3436, edam:operation_3802 ; sc:name "Coral" ; sc:url "https://coral.caleydoapp.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0634, edam:topic_2815 ; sc:citation , "pmcid:PMC6941781", "pubmed:31903446" ; sc:description "CoralP is a user-friendly interactive web application for visualizing both quantitative and qualitative data. Qualitative and quantitative features can be represented in branch colors, node colors, and node sizes. Phosphatases can be organized using the published phosphatome tree or as radial or force directed networks. CoralP is simple to use, well documented, and freely available. It is the first and only dedicated tool for phosphatome visualization and is widely applicable to a variety of data types including those generated from proteomic, genomic, epidemiological, and high-throughput screening experiments." ; sc:featureList edam:operation_0337, edam:operation_3478, edam:operation_3799 ; sc:license "MIT" ; sc:name "CoralP" ; sc:url "http://phanstiel-lab.med.unc.edu/coralp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC7359491", "pubmed:32665017" ; sc:description "CORAZON( CORrelations Analyses Zipper ONline) is a bioinformatic tool that uses artificial intelligence to cluster genes according to their expression in tissues and also a tool to normalize databases. It is a web server for data normalization and unsupervised clustering based on expression profiles. This tool is composed of 3 unsupervised machine learning algorithms: Mean Shift, K-Means and Hierarchical. Unsupervised learning is the machine learning task of inferring a function to describe the hidden structure from unlabeled data. The inductor analyzes the examples provided and tries to determine if some of them can be grouped in any way, forming clusters." ; sc:featureList edam:operation_0313, edam:operation_3192, edam:operation_3435, edam:operation_3463 ; sc:name "CORAZON" ; sc:softwareHelp ; sc:url "http://corazon.integrativebioinformatics.me" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:citation , "pmcid:PMC3851956", "pubmed:24565104" ; sc:description "Biological network alignment and querying." ; sc:featureList edam:operation_3439 ; sc:name "Corbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://doc.aporc.org/wiki/Corbi" ; biotools:primaryContact "Ling-Yun Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2269 ; sc:citation , "pubmed:33470404" ; sc:description "CoRC (COPASI R Connector) is a high-level R API for Complex Pathway Simulator (Copasi)." ; sc:featureList edam:operation_2426, edam:operation_3928 ; sc:license "Artistic-2.0" ; sc:name "CoRC" ; sc:url "https://jpahle.github.io/CoRC/" ; biotools:primaryContact , "Jonas Förster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3673 ; sc:citation , "pubmed:35696018" ; sc:description "The Chordata Olfactory Receptor Database (CORD) build from the annotation data from the command line tool Genome2OR" ; sc:featureList edam:operation_0269, edam:operation_0310, edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CORD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cord.ihuman.shanghaitech.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC7335209", "pubmed:32620861" ; sc:description "The amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions. Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax (https://cordax.switchlab.org), that explores amyloid sequence beyond its current boundaries." ; sc:name "Cordax" ; sc:softwareVersion "1.0" ; sc:url "https://cordax.switchlab.org" ; biotools:primaryContact "Joost Schymkowitz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3407 ; sc:citation , "pmcid:PMC9805595", "pubmed:36448701" ; sc:description "A R package for convenient correlation analysis" ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3766, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "cordial" ; sc:url "https://github.com/CutillasLab/cordial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC8501646", "pubmed:34627139" ; sc:description "R package for visualizing multi-omics differential correlation networks." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "CorDiffViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sqyu/CorDiffViz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0781, edam:topic_3303, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC7305714", "pubmed:32619700" ; sc:description "CORDITE is The Curated CORona Drug InTERactions Database for SARS-CoV-2. CORDITE aggregates all available knowledge on potential drugs for SARS-CoV-2. Since the outbreak in 2019, researchers are trying to find effective drugs against the SARS-CoV-2 virus based on de novo drug design and drug repurposing. The former approach is very time consuming and needs extensive testing in humans, whereas drug repurposing is more promising, as the drugs have already been tested for side effects, etc. At present, there is no treatment for COVID-19 that is clinically effective, but there is a huge amount of data from studies that analyze potential drugs. We developed CORDITE to efficiently combine state-of-the-art knowledge on potential drugs and make it accessible to scientists and clinicians" ; sc:featureList edam:operation_0305 ; sc:name "CORDITE" ; sc:url "https://cordite.mathematik.uni-marburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_2640, edam:topic_3053 ; sc:citation ; sc:description "CoRe is a robustly benchmarked R package for the identification of core fitness genes in genome-wide pooled CRISPR knock-out screens." ; sc:featureList edam:operation_2436, edam:operation_3227, edam:operation_3802 ; sc:name "CoRe" ; sc:url "https://rpubs.com/AleVin1995/CoRe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3316, edam:topic_3444 ; sc:citation , "pmcid:PMC6524794", "pubmed:31100074" ; sc:description "Cloud-ORiented Engine for advanced MRI simulations (coreMRI) - high-performance, publicly available MR simulation platform on the cloud." ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "coreMRI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.coreMRI.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "Core Hunter is a flexible tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general.In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed." ; sc:featureList edam:operation_2425, edam:operation_3429 ; sc:license "Apache-2.0" ; sc:name "Core Hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://www.corehunter.org" ; biotools:primaryContact "Herman De Beukelaer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0749, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC8699717", "pubmed:34898596" ; sc:description "A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data." ; sc:featureList edam:operation_0440, edam:operation_3192, edam:operation_3196, edam:operation_3222, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoRE-ATAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UcarLab/CoRE-ATAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622 ; sc:citation , "pubmed:32886787" ; sc:description "CoreCruncher is a Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. CoreCruncher is a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs." ; sc:featureList edam:operation_0310, edam:operation_3209 ; sc:name "CoreCruncher" ; sc:url "https://github.com/lbobay/CoreCruncher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3175 ; sc:citation , "pmcid:PMC10663985", "pubmed:37878789" ; sc:description "Flexible and efficient program for core-genome alignment of evolutionary diverse genomes." ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_0524, edam:operation_3182 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CoreDetector" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/mfruzan/CoreDetector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0781, edam:topic_3301 ; sc:citation , "pmcid:PMC3630060", "pubmed:23566564" ; sc:description "A webserver for the determination of core genes from sets of viral and small bacterial genomes." ; sc:featureList edam:operation_2454 ; sc:name "CoreGenes3.5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://binf.gmu.edu:8080/CoreGenes3.5/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4565029", "pubmed:25979476" ; sc:description "This package provides methods to identify active transcriptional programs, including methods and classes to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model TF cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary." ; sc:featureList edam:operation_0438 ; sc:license "GPL-3.0" ; sc:name "CoRegNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CoRegNet.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3301, edam:topic_3697 ; sc:citation , "pmcid:PMC5816963", "pubmed:29473009" ; sc:description "Search for a niche associated CORE MICrobiome." ; sc:featureList edam:operation_0324 ; sc:name "COREMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://core-mic.com/" ; biotools:primaryContact "Mark A. Williams", "Richard R. Rodrigue" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2331 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3303 ; sc:citation ; sc:contributor "http://www.coremine.com/medical/helppages/HelpPages.html#5" ; sc:description "This library is ideal for those seeking an overview of a complex subject while allowing the possibility to \"drill down\" to specific details. Search results are presented in a dashboard format comprised of panels containing various categories of information ranging from introductory sources to the latest scientific articles." ; sc:featureList edam:operation_0305, edam:operation_0337, edam:operation_2421 ; sc:funder "http://www.coremine.com/medical/helppages/HelpPages.html#5" ; sc:name "Coremine Medical" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UiO" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.coremine.com/medical" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3176, edam:topic_3295, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC7493859", "pubmed:32938377" ; sc:description "CORENup is a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. 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It is a collection of Perl script for the alignment of SARS-CoV-2 genomes and the functional annotation of genetic variants." ; sc:featureList edam:operation_0362, edam:operation_3431, edam:operation_3672 ; sc:name "CorGAT" ; sc:softwareHelp ; sc:url "http://corgat.cloud.ba.infn.it/galaxy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:16845099" ; sc:description "Measures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters." ; sc:featureList edam:operation_0230, edam:operation_0236, edam:operation_0364, edam:operation_0449 ; sc:name "CorGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://corgen.molgen.mpg.de" ; biotools:primaryContact "Philipp W. Messer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3407, edam:topic_3810 ; sc:citation , "pmcid:PMC7109041", "pubmed:32257241" ; sc:description "The CGDB (Coriander Genome Database) is mainly contained the coriander genome, transcriptome, and metabolome datasets" ; sc:featureList edam:operation_0553, edam:operation_2421, edam:operation_3216, edam:operation_3431, edam:operation_3478 ; sc:name "Coriander Genomics Database" ; sc:url "http://cgdb.bio2db.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199 ; sc:citation ; sc:description "CoRINs (Comparator of Residue Interaction Networks) is a web tool for comparing multiple residue interaction networks (RINs) that generates easy to understand results through interactive tables, graphics and downloable text files. CoRINs reports may be useful in the evaluation of protein conformational variation, as an additional tool to validate models from homology modeling, or to assess the putative impacts of a mutation on the protein structure and activity, by identifying its effects on the protein network." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3925 ; sc:name "CoRINs" ; sc:url "https://github.com/LasisUFRN/CoRINs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780 ; sc:citation ; sc:description "Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project." ; sc:featureList edam:operation_0338, edam:operation_0346 ; sc:name "CorkOakDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-PT" ; sc:softwareHelp ; sc:url "http://corkoakdb.org/" ; biotools:primaryContact "Daniel Sobral" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9547434", "pubmed:36207678" ; sc:description "Comparative Meta RNA-Seq Data Standardized Analysis Pipeline (CMRP) is a processing frame for the standardized analysis of Meta RNA-Seq raw data from wide-ranged species." ; sc:featureList edam:operation_0524, edam:operation_3223, edam:operation_3680, edam:operation_3800, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CoRMAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/rubysheng/CoRMAP.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pubmed:28456158" ; sc:description "It fits correlation motif model to multiple studies to detect study specific differential expression patterns." ; sc:featureList edam:operation_0449 ; sc:license "GPL-2.0" ; sc:name "Cormotif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Cormotif.html" ; biotools:primaryContact "Yingying Wei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional." ; sc:featureList edam:operation_3197 ; sc:license "GPL-2.0" ; sc:name "CorMut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CorMut.html" ; biotools:primaryContact "Zhenpeng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Corna is a Python package that perform Natural Abundance Correction on the output intensity of metabolites, obtained after performing Mass Spectrometry(MS)." ; sc:featureList edam:operation_3632, edam:operation_3799, edam:operation_3803 ; sc:name "Corna" ; sc:url "https://github.com/raaisakuk/NA_Correction" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3071, edam:topic_3523 ; sc:citation ; sc:description "Analysis of combinatorial cell-based RNAi screens." ; sc:featureList edam:operation_1812, edam:operation_2428, edam:operation_2495, edam:operation_3435, edam:operation_3439 ; sc:license "Artistic-2.0" ; sc:name "coRNAi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "https://bioconductor.org/packages/3.4/bioc/html/coRNAi.html" ; biotools:primaryContact "Elin Axelsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Coverage-dependent RNA-Seq analysis of gene expression data without biological replicates." ; sc:featureList edam:operation_2495, edam:operation_3680 ; sc:name "CORNAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/joel-lzb/CORNAS" ; biotools:primaryContact "Tsung Fei Khang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; 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sc:additionalType edam:data_1669 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "This tool allows you to do co-expression analysis using either predefined or user-defined groups of micro array experiments." ; sc:featureList edam:operation_0315 ; sc:name "CorNet Arabidopsis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB", "UGent", "VIB" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://cornet.psb.ugent.be" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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biotools:primaryContact "Shahab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "Fit Corona / COVID cases of your own country with this simple script. 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Feature profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria are provided." ; sc:featureList edam:operation_2945, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "coseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/coseq.html" ; biotools:primaryContact "Andrea Rau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:33241320" ; sc:description "COSIFER (COnSensus Interaction Network InFErence Service) is a Python package for the consensus inference of molecular interaction networks. Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources. COSIFER runs multiple selected inference algorithms on your expression data and returns a consensus interaction network." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3925 ; sc:license "MIT" ; sc:name "COSIFER" ; sc:url "https://ibm.biz/cosifer-aas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3300, edam:topic_3304, edam:topic_3489 ; sc:citation ; sc:description """Time distributed data analysis by Cosinor.Online application. Tools for estimating and predicting the cosinor model version 1.1 from CRAN. cosinor is a set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients. cosinor: Tools for estimating and predicting the cosinor model. Molcan, L. (2019). Time distributed data analysis by Cosinor. Online application. bioRxiv, 805960. Preprint available at BioRxiv, doi: https://doi.org/10.1101/805960. Cosinor Online, cosinor on the web, is a simple web-based application evaluating the presence of 24-h periodicity. 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CoVex integrates virus-human protein interactions, human protein-protein interactions, and drug-target interactions. It allows visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drug candidates. Thus, CoVex is a resource to understand molecular mechanisms of pathogenicity and to prioritize candidate therapeutics." ; sc:featureList edam:operation_3925, edam:operation_3938 ; sc:name "CoVex" ; sc:url "https://exbio.wzw.tum.de/covex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3297, edam:topic_3375, edam:topic_3382, edam:topic_3400 ; sc:citation , "pmcid:PMC9913043", "pubmed:36763096" ; sc:description "This database enables systematic analysis and interpretation of this large-scale dataset by providing a comprehensive view of various features such as affinity, neutralization, in vivo protection and effector functions for each antibody." ; sc:featureList edam:operation_0310, edam:operation_0416, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "COVIC-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://covicdb.lji.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3374, edam:topic_3379, edam:topic_3400, edam:topic_3930 ; sc:citation , "pmcid:PMC7454247" ; sc:description "COVID-19 antibody therapeutics tracker is a global online database of antibody therapeutics for the prevention and treatment of COVID-19." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3454 ; sc:name "COVID-19 Antibody Therapeutics Tracker" ; sc:url "https://chineseantibody.org/covid-19-track/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3360, edam:topic_3384 ; sc:citation ; sc:description "OncoMX has been expanded to include COVID-19 biomarkers." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3436 ; sc:name "COVID-19 biomarkers" ; sc:url "https://data.oncomx.org/covid19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_3303 ; sc:citation , "pmcid:PMC7537053", "pubmed:32981130" ; sc:description "Covid-19.bioreproducibility.org is a web resource for SARS-CoV-2-related structural models. Structural biologists have already determined hundreds of experimental X‐ray, cryo‐EM, and NMR structures of proteins and nucleic acids related to this coronavirus, and this number is still growing. The system can help biomedical researchers, who may not necessarily be experts in structural biology, navigate through the flood of structural models. It aggregates expert‐verified information about SARS‐CoV‐2‐related macromolecular models. In this article," ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3431, edam:operation_3454, edam:operation_3938 ; sc:name "Covid-19.bioreproducibility.org" ; sc:url "http://Covid-19.bioreproducibility.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0769, edam:topic_3299, edam:topic_3305 ; sc:citation ; sc:description "COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking." ; sc:featureList edam:operation_0244, edam:operation_0308, edam:operation_3196, edam:operation_3431, edam:operation_3695 ; sc:license "MIT" ; sc:name "COVID-19 CG" ; sc:url "http://covidcg.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3303, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC8117951", "pubmed:33997112" ; sc:description "COVID-19-CT-CXR is a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3359, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "COVID-19-CT-CXR" ; sc:url "https://github.com/ncbi-nlp/COVID-19-CT-CXR" ; biotools:primaryContact "Zhiyong Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Very basic data analysis and visualization on the spread of the COVID-19 virus in Italy" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "covid-19 data analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.7" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74556-covid-19-data-analysis" ; biotools:primaryContact "Andrea Augello" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3489 ; sc:citation , "pubmed:34048576" ; sc:description "COVID-19 Data Portal is a tool for accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "COVID-19 Data Portal" ; sc:url "https://www.covid19dataportal.org/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0634, edam:topic_3068 ; sc:citation , ; sc:description "COVID-19 Knowledge Graph is a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology." ; sc:license "CC0-1.0" ; sc:name "COVID-19 Knowledge Graph" ; sc:url "https://github.com/covid19kg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0632, edam:topic_3168, edam:topic_3324 ; sc:citation ; sc:description "he SARS-CoV-2 mutation browser is easy, efficient, and user friendly that only deals with novel coronavirus and display the viral genome variation around the globe on a single platform for the convenience of the researchers and virologists. The browser features comprehensive integration of a genomic sequence of SARS-CoV-2along with their metadata information from NGDC, NCBI, and GISAID. Furthermore, it is open access mutation browser that displays the region and gene-wise (5UTR, ORFab, S, E, M, N, 3UTR) distribution of mutation data of particular virus isolate and also provides position and statistics of mutations. Moreover, viral primer sequence information is also displayed on the same page “primer infopedia”." ; sc:featureList edam:operation_0308, edam:operation_3208, edam:operation_3227 ; sc:name "SARS-CoV-2 Mutation Browser" ; sc:softwareVersion "1.3" ; sc:url "http://covid-19.dnageography.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0781, edam:topic_3305, edam:topic_3379 ; sc:citation , "pubmed:33346828" ; sc:description "The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19." ; sc:featureList edam:operation_3280, edam:operation_3431, edam:operation_3625, edam:operation_3938 ; sc:license "CC0-1.0" ; sc:name "COVID-19 Ontology" ; sc:url "https://bioportal.bioontology.org/ontologies/COVID-19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_0769, edam:topic_3063 ; sc:citation , "pubmed:34042709" ; sc:description "COVID-19 preVIEW is a tool for semantic search to explore COVID-19 research preprints." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:name "COVID-19 preVIEW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://preview.zbmed.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315, edam:topic_3324 ; sc:citation ; sc:description """COVID-19 Scenarios is an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2. This tool is based on the SIR model that simulates a COVID19 outbreak. The primary purpose of the tool is to explore the dynamics of COVID19 cases and the associated strain on the health care system in the near future.""" ; sc:featureList edam:operation_1812, edam:operation_2426, edam:operation_3096 ; sc:license "MIT" ; sc:name "COVID-19 Scenarios" ; sc:url "http://covid19-scenarios.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_3063, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC7989301", "pubmed:33674830" ; sc:description "COVID-19 SignSyma is a tool foor fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model." ; sc:featureList edam:operation_0306, edam:operation_3435 ; sc:name "COVID-19 SignSym" ; sc:url "https://clamp.uth.edu/covid/nlp.php" ; biotools:primaryContact , "Masoud Rouhizadeh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3063, edam:topic_3361, edam:topic_3379 ; sc:citation , "pmcid:PMC7337837", "pubmed:32569358" ; sc:description """COVID-19 TestNorm is a tool to normalize COVID-19 testing names to LOINC codes. Large observational data networks that leverage routine clinical practice data in electronic health records (EHRs) are critical resources for research on coronavirus disease 2019 (COVID-19). Data normalization is a key challenge for the secondary use of EHRs for COVID-19 research across institutions. In this study, we addressed the challenge of automating the normalization of COVID-19 diagnostic tests, which are critical data elements, but for which controlled terminology terms were published after clinical implementation. We developed a simple but effective rule-based tool called COVID-19 TestNorm to automatically normalize local COVID-19 testing names to standard LOINC (Logical Observation Identifiers Names and Codes) codes. COVID-19 TestNorm was developed and evaluated using 568 test names collected from 8 healthcare systems""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3799 ; sc:name "COVID-19 TestNorm" ; sc:url "https://clamp.uth.edu/covid/loinc.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0781, edam:topic_3324 ; sc:author "Christoph Schönenberger" ; sc:description "Dashboard showing recent developments of the COVID-19 virus pandemic. The latest open data on the COVID-19 spread are regularly downloaded and displayed in a map, summary tables, key figures and plots." ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "COVID-19 Dashboard" ; sc:url "https://chschoenenberger.shinyapps.io/covid19_dashboard/" ; biotools:primaryContact "Christoph Schönenberger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3418, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC9035978", "pubmed:35468755" ; sc:description "A database for tracking the contribution of genomics and precision health to the COVID-19 pandemic response." ; sc:featureList edam:operation_0306, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "COVID-19 GPH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phgkb.cdc.gov/PHGKB/coVInfoStartPage.action" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3336 ; sc:contributor ; sc:description "Visualises linked human biological data related to SARS-CoV-2 in the form of a knowledge graph, using a range of publicly available data. Includes gene, protein, gene ontology, reaction, pathway, homology, protein domain, phenotype/disease, and GWAS data and the interactions between them. KnetMiner scores and ranks genes to give the most relevant results relating to your query search." ; sc:name "COVID-19 KnetMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://knetminer.org/COVID-19/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3300 ; sc:citation ; sc:description "COVID-19 Living OVerview of Evidence (COVID-19 L·OVE) is a public repository and classification platform for COVID-19 articles." ; sc:featureList edam:operation_2429 ; sc:name "COVID-19 L_OVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://app.iloveevidence.com/covid19" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3305, edam:topic_3308 ; sc:citation , "pmcid:PMC9934388", "pubmed:36801619" ; sc:description "The online platform to query gene expression differences between severe and mild COVID-19 patients in these datasets." ; sc:featureList edam:operation_0560, edam:operation_2238, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "COVID-19 MvsS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kuanrongchan-covid19-severity-app-t7l38g.streamlitapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0781, edam:topic_3345, edam:topic_3517 ; sc:citation , ; sc:description "Phenotype data dictionary for COVID-19 patients within the COVID-19 Host Genetics Initiative, employed in several clinical studies around the hospitals and labs of the network." ; sc:name "COVID-19 phenotype definition" ; sc:url "http://gmql.eu/phenotype/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3305, edam:topic_3379, edam:topic_3382, edam:topic_3400 ; sc:citation , "pmcid:PMC9701211", "pubmed:36435936" ; sc:description "the COVID-19 Seroprevalence Studies Hub, known as COVID-19 SeroHub, is an online dashboard intended to help researchers and policymakers monitor studies of Severe Acute Respiratory" ; sc:featureList edam:operation_0337, edam:operation_0416, edam:operation_3431 ; sc:license "Not licensed" ; sc:name "COVID-19 SeroHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://covid19serohub.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3344 ; sc:description "Covid-19RiskPrediction is a MATLAB script for COVID-19 Patient/Non-Patient Risk Prediction using AI." ; sc:isAccessibleForFree true ; sc:name "Covid-19RiskPrediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74754-covid-19riskprediction" ; biotools:primaryContact "Amburose Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3372 ; sc:citation , "pmcid:PMC7340090", "pubmed:32834624" ; sc:description "COVID-ABS is an agent-based model of COVID-19 epidemic to simulate health and economic effects of social distancing interventions. COVID-ABS is a SEIR (Susceptible-Exposed-Infected-Recovered) agent-based model that aims to simulate the pandemic dynamics using a society of agents emulating people, business and government." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "COVID-ABS" ; sc:url "https://github.com/petroniocandido/COVID19_AgentBasedSimulation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0160, edam:topic_0196, edam:topic_0199, edam:topic_3500 ; sc:citation ; sc:description "COVID-Align is an accurate online alignment of hCoV-19 genomes using a profile HMM." ; sc:featureList edam:operation_0300, edam:operation_0492, edam:operation_3182, edam:operation_3192 ; sc:name "COVID-Align" ; sc:url "https://covalign.pasteur.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3452, edam:topic_3520 ; sc:citation , , ; sc:description "COVID-CT-Mask-Net is a model for prediction COVID-19 from CT Scans Using Regional Features." ; sc:featureList edam:operation_0479, edam:operation_3359, edam:operation_3435 ; sc:name "COVID-CT-Mask-Net" ; sc:url "https://github.com/AlexTS1980/COVID-CT-Mask-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC7906283", "pubmed:33643375" ; sc:description "COVID-DeepPredictor is a recurrent neural network to predict SARS-CoV-2 and other pathogenic viruses." ; sc:featureList edam:operation_3461, edam:operation_3898, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "COVID-DeepPredictor" ; sc:url "http://www.nitttrkol.ac.in/indrajit/projects/COVID-DeepPredictor/" ; biotools:primaryContact "Indrajit Saha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "This graphic interface displays the covid time series (cases, deaths, vaccinations and much more) in many selectable manners." ; sc:featureList edam:operation_0416, edam:operation_0560 ; sc:isAccessibleForFree true ; sc:name "Covid GUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.0.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74973-covid-gui" ; biotools:primaryContact "Peter Seibold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3053, edam:topic_3170, edam:topic_3517 ; sc:citation , "pmcid:PMC9599684", "pubmed:36291657" ; sc:description "A Web-Based Prediction of COVID-19 Host Genes via Network Boosting of Genome-Wide Association Data." ; sc:featureList edam:operation_2454, edam:operation_3196, edam:operation_3925 ; sc:license "Not licensed" ; sc:name "COVID-GWAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://inetbio.org/covidgwab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071 ; sc:citation ; sc:description "COVID-KOP (COVID linked in Knowledge Oriented Pathways) is a biomedical reasoning system combining the knowledge existing in the ROBOKOP knowledge graph and data collected about the COVID-19 pandemic." ; sc:name "COVID-KOP" ; sc:url "https://covidkop.renci.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384, edam:topic_3452, edam:topic_3474, edam:topic_3954 ; sc:citation ; sc:description "Deep Convolutional Neural Network for Severity Assessment of COVID-19 Cases from Chest X-ray Images." ; sc:featureList edam:operation_3443, edam:operation_3927 ; sc:name "COVID-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://covid-net.ml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_3303, edam:topic_3518 ; sc:citation , "pmcid:PMC8570443", "pubmed:34748989" ; sc:description "The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters." ; sc:featureList edam:operation_0314, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "COVID-ONE-hi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.covid-one.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3384, edam:topic_3452, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9015255", "pubmed:35465215" ; sc:description "A clinical decision support system for COVID-19 detection." ; sc:featureList edam:operation_3443, edam:operation_3659, edam:operation_3936 ; sc:license "Not licensed" ; sc:name "COVID-opt-aiNet" ; sc:url "https://github.com/faizakhan1925/COVID-opt-aiNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0781, edam:topic_3170, edam:topic_3305, edam:topic_3474 ; sc:citation ; sc:description "COVID-Predictor is a Machine Learning model to Predict Novel Coronavirus." ; sc:featureList edam:operation_2428, edam:operation_3461, edam:operation_3472 ; sc:name "COVID-Predictor" ; sc:url "http://www.nitttrkol.ac.in/indrajit/projects/COVID-Predictor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0769, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC9012066", "pubmed:35428185" ; sc:description "A webserver for the analysis of SARS-CoV-2 sequencing data." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "COVID-Profiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genomics.lshtm.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3474 ; sc:citation ; sc:description "COVID-SGIS is a smart tool for dynamic monitoring and temporal forecasting of Covid-19." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "COVID-SGIS" ; sc:url "https://github.com/Biomedical-Computing-UFPE/Covid-SGIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3322, edam:topic_3324, edam:topic_3384 ; sc:citation ; sc:description "COVID Term is constructed by Institute of Medical Information, Chinese Academy of Medical Sciences and consists of the bilingual preferred terms, abbreviations, synonyms and some definitions and sources for concepts related with COVID-19 in disease, viruses, clinical manifestation, infected population, epidemic prevention and control, psychological assistance et. al." ; sc:featureList edam:operation_2422 ; sc:name "COVID Term" ; sc:url "http://covidterm.imicams.ac.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3305, edam:topic_3324, edam:topic_3379, edam:topic_3394 ; sc:citation , ; sc:description "COVID-TRACK is a Python based web-application that provides a platform for tracking testing, incidence, hospitalizations, and deaths related to COVID-19 along with various derived quantities. Our application makes the comparison across states in the USA and countries in the world easy to explore, with useful transformation options including per capita, log scale, and/or moving averages." ; sc:featureList edam:operation_2429, edam:operation_3436, edam:operation_3503 ; sc:name "COVID-TRACK" ; sc:url "https://covidtracking.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "The application allows an analysis of COVID 19 cases in the country of interest as well as a curve fit for the next few days" ; sc:isAccessibleForFree true ; sc:name "APP de COVID 19 con MATLAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75152-app-de-covid-19-con-matlab" ; biotools:primaryContact "Carlos Tapia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Linear, exponential, logistic, Gompertz, Gauss, Fourier models fitted to epidemiological data from the COVID-19 outbreak." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "COVID19 Data Fitting" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75016-covid19-data-fitting-with-linear-and-nonlinear-regression" ; biotools:primaryContact "Lorand Gabriel Parajdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2640, edam:topic_3305, edam:topic_3375, edam:topic_3407 ; sc:citation , "pmcid:PMC7454591", "pubmed:32750131" ; sc:description "COVID-19 Drug interactions is a comprehensive, up-to-date, evidence-based COVID19 drug-drug interaction resource." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "COVID- 19 Drug interactions" ; sc:url "http://www.covid19-druginteractions.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3377, edam:topic_3379, edam:topic_3400, edam:topic_3474 ; sc:citation , "pmcid:PMC7952300", "pubmed:33716737" ; sc:description "COVID-19 drug repurposing system for In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19." ; sc:featureList edam:operation_3454, edam:operation_3925, edam:operation_3938 ; sc:license "MIT" ; sc:name "COVID-19 drug repurposing" ; sc:url "https://github.com/muntisa/immuno-drug-repurposing-COVID-19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344, edam:topic_3474 ; sc:description "The example trains a Machine Learning Model to forecast the number of covid-19 cases given the number of cases in previous days." ; sc:isAccessibleForFree true ; sc:name "COVID-19 Corona Forecasting using Machine Learning" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75423-covid-19-corona-forecasting-using-machine-learning" ; biotools:primaryContact "Akhilesh Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3344, edam:topic_3500 ; sc:description "MATLAB script for generating an animation displaying the spread of COVID-19 India and save it as Vid file." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "COVID19 India Spread Animation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75112-covid19-india-spread-animation" ; biotools:primaryContact "Siddharth Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "Shows the actual numbers of people affected with the corona virus COVID-19. Data obtained from https://corona.lmao.ninja/" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "COVID-19 infections" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74540-covid19" ; biotools:primaryContact "ThomasV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3512 ; sc:description "Script for visualizing COVID-19 infections in the European Union" ; sc:isAccessibleForFree true ; sc:name "COVID-19 infections" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75073-visualizacion-covid-19" ; biotools:primaryContact "Emmanuel Olivar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3344 ; sc:description "This model was created based off of fitVirus. This is a data-driven model that obtains up to date data and predicts the spread of COVID-19." ; sc:isAccessibleForFree true ; sc:name "COVID19 Modeling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.6.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74632-covid-19-modeling" ; biotools:primaryContact "JM2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Virus propagation simulator in MATLAB/Simulink" ; sc:isAccessibleForFree true ; sc:name "COVID-19 Propagation Simulator (Simulink)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74821-covid-19-propagation-simulator-simulink" ; biotools:primaryContact "Pavel Roslovets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "Track real time COVID19 cases in India" ; sc:isAccessibleForFree true ; sc:name "COVID19 Realtime tracking simulation for Indian states" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74822-covid19-realtime-tracking-simulation-for-indian-states" ; biotools:primaryContact "Siddharth Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Visualize the spread of COVID 19" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "COVID19 spread visualizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75431-hbarlivecovid19v3" ; biotools:primaryContact "Lateef Adewale Kareem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Using Text Analytics in MATLAB to explore research articles related to COVID-19 and other coronaviruses." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:name "COVID-19 - TextAnalytics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74942-covid-19_textanalytics_matlab" ; biotools:primaryContact "Sohini Sarkar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3324, edam:topic_3344 ; sc:citation ; sc:description "Agent-based Transmission model of COVID-19" ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "COVID-19 Transmission model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://awww.mathworks.com/matlabcentral/fileexchange/75733-transmission-model-of-covid-19" ; biotools:primaryContact "Erik Cuevas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3344, edam:topic_3382, edam:topic_3500 ; sc:description "This code will generate an animation displaying the spread of COVID-19 and save it as a video file. Data is obtained and processed from HDX." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "COVID-19 World Spread Animation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.5.5" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74718-covid-19-world-spread-animation" ; biotools:primaryContact "JM2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , , "pmcid:PMC7928848", "pmcid:PMC8290949", "pubmed:34272225", "pubmed:34505002" ; sc:description "Population-based Forward-time Simulator for the Outbreak of COVID-19" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "COVID19 Outbreak Simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.3" ; sc:url "https://ictr.github.io/covid19-outbreak-simulator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3305 ; sc:citation , "pmcid:PMC8122363", "pubmed:33991092" ; sc:description "The package covid19census provides functions to extract COVID-19 cases, deaths, hospitalizations and test of U.S. and Italy at the county and regional level, respectively, and then combines them with other population metrics (age, sex, prevalence of chronic conditions, income indexes, access to health services and many others)." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3659 ; sc:license "MIT" ; sc:name "covid19census" ; sc:url "https://github.com/c1au6i0/covid19census" ; biotools:primaryContact "Luigi Marchionni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Matlab tool to download and plot Covid-19 data" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "covid19data" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74935-covid19data" ; biotools:primaryContact "Matthias Chung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0634, edam:topic_3308, edam:topic_3336 ; sc:citation , "pubmed:34554255" ; sc:description "Database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "COVID19db" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hpcc.siat.ac.cn/covid19db" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3577 ; sc:citation ; sc:description "Covid19Risk.ai is an open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19." ; sc:featureList edam:operation_2422, edam:operation_3659 ; sc:name "Covid19Risk.ai" ; sc:url "https://covid19risk.ai/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3322, edam:topic_3324, edam:topic_3344 ; sc:description "This simulation shows how COVID-19 Spread World wide" ; sc:isAccessibleForFree true ; sc:name "COVID-19 Spread Model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74720-covid-19-spred-model" ; biotools:primaryContact "Deepesh B" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC10366449", "pubmed:37497545" ; sc:description "COVIDanno, COVID-19 annotation in human, which is an integrated RNA-seq database of SARS-CoV-2-infected in vitro models." ; sc:featureList edam:operation_3223, edam:operation_3672, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "COVIDanno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biomedbdc.wchscu.cn/COVIDanno/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3384, edam:topic_3452, edam:topic_3474, edam:topic_3954 ; sc:citation , "pmcid:PMC7901302", "pubmed:33644298" ; sc:description "COVIDC is an expert system to diagnose COVID-19 and predict its severity using chest CT scans." ; sc:featureList edam:operation_0479, edam:operation_3092, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "COVIDC" ; sc:url "https://covidc.pythonanywhere.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7893172", "pubmed:33603193" ; sc:description "CovidCTNet is an open-source deep learning approach to diagnose covid-19 using small cohort of CT images." ; sc:featureList edam:operation_3443 ; sc:name "CovidCTNet" ; sc:url "https://github.com/mohofar/covidctnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_2269, edam:topic_3474, edam:topic_3948 ; sc:citation , "pmcid:PMC7299140", "pubmed:32555466" ; sc:description "COVIDep provides an up-to-date set of B-cell and T-cell epitopes that can serve as potential vaccine targets for SARS-CoV-2. The identified epitopes are experimentally-derived from the 2003 SARS virus and have a close genetic match with the available SARS-CoV-2 sequences. 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sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0602, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:34581813" ; sc:description "CovPDB, a database solely dedicated to high-resolution cocrystal structures of biologically relevant cP–L complexes, curated from the Protein Data Bank" ; sc:featureList edam:operation_2421, edam:operation_3938, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:name "CovPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pharmbioinf.uni-freiburg.de/covpdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0632, edam:topic_2275, edam:topic_2828 ; sc:citation ; sc:description "CovPepDock is a web application for covalent flexible peptide docking in Rosetta." ; sc:featureList edam:operation_0418, edam:operation_3899, edam:operation_4009 ; sc:name "CovPepDock" ; sc:softwareHelp ; sc:url "https://rosie.graylab.jhu.edu/cov_pep_dock" ; biotools:primaryContact "Nir London" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description "CovRadar is a tool for molecular surveillance of the Corona spike protein. 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It contains cell penetrating peptides (CPPs) alongwith their secondary & tertiary structure. 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The key idea of CRGNet is to iteratively select unlabeled pixels with high confidence to expand the annotated area from the original sparse points" ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CRGNet" ; sc:url "https://github.com/YonghaoXu/CRGNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0659, edam:topic_3673 ; sc:citation , "pubmed:32844531" ; sc:description "CRHP Finder is a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:name "CRHP Finder" ; sc:url "https://cge.cbs.dtu.dk/services/CRHP-Finder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0804, edam:topic_2640, edam:topic_3170, edam:topic_3400 ; sc:citation , "pmcid:PMC7658727", "pubmed:33214875" ; sc:description "The Cancer Research Institute (CRI) iAtlas is an interactive web platform for data exploration and discovery in the context of tumors and their interactions with the immune microenvironment. iAtlas allows researchers to study immune response characterizations and patterns for individual tumor types, tumor subtypes, and immune subtypes. iAtlas supports computation and visualization of correlations and statistics among features related to the tumor microenvironment, cell composition, immune expression signatures, tumor mutation burden, cancer driver mutations, adaptive cell clonality, patient survival, expression of key immunomodulators, and tumor infiltrating lymphocyte (TIL) spatial maps." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3463 ; sc:name "CRI iAtlas" ; sc:url "https://www.cri-iatlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "Used for genetic linkage analysis of diploid species. This version has been upgraded to handle large pedigrees with large numbers of markers on modern hardware." ; sc:featureList edam:operation_0283 ; sc:license "Not licensed" ; sc:name "CRI-MAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , ; sc:url "http://www.animalgenome.org/tools/share/crimap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3382 ; sc:citation ; sc:description "This tool provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity." ; sc:featureList edam:operation_3443 ; sc:license "Artistic-2.0" ; sc:name "CRImage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CRImage.html" ; biotools:primaryContact "Henrik Failmezger", "Yinyin Yuan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pubmed:36349867" ; sc:description "Crimp allows to align clusters across multiple clusterings, based on their matrices of membership coefficients (Q-matrices). This is frequently done to post-process outputs from programs like Structure (Pritchard et al. 2000). Crimp can be used as a much faster and typically more accurate alternative to CLUMPP (Jakobsson & Rosenberg 2007)." ; sc:featureList edam:operation_2424, edam:operation_2928, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Crimp" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/ulilautenschlager/crimp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2275, edam:topic_3384, edam:topic_3489 ; sc:citation ; sc:description "Crimson (cardiovascular integrated modelling & simulation) is an advanced simulation environment for subject-specific hemodynamic analysis. Crimson is integrating best-in-class open source-solutions for parallel flow solvers, fluid-structure interactions, GUI-based boundary condition specification, data assimilation, medical image processing, mesh generation, transitional hemodynamics, and much more." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3096 ; sc:license "AGPL-3.0" ; sc:name "CRIMSON" ; sc:softwareHelp ; sc:url "http://www.crimson.software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0204, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation ; sc:description "CrinetCeRna Interaction NETwork) is a computational R tool to infer genome-wide competing endogenous RNA (ceRNA) interactions and groups." ; sc:featureList edam:operation_0463, edam:operation_2437, edam:operation_3629, edam:operation_3792 ; sc:license "CC-BY-NC-4.0" ; sc:name "Crinet" ; sc:url "https://github.com/bozdaglab/crinet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Computational Resources for predicting protein-macromolecular interactions" ; sc:featureList edam:operation_2945 ; sc:name "CRIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/crip/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0203, edam:topic_2830, edam:topic_3170 ; sc:citation , "pmcid:PMC8600631", "pubmed:34806017" ; sc:description "Complete Reconstruction of Immunoglobulin V-D-J Sequences from RNA-seq" ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CRIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Rashedul/CRIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640 ; sc:author ; sc:citation ; sc:contributor "Chiara Barbera" ; sc:description "CRIS_single-sample is a computational R workflow to replicate the training, testing and biological validation of a multi-label classifier (ML2CRIS) for colorectal cancer intrinsic subtyping." ; sc:name "CRIS_single-sample" ; sc:url "https://github.com/DEIB-GECO/CRIS_single-sample" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:20529923" ; sc:description "Identifies rare and common variants in pooled sequencing data" ; sc:featureList edam:operation_3197 ; sc:name "CRISP" ; sc:softwareHelp ; sc:url "https://bansal-lab.github.io/software/crisp.html" ; biotools:primaryContact "Vikas Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0632, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:32215567" ; sc:description "CRiSP (Cystine-Rich peptide Structure Prediction) is an accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning." ; sc:featureList edam:operation_0471, edam:operation_0474, edam:operation_1850 ; sc:name "CRiSP" ; sc:url "http://wulab.com.cn/CRISP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0659, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:33010154" ; sc:description "CRISP-view is a database of functional genetic screens spanning multiple phenotypes." ; sc:featureList edam:operation_2428, edam:operation_2436, edam:operation_3196 ; sc:name "CRISP-view" ; sc:url "http://crispview.weililab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2885, edam:topic_3170, edam:topic_3512, edam:topic_3912 ; sc:citation , , "pmcid:PMC7256011", "pubmed:32494309" ; sc:description """A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications. Software used to design guide RNA sequences for CRISPR/Cas9 genome editing. Steps to install crispRdesignR (tested in R version 3.4.4):. This software aims to provide all scientifically pertinent information when designing guide RNA sequences for Cas9 genome editing. The DAK1.fasta and DAK1_short.txt file contains a DNA sequence native to the DAK1 gene that can be copied and pasted into crispRdesignR or uploaded as a file (in the GUI version)""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3096 ; sc:name "crispRdesignR" ; sc:url "https://github.com/dylanbeeber/crispRdesignR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3382, edam:topic_3422, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC8921635", "pubmed:35022651" ; sc:description "CRISP: a deep learning architecture for GC × GC–TOFMS contour ROI identification, simulation and analysis in imaging metabolomics" ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CRISP" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/vivekmathema/GCxGC-CRISP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3173 ; sc:citation ; sc:description "CrisPam is a web tool that detects SNP-derived PAMs for allele-specific targeting by the CRISPR/Cas system. The algorithm scans the generation of each reported PAM for a given DNA sequence and its variations. A successful result is such that at least one PAM is generated by a SNP. Thus, the PAM shall be part of the variant allele only and the Cas protein will therefore be able to exclusively bind the variant allele for gene-editing, while the wildtype allele remains unchanged." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3661 ; sc:name "CrisPam" ; sc:url "https://github.com/ristllin/CrisPam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "A CRISPR Interactive database." ; sc:featureList edam:operation_0338 ; sc:isAccessibleForFree true ; sc:name "Crispi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:url "http://crispi.genouest.org/" ; biotools:primaryContact "GenOuest platform" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622, edam:topic_3053 ; sc:citation ; sc:description "Design, evaluate and clone guide sequences for the CRISPR/Cas9 system." ; sc:featureList edam:operation_3649 ; sc:license "CC-BY-4.0" ; sc:name "CRISPOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crispor.tefor.net/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3168, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC7511213", "pubmed:32963098" ; sc:description "CRISPR-CBEI is a web-based designing tool for Cytosine Base Editor mediated gene Inactivation" ; sc:featureList edam:operation_0436, edam:operation_2421, edam:operation_3096 ; sc:license "Apache-2.0" ; sc:name "CRISPR-CBEI" ; sc:url "https://taolab.nwafu.edu.cn/crisprcbei/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3343, edam:topic_3511 ; sc:citation , "pmcid:PMC5584922", "pubmed:28873439" ; sc:description "A web server for designing focused CRISPR screening experiments." ; sc:featureList edam:operation_2478 ; sc:name "CRISPR-FOCUS" ; sc:softwareHelp ; sc:url "http://cistrome.org/crispr-focus/" ; biotools:primaryContact "X. Shirley Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pubmed:28624544" ; sc:description "A convenient, integrated toolkit to expedite all experimental designs and analyses of mutations for CRISPR/Cas9/Cpf1-based genome editing in plants and other organisms." ; sc:featureList edam:operation_0231 ; sc:license "Unlicense" ; sc:name "CRISPR-GE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://skl.scau.edu.cn/home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_2229, edam:topic_3173, edam:topic_3912 ; sc:citation , "pmcid:PMC9307495", "pubmed:35891797" ; sc:description "An online tool for designing highly efficient sgRNAs targeting cell surface proteins" ; sc:featureList edam:operation_0314, edam:operation_3096, edam:operation_3767 ; sc:name "CRISPR-Surfaceome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://crispr-surfaceome.siais.shanghaitech.edu.cn/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_3512 ; sc:citation ; sc:description """protein-centric CRISPR guide design for targeted proteome engineering. A protein-centric CRISPR gRNA design tool for TArgeted Protein Engineering. Existing CRIPSR gRNA design tools target protein-coding regions within genomic loci and non-specifically target the entire input region of DNA. Current tools fail to consider proteomic-based applications, so CRISPR-TAPE has been developed to reduce the substantial time burden associated with manual curation of gRNA libraries and empower the proteomics community. Hello, welcome to CRISPR-TAPE, a protein-centric gRNA design tool.""" ; sc:featureList edam:operation_0363, edam:operation_3695 ; sc:name "CRISPR-TAPE" ; sc:url "http://www.laboratorychild.com/crispr-tape" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1476, edam:format_1929 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1476, edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_1476 ; sc:name "RNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2275, edam:topic_2814, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC10127312", "pubmed:37098485" ; sc:description "Web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins." ; sc:featureList edam:operation_2441, edam:operation_3899, edam:operation_3901, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRISPR-Cas-Docker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.crisprcasdocker.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC10228036", "pubmed:37254060" ; sc:description "Cross-platform graphical analysis tool for high-throughput CRISPR-based genome editing evaluation." ; sc:featureList edam:operation_3096, edam:operation_3359, edam:operation_3695, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRISPR-GRANT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fuhuancheng/CRISPR-GRANT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC9825451", "pubmed:36350608" ; sc:description "CRISPRbase is a comprehensive database curating the outcome and evaluating off-target effects of base editors on various cell types and tissues in dozens of species" ; sc:featureList edam:operation_0314, edam:operation_3096, edam:operation_3227 ; sc:license "Not licensed" ; sc:name "CRISPRbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crisprbase.maolab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3174, edam:topic_3299, edam:topic_3673 ; sc:citation , "pmcid:PMC7968741", "pubmed:33667225" ; sc:description "CRISPRbuilder-TB is a tool that reconstructs the whole CRISPR locus from a Mycobacterium tuberculosis complex genome, by using Whole Genome Sequencing (WGS) data. This allows to deduce the real spoligotype, to detect mutants of spacers and direct repeats, insertion of mobile elements, and duplications. The Cas locus is reconstructed too. This is a semi automatic approach that leads to a set of contigs to assemble manually. Depending on the number, length, and quality of SRAs, the number of contigs can range from 1-2 patterns, in the best case scenario where the good quality of sequences allows a quasi-automatic reconstruction of the CRISPR cut in mobile element positions, to several contigs difficult to process, for too short or polluted reads." ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_3745, edam:operation_3963 ; sc:license "GPL-3.0" ; sc:name "CRISPRbuilder-TB" ; sc:url "https://github.com/cguyeux/CRISPRbuilder-TB" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3474 ; sc:author , ; sc:citation ; sc:description "Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRISPRcasIdentifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BackofenLab/CRISPRcasIdentifier" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0114, edam:topic_0121, edam:topic_3174, edam:topic_3474 ; sc:citation , "pubmed:35998924" ; sc:description "CRISPRCasStack is a toolkit capable of accurately identifying Cas proteins and comprehensively predicting CRISPR-Cas-related components, with the goal of accurately identifying potential Cas proteins that cannot currently be identified based on homology through a machine learning-based approach." ; sc:featureList edam:operation_3096, edam:operation_3767 ; sc:license "Not licensed" ; sc:name "CRISPRCasStack" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/yrjia1015/CRISPRCasStack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0160, edam:topic_0196, edam:topic_3174 ; sc:citation , ; sc:description "CRISPRCasTyper is a automated software tool with improved capabilities for identifying and typing CRISPR arrays and cas loci across prokaryotic sequences." ; sc:featureList edam:operation_0310, edam:operation_0435, edam:operation_0579 ; sc:license "MIT" ; sc:name "CRISPRCasTyper" ; sc:url "http://cctyper.crispr.dk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC9939378", "pubmed:36814834" ; sc:description "A R/Python package and an interactive web application, for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CRISPRcleanR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://crisprcleanr-webapp.fht.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0199, edam:topic_0621, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:18442988" ; sc:description "Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in this tool as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains." ; sc:featureList edam:operation_0237, edam:operation_3196, edam:operation_3197, edam:operation_3432 ; sc:name "CRISPRcompar" ; sc:url "http://crispr.u-psud.fr/CRISPRcompar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_2885 ; sc:citation "pubmed:17537822" ; sc:description "Detects this family of direct repeats found in the DNA of many bacteria and archaea." ; sc:featureList edam:operation_0237, edam:operation_0239, edam:operation_0379, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "CRISPRFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index" ; biotools:primaryContact "Marie Touchon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0203, edam:topic_3474, edam:topic_3930 ; sc:citation , "pubmed:33290505" ; sc:description "CRISPRidentify is a tool to search for CRISPR arrays which utilises machine learning approach for distinguishing false candidates from true CRISPRS. CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, CRISPRidentify approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as an intuitive measure of the likelihood that a given genomic region is a CRISPR array." ; sc:featureList edam:operation_0379, edam:operation_2421, edam:operation_3211 ; sc:name "CRISPRidentify" ; sc:url "https://github.com/BackofenLab/CRISPRidentify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3168, edam:topic_3293, edam:topic_3912 ; sc:citation , "pmcid:PMC10320192", "pubmed:37216595" ; sc:description "CRISPR-oriented web-tool to dissect the key molecular events during the co-evolution of CRISPR and anti-CRISPR mechanisms." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3092, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "CRISPRimmunity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.microbiome-bigdata.com/CRISPRimmunity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0199, edam:topic_0654 ; sc:citation , "pmcid:PMC7355252", "pubmed:32657417" ; sc:description "CRISPRLand, relies on an unexploited observation about the nature of the repair process: the landscape of the DNA repair is highly sparse in the (Walsh–Hadamard) spectral domain. This observation enables our framework to address key shortcomings that limit the interpretability and scaling of current deep-learning-based DNA repair models. In particular. ur proposed framework is based on a divide-and-conquer strategy that uses a fast peeling algorithm to learn the DNA repair models. CRISPRLand captures lower-degree features around the cut site, which enrich for short insertions and deletions as well as higher-degree microhomology patterns that enrich for longer deletions." ; sc:name "CRISPRLand" ; sc:url "https://github.com/UCBASiCS/CRISPRLand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0622, edam:topic_3053, edam:topic_3474 ; sc:citation , "pmcid:PMC8265192", "pubmed:34133710" ; sc:description "CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3695 ; sc:name "CRISPRloci" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rna.informatik.uni-freiburg.de/CRISPRloci/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3466, edam:format_3508, edam:format_3547, edam:format_3579 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:author , "Sita Saunders" ; sc:citation , "pmcid:PMC4147912", "pubmed:23863837", "pubmed:25161238" ; sc:description "Prediction of CRISPR RNA by repeat conservation." ; sc:featureList edam:operation_2454 ; sc:isAccessibleForFree true ; sc:name "CRISPRmap web server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "2.1.3" ; sc:url "http://rna.informatik.uni-freiburg.de/CRISPRmap/" ; biotools:primaryContact , "Sita Saunders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2229, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC9252781", "pubmed:35640601" ; sc:description "CRISPRnano is a javascript-based program that was developed for rapid deep sequencing based genotyping of nuclease edited cell clones." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3196, edam:operation_3227, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "CRISPRnano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.CRISPRnano.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3077, edam:topic_3297, edam:topic_3474 ; sc:citation , "pmcid:PMC8163799", "pubmed:34050182" ; sc:description "CRISPRon is a web application for CRISPR Cas9 on-target predictions. It enhances CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning." ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3431 ; sc:license "AGPL-3.0" ; sc:name "CRISPRon" ; sc:softwareHelp ; sc:url "https://rth.dk/resources/crispr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3512, edam:topic_3912 ; sc:citation , "pubmed:36271848" ; sc:description "Webservers for CRISPR Cas9 on- and off-target predictions." ; sc:featureList edam:operation_0440, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CRISPRon_off" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rth.dk/resources/crispr/crispron/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3474 ; sc:citation ; sc:description "Flexible and efficient tool for single guide RNA (sgRNAs) on-target activity prediction in CRISPR/Cas9 systems." ; sc:featureList edam:operation_0415 ; sc:name "CRISPRpred" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/khaled-rahman/CRISPRpred" ; biotools:primaryContact "M. Sohel Rahman", "Md. Khaledur Rahman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3912 ; sc:citation , "pmcid:PMC7268231", "pubmed:32487025" ; sc:description "CRISPRpred(SEQ) is a method for sgRNA on-target activity prediction that leverages only traditional machine learning techniques and hand-crafted features extracted from sgRNA sequences. We compare the results of CRISPRpred(SEQ) with that of DeepCRISPR, the current state-of-the-art, which uses a deep learning pipeline." ; sc:featureList edam:operation_3096, edam:operation_3937 ; sc:name "CRISPRpred(SEQ)" ; sc:url "https://github.com/Rafid013/CRISPRpredSEQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC8887420", "pubmed:34850137" ; sc:description "CRISPRroots: CRISPR–Cas9-mediated edits with accompanying RNA-seq data assessed for on-target and off-target sites." ; sc:featureList edam:operation_3096, edam:operation_3196, edam:operation_3223, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CRISPRroots" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rth.dk/resources/crispr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622, edam:topic_3053 ; sc:citation , "pmcid:PMC4172692", "pubmed:25247697" ; sc:description "The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not." ; sc:featureList edam:operation_3095 ; sc:license "GPL-2.0" ; sc:name "CRISPRseek" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CRISPRseek.html" ; biotools:primaryContact "Lihua Julie Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053 ; sc:citation ; sc:description "Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis." ; sc:featureList edam:operation_2451 ; sc:license "GPL-3.0" ; sc:name "crisprseekplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/crisprseekplus.html" ; biotools:primaryContact "Alper Kucukural" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , "pubmed:33084893" ; sc:description "crisprSQL is a SQL-based database for CRISPR/Cas9 off-target cleavage assays. It is a one-stop source for epigenetically annotated, base-pair resolved cleavage frequency distributions. This hand-curated dataset can act as an insight into state-of-the-art technologies driving transgenics, inform guide RNA design for genome engineering, and serve as a shared, transparent basis for modelling off-target DNA cleavage of CRISPR/Cas. Attached gene IDs make the high-resolution data usable for informing knockout screens, functional genomics and transcriptomics research." ; sc:featureList edam:operation_2421, edam:operation_3096, edam:operation_3799 ; sc:name "crisprSQL" ; sc:url "http://www.crisprsql.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:description "CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "CRISPRStudio" ; sc:url "https://github.com/moineaulab/CRISPRStudio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3912 ; sc:citation , "pmcid:PMC9486595", "pubmed:36124799" ; sc:description "CRISPRtracrRNA: an end-to-end standalone bioinformatic tool for tracrRNA predictions. In order to robustly predict the new tracrRNA candidates, CRISPRtracrRNA combines different sources of evidence." ; sc:featureList edam:operation_0292, edam:operation_0302, edam:operation_0481 ; sc:license "Not licensed" ; sc:name "CRISPRtracrRNA" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/BackofenLab/CRISPRtracrRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pubmed:27404876" ; sc:description "Provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants." ; sc:featureList edam:operation_0415, edam:operation_0564 ; sc:license "GPL-2.0" ; sc:name "CrispRVariants" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CrispRVariants.html" ; biotools:primaryContact "Helen Lindsay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC9630310", "pubmed:36323688" ; sc:description "A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies." ; sc:featureList edam:operation_3096, edam:operation_3211, edam:operation_3661 ; sc:license "Not licensed" ; sc:name "crisprVerse" ; sc:softwareHelp ; sc:url "https://github.com/crisprVerse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3168 ; sc:citation , "pmcid:PMC9128103", "pubmed:35610585" ; sc:description "A Python package for visualizing and analyzing CRISPR sequences." ; sc:featureList edam:operation_0337, edam:operation_0491, edam:operation_1812 ; sc:license "GPL-3.0" ; sc:name "CrisprVi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/crisprvi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3524 ; sc:citation ; sc:description "Discrete simulation tool for designing pooled genetic screens." ; sc:featureList edam:operation_2426 ; sc:name "CRISPulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crispulator.ucsf.edu/" ; biotools:primaryContact "Martin Kampmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3912 ; sc:citation , "pmcid:PMC6789908", "pubmed:31548381" ; sc:description "Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST | CRISPy-web now detects potential amino acid changes introducable by CRISPR-BEST" ; sc:featureList edam:operation_3096, edam:operation_3280 ; sc:name "crispy" ; sc:url "https://crispy.secondarymetabolites.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0621, edam:topic_3168, edam:topic_3796, edam:topic_3912 ; sc:citation ; sc:description "CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing. 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Users are able to upload their data sets and subsequently apply the standard workflow steps using a project-based structure and an easy to navigate interface. Along the way, the tool provides multiple familiar visualizations such as the hierarchically clustered genes with color-coded clusters, a similar tree for the samples and sample traits, module-trait correlations, and more. In addition, the tool allows for integrating multiple WGCNA projects using a correlation-based approach. Both data and visualizations can be exported" ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:name "crosslinkWGCNA" ; sc:url "https://github.com/LUMC-BioSemantics/crosslinkWGCNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "An efficient tool for converting genome coordinates between assemblies. 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sc:citation ; sc:description "A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis. It runs with data from human (hg19), mouse (mm9) or drosophila (dm3)." ; sc:featureList edam:operation_0445, edam:operation_2403 ; sc:name "CRUNCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://crunch.unibas.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0804, edam:topic_3360, edam:topic_3473, edam:topic_3934 ; sc:citation , "pmcid:PMC10477295", "pubmed:37666818" ; sc:description "A versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "CRUSTY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://crusty.humanitas.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_3071, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7490944", "pubmed:32928113" ; sc:description "CrustyBase is an interactive online database for crustacean transcriptomes. CrustyBase provides an environment for navigating and visualising crustacean transcriptome datasets. Users can search existing transcriptomes or import new datasets of their own." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3680 ; sc:name "CrustyBase" ; sc:url "https://crustybase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3299 ; sc:citation , "pmcid:PMC3762655", "pubmed:23898041" ; sc:description "Visualization platform for comparative genomics analyses in Brassicaceae species." ; sc:featureList edam:operation_3209 ; sc:name "CrusView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cmbb.arizona.edu/?page_id=250" ; biotools:primaryContact "Xiangfeng (Bryan) Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , ; sc:description "Cross-platform suite of analysis tools for interpreting protein mass spectrometry data." ; sc:featureList edam:operation_3214 ; sc:name "Crux" ; sc:url "http://crux.ms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0622, edam:topic_0634, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC8173893", "pubmed:34082700" ; sc:description "Whole Exome Sequencing Data Analyze System. Tool for annotating, interpreting and reporting genetic variants." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "Cruxome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://114.251.61.49:10024/cruxome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:35810958" ; sc:description "A web server for identifying circRNA-RBP variable-length binding sites based on stacked generalization ensemble deep learning network." ; sc:featureList edam:operation_2464, edam:operation_3436, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CRWS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Creates a density map from atomic coordinates, automatically including the density of solvent." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Cryo-EM image simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/33636-cryo-em-image-simulator" ; biotools:primaryContact "Fred Sigworth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0611, edam:topic_0820, edam:topic_2828, edam:topic_3520 ; sc:citation , "pmcid:PMC7494424", "pubmed:31768063" ; sc:description "cryoID is a python-based program that determines the unique identity of the protein(s) in unknown near-atomic resolution cryoEM density maps from a pool of candidate protein sequences." ; sc:featureList edam:operation_0480, edam:operation_2429, edam:operation_3629, edam:operation_3767 ; sc:license "MIT" ; sc:name "cryoID" ; sc:softwareHelp ; sc:url "https://github.com/EICN-UCLA/cryoID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0611, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33542510" ; sc:description "CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction." ; sc:featureList edam:operation_0244, edam:operation_2939, edam:operation_2990, edam:operation_3432, edam:operation_3457, edam:operation_3890 ; sc:license "GPL-3.0" ; sc:name "cryoDRGN" ; sc:url "https://github.com/zhonge/cryodrgn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0611 ; sc:description "Ontology to describe data and workflows in Cryo Electron Microscopy" ; sc:isAccessibleForFree true ; sc:name "CryoEM Ontology" ; sc:url "http://bioportal.bioontology.org/ontologies/CRYOEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_1317, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36967040" ; sc:description "Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning." ; sc:featureList edam:operation_2429, edam:operation_3457 ; sc:isAccessibleForFree true ; sc:name "CryoRes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cryores.zhanglab.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_2065 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0611, edam:topic_2814 ; sc:citation ; sc:description "A program for rapidly solving high-resolution 3D structures of proteins and drug targets from cryo-electron microscopy data." ; sc:featureList edam:operation_0297, edam:operation_2949, edam:operation_3457 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "cryoSPARC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.cryosparc.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3068, edam:topic_3452 ; sc:citation , "pmcid:PMC9248840", "pubmed:35775989" ; sc:description "CryoVR is a virtual reality training tool designed at Purdue University to familiarize users with cryoEM equipment, such as microscopes and sample preparation equipment, through a safe and accessible, virtual environment." ; sc:featureList edam:operation_0307, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CryoVR" ; sc:operatingSystem "Windows" ; sc:url "https://www.purdue.edu/cryoVR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0196, edam:topic_0610, edam:topic_0621 ; sc:citation , "pmcid:PMC7150774", "pubmed:32210056" ; sc:description "CryProcessor is a python-written tool for searching and extracting Cry toxins from illumina sequence data or from the protein fasta files. It includes several parts: an hmm-based scanning for potential Cry toxins, obtaining information about the domains, extracting Cry toxins with 3 domains only and comparing found toxins with Bt nomenclature." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "CryProcessor" ; sc:url "https://lab7.arriam.ru/tools/cry_processor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_2640, edam:topic_2830, edam:topic_3922 ; sc:citation , "pmcid:PMC10233886", "pubmed:37275273" ; sc:description "Integrated database of proteome and immunopeptidome-derived non-canonical cancer proteins." ; sc:featureList edam:operation_0416, edam:operation_0436, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:name "CrypticProteinDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.maherlab.com/crypticproteindb" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC1347441", "pubmed:16381902" ; sc:description "Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium." ; sc:featureList edam:operation_0224 ; sc:name "Cryptosporidium genome resources CryptoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Georgia" ; sc:softwareHelp ; sc:url "http://cryptodb.org/cryptodb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_0659, edam:topic_3168, edam:topic_3500 ; sc:citation , "pmcid:PMC7966988", "pubmed:33748443" ; sc:description "CryptoGenotyper is a bioinformatics tool for rapid Cryptosporidium identification. The CryptoGenotyper is a fast and reproducible tool that can be used to classify the genotype of Cryptosporidium samples by directly analyzing the DNA electropherogram files that correspond to two of its characteristic gene markers: SSU rRNA and gp60." ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3196 ; sc:name "CryptoGenotyper" ; sc:url "https://github.com/phac-nml/CryptoGenotyper" ; biotools:primaryContact "Rebecca A. Guy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3474 ; sc:citation , "pmcid:PMC4764925", "pubmed:26906024" ; sc:description "Integrated crystallization analysis that builds on support-vector regression (SVR) models to facilitate computational protein crystallization prediction, analysis, and design." ; sc:featureList edam:operation_0267, edam:operation_0410, edam:operation_3659 ; sc:name "Crysalis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://nmrcen.xmu.edu.cn/crysalis/" ; biotools:primaryContact "Huilin Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_1317, edam:topic_3448, edam:topic_3557 ; sc:citation ; sc:description "Predict the X-ray solution scattering curve of a known structure, given the atomic coordinates in a PDB file, and fit to an experimental scattering curve." ; sc:featureList edam:operation_2238, edam:operation_2423, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "Crysol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3047 ; sc:citation , "pmcid:PMC8202033", "pubmed:34188619" ; sc:description "CrystalExplorer is a native cross-platform program with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density." ; sc:featureList edam:operation_0337, edam:operation_3351, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "CrystalExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://crystalexplorer.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_1317, edam:topic_3474 ; sc:citation , "pmcid:PMC6782082", "pubmed:31636523" ; sc:description "The site-symmetry induced representations of layer groups on the Bilbao Crystallographic Server." ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3454 ; sc:name "crystals MoS2" ; sc:url "http://www.cryst.ehu.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0605, edam:topic_3315 ; sc:citation ; sc:description "crystIT is a Python tool for calculating various complexity measures of crystal structures based on a standardized CIF-file." ; sc:featureList edam:operation_2409, edam:operation_3454, edam:operation_3891 ; sc:license "MIT" ; sc:name "crystIT" ; sc:url "http://github.com/GKieslich/crystIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382 ; sc:citation , "pubmed:35926337" ; sc:description "CS-CO is a hybrid self-supervised visual representation learning method tailored for H&E-stained histopathological images." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CS-CO" ; sc:url "https://github.com/easonyang1996/CS-CO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , "pubmed:12117802" ; sc:description "Its modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny. It will allow simulations to take such information into account and some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites." ; sc:featureList edam:operation_2421, edam:operation_2479 ; sc:name "CS-PSeq-Gen" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://bioserv.rpbs.univ-paris-diderot.fr/software.html#cspseqgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "Protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as input." ; sc:featureList edam:operation_0477 ; sc:name "CS-ROSETTA3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://haddock.science.uu.nl/enmr/services/CS-ROSETTA3/" ; biotools:primaryContact "WeNMR Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:18515350" ; sc:description "Chemical Shift to 3D Structure is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input." ; sc:featureList edam:operation_0474 ; sc:name "CS23D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs23d.ca" ; biotools:primaryContact "Feedback Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3512, edam:topic_3674 ; sc:citation , "pmcid:PMC6739324", "pubmed:31511570" ; sc:description "Aan improved bioinformatics tool for identifying DNA 6 mA modifications via Chou's 5-step rule | An improved machine-learning based prediction tool for identifying DNA 6mA modifications | csDMA was implemented in python 2.7" ; sc:name "csDMA" ; sc:url "https://github.com/liuze-nwafu/csDMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3173, edam:topic_3512 ; sc:citation , "pmcid:PMC6836739", "pubmed:31649059" ; sc:description """Identification and dynamic quantification of regulatory elements using total RNA. Software for motif discovery and next-gen sequencing analysis. Sequencing the 5' end of cap-protected RNAs enables the identification of Transcription Start Sites (TSS) at nucleotide resolution.""" ; sc:featureList edam:operation_0238, edam:operation_0443, edam:operation_3192, edam:operation_3216, edam:operation_3799 ; sc:name "csRNA-seq" ; sc:url "http://homer.ucsd.edu/homer/ngs/csRNAseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0102, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:22553365" ; sc:description "Comparative Structural Alignment (CSA) is a webserver for computing and comparing protein structure alignments. Different scoring schemes are used to compute score-optimal alignments. Input is two PDB files." ; sc:featureList edam:operation_0295, edam:operation_0477, edam:operation_0503, edam:operation_2488 ; sc:name "CSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csa.project.cwi.nl" ; biotools:primaryContact "I. Wohlers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC6929326", "pubmed:31874601" ; sc:description """a web service for the complete process of ChIP-Seq analysis. BACKGROUND:Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with DNA. At present, most ChIP-seq analysis tools adopt the command line, which lacks user-friendly interfaces. Although some web services with graphical interfaces have been developed for ChIP-seq analysis, these sites cannot provide a comprehensive analysis of ChIP-seq from raw data to downstream analysis. RESULTS:In this study, we develop a web service for the whole process of ChIP-Seq Analysis (CSA), which covers mapping, quality control, peak calling, and downstream analysis. In addition, CSA provides a customization function for users to define their own workflows.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3222 ; sc:name "CSA" ; sc:url "http://compubio.csu.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:description "Matlab codes for diffusion MRI CSA-ODF computation and Hough tractography." ; sc:isAccessibleForFree true ; sc:name "CSA-QBI and Hough Tractography for Diffusion MRI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.13" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/62516-csa-qbi-and-hough-tractography-for-diffusion-mri" ; biotools:primaryContact "Iman Aganj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation , "pmcid:PMC3114017", "pubmed:21554688" ; sc:description "Statistical tools for ChIP-seq data analysis. Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation." ; sc:featureList edam:operation_2478 ; sc:license "Artistic-2.0" ; sc:name "CSAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CSAR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3125, edam:topic_3168 ; sc:citation ; sc:description "A contig scaffolding tool using algebraic rearrangements." ; sc:featureList edam:operation_3216 ; sc:name "CSAR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ablab-nthu/CSAR" ; biotools:primaryContact "Chin Lung Lu", "Hsien-Tai Chiu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_3327 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003, edam:format_3475, edam:format_3547 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3003, edam:format_3475, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_3003, edam:format_3475, edam:format_3547 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3168, edam:topic_3169, edam:topic_3511 ; sc:citation , "pmcid:PMC4066778", "pubmed:24852250" ; sc:description "Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control." ; sc:featureList edam:operation_3230 ; sc:license "GPL-3.0" ; sc:name "csaw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/csaw.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0203, edam:topic_0621 ; sc:citation , "pmcid:PMC7355258", "pubmed:32657415" ; sc:description "CSBFinder-S is a tool for the discovery and ranking of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder-S incorporates efficient algorithms that identify CSBs in large genomic datasets. The discovered CSBs are ranked according to a probabilistic score and clustered to families according to their gene content similarity." ; sc:featureList edam:operation_3432, edam:operation_3695, edam:operation_3802 ; sc:license "Apache-2.0" ; sc:name "CSBFinder-S" ; sc:url "https://github.com/dinasv/CSBFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Web resource that includes a large collection of genome-wide ChIP-Seq experiments performed on TFs, histone modifications, RNA polymerases and others. Enriched peak regions from the ChIP-Seq experiments are crossed with the genomic coordinates of a set of input genes, to identify which of the experiments present a statistically significant number of peaks within the input genes’ loci." ; sc:featureList edam:operation_0349, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "Cscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.beaconlab.it/cscan" ; biotools:primaryContact "Federico Zambelli", "Giulio Pavesi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3053 ; sc:citation ; sc:description "Predicts the oncogenic status (disease-driver or neutral) of somatic point mutations in the coding and non-coding regions of the cancer genome. Enter a mutation or list of mutations (one per line) into the form below using the format chromosome,position,reference,mutant (see Help for more details). Mutations uploaded from a file should use the VCF format with a minimum of five columns (chromosome, position, id, reference, mutant)." ; sc:featureList edam:operation_3202 ; sc:license "CC-BY-4.0" ; sc:name "CScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cscape.biocompute.org.uk/" ; biotools:primaryContact "Mark F. Rogers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_2640 ; sc:citation , "pmcid:PMC7320610", "pubmed:32282885" ; sc:description "CScape-somatic is a web tool for distinguishing driver and passenger point mutations in the cancer genome." ; sc:featureList edam:operation_3227 ; sc:name "CScape-somatic" ; sc:url "http://CScape-somatic.biocompute.org.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2258, edam:topic_2814, edam:topic_3371 ; sc:citation ; sc:description "Predicts individual component's chemical structure in a mixture, utilizing an iterative dynamic programming algorithm, and a database organized from a large collection of natural products." ; sc:featureList edam:operation_2480 ; sc:name "CSCCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://csccp.cmdm.tw/" ; biotools:primaryContact "Yufeng J. Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation , "pubmed:34551437" ; sc:description "Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs." ; sc:featureList edam:operation_0436, edam:operation_0463, edam:operation_3435, edam:operation_3901 ; sc:name "CSCD2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://geneyun.net/CSCD2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_2269, edam:topic_3169, edam:topic_3175 ; sc:citation , "pmcid:PMC10206090", "pubmed:37166448" ; sc:description "CscoreTool-M infers 3D sub-compartment probabilities within cell population." ; 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sc:citation , "pubmed:33247283" ; sc:description "Software for taking care of all algorithmic complexities and numerical workload of the CSD-ISM, including hardware synchronization and image reconstruction." ; sc:featureList edam:operation_3552, edam:operation_3629, edam:operation_3760 ; sc:license "GPL-3.0" ; sc:name "CSD-ISM" ; sc:url "https://projects.gwdg.de/projects/csdism-2020" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0152, edam:topic_0593, edam:topic_0780 ; sc:citation , "pmcid:PMC8968703", "pubmed:35354826" ; sc:description "The Carbohydrate Structure Database is a free curated repository storing various data on glycans of bacterial, fungal and plant origins." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "CSDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://csdb.glycoscience.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0219, edam:topic_0621, edam:topic_0780 ; sc:citation , "pubmed:33242091" ; sc:description "CSDB_GT, a curated glycosyltransferase database with close-to-full coverage on three most studied non-animal species." ; sc:featureList edam:operation_0346, edam:operation_0360, edam:operation_3431 ; sc:name "CSDB_GT" ; sc:url "http://csdb.glycoscience.ru/gt.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation ; sc:description "CSDeconv maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach" ; 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sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "This tool filters sequencing artifacts (reads with all but 3 identical bases)." ; sc:featureList edam:operation_3695 ; sc:name "cshl_fastx_artifacts_filter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "This tool clips adapters from the 3'end of the sequences in a FASTA/FASTQ file." ; sc:featureList edam:operation_0231 ; sc:name "cshl_fastx_clipper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "This tool collapses identical sequences in a FASTA file into a single sequence." ; sc:featureList edam:operation_0232 ; sc:name "cshl_fastx_collapser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library." ; sc:featureList edam:operation_0564 ; sc:name "cshl_fastx_nucleotides_distribution" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Creates quality statistics report for the given Solexa/FASTQ library." ; sc:featureList edam:operation_3218 ; sc:name "cshl_fastx_quality_statistics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Rename the sequence identifiers in a FASTQ/A file." ; sc:featureList edam:operation_3282 ; sc:name "cshl_fastx_renamer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.11" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Reverse-complement each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed." ; sc:featureList edam:operation_0363, edam:operation_3218 ; sc:name "cshl_fastx_reverse_complement" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Trim (cut bases from) sequences in a FASTA/Q file." ; sc:featureList edam:operation_0369 ; sc:name "cshl_fastx_trimmer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932, edam:format_1933 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Split a FASTQ or FASTA file into several files, using barcodes as the split criteria." ; sc:featureList edam:operation_0369 ; sc:name "cshl_princeton_fastx_barcode_splitter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://hannonlab.cshl.edu/fastx_toolkit/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_2269, edam:topic_3170, edam:topic_3500 ; sc:citation , "pmcid:PMC7048296", "pubmed:32069291" ; sc:description "Continuous-State Hidden Markov Models Transcription Factors(TF) (CSHMM-TF) is a method which integrates probabilistic modeling of single cell RNA-seq data with the ability to assign TFs to specific activation points in the model. TFs are assumed to influence the emission probabilities for cells assigned to later time points allowing us to identify not just the TFs controlling each path but also their order of activation." ; sc:featureList edam:operation_0335, edam:operation_2495, edam:operation_3359, edam:operation_3891 ; sc:name "CSHMM-TF" ; sc:url "https://github.com/jessica1338/CSHMM-TF-for-time-series-scRNA-Seq.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0593, edam:topic_3474, edam:topic_3542 ; sc:citation ; sc:description "Prediction of Secondary Structure from Backbone Chemical Shifts and Sequence. Uses Bidirectional Long Short Term Memory and NMR Chemical Shifts." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0319, edam:operation_0474, edam:operation_2488 ; sc:name "CSI-LSTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://csi.wishartlab.com/cgi-bin/index.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1775 ; sc:citation ; sc:description "CSM (Cutoff Scanning Matrix) is a novel structure-based protein function prediction and structural classification method. CSM generates feature vectors that represent distance patterns between protein residues. These feature vectors are then used as evidence for classification." ; sc:featureList edam:operation_1777, edam:operation_2423, edam:operation_2479, edam:operation_2990 ; sc:name "CSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://homepages.dcc.ufmg.br/~dpires/csm/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1476 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2275, edam:topic_2830 ; sc:citation , "pubmed:34734992" ; sc:description "Graph-based antibody-antigen binding affinity prediction and docking scoring function." ; sc:featureList edam:operation_0252, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:name "CSM-AB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; 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CUPP performs unsupervised clustering of proteins for formation of protein groups and can be used for fast annotation of enzyme protein family, subfamily and EC function of carbohydrate-active enzymes." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_0558, edam:operation_3431 ; sc:name "CUPP" ; sc:url "https://cupp.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_2814 ; sc:citation "pubmed:16845001" ; sc:description "Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures." ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_0474, edam:operation_2406, edam:operation_2416 ; sc:name "CUPSAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cupsat.tu-bs.de/" ; biotools:primaryContact "Prof. Dr. Dietmar Schomburg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3301 ; sc:citation ; sc:description "Bioconductor package providing uniformly processed and manually annotated human microbiome profiles for thousands of people. Microbial taxonomy (from MetaPhlAn2) and metabolic functional potential (from HUMAnN2) can be analyzed with respect to numerous participant characteristics and health outcomes, simply and reproducibly on a normal laptop." ; sc:name "curatedMetagenomicData" ; sc:softwareVersion "1.0" ; sc:url "https://waldronlab.io/curatedMetagenomicData/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_0659, edam:topic_3295, edam:topic_3518 ; sc:author ; sc:citation , "pmcid:PMC7553567", "pubmed:33016192" ; sc:description "curatedAdipoArray is a curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3436, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "curatedAdipoArray" ; sc:url "https://bioconductor.org/packages/curatedAdipoArray" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation , "pubmed:35579371" ; sc:description "A GPU-accelerated reference-free compressor for high-throughput sequencing reads of FASTQ files." ; sc:featureList edam:operation_0232, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CURC" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/BioinfoSZU/CURC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0605, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:35368074" ; sc:description "An efficient curriculum learning-based strategy for molecular graph learning." ; sc:featureList edam:operation_0337, edam:operation_3802, edam:operation_4009 ; sc:license "Not licensed" ; sc:name "CurrMG" ; sc:url "https://github.com/gu-yaowen/CurrMG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0091, edam:topic_0194 ; sc:citation , "pmcid:PMC10174701", "pubmed:37180471" ; sc:description "Scripts to curate metadata and sample genomes from GISAID for analysis and display in nextstrain and microreact." ; sc:featureList edam:operation_0324, edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "CurSa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/luisdelaye/CurSa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental introduction of read-pair information into the assembly process. This enables the assembly of larger genomes than would otherwise be possible within existing memory constraints." ; sc:featureList edam:operation_0310, edam:operation_0524 ; sc:name "Curtain" ; sc:softwareHelp ; sc:url "http://code.google.com/p/curtain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0157, edam:topic_3511 ; sc:citation "pubmed:21558323" ; sc:description "Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures." ; sc:featureList edam:operation_0458, edam:operation_0475, edam:operation_2481, edam:operation_2518 ; sc:name "CURVES+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://gbio-pbil.ibcp.fr/cgi/Curves_plus/" ; biotools:primaryContact "R. Lavery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622, edam:topic_3168, edam:topic_3673 ; sc:citation , "pmcid:PMC3899341", "pubmed:24466273" ; sc:description "Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding." ; sc:featureList edam:operation_0292 ; sc:name "CUSHAW3" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cushaw3.sourceforge.net/homepage.htm#latest" ; biotools:primaryContact "Yongchao Li" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Create a codon usage table from nucleotide sequence(s)." ; sc:featureList edam:operation_0284 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cusp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cusp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0621, edam:topic_3301, edam:topic_3407 ; sc:citation , "pmcid:PMC9876896", "pubmed:36697464" ; sc:description "Customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "CusProSe" ; sc:url "https://i2bc.github.io/CusProSe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0781, edam:topic_2830, edam:topic_3379, edam:topic_3930 ; sc:citation ; sc:description "Custommune is an Automated Tool for Designing Personalized and Population-Targeted Peptide Vaccines" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_0560 ; sc:name "Custommune" ; sc:url "http://www.custommune.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2572, edam:format_3016 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2572, edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1106 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2572, edam:format_3016 ; sc:name "dbSNP ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3264 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2572, edam:format_3016 ; sc:name "COSMIC ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2572, edam:format_3016 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170, edam:topic_3366 ; sc:citation ; sc:description "Generate customized protein sequence database from RNA-Seq data for proteomics search." ; sc:featureList edam:operation_0361, edam:operation_3429 ; sc:license "Artistic-2.0" ; sc:name "customProDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/customProDB.html" ; biotools:primaryContact "xiaojing wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3120, edam:topic_3168, edam:topic_3922 ; sc:citation , "pmcid:PMC7684676", "pubmed:33274046" ; sc:description "CusVarDB is a tool for building customized sample-specific variant protein database from next-generation sequencing datasets. CusVarDB is a tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets." ; sc:featureList edam:operation_3211, edam:operation_3227, edam:operation_3631 ; sc:license "CC-BY-4.0" ; sc:name "CusVarDB" ; sc:operatingSystem "Windows" ; sc:url "https://sourceforge.net/projects/cusvardb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation , ; sc:description "Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads." ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3237 ; sc:license "MIT" ; sc:name "Cutadapt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/cutadapt/" ; biotools:primaryContact "Marcel Martin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3175, edam:topic_3316 ; sc:citation , , "pmcid:PMC7477834", "pubmed:32746918" ; sc:description "Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis" ; sc:featureList edam:operation_3196, edam:operation_3199, edam:operation_3228 ; sc:license "MIT" ; sc:name "cuteSV" ; sc:url "https://github.com/tjiangHIT/cuteSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3071, edam:topic_3673 ; sc:citation ; sc:description "Cutevariant is a cross-plateform application dedicated to maniupulate and filter variation from annotated VCF file." ; sc:featureList edam:operation_0224, edam:operation_0484, edam:operation_3227, edam:operation_3661 ; sc:license "GPL-3.0" ; sc:name "Cutevariant" ; sc:url "https://github.com/labsquare/Cutevariant" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Extract codon usage tables from CUTG database." ; sc:featureList edam:operation_1812 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cutgextract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cutgextract.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2715 ; sc:name "Protein ID (CuticleDB)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation , "pmcid:PMC522807", "pubmed:15453918" ; sc:description "A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle." ; sc:featureList edam:operation_0224 ; sc:name "CuticleDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Athens", "University of Georgia" ; sc:softwareHelp ; sc:url "http://biophysics.biol.uoa.gr/cuticleDB/" ; biotools:primaryContact "Biophysics and Bioinformatics Laboratory, University of Athens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3318, edam:topic_3382 ; sc:citation , "pmcid:PMC8218547", "pubmed:34169274" ; sc:description "Advances in a Runtime-Interpreted Analysis Description Language for HEP Data." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.0" ; sc:name "CutLang" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/unelg/CutLang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3169, edam:topic_3534 ; sc:citation , "pmcid:PMC6734249", "pubmed:31500663" ; sc:description "A flexible pipeline for CUT&RUN processing and footprint analysis | We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https: bitbucket.org qzhudfci cutruntools" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3436 ; sc:license "GPL-2.0" ; sc:name "CUT and RUNTools" ; sc:softwareHelp ; sc:url "https://bitbucket.org/qzhudfci/cutruntools/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove a section from a sequence." ; sc:featureList edam:operation_0369 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "cutseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/cutseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3308, edam:topic_3444, edam:topic_3500 ; sc:citation , "pubmed:37343557" ; sc:description "A brain atlas for the camouflaging dwarf cuttlefish, Sepia bandensis." ; sc:name "cuttlebase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.cuttlebase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3673 ; sc:citation ; sc:description "Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s). Cuttlefish is a tool for constructing the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel modeling scheme of the de Bruijn graph vertices as finite-state automata, and constrains the state-space for the automata to enable tracking of their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that the algorithm scales much better than existing approaches, especially as the number and scale of the input references grow." ; sc:featureList edam:operation_0524, edam:operation_3211, edam:operation_3472 ; sc:license "BSD-3-Clause" ; sc:name "Cuttlefish" ; sc:url "https://github.com/COMBINE-lab/Cuttlefish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Script package for quantifying bacterial load within cells using images from a CV1000 microscope" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "CV1000 microscope bacteria quantifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/67277-safire_cv1000" ; biotools:primaryContact "Abigail Reens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3399, edam:topic_3422 ; sc:citation , "pmcid:PMC6705850", "pubmed:31437231" ; sc:description "Prediction model for cardiovascular events or all-cause mortality in incident dialysis patients | Some variables including age, comorbidity of diabetes, and so on at dialysis initiation are associated with patient prognosis. Cardiovascular (CV) events are a major cause of death, and adequate models that predict prognosis in dialysis patients are warranted. Therefore, we created models using some variables at dialysis initiation. We used a database of 1,520 consecutive dialysis patients (median age, 70 years; 492 women [32.4%]) from a multicenter prospective cohort study. We established the primary endpoint as a composite of the incidence of first CV events or all-cause death. A multivariable Cox proportional hazard regression model was used to construct a model. We considered a complex and a simple model" ; sc:featureList edam:operation_3503, edam:operation_3659 ; sc:name "CV event predict" ; sc:url "https://statacademy.shinyapps.io/App_inaguma_20190717/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3371 ; sc:citation ; sc:description "Molecular generative model based on conditional variational autoencoder for de novo molecular design." ; sc:featureList edam:operation_0322 ; sc:license "CC-BY-NC-4.0" ; sc:name "CVAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jaechanglim/CVAE" ; biotools:primaryContact "Woo Youn Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_2640, edam:topic_3170, edam:topic_3379 ; sc:citation , "pmcid:PMC7439093", "pubmed:32449936" ; sc:description "CVCDAP (Cancer Virtual Cohort Discovery Analysis Platform) a web-based platform to deliver an interactive and customizable toolbox off the shelf for cohort-level analysis of TCGA and CPTAC public datasets, as well as user uploaded datasets. CVCDAP allows flexible selection of patients sharing common molecular and/or clinical characteristics across multiple studies as a virtual cohort, and provides dozens of built-in customizable tools for seamless genomic, transcriptomic, proteomic and clinical analysis of a single virtual cohort, as well as, to compare two virtual cohorts with relevance." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3501 ; sc:name "CVCDAP" ; sc:url "https://omics.bjcancer.org/cvcdap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3335, edam:topic_3360, edam:topic_3422 ; sc:citation , "pmcid:PMC8722174", "pubmed:34980174" ; sc:description "Incidence and risk of CVD in people with liver disease" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "CVD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lailab.shinyapps.io/cvd_in_liver_disease/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3403, edam:topic_3474 ; sc:citation , "pmcid:PMC10023204", "pubmed:36965300" ; sc:description "Explainable artificial intelligence determination of the relationship of troponin to D-Dimer, mortality, and CK-MB in COVID-19 patients." ; sc:featureList edam:operation_3659, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "CVD22" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cvd22covid.streamlitapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description "Shiny app for interactive variant prioritisation in precision cancer medicine. Its input file is the output of the Oncotator Variant Annotation tool that summarises variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive prioritisation in this tool is based on known germline and cancer variants, DNA repair genes and functional prediction scores." ; sc:featureList edam:operation_3226 ; sc:license "GPL-3.0" ; sc:name "CVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CVE.html" ; biotools:primaryContact "Andreas Mock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3400, edam:topic_3421, edam:topic_3934 ; sc:citation , "pmcid:PMC6730493", "pubmed:31543876" ; sc:description """A Computational Pipeline for the Diagnosis of CVID Patients. Computational_Pipeline_CVID.""" ; sc:featureList edam:operation_3935 ; sc:name "CVID" ; sc:url "https://github.com/saeyslab/Computational_Pipeline_CVID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32365032" ; sc:description "Conditional Variational Image Deraining (CVID) network for better deraining performance, leveraging the exclusive generative ability of Conditional Variational Auto-Encoder (CVAE) on providing diverse predictions for the rainy image. To perform spatially adaptive deraining, we propose a spatial density estimation (SDE) module to estimate a rain density map for each image. Since rain density varies across different color channels, we also propose a channel-wise (CW) deraining scheme." ; sc:featureList edam:operation_3443 ; sc:name "CVID" ; sc:url "https://github.com/Yingjun-Du/VID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC9191720", "pubmed:35696379" ; sc:description "CView is an alignment visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. The relationship that sequence regions that are currently on screen have to other regions of diversity within the alignment can be observed, thus increasing intuitive insight." ; sc:featureList edam:operation_0291, edam:operation_0292, edam:operation_3196, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "CView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/cview/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC9887406", "pubmed:36726731" ; sc:description "A tool for finding heterogeneously methylated genomic regions using ONT reads." ; sc:featureList edam:operation_3186, edam:operation_3432, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "cvlr" ; sc:url "https://github.com/EmanueleRaineri/cvlr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC9518872", "pubmed:36170233" ; sc:description "An online processing tool for CO2-inhalation and resting-state cerebrovascular reactivity (CVR) MRI data." ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:license "Other" ; sc:name "CVR-MRICloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://braingps.mricloud.org/cvr.v5" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0621, edam:topic_0637, edam:topic_0769, edam:topic_3293 ; sc:citation , "pubmed:15215347", "pubmed:19398429", "pubmed:34119695" ; sc:description "Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0325, edam:operation_0552, edam:operation_3478, edam:operation_3625 ; sc:license "MIT" ; sc:name "CVTree" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/ghzuo/cvtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "CVXB is a tool for image segmentation with artifacts and bias. Region-based image segmentation model with artifacts (outliers) detection and bias correction." ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "CVXB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/49367-cvxb-image-segmentation-with-artifacts-and-bias" ; biotools:primaryContact "Dominique Zosso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31593235" ; sc:description """Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. Here we proposed two novel algorithms, the Direct Subsequence Dynamic Time Warping for nanopore raw signal search (DSDTWnano) and the continuous wavelet Subsequence DTW for nanopore raw signal search (cwSDTWnano), to enable the direct subsequence inquiry and exact mapping in the nanopore raw signal datasets.""" ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_3185 ; sc:name "cwSDTWnano" ; sc:url "https://github.com/icthrm/cwSDTWnano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3168 ; sc:citation ; sc:description "Unified framework for analyzing prion protein gene variability and spatial structure." ; sc:featureList edam:operation_2403 ; sc:name "CWDPRNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ecosystems.psu.edu/research/labs/walter-lab/additional-labs/population-genetics-lab" ; biotools:primaryContact "William L. Miller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Automatically built VM used for a remote CWL training" ; sc:name "CWL Training" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0821, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:32827670" ; sc:description "CWLy-pred is a cell wall lytic enzymes identifier based on improved MRMD feature selection method." ; sc:featureList edam:operation_0335 ; sc:name "CWLy-pred" ; sc:url "http://server.malab.cn/CWLy-pred/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0821, edam:topic_2229, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:32580129" ; sc:description "CWLy-SVM is a Support Vector Machine-based tool for identifying the cell wall lytic enzymes." ; sc:featureList edam:operation_0335, edam:operation_3936, edam:operation_3937 ; sc:name "CWLy-SVM" ; sc:url "http://server.malab.cn/CWLy-SVM/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0204 ; sc:citation ; sc:description "Method used for identification of over-represented words in a set of ranked sequences. By default it is aimed at human miRNA analysis; you give a ranked list of differential expression values of genes across two conditions and it finds words in 3' UTRs of lengths 6 and 7 over-represented in the most regulated genes." ; sc:featureList edam:operation_0238, edam:operation_2495 ; sc:name "cWords" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://servers.binf.ku.dk/cwords/" ; biotools:primaryContact "Simon Horskjær Rasmussen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0593, edam:topic_3332 ; sc:citation ; sc:description "Program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR." ; sc:featureList edam:operation_2406, edam:operation_2426, edam:operation_2481, edam:operation_3445 ; sc:isAccessibleForFree true ; sc:name "CYANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.cyana.org/wiki/index.php/Main_Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation , "pmcid:PMC4752027", "pubmed:26937268" ; sc:description "Simple animations of Cytoscape networks." ; sc:featureList edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "CyAnimator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0" ; sc:url "http://www.cgl.ucsf.edu/cytoscape/CyAnimator/index.shtml" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0804, edam:topic_2229, edam:topic_3474, edam:topic_3934 ; sc:citation , "pubmed:34037686" ; sc:description "CyAnno is a semi-automated approach for cell type annotation of mass cytometry datasets." ; sc:featureList edam:operation_3432, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "CyAnno" ; sc:url "https://github.com/abbioinfo/CyAnno" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0622 ; sc:citation "pubmed:19880388" ; sc:description "CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_2422, edam:operation_3672 ; sc:name "CyanoBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genome.kazusa.or.jp/cyanobase" ; biotools:primaryContact "M. Nakao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1333 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation ; sc:description "Manually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases." ; sc:featureList edam:operation_0253, edam:operation_0338 ; sc:isAccessibleForFree true ; sc:name "CyanoLyase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:url "http://cyanolyase.genouest.org/" ; biotools:primaryContact "GenOuest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_3520 ; sc:citation , "pubmed:36548962" ; sc:description "CyanoMapDB is a database providing cyanobacterial protein-protein interactions (PPIs) with experimental evidence, consisting of 52,304 PPIs among 6,789 proteins from 23 cyanobacterial species." ; sc:featureList edam:operation_0224, edam:operation_2428, edam:operation_3925 ; sc:license "Not licensed" ; sc:name "CyanoMapDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cyanomapdb.msbio.pro/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1900 ; sc:name "NCBI locus tag" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_0601, edam:topic_0622 ; sc:citation , "pmcid:PMC8728175", "pubmed:34614159" ; sc:description "An integrated omics database for functional genomic analysis of cyanobacteria." ; sc:featureList edam:operation_0303, edam:operation_0314, edam:operation_2422, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "CyanoOmicsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cyanoomics.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3174, edam:topic_3407, edam:topic_3697, edam:topic_3941 ; sc:citation , "pubmed:33320930" ; sc:description "CyanoPATH is a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms" ; sc:featureList edam:operation_0533, edam:operation_3660, edam:operation_3926, edam:operation_3929 ; sc:name "CyanoPATH" ; sc:url "http://www.csbg-jlu.info/CyanoPATH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0610, edam:topic_0625, edam:topic_3071, edam:topic_3308 ; sc:citation , "pubmed:33125079" ; sc:description "Cyanorak is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from genomes covering most of the wide genetic diversity known so far within these groups, and which were split into clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites." ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3432 ; sc:name "Cyanorak" ; sc:softwareVersion "2.1" ; sc:url "http://www.sb-roscoff.fr/cyanorak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3170, edam:topic_3360, edam:topic_3474, edam:topic_3934 ; sc:citation ; sc:description "CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data" ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "CYANUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://exbio.wzw.tum.de/cyanus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3170, edam:topic_3518, edam:topic_3520 ; sc:citation "pubmed:22600740" ; sc:description "Cyber-T provides differential analysis tools for high-throughput data such as data from microarrays, next generation sequencing platforms and mass spectrometry. Various statistical analyses are computed using R-code." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3658, edam:operation_3741 ; sc:name "Cyber-T" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cybert.ics.uci.edu/." ; biotools:primaryContact "For bugs and general help (Subject=CyberT)", "For commercial licenses (Subject=CyberT)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3306, edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9270370", "pubmed:35803978" ; sc:description "CyberSco.py is a software written in Python for performing Conditional Microscopy. It was conceived to be available to none expert users with a simple intuitive GUI interface and easy syntax for predefined experiments." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "CyberSco" ; sc:url "https://github.com/Lab513/CyberSco.Py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_3071, edam:topic_3303 ; sc:citation , "pmcid:PMC6937922" ; sc:description "CyBy2 is a library for writing chemical and biological data management systems. It is a strongly typed, purely functional framework for chemical data management. This library provides a set of utility functions and data types for writing purely functional client/server applications for handling and querying chemical and biological data. 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It provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. Included is information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3454 ; sc:name "Cyclebase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cyclebase.org/" ; biotools:primaryContact "Alberto Santos", "Lars Juhl Jensen", "Rasmus Wernersson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:36478276" ; sc:description """CYCLeR is a software package for assembly of circRNA transcripts from RNA-seq data. Takes a set of BSJ prediction files and RNA-seq BAM files as an input and outputs circRNA trascnripts as FASTA, GTF and flat annotation files. 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CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_3196, edam:operation_3432 ; sc:name "CYPminer" ; sc:url "https://github.com/Okweon/CYPminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2258, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:34038112" ; sc:description "CyProduct is a software tool for accurately predicting the byproducts of human Cytochrome P450 metabolism." ; sc:featureList edam:operation_0417, edam:operation_3454, edam:operation_3929 ; sc:name "CyProduct" ; sc:url "https://bitbucket.org/wishartlab/cyproduct/src/master/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769 ; sc:citation , "pmcid:PMC4670004", "pubmed:26672762" ; sc:description "Turbocharging Cytoscape Access for External Tools via a RESTful API. It is a technology that powers Cytoscape Automation, which enables you to create reproducible workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc). This enables Cytoscape to scale to large collections of datasets and larger more complex workflows than is practical via keyboard and mouse." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3760 ; sc:license "MIT" ; sc:name "CyREST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://apps.cytoscape.org/apps/cyrest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_0602 ; sc:citation ; sc:description "Establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller. It can be used as a plug-in, e.g. to run R commands or to be used as a library to allow your plug-in to connect to R." ; sc:featureList edam:operation_3083, edam:operation_3562 ; sc:name "Cyrface" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/saezrodriguez/cyrface/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0202, edam:topic_2815, edam:topic_3369 ; sc:citation , "pubmed:37119813" ; sc:description "Human cysteine database based on experimental quantitative chemoproteomics." ; sc:featureList edam:operation_1830, edam:operation_1831, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "CysDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://backuslab.shinyapps.io/cysdb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0601, edam:topic_3534 ; sc:citation , "pmcid:PMC9677505", "pubmed:36305460" ; sc:description "A comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications." ; sc:featureList edam:operation_0417, edam:operation_1830, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "CysModDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cysmoddb.bioinfogo.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3518 ; sc:citation ; sc:description "Minimal/maximal spanning tree subnetwork discovery. 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CystAnalyser is able to provide users the cystic index, the number of cysts and the cystic size profile." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3891 ; sc:name "CystAnalyser" ; sc:url "https://citius.usc.es/transferencia/software/cystanalyser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0769, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description "Cyto is a docker-based application to run Anduril analysis pipelines on high dimensional cytometry data. Cyto aims to make available new computational cytometry tools to scientists with and without a bioinformatics background. 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In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection." ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "CytoCensus" ; sc:url "http://github.com/hailstonem/CTC_CytoCensus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3168, edam:topic_3170 ; sc:description "This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering." ; sc:featureList edam:operation_2990, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "CytoDx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CytoDx.html" ; biotools:primaryContact "Zicheng Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3325, edam:topic_3400, edam:topic_3474, edam:topic_3520, edam:topic_3934 ; sc:citation , "pmcid:PMC7474669", "pubmed:32801215" ; sc:description """A robust and interpretable end-to-end deep learning model for cytometry data. 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sc:name "CytoML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/CytoML.html" ; biotools:primaryContact "Mike Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3315, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9191702", "pubmed:35696439" ; sc:description "cytoNet is a cloud-based image analysis software designed to quantify the structure of cell communities from microscope images using principles of graph theory." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3927 ; sc:license "Not licensed" ; sc:name "cytoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sample-env-1.myiusswm4v.us-west-2.elasticbeanstalk.com/index2.html" . a sc:SoftwareApplication ; 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sc:isAccessibleForFree true ; sc:name "Cytoscape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.7.1" ; sc:url "http://www.cytoscape.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0602, edam:topic_3382 ; sc:citation "pubmed:20656902" ; sc:description "Web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_1812, edam:operation_3083, edam:operation_3439 ; sc:name "Cytoscape Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cytoscapeweb.cytoscape.org/" ; biotools:primaryContact "Gary D. Bader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC7203740", "pubmed:31971582" ; sc:description "Fiji Macro and GUI for CytoSeg to automatically extract and analyze the actin cytoskeleton from microscopy images. 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The goal of CytoSpill is to compensate the spillover effects in CyTOF data which caused by technical effects without relying on control experiment." ; sc:featureList edam:operation_2454, edam:operation_3432, edam:operation_3435 ; sc:name "CytoSpill" ; sc:url "https://github.com/KChen-lab/CytoSpill" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3168, edam:topic_3395, edam:topic_3934 ; sc:author "Yuting Dai" ; sc:citation , "pmcid:PMC7983272", "pubmed:33752602" ; sc:description "CytoTree is an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. CytoTree is an R package to implement cellular subpopulations identification, trajectory inference, pseudotime estimation and visualization for flow and mass cytometry data." ; sc:featureList edam:operation_2939, edam:operation_3890, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "CytoTree" ; sc:softwareHelp ; sc:url "https://ytdai.github.io/CytoTree/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0625 ; sc:citation , "pmcid:PMC5870853", "pubmed:28165109" ; sc:description "Library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility." ; sc:featureList edam:operation_3197 ; sc:name "cyvcf2" ; sc:softwareHelp ; sc:url "https://github.com/brentp/cyvcf2" ; biotools:primaryContact "Aaron R Quinlan", "Brent S Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0114, edam:topic_0611, edam:topic_0621, edam:topic_3168 ; sc:citation , "pmcid:PMC7537106", "pubmed:33062585" ; sc:description "The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) is a database of barcoded Chytridiomyceta and Blastocladiomycota cultures." ; sc:featureList edam:operation_0324, edam:operation_2421, edam:operation_3200 ; sc:name "CZEUM" ; sc:url "http://czeum.herb.lsa.umich.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3304 ; sc:citation , "pubmed:35965076" ; sc:description "A functional human brain atlas termed D-BFA (DFC-based Brain Functional Atlas)" ; sc:featureList edam:operation_2429, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "D-BFA" ; sc:url "https://github.com/sliderplm/D-BFA-618" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047 ; sc:description "D-cellerate is a web application that provides a graphical interface for Seurat version 2, a popular single-cell RNA-seq (scRNA-seq) package for R. It provides an easy-to-use UI and the ability to export results as an HTML file." ; sc:featureList edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "D-cellerate" ; sc:softwareHelp ; sc:url "https://github.com/BioData-PT/D-cellerate" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_3307 ; sc:description "D-EE is a distributed dimensionality reduction and visualization tool. Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup." ; sc:featureList edam:operation_0571 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "D-EE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/ShaokunAn/D-EE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:citation , "pmcid:PMC5991294", "pubmed:29888139" ; sc:description "Dotplot large Genomes in an Interactive, Efficient and Simple way." ; sc:featureList edam:operation_0490 ; sc:license "GPL-3.0" ; sc:name "D-GENIES" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/genotoul-bioinfo/dgenies" ; biotools:primaryContact "Christophe Klopp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_3170, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC7952457", "pubmed:33707582" ; sc:description "D-miRT is a two-stream convolutional neural network for microRNA transcription start site feature integration and identification." ; sc:featureList edam:operation_0463, edam:operation_2437, edam:operation_3792 ; sc:name "D-miRT" ; sc:operatingSystem "Linux" ; sc:url "http://hulab.ucf.edu/research/projects/DmiRT/" ; biotools:primaryContact "Haiyan Hu", "Xiaoman Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:19465389" ; sc:description "A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains." ; sc:featureList edam:operation_0246, edam:operation_0270, edam:operation_0303, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "d-Omix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biotec.or.th/isl/Domix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0160, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:37468182" ; sc:description "Web server to extract structural features of related but unaligned RNA sequences." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_3469 ; sc:isAccessibleForFree true ; sc:name "D-ORB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://d-orb.major.iric.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:33624749" ; sc:description "d-PBWT is a dynamic positional Burrows-Wheeler transform that can be used for haplotype matching." ; sc:featureList edam:operation_0487, edam:operation_3211, edam:operation_3557 ; sc:name "d-PBWT" ; sc:url "http://genome.ucf.edu/d-PBWT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2258, edam:topic_3336 ; sc:citation , "pubmed:32558380" ; sc:description """D-Peptide Builder is a web Service to Enumerate, Analyze, and Visualize the Chemical Space of Combinatorial Peptide Libraries. Peptide-based drug discovery is re-gaining attention in drug discovery. Similarly, combinatorial chemistry continues to be a useful technique for the rapid exploration of chemical space. A current challenge, however, is the enumeration of combinatorial peptide libraries using freely accessible tools. To facilitate the swift enumeration of combinatorial peptide libraries, we introduce herein D-Peptide Builder. In the current version, the user can build up to pentapeptides, linear or cyclic, using the natural pool of 20 amino acids. The user can use non- and or N-methylated amino acids. The server also enables the rapid visualization of the chemical space of the newly enumerated peptides in comparison with other libraries relevant to drug discovery and preloaded in the server""" ; sc:featureList edam:operation_0337, edam:operation_3631 ; sc:name "D-Peptide Builder" ; sc:url "http://dpeptidebuilder.quimica.unam.mx:4000/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc:description "D-SCRIPT is a deep learning method for predicting a physical interaction between two proteins given just their sequences. It generalizes well to new species and is robust to limitations in training data size. Its design reflects the intuition that for two proteins to physically interact, a subset of amino acids from each protein should be in con-tact with the other. The intermediate stages of D-SCRIPT directly implement this intuition, with the penultimate stage in D-SCRIPT being a rough estimate of the inter-protein contact map of the protein dimer. This structurally-motivated design enhances the interpretability of the results and, since structure is more conserved evolutionarily than sequence, improves generalizability across species." ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3094 ; sc:license "MIT" ; sc:name "D-SCRIPT" ; sc:softwareHelp ; sc:url "https://github.com/samsledje/D-SCRIPT" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3316, edam:topic_3382 ; sc:citation , "pubmed:32196327" ; sc:description "d-SEAMS is a collection of analysis tools for molecular simulations. It has been implemented as a High Performance Cluster enabled engine in C++, with extensions via the Lua scripting interface. The code sheds light on the structures from simulation trajectories, in terms of their topology and it has been tailored for the analysis of nucleating systems. The framework is meant to be interfaced to a large variety of external tools and software, including R and other libraries. It is also the first and at-present only scientific analysis tool to use reproducible builds via nix." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2476 ; sc:name "d-SEAMS" ; sc:url "https://dseams.info" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0623, edam:topic_3320 ; sc:description "d-StructMAn is a new improved implementation of our earlier tool StructMAn, shipped in a convenient and easily installable container form and extended to annotation of short in-frame indels and alterations arising as a consequence of alternative splicing events. d-StructMAn produces a wide range of structural features by combining information from experimentally resolved structures of many related proteins, which is a unique feature of the StructMAn family tools. Additionally to information from experimentally resolved protein structures, d-StructMAn can also harness all protein structure models stored in the AlphaFold Protein Structure Database." ; sc:featureList edam:operation_0477 ; sc:name "d-StructMAn" ; sc:url "https://github.com/kalininalab/d-StructMAn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:35576425" ; sc:description "Dual Disentanglement Network (D2-Net) for brain tumor segmentation with missing modalities, which consists of a modality disentanglement stage (MD-Stage) and a tumor-region disentanglement stage (TDStage)." ; sc:featureList edam:operation_3791 ; sc:license "Apache-2.0" ; sc:name "D2-Net" ; sc:url "https://github.com/CityU-AIM-Group/D2Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2275, edam:topic_3373 ; sc:citation , "pubmed:35443040" ; sc:description "A deep learning platform for predicting drug targets and for virtual screening against COVID-19." ; sc:featureList edam:operation_2476, edam:operation_2489, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "D3AI-CoV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-CoV/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_0749, edam:topic_0821 ; sc:citation , "pmcid:PMC9597563", "pubmed:36327885" ; sc:description "A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2." ; sc:featureList edam:operation_0303, edam:operation_0331, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "D3AI-Spike" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-Spike/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275 ; sc:citation , "pubmed:37536095" ; sc:description "Platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening." ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "D3CARP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.d3pharma.com/D3CARP/index.php" ; biotools:primaryContact "Zhijian Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0821, edam:topic_3534 ; sc:citation , "pubmed:33938221" ; sc:description """D3DistalMutation is a database to explore the effect of distal mutations on enzyme activity. In general, D3DistalMutation describes the effect of distal mutation (mutations more than 10 Å away from the active site) on enzyme activity and classified enzymes into four classes, viz., no activity change, decrease activity, loss of activity and increase activity. The D3DistalMutation provides information including mutation residues, active sites, the closest distances, activity change description and references.""" ; sc:featureList edam:operation_2421, edam:operation_3896, edam:operation_4009 ; sc:name "D3DistalMutation" ; sc:url "http://www.d3pharma.com/D3DistalMutation/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0176, edam:topic_2275, edam:topic_3336 ; sc:citation ; sc:description "D3PM is a Comprehensive Database for Protein Motions Ranging from Residue to Domain" ; sc:featureList edam:operation_0244, edam:operation_0482, edam:operation_2476, edam:operation_2950 ; sc:name "D3PM" ; sc:url "http://www.d3pharma.com/D3PM/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3343 ; sc:citation ; sc:description "D3Similarity is A Ligand-Based Approach for Predicting Drug Targets and for Virtual Screening of Active Compounds Against COVID-19. D3Similarity was developed with two purposes based on the two-dimensional and three-dimensional similarity of molecular structure, one is for predicting target proteins for active compounds observed from experimental studies, and another is for virtual screening via 2D and 3D similarity evaluation. To this end, we developed a database composed of the bioactive molecules with known targets or/and well-explored mechanism related to the whole process of coronavirus infection, replication and release. “TargetPrediction” is for predicting target proteins, while “VirtualScreening” is for virtual screening against target proteins based on the 2D or 3D similarity evaluation." ; sc:featureList edam:operation_0474, edam:operation_2489, edam:operation_3938 ; sc:name "D3Similarity" ; sc:url "https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0634, edam:topic_0749, edam:topic_2275 ; sc:citation , "pmcid:PMC7169934", "pubmed:32318328" ; sc:description "D3Targets-2019-nCoV is a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19." ; sc:featureList edam:operation_2476, edam:operation_3897, edam:operation_3899, edam:operation_3938 ; sc:name "D3Targets-2019-nCoV" ; sc:url "https://www.d3pharma.com/D3Targets-2019-nCoV/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_3375, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description "D4 is a approch of Deep Drug-drug interaction Discovery and Demystification. D4 is a method for predicting drug-drug interactions along with their mechnsims of interaction. It uses 11 different mechanisms at pharmacokinetic, pharmacodynamic, multi-pathway, and pharmacogenetic levels. D4 utlizes a neuro-symbolic deep learning strategies to encode for background knowledge about basic biological processes and phenomena about drugs." ; sc:featureList edam:operation_2409, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "D4" ; sc:url "https://github.com/bio-ontology-research-group/D4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , ; sc:description "The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants | You need to sign in or sign up before continuing | Wellcome Centre for Integrative Neuroscience, University of Oxford's version control server" ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "dHCP" ; sc:url "https://git.fmrib.ox.ac.uk/seanf/dhcp-fmri-pipeline-release" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3512 ; sc:citation , , "pubmed:33051642" ; sc:description """A tool for quantification of mRNA and punctate structures in time-lapse images of single cells. ABSTRACT Many biological processes are regulated by single molecules and molecular assemblies within cells that are visible by microscopy as punctate features, often diffraction limited. Here we present detecting-NEMO (dNEMO), a computational tool optimized for accurate and rapid measurement of fluorescent puncta in fixed-cell and time-lapse images. The spot detection algorithm uses the à trous wavelet transform, a computationally inexpensive method that is robust to imaging noise. By combining automated with manual spot curation in the user interface, fluorescent puncta can be carefully selected and measured against their local background to extract high quality single-cell data. Integrated into the workflow are segmentation and spot-inspection tools that enable almost real-time interaction with images without time consuming pre-processing steps.""" ; sc:featureList edam:operation_0310, edam:operation_3436, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "dNEMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/recleelab/dNEMO-0.9.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0634, edam:topic_3320, edam:topic_3334, edam:topic_3512 ; sc:citation , "pubmed:31834368" ; sc:description """A Bayesian model to integrate changes in splicing and RNA binding protein activity. MOTIVATION:Alternative splicing (AS) is an important mechanism in the generation of transcript diversity across mammals. AS patterns are dynamically regulated during development and in response to environmental changes. Defects or perturbations in its regulation may lead to cancer or neurological disorders, among other pathological conditions. The regulatory mechanisms controlling AS in a given biological context are typically inferred using a two step-framework: differential AS analysis followed by enrichment methods. These strategies require setting rather arbitrary thresholds and are prone to error propagation along the analysis""" ; sc:featureList edam:operation_0438, edam:operation_2436, edam:operation_3659 ; sc:name "dSreg" ; sc:url "https://bitbucket.org/cmartiga/dsreg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , "pmcid:PMC6385470", "pubmed:30791935" ; sc:description "Method for identifying differential reactive regions from RNA structurome profiling data." ; sc:featureList edam:operation_0278, edam:operation_2495, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "dStruct" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AviranLab/dStruct" ; biotools:primaryContact "Krishna Choudhary", "Sharon Aviran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3337, edam:topic_3382 ; sc:citation , "pmcid:PMC9299305", "pubmed:35857792" ; sc:description "An open-source digital system for quantifying immunohistochemical staining with 3,3'-diaminobenzidine (DAB)." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DAB-quant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sarafridov/DAB-quant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3067, edam:topic_3336, edam:topic_3373 ; sc:citation , "pmcid:PMC9198367", "pubmed:35721178" ; sc:description "An end-to-end model DACPGTN for predicting ATC code for a given drug." ; sc:featureList edam:operation_3891, edam:operation_3927, edam:operation_3935, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DACPGTN" ; sc:url "https://github.com/Szhgege/DACPGTN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "De novo peptide sequencing based on a divide-and-conquer algorithm and peptide tandem spectrum simulation" ; sc:featureList edam:operation_3644 ; sc:name "DACSIM" ; sc:url "https://pubs.acs.org/doi/abs/10.1021/ac0491206" ; biotools:primaryContact "Zhongqi Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3295, edam:topic_3518, edam:topic_3678 ; sc:citation ; sc:description "DACT is an R package for testing mediation effects in genome-wide epigenetic studies. DACT leverages the epigenome-wide data to estimate the relative proportions of the three null cases under the composite null hypothesis. The empirical null framework has been employed for large-scale inference." ; sc:featureList edam:operation_0417, edam:operation_2238, edam:operation_3207 ; sc:name "DACT" ; sc:url "https://github.com/zhonghualiu/DACT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625 ; sc:description "Domestic Animal Diversity Information System is a communication and information tool for implementing strategies for the management of animal genetic resources. It provides the user with searchable databases of breed-related information and images, management tools, and a library of references, links and contacts of Regional and National Coordinators for the Management of Animal Genetic Resources. It provides countries with a secure means to control the entry, updating and accessing of their national data." ; sc:featureList edam:operation_2422 ; sc:license "Not licensed" ; sc:name "DAD-IS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.fao.org/dad-is/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC4927377", "pubmed:27214047" ; sc:description "This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. 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sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3316 ; sc:author "Alex Lisovich", "Roger Day" ; sc:citation ; sc:description "An R package for retrieving data from DAVID, the Database for Annotation, Visualization and Integrated Discovery" ; sc:featureList edam:operation_2409, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "DAVIDQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioConductor" ; sc:softwareHelp ; sc:softwareVersion "1.29.0" ; sc:url "http://www.bioconductor.org/packages//2.13/bioc/html/DAVIDQuery.html" ; biotools:primaryContact "Roger Day" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3384, edam:topic_3398 ; sc:citation , "pubmed:35922700" ; sc:description "Distributed automation for XNAT toolkit (DAX) provides large-scale image storage and analysis pipelines with an optimized job management tool for neuroimaging data" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DAX" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/VUIIS/dax" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3169, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7703781", "pubmed:31603498" ; sc:description """A database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DNA regulatory regions. Genome-wide association studies (GWAS) have shown many variants are found within putative enhancer elements. To provide insights into the regulatory role of enhancer-associated noncoding variants in cancer epigenome, and to facilitate the identification of functional noncoding mutations, we present dbInDel, a database where we have comprehensively analyzed enhancer-associated insertion and deletion variants for both human and murine samples using ChIP-Seq data. Moreover, we provide the identification and visualization of upstream TF binding motifs in InDel-containing enhancers. Downstream target genes are also predicted and analyzed in the context of cancer biology.""" ; sc:featureList edam:operation_0438, edam:operation_0452, edam:operation_3226 ; sc:name "dbInDel" ; sc:url "http://enhancer-indel.cam-su.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2640, edam:topic_3168, edam:topic_3295 ; sc:citation , "pubmed:31830689" ; sc:description """Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. An open-access database of DNA mismatch repair (MMR) gene variants in Chinese population. DNA mismatch repair (MMR) genes play an important role in maintaining genomic stability""" ; sc:featureList edam:operation_3225, edam:operation_3461 ; sc:name "dbMMR-Chinese" ; sc:url "https://dbMMR-chinese.fhs.um.edu.mo" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2229, edam:topic_3071, edam:topic_3474 ; sc:citation , "pubmed:33151284" ; sc:description "Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is the manually-curated database. It has been developed to provide the information and analytical resources to the scientific community in order to develop antimicrobial compounds with the high therapeutic index." ; sc:featureList edam:operation_0407, edam:operation_2421, edam:operation_3631 ; sc:name "DBAASP" ; sc:softwareVersion "3" ; sc:url "http://dbaasp.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC8690246", "pubmed:34850155" ; sc:description "DBAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method on genomic and proteomic data." ; sc:featureList edam:operation_0418, edam:operation_0476, edam:operation_2421, edam:operation_3461, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "dbAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://awi.cuhk.edu.cn/dbAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0623, edam:topic_0798, edam:topic_3068 ; sc:citation , "pmcid:PMC10767833", "pubmed:37889074" ; sc:description """Database of anti-prokaryotic immune system genes. dbAPIS serves as a comprehensive data repository for experimentally validated viral anti-prokaryotic immune system (APIS) proteins and their associated protein families.""" ; sc:featureList edam:operation_0477, edam:operation_3092, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "dbAPIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bcb.unl.edu/dbAPIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2815, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC10010469", "pubmed:36913438" ; sc:description "Database of missense single-nucleotide polymorphisms in human aquaporins." ; sc:featureList edam:operation_0308, edam:operation_0331, edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "dbAQP-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.iitk.ac.in/dbAQP-SNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0634, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:20929868" ; sc:description "Comprehensive repositories of new exon boundaries induced by pathogenic mutations in human disease genes. Aberrant 5’- and 3’-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions or elsewhere. Data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the algorithm-estimated splice-site strength." ; sc:featureList edam:operation_0433, edam:operation_0446, edam:operation_2422, edam:operation_2454, edam:operation_3644 ; sc:name "DBASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.dbass.org.uk/" ; biotools:primaryContact "DBASS3 Support", "DBASS5 Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3419, edam:topic_3473, edam:topic_3517 ; sc:citation , "pmcid:PMC9250320", "pubmed:35779245" ; sc:description "A comprehensive bipolar disorder database for genetic research." ; sc:featureList edam:operation_2421, edam:operation_3227, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "dbBIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dbbip.xialab.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3339, edam:topic_3572 ; sc:citation ; sc:description "The database of bacterial quality scores." ; sc:featureList edam:operation_2421 ; sc:name "dBBQs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://arc-gem.uams.edu/dbbqs/" ; biotools:primaryContact "Visanu Wanchai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0160, edam:topic_0623, edam:topic_0736, edam:topic_0821 ; sc:citation "pubmed:22645317" ; sc:description "dbCAN provides automated carbohydrate-active enzyme signature domain-based annotation for a set of proteins. Each carbohydrate-active enzyme has an assigned signature domain." ; sc:featureList edam:operation_0226, edam:operation_0246, edam:operation_0303, edam:operation_0362, edam:operation_3092 ; sc:name "dbCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csbl.bmb.uga.edu/dbCAN/annotate.php" ; biotools:primaryContact "Ying Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_0820, edam:topic_3068, edam:topic_3174 ; sc:citation , "pubmed:32941621" ; sc:description "dbCAN-PUL is a data repository of prokaryotic CAZyme-containing gene clusters that have been experimentally validated to act on a carbohydrate substrate." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3432 ; sc:name "dbCAN-PUL" ; sc:url "http://bcb.unl.edu/dbCAN_PUL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0196, edam:topic_3174, edam:topic_3697, edam:topic_3810 ; sc:citation , , "pmcid:PMC5753378", "pmcid:PMC9825555", "pubmed:30053267", "pubmed:36399503" ; sc:description "A online database dbCAN-seq to provide pre-computed carbohydrate-active enzyme (CAZymes) sequence and annotation data for 5,349 bacterial genomes." ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "dbCAN-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bcb.unl.edu/dbCAN_seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0160, edam:topic_3174 ; sc:citation ; sc:description "Automated Carbohydrate-active enzyme ANnotation. Three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database." ; sc:featureList edam:operation_0362, edam:operation_3431 ; sc:name "dbCAN2" ; sc:softwareHelp ; sc:url "http://cys.bios.niu.edu/dbCAN2/" ; biotools:primaryContact "Yanbin Yin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation ; sc:description "Detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples." ; sc:featureList edam:operation_0445 ; sc:license "GPL-2.0" ; sc:name "DBChIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/DBChIP.html" ; biotools:primaryContact "Kun Liang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0634, edam:topic_2885, edam:topic_3293 ; sc:citation , "pubmed:33196844" ; sc:description "dbCNS is a database for conserved noncoding sequences." ; sc:featureList edam:operation_2421, edam:operation_3478, edam:operation_3745 ; sc:name "dbCNS" ; sc:url "http://yamasati.nig.ac.jp/dbcns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830, edam:topic_3293, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC7679231", "pubmed:33276297" ; sc:description "DBCOVP is a database of coronavirus virulent glycoproteins. A Knowledge Based Resource for Exploring the Functional and Immunological Properties of Coronavirus Virulent Glycoproteins for Application in Vaccine Target Discovery." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2421, edam:operation_3431 ; sc:name "DBCOVP" ; sc:url "http://covp.immt.res.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736 ; sc:citation "pubmed:20530534" ; sc:description "Web server tool that provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding." ; sc:featureList edam:operation_0303, edam:operation_0471, edam:operation_0474, edam:operation_1850, edam:operation_2415 ; sc:name "DBCP" ; sc:url "http://120.107.8.16/dbcp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0654 ; sc:citation "pubmed:21051346" ; sc:description "A database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org) is a database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and--when possible--detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event." ; sc:featureList edam:operation_0282, edam:operation_0452, edam:operation_3224, edam:operation_3280 ; sc:name "dbCRID" ; sc:url "http://c1.accurascience.com/dbCRID/" ; biotools:primaryContact "dbCRID Administrator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2716 ; sc:name "DBD ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation ; sc:description "Predicted transcription factors in completely sequenced genomes." ; sc:featureList edam:operation_0224 ; sc:name "Transcription factor prediction database (DBD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.transcriptionfactor.org/index.cgi" ; biotools:primaryContact "Sarah A. Teichmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_3125 ; sc:citation "pubmed:22693214" ; sc:description "Uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA. Queries can be specified by a PDB ID or the coordinates of a DNA-binding protein in PDB format." ; sc:featureList edam:operation_0415 ; sc:name "DBD2BS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dbd2bs.csie.ntu.edu.tw/" ; biotools:primaryContact "Support Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_2640, edam:topic_2815, edam:topic_3520 ; sc:citation "pubmed:19900968", "pubmed:22096234" ; sc:description "A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_3223, edam:operation_3741 ; sc:name "dbDEPC" ; sc:url "http://lifecenter.sgst.cn/dbdepc/index.do" ; biotools:primaryContact "dbdepc Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9942549", "pubmed:36786403" ; sc:description "a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DBDIpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/DBDIpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:21097891" ; sc:description "The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3197, edam:operation_3661 ; sc:name "dbDNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://goods.ibms.sinica.edu.tw/DNVs/" ; biotools:primaryContact "Mirrian Meng-Ru Ho", "Wen-chang Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC9435744", "pubmed:35977841" ; sc:description "A dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "dbEmbryo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sysomics.com/dbEmbryo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0219, edam:topic_0659, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC9162909", "pubmed:35685362" ; sc:description "A manually curated database of human and mouse essential lncRNA genes." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "dbEssLnc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://esslnc.pufengdu.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1105 ; sc:name "dbEST accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1105 ; sc:name "dbEST accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1105 ; sc:name "dbEST accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1105 ; sc:name "dbEST accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1105 ; sc:name "dbEST accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2532 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2532 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2532 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2532 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation "pubmed:8401577" ; sc:description "Division of GenBank that contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms." ; sc:featureList edam:operation_0224 ; sc:name "dbEST database of EST sequences" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NCBI" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/dbEST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0621, edam:topic_2815, edam:topic_2840 ; sc:citation "pubmed:22102573" ; sc:description "Database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim is to provide a comprehensive database for human pathogenic bacterial exotoxins." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_3092, edam:operation_3439, edam:operation_3461 ; sc:name "DBETH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hpppi.iicb.res.in/btox/" ; biotools:primaryContact "Saikat Chakrabarti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pubmed:35929780" ; sc:description "DBFE is a Python library with feature extraction methods that facilitate classifier learning from distributions of genomic variants." ; sc:featureList edam:operation_3937 ; sc:license "BSD-3-Clause" ; sc:name "DBFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MNMdiagnostics/dbfe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , ; sc:description "Access to entries from various up-to-date biological databases using entry identifiers or accession numbers." ; sc:featureList edam:operation_2422 ; sc:name "dbfetch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/dbfetch/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3173, edam:topic_3325, edam:topic_3678 ; sc:citation , "pmcid:PMC3965052", "pubmed:24297256" ; sc:description "The Database of Genotypes and Phenotypes (dbGAP) is a National Institutes of Health-sponsored repository charged to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in humans. Information in dbGaP is organized as a hierarchical structure and includes the accessioned objects, phenotypes (as variables and datasets), various molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks), analyses and documents." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "dbGAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/gap" ; biotools:primaryContact "Michael Feolo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3335, edam:topic_3676 ; sc:citation , "pubmed:31504194" ; sc:description "An R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP) | Using dbgap2x, R package to explore, download and decrypt phenotypic and genomic data from dbGaP | On dbGaP, the phenotypic files are encrypted. We created a decryption function that uses a dockerized version on sratoolkit. To use that function, you need to have docker installed on your device (www.docker.com). If you are using the dockerized version of this software (available at hub.docker.com/r/gversmee/dbgap2x), docker is already pre-installed, but you'll need to upload your key on the jupyter working directory" ; sc:featureList edam:operation_3196 ; sc:license "Apache-2.0" ; sc:name "dbgap2x" ; sc:url "https://github.com/gversmee/dbgap2x" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3071, edam:topic_3297 ; sc:citation , "pmcid:PMC9985192", "pubmed:36869285" ; sc:description "Contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP)." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "dbGaPCheckup" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/dbGaPCheckup/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3676 ; sc:citation , "pmcid:PMC8163239", "pubmed:34048545" ; sc:description "dbGENVOC, a comprehensive, flexible database framework, developed with an aim to allow potential users to access, query, browse and download clinically relevant somatic and germline variation data from Indian oral cancer patients. This database will store variant calls from various studies that uses massively parallel sequencing to generate genome-scale data." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3227 ; sc:name "dbGENVOC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://research.nibmg.ac.in/dbcares/dbgenvoc/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a BLAST database." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbiblast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbiblast.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a fasta file database." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbifasta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbifasta.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a flat file database." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbiflat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbiflat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a GCG formatted database." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbigcg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbigcg.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0654 ; sc:description "DBindR is a web server for prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature" ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "DBindR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbi.seu.edu.cn/DBindR/DBindR.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_0154, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC10425311", "pubmed:37589022" ; sc:description "Database for lipids and proteins in human lipid metabolism." ; sc:featureList edam:operation_2415, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "DBLiPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lipid.cloudna.cn/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3295, edam:topic_3325 ; sc:citation , "pmcid:PMC4702807", "pubmed:26503248" ; sc:description "Database of autosomal monoallelic expression for investigating whether the gene/gene class of interest is inferred or measured to be monoallelic in mouse or human tissues." ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "dbMAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mae.hms.harvard.edu/aboutmae.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_2640, edam:topic_3577 ; sc:citation , "pubmed:34314366" ; sc:description "A Database for Exploring the Mutation Markers of Anti-Cancer Drug Sensitivity" ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "dbMCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.aielab.cc/dbMCS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0601, edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC7272086", "pubmed:32497121" ; sc:description "dBMHCC is a comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers." ; sc:featureList edam:operation_0417, edam:operation_2421, edam:operation_2489, edam:operation_2495 ; sc:name "dBMHCC" ; sc:url "http://predictor.nchu.edu.tw/dBMHCC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_2229 ; sc:citation , "pubmed:37000408" ; sc:description "A manually curated database of conditional protein mis-localization events." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2489, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "dbMisLoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://dbml.pufengdu.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0659, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC7251985", "pubmed:32227657" ; sc:description "dbMTS is a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions. dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study." ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_3792 ; sc:name "dbMTS" ; sc:url "http://database.liulab.science/dbMTS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3390 ; sc:citation ; sc:description "An open source application suite to store biological studies. The central module (GSCF) stores the study design, which links out to modules that contain the measurements of specific measurement platforms." ; sc:featureList edam:operation_0224 ; sc:name "Nutritional Phenotype Database (dbnp)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://dbnp.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_1775, edam:topic_3077, edam:topic_3325, edam:topic_3574 ; sc:citation , , , "pmcid:PMC4752381", "pubmed:26555599" ; sc:description "Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study." ; sc:featureList edam:operation_3436, edam:operation_3459, edam:operation_3661, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "dbNSFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://sites.google.com/site/jpopgen/dbNSFP" ; biotools:primaryContact "Xiaoming Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3922, edam:topic_3930 ; sc:citation , "pmcid:PMC7043295", "pubmed:32090262" ; sc:description "dbPepNeo is a manually curated database for human tumor neoantigen peptides." ; sc:featureList edam:operation_0252, edam:operation_3435, edam:operation_3646 ; sc:name "dbPepNeo" ; sc:url "http://www.biostatistics.online/dbPepNeo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:37651627" ; sc:description "Supervised learning model for computational recognition of DNA-binding proteins in model organisms." ; sc:featureList edam:operation_0477, edam:operation_3900 ; sc:isAccessibleForFree true ; sc:name "DBPMod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/dbpmod/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3336, edam:topic_3373, edam:topic_3378, edam:topic_3577 ; sc:citation ; sc:description "DBPOM is a comprehensive database of pharmaco-omics for cancer precision medicine." ; sc:featureList edam:operation_2421, edam:operation_3223 ; sc:name "DBPOM" ; sc:url "http://www.dbpom.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_0780 ; sc:citation ; sc:description """DataBase of Plant Research (DBHR) is an online data resource specifically designed for human research, which provides access to almost all latest human database on easy and friendly finding way, the classification based on data type is informative and straightforward, we assign one major category to each database, although one database may correspond to multiple categories. In what follows, we focus on databases categorized as DNA, RNA, protein, expression, pathway and disease. Dr. Shahid. DB-PR ( DataBase of Plants, Research ). Databases of plants have been an integral part of modern biology.""" ; sc:featureList edam:operation_2421 ; sc:name "DBPR" ; sc:url "https://www.habdsk.org/dbpr.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0203, edam:topic_3512 ; sc:citation ; sc:description "A web server for predicting DNA-binding residues in protein sequences" ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "DBPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/dbpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_0621, edam:topic_0637 ; sc:citation , , "pmcid:PMC4385273", "pmcid:PMC7260176", "pubmed:25841437", "pubmed:32472030" ; sc:description "dbPSP (database of Phosphorylation Sites in Prokaryotes) is an updated resource for annotating protein phosphorylation sites (p-sites) in prokaryotes (bacteria and archaea)." ; sc:featureList edam:operation_0361, edam:operation_0417, edam:operation_2421 ; sc:license "CC-BY-3.0" ; sc:name "dbPSP" ; sc:softwareVersion "2.0" ; sc:url "http://dbpsp.biocuckoo.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0601 ; sc:citation , "pmcid:PMC1347446", "pubmed:16381945" ; sc:description "An informative resource for protein post-translational modifications (PTMs)." ; sc:featureList edam:operation_2479 ; sc:name "dbPTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://dbptm.mbc.nctu.edu.tw" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC8728263", "pubmed:34788852" ; sc:description "An updated database for exploring regulatory networks and functional associations of protein post-translational modifications." ; sc:featureList edam:operation_0417, edam:operation_2421, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "dbPTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://awi.cuhk.edu.cn/dbPTM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3172, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC8824206", "pubmed:34851722" ; sc:description "dbPUP is a database of polyphenol utilization proteins (PUPs) that have been experimentally characterized to metabolize polyphenol substrates." ; sc:featureList edam:operation_0303, edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "dbPUP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bcb.unl.edu/dbpup/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3390, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC9504335", "pubmed:36135348" ; sc:description "DbRUSP is an interactive database for the analysis and interpretation of newborn screening (NBS) data and for studying the effects of covariates on blood metabolite levels." ; sc:featureList edam:operation_3643, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "dbRUSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rusptools.shinyapps.io/dbRUSP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0199, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC8119332", "pubmed:33676930" ; sc:description "DBSAV database reports GTS scores of human genes and DeepSAV scores of SAVs in the human proteome, including pathogenic SAVs, benign SAVs, gnomAD SAVs observed in exome sequencing, and all possible SAVs by single nucleotide variations. Each human protein has a designated web page that displays these SAVs along with various sequence, structural and functional properties. This database is a useful resource for mechanistic interpretation of human SAVs and their relationships with protein functions and human diseases." ; sc:featureList edam:operation_3436, edam:operation_3663, edam:operation_4008 ; sc:name "DBSAV database" ; sc:url "http://prodata.swmed.edu/DBSAV" ; biotools:primaryContact "Nick V. Grishin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0654, edam:topic_0659, edam:topic_3168 ; sc:citation ; sc:description """DBSCAN-SWA is a tool for rapid prophage detection and annotation Bacteriophages are viruses that specifically infect bacteria and the infected bacteria are called bacterial hosts of the viruses. Passive replication of the bacteriophage genome relies on integrate into the host's chromosome and becoming a prophage. Prophages coexist and co-evolve with bacteria in the natural environment, having an impact on the entire ecological environment. Therefore, it is very essential to develop effective and accurate tools for identification of prophages. DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes, running faster than any previous tools and presenting great detection power based on the analysis using 184 manually curated prophages.""" ; sc:featureList edam:operation_0337, edam:operation_0436, edam:operation_3092 ; sc:license "GPL-2.0" ; sc:name "DBSCAN-SWA" ; sc:url "https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3304, edam:topic_3500 ; sc:citation , "pmcid:PMC8570685", "pubmed:34625460" ; sc:description "An Open-Source Software for Automated Accurate Analysis of Rodent Behavior in Forced Swim Test and Tail Suspension Test." ; sc:featureList edam:operation_2940, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DBscorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/swanandlab/DBscorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3334 ; sc:citation , "pubmed:36086324" ; sc:description "Deep Brain Stimulation Simulator (DBSim) is a free COMSOL Multiphysics-based stand-alone program developed by the Neuroengineering group for performing patient-specific FEM simulations of DBS based on the data generated by ELMA." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "DBSim" ; sc:url "https://liu.se/en/article/ne-downloads" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1106 ; sc:name "dbSNP ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885, edam:topic_3325, edam:topic_3574 ; sc:citation ; sc:description "Database of single nucleotide polymorphism (dbSNP) contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations." ; sc:featureList edam:operation_2421, edam:operation_3197, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "dbSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NCBI" ; sc:url "http://www.ncbi.nlm.nih.gov/SNP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2885, edam:topic_3297 ; sc:description "GUI for the retrieval of single nucleotide polymorphism data from dbSNP." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "dbSNP tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/12481-dbsnp-tool" ; biotools:primaryContact "Colin Clarke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0621, edam:topic_2885 ; sc:citation "pubmed:21037260" ; sc:description "dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including humans. dbSNP-Q can be used to query human data from dbSNP for a variety tasks such as genomic mapping, SNP/gene functional properties, allele frequency data and information on the underlying experiments. It also includes documentation and download tools." ; sc:featureList edam:operation_0224, edam:operation_0484, edam:operation_2429, edam:operation_3196, edam:operation_3197 ; sc:name "dbSNP-Q" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cgsmd.isi.edu/dbsnpq" ; biotools:primaryContact "dbSNP-Q Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_0821, edam:topic_3569 ; sc:citation ; sc:description "Stand-alone software tool for construction and analysis of mathematical models of biological systems." ; sc:featureList edam:operation_3660 ; sc:license "BSD-2-Clause" ; sc:name "DBSolve Optimum" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.insysbio.ru/en/software/db-solve-optimum" ; biotools:primaryContact "Nail M Gizzatkulov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0157, edam:topic_0623, edam:topic_0820, edam:topic_2814 ; sc:citation , "pubmed:33641184" ; sc:description "DbStRiPs (Database of structural repeats in proteins) is a structural repeat database which classifies a protein structure into a structural repeat family based on graph based structural repeat identification algorithm, PRIGSA2." ; sc:featureList edam:operation_0303, edam:operation_0476, edam:operation_2488, edam:operation_2996, edam:operation_3767 ; sc:name "DbStRiPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinf.iiit.ac.in/dbstrips/" ; biotools:primaryContact "Nita Parekh" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2389 ; sc:name "UniSTS accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pubmed:2781285" ; sc:description "A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences." ; sc:featureList edam:operation_0224 ; sc:name "NCBI database of sequence tagged sites" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/dbSTS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2815, edam:topic_3077, edam:topic_3500 ; sc:citation , "pmcid:PMC4702767", "pubmed:26438538" ; sc:description "A database of super-enhancers in mouse and human genome." ; sc:featureList edam:operation_0338 ; sc:name "dbSUPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://asntech.org/dbsuper/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display information about a public database." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbtell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbtell.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1929 ; sc:name "Database search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , "pubmed:16030071" ; sc:description "Easy-to-use environment for customized fasta database manipulations." ; sc:featureList edam:operation_2425 ; sc:name "dbtoolkit" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://code.google.com/p/dbtoolkit/" ; biotools:primaryContact "Lennart Martens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Collection of programs to manipulate sequence databanks files." ; sc:name "dbtools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@dbtools@0.99c" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_2830 ; sc:citation , "pmcid:PMC8275335", "pubmed:34252932" ; sc:description "Predicting MHC-peptide binding affinity by differential boundary tree." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0479 ; sc:isAccessibleForFree true ; sc:name "DBTpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fpy94/DBT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8535304", "pubmed:34680971" ; sc:description "A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans." ; sc:featureList edam:operation_0314, edam:operation_0464, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "DBtRend" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://trend.pmrc.re.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3173, edam:topic_3340, edam:topic_3512 ; sc:citation "pubmed:19910371", "pubmed:22086958" ; sc:description "DataBase of Transcription Start Sites is a database which contains precise positional information for transcription start sites of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequencing the 5-end of oligo-cap selected cDNAs in humans and mice. 31 different cell types or culture conditions are represented. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated." ; sc:featureList edam:operation_0314, edam:operation_0440, edam:operation_0527, edam:operation_3197, edam:operation_3429 ; sc:name "DBTSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dbtss.hgc.jp/" ; biotools:primaryContact "Y. Suzuki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199 ; sc:description "NCBI's database of genomic structural variation – it contains insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex chromosomal rearrangements" ; sc:featureList edam:operation_3431 ; sc:license "Other" ; sc:name "dbVAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/dbvar" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Compress an uncompressed dbx index." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxcompress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxcompress.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index the EDAM ontology using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxedam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxedam.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a fasta file database using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxfasta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxfasta.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0958 ; sc:name "Tool metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a flat file database using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxflat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxflat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a GCG formatted database using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxgcg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxgcg.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index an obo ontology using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxobo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxobo.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Validate index and report internals for dbx databases." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxreport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxreport.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index a data resource catalogue using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxresource" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxresource.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Dump statistics for dbx databases." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxstat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxstat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Index NCBI taxonomy using b+tree indices." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxtax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxtax.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Uncompress a compressed dbx index." ; sc:featureList edam:operation_0227 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "dbxuncompress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/dbxuncompress.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3510, edam:topic_3520, edam:topic_3922 ; 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Similar to Simula, DE-Sim models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DE-Sim" ; sc:softwareHelp , , , ; sc:url "https://github.com/KarrLab/de-sim" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_3068, edam:topic_3474 ; sc:citation ; sc:description "DE-STRESS (DEsigned STRucture Evaluation ServiceS) is a web application that provides a suite of tools for evaluating protein designs." ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3960, edam:operation_4008 ; sc:name "DE-STRESS" ; sc:url "https://pragmaticproteindesign.bio.ed.ac.uk/de-stress/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6921400", "pubmed:31856811" ; sc:description """Fast read alignment with incorporation of known genomic variants. deBGA-VARA is a novel variation-aware high-throughput sequencing read aligner. VARA is a variation-aware read global alignment algorithm. We developed deBGA-VARA by integrating VARA into deBGA. 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We compute the likelihood of assignment to various samples and assign to the most likely sample. We then compute the assignment quality to avoid ambiguous assignments. This is similar to how mapping quality solves the problem of ambiguous assignments." ; sc:isAccessibleForFree true ; sc:name "deML" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://grenaud.github.io/deML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6913027", "pubmed:31842925" ; sc:description """fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads""" ; sc:featureList edam:operation_0232, edam:operation_0295, edam:operation_0495, edam:operation_2089, edam:operation_3198 ; sc:license "MIT" ; sc:name "deSALT" ; sc:url "https://github.com/ydLiu-HIT/deSALT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Fast and accurate classification of metagenomics long reads with sparse approximate matches | DeSAMBA(de Bruijn graph-based Sparse Approximate Match Block Analyzer) is a tailored long read classification approach using a novel sparse approximate match-based pseudo alignment algorithm. 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DEAP makes significant improvements over existing approaches by including information about pathway structure and discovering the most differentially expressed portion of the pathway. On simulated data, DEAP significantly outperformed traditional methods: with high differential expression, DEAP increased power by two orders of magnitude; with very low differential expression, DEAP doubled the power. DEAP performance was illustrated on two different gene and protein expression studies. DEAP discovered fourteen important pathways related to chronic obstructive pulmonary disease and interferon treatment that existing approaches omitted. 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This is accomplished through comparison of input sequences against a profile hidden Markov (PHMM) model using the Viterbi algorithm and adjustment of the sequence based on the reported Viterbi path (debar depends on functions from the R package aphid for the PHMM structure and for running the Viterbi algorithm)." ; sc:featureList edam:operation_0452, edam:operation_3200 ; sc:license "GPL-3.0" ; sc:name "debar" ; sc:url "https://CRAN.R-project.org/package=debar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269, edam:topic_3518, edam:topic_3519 ; sc:citation , ; sc:description "DEBay is a computational tool for deconvolution of quantitative PCR data for estimation of cell type-specifc gene expression in a mixed population. DEBay estimates cell type-specific gene expression by deconvolution of quantitative PCR data of a mixed population. It will be useful in experiments where the segregation of different cell types in a sample is arduous, but the proportion of different cell types in the sample can be measured. 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An R package for a rapid differential gene presence analysis between similar genomes. deltaRpkm is an R package whose main purpose is to quickly identify genes potentially involved in a given trait by performing a differential analysis of genes coverage between two sets of closely related bacterial genomes. 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Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ΔSCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination).""" ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:name "SCOPE" ; sc:url "https://github.com/msschwartz21/deltascope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0634 ; sc:citation , "pmcid:PMC9235497", "pubmed:35758816" ; sc:description "DEMA (Distance-bounded Energy-field Minimization Algorithm) an algorithm to model and layout biomolecular networks with quantitative properties." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3799, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; 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sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0736, edam:topic_3120, edam:topic_3293 ; sc:citation , "pubmed:33325500" ; sc:description "DeMaSk is a web server and library for deep mutational scanning substitution matrix and its use for variant impact prediction." ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_3663, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "DeMaSk" ; sc:url "https://demask.princeton.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0153, edam:topic_0602, edam:topic_0821, edam:topic_3407 ; sc:citation , "pubmed:32061129" ; sc:description "EMBF is a database of enzymes of microalgal biofuel feedstock." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3660, edam:operation_3929 ; sc:name "dEMBF" ; 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sc:featureList edam:operation_0337 ; sc:name "deMeta" ; sc:url "https://github.com/Computational-NeuroGenetics/deMeta-beta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_0736 ; sc:citation , "pmcid:PMC9252800", "pubmed:35536281" ; sc:description "DEMO (Domain Enhanced MOdeling, version 2) is an significantly improved version for automated assembly of full-length structural models of multi-domain proteins by integrating analogous template alignments with deep-learning predicted inter-domain spatial restraints." ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_0474 ; sc:license "Not licensed" ; sc:name "DEMO2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://zhanggroup.org/DEMO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description "DeMoS (Dense Module based Gene Signature Detection through Quasi-Clique) is an application for performing cervical cancer prognosis." ; sc:featureList edam:operation_0463, edam:operation_3463, edam:operation_3658, edam:operation_3766, edam:operation_3792 ; sc:name "DeMoS" ; sc:url "https://github.com/sahasuparna/DeMoS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0208, edam:topic_3375, edam:topic_3407 ; sc:citation , "pmcid:PMC9484408", "pubmed:36003040" ; sc:description """Pharmacokinetic and toxicodynamic concepts in idiosyncratic, drug-induced liver injury. DemoTox-PK documentation. DemoTox-PK allows the user to visualize how such alterations might lead to a toxic reaction. The illustrations presented provide a framework for conceptualizing idiosyncratic reactions and could serve as a stimulus for future discussion, education, and research into modes of action of IDILI.""" ; sc:featureList edam:operation_0334, edam:operation_0337, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "DemoTox-PK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bhattacharyalab.github.io/DemoTox-PK/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3308 ; sc:citation , "pmcid:PMC5784859", "pubmed:29227470" ; sc:description "Deconvolution of sample identity and identification of multiplets when multiple samples are pooled by barcoded single cell sequencing." ; sc:featureList edam:operation_2423, edam:operation_3197, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "demuxlet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/statgen/demuxlet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8762864", "pubmed:35039061" ; sc:description "DENA (Deeplearning Explore Nanopore m6A). Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data." ; sc:featureList edam:operation_0428, edam:operation_3799, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DENA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/weir12/DENA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3375, edam:topic_3379, edam:topic_3386, edam:topic_3474 ; sc:citation , "pmcid:PMC6820739", "pubmed:31664080" ; sc:description """A web resource for dendrimer pharmacokinetics investigation and prediction. Abstract: The development of nanomedicines currently suffers from a lack of efficient tools to predict pharmacokinetic behaviour without relying upon testing in large numbers of animals, impacting success rates and development costs. The aim of this work was therefore to present dendPoint, the first in silico model to predict the intravenous pharmacokinetic profiles of a commonly explored drug vector, based on dendrimer physicochemical properties""" ; sc:featureList edam:operation_3695 ; sc:name "Dendrimer Pharmacokinetics Prediction (dendPoint)" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/dendpoint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2640 ; sc:citation ; sc:description "De novo Driver Exclusivity is an algorithm to discover mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples." ; sc:featureList edam:operation_2425, edam:operation_2497, edam:operation_3562 ; sc:name "Dendrix" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://compbio.cs.brown.edu/projects/dendrix/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0099, edam:topic_0199, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC6961311", "pubmed:31937348" ; sc:description "DENDRO (Dna based EvolutioNary tree preDiction by scRna-seq technOlogy) is an R package, which takes scRNA-seq data for a tumor (or related somatic tissues) and accurately reconstructs its phylogeny, assigning each single cell from the single cell RNA sequencing (scRNA-seq) data to a subclone." ; sc:featureList edam:operation_2495, edam:operation_3227, edam:operation_3478, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "DENDRO" ; sc:url "https://github.com/zhouzilu/DENDRO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3293, edam:topic_3474 ; sc:citation , "pubmed:33381838" ; sc:description "DendroNet is an approach to train neural networks in the context of evolutionary data. 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Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "For every organization data and its related infrastructure is constantly evolving. As a result, enterprise data will always remain distributed. The Denodo Platform gives IT organizations the flexibility to evolve their data strategies, migrating to the cloud, or logically unifying data warehouses and data lakes, without affecting business. The Denodo Platform also accelerates data provisioning through reduced data replication, it enables consistent security and governance across multiple systems, and it gives your business users the flexibility to choose their preferred applications. The only way you can accomplish this is through a logical data fabric powered by data virtualization. The Denodo Platform is the only solution that can meet this need. 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Subramanian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_2828 ; sc:citation , "pmcid:PMC5947772", "pubmed:29533234" ; sc:description "Diffraction Integration for Advanced Light Source." ; sc:featureList edam:operation_3214 ; sc:name "DIALS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://dials.github.io/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3071, edam:topic_3512 ; sc:citation , "pmcid:PMC9652854", "pubmed:36368948" ; sc:description "DIAMIN is a high-level software library to facilitate the development of distributed applications for the efficient analysis of large-scale molecular interaction networks." ; sc:featureList edam:operation_2422, edam:operation_2949, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DIAMIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ldirocco/DIAMIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. 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Identify conserved regions and design primers based on multiple sequence alignments of putative orthologous sequences from whole‐genome or whole‐transcriptome data." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3478 ; sc:license "GPL-2.0" ; sc:name "discromark" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/hdetering/discomark" ; biotools:primaryContact "Sereina Rutschmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pmcid:PMC4245949", "pubmed:25389269" ; sc:description "Discover discriminative sequence motifs." ; sc:featureList edam:operation_0415 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "discrover" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maaskola/discrover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3344, edam:topic_3500 ; sc:description "A complete GUI for disease detection in animals using color channel extraction." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Disease detection in animals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/73332-disease-detection-in-animals-using-color-channel-extraction" ; biotools:primaryContact "muhammad bilal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_0769, edam:topic_2640, edam:topic_3067, edam:topic_3325 ; sc:citation , "pmcid:PMC6323977", "pubmed:30407550" ; sc:description """Classification, content and workflow expansion. Each import consists of two files: a *_terms.txt file and a *_import.owl file. The .txt file is used to generate the .owl import module using ROBOT extract. This browser does not support visualization of term relationships on the Disease Ontology website. Please use Chrome, Safari or Firefox when using the Disease Ontology website to unlock visualization capabaility. Open the corresponding .txt file and do a text search to ensure the ID has not yet been added. Save the file, and then in terminal, run the desired make command (see below). Name Synonym Definition Subset DOID Alternate ID Xrefs DO_AGR_slim DO_cancer_slim DO_FlyBase_slim DO_GXD_slim DO_IEDB_slim DO_MGI_slim DO_rare_slim NCIthesaurus TopNodes_DOcancerslim.""" ; sc:featureList edam:operation_2421, edam:operation_3280, edam:operation_3559 ; sc:name "disease-ontology" ; sc:url "http://www.disease-ontology.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0634, edam:topic_3063, edam:topic_3325 ; sc:citation , "pmcid:PMC3245088", "pubmed:22080554" ; sc:description "The Disease Ontology (DO) has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts." ; sc:featureList edam:operation_0224, edam:operation_0226, edam:operation_3352, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "CC-BY-1.0" ; sc:name "DO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://disease-ontology.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3063, edam:topic_3325, edam:topic_3366, edam:topic_3489 ; sc:citation , "pubmed:23973272" ; sc:description "Information retrieval tool for accessing and integrating genetic and medical information for health applications. Resorting to this integrated environment, clinicians are able to access and relate diseases data already available in the Internet, scattered along multiple databases." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2497, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "Diseasecard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/diseasecard/" ; biotools:primaryContact "José Luis Oliveira", "Pedro Lopes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3335, edam:topic_3407 ; sc:citation , "pmcid:PMC4086092", "pubmed:24895436" ; sc:description "DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_2495, edam:operation_2990, edam:operation_3223 ; sc:name "DiseaseConnect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://disease-connect.org" ; biotools:primaryContact "Liu Lab (Systems Biology Lab)", "Zhou Lab, University of Southern California" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2769 ; sc:name "Transcript ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , , "pmcid:PMC3245164", "pmcid:PMC8728278", "pubmed:22135302", "pubmed:34792145" ; sc:description "The Human Disease Methylation Database Version 3.0 is a web-based resource that focuses on the abnormal methylome of human diseases." ; sc:featureList edam:operation_0308, edam:operation_3204, edam:operation_3206, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:name "DiseaseMeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.0" ; sc:url "http://218.8.241.243:8080/DiseaseMeth3.0/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3667 ; sc:name "Disease identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3667 ; sc:name "Disease identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3517 ; sc:citation , "pubmed:25484339" ; sc:description "DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "DISEASES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://diseases.jensenlab.org/" ; biotools:primaryContact "Lars Juhl Jensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_3538 ; sc:citation "pubmed:14604535" ; sc:description "A computational tool for prediction of disordered/unstructured regions within a protein sequence." ; sc:featureList edam:operation_0470, edam:operation_0474, edam:operation_1777, edam:operation_2423, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DisEMBL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://dis.embl.de/" ; biotools:primaryContact "Dr Rune Linding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Computational tool for prediction of disordered/unstructured regions within a protein sequence." ; sc:featureList edam:operation_2479 ; sc:name "Disembl WS (jabaws)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.compbio.dundee.ac.uk/jabaws/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3306, edam:topic_3407 ; sc:citation , "pmcid:PMC8963327", "pubmed:35094056" ; sc:description "DisEnrich—the database of human proteome IDRs that are significantly enriched in particular amino acids." ; sc:featureList edam:operation_2949, edam:operation_3501, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "DisEnrich" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://prodata.swmed.edu/DisEnrichDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:description "A visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers." ; sc:featureList edam:operation_2429, edam:operation_2945 ; sc:name "disentangler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20111001" ; sc:url "http://kumasakanatsuhiko.jp/projects/disentangler/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1106 ; sc:name "dbSNP ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID (NCBI)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2376, edam:format_3464, edam:format_3475 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Plug-in", "SPARQL endpoint", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0199, edam:topic_0218, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3325, edam:topic_3342, edam:topic_3344, edam:topic_3345, edam:topic_3366 ; sc:author , "Josep Sauch Pitchard", "Juan Manuel Ramirez Anguita" ; sc:citation , , , , , ; sc:contributor , , ; sc:description """DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated to human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype–phenotype relationships. The current version of DisGeNET (v7.0) contains 1,134,942 gene-disease associations (GDAs), between 21,671 genes and 30,170 diseases, disorders, traits, and clinical or abnormal human phenotypes, and 369,554 variant-disease associations (VDAs), between 194,515 variants and 14,155 diseases, traits, and phenotypes.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3083, edam:operation_3226, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "DisGeNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "Database version 7.0", "DisGeNET Cytoscape App Version 7.0.x", "DisGeNET RDF release 7.0", "Platform v1.1.0", "REST API v1.0.0", "disgenet2r R package Version: 0.0.9" ; sc:url "http://www.disgenet.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10034587", "pubmed:36968431" ; sc:description "Fast and robust method to identify ligand-receptor interactions at subunit level from single-cell RNA-sequencing data." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DiSiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://disir-scrna.streamlitapp.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3542 ; sc:author ; sc:citation , , , "pmcid:PMC3548674", "pubmed:21715467", "pubmed:23368835" ; sc:description "Prediction of cysteine connectivity patterns in a protein chain." ; sc:featureList edam:operation_0267, edam:operation_1829, edam:operation_1830 ; sc:isAccessibleForFree true ; sc:name "DisLocate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/dislocate" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0605 ; sc:citation ; sc:description "DiSMed is a de-identification methodology for Spanish medical texts based on Named Entity Recognition (NER). It is based on spaCy and partially based on the networks designed by Gillaume Genthial implemented on Tensorflow 1. DiSMed includes both the Python code and the curated dataset, available under request under a research use agreement." ; sc:isAccessibleForFree true ; sc:name "DiSMed" ; sc:url "https://github.com/BIMCV-CSUSP/DiSMed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3295 ; sc:citation , "pmcid:PMC4966778", "pubmed:27473283" ; sc:description "DISMISS is a new software package that detects strand-associated DNA methylation from existing MeDIP-Seq analyses" ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "DISMISS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://uhkniazi.github.io/dismiss/" ; biotools:primaryContact "Martin T. Swain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:33064143" ; sc:description "The DiSNEP package implemented the Disease-Specific Network Enhancement Prioritization (DiSNEP) framework. The DiSNEP framework first enhances a comprehensive gene network specifically for a disease through a diffusion process on a gene-gene similarity matrix derived from a disease omics data. The enhanced disease-specific gene network thus better reflects true gene interactions for the disease and may improve prioritizing disease-associated genes subsequently." ; sc:featureList edam:operation_0315, edam:operation_3435, edam:operation_3927 ; sc:name "DiSNEP" ; sc:url "https://github.com/pfruan/DiSNEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_3335 ; sc:citation , "pmcid:PMC7032061", "pubmed:32110491" ; sc:description "DISNET is a framework for extracting phenotypic disease information from public sources." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3907 ; sc:name "DISNET" ; sc:softwareHelp ; sc:url "http://disnet.ctb.upm.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:32176770" ; sc:description """DisoFun is a tool for differentiating isoform functions with collaborative matrix factorization. Description :This page includes the codes of DisoFun which are implemented and tested on Matlab2014a version by Mr. Wang (Keyao Wang, Email: l: keyaowang@email.swu.edu.cn) an) and free for academic usage. You can run it at your own disk. For other purposes, please contact Dr. Yu (Guoxian Yu, Email: l: gxyu@swu.edu.cn). I). If you have any problem on using these codes, just contact us via Email.""" ; sc:featureList edam:operation_0264, edam:operation_3436, edam:operation_3672 ; sc:name "DisoFun" ; sc:url "http://mlda.swu.edu.cn/codes.php?name=DisoFun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0121, edam:topic_0153, edam:topic_0736, edam:topic_3538 ; sc:citation , "pubmed:34487138" ; sc:description "Accurate prediction of disordered lipid binding residues in protein sequences with deep recurrent networks and transfer learning." ; sc:featureList edam:operation_0269, edam:operation_0272, edam:operation_3094, edam:operation_3904 ; sc:name "DisoLipPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biomine.cs.vcu.edu/servers/DisoLipPred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_3306, edam:topic_3474, edam:topic_3538, edam:topic_3542 ; sc:citation , "pubmed:35469832" ; sc:description "DisoMine is a tool that predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure and early folding." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_2476, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "DisoMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bio2byte.be/disomine/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1526 ; sc:name "Protein globularity" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:name "Sequence image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC4380029", "pubmed:25391399" ; sc:description "DISOPRED3 represents the latest release of our successful machine-learning based approach to the detection of intrinsically disordered regions." ; sc:featureList edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "DISOPRED3" ; sc:operatingSystem "Linux" ; sc:softwareVersion "3.1" ; sc:url "http://bioinf.cs.ucl.ac.uk/disopred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0128, edam:topic_0154, edam:topic_3538 ; sc:citation , "pubmed:31889261" ; sc:description "DisoRDPbind is a web predictor of disorder-mediated RNA, DNA and protein binding regions. DisoRDPbind predicts the RNA-, DNA-, and protein-binding residues located in the intrinsically disordered regions." ; sc:featureList edam:operation_0470, edam:operation_0475, edam:operation_2492, edam:operation_3901, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "DisoRDPbind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biomine.cs.vcu.edu/servers/DisoRDPbind/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:33914683" ; sc:description "Disp R-CNN is a tool for shape prior guided instance disparity estimation for 3D object detection." ; sc:license "Apache-2.0" ; sc:name "Disp R-CNN" ; sc:url "https://github.com/zju3dv/disprcnn" ; biotools:primaryContact "Xiaowei Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0601, edam:topic_0634, edam:topic_2229 ; sc:citation , "pmcid:PMC9156858", "pubmed:35685370" ; sc:description "An integrative database of diseases related variations in liquid-liquid phase separation proteins." ; sc:featureList edam:operation_0417, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "DisPhaseDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1.8" ; sc:url "http://disphasedb.leloir.org.ar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0154, edam:topic_0736, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC7461198", "pubmed:32823616" ; sc:description "DispHred is server to predict pH-dependent order-disorder transitions in intrinsically disordered proteins. 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The dockNmine portal aims at gathering public and private data into a unique service. Automated queries on protein targets and ligand definitions are performed to Uniprot, PubChem and ChemBL to enhance the results of pre-computed docking experiments. When available, public data are automatically added to the docking results to produce state-of-the-art protein-ligand binding analysis such as ROC curves or enrichment analysis. Users can also upload their own private data to analyze them automatically""" ; sc:featureList edam:operation_0310, edam:operation_0482, edam:operation_1812, edam:operation_3799, edam:operation_3899 ; sc:name "dockNmine" ; sc:softwareHelp ; sc:url "http://www.ufip.univ-nantes.fr/tools/docknmine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2275, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:33035337" ; sc:description "DockCoV2 is a drug database against SARS-CoV-2. It can be used for coronavirus (SARS-CoV-2) drug screening." ; sc:featureList edam:operation_2421, edam:operation_3899, edam:operation_3938 ; sc:license "GPL-3.0" ; sc:name "DockCoV2" ; sc:url "https://covirus.cc/drugs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3343 ; sc:citation , "pmcid:PMC8442548", "pubmed:34555725" ; sc:description "Open consensus docking and ranking pipeline for virtual screening of small molecules." ; sc:featureList edam:operation_2476, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "dockECR" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/rochoa85/dockECR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation "pubmed:29069297", "pubmed:30367595" ; sc:description """docker4seq provides a general schema and an infrastructure to distribute robust and reproducible workflows. It guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture. docker4seq R package contains all the R functions required to handle all the steps of RNAseq and miRNA-seq workflow.""" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "docker4seq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.2.9" ; sc:url "https://github.com/kendomaniac/docker4seq" ; biotools:primaryContact "Raffaele Calogero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_0769, edam:topic_2275 ; sc:citation , "pubmed:36764832" ; sc:description "An integrated graphic user interface tool for molecular docking and virtual screening." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Dockey" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lmdu/dockey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_2814 ; sc:citation , "pmcid:PMC9667896", "pubmed:36281025" ; sc:description "DOCKGROUND resource for protein recognition studies." ; sc:featureList edam:operation_0337, edam:operation_0477, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "Dockground" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dockground.compbio.ku.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:35792827" ; sc:description "DockingPie is a plugin of the popular molecular graphics system PyMOL that offers a versatile and user-friendly graphical user interface for assisting molecular and consensus docking analyses." ; sc:featureList edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DockingPie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/paiardin/DockingPie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0166, edam:topic_2275 ; sc:citation , "pmcid:PMC9825772", "pubmed:36484688" ; sc:description "An efficient Siamese graph-based neural network method which predicts contact residues between two interacting proteins." ; sc:featureList edam:operation_0244, edam:operation_0272, edam:operation_0478, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "DockNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biosig.lab.uq.edu.au/docknet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3318, edam:topic_3343 ; sc:citation , , "pubmed:34160214" ; sc:description """A Python code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces. Automatization for adsorbing molecules on surfaces and screening the different adsorption modes and molecular configurations.""" ; sc:featureList edam:operation_0478, edam:operation_1816, edam:operation_3359, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "DockOnSurf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/lch_interfaces/dockonsurf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0128, edam:topic_2275 ; sc:citation , "pmcid:PMC4414291", "pubmed:25902779" ; sc:description "A webserver for ranking protein-protein docked poses." ; sc:featureList edam:operation_0482 ; sc:name "DOCKSCORE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/dockscore/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_3307 ; sc:citation , "pmcid:PMC5333608", "pubmed:28344774" ; sc:description "Brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within." ; sc:featureList edam:operation_0224, edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "Dockstore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dockstore.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC8596819", "pubmed:34789335" ; sc:description "A docking wrapper to enhance de novo molecular design." ; sc:featureList edam:operation_0478, edam:operation_3935, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DockStream" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MolecularAI/DockStream" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0209, edam:topic_2275, edam:topic_3930 ; sc:citation ; sc:description "DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market." ; sc:featureList edam:operation_3891, edam:operation_3899, edam:operation_3938 ; sc:name "DockThor-VS" ; sc:url "http://www.dockthor.lncc.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description "DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorporates different ontologies with an accompagnying R package that allows easy access, exploration, and definition of disease concepts of interest. It can work as the intermediate player to facilitate access and exhaustive extraction of information from other life science databases without the need to harmonize these up front." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3280 ; sc:license "GPL-3.0" ; sc:name "DODO" ; sc:url "https://github.com/Elysheba/DO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "Dodona is a free online exercise platform for learning to code. It wants to teach students how to program in the most meaningful and effective way possible, by using different techniques to apply the advantages of personalized coaching in contexts where students usually only have access to traditional coaching (e.g. lectures or exercise sessions) or even no coaching at all (e.g. independent learning or homework)." ; sc:name "Dodona" ; sc:softwareHelp ; sc:softwareVersion "4.2" ; sc:url "https://dodona.ugent.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_3174 ; sc:citation "pubmed:22110030" ; sc:description "The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_0525, edam:operation_3216 ; sc:name "DOE Joint Genome Institute Genome Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.jgi-psf.org/" ; biotools:primaryContact "I.V. Grigoriev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3179, edam:topic_3393, edam:topic_3518 ; sc:citation "pubmed:16179358" ; sc:description "Doelan is an tool designed to monitor the quality of DNA microarray production." ; sc:featureList edam:operation_0309, edam:operation_0560, edam:operation_2428, edam:operation_3218 ; sc:name "Doelan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.transcriptome.ens.fr/doelan/" ; biotools:primaryContact "Doelan Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3678 ; sc:citation , "pmcid:PMC6794737", "pubmed:31615395" ; sc:description """A python package for optimizing processing pipelines using statistical design of experiments (DoE). A systematic approach to optimizing multi-level and multi-step data processing workflows. Optimize your data processing pipelines with doepipeline. The optimization strategy implemented in doepipeline is based on methods from statistical Design of Experiments (DoE). Use it to optimize quantitative and/or qualitative factors of simple (single tool) or complex (multiple tool) pipelines""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3216, edam:operation_3227, edam:operation_3454 ; sc:license "MIT" ; sc:name "doepipeline" ; sc:url "https://github.com/clicumu/doepipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3325, edam:topic_3474 ; sc:citation ; sc:description "Rare variant association test based on position density estimation." ; sc:featureList edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DoEstRare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/DoEstRare/index.html" ; biotools:primaryContact "Elodie Persyn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2878 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structural motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3534 ; sc:citation , ; sc:description "Automated pocket detection and analysis tool enabling the identification of potential binding pockets and subpockets in protein structures. Additionally, global properties, describing size, shape and chemical features of the predicted (sub)pockets, are calculated. Per default, a simple druggability score is provided for each (sub)pocket, based on a linear combination of the three descriptors describing volume, hydrophobicity and enclosure." ; sc:featureList edam:operation_2406 ; sc:name "DoGSiteScorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Hamburg - Center for Bioinformatics" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de/#dogsite" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1070 ; sc:encodingFormat edam:format_1475 ; sc:name "Structure ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3128 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_1317 ; sc:citation , , ; sc:description "Database of local biomolecular conformers, stores DNA structural data including the information about DNA local spatial arrangement." ; sc:featureList edam:operation_0253 ; sc:isAccessibleForFree true ; sc:name "Dolbico" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://dolbico.org/" ; biotools:primaryContact "Bohdan Schneider", "Daniel Svozil", "Filip Lankaš", "Jiří Černý", "Petr Cech" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0736, edam:topic_3325, edam:topic_3512 ; sc:citation , "pmcid:PMC9990413", "pubmed:36896423" ; sc:description "Improve the classification of human missense variants using protein domains information." ; sc:featureList edam:operation_0303, edam:operation_3225, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "DOLPHIN" ; sc:url "https://dolphin.mmg-gbit.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168 ; sc:citation "pmcid:PMC6938066" ; sc:description "DolphinNext is a web server for distributed data processing of high throughput genomics." ; sc:isAccessibleForFree true ; sc:name "DolphinNext" ; sc:url "https://dolphinnext.umassmed.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0736, edam:topic_0821 ; sc:citation ; sc:description "dom2vec is tool for unsupervised protein domain embeddings capture domains structure and function providing data-driven insights into collocations in domain architectures." ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_0337 ; sc:name "dom2vec" ; sc:url "https://github.com/damianosmel/dom2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:16547073", "pubmed:17553833" ; sc:description "Accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_0476, edam:operation_0477, edam:operation_3092 ; sc:name "DOMAC" ; sc:url "http://casp.rnet.missouri.edu/domac.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Method to identify domains in a protein sequence from similarity searches using PSI-BLAST. The identified domains are used in individual PSI-BLAST searches to improve detection of distant homologous sequences. The tool iterates until no new domains are found." ; sc:featureList edam:operation_2403, edam:operation_2451 ; sc:name "DOMAINATION_Domain_Prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ibi.vu.nl/programs/domainationwww/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3300, edam:topic_3384 ; sc:citation , "pmcid:PMC9908850", "pubmed:36610676" ; sc:description "Domain adaptation toolbox for medical data analysis." ; sc:featureList edam:operation_0337, edam:operation_2945, edam:operation_3443, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "DomainATM" ; sc:softwareHelp ; sc:url "https://mingxia.web.unc.edu/domainatm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:description "DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are" ; sc:featureList edam:operation_2479 ; sc:name "DomainFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.4" ; sc:url "http://dirac.cnrs-orleans.fr/plone/Members/hinsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0605, edam:topic_0621, edam:topic_0736, edam:topic_3944 ; sc:citation , "pmcid:PMC9601794", "pubmed:36208126" ; sc:description "Accurate domain structure annotation including those with non-contiguous topologies." ; sc:featureList edam:operation_0224, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "DomainMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FriedLabJHU/DomainMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation , "pubmed:11159328" ; sc:description "DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact." ; sc:featureList edam:operation_2479 ; sc:name "DomainParser" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://csbl.bmb.uga.edu/downloads/indexa.php#domainparser2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1355 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein signature" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1904 ; sc:encodingFormat edam:format_2330 ; sc:name "Locus ID (EntrezGene)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3572 ; sc:citation ; sc:description "Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure." ; sc:featureList edam:operation_2436, edam:operation_2997 ; sc:license "Artistic-2.0" ; sc:name "domainsignatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/domainsignatures.html" ; biotools:primaryContact "Florian Hahne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0623, edam:topic_0736, edam:topic_3299 ; sc:citation , "pubmed:34023887" ; sc:description "DomainViz allows users to identify and visualize protein domains on one or more protein sequences using multiple domain prediction platforms (Pfam and Prosite) to understand the consensus positionality and abundance of different domains within protein groups and families." ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "DomainViz" ; sc:url "https://uhrigprotools.biology.ualberta.ca/domainviz" ; biotools:primaryContact "R Glen Uhrig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0749, edam:topic_3500 ; sc:citation , "pmcid:PMC8743893", "pubmed:35000444" ; sc:description "DomArchive is a data package compiling dominance interaction data published over a century of research. The goal of the package is to facilitate comparative research on the structure and function of dominance hierarchies." ; sc:featureList edam:operation_0310, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "DomArchive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DomArchive/DomArchive" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0602, edam:topic_0736 ; sc:citation ; sc:description "DomFun is a system to assign functions to unknown proteins using a systemic approach without considering their sequence but their domains associated with functional systems. It uses associations calculated between protein domains and functional annotations as training dataset and performs predictions over proteins (using UniProt identifiers) by finding their domains and if they have been associated with functional annotations (in GO molecular functions, biological processes, KEGG and Reactome pathway terms)." ; sc:featureList edam:operation_0303, edam:operation_1777, edam:operation_3928 ; sc:license "MIT" ; sc:name "DomFun" ; sc:url "https://rubygems.org/gems/DomFun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0602, edam:topic_0736, edam:topic_3957 ; sc:citation "pubmed:21113022" ; sc:description "Collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. 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biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3407 ; sc:citation , "pubmed:36940011" ; sc:description "Development and validation of a nomogram to estimate future risk of type 2 diabetes mellitus in adults with metabolic syndrome." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "dynnomapp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lucky0708.shinyapps.io/dynnomapp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602 ; sc:citation , "pmcid:PMC5793847", "pubmed:28472330" ; sc:description "Compute biomolecular systems dynamics for user-uploaded structural coordinates or PDB identifiers, by integrating two widely used elastic network models (ENMs) – the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM)." ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_1839 ; sc:name "DynOmics EMN" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://enm.pitt.edu/" ; biotools:primaryContact "Hongchun Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3360, edam:topic_3398 ; sc:citation , "pmcid:PMC6702040", "pubmed:31431819" ; sc:description "An R method for multiple imputation in R library Dynamic Modeling in R (dynr)." ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3891 ; sc:name "dynr.mi" ; sc:url "https://rdrr.io/cran/dynr/man/dynr.mi.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "dynUGENE is an R package for uncertainty-aware gene regulatory network inference, simulation, and visualization." ; sc:featureList edam:operation_1781, edam:operation_3925, edam:operation_3928 ; sc:name "dynUGENE" ; sc:url "https://tianyulu.shinyapps.io/dynUGENE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0204, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC8287415", "pubmed:34290733" ; sc:description "A Novel Dysregulated Pathway Identification Analysis Method." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "DysPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lemonwang2020/DysPIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3577 ; sc:citation , "pubmed:32717036" ; sc:description "DysRegSig is an R package for identifying gene dysregulations and building mechanistic signatures in cancer. DysRegSig is capable of robustly exploring gene dysregulations from high-dimensional expression data with cooperativity and synergy between regulators and several other transcriptional regulation rules taken into consideration. DysRegSig also offers tools to rank dysregulated regulations and TFs, and construct mechanistic signature with gene dysregulations by using genetic algorithm." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "DysRegSig" ; sc:url "https://github.com/SCBIT-YYLab/DysRegSig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0622, edam:topic_0736, edam:topic_2640, edam:topic_2885 ; sc:citation , "pubmed:25064568" ; sc:description "Identifies cancer driver genes based on linear annotations of biological regions such as protein domains. e-Driver uses information on three-dimensional (3D) structures of the mutated proteins to identify specific structural features. Then, the algorithm analyzes whether these features are enriched in cancer somatic mutations and, therefore, are candidate driver genes." ; sc:featureList edam:operation_2415, edam:operation_2454, edam:operation_2949, edam:operation_3197, edam:operation_3225, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "e-Driver" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/eduardporta/e-Driver" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0202, edam:topic_0634 ; sc:citation , "pmcid:PMC8152780", "pubmed:34068131" ; sc:description "A Novel mHealth System for Remote Monitoring of Symptoms in COVID-19. Application for remote monitoring of vital signs and symptoms." ; sc:featureList edam:operation_0460, edam:operation_2421 ; sc:name "e-CoVig" ; sc:url "https://play.google.com/store/apps/details?id=com.ecovig.app" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:24481216" ; sc:contributor ; sc:description "E-CRISP is a computational tool to design and evaluate guide RNAs for use with CRISPR/Cas9. The web application uses fast algorithms to identify target sequences for use with mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different parameters of how CRISPR constructs can be used in experimental applications, such as knock-out and tagging experiments. E-CRISP can design guide RNAs for genomes of more than 30 organisms." ; sc:featureList edam:operation_0337, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "E-CRISP" ; sc:softwareHelp ; sc:softwareVersion "5.3.0" ; sc:url "http://www.e-crisp.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "Enviromic Assembly for purposes of Genomic Prediction (E-GP). Enviromic assembly increases accuracy and reduces costs of the genomic prediction for yield plasticity" ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3557, edam:operation_3799 ; sc:name "E-GP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gcostaneto/EGP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6859266", "pubmed:31777679" ; sc:description """Augmentation of Doppler Radar Data Using Generative Adversarial Network for Human Motion Analysis. Objectives:Human motion analysis can be applied to the diagnosis of musculoskeletal diseases, rehabilitation therapies, fall detection, and estimation of energy expenditure. To analyze human motion with micro-Doppler signatures measured by radar, a deep learning algorithm is one of the most effective approaches. Because deep learning requires a large data set, the high cost involved in measuring large amounts of human data is an intrinsic problem. The objective of this study is to augment human motion micro-Doppler data employing generative adversarial networks (GANs) to improve the accuracy of human motion classification. Methods:To test data augmentation provided by GANs, authentic data for 7 human activities were collected using micro-Doppler radar.""" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:license "MIT" ; sc:name "e-hir GAN" ; sc:url "https://github.com/isn350/e_hir_GAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3336 ; sc:citation "pubmed:20444867" ; sc:description "e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included." ; sc:featureList edam:operation_2430 ; sc:name "e-LEA3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ipmc.cnrs.fr/lea.html" ; biotools:primaryContact "Dominique Douguet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:33624746" ; sc:description "E-MAGMA is an eQTL-informed method to identify risk genes using genome-wide association study summary statistics." ; sc:featureList edam:operation_3196, edam:operation_3232 ; sc:name "E-MAGMA" ; sc:url "https://github.com/eskederks/eMAGMA-tutorial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2640 ; sc:citation , ; sc:description "e-MutPath is a R library for the identification of candidate cancer mutations based on edge perturbation." ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "e-MutPath" ; sc:url "https://github.com/lyshaerbin/eMutPath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3263, edam:topic_3577 ; sc:citation , "pubmed:34086863" ; sc:description "E-Pedigrees is a large-scale automatic family pedigree prediction application." ; sc:featureList edam:operation_3435, edam:operation_3625 ; sc:license "MIT" ; sc:name "E-Pedigrees" ; sc:url "https://github.com/xiayuan-huang/E-pedigrees" ; biotools:primaryContact "David Page", "Scott J Hebbring" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3263, edam:topic_3305, edam:topic_3368, edam:topic_3489 ; sc:citation , "pmcid:PMC7027209", "pubmed:32066455" ; sc:description "E-PIX® is a record linkage tool for managing multi-million patients in research projects at a large university hospital in Germany. The Record Linkage and ID Management solution E-PIX (Enterprise Identifier Cross Referencing) applies the propabilistic Fellegi-Sunter-algorithm and the Levenshtein distance to avoid duplicate participant entries. The independent software module facilitates participant management and multisite-aggregation of medical research data." ; sc:featureList edam:operation_0224, edam:operation_3907 ; sc:license "AGPL-3.0" ; sc:name "E-PIX" ; sc:url "https://github.com/mosaic-hgw/E-PIX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3263, edam:topic_3303 ; sc:citation ; sc:description "Federated Trusted Third Party as an Approach for Privacy Preserving Record Linkage in a Large Network of University Medicines in Pandemic Research." ; sc:featureList edam:operation_3283, edam:operation_3454, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "E-PIX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://demo.ths-greifswald.de/epix-web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3277 ; sc:citation ; sc:description "E-Predict compares observed hybridization patterns with theoretical energy profiles representing different species. We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications." ; sc:featureList edam:operation_2423, edam:operation_2495 ; sc:name "E-Predict" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://derisilab.ucsf.edu/software/epredict/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2546 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Matteo Manfredi" ; sc:citation ; sc:contributor ; sc:description "E-pRSA is a method for predicting the Relative Solvent Accessibility of residues in a protein chain without requiring previous knowledge of the 3-dimensional structure. E-pRSA is based on embeddings derived from protein language models." ; sc:featureList edam:operation_0384, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "E-pRSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://e-prsa.biocomp.unibo.it/main" ; biotools:primaryContact , "Matteo Manfredi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0092, edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation , "pmcid:PMC4086097", "pubmed:24810851" ; sc:description "Collection of web servers for comparative RNA structure prediction and visualisation." ; sc:featureList edam:operation_0278, edam:operation_0337, edam:operation_0570, edam:operation_2441 ; sc:name "e-RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.e-rna.org" ; biotools:primaryContact "e-RNA Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3523, edam:topic_3678 ; sc:citation "pubmed:14764878", "pubmed:15980541", "pubmed:20444868" ; sc:description "E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design." ; sc:featureList edam:operation_2428 ; sc:name "E-RNAi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://e-rnai.dkfz.de/" ; biotools:primaryContact "E-RNAi Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2640 ; sc:citation ; sc:description "an open-source, browser-based visualization suite to render complex relationships between cancer evolution data in an intuitive, interactive framework for biomedical investigators. It consists of 3 visualization tools: Timescape, Mapscape and Cellscape" ; sc:featureList edam:operation_2426, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "E-scape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.nature.com/articles/nmeth.4303" ; biotools:primaryContact "Maia Smith" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3120, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:36227117" ; sc:description "Embedding of protein sequence and function improves the annotation of human pathogenic variants." ; sc:featureList edam:operation_0331, edam:operation_3461, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "E-SNPs and GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://esnpsandgo.biocomp.unibo.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0622, edam:topic_3398 ; sc:citation , "pmcid:PMC3814377", "pubmed:24003033" ; sc:description "Web tool to design TALENs for genome engineering." ; sc:featureList edam:operation_0477 ; sc:name "E-TALEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.e-talen.org/E-TALEN/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0634, edam:topic_3336, edam:topic_3407 ; sc:citation , "pmcid:PMC9677481", "pubmed:36347537" ; sc:description "An interactive visual exploration platform for target-disease knowledge mapping from literature." ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_3938 ; sc:license "Other" ; sc:name "e-TSN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lilab-ecust.cn/etsn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0199, edam:topic_3120, edam:topic_3305 ; sc:citation , "pmcid:PMC8953562", "pubmed:35341044" ; sc:description "Evolve is a Webtool designed to model mutations in the input protein complex using Modeller." ; sc:featureList edam:operation_0244, edam:operation_0331, edam:operation_0478, edam:operation_0480, edam:operation_3227 ; sc:license "Not licensed" ; sc:name "E-Volve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.dcc.ufmg.br/evolve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0821, edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:18524800" ; sc:description "E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0448, edam:operation_2575, edam:operation_3092 ; sc:name "E1DS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://e1ds.csbb.ntu.edu.tw/" ; biotools:primaryContact "E1DS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_0654, edam:topic_3306, edam:topic_3520 ; sc:citation , "pubmed:34435773" ; sc:description "E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy." ; sc:featureList edam:operation_0244, edam:operation_0278, edam:operation_2476, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "E2EDNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/InfluenceFunctional/E2EDNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0654, edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:15215398" ; sc:description "E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe." ; sc:featureList edam:operation_2429, edam:operation_2451, edam:operation_2871, edam:operation_3211 ; sc:name "E2G" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/e2g/" ; biotools:primaryContact "Alexander Sczyrba", "Jan Krüger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0218, edam:topic_3473 ; sc:citation "pubmed:18483079" ; sc:description "Web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published literature as well as from the biological databases." ; sc:featureList edam:operation_0306 ; sc:name "E3Miner" ; sc:url "http://e3miner.biopathway.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0780, edam:topic_0821, edam:topic_3697 ; sc:citation , "pubmed:31794006" ; sc:description """simultaneous classification and motif identification for enzyme annotation. 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EasyFRAP-web allows large data-sets to be rapidly evaluated and normalized fluorescence recovery curves to be generated and exported. It also performs curve fitting and provides quantitative parameters (mobile fraction and recovery half time) necessary for comparison across data-sets." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "easyFRAP-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:url "https://easyfrap.vmnet.upatras.gr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Suite" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_0821, edam:topic_2275 ; sc:citation , "pubmed:32833550" ; sc:description "EasyAmber is a comprehensive toolbox to automate the molecular dynamics simulation of proteins. EasyAmber is a set of wrapper scripts to automate the molecular dynamics routines implemented in the Amber package. The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility, and supports the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. The easyAmber software takes the molecular dynamics to the next level in terms of usability for complex processing of large volumes of data. It implements advanced MD protocols, but is highly automated and easy-to-operate to attract a broad audience. 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The user can handle simultaneously large data sets of raw data, visualize fluorescence recovery curves, exclude low quality data, perform data normalization, extract quantitative parameters, perform batch analysis and save the resulting data and figures for further use." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-1.0" ; sc:name "easyFRAP" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ccl.med.upatras.gr/easyfrap.html" ; biotools:primaryContact "Zoi Lygerou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0625, edam:topic_3077, edam:topic_3277 ; sc:citation ; sc:description "Process and analyze ecological field sampling data generated using the Fulcrum mobile application." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3196 ; sc:license "Other" ; sc:name "easyFulcrum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://andersenlab.org/easyfulcrum/articles/easyFulcrum.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0622, edam:topic_0780, edam:topic_3489 ; sc:citation , "pubmed:35748710" ; sc:description "EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EasyGDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/noefp/easy_gdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "Fully automated gene prediction for prokaryotes. 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The package allows you to import easily qPCR data files as described in the vignette. 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Chan", "Wei-Chun Kao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070, edam:topic_3407 ; sc:citation , "pubmed:31384918" ; sc:description "An Application for Detection and Analysis of Oscillators Identifies Metabolic Regulation on Genome-Wide Circadian Output | An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators | Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO) | Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2017) | This is the first step in the PAICE (Pipeline for Amplitude Integration of Circadian Exploration) Suite! 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The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids." ; sc:featureList edam:operation_0578, edam:operation_2422 ; sc:license "GPL-2.0" ; sc:name "ecolitk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ecolitk.html" ; biotools:primaryContact "Laurent Gautier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0160, edam:topic_0623, edam:topic_2814 ; sc:citation , "pubmed:33983436" ; sc:description "eCOMPASS (evaluative comparison of multiple protein alignments by statistical score) addresses this problem using a statistical measure of relative alignment quality based on direct coupling analysis (DCA): to maintain protein structural integrity over evolutionary time, substitutions at one residue position typically result in compensating substitutions at other positions. eCOMPASS computes the statistical significance of the congruence between high scoring directly coupled pairs and 3D contacts in corresponding structures, which depends upon properly aligned homologous residues." ; sc:featureList edam:operation_0295, edam:operation_0337, edam:operation_0492, edam:operation_2479 ; sc:name "eCOMPASS" ; sc:url "https://www.igs.umaryland.edu/labs/neuwald/software/compass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0176, edam:topic_0749, edam:topic_2275 ; sc:citation , "pubmed:32323374" ; sc:description "ECONTACT (Energetic CONTributions of Amino acid residues and its possible Cross-Talk) is an approach to identify potential cross-talks between amino acid residues of protein pocket involved in ligand binding. This approach utilizes per-residue energy terms derived from multiple protein-ligand complexes as variables for principal component analysis (PCA) and identifies top cross-talks which can be tested in any protein-ligand complex." ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3431, edam:operation_3891, edam:operation_3938 ; sc:name "ECONTACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.gujaratuniversity.ac.in/econtact/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474 ; sc:citation , "pubmed:31513916" ; sc:description "> HOMEPAGE MISSING! | Improved ensemble convolutional neural networks for RNA binding protein prediction directly from sequence | RNA binding proteins (RBPs) determine RNA process from synthesis to decay, which play a key role in RNA transport, translation and degradation. Therefore, exploring RBPs' function from the amino acid sequence using computational methods has become one of the momentous topics in genome annotation. However, there still have some challenges: (1) shallow feature: Although the sequence determines structure is self-evident, it is difficult to analyze the essential features from simple sequence. (2) Poorly understand: feature-based prediction methods mainly emphasize feature extraction, while in-depth understanding of protein mysteries limits the application of feature engineering. (3) Feature fusion: multi-feature fusion is often used, but the features are not well integrated" ; sc:featureList edam:operation_3902 ; sc:name "econvRBP" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31513916" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC8825466", "pubmed:34927685" ; sc:description "EcoPLOT is an interactive web-application for the analysis of multivariate-biogeochemical datasets." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EcoPLOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cdsanchez18/EcoPLOT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0749, edam:topic_2830, edam:topic_3966 ; sc:citation , "pmcid:PMC10072801", "pubmed:37016299" ; sc:description "EcoSP database is an integrated repository of bacterial O-antigens and K-antigens (Escherichia coli), which collects comprehensive information, including serotypes, coding region sequences, glycosyltransferases, structures, and biosynthetic pathways of K-/O- antigens." ; sc:featureList edam:operation_0252, edam:operation_0417, edam:operation_2421, edam:operation_3431, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "EcoSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ecosp.dmicrobe.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36282847" ; sc:description "An R-package to easily use Transfer Learning for Ecological Studies. A plankton case study." ; sc:featureList edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EcoTransLearn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/IFREMER-LERBL/EcoTransLearn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:15215395" ; sc:description "The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. 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(Galaxy Version 1.0.0)" ; sc:featureList edam:operation_0310, edam:operation_3219, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ECTyper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usegalaxy.eu/root?tool_id=ectyper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0196, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC7147433", "pubmed:32292644" ; sc:description "ECuADOR is a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines." ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_3211, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "ECuADOR" ; sc:url "https://github.com/BiodivGenomic/ECuADOR/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2330 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3617 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3679 ; sc:citation ; sc:description "A web-based tool to support researchers in the planning of animal experiments. 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The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.""" ; sc:featureList edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EDAM-Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://github.com/IFB-ElixirFr/edam-browser" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by definition." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamdef" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamdef.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by has_input relation." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamhasinput" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamhasinput.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by has_output relation." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamhasoutput" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamhasoutput.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by is_format_of relation." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamisformat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamisformat.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by is_identifier_of relation." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamisid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamisid.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find EDAM ontology terms by name." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "edamname" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/edamname.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3170 ; sc:citation , "pmcid:PMC4067528", "pubmed:24929920" ; sc:description "Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)." ; sc:featureList edam:operation_0564, edam:operation_3680 ; sc:license "Artistic-2.0" ; sc:name "EDASeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/EDASeq.html" ; biotools:primaryContact "Davide Risso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3308, edam:topic_3361 ; sc:citation , "pmcid:PMC10665591", "pubmed:38022697" ; sc:description "Extension of GDC data analysis, visualization, and exploration tools." ; sc:featureList edam:operation_2939, edam:operation_3223, edam:operation_3431 ; sc:license "MIT" ; sc:name "eDAVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://edave.pum.edu.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_3299, edam:topic_3474, edam:topic_3794 ; sc:citation , "pubmed:34694393" ; sc:description "Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network." ; sc:featureList edam:operation_3901, edam:operation_3902, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EDCNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yaweiwang1232/EDCNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3324, edam:topic_3379, edam:topic_3418 ; sc:citation , "pmcid:PMC9077850", "pubmed:35526046" ; sc:description "The European & Developing Countries Clinical Trials Partnership (EDCTP) Knowledge Hub." ; sc:featureList edam:operation_0224, edam:operation_0496 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "EDCTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://edctpknowledgehub.tghn.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "This tool can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance." ; sc:featureList edam:operation_0309, edam:operation_3095 ; sc:license "GPL-2.0" ; sc:name "EDDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/EDDA.html" ; biotools:primaryContact "Chia Kuan Hui Burton", "Niranjan Nagarajan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3301 ; sc:citation "pubmed:18332092" ; sc:description "A program for assembling de novo bacterial genomes from short reads produced by Illumina sequencing platform." ; sc:featureList edam:operation_0524, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EDENA" ; sc:operatingSystem "Linux" ; sc:softwareVersion "3" ; sc:url "http://www.genomic.ch/edena" ; biotools:primaryContact "Dr David HERNANDEZ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2259, edam:topic_3053, edam:topic_3517 ; 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sc:featureList edam:operation_0269, edam:operation_2995, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "EMCBOW-GPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/454170054/EMCBOW-GPCR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0611 ; sc:description "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. 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Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, this missing metadata may be found in the narrative of publications describing the research. This respository offers a new metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, and Europe PMC annotations API." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "EMERALD METAGENOMICS ANNOTATIONS PIPELINE" ; sc:operatingSystem "Linux" ; sc:url "https://gitlab.com/maaly7/emerald_metagenomics_annotations" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation , , , ; sc:description "The Extreme-scale Model Exploration with Swift (EMEWS) framework enables the direct integration of multi-language model exploration (ME) algorithms while scaling dynamic computational experiments to very large numbers (millions) of models on all major HPC platforms. EMEWS has been designed for any \"black box\" application code, such as agent-based and microsimulation models or training of machine learning models, that require multiple runs as part of heuristic model explorations. One of the main goals of EMEWS is to democratize the use of large-scale computing resources by making them accessible to more researchers in many more science domains. EMEWS is built on the Swift/T parallel scripting language." ; sc:isAccessibleForFree true ; sc:name "EMEWS" ; sc:softwareHelp ; sc:url "https://emews.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_3957 ; sc:citation , "pubmed:33381837" ; sc:description "Extensible Matrix Factorization (EMF) is an flexible method for imputing genetic interactions with cross-species and side information." ; sc:featureList edam:operation_2421, edam:operation_3557, edam:operation_3799 ; sc:license "MIT" ; sc:name "Extensible Matrix Factorization" ; sc:url "https://github.com/lrgr/EMF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1930 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "EMGB is a CWL-based workflow for metagenomics analyses including a web-based interface for filtering ind querying analysis results" ; sc:featureList edam:operation_0256, edam:operation_0325, edam:operation_0337, edam:operation_2451, edam:operation_3695 ; sc:name "EMGB" ; sc:provider "Bielefeld University", "CeBiTec" ; sc:url "https://emgb.cebitec.uni-bielefeld.de" ; biotools:primaryContact "EMGB Service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "Finds the \"on\" and \"off\" indicies of a single raw surface EMG burst (muscle contraction)." ; sc:isAccessibleForFree true ; sc:name "EMGONOFF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/11049-emgonoff" ; biotools:primaryContact "Kieran Coghlan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0611, edam:topic_3382 ; sc:citation ; sc:description "Accurate automated hole masking algorithm for single-particle cryo-EM image processing." ; sc:featureList edam:operation_3443 ; sc:name "EMHP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/chazbot/emhp" ; biotools:primaryContact "Charles Bowman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3053 ; sc:citation , ; sc:description """EMIRGE (Expectation-Maximization Iterative Reconstruction of Genes from the Environment) reconstructs full length ribosomal genes from short read sequencing data. In the process, it also provides estimates of the sequences' abundances. EMIRGE uses a modification of the EM algorithm to iterate between estimating the expected value of the abundance of all SSU sequences present in a sample and estimating the probabilities for each read that a specific sequence generated that read. At the end of each iteration, those probabilities are used to re-calculate (correct) a consensus sequence for each reference SSU sequence, and the mapping is repeated, followed by the estimations of probabilities. The iterations should usually stop when the reference sequences no longer change from one iteration to the next. Practically, 40-80 iterations is usually sufficient for many samples. 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As sequencing-based reference panels continue to grow, increasingly more markers are being well or better imputed but at the same time, even more markers with relatively low minor allele frequency are being imputed with low imputation quality. Here, we propose new methods that incorporate imputation uncertainty for downstream association analysis, with improved power and/or computational efficiency." ; sc:featureList edam:operation_3557 ; sc:license "GPL-2.0" ; sc:name "EMLRT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://yunliweb.its.unc.edu/emlrt.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Multiple sequence alignment (ClustalW wrapper)." ; sc:featureList edam:operation_0499 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "emma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/emma.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0769, edam:topic_3895, edam:topic_3912 ; sc:citation , "pubmed:35050610" ; sc:description "EMMA-CAD a web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors" ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:name "EMMA-CAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://emma.cailab.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_2058 ; sc:name "Microarray hybridisation data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3161 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "MAGE-compliant software platform for the evaluation of microarry experiment data sets resulting from genome-wide transcriptomics studies. It allows to access the raw transcriptome data sets and provides automated and extensible analysis and visualization pipelines, including but not limited to the normalization of single and multiple microarrays and statistical tests for inferring differentially expressed genes." ; sc:featureList edam:operation_0313, edam:operation_0571, edam:operation_2238, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "EMMA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bielefeld University", "CeBiTec", "bigi" ; sc:softwareHelp , ; sc:softwareVersion "2.8.2" ; sc:url "http://emma.cebitec.uni-bielefeld.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071, edam:topic_3518 ; sc:description "A MAGE-compliant system for the collaborative analysis and integration of microarray data." ; sc:featureList edam:operation_2422 ; sc:name "EMMA2 WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php/UsingTheWSInterface" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3168 ; sc:citation , "pmcid:PMC10704716", "pubmed:38062452" ; sc:description "A new method for computing multiple sequence alignments given a constraint subset alignment." ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:name "EMMA" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/c5shen/EMMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , "pmcid:PMC3092069", "pubmed:20208533" ; sc:description "Efficient Mixed-Model Association eXpedited is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the efficiency obtained by the EMMA algorithm, EMMAX takes advantage of the fact that each locus explains only a small fraction of complex traits allowing the avoidance of repetitive variance component estimation procedures." ; sc:featureList edam:operation_0282 ; sc:license "Not licensed" ; sc:name "EMMAX" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genetics.cs.ucla.edu/emmax/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_1317, edam:topic_2275, edam:topic_3542 ; sc:citation , "pubmed:33954706" ; sc:description "EMNUSS is a deep learning framework for secondary structure annotation in cryo-EM maps." ; sc:featureList edam:operation_0267, edam:operation_0478, edam:operation_2429, edam:operation_2488 ; sc:license "GPL-3.0" ; sc:name "EMNUSS" ; sc:url "http://huanglab.phys.hust.edu.cn/EMNUSS" ; biotools:primaryContact "Sheng-You Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2275, edam:topic_3325, edam:topic_3534 ; sc:citation , "pmcid:PMC6131211", "pubmed:30052959" ; sc:description """A database of comparative structure models of drug-target interactions from the Binding Database. Computational Systems Biology Group. A database of 200,005 comparative models of drug-bound proteins based on 1,391,403 interaction data obtained from the Binding Database. 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Andersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3316 ; sc:author ; sc:citation ; sc:description "The Empusa code generator: bridging the gap between the intended and the actual content of RDF resources" ; sc:featureList edam:operation_0335, edam:operation_3429 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Empusa" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://empusa.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2640, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC5010989", "pubmed:33299129" ; sc:description """a resource for pan-cancer analysis of epithelial-mesenchymal transition genes and signatures. resource for metastatic research.""" ; sc:name "EMTome" ; sc:url "http://www.emtome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3796 ; sc:citation , "pubmed:33459779" ; sc:description "EMU is a tool for large-scale inference of population structure in presence of missingness using EM-PCA." ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3960 ; sc:license "GPL-3.0" ; sc:name "EMU" ; sc:url "https://github.com/rosemeis/emu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3056, edam:topic_3325 ; sc:citation , "pubmed:23757202" ; sc:description "Emory Genetics Laboratory's (EGL) Variant Classification Catalog contains variants of the gene of interest that has been seen and analysed by EGL Genetics." ; sc:featureList edam:operation_3197, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:name "EmVClass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.egl-eurofins.com/emvclass/emvclass.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_3511, edam:topic_3512 ; sc:citation , "pmcid:PMC8344586", "pubmed:27899630", "pubmed:34096994" ; sc:description "A globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. 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Deep neural networks have been successfully applied to many real-world applications.""" ; sc:license "MIT" ; sc:name "EnAET" ; sc:url "https://github.com/maple-research-lab/EnAET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3168 ; sc:citation , "pubmed:32470109" ; sc:description """An encoder for nanopore FASTQ files. ENANO is a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files. We tested ENANO and current state-of-the-art compressors on several publicly available nanopore datasets. The results show that our algorithm consistently achieves the best compression performance on every nanopore dataset, while being computationally efficient in terms of speed and memory requirements when compared to existing alternatives.""" ; sc:featureList edam:operation_1812, edam:operation_3185 ; sc:license "MIT" ; sc:name "ENANO" ; sc:url "https://github.com/guilledufort/EnanoFASTQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3407 ; sc:citation , "pmcid:PMC9849115", "pubmed:36653322" ; sc:description "Manually curated database of experimentally supported endocrine system disease and lncRNA associations." ; sc:featureList edam:operation_2421, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "ENCD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bio-server.cn/ENCD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pmcid:PMC6861419", "pubmed:31781178" ; sc:description "This is the ENCODE-DCC RNA-sequencing pipeline. 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Single-cell RNA sequencing enables us to characterize the cellular heterogeneity in single cell resolution with the help of cell type identification algorithms. However, the noise inherent in single-cell RNA-sequencing data severely disturbs the accuracy of cell clustering, marker identification and visualization. We propose that clustering based on feature density profiles can distinguish informative features from noise. We named such strategy as 'entropy subspace' separation and designed a cell clustering algorithm called ENtropy subspace separation-based Clustering for nOise REduction (ENCORE) by integrating the 'entropy subspace' separation strategy with a consensus clustering method. We demonstrate that ENCORE performs superiorly on cell clustering and generates high-resolution visualization across 12 standard datasets""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "ENCORE" ; sc:softwareHelp ; sc:url "https://github.com/SONG0417/ENCORE_V1.0.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1743 ; sc:name "Atomic coordinate" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0736, edam:topic_0749, edam:topic_2275 ; sc:citation , "pubmed:37423912" ; sc:description "Web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations." ; sc:featureList edam:operation_0337, edam:operation_2492, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EnCPdock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.scinetmol.in/EnCPdock/" ; biotools:primaryContact "Sankar Basu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_0820 ; sc:citation , "pubmed:33513017" ; sc:description "EnCurv method for maintaining membrane curvature in MD simulations." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "EnCurv" ; sc:url "https://github.com/yesint/EnCurv" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_0634, edam:topic_3053, edam:topic_3678 ; sc:citation "pubmed:16680138", "pubmed:18508807" ; sc:description "ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server supports multiple species and integrates multiple genomic data to generate the final prioritization. ENDEAVOUR has been benchmarked in silico and experimentally validated leading to the discovery of novel disease genes in several genetic diseases." ; sc:featureList edam:operation_2409, edam:operation_2428 ; sc:name "ENDEAVOUR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://endeavour.esat.kuleuven.be/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , , "pmcid:PMC9825263", "pmcid:PMC9825747", "pubmed:36515467", "pubmed:36548388" ; sc:description "Cell type deconvolution of spatially resolved transcriptomics data via ensemble learning." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3629 ; sc:license "Not licensed" ; sc:name "EnDecon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Zhangxf-ccnu/EnDecon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC9730666", "pubmed:36482318" ; sc:description "EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-1.0" ; sc:name "EndHiC" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/fanagislab/EndHiC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC7480700" ; sc:description """Dynamic Analysis for Detecting Endianness Bugs. Endicheck is a Valgrind tool to help you detect missing byte-swaps in your program. It is recommended to use --prefix to install into other-than-default location, since you typically do not want to replace your system's installation of Valgrind. Endicheck still contains all the original Valgrind tools, like MemCheck, but it might not contain all the latest updates or distribution patches.""" ; sc:featureList edam:operation_3891 ; sc:name "Endicheck" ; sc:url "http://github.com/rkapl/endicheck" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:37018101" ; sc:description "Ensemble deep learning-based tool for identifying therapeutic peptides with low hemolytic activity." ; sc:featureList edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "EnDL-HemoLyt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://endl-hemolyt.anvil.app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3308, edam:topic_3407, edam:topic_3518 ; sc:citation , "pmcid:PMC6324065", "pubmed:30357379" ; sc:description """a database of endothelial cell transcriptomics data. EndoDB The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) transcriptomics data (Pubmed).""" ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_2939 ; sc:name "EndoDB" ; sc:url "https://vibcancer.be/software-tools/endodb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384, edam:topic_3474, edam:topic_3954 ; sc:citation , "pubmed:32795966" ; sc:description "Deep Super-Resolution for Capsule Endoscopy." ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3799 ; sc:name "EndoL2H" ; sc:url "https://github.com/CapsuleEndoscope/EndoL2H" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3308, edam:topic_3337, edam:topic_3407, edam:topic_3420 ; sc:citation , "pmcid:PMC7455745", "pubmed:32859947" ; sc:description """A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions. EndometDB web frontend works as the input/output layer for the EndometDB, providing user's query for the backend and plotting it after backend has finished processing it. An extensive collection of human samples and data from patients, that aids in the research for better diagnosis or cure for endometriosis.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2495, edam:operation_3454, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "EndometDB" ; sc:url "https://endometdb.utu.fi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "Interpreting tree ensemble machine learning models with endoR." ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "endoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/leylabmpi/endoR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0780, edam:topic_2229 ; sc:citation , "pmcid:PMC8312264", "pubmed:34252921" ; sc:description "Gene tree and species tree reconciliation with endosymbiotic gene transfer." ; sc:featureList edam:operation_0553, edam:operation_3478, edam:operation_3942, edam:operation_3947 ; sc:name "EndoRex" ; sc:url "https://github.com/AEVO-lab/EndoRex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3337, edam:topic_3519 ; sc:citation , "pmcid:PMC8971653", "pubmed:35092277" ; sc:description "A package for the temporal refinement of endometrial biopsies using an initial timing value as provided via urinary ovulation test and the measurement of expression for a panel of time-sensitive genes" ; sc:featureList edam:operation_0314, edam:operation_3454, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EndoTime" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AE-Mitchell/EndoTime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0769, edam:topic_0821 ; sc:citation , "pmcid:PMC10204868", "pubmed:37228581" ; sc:description "Directing Protein Design Choices by Per-Residue Energy Breakdown Analysis with an Interactive Web Application." ; sc:featureList edam:operation_0387, edam:operation_0479, edam:operation_1839, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ENDURE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://endure.kuenzelab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:19402753" ; sc:description "Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. This resource provides a \"systems-wide\" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins." ; sc:featureList edam:operation_0477 ; sc:name "eNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ecoli.med.utoronto.ca/" ; biotools:primaryContact "Andrew Emili" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3408 ; sc:citation , "pmcid:PMC8642973", "pubmed:34863095" ; sc:description "The ENsemble Fusion (EnFusion) repo contains a Dockerfile to build a Docker Image that can overlap outputs from 7 fusion detection algorithms, to identify high confidence fusion events." ; sc:featureList edam:operation_0239, edam:operation_3501 ; sc:isAccessibleForFree true ; 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biotools:primaryContact "Steven Maere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3334, edam:topic_3384, edam:topic_3444, edam:topic_3517 ; sc:citation ; sc:description """Cross-disorder integration and multiscale neural contextualization of multisite neuroimaging datasets. 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Enlighten2 allows to easily prepare and run molecular dynamics simulations of protein-ligand systems. It requires no installation or knowledge of computational chemistry software and can be run on any machine (Windows, Mac or Linux) that has PyMOL and Docker installed. 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Testing it on a set of de novo draft genomes led to the closure of up to 20% of the gaps originally present. It is cross-platform and most of the steps of its pipeline are parallelizable, making easy and fast to improve a draft genome resulting from a de novo assembly." ; sc:featureList edam:operation_0525 ; sc:name "Enly" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-FIRENZE" ; sc:softwareHelp ; sc:softwareVersion "1.2.2" ; sc:url "http://enly.sourceforge.net/" ; biotools:primaryContact "Marco Fondi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3474 ; sc:author ; sc:citation , "pubmed:34050729" ; sc:description "EnMCB is an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models." ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "EnMCB" ; sc:url "https://github.com/whirlsyu/EnMCB/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_2330, edam:format_3578 ; sc:name "Microarray hybridisation data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Microarray hybridisation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518, edam:topic_3572 ; sc:citation , "pmcid:PMC5209853", "pubmed:28049437" ; sc:description "This package provides an efficient data pre-processing tool designed to reduce background noise and improve signal for DNA methylation estimation from Illumina Methylation BeadChip array measurements. 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Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. 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sc:softwareHelp , ; sc:url "http://bioconductor.org/packages/epialleleR/" ; biotools:primaryContact "Oleksii Nikolaienko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3169, edam:topic_3517 ; sc:citation , "pmcid:PMC4747527", "pubmed:26859295" ; sc:description "ePIgenomics ANNOtation tool." ; sc:featureList edam:operation_3197, edam:operation_3225 ; sc:name "ePIANNO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epianno.stat.sinica.edu.tw/index.html" ; biotools:primaryContact "Hsuan-Yu Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3173, edam:topic_3295 ; sc:citation ; sc:description "Enrichment analyses on epigenomic data in a fast and user-friendly way." ; 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sc:name "EPicker" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://thuem.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3295, edam:topic_3360, edam:topic_3674 ; sc:citation , "pmcid:PMC7574234", "pubmed:33081832" ; sc:description "EpiClass is a Optimizing and predicting performance of DNA methylation biomarkers using sequence methylation density information. EpiClass is a software program to distinguish case samples from control samples using methylation density profiles of each sample." ; sc:featureList edam:operation_0308, edam:operation_0417, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:name "EpiClass" ; sc:url "https://github.com/Elnitskilab/EpiClass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3295, edam:topic_3673, edam:topic_3674 ; sc:citation , "pmcid:PMC7546467", "pubmed:32966276" ; sc:description "Epiclomal is a method for probabilistic clustering of sparse single-cell DNA methylation data." ; sc:featureList edam:operation_3207, edam:operation_3432, edam:operation_3557, edam:operation_3919 ; sc:name "Epiclomal" ; sc:url "https://github.com/shahcompbio/Epiclomal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Command-line tool", "Library", "Suite" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3366 ; sc:citation , "pmcid:PMC5919098", "pubmed:27863955" ; sc:description "EPICO / BLUEPRINT Data Analysis Portal, data loading scripts and API" ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "epico-data-analysis-portal" ; sc:softwareHelp ; sc:url "https://github.com/inab/epico-data-analysis-portal/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7029718", "pubmed:32117461" ; sc:description "epiCOLOC is a web-based tool with built-in large-scale and context-dependent epigenomics annotations." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "epiCOLOC" ; sc:softwareHelp ; sc:url "http://mulinlab.org/epicoloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3173 ; sc:citation , "pmcid:PMC10209526", "pubmed:37250110" ; sc:description "R package for the comparison and quality control of epigenomic peak files." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2428, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EpiCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://neurogenomics.github.io/EpiCompare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305 ; sc:citation ; sc:description "Handling, visualisation and analysis of epidemiological contacts. Represent epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "epicontacts" ; sc:softwareHelp , , ; sc:softwareVersion "1.1.1" ; sc:url "http://www.repidemicsconsortium.org/epicontacts/" ; biotools:primaryContact "VP Nagraj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3308, edam:topic_3656 ; sc:citation , "pmcid:PMC9338487", "pubmed:35906531" ; sc:description "EpiConv is an algorithm of clustering scATAC-seq data and correcting batch effects." ; sc:featureList edam:operation_3222, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "epiConv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LiLin-biosoft/epiConv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3305, edam:topic_3419 ; sc:citation , "pubmed:36847716" ; sc:description "A framework for linking online social media in epidemiological cohorts." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Epicosm" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://dynamicgenetics.github.io/Epicosm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3173 ; sc:description "Provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock. Future work will providedata tracks for these information sources and will ID tissue specific regulation information that is helpful in dissecting QTL." ; sc:featureList edam:operation_2422 ; sc:license "Not licensed" ; sc:name "EpiDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://epidb.animalgenome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Matlab Toolbox for epidemic management using partially observable decision process framework for action selection" ; sc:isAccessibleForFree true ; sc:name "Epidemic Management Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75165-epidemic-management-toolbox" ; biotools:primaryContact "Jens Kappey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518 ; sc:citation , , , ; sc:description "It infers the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user." ; sc:featureList edam:operation_3809 ; sc:license "GPL-2.0" ; sc:name "EpiDISH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://www.biosino.org/EpiDISH/" ; biotools:primaryContact "Shijie Charles Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0749, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc:description "EpiDope is a deep neural network for linear B-cell epitope prediction." ; sc:featureList edam:operation_0337, edam:operation_0416, edam:operation_3927 ; sc:license "MIT" ; sc:name "EpiDope" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://github.com/mcollatz/EpiDope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3047, edam:topic_3173, edam:topic_3366 ; sc:citation , "pmcid:PMC4494013", "pubmed:26153137" ; sc:description "EpiFactors is a database for epigenetic factors such as histones, protamines, other proteins and lncRNAs. It compiles functional information about human and mouse epigenetic regulators, their complexes, and expression in multiple cell types to facilitate the work of researchers in the field of epigenetics." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "EpiFactors" ; sc:url "https://epifactors.autosome.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC8448340", "pubmed:34492011" ; sc:description """Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves. Main functions: epiFilter (or epiFilterSm) performs forward filtering to generate causal R estimates; epiSmooth performs backward smoothing to generate R estimates that use all possible information and recursPredict provides one-step-ahead predictions.""" ; sc:featureList edam:operation_3435, edam:operation_3503, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "EpiFilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kpzoo/EpiFilter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC6738191", "pubmed:31543947" ; sc:description "An R package for risk assessment of travel-related spread of disease | ☣✈️ Risk assessment of travel-related disease spread | Predicting Disease Spread from Flow Data | Welcome to the epiflows package! | epiflows is a package for predicting and visualising spread of infectious diseases based on flows between geographical locations, e.g., countries. epiflows provides functions for calculating spread estimates, handling flow data, and visualization" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "epiflows" ; sc:softwareHelp ; sc:url "https://www.repidemicsconsortium.org/epiflows" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_2840, edam:topic_3170 ; sc:citation , "pmcid:PMC4804494", "pubmed:27004791" ; sc:description "Extracting patterns and identifying co-expressed genes from RNA-Seq data." ; sc:featureList edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "EPIG-Seq" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/epig-seq/?source=navbar" ; biotools:primaryContact "Pierre R. Bushel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0821, edam:topic_2885, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "epiGBS2 is an improved protocol and automated snakemake workflow for highly multiplexed reduced representation bisulfite sequencing." ; sc:featureList edam:operation_0484, edam:operation_3186, edam:operation_3192, edam:operation_3919, edam:operation_3933 ; sc:license "MIT" ; sc:name "epiGBS2" ; sc:url "https://github.com/nioo-knaw/epiGBS2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:32289146" ; sc:description "EpiGEN is an epistasis simulation pipeline written in Python. It supports epistasis models of arbitrary size, which can be specified either extensionally or via parametrized risk models. Moreover, the user can specify the minor allele frequencies (MAFs) of both noise and disease SNPs, and provide a biased target distribution for the generated phenotypes to simulate observation bias." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "EpiGEN" ; sc:url "https://github.com/baumbachlab/epigen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3325, edam:topic_3334, edam:topic_3360, edam:topic_3577 ; sc:citation , "pubmed:32623772" ; sc:description "EpigenCentral provides online analyses of epigenetic patterns related to diseases, intended for the broad biomedical community and clinical practitioners. Epigenetic disruptions play a key role in many congenital diseases, such as neurodevelopmental syndromes involving autism and intellectual disabilities." ; sc:featureList edam:operation_3204, edam:operation_3225, edam:operation_3461 ; sc:name "EpigenCentral" ; sc:url "http://epigen.ccm.sickkids.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3295, edam:topic_3299, edam:topic_3300 ; sc:citation , "pmcid:PMC7750963", "pubmed:32573701" ; sc:description "Epigenetic Pacemaker is a fast conditional expectation maximization algorithm for modeling epigenetic state written in Python." ; sc:featureList edam:operation_2238, edam:operation_3204 ; sc:license "MIT" ; sc:name "Epigenetic Pacemaker" ; sc:softwareHelp ; sc:url "https://pypi.org/project/EpigeneticPacemaker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3168, edam:topic_3295, edam:topic_3336 ; sc:citation , "pubmed:33729791" ; sc:description "Epigenetic Target Profiler is a web server to predict epigenetic targets of small molecules. The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for different targets, which involves an under-representation of epigenetic targets, and despite the increasing importance of epigenetic targets in drug discovery, there are no open tools for epigenetic target prediction. In this work, we introduce Epigenetic Target Profiler (ETP), a freely accessible and easy-to-use web application for the prediction of epigenetic targets of small molecules. For a query compound, ETP predicts its bioactivity profile over a panel of 55 different epigenetic targets" ; sc:featureList edam:operation_0303, edam:operation_2489, edam:operation_3938 ; sc:name "Epigenetic Target Profiler" ; sc:url "http://www.epigenetictargetprofiler.com" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:24403540" ; sc:description "A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types." ; sc:featureList edam:operation_0438, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "epigenomix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/epigenomix.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3474 ; sc:citation "pubmed:19208250" ; sc:description "Enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest, and its searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, it can predict the status of genomic regions that were not included in the input dataset." ; sc:featureList edam:operation_2238 ; sc:name "EpiGRAPH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://epigraph.mpi-inf.mpg.de/WebGRAPH/" ; biotools:primaryContact "Dr. Joachim Büch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382 ; sc:citation , "pubmed:31544932" ; sc:description "An open-source platform to quantify epithelial organization | EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any computational or natural tessellation | The EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any made by computational or natural tessellation" ; sc:license "GPL-3.0" ; sc:name "EpiGraph" ; sc:url "https://imagej.net/EpiGraph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Library", "Web API", "Workbench" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0625, edam:topic_3305, edam:topic_3344, edam:topic_3473 ; sc:citation ; sc:description "EpiGraphDB is an analytical platform and database to support data mining in epidemiology. The platform incorporates a graph of causal estimates generated by systematically applying Mendelian randomization to a wide array of phenotypes, and augments this with a wealth of additional data from other bioinformatic sources. EpiGraphDB aims to support appropriate application and interpretation of causal inference in systematic automated analyses of many phenotypes." ; sc:featureList edam:operation_0224, edam:operation_3280, edam:operation_3625 ; sc:name "EpiGraphDB" ; sc:url "https://epigraphdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3295, edam:topic_3674 ; sc:author "Xiaowen Chen" ; sc:citation , "pmcid:PMC7801679", "pubmed:33432081" ; sc:description "epihet is an R-package that calculates the epigenetic heterogeneity between cancer cells and/or normal cells. The functions establish a pipeline that take in bisulfite sequencing data from multiple samples and use the data to track similarities and differences in epipolymorphism,proportion of discordantly methylated sequencing reads (PDR),and Shannon entropy values at epialleles that are shared between the samples.epihet can be used to perform analysis on the data by creating pheatmaps, box plots, PCA plots, and t-SNE plots. MA plots can also be created by calculating the differential heterogeneity of the samples. And we construct co-epihet network and perform network analysis." ; sc:featureList edam:operation_0531, edam:operation_2939, edam:operation_3223, edam:operation_3501, edam:operation_3927, edam:operation_3960 ; sc:license "Artistic-2.0" ; sc:name "epihet" ; sc:url "https://bioconductor.org/packages/release/bioc/html/epihet.html" ; biotools:primaryContact "Sheng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_3063 ; sc:citation , "pmcid:PMC10067149", "pubmed:37016683" ; sc:description "Community-based ontology tailored for semantic interoperability and text mining." ; sc:featureList edam:operation_0306, edam:operation_3352, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Epilepsy Ontology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioportal.bioontology.org/ontologies/EPIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Logical modelling of Epithelial dynamics. Definition, simulation and visualisation of qualitative models for epithelial pattern formation." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "EpiLog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epilog-tool.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3974 ; sc:citation , "pubmed:36107776" ; sc:description "Detecting high-order epistasis interactions using mixed effect conditional inference forest (epiMEIF)." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3791, edam:operation_3799 ; sc:license "Not licensed" ; sc:name "epiMEIF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TAGC-NetworkBiology/epiMEIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0153, edam:topic_3172, edam:topic_3305, edam:topic_3407 ; sc:citation , "pmcid:PMC7660139", "pubmed:31943015" ; sc:description "EpiMetal is an open-source graphical web browser tool for easy statistical analyses in epidemiology and metabolomics." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3659, edam:operation_3799 ; sc:license "MIT" ; sc:name "EpiMetal" ; sc:url "http://EpiMetal.computationalmedicine.fi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_3295 ; sc:citation , "pmcid:PMC4037167", "pubmed:24682734" ; sc:description "A database of curated mutual regulation between miRNAs and epigenetic modifications." ; sc:featureList edam:operation_0224 ; sc:name "EpimiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://210.46.85.180:8080/EpimiR/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3324, edam:topic_3524, edam:topic_3569 ; sc:citation , "pmcid:PMC5931789", "pubmed:29731699" ; sc:description "Mathematical Modeling of Infectious Disease." ; sc:featureList edam:operation_3562 ; sc:license "GPL-3.0" ; sc:name "EpiModel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.epimodel.org/" ; biotools:primaryContact "Samuel Jenness" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3173, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC7114791", "pubmed:32241255" ; sc:description "EpiMOLAS (Epi-genoMics OnLine Analysis System) is an intuitive web-based framework for genome-wide DNA methylation analysis." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3204 ; sc:license "MIT" ; sc:name "EpiMOLAS" ; sc:url "http://symbiosis.iis.sinica.edu.tw/epimolas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC8420331", "pubmed:34313401" ; sc:description "A mathematical dashboard for the analysis of Italian COVID-19 epidemic data." ; sc:featureList edam:operation_2426 ; sc:name "epiMOX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.epimox.polimi.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC7781373", "pubmed:33395407" ; sc:description "EpiMut is software for functional annotation of amino acid substitutions (AASs) in epigenetic factors that is independent from sequence alignments and homology search. It is based on the biochemical and physicochemical characteristics of amino acids and digital signal processing approach in protein sequence analysis." ; sc:featureList edam:operation_0292, edam:operation_0331 ; sc:name "EpiMut" ; sc:softwareHelp ; sc:url "https://www.vin.bg.ac.rs/180/tools/epimut.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295 ; sc:author "Carlos Ruiz-Arenas", "Leire Abarrategui" ; sc:description "The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations." ; sc:featureList edam:operation_0226, edam:operation_2945 ; sc:name "epimutacions" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/epimutacions.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3293, edam:topic_3474, edam:topic_3974 ; sc:citation , "pubmed:35412634" ; sc:description "A nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants." ; sc:featureList edam:operation_2454, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "EPIMUTESTR" ; sc:url "https://github.com/LichtargeLab/EPIMUTESTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:34085237" ; sc:description "Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads." ; sc:featureList edam:operation_3185, edam:operation_3907 ; sc:license "GPL-2.0" ; sc:name "EpiNano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/enovoa/EpiNano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Extension of the original Nested Effects Models (NEM). It is able to take into account double knockouts and infer more complex network signalling pathways." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "epiNEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/epiNEM.html" ; biotools:primaryContact "Martin Pirkl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_2830, edam:topic_3400, edam:topic_3518 ; sc:citation , "pmcid:PMC9581008", "pubmed:36303765" ; sc:description "Platform for Analysis and Visualization of Peptide Immunoarray Data." ; sc:featureList edam:operation_0416, edam:operation_2938, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "EPIphany" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://epiphany.usask.ca/epiphany/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2830, edam:topic_3930, edam:topic_3948, edam:topic_3966 ; sc:citation , "pubmed:37258914" ; sc:description "Resource facilitating epitope-vaccine design against human pathogenic orthopoxviruses." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0479 ; sc:isAccessibleForFree true ; sc:name "EPIPOX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio.med.ucm.es/epipox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0634, edam:topic_0749, edam:topic_3173, edam:topic_3940 ; sc:citation , "pmcid:PMC7319550", "pubmed:32459338" ; sc:description "EpiRegio is a resource of Regulatory EleMents (REMs) associated to protein coding, and non-protein coding genes. For a detailed documentation, please read our documentation." ; sc:featureList edam:operation_0443, edam:operation_2422, edam:operation_2436, edam:operation_2437 ; sc:license "GPL-3.0" ; sc:name "EpiRegio" ; sc:softwareHelp ; sc:url "https://epiregio.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3170, edam:topic_3173, edam:topic_3179 ; sc:citation ; sc:description "An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. EpiRomics is also designed for regulatory network analysis in order to identify enhancer and enhanceosome regions from these data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "epiRomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Huising-Lab/epiRomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3674 ; sc:citation , "pmcid:PMC7650528", "pubmed:32883324" ; sc:description "EPISCORE is a R pacakge for cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. It is a computational algorithm that performs virtual microdissection of bulk tissue DNA methylation data at single cell-type resolution for any solid tissue. EPISCORE applies a probabilistic epigenetic model of gene regulation to a single-cell RNA-seq tissue atlas to generate a tissue-specific DNA methylation reference matrix, allowing quantification of cell-type proportions and cell-type-specific differential methylation signals in bulk tissue data." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3629, edam:operation_3800, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "EPISCORE" ; sc:url "https://github.com/aet21/EpiSCORE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3474 ; sc:citation , "pubmed:32869348" ; sc:description "EPISFA is an unsupervised machine learning method for exploring gene-gene interaction in family-based data." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3935 ; sc:name "EPISFA" ; sc:url "https://github.com/doublexism/episfa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3047, edam:topic_3318 ; sc:citation , "pubmed:36856731" ; sc:description "A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "EPISOL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EPISOLrelease/EPISOL" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_2830, edam:topic_3305, edam:topic_3966 ; sc:citation , "pmcid:PMC8500151", "pubmed:34585726" ; sc:description "Metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species." ; sc:featureList edam:operation_0416, edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "EpiViruSurf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gmql.eu/epivirusurf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3382, edam:topic_3674 ; sc:citation , "pmcid:PMC7315560", "pubmed:32580750" ; sc:description "epiTOC2 is an R-script that aims to estimate the mitotic age of a sample profiled genome-wide at the DNA methylation level. It is based on a mitotic clock model where DNA methylation errors occuring during cell-division accrue in the adult stem cell pool of a tissue, allowing tracking of the number of stem-cell divisions. epiTOC2 not only estimates the cumulative number of stem-cell divisions, but also allows the intrinsic rate of stem-cell division per stem-cell per year to be estimated if the chronological age of the sample(s) is known." ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3891 ; sc:name "epiTOC2" ; sc:url "https://doi.org/10.5281/zenodo.2632938" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0804 ; sc:citation "pubmed:25712691" ; sc:description "Virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly." ; sc:featureList edam:operation_0310, edam:operation_2423, edam:operation_2430, edam:operation_3196 ; sc:name "EpiToolKit" ; sc:softwareHelp ; sc:url "http://www.epitoolkit.de/" ; biotools:primaryContact "Oliver Kohlbacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3930, edam:topic_3948, edam:topic_3966 ; sc:citation , "pmcid:PMC9417011", "pubmed:36018887" ; sc:description "An interactive web application to study predicted T-cell epitopes." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Epitope-Evaluator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fuxmanlab.shinyapps.io/Epitope-Evaluator/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3474, edam:topic_3966 ; sc:citation , "pmcid:PMC10199762", "pubmed:37039696" ; sc:description "Accurate Taxonomy-Aware B-Cell Linear Epitope Prediction." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:name "epitope1D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biosig.lab.uq.edu.au/epitope1d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3966, edam:topic_3967 ; sc:citation ; sc:description "Epitopedia: identifying molecular mimicry of known immune epitopes." ; sc:featureList edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Epitopedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cbalbin-FIU/Epitopedia" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2200, edam:format_2205 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3534 ; sc:author ; sc:description "epitopepredict is a programmatic framework and command line tool designed to aid the process of T cell epitope prediction. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualisation and filtering of the results." ; sc:featureList edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "epitopepredict" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.5.0" ; sc:url "https://github.com/dmnfarrell/epitopepredict" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3324, edam:topic_3966 ; sc:citation , "pubmed:34180989" ; sc:description """Linear Epitope Prediction Using Deep Protein Sequence Embeddings. EpitopeVec predicts linear B-cell epitopes. It takes protein sequences (FASTA format) as input and then lists the peptides (of a given amino acids length) that can be epitopes along with their respective prediction probability.""" ; sc:featureList edam:operation_0252, edam:operation_0267, edam:operation_0416 ; sc:license "GPL-3.0" ; sc:name "EpitopeVec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hzi-bifo/epitope-prediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3173, edam:topic_3512, edam:topic_3940 ; sc:citation , "pmcid:PMC7071901", "pubmed:32094195" ; sc:description "EpiVIA is joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels. EpiVIA parses each read and identifies the chimeric fragments, which are further classified into different categories based on how the read pair is aligned to the combined reference genome." ; sc:featureList edam:operation_1812, edam:operation_3192, edam:operation_3198, edam:operation_3222 ; sc:name "EpiVIA" ; sc:url "https://github.com/VahediLab/epiVIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_0654, edam:topic_3173, edam:topic_3518 ; sc:citation , "pmcid:PMC9308245", "pubmed:35870905" ; sc:description "A Tool for Exploratory Data Analysis and Visualisation within Epigenome Wide Methylation Analyses (EWAS)." ; sc:featureList edam:operation_0337, edam:operation_3204, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "EpiVisR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SteRoe/EpiVisR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3295, edam:topic_3308 ; sc:citation , "pubmed:31782758" ; sc:description "A proactive and automatic visual analytics system integrated with Epiviz that alleviates the burden of manually executing data analysis required to test biologically meaningful hypotheses." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3463 ; sc:name "Epiviz Feed" ; sc:url "https://github.com/epiviz/epiviz-feed-computation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_2640 ; sc:citation , , "pmcid:PMC7695125", "pubmed:32618995" ; sc:description "A library to query and transform genomic data from indexed files" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3211 ; sc:license "MIT" ; sc:name "Epiviz File Server" ; sc:softwareHelp ; sc:url "http://pypi.org/project/epivizFileServer" ; biotools:primaryContact "Hector Corrada Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "This package provides connections to the epiviz web app for interactive visualization of genomic data." ; sc:featureList edam:operation_0224, edam:operation_3208 ; sc:license "Artistic-2.0" ; sc:name "epivizr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/epivizr.html" ; biotools:primaryContact "Hector Corrada Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "API for interactive visualization of genomic data using epiviz web components. 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It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. 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Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC2612013", "pubmed:19038062" ; sc:description "\"ESLpred2\" is an improved version of our previous most popular method, ESLpred, which can predict four major localizations (cytoplasmic, mitochondrial, nuclear and extracellular) with an accuracy of 88%." ; sc:featureList edam:operation_2945 ; sc:name "eslpred2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/eslpred2/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3056, edam:topic_3796 ; sc:citation , "pmcid:PMC9748406", "pubmed:36517735" ; sc:description "A statistical model to infer admixture events from individual genomics data." ; sc:featureList edam:operation_3196, edam:operation_3658, edam:operation_3664, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "eSMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zachary-zzc/eSMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0199, edam:topic_0203, edam:topic_3295, edam:topic_3895 ; sc:citation , "pubmed:34928133" ; sc:description "A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels." ; sc:featureList edam:operation_0284, edam:operation_0554, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "ESO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cs.tau.ac.il/~tamirtul/ESO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC10563827", "pubmed:37815872" ; sc:description "Curated database of biomarker genes and miRNAs associated with esophageal cancer." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "ESOMIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://esomir.dqweilab-sjtu.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_3322, edam:topic_3325, edam:topic_3408, edam:topic_3676 ; sc:citation "pubmed:23962721" ; sc:description "NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders." ; sc:featureList edam:operation_2421, edam:operation_3197, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "ESP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://evs.gs.washington.edu/EVS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0209, edam:topic_3474 ; sc:citation , "pubmed:31553186" ; sc:description "Practical High-Quality Electrostatic Potential Surfaces for Drug Discovery Using a Graph-Convolutional Deep Neural Network | A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces | For generating ligand PQR files, a graph convolutional deep neural network (DNN) model, trained on ESP surfaces derived using DFT calculations for ~100,000 molecules, is used. For proteins, parametrized charges for amino acids are used, which are fully compatible with the ligand ESP surfaces generated using the DNN model" ; sc:featureList edam:operation_0387, edam:operation_0394, edam:operation_0480 ; sc:license "Apache-2.0" ; sc:name "ESP DNN" ; sc:url "https://github.com/AstexUK/ESP_DNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3047, edam:topic_3172, edam:topic_3474 ; sc:citation , "pmcid:PMC10185530", "pubmed:37188731" ; sc:description "A general model to predict small molecule substrates of enzymes based on machine and deep learning." ; sc:featureList edam:operation_1777, edam:operation_3092, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "ESP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://esp.cs.hhu.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3315, edam:topic_3452 ; sc:citation , "pubmed:37100009" ; sc:description "R package for automation, exploitation and processing of DICOM files in medical physics and clinical research." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "espadon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://espadon.cnrs.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC9600499", "pubmed:36349096" ; sc:description "End-to-end differentiable construction of molecular mechanics force fields." ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3893, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "espaloma" ; sc:url "https://github.com/choderalab/espaloma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0593, edam:topic_0602, edam:topic_3306, edam:topic_3365 ; sc:citation , "pmcid:PMC8489228", "pubmed:34605428" ; sc:description "An online data-analysis platform for molecular biophysics." ; sc:featureList edam:operation_0455, edam:operation_0482, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "eSPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spc.embl-hamburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3299 ; sc:citation , "pmcid:PMC7511691", "pubmed:32712417" ; sc:description "ESPRES is a web application for interactive analysis of multiple pressures in aquatic ecosystems." ; sc:featureList edam:operation_0387, edam:operation_2429, edam:operation_3935 ; sc:name "ESPRES" ; sc:url "http://www.espres.eu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2006 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3697 ; sc:citation ; sc:description "An algorithm for hierarchical clustering and taxonomic clustering of next generation sequencing data." ; sc:featureList edam:operation_0291, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "APL-1.0" ; sc:name "ESPRIT-Forest" ; sc:softwareHelp ; sc:url "https://www.acsu.buffalo.edu/~yijunsun/lab/ESPRIT-Forest.html" ; biotools:primaryContact "Yijun Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Efficient disorder prediction tool." ; sc:featureList edam:operation_2945 ; sc:name "ESpritz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://protein.bio.unipd.it/espritz" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3173, edam:topic_3318 ; sc:citation , "pubmed:33523102" ; sc:description """Essential component analysis of Hi-C matrices. Here we introduce essHi-C, a method to isolate the specific, or essential component of Hi-C matrices from the aspecific portion of the spectrum that is compatible with random matrices. Systematic comparisons shows that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices.""" ; sc:featureList edam:operation_3432, edam:operation_3454, edam:operation_3799 ; sc:license "MIT" ; sc:name "essHi-C" ; sc:url "https://github.com/stefanofranzini/essHIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3308, edam:topic_3473, edam:topic_3512 ; sc:citation "pubmed:20034392" ; sc:description "Platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data." ; sc:featureList edam:operation_0226, edam:operation_0310 ; sc:name "est2assembly" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/p/est2assembly/" ; biotools:primaryContact "Dr Alexie Papanicolaou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Align EST sequences to genomic DNA sequence." ; 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sc:applicationSubCategory edam:topic_0078, edam:topic_0196, edam:topic_0203, edam:topic_0654, edam:topic_3512 ; sc:citation "pubmed:16772268", "pubmed:17545197" ; sc:description "Automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level." ; sc:featureList edam:operation_0310, edam:operation_0526, edam:operation_3219 ; sc:name "ESTExplorer" ; sc:url "http://estexplorer.biolinfo.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3315, edam:topic_3360 ; sc:citation , "pubmed:34038548" ; sc:description "EstimAge is a webserver hub for the computation of methylation age." ; sc:featureList edam:operation_3207, edam:operation_3557, edam:operation_3659, edam:operation_3919 ; sc:name "EstimAge" ; sc:softwareHelp ; sc:url "http://estimage.iac.rm.cnr.it" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation "pubmed:18426324", "pubmed:4337382" ; sc:description "Estimate LDL cholesterol based on measured total cholesterol (TC), HDL, and triglycerides (TG)." ; sc:isAccessibleForFree true ; sc:name "Estimate LDL cholesterol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36095-estimate-ldl-cholesterol" ; biotools:primaryContact "Igor Podlubny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3420 ; sc:citation , "pmcid:PMC10416499", "pubmed:37568078" ; sc:description "R package to estimate and monitor the effective reproductive number." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3629, edam:operation_3799, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:name "estimateR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://covid-19-re.github.io/estimateR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:description "A set of MATLAB functions for computing a smooth approximation to the precision-recall curve." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Estimating a smooth precision-recall curve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29250-estimating-a-smooth-precision-recall-curve" ; biotools:primaryContact "Kay H. Brodersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3375 ; sc:citation , "pmcid:PMC7520045", "pubmed:32428223" ; sc:description "ESTIpop is an R package that estimates the parameters of continuous-time Markov branching processes (CTMBPs) with constant or time-dependent rates." ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "ESTIpop" ; sc:url "https://github.com/michorlab/estipop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3512 ; sc:description "Program that performs the preprocessing for cDNA reads. The program detects all the characterstics found within a sequence viz. restriction site, cloning vector, polyA tail, library tag, polyA signal. It also predicts whether the sequence should be used for further processing or should be rejected. If accepted the  region within the sequence which is high quality is also identified." ; sc:featureList edam:operation_0335 ; sc:name "ESTprep" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "3.1.4" ; sc:url "https://genome.uiowa.edu/home.old/pubsoft/software.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2704 ; sc:name "Clone ID (IMAGE)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2292 ; sc:name "GenBank accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation ; sc:description "A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports." ; sc:featureList edam:operation_0224 ; sc:name "ESTs SOURCE" ; sc:provider "Stanford University" ; sc:softwareHelp ; sc:url "http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:description "ESTScan can detect coding regions (CDS) in DNA sequences, even if they are of low quality. It also detects/corrects sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. The program may miss a few translated amino acids at termini, but detects coding regions with high selectivity and sensitivity." ; sc:featureList edam:operation_0226 ; sc:name "ESTscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://myhits.isb-sib.ch/cgi-bin/estscan" ; biotools:primaryContact "ESTScan Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3452, edam:topic_3474, edam:topic_3519 ; sc:citation , "pmcid:PMC8405348", "pubmed:34483709" ; sc:description "An Ensemble Transfer Learning Network for COVID-19 detection from lung CT-scan images." ; sc:featureList edam:operation_3436, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ET-NET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Rohit-Kundu/ET-NET_Covid-Detection" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:34021703" ; sc:description "ET-Score is a scoring function based on Extra Trees algorithm for predicting ligand-protein affinity." ; sc:featureList edam:operation_0478, edam:operation_3092, edam:operation_4009 ; sc:license "GPL-3.0" ; sc:name "ET-Score" ; sc:url "https://github.com/miladrayka/ET_Score" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_1775, edam:topic_2814 ; sc:citation "pubmed:16644792" ; sc:description "Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins." ; sc:featureList edam:operation_2414, edam:operation_2479, edam:operation_3092 ; sc:name "ET Report Maker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mammoth.bcm.tmc.edu/report_maker/" ; biotools:primaryContact "Lisa Beveridge" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find tandem repeats in a nucleotide sequence." ; sc:featureList edam:operation_0379 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "etandem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/etandem.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3068 ; sc:citation "pubmed:16926219", "pubmed:17452348" ; sc:description "Textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query." ; sc:featureList edam:operation_0224, edam:operation_0360, edam:operation_2409, edam:operation_2421 ; sc:name "eTBLAST" ; sc:url "http://etest.vbi.vt.edu/etblast3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3417 ; sc:citation ; sc:description "A common platform that may be used in different calibration scenarios in video based oculography." ; sc:featureList edam:operation_3443 ; sc:license "LGPL-2.0" ; sc:name "ETCAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://github.com/kasprowski/etcal" ; biotools:primaryContact "Pawel Kasprowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3360, edam:topic_3577, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "ETCHING is ultra-fast and high-performing somatic SV detector that significantly reduces the mapping cost by filtering reads matched to pan-genome and normal k-mer sets." ; sc:featureList edam:operation_0308, edam:operation_3198, edam:operation_3216, edam:operation_3435, edam:operation_3472 ; sc:license "MIT" ; sc:name "ETCHING" ; sc:url "http://big.hanyang.ac.kr/ETCHING" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293 ; sc:description "The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org" ; sc:featureList edam:operation_0324, edam:operation_0326 ; sc:name "ete" ; sc:softwareVersion "3.1.2" ; sc:url "http://etetoolkit.org/about/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Ethoflow is a computer vision and artificial intelligence-based software for automatic behavior analysis." ; sc:name "Ethoflow" ; sc:url "https://github.com/bernardesrodrigoc/Ethoflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3500, edam:topic_3679 ; sc:citation , "pubmed:32994566" ; sc:description "EthoLoop is a framework for studying the neuroethology of freely roaming animals. Combining real-time optical tracking and behavioral analysis with remote-controlled stimulus-reward boxes, this system allows direct interactions with animals in their habitat. EthoLoop continuously provides close-up views of the tracked individuals and thus allows high-resolution behavioral analysis using deep-learning methods." ; sc:featureList edam:operation_3890 ; sc:license "LGPL-3.0" ; sc:name "EthoLoop" ; sc:url "http://www.etholoop.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2640, edam:topic_3957 ; sc:citation , "pubmed:35771625" ; sc:description "Extensive Tool for Network Analysis (ETNA) is an user-firendly graphical interface for the network analysis that contains classical measures and simulation-based ones." ; sc:featureList edam:operation_2492, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ETNA" ; sc:url "https://githubtocolab.com/AlicjaNowakowska/ETNA/blob/main/ETNAColab.ipynb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3306, edam:topic_3524, edam:topic_3534 ; sc:citation ; sc:description "An open source framework that allows the automated prediction of ligand-binding free energies requiring the ligand structure as only input." ; sc:featureList edam:operation_0478 ; sc:license "GPL-2.0" ; sc:name "eTOX ALLIES" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GeerkeLab/eTOX-ALLIES" ; biotools:primaryContact "Daan P. Geerke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2815, edam:topic_3500 ; sc:citation , "pubmed:31887789" ; sc:description "ETph is a database for enhancer and their targets in pig and human." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_3799 ; sc:name "ETph" ; sc:url "http://klab.sjtu.edu.cn/enhancer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2259, edam:topic_2640, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:33581336" ; sc:description "A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients." ; sc:featureList edam:operation_2423 ; sc:name "eTumorMetastasis" ; sc:url "https://github.com/WangEdwinLab/eTumorMetastasis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0632, edam:topic_3168, edam:topic_3519 ; sc:citation ; sc:description "EUAdb is database for COVID-19 test development that contains standardized information about Eemergency Use Authorizations-issued tests and is focused on RT-qPCR diagnostic tests, or high complexity molecular-based laboratory developed tests." ; sc:featureList edam:operation_0224, edam:operation_3559, edam:operation_3799 ; sc:name "EUAdb" ; sc:url "http://EUAdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3301 ; sc:author "Christine Nardini", "Xiaoyuan Zhou" ; sc:citation ; sc:description "Package to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases or as unknown based on their ambiguous genus classification. It measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition." ; sc:featureList edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "eudysbiome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioConductor" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/eudysbiome.html" ; biotools:primaryContact "Xiaoyuan Zhou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Gene prediction software for eukaryotic organisms. It is currently mainly tuned for plant and fungal genomes." ; sc:featureList edam:operation_0362 ; sc:name "EuGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/EuGene/" ; biotools:primaryContact "Yves Van de Peer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0780, edam:topic_3512 ; sc:citation "pubmed:12824408" ; sc:description "Gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb." ; sc:featureList edam:operation_0433, edam:operation_2454, edam:operation_2499 ; sc:name "EUGENE HOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl" ; biotools:primaryContact "Sylvain Foissac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0622 ; sc:citation "pubmed:11752277" ; sc:description "Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information." ; sc:featureList edam:operation_0282, edam:operation_2422, edam:operation_2429, edam:operation_2454, edam:operation_2871 ; sc:name "euGenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iubio.bio.indiana.edu:8089/" ; biotools:primaryContact "euGenes Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:name "Sequence accession (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation ; sc:description "European Hepatitis C virus database." ; sc:featureList edam:operation_0224 ; sc:name "European Hepatitis C virus database (euHCVdb)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://euhcvdb.ibcp.fr/euHCVdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0621, edam:topic_3324 ; sc:citation , "pmcid:PMC8728146", "pubmed:34718738" ; sc:description "This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction." ; sc:featureList edam:operation_0224, edam:operation_0238, edam:operation_0239, edam:operation_0245 ; sc:isAccessibleForFree true ; sc:name "Eukaryotic Linear Motif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://elm.eu.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_0780, edam:topic_3500, edam:topic_3512 ; sc:citation ; sc:description "The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanity." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "EukMetaSanity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cjneely10/EukMetaSanity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3500, edam:topic_3512 ; sc:citation "pubmed:19914931" ; sc:description "Integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2422, edam:operation_3429, edam:operation_3431 ; sc:name "Eukaryotic Pathongen Database Resources (EuPathDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://EuPathDB.org" ; biotools:primaryContact "Omar S. Harb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3308, edam:topic_3387 ; sc:description "The EuphausiiDB portal offers the possibility for users to explore an Euphausiidae transcriptom database by using “simple” and “advanced” search functions for a specific taxonomic level, a specific geographic location or project origin, and a specific annotation. Statistical interactive charts, readsets location maps and tables, and the resulting list of datasets are associated with the search functions. For each selected dataset, the user can access readset and assembly short summary pages with cross-references to external databases (EBI SRA, NCBI taxID, WORMS), which allow better traceability and homogeneity across databases, as well as the possibility of downloading all resulting files...The intention is to develop the database continually as the transcriptomes of new species are sequenced and thus provide an up-to-date reference dedicated to the diversity of euphausiids." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "EuphausiiDB" ; sc:softwareHelp ; sc:url "http://euphausiidb.sb-roscoff.fr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219 ; sc:author "Stephan Weise" ; sc:citation , "pmcid:PMC5210606", "pubmed:27580718" ; sc:description "Search catalogue providing information about ex situ plant collections maintained in Europe. It is based on a European network of ex situ National Inventories (NIs). Currently, it comprises information about 1.9 million germplasm accessions from almost 400 holding institutions from 43 countries. It contains both passport data and phenotypic data." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "EURISCO" ; sc:operatingSystem "Linux" ; sc:provider "European Cooperative Programme for Plant Genetic Resources (ECPGR)", "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben" ; sc:softwareHelp ; sc:softwareVersion "1.5.4" ; sc:url "http://eurisco.ecpgr.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0593, edam:topic_3678 ; sc:citation , "pmcid:PMC3055595", "pubmed:21106561" ; sc:description "EuroCarbDB is a repository of carbohydrate structures, experimental evidence, and carbohydrate-oriented research and analysis tools." ; sc:featureList edam:operation_0224, edam:operation_0360, edam:operation_2480, edam:operation_3431 ; sc:name "EuroCarbDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/archive/p/eurocarb/" ; biotools:primaryContact "Stuart M. Haslam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Archive of life sciences journal literature." ; sc:featureList edam:operation_0224 ; sc:name "Europe PMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI Databases" ; sc:softwareHelp ; sc:url "http://europepmc.org/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3505 ; sc:encodingFormat edam:format_2332 ; sc:name "Bibliography" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:author "Literature Services" ; sc:citation ; sc:description "Tool that allows article authors to build a bibliography and export it to ORCID." ; sc:featureList edam:operation_3349 ; sc:name "Europe PMC ORCID Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://europepmc.org/orcid/import" ; biotools:primaryContact "Jo McEntyre" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3505 ; sc:encodingFormat edam:format_2332, edam:format_3475 ; sc:name "Bibliography" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description "Link grants to their articles." ; sc:featureList edam:operation_3349 ; sc:name "Europe PMC plus Grant Linking" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "Mimas", "NCBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://plus.europepmc.org/emss/login/uls.cgi?rss=wt&url=/plus/menu.html" ; biotools:primaryContact "Jo McEntyre" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0971 ; sc:encodingFormat edam:format_3506, edam:format_3508 ; sc:name "Article" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071 ; sc:description "Anyone from at least one of the Europe PMC Funders can submit an author manuscript for inclusion in Europe PubMed Central. 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The core services of INFRAFRONTIER comprise the systemic phenotyping of mouse mutants in the participating mouse clinics, and the archiving and distribution of mouse mutant lines by the European Mouse Mutant Archive (EMMA). EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant mouse strains essential for basic biomedical research. The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. 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The system can be used as a text search engine like PubMed, with additional features to help users to discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_2422, edam:operation_3280 ; sc:name "FACTA plus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://refine1-nactem.mc.man.ac.uk/facta/" ; biotools:primaryContact "Yoshimasa Tsuruoka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "factDesign" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/factDesign.html" ; biotools:primaryContact "Denise Scholtens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC8728199", "pubmed:34755879" ; sc:description "An updated catalog of transcription factor motifs and candidate regulatory motif sites." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0445, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "Factorbook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.factorbook.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC8006390", "pubmed:33781206" ; sc:description "FactorHNE is a factor graph-aggregated heterogeneous network embedding for disease-gene association prediction." ; sc:featureList edam:operation_3436, edam:operation_3927, edam:operation_4009 ; sc:name "FactorHNE" ; sc:url "https://github.com/xasdzxc/FactorHNE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:36516557" ; sc:description "A scalable interpretable approach to context modeling for medical image segmentation." ; sc:featureList edam:operation_3436, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Factorizer" ; sc:url "https://github.com/pashtari/factorizer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:name "Protocol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "FactorViz provides an interactive visualization and reporting environment for exploring the results of the methylome decomposition experiments carried out by MeDeCom or similar deconvolution tools." ; sc:featureList edam:operation_3629 ; sc:name "FactorViz" ; sc:softwareVersion "2.1.0" ; sc:url "https://github.com/CompEpigen/FactorViz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0218, edam:topic_2229 ; sc:citation , "pubmed:33601085" ; sc:description """Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. A web server for predicting of FAD Binding Sites Using Pre-training of Deep Bidirectional Transformers. During cellular respiration in general and electron transport chain in particular, flavin adenine dinucleotide (FAD) plays a vital role.""" ; sc:featureList edam:operation_2575 ; sc:name "FAD-BERT" ; sc:url "http://140.138.155.216/fadbert/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3308, edam:topic_3519, edam:topic_3934 ; sc:citation ; sc:description "FaDA is a user-friendly data visualization and analysis tool developed in R programming with the R Shiny package. FaDA provides users of non-computational background to analyze their data for statistical analysis and quick visualization. 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The prediction is based on the basis of binary pattern of 17 window motif of amino acid sequence by using support vector machines(SVM)." ; sc:featureList edam:operation_2945 ; sc:name "fadpred" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/fadpred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0621, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7901478", "pubmed:33436511" ; sc:description """A Quantification Tool for Prokaryotic Transcriptomic Analyses. Most current available quantification tools for transcriptomics analyses have been designed using human data sets, in which full-length transcript sequences are available. 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The tool accesses FHIR resources, presents metadata to the user, guide the user about the configuration to be applied and then output the processed FHIR resources." ; sc:featureList edam:operation_3283 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "FAIR4Health Data Privacy Tool" ; sc:softwareHelp , ; sc:softwareVersion "v1.1.1" ; sc:url "https://osf.io/ywhrj/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0780, edam:topic_3305, edam:topic_3384, edam:topic_3571 ; sc:citation , "pmcid:PMC10198982", "pubmed:37208467" ; sc:description "A framework for FAIRification processes." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3431, edam:operation_3435, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "FAIR Cookbook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://faircookbook.elixir-europe.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_3620 ; sc:name "Resource metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2332, edam:format_3255 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3307, edam:topic_3391, edam:topic_3678 ; sc:citation ; sc:description "FAIR Data Station for Lightweight Metadata Management & Validation of Omics Studies" ; sc:featureList edam:operation_0336, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "FAIR Data Station" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://fairbydesign.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Best practice database platform for genomics data, developer in the Netherlands. Has diverse implementations including MOLGENIS" ; sc:name "FAIR genomes" ; sc:url "http://fairgenomes.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description "FAIRSCAPE is a reusable computational framework, enabling simplified access to modern scalable cloud-based components. It fully implements the FAIR data principles and extends them to provide FAIR Evidence, including provenance of datasets, software and computations,as metadata for all computed results." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "FAIRSCAPE" ; sc:softwareHelp , ; sc:url "https://fairscape.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0196, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:21576220" ; sc:description "Web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method." ; sc:featureList edam:operation_0310, edam:operation_0322, edam:operation_0477, edam:operation_0479, edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FALC-Loop" ; sc:operatingSystem "Linux" ; sc:url "http://galaxy.seoklab.org/softwares/falc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description "A high-speed FastQC emulation for quality control of sequencing data." ; sc:featureList edam:operation_0337, edam:operation_3198, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "Falco" ; sc:url "https://github.com/smithlabcode/falco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170, edam:topic_3316, edam:topic_3512 ; sc:citation , "pmcid:PMC6936136", "pubmed:31888474" ; sc:description "Falco is a quick and flexible single-cell RNA-seq processing framework on the cloud. Falco is a software bundle that enables bioinformatic analysis of large-scale transcriptomic data by utilising public cloud infrastructure. The framework currently provide supports for single cell RNA feature quantification, alignment and transcript assembly analyses." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3799 ; sc:name "Falco" ; sc:url "https://github.com/VCCRI/Falco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Experimental PacBio diploid assembler." ; sc:featureList edam:operation_0310 ; sc:name "Falcon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pratas/falcon" ; biotools:primaryContact "Thomas Sauter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description """Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. The falcon spectrum clustering tool uses advanced algorithmic techniques for highly efficient processing of millions of MS/MS spectra. First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity searching. The nearest neighbor indexes are used to efficiently compute a sparse pairwise distance matrix without having to exhaustively compare all spectra to each other. 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OBJECTIVE:Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. APPROACH:We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. 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Sorger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1332 ; sc:name "Protein sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "Algorithm for large-scale multiple sequence alignments" ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FAMSA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/refresh-bio/FAMSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3940 ; sc:citation ; sc:description "FAN-C (Framework for the ANalysis of C-like data) provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads." ; sc:featureList edam:operation_0337, edam:operation_3219 ; sc:license "GPL-3.0" ; sc:name "FAN-C" ; sc:softwareHelp ; sc:url "https://github.com/vaquerizaslab/fanc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3169, edam:topic_3170, edam:topic_3263, edam:topic_3673 ; sc:citation , "pubmed:32726397" ; sc:description "FANCY is a fasttool for estimation for of privacy risk in functional genomics data." ; sc:featureList edam:operation_0331, edam:operation_3196, edam:operation_3659 ; sc:name "FANCY" ; sc:url "http://fancy.gersteinlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0196, edam:topic_2640, edam:topic_3175 ; sc:citation , "pmcid:PMC8134938", "pubmed:34027500" ; sc:description "FaNDOM (Fast Nested Distance Aligner for Optical Maps) performs alignment of Bionano Saphyr optical map molecules and contigs to a reference, using a seed-based filter." ; sc:featureList edam:operation_2429, edam:operation_3216, edam:operation_3227, edam:operation_3359 ; sc:name "FaNDOM" ; sc:url "https://github.com/jluebeck/FaNDOM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:35333723" ; sc:description "A Feedback Attention Network for Improved Biomedical Image Segmentation." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3927 ; sc:license "Not licensed" ; sc:name "FANet" ; sc:url "https://github.com/nikhilroxtomar/FANet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3303, edam:topic_3336 ; sc:citation , "pmcid:PMC7753081", "pubmed:33363710" ; sc:description "FangNet is a tool for mining herb hidden knowledge from traditional Chinese medicine clinical effective formulas using structure network algorithm." ; sc:featureList edam:operation_2422, edam:operation_3436 ; sc:name "FangNet" ; sc:url "http://fangnet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3474 ; sc:citation ; sc:description "Machine learning approach to classify genes and genera in the family Geminiviridae." ; sc:featureList edam:operation_2421, edam:operation_2995 ; sc:name "Fangorn Forest (F2)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp" ; biotools:primaryContact "Elizabeth P. B. Fontes", "Fabio R. Cerqueira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Fast Network Motif Detection is for fast network motif detection; it relies on recently developed algorithms to improve the efficiency of network motif detection by some orders of magnitude over existing tools. This facilitates the detection of larger motifs in bigger networks than previously possible. 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3068, edam:topic_3382 ; sc:citation , "pubmed:32519291" ; sc:description "FaReT (Face Research Toolkit) is a free and open-source toolkit of three-dimensional models and software to study face perception." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "FaReT" ; sc:url "https://github.com/fsotoc/FaReT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3305 ; sc:description "fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output." ; sc:featureList edam:operation_3482 ; sc:name "fARGene" ; sc:url "https://github.com/fannyhb/fargene" . a sc:SoftwareApplication ; 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0621, edam:topic_0736, edam:topic_3520 ; sc:citation , "pmcid:PMC10185405", "pubmed:37084276" ; sc:description "Assessing the similarity between proteins using multi-layered feature architectures." ; sc:featureList edam:operation_2421, edam:operation_2474, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/greedyFAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Fas2Nex  can read a .FAS (FASTA) file and save it as .NEX (NEXUS) file (or again as a .fas file) for phylogenetic analysis with PAUP*, with the option of removing columns of characters consisting only of gaps. If necessary, the ends of short sequences in the .fas file will be padded to full length." ; sc:featureList edam:operation_0335, edam:operation_2945 ; sc:name "Fas2Nex" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.famd.me.uk/AGL/AGL_sw.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description "Graphical platform for manipulating sequences and alignments in a batch mode." ; sc:featureList edam:operation_0292 ; sc:name "FasParser2" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "https://github.com/Sun-Yanbo/FasParser/releases" ; biotools:primaryContact "Yan-Bo Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0166 ; sc:citation , "pmcid:PMC7320614", "pubmed:32259206" ; sc:description "FASPR is an open-source tool for fast and accurate protein structural modeling of protein side-chain conformations and packing." ; sc:featureList edam:operation_0249, edam:operation_0384, edam:operation_0394, edam:operation_0479, edam:operation_0480 ; sc:license "MIT" ; sc:name "FASPR" ; sc:url "https://zhanglab.ccmb.med.umich.edu/FASPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:description "FAssign (Fuzzy Assignment) is new algorithm for the protein secondary structure assignment, using fuzzy logic based on backbone angles." ; sc:featureList edam:operation_0319, edam:operation_2479, edam:operation_2488 ; sc:name "FAssign" ; sc:url "http://bs.ipm.ir/softwares/fassign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation ; sc:description "The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools (for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics modeled after the Unix textutils (such as grep, cut, head, tr, etc)." ; sc:featureList edam:operation_2403 ; sc:name "FAST: Fast Analysis of Sequences Toolbox" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "https://github.com/tlawrence3/FAST" ; biotools:primaryContact "Takashi Abe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "A fast method to compute AUC (area under the curve)." ; sc:isAccessibleForFree true ; sc:name "Fast AUC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50962-fast-auc" ; biotools:primaryContact "Lior Kirsch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:description "Rapid fitting of Gaussian PSF models to a list of candidate positions in an image." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Fast Gaussian Point Spread Function Fitting (MEX)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/52417-fast-gaussian-point-spread-function-fitting-mex" ; biotools:primaryContact "Simon Christoph Stein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769 ; sc:citation , , "pubmed:33006480" ; sc:description "Fast-GBS is an analysis toolkit for genotyping-by-sequencing data. 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It can also change sequences by deleting specified characters or whitespace, introduce newlines for readibility, or change sequence case." ; sc:featureList edam:operation_0335 ; sc:name "FASTA Canonical Sequences" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=15" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , ; sc:description "File conversion." ; sc:featureList edam:operation_0335 ; sc:name "fasta_to_phylip" ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/fredericlemoine/goalign" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0637, edam:topic_0749, edam:topic_3500, edam:topic_3577 ; sc:citation , "pubmed:32623815" ; sc:description "Fastachar is a graphical user interface that allows a simple comparison of two sets of DNA sequences. 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Although it is uncommon, the FASTAFS format denotes the index (a typical header) after the data. The reason for this location is that most metadata can only be known after converting the entire FASTA file to FASTAFS. For instance, the number of nucleotides encoded within 2bit data, the number of N-characters or the checksum.""" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3357 ; sc:license "GPL-2.0" ; sc:name "FASTAFS" ; sc:softwareHelp ; sc:url "https://github.com/yhoogstrate/fastafs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:description "FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. 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FastBMD is a computationally efficient implementation of the National Toxicology Program Approach to Genomic Dose-Response Modeling. Key features include a simplified workflow, ability to download results at each step, and interactive exploration of pathway-level BMDs. In addition to model organisms, FastBMD is designed to support non-model organisms by enabling an annotation-free pipeline that includes feature sensitivity-based point-of-departure analysis. The final part of the analysis is designed to allow users to interactively explore BMDs at different levels of organization:." ; sc:featureList edam:operation_3435 ; sc:name "FastBMD" ; sc:url "http://www.fastbmd.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "FastCodeML is a collection of optimization strategies for fast detection of positive selection on phylogenetic trees." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "FastCodeML" ; sc:url "https://gitlab.sib.swiss/phylo/fastcodeml" ; biotools:primaryContact "Nicolas Salamin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0736, edam:topic_2275, edam:topic_3557 ; sc:citation "pubmed:15713734", "pubmed:16506242", "pubmed:17537824" ; sc:description "FastContact is a free energy scoring tool for protein-protein complex structures." ; sc:featureList edam:operation_0321, edam:operation_0478, edam:operation_0482, edam:operation_2492 ; sc:name "FastContact" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://structure.pitt.edu/servers/fastcontact/" ; biotools:primaryContact "Camacho CJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC9837158", "pubmed:36694721" ; sc:description "A tool for identification of adapters and other sequence patterns in next generation sequencing (NGS) data." ; sc:featureList edam:operation_0363, edam:operation_1812, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FastContext" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/FastContext" . a sc:SoftwareApplication ; 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It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files." ; sc:featureList edam:operation_0236, edam:operation_2238, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "FastQC" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" ; biotools:primaryContact "Simon Andrews" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1932, edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation , ; sc:description "Reports from FastQC with option for long reads." ; sc:featureList edam:operation_3218 ; sc:name "fastqc_toolshed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_3168, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:34623374" ; sc:description "A FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model." ; sc:featureList edam:operation_0524, edam:operation_2409, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FastqCLS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/krlucete/FastqCLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:description "Compute quality stats for FASTQ files and print those stats as emoji... for some reason." ; sc:featureList edam:operation_3218 ; sc:name "FASTQE" ; sc:url "https://fastqe.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0749, edam:topic_0798, edam:topic_3168, edam:topic_3895 ; sc:citation , "pmcid:PMC7515713", "pubmed:32813015" ; sc:description "FASTQINS is a Python pipeline to map transponson insertions from Tn-seq data." ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "FASTQINS" ; sc:url "https://github.com/CRG-CNAG/fastqins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_2885, edam:topic_3168 ; sc:citation , ; sc:description "FASTQuick is an ultra-fast QC tool for NGS sequencing fastq files. It generates a comprehensive list of QC statistics, including ancestry and contamination estimation, at ~50x faster turnaround time than alignment-based QC tools." ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3218 ; sc:license "MIT" ; sc:name "FASTQuick" ; sc:url "https://github.com/Griffan/FASTQuick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3572 ; sc:citation ; sc:description "Checking that FastQ files are follows standards." ; sc:featureList edam:operation_3218 ; sc:name "FastQValidator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/FastQValidator" ; biotools:primaryContact "The Center for Statistical Genetics at the University of Michigan School of Public Health" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC3606433", "pubmed:23533605" ; sc:description "fastqz is a compressor for the most common (Sanger format) FASTQ files produced by DNA sequencing machines. 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sc:url "http://www.bioinformatics.nl/cgi-bin/emboss/featmerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622, edam:topic_3175, edam:topic_3511 ; sc:citation , "pubmed:25934264" ; sc:description "Tool for integrated annotation of sequence features and variation, facilitating interpretation in genomics experiments." ; sc:featureList edam:operation_3661 ; sc:name "FEATnotator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/featnotator/" ; biotools:primaryContact "Mockaitis K." . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; 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Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. 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It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed." ; sc:featureList edam:operation_2495, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "FEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FEM.html" ; biotools:primaryContact "Zhen Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC8641482", "pubmed:34909283" ; sc:description "Mining biological meaning from cell level in single-cell RNA sequencing data." ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/qingyunpkdd/single_cell_fem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3304 ; sc:citation , "pmcid:PMC7498500", "pubmed:32306231" ; sc:description "FEMfuns (Finite Element Method for useful neuroscience simulations) is a volume conduction modeling pipeline that includes resistive, capacitive or dispersive tissue and electrodes. 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The original paper can be found." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "FEMfuns" ; sc:url "https://github.com/meronvermaas/FEMfuns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3444, edam:topic_3452 ; sc:description "These models could be run by the matlab for femlab GUI I posted earlier." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Matlab for Femlab models" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36556-matlab-for-femlab-models" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3318 ; sc:citation , "pubmed:34519200" ; sc:description "A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations." ; sc:featureList edam:operation_0455, edam:operation_2476, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FEPrepare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://feprepare.vi-seem.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0749, edam:topic_3474, edam:topic_3510 ; sc:citation , "pubmed:35696075" ; sc:description "A Tool for Feature Extraction from Protein Sequence." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0417, edam:operation_2422, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FEPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dukkakc/FEPS_CFS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3299 ; sc:citation , , "pubmed:33208064", "pubmed:33238837" ; sc:description "FermatS is a numerical representation for protein sequence comparison and DNA-binding protein identification." ; sc:featureList edam:operation_2451, edam:operation_3659, edam:operation_3767, edam:operation_3900, edam:operation_3901 ; sc:name "FermatS" ; sc:url "https://github.com/GaoYa1122/FermatS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0780, edam:topic_0821, edam:topic_3390 ; sc:citation , "pmcid:PMC8055555", "pubmed:33898816" ; sc:description "FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3646 ; sc:name "FermFooDb" ; sc:url "https://webs.iiitd.edu.in/raghava/fermfoodb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2640, edam:topic_3047, edam:topic_3172 ; sc:citation , "pmcid:PMC7100629", "pubmed:32219413" ; sc:description "FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations." ; sc:featureList edam:operation_2437, edam:operation_3778 ; sc:name "FerrDb" ; sc:url "http://www.zhounan.org/ferrdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2830, edam:topic_3500, edam:topic_3574 ; sc:citation , "pubmed:34954426" ; sc:description "A Straight Pipeline for Functional Gene Annotation and Disease Mutation Discovery" ; sc:featureList edam:operation_2421, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "FertilityOnline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mcg.ustc.edu.cn/bsc/spermgenes2.0/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3361, edam:topic_3489 ; sc:citation , "pmcid:PMC6994642", "pubmed:32021811" ; sc:description "FESTIval is a versatile framework for conducting experimental evaluations of spatial indices. 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Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc." ; sc:featureList edam:operation_0296, edam:operation_0303, edam:operation_0314, edam:operation_3092 ; sc:name "FFAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ffas.godziklab.org" ; biotools:primaryContact "FFAS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3321, edam:topic_3474 ; sc:citation , "pmcid:PMC4048315", "pubmed:24905468" ; sc:description "Fast Family-Based Sequence Kernel Association Test." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "FFBSKAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mga.bionet.nsc.ru/soft/FFBSKAT/" ; biotools:primaryContact "G.R. Svishcheva", "N.M. Belonogova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:citation , "pubmed:33306465" ; sc:description "FFD is a fast scale-invariant feature detector for computer vision tasks. Features include extracting matching features across a given pair of images." ; sc:featureList edam:operation_2426, edam:operation_3443 ; sc:name "FFD" ; sc:url "https://github.com/mogvision/FFD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Methods for computing the (NP-hard) family-free DCJ similarity, which is a large-scale rearrangement measure for comparing two given genomes." ; sc:featureList edam:operation_3438 ; sc:license "GPL-3.0" ; sc:name "ffdcj-sim" ; sc:softwareHelp ; sc:url "https://git.facom.ufms.br/diego/ffdcj-sim" ; biotools:primaryContact "Diego P. Rubert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2814 ; sc:citation ; sc:description "Software package designed to perform continuum mechanics simulations of proteins and other globular macromolecules. It combines conventional finite element methods with stochastic thermal noise, and is appropriate for simulations of large proteins and protein complexes at the mesoscale (length-scales in the range of 5 nm to 1 μm), where there is currently a paucity of modelling tools." ; sc:featureList edam:operation_0477 ; sc:name "Fluctuating Finite Element Analysis (FFEA)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://ffea.readthedocs.io/en/stable/" ; biotools:primaryContact "Sarah A. 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The database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets." ; sc:featureList edam:operation_0525, edam:operation_2454, edam:operation_2495 ; sc:name "FGDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.gsf.de/genre/proj/FGDB/" ; biotools:primaryContact "FGDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0769, edam:topic_3292, edam:topic_3520 ; sc:citation , "pmcid:PMC8050109", "pubmed:33897975" ; sc:description "FGDB is a database of follicle stimulating hormone glycans. FGDB provides fucosylated and non-fucosylated glycans associated with Follicle Stimulating Hormones (FSH) in human." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_4009 ; sc:name "FGDB" ; sc:url "https://fgdb.unmc.edu/" ; biotools:primaryContact "Chittibabu Guda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0622 ; sc:citation , "pubmed:14734324" ; sc:description "The FGDP (functional genomics data pipeline) is a Java-based, Microarray or Genechip data analysis system. The FGDP provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed, and provides a web server and interface for presenting results" ; sc:featureList edam:operation_2495 ; sc:name "FGDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation ; sc:description "HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences." ; sc:featureList edam:operation_2454 ; sc:name "FGENESH" ; sc:url "http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0623, edam:topic_3293, edam:topic_3500 ; sc:citation "pubmed:17584790" ; sc:description "Resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations)." ; sc:featureList edam:operation_0323, edam:operation_0553, edam:operation_0554, edam:operation_2454 ; sc:name "FGF" ; sc:url "http://fgf.genomics.org.cn/service/index.jsp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3181 ; sc:name "Sequence assembly report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0196, edam:topic_0797 ; sc:author "Ousmane Cissé" ; sc:citation ; sc:contributor "Jason Stajich" ; sc:description "Genome completeness assessment tool focused on Fungi" ; sc:featureList edam:operation_3180 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FGMP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0.0" ; sc:url "http://github.com/stajichlab/FGMP" ; biotools:primaryContact "Ousmane Cissé" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4426835", "pubmed:25600944" ; sc:description "Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "FGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FGNet.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction." ; sc:featureList edam:operation_2436 ; sc:license "MIT" ; sc:name "fgsea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/fgsea.html" ; biotools:primaryContact "Alexey Sergushichev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC9235494", "pubmed:35758819" ; sc:description "The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance." ; sc:featureList edam:operation_0524, edam:operation_3096, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FGTED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Kingsford-Group/gtedemedtest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3512, edam:topic_3673 ; sc:citation , "pmcid:PMC7319540", "pubmed:32421816" ; sc:description "FGviewer is an online visualization tool for functional features of human fusion genes. FGviewer is aiming for the effective visualization of the functional features of fusion genes for better prioritization of therapeutic target selection. FGviewer provides functional feature annotations at four different levels: DNA-, RNA-, protein-, and pathogenic-levels. The same breakpoint line across four tiers will classify between FG involving or non-involving zone with multiple types of functional features. Those features include fusion mRNA and amino acid sequences based on the user’s breakpoint coordinates, swapped gene expression regulatory (i.e., transcription factor or miRNA binding sites), protein functional features (i.e., protein domains, protein- protein interactions, binding sites of all molecules, secondary structure level feature, etc.), clinically relevant variants, etc." ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_3672 ; sc:name "FGviewer" ; sc:url "https://ccsmweb.uth.edu/FGviewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3063 ; sc:citation , , "pmcid:PMC7066811", "pubmed:32160884" ; sc:description "FHIR PIT (Health Level 7 Fast Healthcare Interoperability Resources Patient data Integration Tool) is an open software application for spatiotemporal integration of clinical data and environmental exposures data. FHIR PIT (Patient data Integration Tool) uses geocodes and time stamps of varying resolution (e.g., hour, year) to integrate the clinical data with environmental exposures data from multiple sources before stripping the data of PHI (including the geocodes and time stamps) and binning feature variables to create ICEES tables. Of note, FHIR PIT is modular and extensible and can be adapted for virtually any type of data that requires geocodes and dates for integration with personally identifiable information." ; sc:license "MIT" ; sc:name "FHIR PIT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/NCATS-Tangerine/FHIR-PIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3384, edam:topic_3452, edam:topic_3474, edam:topic_3954 ; sc:citation , "pmcid:PMC10326955", "pubmed:37415138" ; sc:description "Python package to query FHIR servers. This package is meant to provide a simple abstraction to query and structure FHIR resources as pandas DataFrames." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3283, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FHIR-PYrate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UMEssen/FHIR-PYrate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3063, edam:topic_3366, edam:topic_3404, edam:topic_3577 ; sc:citation , "pubmed:34042754" ; sc:description "FhirSpark is a tool for implementing a mediation layer to bring Fast Healthcare Interoperability Resources (FHIR) to the cBioPortal for cancer genomics." ; sc:featureList edam:operation_3435 ; sc:name "FhirSpark" ; sc:url "https://github.com/buschlab/fhirspark" ; biotools:primaryContact "Niklas Reimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3174 ; sc:citation ; sc:description "\"FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS).\"" ; sc:featureList edam:operation_0292 ; sc:name "FHiTINGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/fhitings/" ; biotools:primaryContact "Jordan Peccia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3068, edam:topic_3421, edam:topic_3512 ; sc:citation , "pmcid:PMC7006814", "pubmed:32076423" ; sc:description "FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR)." ; sc:featureList edam:operation_2422, edam:operation_3225, edam:operation_3461 ; sc:name "FHLdb" ; sc:url "https://www.biotoclin.org/FHLdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_0602, edam:topic_2275 ; sc:citation "pubmed:20460459" ; sc:description "FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function." ; sc:featureList edam:operation_0322, edam:operation_0474, edam:operation_0478, edam:operation_0479, edam:operation_0480 ; sc:name "FiberDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/FiberDock/" ; biotools:primaryContact "FiberDock Administrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "FiberQ is a MATLAB script for automatic quantification of dna fibers from fluorescent images" ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "FiberQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/69788-fiberq" ; biotools:primaryContact "Pierre Ghesquiere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3047 ; sc:citation ; sc:description "FiberSim is software for spatially-explicit modeling of half-sarcomeres. The code tracks the position and status of each myosin head, each binding site on actin, and each molecule of myosin-binding protein C." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FiberSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://campbell-muscle-lab.github.io/FiberSim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:34736226" ; sc:description "Pulmonary fibrosis prognosis prediction using a convolutional self attention network." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Fibro-CoSANet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zabir-nabil/Fibro-CoSANet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_3169, edam:topic_3170, edam:topic_3674 ; sc:citation , "pubmed:35277958" ; sc:description "A manually curated resource for multi-omics level evidence integration of fibrosis research" ; sc:featureList edam:operation_2421, edam:operation_3223, edam:operation_3431 ; sc:name "FibROAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.fibroad.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0659, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8571330", "pubmed:34741074" ; sc:description "Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. 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Fiddle is a “matchmaking” tool designed to help researchers to identify the publication format that will work best for a particular dataset that may be hard to publish in traditional journals." ; sc:featureList edam:operation_3357, edam:operation_3431 ; sc:license "MIT" ; sc:name "Fiddle" ; sc:url "http://s-quest.bihealth.org/fiddle/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_2259, edam:topic_2269, edam:topic_3474 ; sc:citation ; sc:description "FIDDLE (Finding Interactions using Diagram Driven modeL Extension) is a tool to automatically assemble or extend models with the knowledge extracted from published literature." ; sc:featureList edam:operation_0310, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "FIDDLE" ; sc:url "https://bitbucket.org/biodesignlab/fiddle/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:name "Pathway or network report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308 ; sc:citation ; sc:description "A web server designed to facilitate the functional interpretation of differential expression analysis. It is aimed at allowing experimentalists to \"play with\" their RNA-Seq data in an easy and at the same time exhaustive fashion within a single tool." ; sc:featureList edam:operation_3501 ; sc:name "FIDEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.biocomputing.it/fidea" ; biotools:primaryContact "Luigi Grassi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3334 ; sc:description "Run-time filter design and execution library." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "fidlib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://uazu.net/fidlib/" ; biotools:primaryContact "Jim Peters" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation , "pubmed:31114899" ; sc:description "Fido-SNP: Predicting the impact of genetic variants in dog genome" ; sc:featureList edam:operation_0331, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "fidosnp" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "web-server" ; sc:url "http://snps.biofold.org/fido-snp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "A functional site- and physicochemical interaction-annotated domain profile database, from which a sequence-based method is developed for predicting both PFSs and PLIs. 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Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population." ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_2422, edam:operation_3197, edam:operation_3431 ; sc:name "FINDbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.findbase.org" ; biotools:primaryContact "FINDbase Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3468 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:author ; sc:description "findCPcli is a command line python-tool for the computation of chokepoint reactions in genome-scale metabolic models. The main purpose of the tool is to compute chokepoints by taking into account both the topology and the dynamic information of the network. In addition to the computation of chokepoints, findCPcli can compute and remove dead-end metabolites, find essential reactions and update the flux bounds of the reactions according to the results of Flux Variability Analysis." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "findCPcli" ; sc:softwareHelp , ; sc:url "https://github.com/findCP/findCPcli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences." ; sc:featureList edam:operation_0264, edam:operation_0310, edam:operation_0527, edam:operation_3192, edam:operation_3662 ; sc:name "FINDER" ; sc:url "https://github.com/sagnikbanerjee15/Finder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3372 ; sc:citation ; sc:description "Findere is a simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure (AMQ)." ; sc:featureList edam:operation_0224, edam:operation_3472, edam:operation_3695 ; sc:license "AGPL-3.0" ; sc:name "findere" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/lrobidou/findere" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3292 ; sc:citation ; sc:description "Determine metal coordination geometry." ; sc:featureList edam:operation_2422 ; sc:name "FindGeo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CERM" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://metalweb.cerm.unifi.it/tools/findgeo/" ; biotools:primaryContact "Claudia Andreini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3940 ; sc:citation , "pmcid:PMC8988339", "pubmed:35392802" ; sc:description "An R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data." ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "FindIT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/devel/bioc/html/FindIT2.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2024 ; sc:name "Enzyme kinetics data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2026 ; sc:name "Hanes Woolf plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2978 ; sc:name "Reaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2025 ; sc:name "Michaelis Menten plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0821 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Calculate and plot enzyme reaction data." ; sc:featureList edam:operation_0334 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "findkm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/findkm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301 ; sc:citation ; sc:description "A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. It provides many novel approaches to doing pangenomic analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible." ; sc:featureList edam:operation_3209 ; sc:license "GPL-2.0" ; sc:name "FindMyFriends" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FindMyFriends.html" ; biotools:primaryContact "Thomas Lin Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3337 ; sc:citation , "pubmed:35394020" ; sc:description "An R package to automatically select number of principal components in single-cell analysis." ; sc:featureList edam:operation_3435, edam:operation_3891, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "findPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/haotian-zhuang/findPC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries." ; sc:featureList edam:operation_0258, edam:operation_0335, edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "FindPeaks 4.0 (Vancouver Short Read Package)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vancouvershortr.sourceforge.net/" ; biotools:primaryContact "Anthony Fejes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_1775, edam:topic_3520 ; sc:description "Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage." ; sc:featureList edam:operation_2479 ; sc:name "FindPept" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/findpept/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "We developed a comprehensive pipeline for annotating predicted NLR genes from a non-masked genome fasta file input. We identify loci using NLR-annotator software (Steuernagel et al. 2020), tblastn (Altschul et al. 1990) and Hidden Markov Model (HMM) (Eddy 2010). The unmasked loci identified through these methods, and including 20 kb flanking regions, are then annotated with Braker2 software (Hoff et al. 2019) using experimentally validated resistance genes as reference (Kourelis et al. 2021). Annotated amino acid fasta files are screened for domains using Interproscan (Jones et al. 2014) and the predicted coding and amino acid sequences containing both NB-ARC and LRR domains are located back to scaffolds/chromosomes and extracted in fasta and gff3 format." ; sc:featureList edam:operation_3672 ; sc:name "FindPlantNLRs" ; sc:softwareHelp ; sc:url "https://github.com/ZhenyanLuo/FindPlantNLRs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749 ; sc:citation , ; sc:description "Program to search for a promoter motif and optionally, an adapter sequence from a source species on a target species." ; sc:featureList edam:operation_0239 ; sc:name "findpromoter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/findpromoter/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2275, edam:topic_3375, edam:topic_3957 ; sc:citation , "pmcid:PMC8632724", "pubmed:34901479" ; sc:description "A web server for in silico D-peptide ligand identification." ; sc:featureList edam:operation_2476, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "finDr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://findr.biologie.uni-freiburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325, edam:topic_3571 ; sc:citation , "pubmed:23462700" ; sc:description "A search engine for rare diseases." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "FindZebra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.findzebra.com/raredisease" ; biotools:primaryContact "FindZebra Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654, edam:topic_3293, edam:topic_3944 ; sc:citation ; sc:description "An automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "findZX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hsigeman/findZX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0637, edam:topic_3520 ; sc:citation , "pmcid:PMC9998077", "pubmed:36910011" ; sc:description "Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics." ; sc:featureList edam:operation_3643, edam:operation_3649, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FineFDR" ; sc:url "https://github.com/Biocomputing-Research-Group/FDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3174, edam:topic_3299, edam:topic_3673, edam:topic_3796 ; sc:citation , "pmcid:PMC8684245", "pubmed:34922440" ; sc:description "This stand-alone program implements the Fine-Mapping of Adaptive Variation (FineMAV) statistic for detection of positively selected variants." ; sc:featureList edam:operation_3196, edam:operation_3208, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FineMAV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/fadilla-wahyudi/finemav" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2229, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8219044", "pubmed:34169280" ; sc:description "FINER is a unified deep learning framework to jointly predict protein isoform functions and isoform-isoform interactions." ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FINER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/haochenucr/FINER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0654, edam:topic_3176 ; sc:citation ; sc:description "FineStr (pronounced as (fi-nes’tru), from Latin fenestra—window, and from fine structure]) server allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them." ; sc:featureList edam:operation_2429 ; sc:name "FineStr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://www.cs.bgu.ac.il/~nucleom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3056 ; sc:citation ; sc:description "fineSTRUCTURE is an algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals. Full assignment uncertainty is given." ; sc:featureList edam:operation_3197 ; sc:license "Other" ; sc:name "fineSTRUCTURE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://paintmychromosomes.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0623 ; sc:author "Terri Attwood" ; sc:citation , ; sc:description "Scan a protein sequence against PRINTS to identify the closest matching PRINTS sequence motifs/fingerprints." ; sc:featureList edam:operation_0239, edam:operation_3092 ; sc:name "FingerPRINTScan (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Manchester" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/pfa/fingerprintscan/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC7890800", "pubmed:33602113" ; sc:description """High quality somatic mutations using filters for next generation sequencing. FiNGS: Filters for Next Generation Sequencing. We have developed Filters for Next Generation Sequencing (FiNGS), software written specifically to address these filtering issues. FiNGS can implement the ICGC filtering standards and has filters and thresholds that are fully configurable, which substantially increases the precision of results and provides high quality variants for further analysis.""" ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "FiNGS" ; sc:url "https://github.com/cpwardell/FiNGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0202, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC10326304", "pubmed:37348543" ; sc:description "Genetic fine-mapping from summary data using a nonlocal prior improves the detection of multiple causal variants." ; sc:featureList edam:operation_0282, edam:operation_0488, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FiniMOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vkarhune.github.io/finimom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3304 ; sc:citation , "pubmed:36579658" ; sc:description "Find Neuropyhsiological Networks (FiNN). A Python Toolbox for the analysis of electrophysiological data." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FiNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/neurophysiological-analysis/FiNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3300, edam:topic_3577, edam:topic_3673 ; sc:author ; sc:citation , , "pmcid:PMC9094564", "pubmed:35486646" ; sc:contributor , ; sc:description """FINSURF (Functional Identification of Non-coding Sequences Using Random Forests) is a tool designed to analyse lists of sequences variants in the human genome. It assigns a score to each variant, reflecting its functional importance and therefore its likelihood to disrupt the physiology of its carrier. FINSURF scores Single Nucleotide Variants (SNV), insertions and deletions. Among SNVs, transitions and transversions are treated separately. Insertions are characterised by a score given to each base flanking the insertion point. Deletions are characterised by a score at every deleted base. FINSURF can (optionally) use a list of known or suspected disease genes, in order to restrict results to variants overlapping cis-regulatory elements linked to these genes. For a variant of interest, users can generate a graphical representation of "feature contributions », showing the relative contributions of genomic, functional or evolutionary information to its score.""" ; sc:featureList edam:operation_0337, edam:operation_0438, edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "CECILL-C" ; sc:name "FINSURF" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://www.finsurf.bio.ens.psl.eu/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512, edam:topic_3934 ; sc:citation , , "pmcid:PMC10078054", "pmcid:PMC10122391", "pubmed:37024957", "pubmed:37085832" ; sc:description "Droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing." ; sc:featureList edam:operation_0314, edam:operation_3891, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FIPRESCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hz1010/FIPRESCI_data_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0654 ; sc:citation ; sc:description "A motif discovery and characterization program based on mutual information" ; sc:featureList edam:operation_0438 ; sc:name "FIRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1a" ; sc:url "https://tavazoielab.c2b2.columbia.edu/FIRE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0749 ; sc:citation ; sc:description "Motif discovery and characterization program for proteins based on mutual information" ; sc:featureList edam:operation_0238, edam:operation_2479 ; sc:name "FIRE-pro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://tavazoielab.c2b2.columbia.edu/FIRE-pro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7788093", "pubmed:33489005" ; sc:description """Detecting frequently interacting regions from Hi-C data. The University of North Carolina at Chapel Hill. FIREcaller: an R package for detecting frequently interacting regions from Hi-C data. Hi-C experiments have been widely adopted to study chromatin spatial organization, which plays important roles in genome function. Frequently interacting regions (FIREs) are more informative for tissue-specific chromatin interactions than the well-established Hi-C readouts, such as A/B compartments, topologically associating domains (TADs) and chromatin loops.""" ; sc:featureList edam:operation_3223, edam:operation_3226, edam:operation_3435 ; sc:name "FIREcaller" ; sc:url "https://yunliweb.its.unc.edu/FIREcaller" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2007 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_2330 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_3510, edam:topic_3534 ; sc:author , ; sc:citation , , "pmcid:PMC1716728", "pmcid:PMC3965074", "pubmed:17132832", "pubmed:24243844" ; sc:description "A curated inventory of catalytic and biologically relevant small ligand-binding sites." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "FireDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://firedb.bioinfo.cnio.es/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "Database of PDB structures and their associated ligands. It also contains the largest set of reliably annotated functionally important residues." ; sc:featureList edam:operation_0482, edam:operation_2422, edam:operation_2479 ; sc:name "firedb WS" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "CNIO", "cnio.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://firedb.bioinfo.cnio.es/rest/FireDB_rest.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_0602, edam:topic_2275, edam:topic_2830 ; sc:citation "pubmed:18424796" ; sc:description "The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space." ; sc:featureList edam:operation_0322, edam:operation_0478, edam:operation_0480, edam:operation_0482, edam:operation_3456 ; sc:name "FireDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/FireDock/" ; biotools:primaryContact "FireDock Administrator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_1964, edam:format_3508 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_2814 ; sc:author , , ; sc:citation , "pmcid:PMC5570187", "pubmed:28449074" ; sc:contributor , , , , , "Czech Science Foundation", "European Regional Development Fund", "Ministry of Education of the Czech Republic", "Tomas Martinek" ; sc:description "FireProt is a web server for an automated design of thermostable mutants. The design of thermostable mutants is based on the integration of structural and evolutionary information obtained from several bioinformatics databases and computational tools." ; sc:featureList edam:operation_0331, edam:operation_2406 ; sc:funder "Czech Science Foundation", "European Regional Development Fund", "Ministry of Education of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "FireProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , ; sc:softwareVersion "1.3" ; sc:url "https://loschmidt.chemi.muni.cz/fireprot/" ; biotools:primaryContact "FireProt team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1984 ; sc:name "Protein sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3293 ; sc:author , ; sc:contributor , , "Rayyan Khan" ; sc:description "FireProt-ASR is a web server for an automated calculation of ancestral sequences. Fireprot-ASR allows you to perform ancestral sequence reconstruction starting from a single protein sequence. The pipeline first compiles a dataset of catalytically similar protein sequences, aligns them, construct their phylogenetic tree, and then reconstruct ancestral nodes. It also allows user to input their own data and start from a different point in the pipeline." ; sc:featureList edam:operation_0346, edam:operation_0492, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "FireProt ASR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , , ; sc:softwareVersion "1.1" ; sc:url "https://loschmidt.chemi.muni.cz/fireprotasr/" ; biotools:primaryContact "FireProt ASR team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0199, edam:topic_0219, edam:topic_0621, edam:topic_3068, edam:topic_3474 ; sc:author , ; sc:citation , "pubmed:33166383" ; sc:contributor , ; sc:description "FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. Proteins find their use in numerous biomedical and biotechnological applications. Naturally occurring proteins usually cannot withstand harsh industrial environments since they have evolved to function under mild conditions. Increasing protein stability is one of the key determinants of protein applicability. The predictive power of the current computational tools is compromised by the limited experimental data that would allow a rigorous training and testing." ; sc:featureList edam:operation_0331, edam:operation_1839, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "FireProtDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://loschmidt.chemi.muni.cz/fireprotdb" ; biotools:primaryContact "FireProt team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0166, edam:topic_0736, edam:topic_3448, edam:topic_3542 ; sc:citation , "pubmed:32112578" ; sc:description "FiRES (Find Repeated Elements in Structure) is a computational method for de novo identification of proteins with repeated elements. It relies on a topology-independent structure alignment method to identify repeating elements in protein structure. FiRES can be used for the discovery of proteins containing similar structural elements with less than 20% identical residues." ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_0337, edam:operation_3767 ; sc:name "FiRES" ; sc:url "http://fires.ifc.unam.mx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "Predicts functional residues from structural templates and alignment reliability. It runs HHsearch and PSI-BLAST programs to generate alignments. Profiles are generated from a local 70% non-redundant database. Alignments are generated between the target sequences and FireDB templates." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "firestar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CNIO", "cnio.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://firedb.bioinfo.cnio.es/Php/FireStar.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "This tool predicts functional residues from structural templates and alignment reliability. It runs HHsearch and PSI-BLAST programs to generate alignments. Profiles are generated from a local 70% non-redundant database. Alignments are generated between the target sequences and FireDB templates." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "firestar WS" ; sc:provider "CNIO", "cnio.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://firedb.bioinfo.cnio.es/Php/fstarTEXT.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3053 ; sc:citation ; sc:description """Coessential Genetic Networks Reveal the Organization and Constituents of a Dynamic Cellular Stress Response. Summary The interrelated programs essential for cellular fitness in the face of stress are critical to understanding tumorigenesis, neurodegeneration, and aging. However, modelling the combinatorial landscape of stresses experienced by diseased cells is challenging, leaving functional relationships within the global stress response network incompletely understood. Here, we leverage genome-scale fitness screening data from 625 cancer cell lines, each representing a unique biological context, to build a network of “coessential” gene relationships centered around master regulators of the response to proteotoxic, oxidative, hypoxic, and genotoxic stress.""" ; sc:name "Fireworks" ; sc:url "http://fireworks.mendillolab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "FIRM is an R package for accurate integration of heterogeneous scRNA-seq datasets across multiple platforms, which specifically accounts for the heterogeneity in cell type composition between SS2 and 10X datasets. The integrated datasets generated using FIRM show accurate mixing of shared cell type identities and superior preservation of original structure for each dataset." ; sc:featureList edam:operation_3891 ; sc:name "FIRM" ; sc:url "https://github.com/mingjingsi/FIRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC7648056", "pubmed:33159146" ; sc:description "FIRM-AVP is a tool for antiviral peptide prediction. It is used for better understanding and prediction of antiviral peptides through primary and secondary structure feature importance." ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_3936 ; sc:name "FIRM-AVP" ; sc:url "https://msc-viz.emsl.pnnl.gov/AVPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3383, edam:topic_3444 ; sc:citation ; sc:description "Volumetric visualization tool which runs in all modern web browsers." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "First Person Bioimage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://fpb.ceb.cam.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0654, edam:topic_0749, edam:topic_2815, edam:topic_3512 ; sc:citation "pubmed:11726928" ; sc:description "First Exon Finder (FirstEF) is a 5' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree." ; sc:featureList edam:operation_0430, edam:operation_0440, edam:operation_0446 ; sc:name "FirstEF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rulai.cshl.org/tools/FirstEF/" ; biotools:primaryContact "Ivo Grosse", "Ramana Davuluri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0199, edam:topic_0749, edam:topic_2269 ; sc:citation "pubmed:12874379", "pubmed:15932904", "pubmed:18442989" ; sc:description "Tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR." ; sc:featureList edam:operation_0331, edam:operation_3095, edam:operation_3664 ; sc:name "Firth Software Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://guinevere.otago.ac.nz/stats.html" ; biotools:primaryContact "Andrew Firth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0623, edam:topic_0736, edam:topic_3168 ; sc:citation "pubmed:16844969" ; sc:description "Server for the identification of remote sequence homologues on the basis of protein domains." ; sc:featureList edam:operation_0245, edam:operation_0246, edam:operation_0303, edam:operation_0483, edam:operation_0491 ; sc:name "FISH" ; sc:url "http://max.ucmp.umu.se/sahmm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pmcid:PMC3941796", "pubmed:24564523" ; sc:description "FISH Amyloid is a new method for finding amyloidogenic segments in proteins based on site specific co-occurrence of aminoacids." ; sc:featureList edam:operation_2479 ; sc:name "FISH Amyloid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comprec-lin.iiar.pwr.edu.pl/fishInput/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3382 ; sc:description "Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.FISH Finder is a graphical software tool to automatically analyze FISH images that vary significantly." ; sc:featureList edam:operation_3443 ; sc:name "FISH Finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.27" ; sc:url "https://code.google.com/p/fishfinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_2885 ; sc:citation ; sc:description "Visualizes data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. It comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats." ; sc:featureList edam:operation_2495 ; sc:name "FISH Oracle" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/fish-oracle-2.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Family Identification with Structure Anchored Hidden Markov Models." ; sc:featureList edam:operation_2423 ; sc:name "FISH - profile search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://babel.ucmp.umu.se/fish/hmmsearch.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Family Identification with Structure Anchored Hidden Markov Models." ; sc:featureList edam:operation_2423 ; sc:name "FISH - sequence search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://babel.ucmp.umu.se/fish/hmmpfam.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "This software provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis." ; sc:featureList edam:operation_3443 ; sc:license "Artistic-2.0" ; sc:name "FISHalyseR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FISHalyseR.html" ; biotools:primaryContact "Andreas Heindl", "Karesh Arunakirinathan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3344 ; sc:citation , "pmcid:PMC3001747", "pubmed:21092291" ; sc:description "Fisher's Exact mid-P method to test row/col independence of a 2x2 contingency table." ; sc:isAccessibleForFree true ; sc:name "Fishers Exact with mid-P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29819-fisher-s-exact-with-mid-p-method" ; biotools:primaryContact "Steinar Thorvaldsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Database and analysis platform for gene expression and alternative splicing of fish species." ; sc:featureList edam:operation_0264, edam:operation_2422, edam:operation_2436, edam:operation_3223, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "FishExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo.njau.edu.cn/fishExp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0203, edam:topic_0621, edam:topic_0659 ; sc:citation , "pmcid:PMC8826519", "pubmed:35020925" ; sc:description "FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles." ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "FishmiRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.fishmirna.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_0621 ; sc:citation ; sc:description """FishPhyloMaker is an R package to generate phylogenies for ray-finned fishes. The package has two functions FishTaxaMaker and FishPhyloMaker. The first generate a data frame from fish species names provided by the user, checking the validity of these names and possible synonyms by using the information presented in Fishbase database through the package rfishbase . Species that were not found in Fishbase are printed in the command line, and the user must inform manually the Family and the Order of these species.""" ; sc:featureList edam:operation_0326, edam:operation_0539, edam:operation_0544, edam:operation_3942 ; sc:license "MIT" ; sc:name "FishPhyloMaker" ; sc:url "https://gabrielnakamura.github.io/FishPhyloMaker/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3452 ; sc:citation , "pmcid:PMC5100182", "pubmed:27821060" ; sc:description "fishplot is an R package that accurately and intuitively displays changes in tumor clonal structure over time." ; sc:featureList edam:operation_3480 ; sc:license "Apache-2.0" ; sc:name "fishplot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/chrisamiller/fishplot" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC8928902", "pubmed:35342596" ; sc:description "FishSizer is an open-source software developed to assist researchers in the use of estimating length and depth of fish larvae by semi-automatization of the process." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FishSizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jeppehave/FishSizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "FiSiPred: This method predict dihedral angles of amino acids of a protein using very simple technique. This server allows users to predict dihedral angles using average based prediction (ABP) and secondary structure assisted average angle based prediction (SABP) methods." ; sc:featureList edam:operation_2945 ; sc:name "fisipred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/fisipred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "FIST (Fast Imputation of Spatially-resolved transcriptomes by graph-regularized Tensor completion) is a graph-regularized tensor completion model for imputing the missing mRNA expressions in sptRNA-seq data." ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3557 ; sc:name "FIST" ; sc:url "https://github.com/kuanglab/FIST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3516, edam:topic_3518 ; sc:citation , "pmcid:PMC6425654", "pubmed:30894135" ; sc:description "R package for genotype calling for tetraploids with multiple population and parental data support." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "fitTetra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://cran.r-project.org/package=fitPoly" ; biotools:primaryContact "Roeland E. Voorrips" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:26656006" ; sc:description "Python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics." ; sc:featureList edam:operation_3439 ; sc:name "Fitchi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.evoinformatics.eu/fitchi.htm" ; biotools:primaryContact "Michael Matschiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Fitting procedure for the parameters of the Branching Process model for COVID19 (SARS-CoV-2) epidemics." ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "fitCOVID19_BranchingProcess" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75382-fitcovid19_branchingprocess" ; biotools:primaryContact "Plamen Trayanov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pubmed:35870444" ; sc:description "Accurate inference of single-cell developmental potential using sample-specific gene weight." ; sc:featureList edam:operation_3463, edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FitDevo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jumphone/fitdevo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0749, edam:topic_2275 ; sc:citation , "pubmed:35289358" ; sc:description "FitDock is a novel protein–ligand docking method which outperforms state-of-the-art methods in terms of accuracy and speed, if the template is available." ; sc:featureList edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FitDock" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://cao.labshare.cn/fitdock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "FitHiC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FitHiC.html" ; biotools:primaryContact "Ruyu Tan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0621, edam:topic_0654, edam:topic_3169, edam:topic_3400 ; sc:citation , "pmcid:PMC7451401", "pubmed:31980751" ; sc:description "Fit-Hi-C (FitHiC) is a Python tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3695, edam:operation_3799 ; sc:license "MIT" ; sc:name "FitHiC" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/ay-lab/fithic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0082 ; sc:citation "pubmed:26894674" ; sc:description "Framework for fitting conformations on a fixed backbone into electron density." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "Fitmunk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://witold.med.virginia.edu/fitmunk/server/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:19210776" ; sc:description "Computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user." ; sc:featureList edam:operation_0438 ; sc:name "FiToM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://erilllab.umbc.edu/research/software/fitom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC7676476", "pubmed:33575635" ; sc:description """Forest of imputation trees for recovering true signals in single-cell open chromatin profiles. Forest of Imputation Trees (FITs) is a method to impute highly sparse and noisy data-sets from single cell epigenome profiling. FITs work in two phases. It has been made so to handle very large read-count matrixes and to get better imputation. In phase-1 it builds multiple imputation trees and from every tree it extracts 1 or 2 imputed version of original read-count matrix. One can run phase-1 of FITs in parallel processing mode also, where multiple trees can be build using several processors.After phase-1, the phase-2 part of FITs is used to accumulate the most relevant imputed version for every cell.""" ; sc:featureList edam:operation_3454, edam:operation_3557 ; sc:name "FITs" ; sc:url "https://reggenlab.github.io/FITs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3344 ; sc:description "Estimation of coronavirus COVID-19 epidemic size by the logistic model" ; sc:featureList edam:operation_3454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "fitVirus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74411-fitvirus" ; biotools:primaryContact "milan batista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3344 ; sc:description "Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model" ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "fitVirusCOVID19" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "5.2.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74658-fitviruscovid19" ; biotools:primaryContact "milan batista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model. Code receives and plots data for the US obtained over the web." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "fitVirusCV19-state" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.6" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74813-fitviruscv19_state-united-states-covid-19-sir-model" ; biotools:primaryContact "JM2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344, edam:topic_3382 ; sc:description "Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model. Code receives and plots most recent data from HDX." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "fitVirusCV19v3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.4.8" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74676-fitviruscv19v3-covid-19-sir-model" ; biotools:primaryContact "JM2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Estimation of coronavirus COVID-19 epidemic evaluation by the SIR model. Code receives and plots most recent data from HDX." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "fitVirusCV19varW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74977-fitviruscv19varw-variable-weight-fitting-of-sir-model" ; biotools:primaryContact "Lateef Adewale Kareem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Fivepseq is a software package for analysis of 5prime endpoints distribution in RNA sequencing datasets. This is particularly useful for techniques that capture 5prime monophosphorylated RNAs, such as 5PSeq, PARE-seq or GMUC. It may also be useful for ribosome profiling datasets and alike." ; sc:featureList edam:operation_3563, edam:operation_3800 ; sc:license "BSD-3-Clause" ; sc:name "fivepseq" ; sc:softwareHelp ; sc:url "http://pelechanolab.com/software/fivepseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3173 ; sc:citation ; sc:description """An interactive multi-tissue eQTL browser. FIVEx: Functional Interpretation and Visualization of Expression.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3232 ; sc:license "MIT" ; sc:name "FIVEx" ; sc:url "https://eqtl.pheweb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC3945112", "pubmed:24603409" ; sc:description "Over-dispersion correction technique that serves to de-duplicate counts." ; sc:featureList edam:operation_3219, edam:operation_3563 ; sc:license "Not licensed" ; sc:name "FixSEQ" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/thashim/fixseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3511 ; sc:citation "pubmed:26538306" ; sc:description "Feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats." ; sc:featureList edam:operation_0415 ; sc:name "Fizzy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EESI/Fizzy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:encodingFormat edam:format_2545 ; sc:name "Tool name (FASTA)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622 ; sc:citation ; sc:description "Pipeline for Single Nucleotide Variants (SNVs) and Copy Number Variation (CNVs) variant calling" ; sc:featureList edam:operation_0362, edam:operation_3227, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "FJD-pipeline" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/TBLabFJD/VariantCallingFJD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10767854", "pubmed:37823705" ; sc:description """Integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing. Circular RNAs (circRNAs) are a class of functional RNA molecules with a continuous loop structure characterized by back-splice junctions (BSJs).""" ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0463 ; sc:isAccessibleForFree true ; sc:name "FL-circAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cosbi.ee.ncku.edu.tw/FL-circAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3474 ; sc:citation ; sc:description "FL-QSAR is a federated learning based QSAR prototype for collaborative drug discovery. FL-QSAR is an horizontal federated-learning based QSAR framework that enables clients to simulate the scenario of n clients with and without HFL(horizontal federated-learning). FL-QSAR is also a demo framework designed to help users better understanding the workflow and the underline mechanism of applying HFL for QSAR modeling. Meanwhile, FL-QSAR can be easily extended to other deep learning algorithms for solving various drug-related learning tasks." ; sc:featureList edam:operation_3625, edam:operation_3799, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "FL-QSAR" ; sc:url "https://github.com/bm2-lab/FL-QSAR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3473 ; sc:citation ; sc:description "Forensic loci allele database." ; sc:featureList edam:operation_0338 ; sc:name "FLAD" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:url "http://forensic.ugent.be/FLAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data." ; sc:featureList edam:operation_3214 ; sc:license "GPL-2.0" ; sc:name "flagme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/flagme.html" ; biotools:primaryContact "Mark Robinson", "Riccardo Romoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0114, edam:topic_0196, edam:topic_0621, edam:topic_3293 ; sc:citation , "pubmed:32956448" ; sc:description "FlaGs (Flanking Genes) web- and command-line tool that clusters neighbourhood-encoded proteins into homologous groups and outputs the identity of the groups, a graphical visualization of the gene neighbourhood and its conservation, and optionally, a phylogenetic tree annotated with flanking gene conservation." ; sc:featureList edam:operation_0224, edam:operation_0435, edam:operation_0558, edam:operation_0567 ; sc:license "GPL-3.0" ; sc:name "FlaGs" ; sc:url "http://www.webflags.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0219, edam:topic_0659, edam:topic_3170 ; sc:citation "pubmed:25338717" ; sc:description "Method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs)." ; sc:featureList edam:operation_0361, edam:operation_3680 ; sc:name "FlaiMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yhoogstrate/flaimapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2258, edam:topic_2269, edam:topic_3474 ; sc:citation ; sc:description "Flame is an open source framework for model development, hosting, and usage in production environments. Flame is a web application, with a Python backend and a web-based graphic interface, which can be used as a desktop application or installed in a server receiving requests from multiple users. Models can be built starting from any collection of biologically annotated chemical structures, since the software supports structural normalization, molecular descriptor generation and machine learning building, using predefined workflows. The model building workflow can be customized from the graphic interface, selecting the type of normalization, molecular descriptors, and machine learning algorithm to be used from a panel of state-of-the-art methods implemented natively." ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Flame" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/phi-grib/flame" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC8301326", "pubmed:34356520" ; sc:description "Functional enrichment analysis using multiple lists" ; sc:featureList edam:operation_2436, edam:operation_2940, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Flame" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://bib.fleming.gr:3838/Flame/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3930 ; sc:citation ; sc:description "FLAME (Coakley et al., 2012) is an open-source, generic formal framework for agent-based modelling that allows parallelisation using MPI, and developers can use it to create models and tools. Implementing a Flame simulation is done by using finite-state automata with memory (Coakley et al., 2006). This tool has been adapted to be used with distributed GPUs using the OpenCL standard (Richmond et al., 2010). Examples of uses of FLAME range from bioreactor studies (Kaul et al., 2013) to immunogenic studies (Kabiri Chimeh et al., 2019) or also epidermis modelling (Li et al., 2013)." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Flame GPU 2" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://flamegpu.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0749, edam:topic_0798, edam:topic_3305 ; sc:citation ; sc:description """A tool for comparative genomics of gene flanking regions. Flanker is a tool for studying the homology of gene-flanking sequences. It will annotate FASTA/multi-FASTA files for specified genes, then write the flanking sequences to new FASTA files. 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Our early work has shown the accuracy of it is higher than the accuracy of traditional methods, especially for RNAs without pseudoknots." ; sc:featureList edam:operation_0278 ; sc:name "FledFold" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.jlucomputer.com/fledfold.php" ; biotools:primaryContact "Hao Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:34331052" ; sc:description "This toolset can be used to analyze the sequencing data generated either by Nanopore or by PacBio using the FLEP-seq method." ; sc:featureList edam:operation_0232, edam:operation_0428, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:name "FLEP-seq" ; sc:url "https://github.com/ZhaiLab-SUSTech/FLEPSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0625, edam:topic_2229 ; sc:citation , "pmcid:PMC8138267", "pubmed:34018332" ; sc:description "FLEX (Functional evaluation of experimental perturbations) is an R package and a pipeline that utilizes several functional annotation resources to establish reference standards for systematic evaluation of genome-wide CRISPR screens." ; sc:featureList edam:operation_2940, edam:operation_3435, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "FLEX" ; sc:url "https://github.com/csbio/FLEX_R" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:24832523" ; sc:description "Flexible barcode and adapter removal. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided. It increases read mapping rates and improves genome as well as transcriptome assemblies. 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The method automatically identifies hinge regions and rigid parts using HingeProt and then docks the input molecules while explicitly considering the hinges and possible protein motions." ; sc:featureList edam:operation_2492 ; sc:name "FlexDock" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/FlexDock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "FlexDotPlot is a universal and modular dot plot visualization tool for complex multifaceted data." ; sc:featureList edam:operation_0490, edam:operation_2937, edam:operation_2943 ; sc:name "FlexDotPlot" ; sc:url "https://github.com/Simon-Leonard/FlexDotPlot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC4678642", "pubmed:26666757" ; sc:description "Combining metabolic flux and regulatory network analyses." ; sc:featureList edam:operation_2497 ; sc:license "GPL-1.0" ; sc:name "FlexFlux" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://lipm-bioinfo.toulouse.inra.fr/flexflux/" ; biotools:primaryContact "Ludovic Cottret" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc:citation , "pmcid:PMC1239896", "pubmed:16199517" ; sc:description """Flexgsea is a R package to do gene set enrichment analysis. Main advantages: - Allows user defined functions. So you can use you favorite package for differential expression. - Calculates significance by sample permutation. - Parallelization using the foreach package. - Can calculate normalized enrichment scores (NES) and significance based on that. - Implements the weighted KS-like statistic.""" ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "flexgsea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NKI-CCB/flexgsea-r" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "Flexible cFDR (conditional false-discovery rate) is an extension of the cFDR framework that supports continuous auxiliary data from any arbitrary distribution, extending its use beyond only GWAS. As in the existing cFDR framework, the method requires GWAS test statistics for the trait of interest and auxiliary SNP-level data to output quantities analogous to p-values (called “v-values”), meaning that the method can be applied iteratively to incorporate additional layers of auxiliary data." ; sc:featureList edam:operation_0484, edam:operation_2238, edam:operation_3891 ; sc:license "MIT" ; sc:name "Flexible cFDR" ; sc:softwareHelp ; sc:url "https://github.com/jamesliley/cfdr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33051680" ; sc:description "flexiMAP (flexible Modeling of Alternative PolyAdenylation) is a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data. It is a beta-regression-based method implemented in R, for discovering differential alternative polyadenylation events in standard RNA-seq data. Importantly, flexiMAP allows the modeling of multiple known covariates that often confound the results of RNA-seq data analysis." ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3563 ; sc:license "MIT" ; sc:name "flexiMAP" ; sc:url "https://github.com/kszkop/flexiMAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "FLEXIQuant-LF is a tool for robust regression to quantify protein modification extent in label-free proteomics data." ; sc:featureList edam:operation_0417, edam:operation_3634, edam:operation_3645, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "FLEXIQuant-LF" ; sc:url "https://github.com/SteenOmicsLab/FLEXIQuantLF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0081, edam:topic_0091, edam:topic_3292, edam:topic_3332 ; sc:citation , "pubmed:18544548", "pubmed:19429600", "pubmed:21070939", "pubmed:22437851", "pubmed:23685436", "pubmed:23740746", "pubmed:25348211", "pubmed:26605625", "pubmed:26612862" ; sc:description "FlexPortal is a web portal containing a series of tools and databases related to macromolecular structure flexibility, developed to offer an integrated approach to study flexibility. Tools such as molecular dynamics atomistic and coarse-grained simulations, proteins and nucleic acids dynamics and flexibility analyses and structures and trajectories databases/repositories are integrated in a publicly available web interface." ; sc:featureList edam:operation_0570, edam:operation_2406, edam:operation_2421, edam:operation_2422, edam:operation_2476, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "FlexPortal" ; sc:operatingSystem "Linux" ; sc:provider "IRB-BSC", "irbbarcelona.org" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mmb.irbbarcelona.org/FlexPortal/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pubmed:18186479", "pubmed:19238251" ; sc:description "FlexPred is a web-server for predicting residue positions involved in conformational switches in proteins.The server accepts either a protein sequence or a PDB file to predict residue positions involved in conformational switches." ; sc:featureList edam:operation_2479 ; sc:name "FlexPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://flexpred.rit.albany.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation "pubmed:12112693" ; sc:description "Detect the optimal flexible structural alignment of a pair of protein structures. 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sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation ; sc:description "Web portal offering a complete set of macromolecular flexibility analyses from a coarse-grained or atomistic MD trajectory" ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:name "FlexServ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://mmb.irbbarcelona.org/FlexServ" ; biotools:primaryContact "Institute for Research in Biomedicine Barcelona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3071, edam:topic_3174 ; sc:citation , "pubmed:34469515" ; sc:description "FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FlexTaxD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FOI-Bioinformatics/flextaxd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3673, edam:topic_3810 ; sc:citation ; sc:description "FlexTyper is a tool which enables the creation of an FM-index of raw, next generation sequencing data to enable rapid and flexible sequence queries." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3198, edam:operation_3211, edam:operation_3472 ; 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FlyBrainLab is designed with three main capabilities in mind: (i) 3D exploration and visualization of fruit fly brain data, (ii) creation of executable circuits directly from the explored and visualized fly brain data, and (iii) interactive exploration of the functional logic of the devised executable circuits. 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It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc." ; sc:featureList edam:operation_3283, edam:operation_3435, edam:operation_3443 ; sc:license "BSD-3-Clause" ; sc:name "fMRIPrep" ; sc:softwareHelp ; sc:url "https://github.com/poldracklab/fmriprep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3512 ; sc:citation ; sc:description "A new tool for detection and identification of clusters of sequential motifs with varying characteristics inside genomic sequences." ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "FMSClusterFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://fmsclusterfinder.fmsbiog.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:23929859" ; sc:description "Software tool to compute the MTP of a physical map based purely on restriction fingerprint data (and the contigs). It completely ignores the ordering of clones obtained by the physical map algorithm." ; sc:featureList edam:operation_0310 ; sc:name "FMTP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.mscs.mu.edu/~bozdag/FMTP/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053 ; sc:citation , "pmcid:PMC6048286", "pubmed:30042776" ; sc:description "Software to Identify Homozygous Lesions in Deletion Mutant Populations." ; sc:featureList edam:operation_3197 ; sc:name "FNBtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/noble-research-institute/fnbtools" ; biotools:primaryContact "Jiangqi Wen", "Liang Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0804, edam:topic_2885, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description """Dissecting molecular regulatory mechanisms underlying noncoding susceptibility SNPs associated with 19 autoimmune diseases using multi-omics integrative analysis. fnGWAS, an integrative analysis frame designed for dissecting molecular mechanisms underlying noncoding GWAS SNPs through incorporating diverse functional cell-specific multi-omics data. Dissecting the functionality of noncoding GWAS SNPs. Just select interested autoimmune diseases (or select all without disease limitation) , select type and enter correspond SNPs/CotoBand/Target Gene. fnGWAS is an integrated analysis pipeline for dissecting molecular mechanisms :. 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It provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated." ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "FourCSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/FourCSeq.html" ; biotools:primaryContact "Felix A. Klein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3399 ; sc:citation , , "pmcid:PMC7039948", "pubmed:32094335" ; sc:description "Fox Insight Collects Online, Longitudinal Patient-Reported Outcomes and Genetic Data on Parkinson's Disease | Fox DEN provides investigators with a tool to explore, download and apply statistical models on aggregated data collected for the Fox Insight online clinical study. The Fox Insight study collects patient-reported outcomes and genetic data from people with Parkinson's disease and their loved ones" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3436 ; sc:name "Fox Insight" ; sc:url "https://foxden.michaeljfox.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_2828, edam:topic_3448, edam:topic_3452 ; sc:citation "pubmed:20507903" ; sc:description "Fast X-ray Scattering (FoXS) is a web server for computing the small angle x-ray scattering (SAXS) structure profile of a molecule in solution and for comparing the computed profile to the experimental profile." ; sc:featureList edam:operation_0295, edam:operation_0297 ; sc:name "FoXS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://salilab.org/foxs" ; biotools:primaryContact "FoXS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0634, edam:topic_3375, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC10462816", "pubmed:37649967" ; sc:description "Extensive library of fingerprint-based molecular activity prediction tools." ; sc:featureList edam:operation_3435, edam:operation_3461, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "FP-MAP" ; sc:url "https://gitlab.com/vishsoft/fpmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3375, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC8479898", "pubmed:34583740" ; sc:description "FPADMET is a compilation of molecular fingerprint-based predictive models for ADMET properties." ; sc:featureList edam:operation_0303, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FPADMET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/vishsoft/fpadmet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:description "FPB is a new data-independent tool suitable for large scale projects as well as mapping of few clones." ; sc:featureList edam:operation_2429 ; sc:name "FPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://services.appliedgenomics.org/software/fpb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , ; sc:description "An easy-to-use open source visualization tool that permits researchers to share their volumetric image data online and third parties to interact with, and explore, datasets in their entirety." ; sc:featureList edam:operation_3443 ; sc:license "CC-BY-SA-4.0" ; sc:name "FPBioimage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://fpb.ceb.cam.ac.uk/" ; biotools:primaryContact "Clemens F. Kaminski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3341, edam:topic_3500 ; sc:citation "pubmed:11934749", "pubmed:9367125" ; sc:description "FPC is a tool to assemble contigs from a set of clones and their restriction fragments." ; sc:featureList edam:operation_0310, edam:operation_0523, edam:operation_0524, edam:operation_2429 ; sc:name "FPC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.agcol.arizona.edu/software/fpc/" ; biotools:primaryContact "FPC Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2259, edam:topic_3473 ; sc:citation "pubmed:25402006" ; sc:description "Data mining-based method for proteome-wide PPI prediction." ; sc:featureList edam:operation_2464 ; sc:name "FpClass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dcv.uhnres.utoronto.ca/FPCLASS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3420 ; sc:citation , "pmcid:PMC8008158", "pubmed:33842844" ; sc:description "The fpemlocal package is the one-country implementation of FPEM (family planning estimation model) designed with tidyverse philosophy. The model in this package uses global model results from the package FPEMglobal to aid in the estimation of country level family planning indicators. fpemlocal comes equiped with survey data, country unit data, and country population count data, to produce one-country runs. Running FPEM is divided into three main functions." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:license "MIT" ; sc:name "FPEM" ; sc:url "https://github.com/AlkemaLab/fpemlocal" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation ; sc:description "FPfilter is a false-positive specific filter for vcf files from whole genome sequencing. It is proved to be more false-positive specific than GATK hard filter." ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "FPfilter" ; sc:url "https://github.com/yuxiangtan/FPfilter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "An FPGA-accelerated implementation of GWAS permutation testing designed primarily for AWS EC2 F1 (f1.2xlarge) instances." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FPGA_perm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v1.0.0" ; sc:url "https://github.com/witseie/fpgaperm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "The FPM app is an open-source application for simple and intuitive Fourier ptychographic reconstruction. FPM is a computational microscopy technique that allows obtaining microscopic image of a measured sample with much higher resolution than it would follow from the numerical aperture (NA) of used microscope objective." ; sc:featureList edam:operation_3454 ; sc:license "GPL-2.0" ; sc:name "FPM" ; sc:url "https://github.com/MRogalski96/FPM-app" ; biotools:primaryContact , "Piotr Zdańkowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pubmed:34890327" ; sc:description "Fast Parameter-free Multi-view Subspace Clustering with Consensus Anchor Guidance." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "FPMVS-CAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wangsiwei2010/FPMVS-CAG" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2878 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structural motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166 ; sc:citation "pubmed:19486540", "pubmed:20478829" ; sc:description "Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket)." ; sc:featureList edam:operation_3351 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Fpocket" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::fpocket" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC9414105", "pubmed:36008829" ; sc:description "Protein pocket hunting in a web browser." ; sc:isAccessibleForFree true ; sc:name "FPocketWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://durrantlab.com/fpocketweb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0166, edam:topic_0623, edam:topic_3534 ; sc:citation "pubmed:19880384" ; sc:description "Relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. To identify protein binding sites, we model the shape of a split pocket induced by a binding ligand. This database provides an easily accessible resource for studying functional surfaces, assessing conformational changes between bound and unbound forms and analyzing functional divergence." ; sc:featureList edam:operation_0245, edam:operation_0384, edam:operation_0387, edam:operation_2575 ; sc:name "fPOP" ; sc:url "http://pocket.uchicago.edu/fpop/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pubmed:24068034" ; sc:description "FPSAC (Fast Phylogentic Scaffolding of Ancient Contigs) is a software for fast phylogenetic scaffolding of ancient contigs. The author apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome." ; sc:featureList edam:operation_3216 ; sc:name "FPSAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://paleogenomics.irmacs.sfu.ca/FPSAC/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3393 ; sc:citation ; sc:description "Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool." ; sc:featureList edam:operation_3218 ; sc:license "MIT" ; sc:name "FQC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/pnnl/fqc" ; biotools:primaryContact "Joseph Brown" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation , ; sc:description "Mini workflow for preprocessing fastq files, it includes quality trimming, duplicate and artefacts filters for FASTQ read files." ; sc:featureList edam:operation_3192, edam:operation_3695 ; sc:name "fqcleaner" ; sc:softwareVersion "0.4.1.1" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Convert quality scoring to Sanger in FASTQ files." ; sc:featureList edam:operation_0233 ; sc:name "fqconvert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation , ; sc:description "Detect duplicate reads. Outputs a list of read names corresponding to reads already seen in the dataset with a better quality sum score (duplicates)." ; sc:featureList edam:operation_3218, edam:operation_3230 ; sc:name "fqduplicate" ; sc:softwareVersion "1.0" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931, edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1931 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3077 ; sc:citation , ; sc:description "Extract a subset of fastq reads." ; sc:featureList edam:operation_0224 ; sc:name "fqextract" ; sc:softwareVersion "1.0.1" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation , ; sc:description "Output reads with low quality bases trimmed (at the extremities) or masked and/or with quality descreased to the minimum. Output an extra singlet dataset if paired-end data provided." ; sc:featureList edam:operation_3192 ; sc:name "fqquality" ; sc:softwareVersion "1.0" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_3071 ; sc:citation , ; sc:description "List names of sequences from FASTQ formatted files." ; sc:featureList edam:operation_0335 ; sc:name "fqseqname" ; sc:softwareVersion "1.0" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1933 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation , ; sc:description "List names of sequence pairs from two FASTQ formatted files." ; sc:featureList edam:operation_2422 ; sc:name "fqseqpair" ; sc:softwareVersion "1.0" ; sc:url "ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools/README" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2269 ; sc:citation , "pmcid:PMC6969201", "pubmed:31953467" ; sc:description "FQSqueezer is a FASTQ compressor based on k-mer statistics." ; sc:featureList edam:operation_0363, edam:operation_3227, edam:operation_3472 ; sc:name "FQSqueezer" ; sc:url "https://github.com/refresh-bio/fqsqueezer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "A package that provides tools for efficient FASTQ files manipulation." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "fqtools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@fqtools@1.1" ; biotools:primaryContact "Nicolas Joly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3511 ; sc:citation ; sc:description "Utility for filtering and trimming high-throughput next-gen reads." ; sc:featureList edam:operation_3192, edam:operation_3695 ; sc:name "fqtrim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.95" ; sc:url "http://ccb.jhu.edu/software/fqtrim/index.shtml" ; biotools:primaryContact "Geo Pertea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "FR-Match is a tool for robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test." ; sc:featureList edam:operation_0313, edam:operation_3891, edam:operation_3935 ; sc:license "MIT" ; sc:name "FR-Match" ; sc:url "https://github.com/JCVenterInstitute/FRmatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382 ; sc:citation , "pubmed:35788455" ; sc:description "Full-Resolution Network and Dual-Threshold Iteration for Retinal Vessel and Coronary Angiograph Segmentation." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "FR-UNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lseventeen/FR-UNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC7702219", "pubmed:33252656" ; sc:description """Ridge regression (RR) is a regularization technique that penalizes the L2-norm of the coefficients in linear regression. One of the challenges of using RR is the need to set a hyperparameter (α) that controls the amount of regularization. Cross-validation is typically used to select the best α from a set of candidates. However, efficient and appropriate selection of α can be challenging, particularly where large amounts of data are analyzed. Because the selected α depends on the scale of the data and predictors, it is also not straightforwardly interpretable. In fracridge, we reparameterize RR in terms of the ratio γ between the L2-norms of the regularized and unregularized coefficients. This approach, called fractional RR (FRR), has several benefits: the solutions obtained for different γ are guaranteed to vary, guarding against wasted calculations, and automatically span the relevant range of regularization, avoiding the need for arduous manual exploration.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "BSD-2-Clause" ; sc:name "fracridge" ; sc:softwareVersion "1.2.1" ; sc:url "https://nrdg.github.io/fracridge/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3056, edam:topic_3524 ; sc:citation ; sc:description "Multi-scenario genome-wide medical population genetics simulation framework." ; sc:featureList edam:operation_2426 ; sc:name "FractalSIM" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://web.cbio.uct.ac.za/~emile/software.html" ; biotools:primaryContact "Emile Chimusa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3314 ; sc:citation , "pubmed:33769437" ; sc:description "FraGAT is a fragment-oriented multi-scale graph attention model for molecular property prediction." ; sc:featureList edam:operation_0478, edam:operation_3454, edam:operation_3927, edam:operation_4009 ; sc:name "FraGAT" ; sc:url "https://github.com/ZiqiaoZhang/FraGAT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0736, edam:topic_3382 ; sc:citation ; sc:description "Guided modeling of missing segments such as loops or hinge regions into cryo-Electron Microscopy (cryo-EM) density maps [1]. Segments of up to 3-35 residues length can be effectively modeled into maps of different resolution." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3431 ; sc:name "FragFit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.52" ; sc:url "http://proteinformatics.charite.de/ngl-tools/fragfit/start.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053 ; sc:citation , "pubmed:20805240" ; sc:description "Application for finding (fragmented) genes in short reads" ; sc:featureList edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "FragGeneScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/fraggenescan/" ; biotools:primaryContact "Wazim MohammedIsmail", "Yuzhen Ye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3174 ; sc:citation , "pmcid:PMC9148508", "pubmed:35643462" ; sc:description "FragGeneScanRs is written in Rust, so first head over to their installation instructions. Afterwards, you can install the crate from crates.io with cargo install frag_gene_scan_rs The installation progress may prompt you to add a directory to your path so you can easily execute it." ; sc:featureList edam:operation_0310, edam:operation_2409, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FragGeneScanRs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/unipept/FragGeneScanRs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "Protein fragment picker that allows protein fragment databases to be created and queried. It can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. It also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput." ; sc:featureList edam:operation_0227, edam:operation_2409, edam:operation_2451, edam:operation_2997 ; sc:license "LGPL-2.1" ; sc:name "Fragger" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/UnixJunkie/fragger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "Residue-residue contact prediction." ; sc:featureList edam:operation_2423 ; sc:name "FragHMMent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://predictioncenter.org/Services/FragHMMent/descr.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3303, edam:topic_3379 ; sc:citation , "pmcid:PMC9159630", "pubmed:35648746" ; sc:description "Assessing and visualizing fragility of clinical results with binary outcomes in R using the fragility package." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "fragility" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=fragility" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_2830, edam:topic_3336, edam:topic_3895 ; sc:citation , "pmcid:PMC9295698", "pubmed:35797032" ; sc:description "A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "FRAGLER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AstraZeneca/fragler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3316, edam:topic_3336, edam:topic_3365, edam:topic_3489 ; sc:citation , "pmcid:PMC8171072", "pubmed:34076593" ; sc:description "The FragMAXapp is a web application for processing and visualisation of macromolecular crystallography data, with the focus on fragment screening campaigns." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "FragMAXapp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://maxiv.lu.se/fragmax/fragmaxapp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2165 ; sc:name "Protein ionisation curve" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Analyzing MS/MS fragmentation data." ; sc:featureList edam:operation_0337 ; sc:name "Fragmentation Analyzer" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.5.13" ; sc:url "http://compomics.github.io/projects/fragmentation-analyzer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:20049869" ; sc:description "A tool for analyzing MS/MS fragmentation data." ; sc:featureList edam:operation_3214 ; sc:name "FragmentationAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compomics.github.io/projects/fragmentation-analyzer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_0821, edam:topic_3534 ; sc:citation "pubmed:20965964" ; sc:description "A resource for the comparison of fragments found in metabolites, drugs or toxic compounds. We generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. It provides a variety of search options. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments binding sites and classification of fragments." ; sc:featureList edam:operation_0394, edam:operation_0398, edam:operation_2929 ; sc:name "FragmentStore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/fragment_store" ; biotools:primaryContact "Catherine Sargent", "Jessica Ahmed", "Paul Thaben", "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0749, edam:topic_2275, edam:topic_3375 ; sc:citation , "pubmed:32027130" ; sc:description "FrAG is a tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand conformational space." ; sc:featureList edam:operation_2476, edam:operation_3899, edam:operation_3938 ; sc:license "MIT" ; sc:name "FragPELE" ; sc:softwareHelp ; sc:url "https://github.com/carlesperez94/frag_pele" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3511 ; sc:citation , "pmcid:PMC5054030", "pubmed:16689703" ; sc:description "It implements an efficient algorithm for detecting nucleotide pattern fragments in genomes that occur in a given order. For each pattern a tolerance can be specified separately." ; sc:featureList edam:operation_0253 ; sc:license "GPL-3.0" ; sc:name "fragrep" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://www.bioinf.uni-leipzig.de/Software/fragrep/" ; biotools:primaryContact "Mosig A" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:33275427" ; sc:description "FragRep is a web server for structure-based ligand design by fragment replacement. FragRep is a powerful computational tool for the rapid generation of ligand design ideas; either in scaffold hopping or bioisosteric replacing." ; sc:featureList edam:operation_3216, edam:operation_3899, edam:operation_3938 ; sc:name "FragRep" ; sc:url "http://xundrug.cn/fragrep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166 ; sc:citation "pubmed:24603983" ; sc:description "Web application designed to sample alternative protein backbone conformations in loop regions using the geometrical constrains of smotifs." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "Frag r Us" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinsilico.org/FRAGRUS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3474 ; sc:citation "pubmed:27153697" ; sc:description "Database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model." ; sc:featureList edam:operation_0267, edam:operation_2479 ; sc:name "FRAGSION" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sysbio.rnet.missouri.edu/FRAGSION/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:33724022" ; sc:description "FRAGSITE is a fragment-based machine learning algorithm that scores protein-ligand binding for ligand virtual screening." ; sc:featureList edam:operation_3216, edam:operation_3899, edam:operation_3938 ; sc:name "FRAGSITE" ; sc:url "http://sites.gatech.edu/cssb/FRAGSITE" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3174 ; sc:citation , "pmcid:PMC7045542", "pubmed:32102653" ; sc:description "FRAGTE is a completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes." ; sc:featureList edam:operation_0310, edam:operation_0491, edam:operation_3454 ; sc:name "FRAGTE" ; sc:url "https://github.com/Yizhuangzhou/FRAGTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0196, edam:topic_3170 ; sc:citation , "pmcid:PMC4712544", "pubmed:26763976" ; sc:description "A transcriptome assembly and mRNA annotation pipeline, which utilizies external and newly developed software components." ; sc:featureList edam:operation_0310, edam:operation_0361 ; sc:name "FRAMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/gengit/FRAMA" ; biotools:primaryContact "Bens M", "Szafranski K" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0621, edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:12824407" ; sc:description "Program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts." ; sc:featureList edam:operation_0265, edam:operation_0436, edam:operation_0489, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "FrameD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genoweb.toulouse.inra.fr/FrameD/FD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3170 ; sc:citation ; sc:description "Sensitive peptide detection on noisy matured sequences. A self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities." ; sc:featureList edam:operation_3767 ; sc:name "FrameDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://iant.toulouse.inra.fr/FrameDP" ; biotools:primaryContact "Erika Sallet", "Jérôme Gouzy", "Ludovic Cottret", "Sébastien Carrere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3070, edam:topic_3318, edam:topic_3344 ; sc:description "Analyzes fluorescence recovery after photobleaching (FRAP) data using the Hankel transform method." ; sc:isAccessibleForFree true ; sc:name "FRAP analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29388-frap_analysis" ; biotools:primaryContact "Peter Jönsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "FRAP.zip is a MATLAB GUI for analysis of FRAP data." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "FRAP.zip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47327-frap-zip" ; biotools:primaryContact "Advanced Imaging Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "FRC-QE is a robust and comparable 3D microscopy image quality metric for cleared organoids." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:name "FRC-QE" ; sc:url "https://github.com/PreibischLab/FRC-QE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0218, edam:topic_0637, edam:topic_2258 ; sc:citation , "pubmed:32120139" ; sc:description "FRCD (Food Risk Component Database) is a comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis." ; sc:featureList edam:operation_0360, edam:operation_3216 ; sc:name "FRCD" ; sc:url "http://www.rxnfinder.org/frcd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0593, edam:topic_2229, edam:topic_3344, edam:topic_3474 ; sc:citation ; sc:description "Colocalization of Fluorescence and Raman Microscopic Images for Training Data Collection" ; sc:featureList edam:operation_3214, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "frcoloc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46608-frcoloc" ; biotools:primaryContact "Sascha D. Krauß" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2209 ; sc:encodingFormat edam:format_3016 ; sc:name "Mutation ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:35420988" ; sc:description "An ensemble predictor with effective feature representation for deleterious synonymous mutation in human genome." ; sc:featureList edam:operation_0253, edam:operation_0433, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "frDSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://frdsm.xialab.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814 ; sc:citation ; sc:description "FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures." ; sc:featureList edam:operation_0271, edam:operation_2421, edam:operation_2423, edam:operation_2479 ; sc:name "FREAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.1" ; sc:url "http://opig.stats.ox.ac.uk/webapps/fread/php/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:name "Sequence composition plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate residue/base frequency table or plot." ; sc:featureList edam:operation_0236 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "freak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/freak.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_1317 ; sc:citation ; sc:description "Program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Frealign" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://emlab.rose2.brandeis.edu/frealign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:19439514" ; sc:description "a frequency-based, de novo short-read clustering method that organizes erroneous short sequences originating in a single abundant sequence into a tree structure. In this structure, each “child” sequence is considered to be derived from its “parent” sequence with one mutation through sequencing errors. The root node is the most frequently observed sequence that represents all erroneous reads in the entire tree." ; sc:featureList edam:operation_3198 ; sc:name "FreClu" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://mlab.cb.k.u-tokyo.ac.jp/%7Equwei/DeNovoShortReadClustering/" ; biotools:primaryContact "Shinichi Morishita" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "FRED is a framework for T-cell epitope detection that offers consistent, easy, and simultaneous access to well established prediction methods for MHC binding and antigen processing. 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It provides different semantic similarity measures for Gene Ontology terms and offers functional similarity values for proteins contained in UniProtKB and for protein families/domains in Pfam and SMART. Users can perform semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. It also supports prioritizing disease gene candidates." ; sc:featureList edam:operation_1777, edam:operation_2414, edam:operation_2495, edam:operation_3672 ; sc:name "FunSimMat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.funsimmat.de" ; biotools:primaryContact "FunSimMat Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation ; sc:description "A modular and extensible classifier for the prediction of functional sites in DNA." ; sc:featureList edam:operation_2403 ; sc:name "FunSiP" ; sc:operatingSystem "Linux", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/supplementary_data/mibel/FunSiP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308, edam:topic_3321 ; sc:citation "pubmed:22829724" ; sc:description "Software that can be used to analyse differential expression data from RNAseq and can integrate these analyses with data from proteomic studies." ; sc:featureList edam:operation_3223 ; sc:name "FunSys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/funsysufpa/" ; biotools:primaryContact "Debmalya Barh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation ; sc:description "Web server attempts to automatically infer which functional specificities and commonalities exist among different taxa." ; sc:featureList edam:operation_3460 ; sc:name "Funtaxis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Department of Molecular Medicine, University of Padua" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.medcomp.medicina.unipd.it/funtaxis" ; biotools:primaryContact "Stefano Toppo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0637 ; sc:citation , "pmcid:PMC10500080", "pubmed:37672040" ; sc:description "A simple and light solution to investigate protein functions in all living organisms." ; sc:featureList edam:operation_2421, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "FunTaxIS-lite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.medcomp.medicina.unipd.it/funtaxis-lite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3071, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:26500152" ; sc:description "The R package which provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types." ; sc:featureList edam:operation_3435 ; sc:name "funtooNorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GreenwoodLab/funtooNorm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0736, edam:topic_0821, edam:topic_3293 ; sc:citation "pubmed:22006843" ; sc:description "Provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH." ; sc:featureList edam:operation_0323, edam:operation_0499, edam:operation_0504, edam:operation_3432 ; sc:name "FunTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/FunTree/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0634, edam:topic_0736, edam:topic_0821 ; sc:citation , "pmcid:PMC6868392", "pubmed:31584091" ; sc:description """identifying protein positions for variation driven functional tuning. 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sc:license "Not licensed" ; sc:name "FusionM4Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pixixiaonaogou/MLSDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation "pubmed:21593131" ; sc:description "Detects fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq studies and characterize fusion junctions at base-pair resolution." ; sc:featureList edam:operation_3199 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "FusionMap" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.arrayserver.com/wiki/index.php?title=FusionMap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3295, edam:topic_3512, edam:topic_3930 ; 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Morganella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3673, edam:topic_3697, edam:topic_3810 ; sc:citation ; sc:description """An integrated metagenomics suite. Metagenomics data analysis software. Metagenomics analysis tool: simplest, fastest and accurate solution for metagenomics data. The easiest, most accurate and reliable cloud software for Metagenomics Analysis. Gaia 2.0 uses the best, most up to date and reliable scientific methods and algorithms, and you don’t even need any bioinformatics knowledge to run it!. GAIA has a reliable upload system with integrated recovery and resume functions to allow you to quickly and securely upload your data. You can also upload it directly from your Google Drive. 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The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations." ; sc:isAccessibleForFree true ; sc:name "Galaxy-SynBioCAD" ; sc:url "https://galaxy-synbiocad.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_1317, edam:topic_2814, edam:topic_3307, edam:topic_3332 ; sc:citation ; sc:description "The Galaxy7TM server improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods." ; sc:name "Galaxy7TM" ; sc:url "https://galaxy.seoklab.org/7TM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0622, edam:topic_3172 ; sc:citation ; sc:description """Galaxy Australia is a hosted instance of the Galaxy web-based platform for data intensive biological research, for all Australian researchers. 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Graph Theoretical Analysis of Task-based Functional Dynamics Toolbox. Graph theoretical analysis of task-related functional dynamics (GAT-FD) is a systematically integrated user-friendly toolkit to characterize the functional dynamics for task-related fMRI data based on graph theoretical techniques. 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sc:citation , , ; sc:description "This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. 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Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pubmed:31406990" ; sc:description "Haplotype-aware graph indexes | This is a reimplementation of the Generalized Compressed Suffix Array (GCSA), a BWT-based index for directed graphs | The old implementation indexed all paths in a directed acyclic graph, which had to be determinized before index construction. GCSA2 approximates the graph with a de Bruijn graph (with k = 256 or less), allowing it to index more complex graphs as well as graphs containing cycles. The order of the de Bruijn graph limits the length of the queries the index is able to answer correctly. 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The Next Generation Cancer Knowledge Network.""" ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3211, edam:operation_3227, edam:operation_3431 ; sc:name "GDportal" ; sc:url "https://gdc.cancer.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2885, edam:topic_3318, edam:topic_3512 ; sc:citation "pubmed:15357877", "pubmed:17932055" ; sc:description "Contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map." ; sc:featureList edam:operation_0282, edam:operation_0526, edam:operation_2429, edam:operation_2871, edam:operation_2944 ; sc:name "Genome Database for Rosaceae (GDR)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rosaceae.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed." ; sc:featureList edam:operation_0226, edam:operation_0362, edam:operation_2409, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "GDSArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GDSArray.html" ; biotools:primaryContact "Qian Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3373 ; sc:citation ; sc:description "Mining pharmacogenomic interactions in cancer." ; sc:featureList edam:operation_2949 ; sc:name "GDSCTools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://gdsctools.readthedocs.io/en/master/" ; biotools:primaryContact "Julio Saez-Rodriguez", "Mathew J Garnett", "Thomas Cokelaer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2921 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330, edam:format_2921 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , "pmcid:PMC5860110", "pubmed:28334390" ; sc:description "This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. It offers efficient operations designed for integers of less than 8 bits (single genetic/genomic variant fewer bits than a byte)." ; sc:featureList edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "gdsfmt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gdsfmt.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:19732865" ; sc:description "Software package for genome-wide association analysis." ; sc:featureList edam:operation_2403 ; sc:name "GDT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://people.virginia.edu/~wc9c/GDT/" ; biotools:primaryContact "Wei-Min Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Performs various functions on GenomeDiff formatted files." ; sc:name "gdtools" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3071 ; sc:citation , , ; sc:description "Merge multiple GenomeDiff input files." ; sc:featureList edam:operation_0232 ; sc:name "gdtools_annotate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533 ; sc:citation , , ; sc:description "Input a single Genome Diff, and as many reference files as you like. Using the Genome Diff, this will apply all the mutations to the reference sequences, output is to a single file that includes all the references in the requested format." ; sc:featureList edam:operation_3202, edam:operation_3429 ; sc:name "gdtools_apply" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533 ; sc:citation , , ; sc:description "Compare control versus test mutations Input a single Genome Diff, and as many reference files as you like. Using the Genome Diff, this will apply all the mutations to the reference sequences, output is to a single file that includes all the references in the requested format." ; sc:featureList edam:operation_0256 ; sc:name "gdtools_check" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3071 ; sc:citation , , ; sc:description "Creates a Genome Variation Format (GVF) file of mutations present in an input Genome Diff file." ; sc:featureList edam:operation_0335 ; sc:name "gdtools_gd2gvf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3071 ; sc:citation , , ; sc:description "Creates a Variant Call Format (VCF) file of mutations present in an input Genome Diff file." ; sc:featureList edam:operation_0335 ; sc:name "gdtools_gd2vcf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2533 ; sc:citation , ; sc:description "Creates a new Genome Diff file with mutations that are present in ALL input Genome Diff files." ; sc:featureList edam:operation_3202, edam:operation_3436 ; sc:name "gdtools_intersect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2533, edam:topic_3071 ; sc:citation , ; sc:description "Remove mutation predictions in masked regions Creates a GD file where mutations in the input GD that are located within certain regions of the reference genome are removed. These regions are defined as MASK entries in the mask GD file. Mutations that overlap only masked reference bases (and therefore do not overlap any unmasked bases) are removed." ; sc:featureList edam:operation_3096 ; sc:name "gdtools_mask" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2533 ; sc:citation , , ; sc:description "Predicts mutations from the evidence entries in the input GD file. Any mutation entries (three-letter code lines) already present in the input GD file will be removed." ; sc:featureList edam:operation_3202 ; sc:name "gdtools_mutations" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2533 ; sc:citation , ; sc:description "Creates a GD file of mutations that have been normalized to the input reference files." ; sc:featureList edam:operation_3435 ; sc:name "gdtools_normalize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2533, edam:topic_3071 ; sc:citation , , ; sc:description "Takes a GenomeDiff file and removes all of the entries that are NOT used as evidence by a mutation. Outputs to a new GenomeDiff file if specified. If no output is specified, verbose will still inform what evidence isn't being used." ; sc:featureList edam:operation_3096 ; sc:name "gdtools_not-evidence" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_2533, edam:topic_3053 ; sc:citation , ; sc:description "Create a file containing random mutations." ; sc:featureList edam:operation_0367 ; sc:name "gdtools_simulate-mutations" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622 ; sc:citation , , ; sc:description "Creates a new Genome Diff file that contains all entries that are still present in the input file after removing mutations that are in any of the subtracted Genome Diff files. All evidence and validation entries are retained in the output file." ; sc:featureList edam:operation_2121 ; sc:name "gdtools_subtract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3071 ; sc:citation , , ; sc:description "Creates a GD file with entries that exist in any input GD file. Duplicate entries are merged into a single entry." ; sc:featureList edam:operation_0232, edam:operation_3429 ; sc:name "gdtools_union" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3572 ; sc:citation , ; sc:description "Validates whether the format of the input Genome Diff files is correct." ; sc:featureList edam:operation_2428 ; sc:name "gdtools_validate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0199 ; sc:citation , , ; sc:description "Variant Call Format(VCF) to GD." ; sc:featureList edam:operation_0335 ; sc:name "gdtools_vcf2gd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.26" ; sc:url "http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_usage.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:35901457" ; sc:description "GE-Impute is an imputation method for scRNA-seq data based on graph embeddings." ; sc:featureList edam:operation_0244, edam:operation_0314, edam:operation_3463, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GE-Impute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wxbCaterpillar/GE-Impute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description """Genomic evolutionary analysis in R with geaR. The package geaR is designed to aid with evolutionary and population genetic analysis across whole genome genotype data in the GDS format.""" ; sc:featureList edam:operation_3196, edam:operation_3216, edam:operation_3918 ; sc:license "MIT" ; sc:name "geaR" ; sc:softwareHelp ; sc:url "https://github.com/CMWbio/geaR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1628, edam:format_1632, edam:format_3000 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1711 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2331, edam:format_3020 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_3464 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199 ; sc:author "Tobias Rausch" ; sc:citation , "pmcid:PMC7071639", "pubmed:32171249" ; sc:description "Gear is a genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses." ; sc:featureList edam:operation_0233, edam:operation_2403, edam:operation_3182, edam:operation_3185, edam:operation_3197, edam:operation_3203, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Gear-Genomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.gear-genomics.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_2275, edam:topic_3303 ; sc:citation "pubmed:26250822" ; sc:description "Ultra-fast automated docking program, designed to predict how small ligands bind to pharmacologically relevant macromolecules. 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The implemented tool includes the traditional capabilities of this type of software, incorporating the concept of layers from image editing software to represent different comparisons. An innovative feature is the integration of the Evolutionary Events timeline. 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Welcome to GECO (Gene Expression Clustering Optimization), the straightforward, user friendly Streamlit app to visualize and investigate data patterns with non-linear reduced dimensionality plots. 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It utilizes the evolutionary computing strategies for solving the so-called Graph Edit Distance problem." ; sc:featureList edam:operation_0277, edam:operation_2497 ; sc:name "GEDEVO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bmb.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://gedevo.compbio.sdu.dk/" ; biotools:primaryContact "Jan Baumbach" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Extension of the idea implemented in GEDEVO to multiple input networks which aims to minimize the sum of GEDs between every pair of input networks." ; sc:featureList edam:operation_0277, edam:operation_2497 ; sc:name "GEDEVO-M" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bmb.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://gedevo.compbio.sdu.dk/" ; biotools:primaryContact "Jan Baumbach" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC7003401", "pubmed:32024475" ; sc:description """Applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes. GeDi: Generalised suffix array-based Direct SNV caller. Generalised suffix array-based Direct SNV caller, or GeDi, detects somatic Single Nucleotide Variants (SNVs) within paired tumour-control NGS datasets.""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:license "MIT" ; sc:name "GeDi" ; sc:url "https://github.com/izaak-coleman/GeDi" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation ; sc:description "An R package for integration of transcriptomic data from multiple high-throughput platforms." ; sc:featureList edam:operation_2939, edam:operation_3282, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GEDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MNStokholm/GEDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "A database of gene-disease pathway association, along with tools to identify i) disease-disease comorbidity, ii) pathway enrichment, iii) disease enrichment, iv) disease enrichment using GO terms, v) polypharmacological target prediction and vi) Venn of genes, pathways, domains, GO terms, and custom list" ; sc:featureList edam:operation_3501 ; sc:name "GeDiPNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gedipnet.bicnirrh.res.in/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0632, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8554027", "pubmed:34722482" ; sc:description "The Genome Editing automated Design platform for point mutation construction in Corynebacterium glutamicum." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "GEDpm-cg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gedpm-cg.biodesign.ac.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_0622 ; sc:description "Application that holds Gene Feature data. It has been designed with the needs of researchers wanting to keep, share and annotate sequence and feature data. Gee Fu is a Ruby on Rails based RESTful web-service application that stores and serves sequence assembly and genome feature data on request." ; sc:featureList edam:operation_0310 ; sc:name "Gee Fu" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1.2" ; sc:url "https://github.com/danmaclean/gee_fu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3508, edam:format_3579, edam:format_3604 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3509 ; sc:encodingFormat edam:format_3508, edam:format_3579, edam:format_3604 ; sc:name "Ontology mapping" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3572 ; sc:citation ; sc:description "Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, etc." ; sc:featureList edam:operation_2436 ; sc:license "GPL-2.0" ; sc:name "geecc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/geecc.html" ; biotools:primaryContact "Markus Boenn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Calculate fractional GC content of nucleic acid sequences." ; sc:featureList edam:operation_0430 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "geecee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/geecee.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:21803806" ; sc:description "Database tool for genomic assembly and feature data" ; sc:featureList edam:operation_0310 ; sc:name "GeeFu" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "https://github.com/danmaclean/gee_fu" ; biotools:primaryContact "Dan MacLean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3293, edam:topic_3303, edam:topic_3360, edam:topic_3697 ; sc:citation ; sc:description "Detecting Sparse Microbial Association Signals Adaptively From Longitudinal Microbiome Data Based on Generalized Estimating Equations." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GEEMiHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xpjiang-ccnu/GEEMiHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2640, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC8039533", "pubmed:33854526" ; sc:description "GeenaR is a tool for MALDI/ToF MS spectra analysis." ; sc:featureList edam:operation_3192, edam:operation_3215, edam:operation_3627, edam:operation_3860, edam:operation_3891 ; sc:name "GeenaR" ; sc:softwareHelp ; sc:url "http://proteomics.hsanmartino.it/geenar/" ; biotools:primaryContact "Eugenio Del Prete", "Paolo Romano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0160, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC7879670", "pubmed:33579334" ; sc:description """Gene function finding through cross-organism ensemble learning. GeFF (Gene Function Finder) is a Web-based portal providing an intuitive interface both to compute novel predicted annotations for multiple organisms (all organisms in the Entrez Gene database) and to browse a database of:. Known annotations of the genes of all organisms in the Entrez Gene database to Gene Ontology (GO) terms describing the gene biological function features,.""" ; sc:featureList edam:operation_2422, edam:operation_2454, edam:operation_3672, edam:operation_3778 ; sc:name "GeFF" ; sc:url "http://tiny.cc/geff/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description """Scalable and flexible gene-environment interaction analysis in millions of samples. GEM (Gene-Environment interaction analysis for Millions of samples) is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference.""" ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3435 ; sc:name "GEIA" ; sc:url "https://github.com/large-scale-gxe-methods/GEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:24728855" ; sc:description "R package for the comparative analysis of evolutionary radiations." ; sc:featureList edam:operation_0323 ; sc:name "GEIGER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/geiger/" ; biotools:primaryContact "Matt Pennell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3068 ; sc:citation , "pubmed:35485739" ; sc:description "An R package for gene-environment interaction analysis incorporating prior information." ; sc:featureList edam:operation_0306, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GEInfo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=GEInfo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3068 ; sc:citation , "pubmed:33961050" ; sc:description "GEInter is an R package for robust gene-environment interaction analysis." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "GEInter" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=GEInter" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0781 ; sc:citation "pubmed:26049161" ; sc:description "Identify integrations of DNA elements on a genome-wide scale." ; sc:featureList edam:operation_0415 ; sc:name "GeIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.nhgri.nih.gov/software/GeIST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "A free 1D gel electrophoresis image analysis software .The process of gel image analysis is straightforward and covers all the main aspects of evaluation from automatic lane detection to precise molecular weight calculations. Many tools help you to improve the accuracy of gel evaluation. You may obtain the gel image with a common digital camera, or even with your cell phone, and use it to get the results in just a few seconds." ; sc:featureList edam:operation_2423, edam:operation_3443 ; sc:name "Gel Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2010a" ; sc:url "http://www.gelanalyzer.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3382, edam:topic_3500, edam:topic_3520 ; sc:citation "pubmed:14681486" ; sc:description "Database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available." ; sc:featureList edam:operation_0224, edam:operation_0398, edam:operation_2929, edam:operation_3092, edam:operation_3767 ; sc:name "GELBANK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gelbank.anl.gov/" ; biotools:primaryContact "György Babnigg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3071, edam:topic_3293 ; sc:citation "pubmed:25725494" ; sc:description "General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques." ; sc:featureList edam:operation_0323, edam:operation_2426 ; sc:name "GeLL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phylo.bio.ku.edu/GeLL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3361 ; sc:description "Software for the analysis of DNA fingerprints (AFLP, t-RFLP, RAPD, ERIC-PCR, RFLP-PCR). It works in a fast and efficient way with trace files (FSA files) as well as with gel image files (TIFF, JPG, BMP, etc.) and handles AFLP, t-RFLP, ERIC-PCR, RFLP-PCR or RAPD data." ; sc:featureList edam:operation_3443 ; sc:name "GelQuest" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.1.7" ; sc:url "http://www.sequentix.de/gelquest/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3382, edam:topic_3520 ; sc:citation "pubmed:14764570" ; sc:description "Platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank's repository." ; sc:featureList edam:operation_2409, edam:operation_3443, edam:operation_3553 ; sc:name "GelScape and GelBank" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.gelscape.ualberta.ca/" ; biotools:primaryContact "Nelson Young" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Developed at Reed College which calculates DNA fragment sizes from gel electrophoresis migration data. It runs on a Macintosh computer only. The first step in using the this program is to enter data for a known marker. Both the distances traveled and the fragment sizes are entered. Then the distances migrated by up to 19 sets of DNA fragments are entered, and the program calculates the sizes of these fragments using a cubic-spline interpolation." ; sc:featureList edam:operation_3443 ; sc:name "GelyMac" ; sc:operatingSystem "Mac" ; sc:url "http://academic.reed.edu/biology/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3517 ; sc:citation , , , "pmcid:PMC3348564", "pmcid:PMC4970299", "pubmed:22492648", "pubmed:24626854", "pubmed:27480116" ; sc:description "Tools for analyzing EWAS, methQTL and GxE genome widely." ; sc:featureList edam:operation_3196, edam:operation_3232 ; sc:license "Artistic-2.0" ; sc:name "GEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GEM.html" ; biotools:primaryContact , "Hong Pan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2259, edam:topic_3473 ; sc:citation ; sc:description "GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data." ; sc:featureList edam:operation_0224, edam:operation_2421 ; sc:name "GEM-TREND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cgs.pharm.kyoto-u.ac.jp/network/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:encodingFormat edam:format_2182 ; sc:name "Tool name (FASTA)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2573, edam:format_3285 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:author "Alejandro Chacon", "Santiago Marco-Sola", "Simon Heath" ; sc:citation , , , "pubmed:23103880", "pubmed:26094690", "pubmed:27604516" ; sc:contributor "Paolo Ribeca" ; sc:description "High-performance mapping for aligning sequenced reads against large reference genomes (e.g. human genome). In particular, it is designed to obtain best results when mapping sequences up to 1K bases long. It indexes the reference genome using a custom FM-Index design, and performs an adaptive gapped search based on the characteristics of the input and the user settings." ; sc:featureList edam:operation_0292, edam:operation_0495, edam:operation_0496, edam:operation_3198, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GEM-Mapper v3" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "v3.6" ; sc:url "https://github.com/smarco/gem3-mapper" ; biotools:primaryContact "Santiago Marco-Sola" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3315, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC8545347", "pubmed:34695175" ; sc:description "Scalable and flexible gene-environment interaction analysis in millions of samples." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/large-scale-gxe-methods/GEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation ; sc:description "A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper" ; sc:featureList edam:operation_0224, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "GEM library" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://gemlibrary.sourceforge.net/" ; biotools:primaryContact "Paolo Ribeca", "Report a bug" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3306, edam:topic_3315 ; sc:description "This method introduces gene set enrichment for mathematical biology (GEMB). Typically, gene-set analyses measure the association between a disease of interest and a set of genes related to a biological pathway. These analyses often incorporate gene network properties to account for differential contributions of each gene. With GEMB, we extend this concept further, defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict the effects of genetic perturbations on a particular downstream function." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "GEMB" ; sc:url "https://github.com/cochran4/GEMB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "GEMDeCan (Gene Expression and Methylation based Deconvolution for Cancer) is a tool for improved tumor immune microenvironment profiling through novel gene expression and DNA methylation signatures predicts immunotherapy response." ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_3629 ; sc:name "GEMDeCan" ; sc:url "https://github.com/VeraPancaldiLab/GEMDeCan" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Generate error models from real data for GemReads." ; sc:featureList edam:operation_2426 ; sc:name "gemerr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6" ; sc:url "https://sourceforge.net/projects/gemsim/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_3277, edam:topic_3474, edam:topic_3520 ; sc:citation , , "pmcid:PMC9216561", "pubmed:35657113" ; sc:description "Interactive interface for transformer-based Genomic Metadata Integration." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GeMI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gmql.eu/gemi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3324, edam:topic_3399 ; sc:citation "pubmed:19850722" ; sc:description "The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool." ; sc:featureList edam:operation_2422, edam:operation_3282, edam:operation_3461 ; sc:name "Gemina" ; sc:url "https://sourceforge.net/projects/gemina/" ; biotools:primaryContact "L. M. Schriml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC3715403", "pubmed:23874191" ; sc:description "GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics." ; sc:featureList edam:operation_2403, edam:operation_3197 ; sc:license "MIT" ; sc:name "GEMINI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gemini.readthedocs.io/en/latest/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:19376825" ; sc:description "Gemma is an open source database, analysis software system and web site for expression data re-use and meta-analysis. It currently contains analyzed data from over 3300 expression profiling studies, yielding billions of data points that can be searched and explored. Gemma offers web-based access to differential expression results and coexpression data in a meta-analysis framework." ; sc:featureList edam:operation_3223 ; sc:name "Gemma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://chibi.ubc.ca/Gemma" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:22706312" ; sc:description "Test for association in genome-wide association studies (GWAS) using a standard linear mixed model to account for population stratification and sample structure. It calculates exact Wald or likelihood ratio test statistics and p-values, and is computationally efficient for large GWAS." ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "GEMMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.xzlab.org/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3316, edam:topic_3512 ; sc:citation , "pmcid:PMC9063052", "pubmed:35501696" ; sc:description "GEMmaker is a Nextflow workflow for large-scale gene expression sample processing, expression-level quantification and Gene Expression Matrix (GEM) construction." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GEMmaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/SystemsGenetics/GEMmaker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077 ; sc:author "Paolo Ribeca" ; sc:citation ; sc:contributor "Santiago Marco Sola" ; sc:description "A set of very optimized tools for indexing/querying huge genomes/files. 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In addition it provides some tools for the developer." ; sc:featureList edam:operation_2495 ; sc:name "genArise" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genArise.html" ; biotools:primaryContact "IFC Development Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815 ; sc:citation ; sc:description "Information on gene mapping and genetic diseases." ; sc:featureList edam:operation_0224 ; sc:name "GenAtlas human gene database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UNIVERSITE PARIS DESCARTES" ; sc:softwareHelp ; sc:url "http://www.dsi.univ-paris5.fr/genatlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0634, edam:topic_1775, edam:topic_3053, edam:topic_3325, edam:topic_3366 ; sc:citation "pubmed:9835018" ; sc:description "The Genatlas database provides information on the structure, expression and function of genes, gene mutations and their consequences on diseases." ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3436, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Genatlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genatlas.org" ; biotools:primaryContact "Alexandra Caude", "Claude Mugnier", "Marie-Liesse Chauvet", "Martine Lemerrer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3295, edam:topic_3315 ; sc:citation ; sc:description """A New Tool for Modelling and Analyzing Cancer Gene Regulatory Networks Using Delayed Nonlinear Variable Order Fractional System. Gene Regulatory Network Analysis by Variable Fractional Order Systems.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3435 ; sc:license "Apache-2.0" ; sc:name "GENAVOS" ; sc:url "https://github.com/hanif-y/GENAVOS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:name "Sequence accession (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2532 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A comprehensive database of public nucleotide sequences for more than 300 000 organisms named, from small and large-scale sequencing projects. Data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage." ; sc:featureList edam:operation_0224 ; sc:name "GenBank nucleotide sequence database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NCBI" ; sc:url "http://www.ncbi.nlm.nih.gov/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2549 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3053, edam:topic_3071 ; sc:citation , ; sc:description "Convert a GenBank, EMBL or UniProt file into a GFF file." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:name "genbank2gff3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.3" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/genbankconverters/genbank2GFF3/0.0.3" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3053 ; sc:citation , ; sc:description "Convert a Genbank/EMBL file into the .ffn (gene) file, .faa (protein fasta file) and ptt file (protein table), or sequin file." ; sc:featureList edam:operation_0335 ; sc:name "genbank_convertor" ; sc:softwareVersion "0.0.1" ; sc:url "https://bioweb.pasteur.fr/packages/pack@pf1-tools@0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:citation , ; sc:description "Convert a Genbank file into the .ffn (gene) file." ; sc:featureList edam:operation_0335 ; sc:name "genbank_to_gene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.0.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/genbank_to_gene/genbank_to_gene/0.0.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Reads Genbank files." ; sc:featureList edam:operation_1812 ; sc:license "Artistic-2.0" ; sc:name "genbankr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genbankr.html" ; biotools:primaryContact "Gabriel Becker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "GENBMAP (Genetical Bandwith Mapping) is a software for the study of the spatial genetic structure. It was developped by Alain Cercueil, O. Fran?ois and S. Manel. The method is essentially descriptive, and allows an user to analyze genotypes and geographic coordinates simultaneously through a two dimensional graphical representation. GenBMAP provides a basis for the interpretation of the genetic structure of a population." ; sc:featureList edam:operation_2429 ; sc:name "GENBMAP" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://membres-timc.imag.fr/Olivier.Francois/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3473 ; sc:citation "pubmed:24764463" ; sc:description "Literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. It can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords." ; sc:featureList edam:operation_2497 ; sc:name "GenCLiP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "GenCLiP 2.0, GenCLiP 3" ; sc:url "http://cismu.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:16336639" ; sc:description "New genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods." ; sc:featureList edam:operation_0313 ; sc:name "GenClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.math.unipa.it/~lobosco/genclust/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3071 ; sc:citation "pubmed:11072342" ; sc:description "Efficient compression algorithm for DNA sequences. Data compression has became a tool to retrieve information hidden in genetic sequences." ; sc:featureList edam:operation_0335 ; sc:name "GenCompress" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www1.spms.ntu.edu.sg/~chenxin/GenCompress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC6933617", "pubmed:31881822" ; sc:description """an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. Generate consensus reads to reduce sequencing noises and remove duplications. A fast tool to remove sequencing duplications and eliminate sequencing errors by generating consensus reads. gencore is a tool for fast and powerful deduplication for paired-end next-generation sequencing (NGS) data. It is much faster and uses much less memory than Picard and other tools. It generates very informative reports in both HTML and JSON formats. It's based on an algorithm for generating consensus reads, and that's why it's named gencore""" ; sc:featureList edam:operation_0232, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "gencore" ; sc:url "https://github.com/OpenGene/gencore" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1927, edam:format_1936 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1927, edam:format_1936 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC153740", "pubmed:12682369" ; sc:description "Genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. This annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GenDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bigi" ; sc:softwareHelp ; sc:softwareVersion "2.4" ; sc:url "http://gendb.computational.bio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1929, edam:format_1939 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1927, edam:format_1936 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC3888431", "pubmed:24427317" ; sc:contributor ; sc:description "This tool was developed based on the GenDB genome annotation system that was originally designed for prokaryotic genomes only. The system has been adapted to facilitate the creation and functional annotation of sequence features that are specific for eukaryotic genomes, e.g. intron and exon gene structures." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GenDBE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bigi" ; sc:softwareHelp ; sc:softwareVersion "2.4" ; sc:url "https://gendbe.computational.bio.uni-giessen.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0157, edam:topic_3053, edam:topic_3168, edam:topic_3500 ; sc:citation "pubmed:16845034" ; sc:description "Prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence." ; sc:featureList edam:operation_0436, edam:operation_0489 ; sc:name "GenDecoder" ; sc:url "http://darwin.uvigo.es/software/gendecoder.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0634, edam:topic_3067, edam:topic_3391 ; sc:citation "pubmed:19498079" ; sc:description "Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to OMIM data. This approach assists in interpreting -omic data for its molecular and clinical aspects." ; sc:featureList edam:operation_0314 ; sc:name "Gendoo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gendoo.dbcls.jp" ; biotools:primaryContact "Takeru Nakazato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0804, edam:topic_3308, edam:topic_3325, edam:topic_3400, edam:topic_3518 ; sc:citation , "pmcid:PMC6749933", "pubmed:31559014" ; sc:description """A curated transcriptome dataset collection to investigate inborn errors of immunity. Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3223 ; sc:name "Gene" ; sc:url "http://pid.gxbsidra.org/dm3/geneBrowser/list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pubmed:34555591" ; sc:description "Gene Bench is a benchmark-ing framework used in analyzing methods that detect differentially expressed genes from biological samples. Besides being a benchmarking framework it also contains some commonly used Differential genes detection algorithms:" ; sc:featureList edam:operation_0571, edam:operation_2454, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Gene-Bench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/raduangelescu/GeneBench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204 ; sc:citation ; sc:description "Computational tool for helping users identify new members of a pathway of interest, as well as the RNA expression datasets in which that pathway is relevant." ; sc:featureList edam:operation_0313, edam:operation_2495 ; sc:name "CLIC (Clustering by Inferred Co-expression)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.gene-clic.org/" ; biotools:primaryContact "Jun S. Liu", "Sarah E. Calvo", "Vamsi K. Mootha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:21998647" ; sc:description "GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression." ; sc:featureList edam:operation_2495 ; sc:name "GENE-Counter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/genecounter/" ; biotools:primaryContact "Jeff H. Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_3179, edam:topic_3518 ; sc:description "Returns a colormap for visualizing gene expression." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Gene Expression Colormap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/6481-gene-expression-colormap" ; biotools:primaryContact "Michael Driscoll" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0632 ; sc:citation , "pubmed:33352459" ; sc:description """A tool to design polynucleotide probes for targeting microbial genes. probe designer for geneFISH and phageFISH.""" ; sc:featureList edam:operation_2419 ; sc:name "Gene-PROBER" ; sc:url "http://gene-prober.icbm.de/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3172, edam:topic_3337, edam:topic_3676 ; sc:citation , "pmcid:PMC9071452", "pubmed:35474393" ; sc:description "Identifying genes with similar continuous trait fingerprints from phenome-wide association analyses." ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3432, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:name "Gene-SCOUT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genescout.public.cgr.astrazeneca.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3053, edam:topic_3373 ; sc:citation ; sc:description "Computational tool for pathway-based rational drug repositioning." ; sc:featureList edam:operation_2497 ; sc:name "Gene2drug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gene2drug.tigem.it/" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0196, edam:topic_0632, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:15215375" ; sc:description "Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR)." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3198 ; sc:name "Gene2Oligo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://berry.engin.umich.edu/gene2oligo/" ; biotools:primaryContact "Jean-Marie Rouillard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:21646335" ; sc:description "The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG." ; sc:featureList edam:operation_0361, edam:operation_3672 ; sc:name "Gene3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gene3d.biochem.ucl.ac.uk/Gene3D/" ; biotools:primaryContact "Jonathan Lees" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1040 ; sc:name "CATH domain ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2701 ; sc:name "CATH node ID (family)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2701 ; sc:name "CATH node ID (family)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623 ; sc:citation ; sc:description "Structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc." ; sc:featureList edam:operation_0224 ; sc:name "Gene3D structural" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UCL" ; sc:softwareHelp ; sc:url "http://gene3d.biochem.ucl.ac.uk/Gene3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8558372", "pubmed:34733322" ; sc:description "An Integrated Genetic Database for Hearing Loss." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3226, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:name "Gene4HL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genemed.tech/gene4hl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description """a comprehensive genetic database of Parkinson's disease. Gene4PD: an integrative genomic database and analytic platform for Parkinson's disease. Rare variants identified from PD patients.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3766 ; sc:name "Gene4PD" ; sc:url "http://genemed.tech/gene4pd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC6639926", "pubmed:31319791" ; sc:description "R package to define gene families and their expression in legumes and beyond." ; sc:featureList edam:operation_0552, edam:operation_0553, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "geneHummus" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.11" ; sc:url "https://cran.r-project.org/package=geneHummus" ; biotools:primaryContact "Jose V. Die" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3320, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:22123740" ; sc:description "The Gene Array Analyzer (GAA) allow to process CEL files from GeneChip�� Gene 1.0 ST Arrays. Various processing steps and visualizations are implemented to identify alternative splicing events. Three simple steps have to be performed to submit a set of CEL files. After the processing is completed the results can be viewed in the browser." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_2499, edam:operation_3223 ; sc:name "Gene Array Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gaa.mpi-bn.mpg.de" ; biotools:primaryContact "Gene Array Analyzer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_0654, edam:topic_3321 ; sc:citation "pubmed:18974334" ; sc:description "See if you can generate and collect three types of protein, then move on to explore the factors that affect protein synthesis in a cell." ; sc:featureList edam:operation_2495 ; sc:name "Gene Expression" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phet.colorado.edu/en/simulation/gene-expression-basics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3678 ; sc:citation "pubmed:22064864" ; sc:description "Semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223 ; sc:name "Gene Expression Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/gxa/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2815, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:21177656" ; sc:description "Database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that leverages information from the GEO and ArrayExpress public repositories to build statistical models that permit converting data from a single microarray into expressed/unexpressed calls for each gene. For selected platforms, users may upload data and obtain results." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3223, edam:operation_3432 ; sc:name "Gene Expression Barcode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://barcode.luhs.org/" ; biotools:primaryContact "Rafael A. Irizarry" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0780, edam:topic_3170, edam:topic_3172 ; sc:citation ; sc:description "Visualize and compare gene expression from standard transcriptome (RNA-Seq) data, cluster samples and genes, and infer enrichment of gene function in gene-sets." ; sc:featureList edam:operation_0571, edam:operation_2939, edam:operation_3501, edam:operation_3891, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Gene Expression Plots" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://usadellab.github.io/GeneExpressionPlots/#/data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_0797 ; sc:citation ; sc:description "Genomic neighborhood data visualization web application." ; sc:featureList edam:operation_3208, edam:operation_3209 ; sc:name "Gene Graphics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://katlabs.cc/genegraphics/" ; biotools:primaryContact "Katherine J Harrison", "Rémi Zallot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0654, edam:topic_2533 ; sc:citation "pubmed:18974334" ; sc:description "Explore the effects of mutations within the lac operon by adding or removing genes from the DNA." ; sc:featureList edam:operation_2495 ; sc:name "Gene Machine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phet.colorado.edu/en/simulation/gene-machine-lac-operon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0621, edam:topic_0780, edam:topic_3053 ; sc:citation , "pubmed:33290552" ; sc:description """The Gene Ontology resource. Source ontology files for the Gene Ontology. The Gene Ontology (GO) project is a major bioinformatics initiative to develop a computational representation of our evolving knowledge of how genes encode biological functions at the molecular, cellular and tissue system levels.""" ; sc:featureList edam:operation_2422, edam:operation_3501, edam:operation_3559, edam:operation_3672, edam:operation_3778 ; sc:name "Gene Ontology" ; sc:softwareHelp , ; sc:url "http://geneontology.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0203 ; sc:description "Gene Ontology Browser (GOBrowser) is an interactive tool for mapping microarray gene expression data onto the GeneOntology directed acyclic graph." ; sc:featureList edam:operation_2429, edam:operation_2495 ; sc:name "Gene Ontology Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.92" ; sc:url "http://bioinformatics.mdanderson.org/main/MicroarrayGOBrowser:Overview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2815, edam:topic_3489, edam:topic_3512 ; sc:citation "pubmed:16371163" ; sc:description "Database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access." ; sc:featureList edam:operation_2454, edam:operation_3224, edam:operation_3672 ; sc:name "Gene Set Builder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cisreg.ca/gsb/" ; biotools:primaryContact "Wyeth W Wasserman" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1150 ; sc:name "Disease ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "Disease enrichment analysis on gene sets." ; sc:featureList edam:operation_3501 ; sc:name "Gene set to diseases" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm.uni-mainz.de/geneset2diseases" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1081 ; sc:encodingFormat edam:format_2332 ; sc:name "Genotype and phenotype annotation ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "Open source tool for marker-assisted gene pyramiding." ; sc:featureList edam:operation_3196 ; sc:license "Apache-2.0" ; sc:name "Gene Stacker" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.9" ; sc:url "http://genestacker.ugent.be/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3620, edam:format_3752 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3518 ; sc:citation , "pmcid:PMC9325790", "pubmed:35882976" ; sc:description "A web tool that autocorrects and updates for Excel misidentified gene names." ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Gene Updater" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kuanrongchan-date-to-gene-converter-date-gene-tool-oodr7h.streamlitapp.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:name "GO-term enrichment data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3315, edam:topic_3518 ; sc:citation , "pmcid:PMC10111666", "pubmed:37069540" ; sc:description "Web application for the analysis and comparison of gene expression data." ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "Genealyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://genealyzer.item.fraunhofer.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test." ; sc:featureList edam:operation_0314, edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "GeneAnswers" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneAnswers.html" ; biotools:primaryContact "Gang Feng", "Lei Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3391 ; sc:citation ; sc:description "Real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization." ; sc:featureList edam:operation_3559 ; sc:name "GENEASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.cchmc.org/mershalab/GENEASE/login.html" ; biotools:primaryContact "Tesfaye B Mersha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format." ; sc:featureList edam:operation_3197 ; sc:license "Artistic-2.0" ; sc:name "geneAttribution" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/geneAttribution.html" ; biotools:primaryContact "Arthur Wuster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3077, edam:topic_3574 ; sc:citation , "pmcid:PMC5199132", "pubmed:28025344" ; sc:contributor ; sc:description "GeneBase 1.1 is a tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank." ; sc:featureList edam:operation_0338 ; sc:license "Apache-2.0" ; sc:name "GeneBase" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://apollo11.isto.unibo.it/software/GeneBase/GeneBase_1.1/" ; biotools:primaryContact "Maria Chiara Pelleri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2229, edam:topic_3168, edam:topic_3308 ; sc:citation ; sc:description "geneBasisR is a package that selects an optimal targeted gene panel (based on scRNA-seq data) as a function of designated number of genes, and provides evaluation of any selected gene panel on -cell type/-cell and -gene levels. It is a package for gene selection using k-NN graphs." ; sc:featureList edam:operation_3435, edam:operation_3463, edam:operation_3557 ; sc:license "MIT" ; sc:name "geneBasis" ; sc:url "https://github.com/MarioniLab/geneBasisR" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3175 ; sc:citation ; sc:description "Recurrent breakpoint gene detection on copy number aberration profiles." ; sc:featureList edam:operation_3227 ; sc:license "GPL-2.0" ; sc:name "GeneBreak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneBreak.html" ; biotools:primaryContact "Evert van den Broek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3673 ; sc:citation ; sc:description """Variant simulation to improve the diagnosis of Mendelian rare genetic diseases. GeneBreaker - Mendelian Disease Simulator. GeneBreaker is a tool which facilitates the creation of rare genetic disease scenarios, allowing user to make novel variants of multiple classes or draw from databases of known pathogenic events.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:name "GeneBreaker" ; sc:url "http://GeneBreaker.cmmt.ubc.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Web service which allows users to search genes based on their locus tags." ; sc:featureList edam:operation_2422 ; sc:name "GeneByLocusTag" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/TextIDsOrganism/GeneIds/GeneByLocusTag.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_3325, edam:topic_3366, edam:topic_3574 ; sc:citation , , "pubmed:12424129", "pubmed:9097728", "pubmed:9789091" ; sc:description "Database of human genes, their products, and involvement in diseases. It automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:name "GeneCards" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genecards.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_1775, edam:topic_3518 ; sc:citation "pubmed:18480120" ; sc:description "Suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profiling, as well as tools that combine co-expression analysis with BLAST for functional inferencing. Arabidopsis thaliana and Barley are featured plants." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3463, edam:operation_3766 ; sc:name "GeneCAT" ; sc:url "http://genecat.mpg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:36803795" ; sc:description "GENECI (GEne NEtwork Consensus Inference) is a software package whose main functionality consists of an evolutionary algorithm to determine the optimal ensemble of machine learning techniques for genetic network inference based on the confidence levels and topological characteristics of its results." ; sc:featureList edam:operation_2437, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GENECI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AdrianSeguraOrtiz/GENECI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3489 ; sc:citation "pubmed:17594234" ; sc:description "Generalized query application that allows you to specify sophisticated sets of queries and generates a table of the number of bio-related records found for each query. The table can be presented as a Web page or in a standard spreadsheet format that will allow you to view the full output of only those queries that generate an interesting number of records." ; sc:featureList edam:operation_2421 ; sc:name "GeneCite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/wrair/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3063, edam:topic_3518 ; sc:description "This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input." ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "geneClassifiers" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/geneClassifiers.html" ; biotools:primaryContact "R Kuiper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3170, edam:topic_3308, edam:topic_3518, edam:topic_3895 ; sc:citation , , "pmcid:PMC9581002", "pubmed:36227547", "pubmed:36303746" ; sc:description "A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis." ; sc:featureList edam:operation_0314, edam:operation_0571, edam:operation_2436, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GeneCloudOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://combio-sifbi.org/GeneCloudOmics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:19390667" ; sc:description "Computer software which can be used as a tool for exploratory analysis of gene expression microarray data. The development of this software was motivated by surging interest to search for interpretable biological structure in gene expression microarray data." ; sc:featureList edam:operation_0313, edam:operation_2495 ; sc:name "GENECLUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/GENECLUST:Overview" ; biotools:primaryContact "Bradley Broom", "Kim-Anh Do", "Paul Roebuck", "Rumiana Nikolova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:36754847" ; sc:description "GeneClust is a computational feature selection method for scRNA-seq cell clustering. GeneClust groups genes into clusters from which genes are evaluated and selected with the aim of maximizing relevance, minimizing redundancy and preserving complementarity." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3501, edam:operation_3680, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "GeneClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ToryDeng/scGeneClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "GeneCodis is a web-based tool for the ontological analysis of lists of genes, proteins, and regulatory elements like miRNAs, transcription factors, and CpGs." ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3792 ; sc:name "GeneCodis" ; sc:url "https://genecodis.genyo.es" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0659, edam:topic_3518 ; sc:citation "pubmed:19465387", "pubmed:22573175" ; sc:description "Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and modular patterns of interrelated annotations. Noisy and redundant output data has been removed from enrichment results, and greater comparative analyses are possible." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3672 ; sc:name "GeneCodis3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genecodis.cnb.csic.es/" ; biotools:primaryContact "GeneCoDis3 Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:name "Database ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3053 ; sc:citation , "pubmed:34715518" ; sc:description "A web application server for constructing cancer patient-specific gene correlation networks with prognostic gene pairs." ; sc:featureList edam:operation_0337, edam:operation_2454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "GeneCoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://geneconet.inha.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3172, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC9073678", "pubmed:35285473" ; sc:description "GeneCup automatically extracts information from PubMed and NHGRI-EBI GWAS catalog on the relationship of any gene with a custom list of keywords hierarchically organized into an ontology." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GeneCup" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hakangunturkun/GeneCup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0607, edam:topic_0622, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:description "Genedata Expressionist performs efficient and quality compliant analysis of next generation sequencing (NGS) and other genomic profiling data" ; sc:featureList edam:operation_0292, edam:operation_2238, edam:operation_2403, edam:operation_2495, edam:operation_3186, edam:operation_3198, edam:operation_3208, edam:operation_3218, edam:operation_3432, edam:operation_3680 ; sc:name "Genedata Expressionist" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://www.genedata.com/products/expressionist/" ; biotools:primaryContact "Genedata Expressionist Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units)." ; sc:featureList edam:operation_0224 ; sc:name "GeneDB database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Sanger Institute" ; sc:softwareHelp ; sc:url "http://www.genedb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3063, edam:topic_3325 ; sc:citation , "pmcid:PMC2587712", "pubmed:19057649" ; sc:description "Provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. Thus, allowing an interactive and explorative approach to the hunt for the candidate gene." ; sc:featureList edam:operation_2403, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "GeneDistiller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genedistiller.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0634, edam:topic_0749, edam:topic_3068, edam:topic_3577 ; sc:citation , "pubmed:33737208" ; sc:description "GeneDive is a powerful but easy-to-use application that can search, sort, group, filter, highlight, and visualize interactions between drugs, genes, and diseases (DGR). GeneDive also facilitates topology discovery through the various search modes that reveal direct and indirect interactions between DGR." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3625 ; sc:name "GeneDive" ; sc:url "http://www.genedive.net" ; biotools:primaryContact "Anagha Kulkarni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3295, edam:topic_3512, edam:topic_3674 ; sc:citation ; sc:description """an R package for Gene-based Differentially Methylated Regions analysis. Gene-based differentially methylated regions analysis. GeneDMRs is an R package to detect the differentially methylated regions based on genes (DMG), gene body (DMP, DME, DMI), CpG islands and gene body interacted with CpG island features (e.g., DMG/DMP/DME/DMI_CpG island and DMG/DMP/DME/DMI_CpG island shore).""" ; sc:featureList edam:operation_0430, edam:operation_0440, edam:operation_3192, edam:operation_3196, edam:operation_3204 ; sc:license "LGPL-3.0" ; sc:name "GeneDMRs" ; sc:url "https://github.com/xiaowangCN/GeneDMRs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3315 ; sc:citation , "pubmed:33279968" ; sc:description """An interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Gene Circuit Explorer (GeneEx) is a systems-biology tool to visualize and simulate gene regulatory circuits (GRCs).""" ; sc:featureList edam:operation_0337, edam:operation_3566, edam:operation_3927 ; sc:license "MIT" ; sc:name "GeneEx" ; sc:url "https://geneex.jax.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3474, edam:topic_3518, edam:topic_3678 ; sc:citation "pubmed:12618382" ; sc:description "Tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, classification and normalization." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3223 ; sc:name "Gene Expression Data Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.upmc.edu/GE2/GEDA.html" ; biotools:primaryContact "James Lyons-Weiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3179, edam:topic_3518 ; sc:citation , "pubmed:34902129" ; sc:description "An R Package to Facilitate Data Reading from Gene Expression Omnibus (GEO)." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "geneExpressionFromGEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/davidechicco/geneExpressionFromGEO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634 ; sc:citation ; sc:description "This package implements the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. Its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest." ; sc:featureList edam:operation_3463 ; sc:license "GPL-2.0" ; sc:name "GeneExpressionSignature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneExpressionSignature.html" ; biotools:primaryContact "Fei Li", "Lu Han", "Yang Cao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2731 ; sc:name "Protein family ID (GeneFarm)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0780 ; sc:citation ; sc:description "Structural and functionnal annotation of plant gene and protein families by a network of experts." ; sc:featureList edam:operation_0224 ; sc:name "GeneFarm" ; sc:url "http://urgi.versailles.inra.fr/Genefarm/index.htpl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3053, edam:topic_3168, edam:topic_3518 ; sc:citation "pubmed:18370116" ; sc:description "Java based graphical user interface for prediction of gene function using multiple sources of data." ; sc:featureList edam:operation_3672 ; sc:name "GeneFAS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://digbio.missouri.edu/software/genefas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23585840" ; sc:description "Tool that can compute all attractors in synchronous dynamic models and asynchronous dynamic models. It is helpful for biologist to deep understand the genetic regulatory networks." ; sc:featureList edam:operation_1781 ; sc:name "GeneFAtt" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/desheng619/download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3321 ; sc:citation ; sc:description "Some basic functions for filtering genes." ; sc:featureList edam:operation_3695 ; sc:license "Artistic-2.0" ; sc:name "genefilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genefilter.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3053 ; sc:description "GeneFinder is a software package for linkage analysis with a variety of extensions.  GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc." ; sc:featureList edam:operation_0283 ; sc:name "GeneFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.7" ; sc:url "http://people.virginia.edu/~wc9c/genefinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0632, edam:topic_3168, edam:topic_3511 ; sc:citation "pubmed:8877506" ; sc:description "Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences." ; sc:featureList edam:operation_0308, edam:operation_2419, edam:operation_3237 ; sc:name "Genefisher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/genefisher/" ; biotools:primaryContact "R. Giegerich" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1210, edam:format_1219, edam:format_1921, edam:format_1925, edam:format_1929, edam:format_1942, edam:format_1948, edam:format_1982, edam:format_1997, edam:format_2330, edam:format_2555 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1209, edam:format_1210, edam:format_1215, edam:format_1925, edam:format_1927, edam:format_1929, edam:format_1930, edam:format_1942, edam:format_1948, edam:format_2330, edam:format_2332 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1240 ; sc:name "PCR primers" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Chris Schleiermacher", "Daniel Hagemeier", "Thomas Gatter" ; sc:citation "pubmed:8877506" ; sc:description "Based on the assumption that genes with related function from different organisms show high sequence similarity, degenerate primers can be designed from sequences of homologues genes. It is an interactive web-based program for designing degenerate primers." ; sc:featureList edam:operation_0308 ; sc:isAccessibleForFree true ; sc:name "genefisher2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bibiserv.cebitec.uni-bielefeld.de/genefisher2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3314, edam:topic_3318, edam:topic_3512 ; sc:citation "pubmed:11836228", "pubmed:12824434" ; sc:description "Tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA." ; sc:featureList edam:operation_2454, edam:operation_2944 ; sc:name "GeneFizz" ; sc:url "http://pbga.pasteur.fr/GeneFizz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description """Updated co-expression databases and tools for human and mouse genes and transcripts. A guilt-by-association tool to find co-expressed genes and functions. GeneFriends employs a RNAseq based gene co-expression network for candidate gene prioritization, based on a seed list of genes, and for functional annotation of unknown genes in human and mouse.""" ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3672 ; sc:name "GeneFriends" ; sc:url "http://www.genefriends.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3518 ; sc:citation , "pubmed:26607490" ; sc:description "Functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis." ; sc:featureList edam:operation_0282, edam:operation_2495 ; sc:license "Artistic-2.0" ; sc:name "genefu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genefu.html" ; biotools:primaryContact , "Markus Schroeder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203 ; sc:citation ; sc:description "R based genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias. It includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure that this package functions properly." ; sc:featureList edam:operation_0286, edam:operation_2963 ; sc:license "GPL-2.0" ; sc:name "GeneGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneGA.html" ; biotools:primaryContact "Zhenpeng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168 ; sc:citation ; sc:description "The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results." ; sc:featureList edam:operation_0314 ; sc:license "GPL-2.0" ; sc:name "GeneGeneInteR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneGeneInteR.html" ; biotools:primaryContact "Magalie Houee-Bigot", "Mathieu Emily" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0203, edam:topic_3120, edam:topic_3168, edam:topic_3678 ; sc:citation , "pmcid:PMC4086129", "pubmed:24782527" ; sc:description "GeneGenie is an optimised oligomer design web server for doing directed evolution." ; sc:featureList edam:operation_0284, edam:operation_0286, edam:operation_3198 ; sc:name "GeneGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://g.gene-genie.appspot.com" ; biotools:primaryContact "Neil Swainston" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0623, edam:topic_3293 ; sc:citation ; sc:description "GeneGrouper is a command-line tool that finds gene clusters in a set of genomes and bins them into groups of similar gene clusters." ; sc:featureList edam:operation_0553, edam:operation_3432, edam:operation_3663 ; sc:license "MIT" ; sc:name "GeneGrouper" ; sc:url "https://github.com/agmcfarland/GeneGrouper" ; biotools:primaryContact "Erica M. Hartmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_2269, edam:topic_3168 ; sc:citation , "pmcid:PMC10186671", "pubmed:37189023" ; sc:description "R package for gene haplotypic statistics and visualization." ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "geneHapR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitee.com/zhangrenl/genehapr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_2815, edam:topic_3337, edam:topic_3512 ; sc:citation "pubmed:15073007", "pubmed:17545196" ; sc:description "Tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3463 ; sc:name "GeneHub-GEPIS" ; sc:url "http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation "pmcid:PMC1915045", "pubmed:8651312" ; sc:description "Allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is used in exact computation of multipoint LOD scores and in a method of non-parametric linkage analysis. The multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data." ; sc:featureList edam:operation_0283, edam:operation_2429 ; sc:name "GENEHUNTER" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2.1" ; sc:url "http://www.broadinstitute.org/ftp/distribution/software/genehunter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2269, edam:topic_3053 ; sc:citation , , ; sc:description "It is a modification of the GENEHUNTER software package . It allows for a parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. Therefore, a disease model which accounts for imprinting includes four penetrances instead of only three." ; sc:featureList edam:operation_0283 ; sc:name "GENEHUNTER-IMPRINTING" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1r3" ; sc:url "http://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html#c63682" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0114, edam:topic_0654, edam:topic_3321, edam:topic_3511 ; sc:author "Roderic Guigo" ; sc:citation , , "pubmed:18428791" ; sc:contributor , "Tyler Alioto" ; sc:description "Ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Geneid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Centre for Genomic Regulation (CRG), Parc de Recerca Biomedica (PRBB)" ; sc:softwareHelp , ; sc:softwareVersion "1.4.4" ; sc:url "http://genome.crg.es/software/geneid/index.html" ; biotools:primaryContact "Francisco Camara", "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2815, edam:topic_3295, edam:topic_3325, edam:topic_3512 ; sc:citation , , "pmcid:PMC1866410", "pubmed:10079240", "pubmed:10094809" ; sc:description "Catalogue of genes (from different species including human) that contains general information about a gene as well as whether it is imprinted and which allele is expressed." ; sc:featureList edam:operation_2495, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "Geneimprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.geneimprint.com/site/genes-by-species" ; biotools:primaryContact "Dr. Randy L. Jirtle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622, edam:topic_3056, edam:topic_3170, edam:topic_3173, edam:topic_3174, edam:topic_3175, edam:topic_3293 ; sc:citation "pubmed:22543367" ; sc:description "Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research." ; sc:featureList edam:operation_0238, edam:operation_0292, edam:operation_0310, edam:operation_0337, edam:operation_3180, edam:operation_3198, edam:operation_3200, edam:operation_3208, edam:operation_3227 ; sc:name "Geneious" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.geneious.com" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3173, edam:topic_3174, edam:topic_3308 ; sc:citation , "pubmed:33080015" ; sc:description """Interfaces for the exploration of space omics data. The NASA GeneLab Data Processing team and Analysis Working Group members have created standard pipelines for processing omics data from spaceflight and space-relevant experiments. This repository contains the processing pipelines that have been standardized to date for the assay types indicated below.""" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3680 ; sc:name "GeneLab" ; sc:url "https://genelab.nasa.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3071, edam:topic_3678 ; sc:citation ; sc:description "A data management system designed to facilitate genetic studies of complex traits. Genetic analyses of complex traits are challenging, and high quality data-management systems are often critical to the success of these projects. So, we have developed it, that enables genotypic data to be merged easily with pedigree and extensive phenotypic data. It was designed specifically to facilitate large-scale, genetic linkage or association studies and is a powerful tool for complex trait mapping." ; sc:featureList edam:operation_2428, edam:operation_2429, edam:operation_2945 ; sc:name "GeneLink" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.7" ; sc:url "http://research.nhgri.nih.gov/genelink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3169, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:35961023" ; sc:description "A supervised GRN inference framework, GENELink, to predict potential interactions from scRNA-seq data and gene linkage topology." ; sc:featureList edam:operation_0314, edam:operation_2437, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GENELink" ; sc:url "https://github.com/zpliulab/GENELink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:20576703", "pubmed:20926419", "pubmed:23794635" ; sc:description "Web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_2454, edam:operation_3766 ; sc:name "GeneMANIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genemania.org" ; biotools:primaryContact "GeneMANIA team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_1775 ; sc:citation "pubmed:20926419" ; sc:description "The plugin brings fast gene function prediction capabilities to the desktop. It identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data." ; sc:featureList edam:operation_0314, edam:operation_2454, edam:operation_3439 ; sc:name "GeneMania Cytoscape plugin" ; sc:url "http://www.genemania.org/plugin/" ; biotools:primaryContact "Gary Bader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation , ; sc:description "A family of gene prediction programs: Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes; Gene Prediction in Eukaryotes; Gene Prediction in Transcripts; Gene Prediction in Viruses, Phages and Plasmids." ; sc:featureList edam:operation_2454 ; sc:name "GeneMark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://exon.gatech.edu/GeneMark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3174, edam:topic_3320, edam:topic_3512, edam:topic_3941 ; sc:citation ; sc:description """Eukaryotic gene prediction with self-training in the space of genes and proteins. Experiments for ProtHint and GeneMark-EP/EP+ projects.""" ; sc:featureList edam:operation_0310, edam:operation_2454, edam:operation_3092 ; sc:name "GeneMark-EP" ; sc:url "http://topaz.gatech.edu/GeneMark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3174, edam:topic_3673, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC8153819", "pubmed:34056597" ; sc:description """GeneMark-HM is a pipeline for protein coding gene prediction in assembled metagenomes from human microbiome (HM). Pipeline integrates three algorithms from GeneMark gene finder family, MetaGeneMark-2, GeneMarkS-2 and Genemark.hmm-2, into a workflow with parameters optimized for analysis of human metagenomes.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "GeneMark-HM" ; sc:url "http://exon.gatech.edu/GeneMark/hmmchoice.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_2229, edam:topic_3053, edam:topic_3170 ; sc:citation , "pmcid:PMC8577352", "pubmed:34764987" ; sc:description "A Database and User Interface for scRNA-seq Marker Genes." ; sc:featureList edam:operation_2422, edam:operation_2454, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GeneMarkeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny.ph.iu.edu/GeneMarkeR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0622, edam:topic_3321 ; sc:citation "pubmed:26220891" ; sc:description "Web site designed to enable connections between clinicians and researchers from around the world who share an interest in the same gene or genes." ; sc:featureList edam:operation_2478 ; sc:name "GeneMatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.genematcher.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0798, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description """An R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. GeneMates: an R package identifying horizontal gene co-transfer between bacteria.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3659 ; sc:license "Apache-2.0" ; sc:name "GeneMates" ; sc:url "http://github.com/wanyuac/GeneMates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "A collection of meta-analysis tools for analysing high throughput experimental data." ; sc:featureList edam:operation_2403 ; sc:license "Artistic-2.0" ; sc:name "GeneMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneMeta.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:17683609" ; sc:description "Package for analyzing gene expression (time series) data with focus on the inference of gene networks." ; sc:featureList edam:operation_3083 ; sc:name "GeneNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://strimmerlab.org/software/genenet/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:25319962" ; sc:description "Assess connectivity among a set of genes of interest (‘seed-genes’) within a biological network of their choosing." ; sc:featureList edam:operation_2495, edam:operation_2497 ; sc:name "GeneNet Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://avigailtaylor.github.io/gntat14/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26886731" ; sc:description "Software to qualitatively infer dynamic gene regulatory interactions from gene expression data. From the time-series data of gene expression, the software identifies not only gene regulatory interactions but also the temporal aspects of the regulatory interactions using two types of scores, R1 and R2. As for the temporal aspect of gene regulatory relations, it identifies the order of the gene regulatory relations and the pace of the relations." ; sc:featureList edam:operation_1781 ; sc:name "GeneNetFinder" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bclab.inha.ac.kr/GeneNetFinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3308 ; sc:citation , "pubmed:33712625" ; sc:description "GeneNetFusion is a computatinal pipeline for the construction of fused co-expression networks and the extraction of relevant gene biomarkers." ; sc:name "GeneNetFusion" ; sc:url "https://github.com/DEIB-GECO/GeneNetFusion" ; biotools:primaryContact "Marco Masseroli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC9665865", "pubmed:36179082" ; sc:description "Tests for Gaussian graphical models with shrinkage." ; sc:featureList edam:operation_0314, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GeneNetTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/V-Bernal/GeneNetTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0602, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:25295303" ; sc:description "Java application for network analysis. The application uses the metabolic pathways stored in kegg to rate the validity of an input network." ; sc:featureList edam:operation_2497 ; sc:name "GeneNetVal" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://fgomezvela.github.io/GeneNetVal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3055, edam:topic_3295, edam:topic_3298, edam:topic_3512 ; sc:citation ; sc:description """A continuously updated tool for systems genetics analyses. GeneNetwork displays the additive values on the far right of many trait QTL maps, usually as red or green lines along the maps.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3359, edam:operation_3891 ; sc:name "GeneNetwork" ; sc:url "http://genenetwork.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3169 ; sc:citation ; sc:description "Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, this tool generates a regulatory network of the TF." ; sc:featureList edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "GeneNetworkBuilder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html" ; biotools:primaryContact "Jianhong Ou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_2640, edam:topic_3382, edam:topic_3966 ; sc:citation , "pubmed:36999902" ; sc:description "Bioinformatics toolbox for genomics-guided neoepitope prediction." ; sc:featureList edam:operation_0560, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "GeNeo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://neo.engr.uconn.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Test two sets of gene lists and visualize the results." ; sc:featureList edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "GeneOverlap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneOverlap.html" ; biotools:primaryContact "Mount Sinai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3053, edam:topic_3321, edam:topic_3512 ; sc:citation "pubmed:25434742" ; sc:description "Standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats." ; sc:featureList edam:operation_2478 ; sc:name "GenePainter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.motorprotein.de/genepainter.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:15223345" ; sc:description "Genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. 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Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies." ; sc:featureList edam:operation_0337 ; sc:name "Genes2WordCloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.maayanlab.net/G2W/create_wordcloud.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157 ; sc:description "Web service that retrieves all genes whose encoding protein has an epitope identified by the Immune Epitope Database and Analysis Resource with the confidence specified by the user." ; sc:featureList edam:operation_0236, edam:operation_2403 ; sc:name "Genes by Epitopes Presence" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/Proteinfeatures/epitopepresence/GenesWithEpitopes.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0157 ; sc:description "Web service that retrieves all genes whose protein product has an isoelectric point in a range that user specify." ; sc:featureList edam:operation_0236 ; sc:name "Genes by Isoelectric Point" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/contact.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157 ; sc:description "Web service that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify." ; sc:featureList edam:operation_0236, edam:operation_2479 ; sc:name "Genes by Molecular Weight" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/Proteinattribute/molecularweight/GeneByMolecularWeight.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "A web service which allows users to search genes based on an organism or a list of organisms." ; sc:featureList edam:operation_2422 ; sc:name "Genes by Organism" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/TextIDsOrganism/Organism/GenesByTaxon.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157 ; sc:description "Web service which allows users to search genes based on organism and other criteria such as minimum signalp sum score, minimum signalp D score and minimum signalp probability." ; sc:featureList edam:operation_0236, edam:operation_2479 ; sc:name "Genes by Predicted Signal Peptide" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/Proteinfeatures/predictedsignalpeptide/GenesWithSignalPeptide.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:description "Web service that retrieves all genes having number of predicted transmembrane domains in a range that user specify." ; sc:featureList edam:operation_2479 ; sc:name "Genes by Transmembrane Domain Count" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mango.ctegd.uga.edu/jkissingLab/SWS/ToxodbAnnotatedWebservices/SearchForGenes/Proteinfeatures/transmembranedomaincount/GenesByTransmembraneDomains.sawadl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2533 ; sc:citation "pubmed:21037276" ; sc:description "Tool for high-throughput detection and annotation of rare sequence variants. Although analysis of sequence electropherograms can be done by eye, this is very laborious and error-prone, especially when analyzing large volumes of data." ; sc:featureList edam:operation_0484 ; sc:name "GeneScreen" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/genescreen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2815, edam:topic_3053, edam:topic_3574 ; sc:citation "pubmed:15980578" ; sc:description "Allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases." ; sc:featureList edam:operation_0314, edam:operation_2421 ; sc:name "GeneSeeker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.cmbi.ru.nl/GeneSeeker/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:36355333" ; sc:description "This web-tool enables the researchers to find differentially expressed genes using different machine learning algorithms." ; sc:featureList edam:operation_0337, edam:operation_2454, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GeneSelectML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.softmed.hacettepe.edu.tr/GeneSelectML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Gene selection based on a mixture of marginal distributions." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "GeneSelectMMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneSelectMMD.html" ; biotools:primaryContact "Weiliang Qiu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053 ; sc:citation ; sc:description "Filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list. The stability of the findings can be considered in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods to find a synthesis." ; sc:featureList edam:operation_2495, edam:operation_3695 ; sc:license "GPL-2.0" ; sc:name "GeneSelector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneSelector.html" ; biotools:primaryContact "Martin Slawski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621, edam:topic_0780, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:12824374", "pubmed:14681433", "pubmed:16219921" ; sc:description "Method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes." ; sc:featureList edam:operation_0433, edam:operation_0476, edam:operation_0526, edam:operation_2454 ; sc:name "GeneSeqer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.plantgdb.org/search/misc/PublicPlantSeq.php" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description "The Ensembl GeneTrees pipeline as a Galaxy workflow." ; sc:featureList edam:operation_0291, edam:operation_0323, edam:operation_0492 ; sc:license "MIT" ; sc:name "GeneSeqToFamily" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily" ; biotools:primaryContact "Anil S Thanki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0659, edam:topic_3518 ; sc:citation "pubmed:19420064" ; sc:description "GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output." ; sc:featureList edam:operation_0314, edam:operation_0443, edam:operation_2436, edam:operation_2454, edam:operation_3223 ; sc:name "GeneSet2miRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.helmholtz-muenchen.de/proj/gene2mir/" ; biotools:primaryContact "GeneSet2miRNA Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3179, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC7542881", "pubmed:33028195" ; sc:description """A tool for summarizing and integrating gene-set analysis results. Gene-set analysis (GSA) tools aim to provide biological context by identifying gene-sets associated with a given trait or traits of interest. Gene-set analysis tools are frequently gene-centric, using as input results from studies using RNA-seq or microarrays data (e.g. Ingenuity or GSEA among many others), but it has also been adapted for interval-based analysis derived from data-types such as DNA methylation or ChIP/ATAC-seq.""" ; sc:featureList edam:operation_2436, edam:operation_2938, edam:operation_3432, edam:operation_3642 ; sc:license "GPL-3.0" ; sc:name "GeneSetCluster" ; sc:url "https://github.com/TranslationalBioinformaticsUnit/GeneSetCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation "pubmed:19834153" ; sc:description "This tool builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts." ; sc:featureList edam:operation_0571, edam:operation_2495 ; sc:name "GeneShelf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hcil.snu.ac.kr/research/geneshelf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3512 ; sc:citation "pubmed:19934259", "pubmed:22110038" ; sc:description "Manually curated database of gene expression signatures. It focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcribe gene signatures. Gene signatures are mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. It provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232, edam:operation_3501 ; sc:name "GeneSigDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.dfci.harvard.edu/genesigdb" ; biotools:primaryContact "John Quackenbush" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC9987115", "pubmed:36879282" ; sc:description "Influence network model uncovers relations between biological processes and mutational signatures." ; sc:featureList edam:operation_0314, edam:operation_3280, edam:operation_3660, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "GENESIGNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ncbi/GeneSigNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:12824313" ; sc:description "GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers." ; sc:featureList edam:operation_0267, edam:operation_0268, edam:operation_0474, edam:operation_3350 ; sc:name "GeneSilico" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://genesilico.pl/meta2/" ; biotools:primaryContact "Lukasz Kozlowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a PCA on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "GENESIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GENESIS.html" ; biotools:primaryContact "Matthew P. Conomos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation "pubmed:11836235" ; sc:description "Various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines." ; sc:featureList edam:operation_2495 ; sc:name "Genesis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.tugraz.at/genesisclient/genesisclient_description.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3444, edam:topic_3520 ; sc:citation , "pmcid:PMC9082496", "pubmed:35050622" ; sc:description "GENESIS (GENEration of Supersequences In Silico) systematically generates pulse programs for arbitrary NOAH supersequences compatible with Bruker spectrometers." ; sc:featureList edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GENESIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nmr-genesis.co.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Collates data from bioinformatics resources and provides automated gene-centric annotations." ; sc:featureList edam:operation_2422 ; sc:name "geneSmash" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://app1.bioinformatics.mdanderson.org/genesmash/_design/basic/api.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2805 ; sc:name "GeneSNP ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815, edam:topic_2885 ; sc:description "Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies." ; sc:featureList edam:operation_0224 ; sc:name "GeneSNPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.utah.edu/genesnps/" ; biotools:primaryContact "Colleen Davis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797 ; sc:citation ; sc:description "GENESPACE: an R package for synteny- and orthology-constrained comparative genomics" ; sc:featureList edam:operation_2403, edam:operation_3182 ; sc:name "GENESPACE" ; sc:url "https://github.com/jtlovell/GENESPACE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3320 ; sc:citation "pubmed:11222768" ; sc:description "A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice." ; sc:featureList edam:operation_0433, edam:operation_2454, edam:operation_2499 ; sc:name "GeneSplicer" ; sc:operatingSystem "Linux" ; sc:url "http://cbcb.umd.edu/software/GeneSplicer/" ; biotools:primaryContact "GeneSplicer team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654 ; sc:citation "pubmed:22962453" ; sc:description "Tool to assemble genes using network matching algorithm. Given an already-assembled dataset, it is capable of assembling contigs together to form more complete genes with the help of a reference gene set. Currently the assembly software that is supported SOAPdenovo." ; sc:featureList edam:operation_0525 ; sc:name "GeneStitch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://omics.informatics.indiana.edu/GeneStitch/" ; biotools:primaryContact "Yu-Wei Wu", "Yuzhen Ye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3321 ; sc:citation "pubmed:26055097" ; sc:description "Mobile application that provides users with a synopsis regarding the information of human genes from various points of view. Synopsis is given as a little story, while, users may perform queries regarding a gene of interest. It is developed for Android and provides general, functional, clinical and network information for known and predicted human genes." ; sc:featureList edam:operation_2421 ; sc:name "GeneStoryTeller" ; sc:softwareHelp ; sc:url "http://bioserver-3.bioacademy.gr/Bioserver/GeneStoryTeller/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:description "It can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products." ; sc:featureList edam:operation_1777, edam:operation_2499 ; sc:license "BSD-3-Clause" ; sc:name "GeneStructureTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneStructureTools.html" ; biotools:primaryContact "Beth Signal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:22826540" ; sc:description "Web-based platform, that can filter, reduce and prioritize human sequence variants from NGS data and assist in the interpretation of personal variants in clinical context." ; sc:featureList edam:operation_0337, edam:operation_2403, edam:operation_3187, edam:operation_3197, edam:operation_3225, edam:operation_3227 ; sc:name "GeneTalk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.gene-talk.de" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634 ; sc:citation , "pmcid:PMC4460584", "pubmed:26040557" ; sc:description "Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier." ; sc:featureList edam:operation_2995 ; sc:license "GPL-2.0" ; sc:name "geNetClassifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/geNetClassifier.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0769, edam:topic_0798, edam:topic_3170 ; sc:citation ; sc:description """A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data. GeneTEFlow is a reproducible and platform-independent workflow for the comprehensive analysis of gene and locus-specific TEs expression from RNA-Seq data using Nextflow and Docker technologies.""" ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_3192, edam:operation_3223, edam:operation_3800 ; sc:name "GeneTEFlow" ; sc:url "https://github.com/zhongw2/GeneTEFlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0625, edam:topic_3500, edam:topic_3673 ; sc:citation ; sc:description """A customizable multilayer approach to genomic variant prioritization and interpretation. GeneTerpret: a new way to interpret and visualize genomic variants data. GeneTerpret: a new way to interpret and visualize genomic variants dataGeneTerpret: a new way to interpret and visualize genomic variants dataGeneTerpret: a new way to interpret and visualize genomic variants data.""" ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:name "GeneTerpret" ; sc:url "https://geneterpret.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3063 ; sc:citation "pmcid:PMC1525324", "pubmed:16888670" ; sc:description "A medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons." ; sc:featureList edam:operation_0282, edam:operation_1812, edam:operation_2429, edam:operation_3096, edam:operation_3224 ; sc:name "GeneTests" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.geneclinics.org/" ; biotools:primaryContact "Roberta A. Pagon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2640, edam:topic_3063, edam:topic_3077 ; sc:citation , "pmcid:PMC8476929", "pubmed:34595403" ; sc:description "GENomics Report TEXt mining R package and Shiny application designed to capture real-world clinico-genomic data." ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GENETEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TheMillerLab/genetex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0623 ; sc:citation ; sc:description "Allows searching information in GenBank and also in other NCBI databases through the interactive orchestration of NCBI Web services." ; sc:featureList edam:operation_2421 ; sc:name "Genetic Revision" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zti.polsl.pl/dmrozek/science/sgb/sgb.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:34506278" ; sc:description "Automatically Designed Deep Networks for Retinal Vessel Segmentation Using a Genetic Algorithm." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Genetic U-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/96jhwei/Genetic-U-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "This package contains functions useful for designing genetics studies, including power and sample-size calculations." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "GeneticsDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneticsDesign.html" ; biotools:primaryContact "The R Genetics Project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities." ; sc:featureList edam:operation_0324 ; sc:license "GPL-2.0" ; sc:name "GeneticsPed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GeneticsPed.html" ; biotools:primaryContact "David Henderson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3321 ; sc:citation "pubmed:25861967" ; sc:description "This tool replaces the knowledge-based inference traditionally used in candidate disease gene prioritization, instead using experimental data from tissue-specific gene expression data sets." ; sc:featureList edam:operation_2495 ; sc:name "GeneTIER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dna2.leeds.ac.uk:8080/expression/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3337, edam:topic_3958 ; sc:citation , "pmcid:PMC10584998", "pubmed:37853040" ; sc:description "An alignment-free method for gene copy number estimation directly from next-generation sequencing reads." ; sc:featureList edam:operation_3196, edam:operation_3233, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GeneToCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bioinfo-ut/GeneToCN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1904 ; sc:name "Locus ID (EntrezGene)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3174, edam:topic_3342 ; sc:citation , "pmcid:PMC9332626", "pubmed:35892968" ; sc:description "A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "GeneToList" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.genetolist.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2331 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation "pubmed:17526521" ; sc:description "GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes." ; sc:featureList edam:operation_2436 ; sc:name "GeneTrail" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetrail.bioinf.uni-sb.de/index.php" ; biotools:primaryContact "GeneTrail Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2331 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation , "pubmed:26787660" ; sc:description "GeneTrail 2 is a web-interface providing access to different tools for the statistical analysis of molecular signatures. GeneTrail2 allows the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results." ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:name "GeneTrail2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "lumc.nl" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://genetrail2.bioinf.uni-sb.de/" ; biotools:primaryContact "Prof. Dr. Hans-Peter Lenhof" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0208, edam:topic_0602, edam:topic_0736 ; sc:citation ; sc:description """Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses. Reranked gene lists. Our final product is the set of top genes defined by (Def. def-genetrank), possibly accumulated over several values of the restart rate (Def. eq-topkler).""" ; sc:featureList edam:operation_2436, edam:operation_2437, edam:operation_3223 ; sc:name "GENetRank" ; sc:url "https://sbl.inria.fr/doc/Genetrank-user-manual.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_2533, edam:topic_3293 ; sc:citation "pubmed:10792974" ; sc:description "Software for the estimation of mutation, migration and growth rates, and ancestral inference such as the time to the most recent common ancestor of a sample of DNA sequences." ; sc:featureList edam:operation_0323 ; sc:name "Genetree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.stats.ox.ac.uk/~griff/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769, edam:topic_0780, edam:topic_3293 ; sc:citation , "pubmed:32979565" ; sc:description """A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. Multilevel homolog-identification pipeline.""" ; sc:featureList edam:operation_0310, edam:operation_0553, edam:operation_3663 ; sc:name "GeneTribe" ; sc:url "https://chenym1.github.io/genetribe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3324, edam:topic_3335 ; sc:citation ; sc:description """Mining transcriptomics and clinical data reveals ACE2 expression modulators and identifies cardiomyopathy as a risk factor for mortality in COVID-19 patients. GENEVA allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contains conditions modulating a gene or a gene signature. See the Help page fore more detail.""" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3223 ; sc:name "GENEVA" ; sc:url "http://genevatool.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2085 ; sc:encodingFormat edam:format_2331 ; sc:name "Structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0219, edam:topic_0654 ; sc:author "WurmLab" ; sc:citation , "pmcid:PMC4866521", "pubmed:26787666" ; sc:description "Tool to identify problematic gene predictions based on comparisons between gene predictions and similar sequences in public databases (e.g., SwissProt)." ; sc:featureList edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "GeneValidator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "1.6.12" ; sc:url "https://wurmlab.github.io/tools/genevalidator/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622, edam:topic_3360 ; sc:citation ; sc:description "High performance search engine for gene expression. It integrates thousands of manually curated, well described public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts such as diseases, drugs, tissues, cancers, cell lines or genotypes. The high diversity of curated experiments allows the tool to project your genes or your data against a broad spectrum of reference profiles and datasets." ; sc:featureList edam:operation_0224, edam:operation_0571, edam:operation_2495, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "Genevestigator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genevestigator.com/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2885, edam:topic_3068 ; sc:citation "pubmed:22693219" ; sc:description "Webserver that lets you search scientific articles using keywords and identifiers for specific biological entities. It has advanced features like: recognizing biological entities like genes and SNPs." ; sc:featureList edam:operation_0305, edam:operation_3280, edam:operation_3501, edam:operation_3778 ; sc:name "GeneView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bc3.informatik.hu-berlin.de/" ; biotools:primaryContact "GeneView Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:description "A native genome browser for the iPad/iPhone.The genome at your fingertips (literally): Tap, scroll and pinch your way through the chromosomes, genes and genomic data." ; sc:featureList edam:operation_3208 ; sc:name "GeneWall Genome Browser" ; sc:operatingSystem "Mac" ; sc:softwareVersion "3.0.1" ; sc:url "http://www.wobblebase.com/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625, edam:topic_3518, edam:topic_3678 ; sc:citation "pubmed:22080549" ; sc:description "Curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes." ; sc:featureList edam:operation_3224, edam:operation_3232, edam:operation_3436, edam:operation_3501 ; sc:name "GeneWeaver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ontologicaldiscovery.org/" ; biotools:primaryContact "Elissa J. Chesler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Ewan Birney" ; sc:citation , ; sc:description "Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors." ; sc:featureList edam:operation_0491, edam:operation_0495 ; sc:name "GeneWise (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/psa/genewise" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3519 ; sc:description "GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis." ; sc:featureList edam:operation_0308, edam:operation_2409, edam:operation_2945, edam:operation_3096 ; sc:name "GenEx" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "6.0.1" ; sc:url "http://www.gene-quantification.de/genex.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_3489 ; sc:citation , "pmcid:PMC6836710", "pubmed:31697362" ; sc:description """Enabling semantic queries across federated bioinformatics databases. Ontology Documentation generated by WIDOCO. Gene expression (GenEx) semantic model.""" ; sc:featureList edam:operation_0224, edam:operation_3282 ; sc:name "GenEx_ontology" ; sc:url "https://biosoda.github.io/genex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0602, edam:topic_3053, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC5899412", "pubmed:29653518" ; sc:description "Tool to infer or validate genetic networks based on expression time series data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "Genexpi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/cas-bioinf/genexpi/wiki" ; biotools:primaryContact "Martin Modrák" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation ; sc:description "This tool annotates a histone modification ChIP-seq peak input file with functionally important genomic features (e.g., genes associated with peaks) based on optimization calculations. It extends the boundaries of every gene in a genome by some distance in DNA base pairs, incorporating cis-regulatory elements (CREs), such as enhancers and promoters, as well as downstream elements that are important to the function of the gene relative to an epigenetic histone modification ChIP-seq dataset." ; sc:featureList edam:operation_0361 ; sc:license "GPL-3.0" ; sc:name "geneXtendeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/geneXtendeR.html" ; biotools:primaryContact "Bohdan Khomtchouk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_3500, edam:topic_3512 ; sc:citation "pubmed:16925843" ; sc:description "Highly reconfigurable gene finder written in C++. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well." ; sc:featureList edam:operation_0430, edam:operation_2454, edam:operation_3197, edam:operation_3223 ; sc:name "GeneZilla" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.genezilla.org" ; biotools:primaryContact "Bill Majoros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3297 ; sc:citation ; sc:description "Geniac is an automatic configuration generator and Installer for nextflow pipelines. With the advent of high-throughput biotechnological platforms and their ever-growing capacity, life science has turned into a digitized, computational and data-intensive discipline. As a consequence, standard analysis with a bioinformatics pipeline in the context of routine production has become a challenge such that the data can be processed in real-time and delivered to the end-users as fast as possible. The usage of workflow management systems along with packaging systems and containerization technologies offer an opportunity to tackle this challenge. While very powerful, they can be used and combined in multiple ways thus increasing their usage complexity" ; sc:featureList edam:operation_1812 ; sc:license "CECILL-2.1" ; sc:name "Geniac" ; sc:url "https://geniac.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "Analyze English sentences and output the base forms, part-of-speech tags, chunk tags, and named entity tags. The tagger is specifically tuned for biomedical text such as MEDLINE abstracts." ; sc:featureList edam:operation_0306 ; sc:name "geniatagger" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.nactem.ac.uk/tsujii/GENIA/tagger/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1088 ; sc:name "Article ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1869 ; sc:name "Organism identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "Genes prioritization for topics of interest using gene-related PubMed abstracts." ; sc:featureList edam:operation_0305 ; sc:name "Genie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm.uni-mainz.de/medlineranker" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:description "An Open Source MPEG-G Codec to compress and decompress FASTQ-files." ; sc:isAccessibleForFree true ; sc:name "Genie" ; sc:url "https://github.com/mitogen/genie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3474 ; sc:citation "pubmed:20927193" ; sc:description "Algorithm for the inference of gene regulatory networks from expression data. 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The interaction with the Genomatix Pathway System enables to explore networks of affected genes and allows for an in-depth assessment of the biological background of variants under investigation." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3661 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "GeneGrid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://genegrid.genomatix.com/grid/home" ; biotools:primaryContact "Contact Form", "GeneGrid Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3293, edam:topic_3305, edam:topic_3697 ; sc:citation ; sc:description """Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. Tools for sampling viral genomes across time of isolation, location of isolation, and genome divergence.""" ; sc:featureList edam:operation_0337, edam:operation_0496, edam:operation_3096 ; sc:license "BSD-3-Clause" ; sc:name "genome-sampler" ; sc:url "https://caporasolab.us/genome-sampler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3316 ; sc:citation , "pmcid:PMC6744645", "pubmed:31519212" ; sc:description "A practical guide to sketching algorithms for processing the flood of genomic data | online notebooks for a review of genome sketching" ; sc:featureList edam:operation_0524, edam:operation_3431, edam:operation_3472 ; sc:license "MIT" ; sc:name "genome-sketching" ; sc:url "https://github.com/will-rowe/genome-sketching" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3474 ; sc:citation "pubmed:20835884" ; sc:description "Genome-wide evaluation under a multiple variance component model by using the maximum likelihood (ML) method and the MCMC implemented Bayesian method." ; sc:featureList edam:operation_2403 ; sc:name "Genome-wide Evaluation" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://statgen.ucr.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:citation , "pubmed:35696018" ; sc:description "Genome2OR is a genetic annotation tool based on HMMER, MAFFT and CD-HIT." ; sc:featureList edam:operation_0226, edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Genome2OR" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/ToHanwei/Genome2OR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0798 ; sc:citation , "pmcid:PMC4744444", "pubmed:26855675" ; sc:description "Genome ARTIST is a pairwise gapped aligner tool which works out issues in mapping the hits of artificial transposons at nucleotide lever accuracy in insertion mutagenesis experiments." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "Genome ARTIST" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.19" ; sc:url "http://www.genomeartist.ro/index.html" ; biotools:primaryContact "Alexandru Al. Ecovoiu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3053, edam:topic_3315 ; sc:citation "pubmed:11483581" ; sc:description "Python/pyrex implementation of the Bayesian classifier of genomic signatures." ; sc:featureList edam:operation_2451, edam:operation_2995 ; sc:name "Genome Classifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sandberg.cmb.ki.se/genomeclass/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2259 ; sc:citation ; sc:description "Open source and high-performance HTML5 web-based genome browser. It allows to browse several genomes and annotations by fetching data from CellBase high-performance REST web services. Custom data (BAMs, VCFs, ...) can also be loaded from remote servers and local disk by using OpenCGA server." ; sc:featureList edam:operation_3208 ; sc:name "Genome Maps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "cipf.es", "http://bioinfo.cipf.es" ; sc:softwareHelp , ; sc:softwareVersion "3" ; sc:url "http://www.genomemaps.org/" ; biotools:primaryContact "babelomics@cipf.es (Francisco García)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0654, edam:topic_3047, edam:topic_3070 ; sc:citation "pubmed:19166610" ; sc:description "Searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk." ; sc:featureList edam:operation_3208 ; sc:name "Genome Projector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.g-language.org/GenomeProjector/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Genome Search Toolkit is a set of scripts for managing massive local homology searches." ; sc:featureList edam:operation_2421 ; sc:name "Genome Search Toolkit" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "0.2.1" ; sc:url "http://kirill-kryukov.com/study/tools/gst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3175 ; sc:citation ; sc:description "Discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals. It looks both across and within a set of sequenced genomes to detect variation. The methods are adaptive and support heterogeneous data sets. A minimum of 20 to 30 genomes are required to get acceptable results, but the method gains power across genomes and processing more genomes provide better results." ; sc:featureList edam:operation_3197, edam:operation_3228 ; sc:license "Not licensed" ; sc:name "Genome STRiP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://software.broadinstitute.org/software/genomestrip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0749 ; sc:citation "pubmed:21593125" ; sc:description "Tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_3208 ; sc:name "Genome Surveyor" ; sc:url "http://veda.cs.uiuc.edu/gs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0623, edam:topic_2885, edam:topic_3293 ; sc:citation , "pmcid:PMC6868693", "pubmed:31752672" ; sc:description """Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes. The draft genomes now can be analyzed. Initiate the GTN with "gtn_CompleteOnly.pl" if your data consist of complete genomes only, or utilize "gtn_WithDraft.pl". The GTN firstly locates the synteny block in genomes if draft data exist. The Markov Cluster Algorithm is introduced to assign the gene families. The Markov Cluster (MCL) Algorithm is introduced in this version. This algorithm is also used in many clustering tool, such as orthoMCL,. Unique gene connection information will be yielded as a result file.""" ; sc:featureList edam:operation_0323, edam:operation_0551, edam:operation_0552, edam:operation_0557, edam:operation_3432 ; sc:name "genome topology network" ; sc:url "https://github.com/0232/Genome_topology_network" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0204, edam:topic_1775, edam:topic_3175 ; sc:description "A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline." ; sc:featureList edam:operation_0338, edam:operation_0361, edam:operation_2409, edam:operation_3197 ; sc:name "Genome Trax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biobase-international.com/product/genome-trax" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_0622, edam:topic_2815 ; sc:citation ; sc:description "Visualize chromosomal abnormalities in the Human Genome using a U-shape layout." ; sc:featureList edam:operation_3197, edam:operation_3208 ; sc:name "Genome U-Plot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/gaitat/GenomeUPlot" ; biotools:primaryContact "George Vasmatzis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Genome Alignment Tools are tools for improving the sensitivity and specificity of genome alignments." ; sc:featureList edam:operation_0292, edam:operation_0491 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Genome Alignment Tools" ; sc:url "https://github.com/hillerlab/GenomeAlignmentTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622, edam:topic_3053, edam:topic_3168, edam:topic_3673, edam:topic_3676 ; sc:description "A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud." ; sc:featureList edam:operation_0337, edam:operation_0564, edam:operation_3184, edam:operation_3227 ; sc:name "GenomeBrowse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.goldenhelix.com/GenomeBrowse/index.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """GenomeChronicler. An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing. singularity container and workflow management.""" ; sc:featureList edam:operation_2422, edam:operation_2939, edam:operation_3196, edam:operation_3227, edam:operation_3431 ; sc:license "MIT" ; sc:name "GenomeChronicler" ; sc:url "https://singularity-hub.org/collections/3664" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_3464 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0625 ; sc:citation , "pmcid:PMC5210668", "pubmed:27789686" ; sc:contributor "Michael Boutros" ; sc:description "Database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "GenomeCRISPR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genomecrispr.dkfz.de" ; biotools:primaryContact "Ulrike Hardeland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:26093150" ; sc:description "SVG based genome viewer written in javascript using D3." ; sc:featureList edam:operation_3208 ; sc:name "GenomeD3Plot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/brinkmanlab/GenomeD3Plot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation ; sc:description "Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint." ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "Genomedata" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://noble.gs.washington.edu/proj/genomedata/" ; biotools:primaryContact "Jay Hesselberth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0622 ; sc:citation ; sc:description "Software for comparing contact maps from HiC, CaptureC and other 3D genome data." ; sc:featureList edam:operation_3209 ; sc:name "GenomeDISCO" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/kundajelab/genomedisco" ; biotools:primaryContact "Anshul Kundaje", "Oana Ursu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3418, edam:topic_3676 ; sc:citation ; sc:description """A platform for phenotype-guided medical genomic diagnosis. Genomic and Phenotypic filters for the Genome Diver project.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3695, edam:operation_3920 ; sc:name "GenomeDiver" ; sc:url "https://github.com/GenomeDiver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This tool uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. Genomic information is plotted together with your data. Plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system." ; sc:featureList edam:operation_3208 ; sc:license "Artistic-2.0" ; sc:name "GenomeGraphs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html" ; biotools:primaryContact "Steffen Durinck" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0987 ; sc:encodingFormat edam:format_2330 ; sc:name "Chromosome name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0987 ; sc:encodingFormat edam:format_2330 ; sc:name "Chromosome name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., \"chr1\" versus \"1\"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order." ; sc:featureList edam:operation_2409, edam:operation_3282 ; sc:license "Artistic-2.0" ; sc:name "GenomeInfoDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'." ; sc:featureList edam:operation_3197 ; sc:license "Artistic-2.0" ; sc:name "genomeIntervals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genomeIntervals.html" ; biotools:primaryContact "Julien Gagneur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3577 ; sc:citation ; sc:description "Genome browser specialized in next-generation sequencing data. Advantages are intuitive interface and smooth drag'n drop response." ; sc:featureList edam:operation_0337 ; sc:name "GenomeJack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genomejack.net/english/gj_browser.html" ; biotools:primaryContact "GenomeJack Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622 ; sc:citation "pubmed:19761611" ; sc:description "A short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single reference." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:name "GenomeMapper" ; sc:operatingSystem "Linux" ; sc:url "http://1001genomes.org/software/genomemapper.html" ; biotools:primaryContact "Korbinian Schneeberger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_0654 ; sc:citation "pubmed:25697648" ; sc:description "Mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs." ; sc:featureList edam:operation_0308, edam:operation_3218 ; sc:name "GenomeMasker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ut.ee/?page_id=167" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0602 ; sc:citation "pubmed:12539951", "pubmed:9697222" ; sc:description "Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W)." ; sc:featureList edam:operation_0224, edam:operation_0253, edam:operation_0276, edam:operation_2421 ; sc:name "GenomeNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genome.ad.jp/" ; biotools:primaryContact "Feedback Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3173, edam:topic_3676 ; sc:citation , "pmcid:PMC7884056", "pubmed:33434514" ; sc:description "Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint." ; sc:featureList edam:operation_0314, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "GenomePaint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://genomepaint.stjude.cloud/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3070 ; sc:citation ; sc:description "Tool that permits multi-level partitioning of large scale DNA constructs for synthetic biology applications. The partitioning algorithm fragments large DNA sequences into smaller, fabricable DNA blocks sharing flanking homologies for in vitro and in vivo DNA assembly. Overlapping homology regions between adjacent DNA blocks are optimized to remove hairpin, sequence repeats and any pattern that interferes with the DNA assembly process. Segments, blocks and sub-blocks that build the blueprint for hierarchical DNA assembly are listed in a GenBank output file." ; sc:featureList edam:operation_2478 ; sc:name "GenomePartitioner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://christenlab.ethz.ch/GenomePartitioner/upload_form_v6.php" ; biotools:primaryContact "Beat Christen", "Matthias Christen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "The goal is to have a simple and straightforward way to download and use genomic sequences. Currently, genomepy supports UCSC, Ensembl and NCBI." ; sc:name "genomepy" ; sc:url "https://github.com/vanheeringen-lab/genomepy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Genomer is command line glue for genome projects. It simplifies the small but tedious tasks required when finishing a genome. Genomer makes it easy to reorganise contigs in a genome, map annotations on to the genome and generate the files required to submit a genome." ; sc:featureList edam:operation_3216 ; sc:name "Genomer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "http://next.gs/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2751 ; sc:name "GenomeReviews ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2711 ; sc:encodingFormat edam:format_2331 ; sc:name "Genome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "Annotated view of the genomic sequence of organisms with completely deciphered genomes. 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The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits." ; sc:featureList edam:operation_2499 ; sc:name "GenomeScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genes.mit.edu/genomescan/" ; biotools:primaryContact "Chris Burge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC9580848", "pubmed:36304311" ; sc:description "The genomeSidekick data analysis tool is a simple and efficient application that allows users to analyze and visualize RNA-seq and ATAC-seq data without having to learn the nitty gritty bioinformatics. This document will provide a comprehensive overview of the functions and capabilities of each tab within the application. For your convenience, the app can be used both online as a website or locally run in your RStudio. If you run into any problems while using the app in RStudio, refer to the Troubleshooting section to see some common errors and solutions that may occur." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "genomeSidekick" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://genomesidekick.shinyapps.io/genomesidekick/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3516 ; sc:description "Visualize and analyze data generated on Illumina array platforms with GenomeStudio Software. This solution supports the genotyping analysis of microarray data. Performance-optimized tools and a graphical interface enable you to convert data into meaningful results." ; sc:featureList edam:operation_3196, edam:operation_3233 ; sc:license "Proprietary" ; sc:name "GenomeStudio" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.illumina.com/techniques/microarrays/array-data-analysis-experimental-design/genomestudio.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174 ; sc:citation ; sc:description "Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. 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It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. 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Mena-Chalco" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package developed for the accurate annotation of genes and quantitative trait loci (QTLs) located in regions identified in common genomic analyses performed in livestock, such as Genome-Wide Association Studies and transcriptomics using RNA-Sequencing. 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This information is then stored in a local database that keeps track of the relationship between transcripts, exons, CDS and genes." ; sc:featureList edam:operation_2409, edam:operation_2422 ; sc:license "Artistic-2.0" ; sc:name "GenomicFeatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. 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More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively." ; sc:featureList edam:operation_0361, edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "GenomicRanges" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , "pmcid:PMC4621043", "pubmed:26501966" ; sc:contributor "funding from the NeCTAR project" ; sc:description "A virtual laboratory for genomics research and training." ; sc:featureList edam:operation_2945 ; sc:funder "funding from the NeCTAR project" ; sc:name "Genomics Virtual Lab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "The University of Queensland (RCC)", "Victorian Life Sciences Computation Initiative (VLSCI)", "unimelb.edu.au" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://genome.edu.au/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description "Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor." ; sc:featureList edam:operation_0226 ; sc:license "Artistic-2.0" ; sc:name "GenomicScores" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomicScores.html" ; biotools:primaryContact "Robert Castelo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3518, edam:topic_3697 ; sc:citation ; sc:description "GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases." ; sc:featureList edam:operation_2436, edam:operation_2939, edam:operation_3431, edam:operation_3891, edam:operation_3935 ; sc:license "Artistic-2.0" ; sc:name "GenomicSuperSignature" ; sc:url "https://github.com/shbrief/GenomicSuperSignaturePaper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169, edam:topic_3170 ; sc:citation "pubmed:22113082" ; sc:description "GenomicTools is a platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq." ; sc:featureList edam:operation_0531, edam:operation_3209, edam:operation_3222 ; sc:license "GPL-2.0" ; sc:name "GenomicTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://code.google.com/p/ibm-cbc-genomic-tools/" ; biotools:primaryContact "A. Tsirigo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges BioConductor package." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "GenomicTuples" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenomicTuples.html" ; biotools:primaryContact "Peter Hickey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "Tools for storing, accessing, analyzing and visualizing genomic data." ; sc:featureList edam:operation_2403, edam:operation_3208, edam:operation_3431 ; sc:license "Artistic-2.0" ; sc:name "Genominator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Genominator.html" ; biotools:primaryContact "James Bullard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:description "Parallel genome assembly system built from the ground up with scalability in mind. It can assemble large and high-coverage genomes from fastq files in a short time and produces assemblies similar to Velvet or Ray in quality." ; sc:featureList edam:operation_0525 ; sc:name "Genomix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.11" ; sc:url "https://github.com/uci-cbcl/genomix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:16652332" ; sc:description "Platform independent Java program for the analysis of genome wide association experiments. The software implements the workflow of an association experiment, including data management, single-point and haplotype analysis, “lead” definition, and data visualization." ; sc:featureList edam:operation_2403, edam:operation_3208 ; sc:name "Genomizer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.ikmb.uni-kiel.de/resources/download-tools/software/genomizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_2533, edam:topic_2640 ; sc:citation "pubmed:25192740" ; sc:description "Software package for internal tandem duplication detection from cancer genome sequencing data." ; sc:featureList edam:operation_0379 ; sc:name "Genomon ITDetector" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ken0-1n/Genomon-ITDetector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:17570856" ; sc:description "Software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design." ; sc:featureList edam:operation_3208 ; sc:name "Genomorama" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://public.lanl.gov/jgans/genomorama/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_2330 ; sc:name "Genotype/phenotype report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3299 ; sc:citation ; sc:description "A genotype network is a graph in which vertices represent genotypes that have the same phenotype. This tool provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network; (iii) multiple interactive visualizations." ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3562 ; sc:name "Genonets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ieu-genonets.uzh.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3337, edam:topic_3577, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:32249310" ; sc:description """Cataloging large-scale phenotypic and next-generation sequencing data within human datasets. GenoPheno-CatalogShiny is an R Shiny App developed to provide a dynamic on-line catalog with datasets containing both, genomic sequencing and clinical data for the same patients.""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3695 ; sc:license "Apache-2.0" ; sc:name "GenoPheno" ; sc:url "https://avillachlab.shinyapps.io/genophenocatalog/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0769, edam:topic_3674 ; sc:citation ; sc:description "Genopo (a.k.a. F5N) is a nanopore sequencing analysis toolkit for Android smartphones." ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3919 ; sc:license "MIT" ; sc:name "Genopo" ; sc:url "https://play.google.com/store/apps/details?id=com.mobilegenomics.genopo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_3334, edam:topic_3520 ; sc:citation ; sc:description """An open-source software for robust and standardized integration of proteomic and genetic data. Genoppi is an open-source software for performing quality control and analyzing quantitative proteomic data. In particular, it streamlines the integration of proteomic data with external datasets such as known protein-protein interactions in published literature, data from genetic studies, gene set annotations, or other user-defined inputs.""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3435, edam:operation_3799 ; sc:license "MIT" ; sc:name "Genoppi" ; sc:url "http://github.com/lagelab/Genoppi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:23042248" ; sc:description "GenoREAD is a web-based, sequence verification software that can be used to compare Sanger sequencing trace files against a reference sequence. Users can either submit their sequencing results one clone at a time, or they can submit a series of clones (as a project) to run at once. Results can be viewed online or downloaded." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3198 ; sc:name "GenoREAD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/genoread/" ; biotools:primaryContact "Jean Peccoud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0625, edam:topic_0780, edam:topic_3500 ; sc:citation ; sc:description "A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life." ; sc:featureList edam:operation_0553, edam:operation_2495, edam:operation_3672, edam:operation_3947 ; sc:name "GenOrigin" ; sc:url "http://genorigin.chenzxlab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0204, edam:topic_0602, edam:topic_2259, edam:topic_3518 ; sc:citation "pubmed:25717191" ; sc:description "Several tools to perform reconstruction of gene regulatory networks from microarray data and connectivity information." ; sc:featureList edam:operation_3439 ; sc:name "GeNOSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://140.113.239.45/GeNOSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:33532816" ; sc:description """Online exploration of quantitative profiles along genomes via interactively customized graphical representations. Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations.""" ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_2928, edam:operation_3553, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Genoscapist" ; sc:url "https://genoscapist.migale.inrae.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "This tool provides an extension of the RangedSummarizedExperiment class with additional API features. This new class provides convenient and fast methods for working with segmented genomic data. Additionally, this extension provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome)." ; sc:featureList edam:operation_3233 ; sc:license "Artistic-2.0" ; sc:name "genoset" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genoset.html" ; biotools:primaryContact "Peter M. Haverty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0654, edam:topic_2533, edam:topic_3516 ; sc:citation "pubmed:24135263" ; sc:description "Free tool to identify length variation of microsatellites from short sequence reads. Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise including PCR amplification errors, individual cell mutation, misalignment or mis-mapping caused by the repetitive nature of the microsatellites." ; sc:featureList edam:operation_3196 ; sc:name "GenoTan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genotan.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330, edam:format_3016 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330, edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3572 ; sc:citation ; sc:description "Takes in a gVCF or VCF and reports metrics to assess quality of calls." ; sc:featureList edam:operation_3218 ; sc:name "genotypeeval" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genotypeeval.html" ; biotools:primaryContact "Jennifer Tom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0654, edam:topic_3318 ; sc:citation , "pmcid:PMC7488165", "pubmed:32944061" ; sc:description """Graphical genotyping on genetic and sequence-based maps. GenoTypeMapper (GTM) is a software to compare, visualize and analyze genomic data of one or two genetic or physical maps. More information about the software can be obtained by reading the corresponding article, which is a prerequisite to understand the idea and theoretical background of this software. GTM is available for download, together with a small manual and testdata.""" ; sc:featureList edam:operation_0282, edam:operation_2944, edam:operation_3196 ; sc:name "GenoTypeMapper" ; sc:url "http://www.genotypemapper.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3169, edam:topic_3175, edam:topic_3940 ; sc:citation ; sc:description """Here, we present GENome Organisation Visual Analytics (GENOVA): a software suite to perform in-depth analyses on various levels of genome organisation, using Hi-C data. GENOVA facilitates the comparison between multiple datasets and supports the majority of mapping-pipelines. The increase in interest for Hi-C methods in the chromatin community has led to a need for more user-friendly and powerful analysis methods. The few currently available software packages for Hi-C do not allow a researcher to quickly summarize and visualize their data. An easy to use software package, which can generate a comprehensive set of publication-quality plots, would allow researchers to swiftly go from raw Hi-C data to interpretable results.""" ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "GENOVA" ; sc:url "http://github.com/dewitlab/GENOVA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0654, edam:topic_2533, edam:topic_3053 ; sc:citation "pubmed:22594998" ; sc:description "Freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results." ; sc:featureList edam:operation_3197 ; sc:name "Genovar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genovar.sourceforge.net/" ; biotools:primaryContact "Kwang Su Jung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3263, edam:topic_3316, edam:topic_3489 ; sc:citation , "pmcid:PMC8319889", "pubmed:34325724" ; sc:description "GenoVault is a private cloud-based central repository for storage and retrieval of genomics data generated in various research labs in various organizations. The solution is delivered in the form of a software suite called “GenoVault”, that enables quick archival and retrieval of data along with analytical support." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "GenoVault" ; sc:url "https://github.com/bioinformatics-cdac/GenoVault" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:name "Histogram" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0797, edam:topic_0798, edam:topic_3174 ; sc:citation , "pmcid:PMC10104344", "pubmed:37014908" ; sc:description "Open-source automated circular genome visualizer for bacteria and archaea." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-1.0" ; sc:name "GenoVi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/robotoD/GenoVi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3168 ; sc:description "A feature rich NGS assembly viewer/browser." ; sc:featureList edam:operation_0337 ; sc:name "GenoViewer" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/astrid/GenoViewer" ; biotools:primaryContact "AstridBio Technologies Kft." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0634, edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:26504140" ; sc:description "Post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. 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It alleviates the multiple hypothesis problems and the need for P value corrections, which often lead to massive numbers of false negatives." ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "genphen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/genphen.html" ; biotools:primaryContact "Simo Kitanovski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0128, edam:topic_0203, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description """Standalone software for creating protein interaction networks from genomes. Ab initio protein interation network generator.""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "GENPPI" ; sc:url "http://github.com/santosardr/genppi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_2187 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_3534 ; sc:citation , "pmcid:PMC5570222", "pubmed:28498966" ; sc:description "Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. Binding sites are defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach" ; sc:featureList edam:operation_0417, edam:operation_2575 ; sc:name "GenProBiS" ; sc:url "http://genprobis.insilab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2840, edam:topic_3474 ; sc:citation , "pubmed:33772575" ; sc:description "genra-py is a Python package for GenRA. Genralised Read-Across (GenRA) is a computational toxicology tool to mimic a human expert’s manual reasoning based on similarity-weighted activity." ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "genra-py" ; sc:url "http://github.com/i-shah/genra-py" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis." ; sc:featureList edam:operation_0256 ; sc:license "Artistic-2.0" ; sc:name "GenRank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenRank.html" ; biotools:primaryContact "Chakravarthi Kanduri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC9048672", "pubmed:35266528" ; sc:description "GenRisk is a package that implements different gene-based scoring schemes to analyze and find significant genes within a phenotype in a population." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3659, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GenRisk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/AldisiRana/GenRisk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0602, edam:topic_0634, edam:topic_2259 ; sc:citation "pubmed:22698142" ; sc:description "Simulate interactions among two genetic and one environmental factor and also allows for epistatic interactions. It is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered." ; sc:featureList edam:operation_3439 ; sc:name "GENS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/gensim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3071 ; sc:citation "pubmed:22945945" ; sc:description "Program designed for specified-sequence retrieval and extraction from large-scale sequence sets in NCBI GenBank flatfile format." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:name "GenScalpel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/archive/p/genscalpel/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0654, edam:topic_3321 ; sc:citation "pubmed:9149143" ; sc:description "Identify complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands." ; sc:featureList edam:operation_2454 ; sc:name "GENSCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genes.mit.edu/GENSCANinfo.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation ; sc:description "A user friendly framework for re-sequencing in a diagnostics context: searching for mutations/variants, especially on well known genes." ; sc:featureList edam:operation_0292, edam:operation_0564, edam:operation_3198, edam:operation_3202, edam:operation_3226 ; sc:isAccessibleForFree false ; sc:license "Unlicense" ; sc:name "GensearchNGS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.phenosystems.com/www/index.php/products/gensearchngs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. 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sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "AT-CUBE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genskew.csb.univie.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2259, edam:topic_3524 ; sc:citation ; sc:description "Generating Series for testing Structural Identifiability." ; sc:featureList edam:operation_2423 ; sc:name "GenSSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/genssi-developer/GenSSI" ; biotools:primaryContact "Jan Hasenauer", "Thomas Ligon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_3474 ; sc:citation ; sc:description "GenTB is a user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. genTB is an analysis tool for Mycobacterium tuberculosis genomic data that offers three main features: a means for sharing, citing and crediting TB data and metadata, the prediction of resistance on genotype using a machine learning algorithm, and geographic resistance and mutation data mapping." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:name "GenTB" ; sc:url "https://gentb.hms.harvard.edu" ; biotools:primaryContact , "Maha R Farhat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3519, edam:topic_3912 ; sc:description "Software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more." ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GENtle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.9.4" ; sc:url "http://gentle.magnusmanske.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation ; sc:description """Distinguish genuine untargeted metabolic features without quality control samples. distinguish genuine signal of untargeted metabolites from measurement artifacts without QC samples.""" ; sc:featureList edam:operation_2428 ; sc:license "GPL-2.0" ; sc:name "genuMet" ; sc:url "https://github.com/liucaomics/genuMet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_2840, edam:topic_3382 ; sc:citation ; sc:description "Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation." ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3891, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GenUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/martin-sicho/genui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0797, edam:topic_3299 ; sc:citation , "pubmed:34951622" ; sc:description "A gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids." ; sc:featureList edam:operation_0525, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GEnView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EbmeyerSt/GEnView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0749, edam:topic_3308 ; sc:citation ; sc:description """Rapid Identification of Discriminative and Explainable Feature Pairs for Genomic Analysis. Genvisage - Rapid Identification of Discriminative Feature Pairs for Genomic Analysis.""" ; sc:featureList edam:operation_3435, edam:operation_3802, edam:operation_3937 ; sc:name "GENVISAGE" ; sc:url "http://genvisage.knoweng.org:443/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Genomic visualization software package that is fully integrated with Lasergene and is designed to support easy generation of publication quality graphics and maps." ; sc:featureList edam:operation_0337 ; sc:name "GenVision" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dnastar.com/t-products-genvision.aspx" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC5039916", "pubmed:27288499" ; sc:description "Produce highly customizable publication quality graphics for genomic data primarily at the cohort level." ; sc:featureList edam:operation_3208 ; sc:license "GPL-3.0" ; sc:name "GenVisR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GenVisR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3071, edam:topic_3810, edam:topic_3912 ; sc:citation , "pmcid:PMC10409678", "pubmed:37278871" ; sc:description "Tool for visualizing agroclimate to inform research and regulatory risk assessment." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "GEnZ Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://foodsystems.org/resources/genz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2269, edam:topic_3542 ; sc:citation , "pubmed:32604028" ; sc:description """A PyMOL plugin for protein structure ensembles analysis. The Geo Measures Plugin can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface.""" ; sc:featureList edam:operation_2476, edam:operation_2488, edam:operation_3890, edam:operation_3891 ; sc:name "Geo-Measures" ; sc:url "https://pymolwiki.org/index.php/Geo_Measures_Plugin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203 ; sc:description "GEO Platform Annotation Table Reader is MATLAB tool that reads and parses platform annotation table (*.annot) from GEO." ; sc:featureList edam:operation_1812, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "GEO Platform Annotation Table Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43153-geo-platform-annotation-table-reader" ; biotools:primaryContact "Sisi Ma" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1566 ; sc:name "Protein-ligand interaction report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_3474, edam:topic_3511, edam:topic_3534 ; sc:citation , "pmcid:PMC10250245", "pubmed:37070217" ; sc:description "Segmentation of nucleic acid binding interface on protein surface with geometric deep learning." ; sc:featureList edam:operation_0415, edam:operation_0420, edam:operation_2464, edam:operation_2492, edam:operation_3897 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GeoBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.zpliulab.cn/GeoBind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0781, edam:topic_3077 ; sc:citation ; sc:description "Command-line software package developed to address sparse or incomplete metadata in GenBank sequence records that relate to the location of the infected host (LOIH) of viruses. Given a set of GenBank accession numbers corresponding to virus GenBank records, it extracts, integrates and normalizes geographic information reflecting the LOIH of the viruses using integrated information from GenBank metadata and related full-text publications." ; sc:featureList edam:operation_0224 ; sc:name "GeoBoost" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://drive.google.com/drive/u/1/folders/0B_4ZL2GZpq2yeHRxMmRvYlNPY2s" ; biotools:primaryContact "Tasnia Tahsin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_3297, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC7755405", "pubmed:32683454" ; sc:description """A natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. GeoBoost2 (part of the ZoDo project) is a system for extracting the location of infected hosts (LOIH) for a given set of GenBank metadata accessions. This involves API implementations that utilize NCBI API's for accessing and parsing information and delivering it to the researcher interested in investigating a set of sequences. You can also use this tool mine Geographic Locations in scientific articles (available as abstracts on PubMed or PMC-OA) or text files.""" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3907 ; sc:license "Apache-2.0" ; sc:name "GeoBoost2" ; sc:url "https://zodo.asu.edu/geoboost2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3318, edam:topic_3393, edam:topic_3489 ; sc:citation , "pmcid:PMC7182183", "pubmed:32330167" ; sc:description """A global database of political administrative boundaries. geoBoundaries by the William & Mary geoLab. Create dynamic maps, analyze and build location-aware and geospatial applications with your data using the power of PostGIS in the cloud.""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_2944, edam:operation_3431 ; sc:name "geoBoundaries" ; sc:url "http://www.geoboundaries.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_2640, edam:topic_3518 ; sc:citation , "pubmed:34935889" ; sc:description "Bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO)." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "geoCancerPrognosticDatasetsRetriever" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AbbasAlameer/geoCancerPrognosticDatasetsRetriever" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:32125609" ; sc:description """A Slicer Toolbox for Targeting Brain Stimulation. 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public.""" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "GeodesicSlicer" ; sc:url "http://www.slicer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:10736051" ; sc:description "Program for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. In the NCA, population structure can be separated from population history when it is assessed through rigorous and objective statistical tests using the temporal information contained in the a genealogy." ; sc:featureList edam:operation_0324 ; sc:name "GEODIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://darwin.uvigo.es/software/geodis.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3382, edam:topic_3518 ; sc:citation ; sc:description "An R/Bioconductor package for gene expression analysis and visualisation." ; sc:featureList edam:operation_0571, edam:operation_2939, edam:operation_3223, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GEOexplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/GEOexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0176, edam:topic_0602, edam:topic_3398 ; sc:citation , "pmcid:PMC9308565", "pubmed:35549473" ; sc:description "GeomBD3 is a rigid body Brownian dynamics software package for simulating association rates and molecular recognition in biological or engineered systems." ; sc:featureList edam:operation_2476, edam:operation_3893, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GeomBD3" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/chang-group/GeomBD3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3518 ; sc:citation , "pmcid:PMC2639278", "pubmed:18842599" ; sc:description "A thin wrapper around the SQLite database along with associated documentation. Access to the metadata associated with samples, platforms, and datasets much more feasible." ; sc:featureList edam:operation_2421 ; sc:license "Artistic-2.0" ; sc:name "GEOmetadb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GEOmetadb.html" ; biotools:primaryContact "Jack Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:18631022" ; sc:description "Python program to compute the geodesic path between two phylogenetic trees." ; sc:featureList edam:operation_0325 ; sc:name "GeoMeTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cibiv.at/software/geometree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3070, edam:topic_3344 ; sc:description "This is fast implementation of bolstered error estimation algorithm for linear SVM classification." ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "Geometric Gaussian-Kernel Bolstered Error Estimation for Linear Classification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/40118-geometric-gaussian-kernel-bolstered-error-estimation-for-linear-classification" ; biotools:primaryContact "Arsen Arakelyan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0623, edam:topic_2814, edam:topic_3318, edam:topic_3534 ; sc:citation ; sc:description """Geometricus Represents Protein Structures as Shape-mers Derived from Moment Invariants. 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Rarey) at ZBH, Hamburg, including DoGSite Scorer, EDIA, PPI, PoseView, SIENA and ProToss.""" ; sc:featureList edam:operation_2421 ; sc:name "GeoMine" ; sc:url "https://proteins.plus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3056, edam:topic_3299, edam:topic_3796 ; sc:citation , "pmcid:PMC8476160", "pubmed:34117771" ; sc:description "Forward-time, individual-based, landscape genomic simulation in Python." ; sc:featureList edam:operation_2426, edam:operation_3454, edam:operation_3891 ; sc:license "MIT" ; sc:name "Geonomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/drewhart/geonomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC8366979", "pubmed:34347784" ; sc:description "GeoPPI is a deep learning based framework that uses deep geometric representations of protein complexes to model the effects of mutations on the binding affinity." ; sc:featureList edam:operation_0331, edam:operation_0478, edam:operation_2492, edam:operation_3227, edam:operation_4009 ; sc:license "MIT" ; sc:name "GeoPPI" ; sc:url "https://github.com/Liuxg16/GeoPPI" ; biotools:primaryContact , "Sen Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3071 ; sc:citation , "pubmed:17496320" ; sc:description "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. 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Instead of directly searching the term, it can find all the gene names contained in the search term and search all the alias of the gene names simultaneously in GEO database. It also provides other functions such as summarizing common biology keywords in the search results." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "GEOsearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioConductor" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GEOsearch.html" ; biotools:primaryContact "Zhicheng Ji" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:20939882" ; sc:description "Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. 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It draws upon differential geometry and random field theory, by leveraging the procedures used in statistical parametric mapping (SPM): a framework for making topological inferences about spatially structured effects, with well-behaved spatial dependencies." ; sc:featureList edam:operation_2429, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "GeoSPM" ; sc:url "https://github.com/high-dimensional/geospm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0654 ; sc:citation "pubmed:15088382" ; sc:description "Complete system used to store and analyze gene expression data. It has a relational database, a web interface, and an analysis suite. There is also a repository for each user’s files, and a comprehensive security system. The program is intended to be a multiuser archive for gene chip data, as well as a friendly, powerful analysis tool for end users. It includes workflow management features for the microarray center, and for the individual research labs." ; sc:featureList edam:operation_2495 ; sc:name "GEOSS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://va-genex.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit)." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "GEOsubmission" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GEOsubmission.html" ; biotools:primaryContact "Alexandre Kuhn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as \"drug set enrichment analysis\" and \"gene2drug\" drug discovery analysis respectively." ; sc:featureList edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "gep2pep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gep2pep.html" ; biotools:primaryContact "Francesco Napolitano" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0862 ; sc:name "Dotplot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797 ; sc:author "Jan Krumsiek" ; sc:citation , "pubmed:17309896" ; sc:description "Genome pair rapid dotter." ; sc:featureList edam:operation_0490 ; sc:isAccessibleForFree true ; sc:name "Gepard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "AT-CUBE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.helmholtz-muenchen.de/icb/gepard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_1775, edam:topic_3518 ; sc:citation "pubmed:12824345", "pubmed:15215434", "pubmed:15980548", "pubmed:16845056", "pubmed:18508806" ; sc:description "Collection of tools for the analysis of microarray data. It includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps." ; sc:featureList edam:operation_0313, edam:operation_2495, edam:operation_3223, edam:operation_3463 ; sc:name "GEPAS" ; sc:url "http://www.gepas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "GEPAT (Genome Expression Pathway Analysis Tool) is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data." ; sc:featureList edam:operation_2495, edam:operation_3928 ; sc:name "GEPAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gepat.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0196, edam:topic_0203, edam:topic_0218, edam:topic_0623 ; sc:citation , "pmcid:PMC10320155", "pubmed:37224532" ; sc:description "Large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_2422, edam:operation_3625, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:name "GePI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gepi.coling.uni-jena.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3518 ; sc:citation , "pmcid:PMC5570223", "pubmed:28407145" ; sc:description "Gene Expression Profiling Interactive Analysis. Interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3463 ; sc:name "GEPIA" ; sc:softwareHelp ; sc:url "http://gepia.cancer-pku.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0610, edam:topic_0625, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:34877793" ; sc:description "The Gene Expression Database of Poplar under Stress." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:name "GEPSdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gepsdb.ahau-edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3517, edam:topic_3974 ; sc:citation ; sc:description "GEPSi is a toolkit to simulate phenotypes for GWAS analysis, given input genotype data for a population." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "GEPSi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/clara-parabricks/GEPSi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "A sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits." ; sc:featureList edam:operation_2429, edam:operation_3659 ; sc:name "geQTL" ; sc:operatingSystem "Linux" ; sc:url "http://www.cs.unc.edu/~weicheng/" ; biotools:primaryContact "Wei Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3293, edam:topic_3295, edam:topic_3810 ; sc:citation , "pubmed:37310261" ; sc:description "Interactive multi-omics database for cross-species data mining in horticultural crops." ; sc:featureList edam:operation_0324, edam:operation_2495, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "GERDH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://dphdatabase.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2835 ; sc:name "Gene ID (VBASE2)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2815, edam:topic_2830 ; sc:citation ; sc:description "An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. 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It supports the complete life cycle of research data management, from planning, through acquisition, to publication. Research data are constantly increasing in both size and complexity, offering not only new analytical possibilities, but also posing new challenges to data processing, integration and safeguarding." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3436 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:name "GFBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.gfbio.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:25400907" ; sc:description "Cytoscape app designed to visualize and analyze the functional dissimilarity of gene networks. 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The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. 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This is a customizable LAMP primer sets designing system: GLAPD (whole genome based LAMP primer design for a set of target genomes).""" ; sc:featureList edam:operation_0308, edam:operation_0346, edam:operation_0525 ; sc:license "GPL-2.0" ; sc:name "GLAPD" ; sc:url "http://cgm.sjtu.edu.cn/GLAPD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. 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In this GUI, sync events can be shown, and data can be optionally annotated (e.g. as slow and fast phase intervals) by hand or by a classifier algorithm, or such annotations can be loaded from file.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3454 ; sc:name "GlassesViewer" ; sc:url "https://github.com/dcnieho/GlassesViewer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1246 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence cluster (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_3464 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0659 ; sc:description "GLobal Automated sRNA Search go, combines iterative BLAST searches, pairwise identity filtering, and structure based clustering in an automated prediction pipeline to find sRNA homologs from scratch. The web server provides predefined parameter sets for a non-expert usage as well as enables a manual setup of the query parameters. The returned GLASSgo result is in FASTA format, whereby the first entry represents the input sequence." ; sc:featureList edam:operation_0337, edam:operation_0438 ; sc:isAccessibleForFree true ; sc:name "GLASSgo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.informatik.uni-freiburg.de/GLASSgo/Input.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3053, edam:topic_3334, edam:topic_3407 ; sc:citation , "pmcid:PMC9673420", "pubmed:36401306" ; sc:description "A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma." ; sc:featureList edam:operation_3501 ; sc:license "CC-BY-4.0" ; sc:name "Glaucoma-TrEl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.jveralab.net/glaucoma-trel/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3379, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9388536", "pubmed:35982106" ; sc:description "A deep-learning algorithm for the diagnosis of primary open-angle glaucoma from fundus photographs." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3927 ; sc:license "BSD-3-Clause" ; sc:name "GlaucomaNet" ; sc:url "https://github.com/bionlplab/GlaucomaNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC8165803", "pubmed:34058973" ; sc:description "GLEANER is a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. 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Based on a generalization of the diffusion state distance, we design a new embedding-based link prediction method called global and local integrated diffusion embedding (GLIDE)""" ; sc:featureList edam:operation_2492, edam:operation_3435, edam:operation_3927 ; sc:name "GLIDE" ; sc:url "https://bitbucket.org/kap_devkota/glide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_3517 ; sc:citation , "pmcid:PMC9237677", "pubmed:35575379" ; sc:description "GLIDER, a method that replaces a protein-protein interaction or association network with a new graph-based similarity network." ; sc:featureList edam:operation_2492, edam:operation_3501, edam:operation_3927 ; sc:license "Not licensed" ; sc:name "GLIDER" ; sc:url "https://github.com/kap-devkota/GLIDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3170 ; sc:citation ; sc:description "Generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information." ; sc:featureList edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "Glimma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Glimma.html" ; biotools:primaryContact "Shian Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation , , , "pmcid:PMC147303", "pmcid:PMC148753", "pubmed:10556321", "pubmed:9421513" ; sc:description "System for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. It uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA." ; sc:featureList edam:operation_2454 ; sc:name "Glimmer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/glimmer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622 ; sc:citation ; sc:description "A new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons." ; sc:featureList edam:operation_2454, edam:operation_3662 ; sc:license "Artistic-1.0" ; sc:name "Glimmer-HMM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/glimmerhmm/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0912 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1249 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence length" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1353 ; sc:name "Sequence motif" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0914 ; sc:encodingFormat edam:format_2330 ; sc:name "Codon usage data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC3245904", "pubmed:22102569" ; sc:description """Glimmer-MG is a system for finding genes in environmental shotgun DNA sequences. Glimmer-MG (Gene Locator and Interpolated Markov ModelER - MetaGenomics) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Licensed under Artistic License.""" ; sc:featureList edam:operation_2422, edam:operation_2454, edam:operation_3937 ; sc:license "Other" ; sc:name "Glimmer-MG" ; sc:softwareHelp ; sc:url "https://github.com/davek44/Glimmer-MG" ; biotools:primaryContact "David R. Kelley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3462 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , ; sc:description "GLIMPSE2 is a set of tools that allow fast whole-genome imputation and phasing of low-coverage sequencing data." ; sc:featureList edam:operation_3454, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GLIMPSE2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.1" ; sc:url "https://odelaneau.github.io/GLIMPSE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3173, edam:topic_3674 ; sc:citation ; sc:description "User-friendly toolset for the analysis of high-throughput DNA-methylation array data." ; sc:featureList edam:operation_3206 ; sc:name "GLINT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cozygene/glint/releases" ; biotools:primaryContact "Elior Rahmani", "Eran Halperin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10350252", "pubmed:37454191" ; sc:description "Database for visualization of molecular profiles to improve prognosis of brain cancer." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_0337, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Glioma-BioDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glioma-biodp.nci.nih.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3334, edam:topic_3360, edam:topic_3384, edam:topic_3577 ; sc:citation , "pmcid:PMC9446481", "pubmed:36081550" ; sc:description "An integrated database for knowledge exploration of diagnostic biomarkers in gliomas." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GlioMarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gliomarker.prophetdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0634, edam:topic_3334, edam:topic_3510 ; sc:citation , "pmcid:PMC7396318", "pubmed:32743661" ; sc:description """A comprehensive web-based tool to access and analyze glia secretome data. Gliome Database has the following feature regarding glia-secreted proteins.""" ; sc:featureList edam:operation_0418, edam:operation_0422, edam:operation_2421 ; sc:name "Gliome database" ; sc:url "http://www.gliome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3669 ; sc:name "Training material" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3669 ; sc:name "Training material" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0219, edam:topic_3307, edam:topic_3366 ; sc:author "Yann Haefliger" ; sc:description "Glittr is a web application that helps you find and compare bioinformatics training material on GitHub and GitLab." ; sc:featureList edam:operation_0224, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Glittr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "https://glittr.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33295604" ; sc:description """Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data. Fit Gamma-Poisson Generalized Linear Models Reliably. The core design aims of glmGamPoi are:.""" ; sc:featureList edam:operation_3659, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "glmGamPoi" ; sc:url "http://github.com/const-ae/glmGamPoi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269 ; sc:citation "pubmed:26315909" ; sc:description "R package for variable selection and predictive modeling of structured genomic data." ; sc:featureList edam:operation_2478 ; sc:name "glmgraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/glmgraph/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script", "Suite" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC9708069", "pubmed:36444984" ; sc:description "GLMsingle is a toolbox for obtaining accurate single-trial estimates in fMRI time-series data. We provide both MATLAB and Python implementations." ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "GLMsingle" ; sc:url "https://github.com/cvnlab/GLMsingle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9207519", "pubmed:35747553" ; sc:description "Holistic glomerular detection, segmentation, and lesion characterization with large-scale web image mining." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Glo-In-One" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hrlblab/Glo-In-One" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2332, edam:format_2333, edam:format_2350 ; sc:name "Biodiversity data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2332, edam:format_2333, edam:format_3464 ; sc:name "Biodiversity data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3810 ; sc:description "It is a global entry point to information and knowledge for strengthening the capacity for PGRFA conservation, management and utilization. The site is managed by the FAO Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). It provides access to accessions of ex situ and in situ plant material available in decentralized collections through the use of DOIs assigned to plant material." ; sc:featureList edam:operation_0227, edam:operation_0337, edam:operation_2945, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-3.0" ; sc:name "Global Information System on Plant Genetic Resources for Food and Agriculture (GLIS)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://glis.fao.org/glis/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "We give the following arguments in support this approach: After normalization, gene-expression-data appears symmetrical and outliers are no problem, least squares should be robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals can’t be expected. Application of ordinary least squares gives unbiased, no longer optimal estimates." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "GlobalAncova" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GlobalAncova.html" ; biotools:primaryContact "Manuela Hummel" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3299, edam:topic_3810 ; sc:author "Tomas Vetrovsky" ; sc:citation ; sc:contributor "Tomas Vetrovsky" ; sc:description """User interface to data from high-throughput sequencing studies of fungal communities across terrestrial biomes. Includes sequencing data, sample locations, sample metadata.""" ; sc:featureList edam:operation_0226, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "GlobalFungi" ; sc:softwareHelp ; sc:url "https://globalfungi.com/" ; biotools:primaryContact "Tomas Vetrovsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269 ; sc:citation , "pubmed:21813478" ; sc:description "Learning Globally Optimal Dynamic Bayesian Network with the Mutual Information Test (MIT) Criterion" ; sc:featureList edam:operation_1781, edam:operation_2238, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "GlobalMIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32428-globalmit-toolbox" ; biotools:primaryContact "Xuan Vinh Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3170 ; sc:citation , "pmcid:PMC4782413", "pubmed:26951498" ; sc:description "The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size." ; sc:featureList edam:operation_2238, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "globalSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/globalSeq.html" ; biotools:primaryContact "Armin Rauschenberger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pubmed:26282998" ; sc:description "Tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms." ; sc:featureList edam:operation_3224 ; sc:license "GPL-2.0" ; sc:name "globaltest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/globaltest.html" ; biotools:primaryContact "Jelle Goeman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Identify, date and describe admixture events occurring in the ancestral history of a given target population within the last ~4,500 years." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "GLOBETROTTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://paintmychromosomes.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0121, edam:topic_0736, edam:topic_3538 ; sc:citation "pubmed:12824398" ; sc:description "Plot the tendency towards globularity for a given protein sequence. 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GLU: A tool for analysing continuously measured glucose in epidemiology. GLU is described in the paper: L.A.C. Millard et al. GLU: A tool for analysing continuously measured glucose in epidemiology, bioRxiv, 2018. GLU is a tool for analysing continuous glucose monitoring (CGM) data in epidemiology.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3557, edam:operation_3659 ; sc:license "MIT" ; sc:name "GLU" ; sc:softwareHelp ; sc:url "https://github.com/MRCIEU/GLU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3361, edam:topic_3407 ; sc:citation , "pubmed:36088892" ; sc:description "Gluclas (GLUcose CLamp ASsistant) is a free software for suggesting glucose infusion rate adjustments during manual glucose clamp experiments." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "Gluclas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jp993/gluclas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_3068 ; sc:citation , "pubmed:36680885" ; sc:description "A comprehensive, curated resource of glucokinase modulators for clinical and molecular research." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "GlucoKinaseDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glucokinasedb.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3300, edam:topic_3390 ; sc:description "Modeling of glucose/insulin dynamics" ; sc:isAccessibleForFree true ; sc:name "Glucose Insulin modeling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42362-glucose-insulin-modeling" ; biotools:primaryContact "DaveA Albers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3366 ; sc:citation ; sc:description "Graph-linked unified embedding for single-cell multi-omics data integration." ; sc:featureList edam:operation_3096, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GLUE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gao-lab/GLUE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0821, edam:topic_2275 ; sc:citation , "pmcid:PMC7329481", "pubmed:32611314" ; sc:description """A database for improving the rational design of glucose-tolerant β-glucosidases. 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It assists glycobiologists in designing enzyme mixtures that can be used to guide the precise determination of glycan structures." ; sc:featureList edam:operation_0417, edam:operation_2476 ; sc:name "GlycoDigest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.glycodigest.org/" ; biotools:primaryContact , "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0749, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC9750110", "pubmed:36282863" ; sc:description "A GlycoEnzyme Pathway and Molecular Function Ontology.." ; sc:featureList edam:operation_3454, edam:operation_3501, edam:operation_3672, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "GlycoEnzOnto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/neel-lab/GlycoEnzOnto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "GlycoEP is a new webserver for more accurate prediction of N-linked, O-linked and C-linked glycosites in eukaryotic glycoproteins using two larger datasets, namely, standard and advanced datasets." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "GlycoEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/glycoep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_3520 ; sc:citation "pubmed:15215392" ; sc:description "Tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra." ; sc:featureList edam:operation_3214, edam:operation_3215, edam:operation_3627, edam:operation_3694 ; sc:name "GlycoFragment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.glycosciences.de/tools/GlycoFragments/fragment.php4" ; biotools:primaryContact "Lohmann K.K." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3382 ; sc:citation , "pmcid:PMC7267839", "pubmed:32170934" ; sc:description """Welcome to the GlycoGlyph Introduction Tutorial. 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The database is a unified resource for carbohydrate structures. It retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases." ; sc:featureList edam:operation_0337, edam:operation_0339, edam:operation_0360, edam:operation_0570, edam:operation_3431 ; sc:name "GlycomeDB" ; sc:softwareHelp ; sc:url "http://www.glycome-db.org" ; biotools:primaryContact "Rene Ranzinger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0844 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular mass" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_2330 ; sc:name "Chemical formula" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121, edam:topic_0122, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides." ; sc:featureList edam:operation_0416, edam:operation_0417, edam:operation_0476, edam:operation_3644 ; sc:name "GlycoMod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/glycomod/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:encodingFormat edam:format_1963 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0982 ; sc:encodingFormat edam:format_1963 ; sc:name "Molecule identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:30574787" ; sc:description "Platform for gathering, monitoring, integrating and visualizing glycomics data." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GlyConnect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://glyconnect.expasy.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3068, edam:topic_3520 ; sc:citation ; sc:description "GlyConnect Compozitor is a glycan composition visualising and comparative tool associated with the GlyConnect database." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "GlyConnect Compozitor" ; sc:url "https://glyconnect.expasy.org/compozitor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0602, edam:topic_0625, edam:topic_0821 ; sc:citation ; sc:description """A database of monosaccharide biosynthesis pathways. Monosaccharide Biosynthesis Pathways Database. Pathways for monosaccharide biosynthesis. Welcome to MonoPathDB, a database of biosynthesis pathways and enzymes for monosaccharides.""" ; sc:featureList edam:operation_3208, edam:operation_3896, edam:operation_3929 ; sc:name "GlycoPathDB" ; sc:url "http://www.bio.iitb.ac.in/glycopathdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3071, edam:topic_3473 ; sc:citation "pubmed:25143288" ; sc:description "Web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics (CFG)." ; sc:featureList edam:operation_2480 ; sc:name "GlycoPattern" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://glycopattern.emory.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2229, edam:topic_3168, edam:topic_3520 ; sc:citation , "pubmed:33174597" ; sc:description """GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Loading GlycoPOST Application.""" ; sc:featureList edam:operation_3431, edam:operation_3627, edam:operation_3860 ; sc:name "GlycoPOST" ; sc:url "https://glycopost.glycosmos.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3392279", "pubmed:22808107" ; sc:description "GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s), where N-glycosite is an Asn residue and O-glycosite could be a serine or threonine residue having a glycan attached covalently and enzymatically at amide or hydroxyl group respectively." ; sc:featureList edam:operation_2945 ; sc:name "glycopp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/glycopp/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2796 ; sc:name "Linucs ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2752 ; sc:name "GlycoMap ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2313 ; sc:encodingFormat edam:format_2331 ; sc:name "Carbohydrate report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2753 ; sc:encodingFormat edam:format_2331 ; sc:name "Carbohydrate conformational map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2313 ; sc:encodingFormat edam:format_2331 ; sc:name "Carbohydrate report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152 ; sc:citation ; sc:description "Carbohydrate structure database." ; sc:featureList edam:operation_0224 ; sc:name "Glycosciences" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.glycosciences.de/sweetdb/index.php" ; biotools:primaryContact "Thomas Lütteke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_3520 ; sc:citation "pubmed:15215392" ; sc:description "Takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures." ; sc:featureList edam:operation_2421, edam:operation_3215, edam:operation_3627 ; sc:name "GlycoSearchMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.glycosciences.de/sweetdb/start.php?action=form_ms_search" ; biotools:primaryContact "Lohmann K.K." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0122, edam:topic_0601 ; sc:citation ; sc:description "Selectively align amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., \"fucosylated\") or specific, such as precise composition, and are proposed in a drop-down list." ; sc:featureList edam:operation_0417 ; sc:name "GlycoSiteAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycoproteome.expasy.org/glycositealign/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2258, edam:topic_3292, edam:topic_3297 ; sc:citation , "pmcid:PMC10284107", "pubmed:37129482" ; sc:description "Integration efforts between GlyCosmos and PubChem." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "GlyCosmos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glycosmos.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0121, edam:topic_0122, edam:topic_0621, edam:topic_0749, edam:topic_2815, edam:topic_3520 ; sc:citation "pubmed:20501599" ; sc:description "Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG)." ; sc:featureList edam:operation_0417, edam:operation_0477, edam:operation_2406, edam:operation_2480, edam:operation_2483, edam:operation_2487 ; sc:name "GlycoViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.glycoviewer.babs.unsw.edu.au" ; biotools:primaryContact "M. Wilkins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0153, edam:topic_0160, edam:topic_3474 ; sc:citation ; sc:description "glycoworkis a Python package for glycan data science and machine learning." ; sc:featureList edam:operation_0292, edam:operation_0337 ; sc:license "MIT" ; sc:name "glycowork" ; sc:url "https://bojarlab.github.io/glycowork/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3520 ; sc:citation ; sc:description "Algorithm for assigning glycan compositions from LC-MS data by exploring biosynthetic network relationships among glycans." ; sc:featureList edam:operation_3214, edam:operation_3629 ; sc:name "GlycReSoft" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.3.7" ; sc:url "http://www.bumc.bu.edu/msr/glycresoft/" ; biotools:primaryContact "Joseph Zaia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures." ; sc:featureList edam:operation_0417 ; sc:name "Glydin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycoproteome.expasy.org/epitopes/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34559595" ; sc:description "A webserver for predicting glycosylation sites on small RNAs." ; sc:featureList edam:operation_0417, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:name "GlyinsRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rnanut.net/glyinsrna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0601, edam:topic_0621, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC10035253", "pubmed:36959676" ; sc:description "Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES." ; sc:featureList edam:operation_0478, edam:operation_0570, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GlyLES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kalininalab/GlyLES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0152, edam:topic_0154, edam:topic_0593, edam:topic_3444 ; sc:citation "pubmed:11752350", "pubmed:16459020", "pubmed:16845109", "pubmed:1757506", "pubmed:9691437" ; sc:description "GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure." ; sc:featureList edam:operation_0474 ; sc:name "GlyNest and CASPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:29518231" ; sc:description "Web interface to upload, visualize and interactively compare glycan expression profiles. The tool can process N- or O-linked glycan expression data." ; sc:featureList edam:operation_0417 ; sc:name "Glynsight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://glycoproteome.expasy.org/glynsight/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3360, edam:topic_3520 ; sc:citation ; sc:description """An automated workflow for quantitative N- and O-linked glycoproteomic data analysis. A automated script for processing and combining Byonic and PD standard output. Pythons 3.4+ with the following packages installed. The program can be run from the location of the script using python main.py. The following parameters can be used for operating the script within the commandline.""" ; sc:featureList edam:operation_1812, edam:operation_3695, edam:operation_3799 ; sc:license "MIT" ; sc:name "GlypNirO" ; sc:url "https://github.com/bschulzlab/glypniro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation "pubmed:15980456" ; sc:description "Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure." ; sc:featureList edam:operation_0429, edam:operation_0474, edam:operation_0477 ; sc:name "Glyprot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.glycosciences.de/modeling/glyprot/php/main.php" ; biotools:primaryContact "Andreas Bohne-Lang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBind or GlycomeDB." ; sc:featureList edam:operation_3504 ; sc:name "GlyS3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycoproteome.expasy.org/substructuresearch" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0166, edam:topic_3068 ; sc:citation , "pubmed:33125071" ; sc:description """The international glycan repository GlyTouCan version 3.0. GlyTouCan is the international glycan structure repository. This repository is a freely available, uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s). Any glycan structure, ranging in resolution from monosaccharide composition to fully defined structures can be registered as long as there are no inconsistencies in the structure.""" ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_3431 ; sc:name "GlyTouCan" ; sc:url "https://glytoucan.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:35533298" ; sc:description "GM-Pep is an integrated approach contained two parts, one is multi-class generator (CVAE model) which was responsibility for generating potential drug-like peptides, the other is multi-classifier (Deep-Multiclassifier) which predicted bioactivity probability of generated peptides by CVAE model." ; sc:featureList edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GM-Pep" ; sc:url "https://github.com/TimothyChen225/GM-Pep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:36752023" ; sc:description "Prediction of cancer driver genes based on gene-miRNA regulatory network with graph convolutional model" ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_2437, edam:operation_3436, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GM-GCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/weiba/GM-GCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_0769 ; sc:citation , "pubmed:36634285" ; sc:description "A parameter-space mapping strategy for force-field calibration." ; sc:featureList edam:operation_2429, edam:operation_3893 ; sc:isAccessibleForFree true ; sc:name "gmak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/mssm-labmmol/gmak" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pubmed:15728110" ; sc:description "Genomic Mapping and Alignment Program for mRNA and EST Sequences." ; sc:featureList edam:operation_0282, edam:operation_0292 ; sc:name "GMAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://research-pub.gene.com/gmap/" ; biotools:primaryContact "Thomas Wu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2306 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , , ; sc:description "A database genome index for GMAP and GSNAP." ; sc:featureList edam:operation_3211 ; sc:name "gmap_build" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2013-01-23" ; sc:url "http://research-pub.gene.com/gmap/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2306 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation , , ; sc:description "Create a map store for known genes or SNPs." ; sc:featureList edam:operation_0282, edam:operation_2403 ; sc:name "gmap_iit_store" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2013-01-23" ; sc:url "http://research-pub.gene.com/gmap/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885 ; sc:citation , , ; sc:description "Build index files for known SNPs." ; sc:featureList edam:operation_0227, edam:operation_3197 ; sc:name "gmap_snpindex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2015-07-23" ; sc:url "http://research-pub.gene.com/gmap/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_2572 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330, edam:format_2572 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2330, edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2330, edam:format_2572 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170 ; sc:citation ; sc:description "GSNAP and GMAP are a pair of tools to align short-read data. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool." ; sc:featureList edam:operation_2478, edam:operation_3198 ; sc:license "Artistic-2.0" ; sc:name "gmapR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gmapR.html" ; biotools:primaryContact "Michael Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_2269 ; sc:citation , "pmcid:PMC5020087", "pubmed:27679641" ; sc:description "Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrates SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features." ; sc:featureList edam:operation_0253 ; sc:license "GPL-3.0" ; sc:name "GMATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v21" ; sc:url "https://sourceforge.net/projects/gmata/" ; biotools:primaryContact "Xuewen Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "GMATo is a novel soft for faster and accurate microsatellite mining at any length and comprehensive statistical analysis for DNA sequences in any genome at any size, with easily customized parameters control for biologists and bio-informatician, running easily at common computers with Windows, Linux, MAC OS etc multiple platforms (platform independently) with both graphic and command interface programmed in Java and Perl computing language." ; sc:featureList edam:operation_2238 ; sc:name "GMATo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://sourceforge.net/projects/gmato/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26261222" ; sc:description "Fill and close the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads." ; sc:featureList edam:operation_3217 ; sc:name "GMcloser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/gmcloser/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3071 ; sc:citation ; sc:description "Database which facilitates the search and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS)." ; sc:featureList edam:operation_2422 ; sc:name "Golm Metabolome Database (GMD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://gmd.mpimp-golm.mpg.de/REST/default.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Package for non-parametric distance measurement between two discrete frequency distributions." ; sc:featureList edam:operation_3432 ; sc:name "GMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp , ; sc:softwareVersion "0.3.3" ; sc:url "http://CRAN.R-project.org/package=GMD" ; biotools:primaryContact "Albin Sandelin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation , , "pmcid:PMC5320543", "pubmed:17503330", "pubmed:28479868" ; sc:description "Nonparametric and genetic model-free alternative to linear or logistic regression for detecting and characterizing nonlinear interactions among discrete genetic and environmental attributes. Compared with the MDR method, this method permits adjustment for discrete and quantitative covariates and is applicable to both dichotomous and continuous phenotypes in different population-based study designs. It will increase the precision accuracy and help users draw a more meaningful conclusion." ; sc:featureList edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "GMDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ssg.uab.edu/gmdr/" ; biotools:primaryContact "Xiang-Yang Lou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC9580954", "pubmed:36304322" ; sc:description "An R Package to Apply Embedding Techniques to Microbiome Data." ; sc:featureList edam:operation_3695, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GMEmbeddings" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MaudeDavidLab/GMEmbeddings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3047, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:35451457" ; sc:description "High-throughput Analysis of Biomolecular Data using Graph-based Multiple Hierarchical Consensus Clustering." ; sc:featureList edam:operation_3223, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GMHCC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yifuLu/GMHCC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0622, edam:topic_0634, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC7488130", "pubmed:32912170" ; sc:description """A shiny application for the identification of gene-targeted drugs for precision medicine. This is the offical repository of GMIEC-shiny. GMIEC is a shiny application to integrate multi-omics data. GMIEC is a new user-friendly and flexible application that allows to integrate gene-expression, copy-number variation, methylation, Chromatin Immuno-Precipitation followed by sequencing (ChIP-seq) data, and mutations at the level of single patient. 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It can also easily combined with Subset-quantile Within Array Normalization(SWAN) or Beta-Mixture Quantile (BMIQ) Normalisation to remove probe design bias." ; sc:featureList edam:operation_3204, edam:operation_3431, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GMQN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MengweiLi-project/gmqn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease." ; sc:featureList edam:operation_3197 ; sc:license "GPL-2.0" ; sc:name "GMRP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GMRP.html" ; biotools:primaryContact "Yuan-De Tan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, SNP detection, splice analyses and genomic enrichments." ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_3198 ; sc:name "Genomatix Mining Station (GMS)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genomatix.de/en/index.html" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_3512 ; sc:citation ; sc:description """Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights. 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It assists you in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Moreover, it allows you to simulate the qualitative behavior of the network in response to external perturbations." ; sc:featureList edam:operation_1781 ; sc:name "GNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibis.inrialpes.fr/article122.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23230149" ; sc:description "Open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks." ; sc:featureList edam:operation_3439 ; sc:name "GNAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/gnatmatlab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_2814 ; sc:citation , "pmcid:PMC6001793", "pubmed:29396867" ; sc:description "Software package intended primarily for the processing of multicomponent high resolution NMR datasets such as those acquired in diffusion, relaxation and kinetic experiments." ; sc:featureList edam:operation_3214 ; sc:license "GPL-3.0" ; sc:name "GNAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.nmr.chemistry.manchester.ac.uk/?q=node/430" ; biotools:primaryContact "Mathias Nilsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3321 ; sc:citation "pubmed:25935118" ; sc:description "Java-based software tool for analyzing gene networks coherence using direct and indirect relationships." ; sc:featureList edam:operation_2497 ; sc:name "GNC" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://fgomezvela.github.io/GNC/" ; biotools:primaryContact "Francisco Gómez Vela", "José Antonio Lagares", "Norberto Díaz-Díaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:33270838" ; sc:description """An R package for constructing gene regulatory networks from transcriptomic data. Gene regulatory network modeling tool (GNET2). GNET2 has been developed and used by the Bioinformatics, Data Mining and Machine Learning Laboratory (BDM) . Help from every community member is very valuable to make the package better for everyone. Checkout the Lab Page.""" ; sc:featureList edam:operation_0337, edam:operation_1781, edam:operation_2437 ; sc:name "GNET2" ; sc:url "https://github.com/jianlin-cheng/GNET2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3390, edam:topic_3810 ; sc:citation , "pmcid:PMC9007240", "pubmed:35434472" ; sc:description "Global Nutrition and Health Atlas (GNHA)." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "GNHA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sites.tufts.edu/gnha/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:34003445" ; sc:description "GNIAP is a R package for gene co-expression network inference and assessment. Can be either GPL-3 or MIT license." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3766 ; sc:name "GNIAP" ; sc:softwareHelp ; sc:url "https://github.com/ozgurcingiz/GNIAP" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047, edam:topic_3474 ; sc:citation ; sc:description """Molecular Docking with Deep Learning. gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina.""" ; sc:featureList edam:operation_0478, edam:operation_3893, edam:operation_4009 ; sc:name "Gnina" ; sc:url "https://github.com/gnina/gnina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0622, edam:topic_3170 ; sc:citation , "pubmed:33576787" ; sc:description """Inference of gene regulatory networks using pseudo-time series data. GNIPLR (gene networks inference based on projection and lagged regression) is a method for constructing gene regulatory network.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3659 ; sc:name "GNIPLR" ; sc:url "https://github.com/zyllluck/GNIPLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3295, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "Disease subnetwork detection with explainable Graph Neural Networks." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GNN-SubNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pievos101/GNN-SubNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:35389867" ; sc:description "A Hierarchical and Adaptive Graph Neural Network for Parameter Space Exploration of Unstructured-Mesh Ocean Simulations." ; sc:featureList edam:operation_2426, edam:operation_3799, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GNN-Surrogate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/trainsn/GNN-Surrogate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:36790067" ; sc:description "Using Graph Neural Networks for Site-of-Metabolism Prediction and its Applications to Ranking Promiscuous Enzymatic Products." ; sc:featureList edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GNN-SOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HassounLab/GNN-SOM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0769, edam:topic_3298, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:35608290" ; sc:description "A graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits." ; sc:featureList edam:operation_0276, edam:operation_0282 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GNNHap" ; sc:url "https://github.com/zqfang/gnnhap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC8650344", "pubmed:34876032" ; sc:description "An efficient scRNA-seq dropout imputation method using graph attention network." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "GNNImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Lav-i/GNNImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3168, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC9462789", "pubmed:36084008" ; sc:description "Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences by providing extensible APIs and implementing the glue required for combining feature sets and models for genome-wide prediction." ; sc:featureList edam:operation_0438, edam:operation_2404, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Gnocis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/bjornbredesen/gnocis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3077, edam:topic_3325, edam:topic_3366 ; sc:citation , "pmcid:PMC5018207", "pubmed:27535533" ; sc:description "Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "ODbL-1.0" ; sc:name "gnomAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gnomad.broadinstitute.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3320, edam:topic_3325, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC7334198", "pubmed:32461655" ; sc:description """Transcript expression-aware annotation improves rare variant interpretation. The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3436, edam:operation_3675 ; sc:name "gnomADsup1" ; sc:url "https://gnomad.broadinstitute.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_2885, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:24478219" ; sc:description "Interactive whole-genome analysis pipeline to prioritize disease-linked variants, genes, and pathways." ; sc:featureList edam:operation_3227 ; sc:name "gNOME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gnome.tchlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3697, edam:topic_3922, edam:topic_3941 ; sc:citation ; sc:description """A multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Support: https://gitlab.com/gaspilleura/gnomo/.""" ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3192 ; sc:license "Apache-2.0" ; sc:name "gNOMO" ; sc:url "https://gitlab.com/rki_bioinformatics/gnomo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3360 ; sc:citation , "pmcid:PMC9051584", "pubmed:35677713" ; sc:description "An R Shiny app supporting cancer genomics survival analysis with cBioPortal." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GNOSIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://lydiaking.shinyapps.io/GNOSIS/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0780, edam:topic_3053 ; sc:citation , , , ; sc:description "A multispecies integrative information system dedicated to plant and fungi pests.. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment" ; sc:featureList edam:operation_0224, edam:operation_0227, edam:operation_2409, edam:operation_3208, edam:operation_3559 ; sc:license "CC-BY-4.0" ; sc:name "Genetic and Genomic Information System (GnpIS)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "18.2" ; sc:url "https://urgi.versailles.inrae.fr/gnpis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3292, edam:topic_3297, edam:topic_3520 ; sc:citation , "pmcid:PMC5321674", "pubmed:27504778" ; sc:description "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication." ; sc:featureList edam:operation_3431, edam:operation_3629, edam:operation_3637, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GNPS" ; sc:softwareHelp , , , ; sc:url "https://gnps.ucsd.edu/" ; biotools:primaryContact "Mingxun Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269, edam:topic_3524 ; sc:citation "pubmed:19304877" ; sc:description "Simulation and statistical inference tool for algebraic or differential equation systems. Other programs have been created to the same end, the Matlab family of graphical interactive programs being some of the more general and easy to use. Still, many available tools are not optimal for performing computer intensive and sophisticated Monte Carlo analyses." ; sc:featureList edam:operation_3658 ; sc:name "GNU MCSim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.gnu.org/software/mcsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622 ; sc:citation "pubmed:19861355" ; sc:description "The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine." ; sc:featureList edam:operation_3198 ; sc:name "Gnumap" ; sc:operatingSystem "Linux" ; sc:url "http://dna.cs.byu.edu/gnumap/" ; biotools:primaryContact "Dr. Mark Clement", "Dr. Quinn Snell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation ; sc:description """Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread. Gene Novelty Unit-based Virus IDentification for SARS-CoV-2.""" ; sc:featureList edam:operation_2871, edam:operation_3227, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "GNUVID" ; sc:url "https://github.com/ahmedmagds/GNUVID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0114, edam:topic_0154, edam:topic_0203, edam:topic_3500 ; sc:citation "pubmed:19920128", "pubmed:22102568" ; sc:description "The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the domains. Gene product annotation continues to increase both in the number of total annotations and in species coverage. Tools have seen major improvements in functionality, speed and usage." ; sc:featureList edam:operation_3501, edam:operation_3559, edam:operation_3672 ; sc:name "Gene Ontology (GO)" ; sc:softwareHelp ; sc:url "http://www.geneontology.org/" ; biotools:primaryContact "Helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation ; sc:description """a highly controlled workflow to discover gene essentiality in loss-of-function screens. SUMMARY Genome-wide CRISPR screens are an effective discovery tool for genes that underlie diverse cellular mechanisms that can be scored through cell fitness. Loss-of-function screens are particularly challenging compared to gain-of-function because of the limited dynamic range of decreased sgRNA sequence detection. Here we describe G uide- O nly control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, T oolset for the R anked A nalysis of GO- C RISPR S creens (TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer and demonstrate superior performance to standard screening methods ||| HOMEPAGE MISSING! ||| CORRECT NAME OF TOOL COULD ALSO BE 'TRACS'""" ; sc:featureList edam:operation_3219, edam:operation_3435, edam:operation_3928 ; sc:name "GO-CRISPR" ; sc:url "https://github.com/developerpiru/TRACS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "GO-Elite is designed to identify a minimal non-redundant set of biological Ontology terms or pathways to describe a particular set of genes or metabolites." ; sc:featureList edam:operation_2497 ; sc:name "GO-Elite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.5" ; sc:url "http://www.genmapp.org/go_elite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3053, edam:topic_3299 ; sc:citation ; sc:description """Summary Visualisations of Gene Ontology Terms with GO-Figure!. GO-Figure! offers a simple solution for command-line plotting of informative summary visualisations of lists of GO terms, designed to support exploratory data analyses and multiple dataset comparisons.""" ; sc:featureList edam:operation_2436, edam:operation_2940, edam:operation_3559 ; sc:name "GO-Figure" ; sc:url "https://gitlab.com/evogenlab/GO-Figure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "GO2MSIG generates collections of gene sets in MSigDB format based on the Gene Ontology (GO) project hierarchy and gene association data, for use with the Gene Set Enrichment Analysis (GSEA) implementation available at the Broad Institute. This enables rapid creation of gene set collections for multiple species." ; sc:featureList edam:operation_3501 ; sc:name "GO2MSIG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20131106" ; sc:url "http://www.bioinformatics.org/go2msig/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0621, edam:topic_0769, edam:topic_3474 ; sc:citation , "pubmed:36786404" ; sc:description "A shared hub for universal benchmarking of machine learning-based protein functional annotations." ; sc:featureList edam:operation_3359, edam:operation_3672, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GO bench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.gobench.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0089 ; sc:citation , ; sc:description "A tool for GO term enrichment analysis." ; sc:featureList edam:operation_3501 ; sc:name "GO enrichment analysis tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://geneontology.org/page/go-enrichment-analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3308 ; sc:citation ; sc:description "Rapid web-based functional annotation tool for genomic and transcriptomic data." ; sc:featureList edam:operation_3672 ; sc:license "CC-BY-4.0" ; sc:name "GO FEAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://computationalbiology.ufpa.br/gofeat/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "A tool for finding significant GO terms shared among a list of genes from your organism of choice." ; sc:featureList edam:operation_2495 ; sc:name "Generic GO Term Finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://go.princeton.edu/cgi-bin/GOTermFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:description "A tool for mapping the granular GO annotations for genes in a list to a set of broader, high-level GO parents terms." ; sc:featureList edam:operation_2495 ; sc:name "Generic GO Term Mapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://go.princeton.edu/cgi-bin/GOTermMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0219, edam:topic_0621, edam:topic_0780 ; sc:citation "pubmed:22123736" ; sc:description "The UniProt GO annotation program aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). The assignment of GO terms to UniProt records is an integral part of UniProt biocuration. UniProt manual and electronic GO annotations are supplemented with manual annotations supplied by external collaborating GO Consortium groups, to ensure a comprehensive GO annotation dataset is supplied to users." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_3672, edam:operation_3778 ; sc:name "GOA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/GOA/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1864 ; sc:encodingFormat edam:format_2060 ; sc:name "Map set data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2549 ; sc:name "Ontology" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:encodingFormat edam:format_2330 ; sc:name "GO-term enrichment data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_3520 ; sc:description "Sorts protein identifications under GOA slim terms." ; sc:featureList edam:operation_2436, edam:operation_3502, edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "goa_gubbar" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.ms-utils.org/goa_gubbar/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "A set of command line tools to manipulate multiple alignments." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "goalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fredericlemoine/goalign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:22004759" ; sc:description "Generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys." ; sc:featureList edam:operation_0474 ; sc:name "GOAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cssb.biology.gatech.edu/GOAP/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3050, edam:topic_3673, edam:topic_3944 ; sc:citation , "pmcid:PMC9971660", "pubmed:36864925" ; sc:description "A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3096, edam:operation_3216, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GoaT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://goat.genomehubs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3390, edam:topic_3407, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC6802673", "pubmed:31649832" ; sc:description """Machine learning classification models for fetal skeletal development performance prediction using maternal bone metabolic proteins in goats. 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Bennett" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2195, edam:format_2330 ; sc:name "Ontology" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2195, edam:format_2330 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3572 ; sc:citation , "pubmed:17098774" ; sc:description "A set of tools for interacting with GO and microarray data. 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Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics." ; sc:featureList edam:operation_3083, edam:operation_3439 ; sc:name "GoSurfer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://systemsbio.ucsd.edu/GoSurfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. 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Gram-Positive Protein Prediction Pipeline. GP4 - Gram Positive Protein Prediction Pipeline.""" ; sc:featureList edam:operation_0418, edam:operation_2489, edam:operation_3802 ; sc:name "GP4" ; sc:url "http://gp4.hpc.rug.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31710658" ; sc:description """Rendering glycans and annotating glycopeptide mass spectra. Find information on common issues. Ask questions and find answers from other users. gpAnnotate: A program for the detailed annotation of MS/MS glycoproteomics spectra using DrawGlycan-SNFG sketches. The Glycopeptide Spectrum Annotation program ( gpAnnotate ) is designed to annotate individual glycoproteomics MS/MS spectrum for several established mass spectrometry fragmentation modes:""" ; sc:featureList edam:operation_0337, edam:operation_3755, edam:operation_3860 ; sc:name "gpAnnotate" ; sc:url "https://virtualglycome.org/gpAnnotate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:25393678" ; sc:description "Statistical approach to prioritizing GWAS results by integrating pleiotropy information and annotation data." ; sc:featureList edam:operation_2238 ; sc:name "GPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dongjunchung.github.io/GPA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:34849578" ; sc:description "Statistical Approach for Functional-Annotation-Tree-Guided Prioritization of GWAS Results." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557, edam:operation_3659, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GPA-Tree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://dongjunchung.github.io/GPATree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0199, edam:topic_3673 ; sc:citation , "pmcid:PMC6612806", "pubmed:31510683" ; sc:description "Efficient merging of genome profile alignments | André Hennig authored Jul 17, 2019" ; sc:featureList edam:operation_0295, edam:operation_0300, edam:operation_3182 ; sc:name "GPalignment" ; sc:url "https://lambda.informatik.uni-tuebingen.de/gitlab/ahennig/GPA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC7788535", "pubmed:33413089" ; sc:description """Modeling drug mechanism of action with large scale gene-expression profiles using GPAR. GPAR Genetic Profile-Activity Relationship. GPAR provides drug repurposing and MOAs prediction services. Using gene expression profile data and Deep Learning, to build models, to make predictions.""" ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_2436, edam:operation_4009 ; sc:name "GPAR" ; sc:url "http://gpar.idrug.net.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31070701" ; sc:description "Human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks." ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "gpart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/gpart" ; biotools:primaryContact "Sun Ah Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3574, edam:topic_3577 ; sc:citation , "pmcid:PMC8042245", "pubmed:33868597" ; sc:description "GPCards is an integrated database of genotype-phenotype correlations in human genetic diseases." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3226 ; sc:name "GPCards" ; sc:softwareHelp ; sc:url "http://genemed.tech/gpcards/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170 ; sc:citation ; sc:description """Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments. GPcounts is Gaussian process regression package for counts data with negative binomial and zero-inflated negative binomial likelihoods described in the paper "Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments". It is implemented using the GPflow library.""" ; sc:featureList edam:operation_3563, edam:operation_3565, edam:operation_3659 ; sc:license "Apache-2.0" ; sc:name "GPcounts" ; sc:url "https://github.com/ManchesterBioinference/GPcounts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121 ; sc:citation "pubmed:19037861" ; sc:description "2-layer predictor: the 1st layer prediction engine is for identifying a query protein sequence as GPCR on non-GPCR; if it is a GPCR protein, the process will be automatically continued with the 2nd-layer prediction engine to further identify its type among the following six main functional classes: (1) rhodopsin-like, (2) secretin-like, (3) metabotrophic/glutamate/pheromone, (4) fungal pheromone, (5) cAMP receptor, and (6) Frizzled/Smoothemed family" ; sc:featureList edam:operation_2423 ; sc:name "GPCR-CA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/GPCR-CA" ; biotools:primaryContact "Xuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_1317 ; sc:citation ; sc:description """GPCR-EXP is a database that specializes in curating experimental and predicted structures of G protein-coupled receptors (GPCR). Structure-related data for experimental structures, such as resolution, publication information, and biological ligand, from the Protein Databank (PDB) are extracted and incorporated into the database. Additionally, all GPCRs from the human genome have been modelled using GPCR-I-TASSER and have been included. Easy-to-read tables have been constructed to faciliate the browsing of: 1. Experimental PDB Structures 2. Predicted GPCR Structures and Functions for Human Genome Furthermore, database statistics can be accessed to provide a glimpse into the current state of GPCR structural biology, while all PDB structures and data are freely available for download.""" ; sc:name "Experimentally-Solved and Predicted GPCR Structures (GPCR-EXP)" ; sc:url "https://zhanggroup.org/GPCR-EXP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0820, edam:topic_2814 ; sc:citation "pubmed:27166369" ; sc:description "Centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs)." ; sc:featureList edam:operation_0292, edam:operation_0477, edam:operation_2476 ; sc:name "GPCR-ModSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://open.gpcr-modsim.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0623, edam:topic_0820, edam:topic_3300, edam:topic_3510 ; sc:citation , "pmcid:PMC7678784", "pubmed:33216895" ; sc:description """A database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors. To analyze the sequence either upload a file with the sequences in FASTA format, or copy and paste the sequence(s) inside the text area below.""" ; sc:featureList edam:operation_0224, edam:operation_0253, edam:operation_0269, edam:operation_2995, edam:operation_3431 ; sc:name "GPCR-PEnDB" ; sc:url "http://gpcr.utep.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2814, edam:topic_3307 ; sc:citation ; sc:description "The G Protein-Coupled Receptors-Sequence Analysis and Statistics (GPCR-SAS) web application provides a set of tools to perform comparative analysis of sequence positions between receptors, based on a curated structural-informed multiple sequence alignment. The analysis tools include: (i) percentage of occurrence of an amino acid or motif and entropy at a position or range of positions, (ii) covariance of two positions, (iii) correlation between two amino acids in two positions (or two sequence motifs in two ranges of positions), and (iv) snake-plot representation for a specific receptor or for the consensus sequence of a group of selected receptors. The analysis of conservation of residues and motifs across transmembrane (TM) segments may guide the design of more selective ligands or help to rationalize activation mechanisms, among others. As an example, here we analyze the amino acids of the \"transmission switch\", that initiates receptor activation following ligand binding." ; sc:name "GPCR-SAS" ; sc:url "http://lmc.uab.cat/gpcrsas/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_1929 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2275 ; sc:citation ; sc:description "GPCR-Sequence-Structure-Feature-Extractor (SSFE). Provides template suggestions and homology models of Class A GPCRs. Identifies key sequence and structural motifs in Class A GPCRs to guide template selection and build homology models." ; sc:featureList edam:operation_0477, edam:operation_0482, edam:operation_2929 ; sc:name "GPCR-SSFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://www.ssfa-7tmr.de/ssfe2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "dysregulation of GPCR ligand signaling systems in cancer genomics database" ; sc:name "GCA, GPCR Cancer Axes" ; sc:url "https://gpcrcanceraxes.bioinfolab.sns.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0202, edam:topic_3332, edam:topic_3336 ; sc:citation ; sc:description "GPCR target/ off-target/ site effect prediction using a docking approach, included body distribution database" ; sc:name "GPCR Panel" ; sc:url "https://gpcrpanel.cmdm.tw/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0820, edam:topic_2258 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "BLAST search of against GPCR domains stored in GPCR SARfari." ; sc:featureList edam:operation_0346 ; sc:name "GPCR SARfari BLAST Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/protein" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0820 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "Search against small molecules stored in GPCR SARfari database." ; sc:featureList edam:operation_0339 ; sc:name "GPCR SARfari Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/sarfari/gpcrsarfari/compound" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "GPCRana allows the quantitative conformational analysis of GPCR structures" ; sc:name "GPCRana" ; sc:url "https://gpcranalysis.com/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128 ; sc:citation "pubmed:22691703" ; sc:description "Allows the user to upload a GPCR sequence, choose a ligand in a library and obtain the 3D structure of the free receptor and ligand-receptor complex." ; sc:featureList edam:operation_0477, edam:operation_0482 ; sc:name "GPCRautomodel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genome.jouy.inra.fr/GPCRautomodel" ; biotools:primaryContact "Jean-François Gibrat" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:name "Phylogenetic tree image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_1317, edam:topic_2275, edam:topic_3293, edam:topic_3510, edam:topic_3534, edam:topic_3542 ; sc:citation , , , , , , , "pubmed:34759374", "pubmed:36395823" ; sc:description "GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs). GPCRdb curates sequence alignments, structures and receptor mutations from literature. Interactive diagrams visualise receptor residues (e.g. snakeplot and helix box plot) and relationships (e.g phylogenetic trees)." ; sc:featureList edam:operation_0240, edam:operation_0291, edam:operation_0337, edam:operation_0346, edam:operation_0477, edam:operation_2451, edam:operation_2928, edam:operation_2990 ; sc:isAccessibleForFree true ; sc:name "GPCRDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GPCRDB" ; sc:softwareHelp , ; sc:url "https://gpcrdb.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A hidden Markov model for GPCR detection." ; sc:featureList edam:operation_2423 ; sc:name "GPCRHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://gpcrhmm.sbc.su.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2275 ; sc:citation ; sc:description "Predict structures of G-protein-coupled receptors (GPCRs) using advanced homology modeling tools: profile-profile alignment, multiple structural templates, and Z coordinate-based filtering of resulting models. Two distinct loop modeling techniques are employed - Modeller and Rosetta - and the BCL::Score (membrane-fitted knowledge-based energy function) is used to score the final ranking list of GPCR models." ; sc:featureList edam:operation_0300, edam:operation_0477 ; sc:name "GPCRM" ; sc:softwareHelp , , ; sc:url "http://gpcrm.biomodellab.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3307, edam:topic_3474 ; sc:citation "pubmed:15215416" ; sc:description "Tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence." ; sc:featureList edam:operation_0224, edam:operation_0269, edam:operation_0270, edam:operation_2454 ; sc:name "GPCRpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/gpcrpred/" ; biotools:primaryContact "Dr. G.P.S. Raghava" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1131 ; sc:name "Protein family name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0820 ; sc:citation ; sc:description "GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases." ; sc:featureList edam:operation_0224 ; sc:name "GPCRs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gpcrdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0157, edam:topic_0623, edam:topic_3510 ; sc:citation "pubmed:15980444" ; sc:description "Tool for predicting amine-binding receptors based on a protein sequence provided by the user." ; sc:featureList edam:operation_0269, edam:operation_2479, edam:operation_3092 ; sc:name "GPCRsclass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/gpcrsclass/" ; biotools:primaryContact "G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0199, edam:topic_0820, edam:topic_3293, edam:topic_3382 ; sc:citation , "pmcid:PMC8262697", "pubmed:34060630" ; sc:description "GPCRsignal: web server for analysis of the interface between G protein-coupled receptors and their effector proteins by dynamics and mutations." ; sc:featureList edam:operation_0244, edam:operation_0269, edam:operation_0477, edam:operation_2476, edam:operation_2995 ; sc:isAccessibleForFree true ; sc:name "GPCRsignal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gpcrsignal.biomodellab.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33734318" ; sc:description "GPDBN is a deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction." ; sc:featureList edam:operation_0314, edam:operation_3443, edam:operation_3927 ; sc:name "GPDBN" ; sc:url "https://github.com/isfj/GPDBN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0208, edam:topic_2640, edam:topic_3517 ; sc:citation , "pubmed:34534336" ; sc:description "GPEdit systematically investigated the impact of genetic variants and pharmacogenomics landscape of RNA editing event across multiple cancer types." ; sc:featureList edam:operation_0282, edam:operation_3096, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "GPEdit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hanlab.uth.edu/GPEdit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_2275, edam:topic_2814 ; sc:description "GPUFRAGFOLD is a CUDA ACELERATED Protein Structure Prediction Tool." ; sc:featureList edam:operation_0271, edam:operation_0310, edam:operation_0474, edam:operation_2423 ; sc:name "GPGPUFRAGFOLD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "http://bioinfadmin.cs.ucl.ac.uk/downloads/gpufragfold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053, edam:topic_3277 ; sc:citation ; sc:description "GPHMM (Global Parameter Hidden Markov Model) is a novel statistical method dedicated to identify copy number alteration and loss of heterozygosity (LOH) in tumor samples using whole genome SNP arrays." ; sc:featureList edam:operation_3196 ; sc:name "GPHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://bioinformatics.ustc.edu.cn/gphmm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3366 ; sc:citation , ; sc:description "Genomic and Proteomic Knowledge Base (GPKB), based on the Genomic and Proteomic Data Warehouse (GPDW), is an integrative database of annotation data from several sources." ; sc:name "GPKB" ; sc:url "http://www.bioinformatics.deib.polimi.it/GPKB/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3373, edam:topic_3375 ; sc:description "The app is used for PKPD Modeling and Simulation." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "gPKPDSimToolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65399-gpkpdsimtoolbox" ; biotools:primaryContact "Iraj Hosseini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , "pmcid:PMC1950838", "pubmed:17701901" ; sc:description "gPLINKis a Java program that provides a simple form interface to the more commonly-usedPLINKcommands (i.e. instead of using the command line options).gPLINKprovides menus and dialogs to create validPLINKcommands, executes them, keeps a record of all commands run in a project, keeps track of input and output files, allows annotation of result files and facilitates integration withHaploview." ; sc:featureList edam:operation_3197 ; sc:license "GPL-2.0" ; sc:name "gPLINK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://zzz.bwh.harvard.edu/plink/gplink.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification." ; sc:featureList edam:operation_2990 ; sc:license "Artistic-2.0" ; sc:name "gpls" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gpls.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation , "pmcid:PMC5048067", "pubmed:27318200" ; sc:description "Genome Puzzle Master (GPM) enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules." ; sc:featureList edam:operation_3217 ; sc:license "Other" ; sc:name "GPM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Jianwei-Zhang/LIMS" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3711 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3520, edam:topic_3542 ; sc:citation "pubmed:11701329" ; sc:description "This tool was primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_2478, edam:operation_2479, edam:operation_3214, edam:operation_3646, edam:operation_3694 ; sc:name "GPMAW" ; sc:operatingSystem "Windows" ; sc:softwareHelp , , ; sc:url "http://www.gpmaw.com/" ; biotools:primaryContact "Lighthouse data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1775 ; sc:description "GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest." ; sc:featureList edam:operation_0236, edam:operation_0405, edam:operation_2479 ; sc:name "GPMAW lite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.alphalyse.com/gpmaw_lite.html" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071 ; sc:citation ; sc:description "A REST API used to access mass spectrometry-based experimental proteomics data and information stored in GPMDB." ; sc:featureList edam:operation_2422 ; sc:name "GPMDB API" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://wiki.thegpm.org/wiki/GPMDB_REST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3324, edam:topic_3837 ; sc:citation , "pubmed:36917170" ; sc:description "GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences." ; sc:featureList edam:operation_0292, edam:operation_3198, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "GPMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bgi-LUSH/GPMeta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3321 ; sc:citation "pubmed:22369687" ; sc:description "Integrated system for identifying promoter regions and annotating regulatory features in user-input sequences." ; sc:featureList edam:operation_0438 ; sc:name "GPMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gpminer.mbc.nctu.edu.tw/" ; biotools:primaryContact "Tzong-Yi Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097 ; sc:citation "pubmed:22000802" ; sc:description "Web server for comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments" ; sc:featureList edam:operation_0300 ; sc:name "GPPAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protein.cau.edu.cn/gppat/" ; biotools:primaryContact "Ziding Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pubmed:31603766" ; sc:description """Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. General Parsimony Phylogeny models from Frequencies. gppf [-h] -m {perfect,persistent,dollo,caminsokal} -f FILE [-k K] -t TIME -c CLONES [-e]. To reproduce experiments described in the paper the following are also required:. ./gppf -m dollo -f data/simulated/n10_m20/21.sim -t 300 -c 1 -k 4 -e starts a Dollo(4) model with a time limit of 300 seconds (5 minutes), with a clone limit of 100% and with a experimental-format output.""" ; sc:license "MIT" ; sc:name "gppf" ; sc:url "https://github.com/AlgoLab/gppf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0769, edam:topic_2640 ; sc:citation , "pmcid:PMC7725124", "pubmed:33297943" ; sc:description """An ILP-based approach for inferring cancer progression with mutation losses from single cell data. Running the entire gpps pipeline. We provide gpps, that can be used to infer cancer progressions from single cell data. Differently from the previous tool. gpps employs a maximum likelihood search to find the best tree that explain the input, starting from single cell data.""" ; sc:featureList edam:operation_3227, edam:operation_3478 ; sc:name "gpps" ; sc:url "https://github.com/AlgoLab/gpps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_1775, edam:topic_2814, edam:topic_3307 ; sc:citation ; sc:description "A webserver for quantitative analysis of GPCR structures and comparison of residue-residue contact scores (RRCS) between two structures, activation pathway analysis, ligand-receptor interaction analysis and RRCS analysis between transmembrane helices." ; sc:name "GPCRana" ; sc:url "http://gpcranalysis.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474 ; sc:citation , "pubmed:32805275" ; sc:description """An improved machine learning-based model for predicting internal m7G modifications using sequence properties. An improved machine-learning based prediction tool for identifying RNA m7G modifications. m7Gpredictor was implemented in python 2.7.""" ; sc:featureList edam:operation_3937 ; sc:name "GPredictor" ; sc:url "https://github.com/NWAFU-LiuLab/m7Gpredictor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC3116489", "pubmed:21599902" ; sc:description "The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "gprege" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gprege.html" ; biotools:primaryContact "Alfredo Kalaitzis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3519 ; sc:citation , "pmcid:PMC8082839", "pubmed:33926379" ; sc:description "GPrimer is a fast GPU-based pipeline for primerdesign for qPCR experiments." ; sc:featureList edam:operation_0308, edam:operation_3237, edam:operation_3695 ; sc:name "GPrimer" ; sc:url "https://github.com/qhtjrmin/GPrimer" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_1964 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3475 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0622, edam:topic_1775 ; sc:citation , "pubmed:27098042" ; sc:description "gProfileR performs functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the 'g:Profiler' toolkit. 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Kinase-specific Phosphorylation Site Prediction.""" ; sc:featureList edam:operation_0417, edam:operation_3454, edam:operation_3755 ; sc:name "GPS-Palm" ; sc:url "http://gpspalm.biocuckoo.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0166, edam:topic_0602, edam:topic_3510 ; sc:citation , "pmcid:PMC4086084", "pubmed:24880689" ; sc:description "GPS-SUMO (small ubiquitin-like modifiers) is a tool for the prediction of sumoylation sites and SUMO-interaction motifs in proteins." ; sc:featureList edam:operation_0417, edam:operation_2492, edam:operation_2575, edam:operation_3092 ; sc:name "GPS-SUMO" ; sc:url "http://sumosp.biocuckoo.org" ; biotools:primaryContact "Jian Ren", "Yu Xue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0821, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:35037020" ; sc:description "Hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites." ; sc:featureList edam:operation_0417, edam:operation_3659, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "GPS-Uber" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gpsuber.biocuckoo.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3305, edam:topic_3318 ; sc:citation , "pmcid:PMC8915920", "pubmed:35281484" ; sc:description "A Python library for building spatial data and extracting spatial measures from raw GPS data." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GPS2space" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shuai-zhou/GPS2space" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC9825484", "pubmed:36416261" ; sc:description "A comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets." ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "GPSAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.gpsadb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0621, edam:topic_0623 ; sc:citation "pubmed:15613390" ; sc:description "Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2422, edam:operation_3092, edam:operation_3280 ; sc:name "GPSDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gpsdb.expasy.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0821, edam:topic_2275, edam:topic_3673 ; sc:citation , "pmcid:PMC7416605", "pubmed:32849454" ; sc:description """Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum mycotoxinivorans. Genome-scaled Prediction of Substrate-specific Enzymes The workflow:. Before run GPSE to a genome or a dataset of sequences, users should carefully modify the GPSEcfg.py file and change every path according to the system!.""" ; sc:featureList edam:operation_0477, edam:operation_0478, edam:operation_0553, edam:operation_3461 ; sc:license "MIT" ; sc:name "GPSE" ; sc:url "https://github.com/JinyuanSun/GPSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:20671027" ; sc:description "Analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons" ; sc:featureList edam:operation_3223, edam:operation_3800 ; sc:name "GPSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www-rcf.usc.edu/%7Eliangche/software.html" ; biotools:primaryContact "Liang Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC8756198", "pubmed:34672337" ; sc:description "An R Package for Comparing Genomic-binding Profile Similarity among Transcriptional Regulators using Customizable Databases." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GPSmatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bao-Lab/GPSmatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0625, edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC7313177", "pubmed:32576192" ; sc:description """The genetic and pharmacogenomic landscape of snoRNAs in human cancer. G enetic and p harmacogenomic landscape of sno RNAs in cancer. GPSno systematically investigated the impact of genetic variants and pharmacogenomics landscape of snoRNAs in multiple cancer types by using thousands of data from The Cancer Genome Atlas (TCGA).""" ; sc:featureList edam:operation_0224, edam:operation_0484, edam:operation_3196 ; sc:name "GPSno" ; sc:url "http://hanlab.uth.edu/GPSno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "GPSR 1.0: This package developed mainly for UNIX machines. It can be downloaded from webs.iiitd.edu.in/raghava/gpsr/" ; sc:featureList edam:operation_2945 ; sc:name "gpsr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/gpsr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_1775, edam:topic_3053, edam:topic_3064 ; sc:citation "pubmed:22570409" ; sc:description "High-throughput profiling experiments based on for example microarrays or proteomics yield genes potentially important for a given biological process." ; sc:featureList edam:operation_2423, edam:operation_3224 ; sc:name "GPSy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gpsy.genouest.org/" ; biotools:primaryContact "Frederic Chalmel", "GenOuest BioInformatics Platform" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:description "GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads." ; sc:featureList edam:operation_2429 ; sc:name "GPU-BSM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.7.0" ; sc:url "http://www.itb.cnr.it/web/bioinformatics/gpu-bsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_1317 ; sc:citation , , "pmcid:PMC3936136", "pubmed:24481593" ; sc:description "The GPU-based implementation of the CASSERT algorithm for protein 3D structure similarity searching. 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For more choices between individual optimizations, go back to commit e472745e.""" ; sc:featureList edam:operation_0495, edam:operation_0524, edam:operation_3472 ; sc:name "GPU-Darwin" ; sc:url "https://github.com/Tongdongq/darwin-gpu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3474 ; sc:description "An open-source, docker-based, and GPU-enabled jupyterlab notebook has been developed that can run on any compute infrastructure for rapid prototyping and developing end-to-end AI projects. In addition, with such a notebook, long-running AI model training programs can be executed remotely. Other features include GPU support for faster training, git integration for version control, the option of creating and executing pipelines of notebooks, and the availability of multiple dashboards for monitoring compute resources." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GPU-enabled docker container with Jupyterlab for AI" ; sc:operatingSystem "Linux" ; sc:softwareVersion "0.1" ; sc:url "https://github.com/anuprulez/ml-jupyter-notebook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0196, edam:topic_0736 ; sc:citation , "pmcid:PMC8896630", "pubmed:34978562" ; sc:description "A GPU accelerated I-TASSER protein structure prediction tool." ; sc:featureList edam:operation_0302, edam:operation_0474, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:name "GPU-I-TASSER" ; sc:operatingSystem "Windows" ; sc:url "https://zhanggroup.org/GPU-I-TASSER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2885, edam:topic_3053 ; sc:description "GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction." ; sc:featureList edam:operation_2421 ; sc:name "GPU3SNP" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://sourceforge.net/projects/gpu3snp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2269, edam:topic_3293, edam:topic_3382 ; sc:citation "pubmed:26012905" ; sc:description "Modified version of MrBayes that enables running Metropolis coupled  Markov  chain Monte Carlo (MC)^3 sampling on a Graphics Processing Unit (GPU)." ; sc:featureList edam:operation_2409 ; sc:name "GPU MrBayes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mrbayes-gpu/" ; biotools:primaryContact "Ming-Ming Ren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation ; sc:description "A GPU-accelerated CUDA implementation of the Levenberg-Marquardt algorithm. It was developed to meet the need for a high performance, general- purpose nonlinear curve fitting software library which is publicly available and open source." ; sc:featureList edam:operation_2425 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Gpufit" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gpufit/Gpufit" ; biotools:primaryContact "Mark Bates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:22662128" ; sc:description "GPU-accelerated ultra-fast and energy-efficient motif analysis program." ; sc:featureList edam:operation_2404 ; sc:name "GPUmotif" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/gpumotif/" ; biotools:primaryContact "Zhaohui Qin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_0659 ; sc:citation ; sc:description "Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "gpuZoo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://netzoo.github.io/zooanimals/gpuzoo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_3314 ; sc:citation , "pubmed:34470369" ; sc:description "The Ghent Quantum Chemistry Package (GQCP) is an open-source electronic structure software package that aims to provide an intuitive and expressive software framework for electronic structure software development. Its high-level interfaces (accessible through C++ and Python) have been specifically designed to correspond to theoretical concepts, while retaining access to lower-level intermediates and allowing structural run-time modifications of quantum chemical solvers. GQCP focuses on providing quantum chemical method developers with the computational \"building blocks\" that allow them to flexibly develop proof of principle implementations for new methods and applications up to the level of two-component spinor bases." ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "GQCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gqcg.github.io/GQCP/landing-page.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0769, edam:topic_3375 ; sc:citation , "pmcid:PMC7080534", "pubmed:31957304" ; sc:description """A SimBiology-Based GUI for Standardized QSP Model Development and Application. version 1.0.2 (74.9 MB) by Iraj Hosseini. https://github.com/feigelman/gQSPsim-release. 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This Python module is designed to be run with OpenMM in order to simulate grand canonical Monte Carlo (GCMC) insertion and deletion moves of water molecules. This allows the particle number to vary according to a fixed chemical potential, and offers enhanced sampling of water molecules in occluded binding sites. The theory behind our work on GCMC sampling can be found in the References section below.""" ; sc:featureList edam:operation_0387, edam:operation_2476, edam:operation_3938 ; sc:license "MIT" ; sc:name "grand" ; sc:softwareHelp ; sc:url "https://github.com/essex-lab/grand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3308 ; sc:citation ; sc:description "GRAND is a collection of gene regulatory networks derived from human tissues, cancer, cell lines, and small molecule drugs. These networks are bipartite graphs linking either transcription factors (TFs) or miRNAs to their target genes. 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Meier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "An R package for graph theoretic association tests." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "GraphAT" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GraphAT.html" ; biotools:primaryContact "Thomas LaFramboise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_2830, edam:topic_3474, edam:topic_3966 ; sc:citation , "pubmed:37039829" ; sc:description "Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model." ; sc:featureList edam:operation_0252, edam:operation_0267, edam:operation_0416, edam:operation_0474 ; sc:license "Not licensed" ; sc:name "GraphBepi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biomed.nscc-gz.cn/apps/GraphBepi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:32167528" ; sc:description """Refined binning of metagenomic contigs using assembly graphs. GraphBin is a NGS data-based metagenomic contig bin refinment tool that makes use of the contig connectivity information from the assembly graph to bin contigs. It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis-binned contigs and predict the labels of contigs which are discarded due to short length.""" ; sc:featureList edam:operation_0310, edam:operation_3731, edam:operation_3798 ; sc:license "GPL-2.0" ; sc:name "GraphBin" ; sc:url "https://github.com/Vini2/GraphBin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0654, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:33577689" ; sc:description """Protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. We collect two nucleic acid-binding protein benchmark datasets from BioLiP database(1), and split them to the training and test sets according to the release date. In addition, we compare GraphBind with state-of-the-art methods for predicting small ligand-binding residues, including Ca2+, Mn2+, Mg2+, ATP and HEME. GraphBind only predicts one protein chain once, please input 1-character chain ID (case sensitive) in the text boxes.""" ; sc:featureList edam:operation_0321, edam:operation_0415, edam:operation_0475, edam:operation_2575, edam:operation_3359 ; sc:name "GraphBind" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3468, edam:format_3752 ; sc:name "Gene expression profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC9490469", "pubmed:36159985" ; sc:description "A shiny web app to easily perform popular visualization analysis for omics data." ; sc:featureList edam:operation_0490, edam:operation_2939, edam:operation_2940, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "GraphBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.graphbio1.com/en/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3297 ; sc:citation ; sc:description "Chaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs." ; sc:featureList edam:operation_0292, edam:operation_0524, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GraphChainer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/algbio/GraphChainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:citation ; sc:description "GraphClust can be used for structural clustering of RNA sequences. 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It automates tasks of finding the best fitting model for the network data, pairwise comparisons of networks, alignment of two networks using GRAAL algorithm (a better network alignment algorithm, MI-GRAAL, is also available for download), and provides capabilities of clustering network nodes based on their topological surrounding in the network." ; sc:featureList edam:operation_2497, edam:operation_2928, edam:operation_3432 ; sc:name "GraphCrunch" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.1" ; sc:url "http://bio-nets.doc.ic.ac.uk/graphcrunch2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3474, edam:topic_3577 ; sc:citation ; sc:description "Graph convolutional networks for drug response prediction." ; sc:featureList edam:operation_3435, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "GraphDRP" ; sc:url "https://github.com/hauldhut/GraphDRP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3373, edam:topic_3377, edam:topic_3474 ; sc:citation , "pubmed:33119053" ; sc:description """Predicting drug-target binding affinity with graph neural networks. 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Through a set of instructions, they are able to convert relationships into nodes and edges. This tool (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence." ; sc:featureList edam:operation_0415, edam:operation_3459 ; sc:name "GraPPLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://grapple.mpimp-golm.mpg.de/" ; biotools:primaryContact "Liam Childs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_3168, edam:topic_3678 ; sc:citation ; sc:description "GRASP is a gene annotation tool for metagenomic studies. GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose." ; sc:featureList edam:operation_0224, edam:operation_0226, edam:operation_0310 ; sc:name "GRASP" ; sc:operatingSystem "Linux" ; sc:softwareVersion "0.0.4" ; sc:url "http://sourceforge.net/projects/grasp-release/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:33381849" ; sc:description """A graph-based residue neighborhood strategy to predict binding sites. The discovery of protein-ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles. Detecting protein-ligand-binding sites experimentally is time-consuming and expensive.""" ; sc:featureList edam:operation_0250, edam:operation_2464, edam:operation_3897 ; sc:name "GRaSP-py" ; sc:url "https://github.com/charles-abreu/GRaSP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0209, edam:topic_3047, edam:topic_3474, edam:topic_3534 ; sc:citation , "pmcid:PMC9252730", "pubmed:35524575" ; sc:description "A machine learning strategy to predict binding sites based on residue neighborhood graphs." ; sc:featureList edam:operation_0474, edam:operation_1839, edam:operation_2492, edam:operation_2575, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GRaSP-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/charles-abreu/GRaSP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0821, edam:topic_3512, edam:topic_3945 ; sc:citation , "pmcid:PMC9632902", "pubmed:36279274" ; sc:description "Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)." ; sc:featureList edam:operation_0323, edam:operation_0337, edam:operation_3192, edam:operation_3745, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "GRASP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://grasp.scmb.uq.edu.au" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC8982879", "pubmed:35324898" ; sc:description "Fast protein structure comparison through effective representation learning with contrastive graph neural networks." ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_2487, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "GraSR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/GraSR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3298, edam:topic_3382, edam:topic_3810 ; sc:citation , "pubmed:33914380" ; sc:description "Grass Vein Image Quantification (GrasVIQ) is an image analysis framework for automatic quantification of veins in grass leaves. Designed specifically for parallel venation, GrasVIQ automatically segments veins from images of cleared grass leaves using thresholding and edge detection techniques. Veins are quantified and classified into orders, and spatial parameters, such as vein width and interveinal distance, are calculated automatically. For more details, please see." ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3799 ; sc:name "grasviq" ; sc:url "https://www.github.com/gaoke379/GrasVIQ" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3299 ; sc:citation "pubmed:15248131" ; sc:description "Software for relative rate tests with groups supporting all models of nucleotide substitution known by PAUP*." ; sc:featureList edam:operation_2478 ; sc:name "GRate" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfweb.info/Software/GRate" ; biotools:primaryContact "Kai Müller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3404 ; sc:citation , "pubmed:36260573" ; sc:description "Grouping Augmented Views from Independent Sources for Dermatology Analysis." ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "GraVIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bit.ly/3xiFyjx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3373, edam:topic_3376 ; sc:citation , "pmcid:PMC5655815", "pubmed:29065900" ; sc:description "Online tool for calculating and mining dose–response data." ; sc:featureList edam:operation_3438 ; sc:name "GRcalculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.grcalculator.org/grcalculator/" ; biotools:primaryContact "Nicholas A. Clark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:23499845" ; sc:description "Novel computational program to characterize the zinc-binding sites in protein structures, by restricting the distances between zinc and its coordinating atoms." ; sc:featureList edam:operation_2575 ; sc:name "GRE4Zn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gre4zn.biocuckoo.org/" ; biotools:primaryContact "Haiyan Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_0622 ; sc:citation , "pmcid:PMC4514817", "pubmed:26208093" ; sc:description "A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species" ; sc:featureList edam:operation_0237 ; sc:name "GREAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://resource.ibab.ac.in/GREAM/" ; biotools:primaryContact "Kshitish K. Acharya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3295 ; sc:citation , "pubmed:35959979" ; sc:description "A comprehensive enrichment analysis software for human genomic regions." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GREAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.liclab.net/Greap/view/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. It assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes." ; sc:featureList edam:operation_0438 ; sc:name "GREAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bejerano.stanford.edu/great/public/html/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2755 ; sc:encodingFormat edam:format_1964 ; sc:name "Transcription factor name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:encodingFormat edam:format_1964 ; sc:name "Locus ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1016 ; sc:encodingFormat edam:format_1964 ; sc:name "Sequence position" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3475 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2259 ; sc:citation ; sc:contributor "François Bucchini" ; sc:description "This tool performs, in a systematic way, an automated analysis of regular arrangements in organisms having multiple chromosomes, for different transcription factors (or regulators, conditions) at the same time. It reports and allows identification of periodic regions of target genes for the different conditions, on each chromosome." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "GREAT:SCAN:multipatterns" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Institute of Systems and Synthetic Biology", "issb.genopole.fr" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://absynth.issb.genopole.fr/Bioinformatics/tools/GREAT/index" ; biotools:primaryContact "MEGA team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:encodingFormat edam:format_1964 ; sc:name "Locus ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1016 ; sc:encodingFormat edam:format_1964 ; sc:name "Sequence position" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3475 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2259 ; sc:citation , "pmcid:PMC4987929", "pubmed:27151196" ; sc:contributor "François Bucchini" ; sc:description "Performs an automated and systematic analysis of periodic patterns in the position of a set of genomic features of interest along the genome. A complete analysis runs: detection of all possible periods from the positions of the genomic features, clustering of genomic features that are “in-phase” for every significant period found, and mapping of all the regions of the genome showing periodicities. Each step generates rich and interactive visualisations as well as machine-readable files." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "GREAT:SCAN:patterns" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Institute of Systems and Synthetic Biology", "issb.genopole.fr" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://great-portal.org/patterns/" ; biotools:primaryContact "MEGA team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344 ; sc:citation ; sc:description "The well known greedy algorithm for solving Set Cover problem, with a few changes" ; sc:isAccessibleForFree true ; sc:name "Greedy algorithm for Set Cover problem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29650-greedy-algorithm-for-set-cover-problem" ; biotools:primaryContact "Fabio Gori" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194 ; sc:citation ; sc:description """Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees. GreedyRFS is a heuristic method developed for the Robinson-Foulds Supertree problem. It takes a set of binary source trees which have overlapping leaf sets as input and outputs a binary supertree on the union of leaves. This heuristic relies on an exact algorithm for the Robinson-Foulds Supertree problem on two source trees. It repeatedly chooses two trees from the source trees (according to some greedy criterion) and merges them using the exact algorithm until only one supertree remains. (A paper detailing the algorithm and experimental results is submitted to SODA and will be available in the future.).""" ; sc:featureList edam:operation_0544, edam:operation_0556, edam:operation_3478 ; sc:name "GreedyRFS" ; sc:url "http://github.com/yuxilin51/GreedyRFS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0622, edam:topic_0625, edam:topic_0749, edam:topic_3673 ; sc:citation ; sc:description """A framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing. Genomic Regulatory Elements ENcyclopedia. This is the home of the GREEN-DB and companion tools (GREEN-VARAN). Genomic Regulatory Elements ENcyclopedia Database A collection of ~2.4M regulatory regions in the human genome, with information about controlled genes, tissues of activity and associated phenotypes. GREEN-DB is available for free for academic usage in a Zenodo repository.""" ; sc:featureList edam:operation_0438, edam:operation_3225, edam:operation_3226 ; sc:license "MIT" ; sc:name "GREEN-DB" ; sc:url "https://github.com/edg1983/GREEN-VARAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC8224424", "pubmed:34194954" ; sc:description "Quantifying the Carbon Footprint of Computation." ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Green Algorithms" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.green-algorithms.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0623, edam:topic_0659, edam:topic_0780 ; sc:citation , "pmcid:PMC8728176", "pubmed:34723326" ; sc:description "A comprehensive database of plant long non-coding RNAs." ; sc:featureList edam:operation_0291, edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GreeNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://greenc.sequentiabiotech.com/wiki2/Main_Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_2269, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7278087", "pubmed:32510565" ; sc:description """A database for plant circRNAs that act as miRNA decoys. Circular RNAs (circRNAs) are a novel type of RNAs that form covalently closed loop structures with neither 5'- 3' polarities nor polyadenylated tails. GreenCircRNA(v1.0) is the most comprehensive database containing 213,494 circRNA informations from over 4100 RNA-seq datasets across 69 different species. Based on these candidate circRNAs, we futher predicted them acting as miRNA decoys and their potential networks involving circRNA-miRNA-mRNA in the corresponding species. This database allows users not only to search, browse and freely download circRNAs with relative informations, such as full-length, graphical, parental gene and interaction network, but also provide some tools for analyze circRNAs. A Wiki-database of plant CircRNAs(v1.0).""" ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:name "GreenCircRNA" ; sc:url "http://greencirc.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_0780, edam:topic_3957 ; sc:citation , "pmcid:PMC8509195", "pubmed:34639237" ; sc:description "A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "GreeningDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.usu.edu/GreeningDB/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3154 ; sc:name "Protein alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0623, edam:topic_0780, edam:topic_3293 ; sc:citation , "pubmed:20864446" ; sc:description "A database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families." ; sc:featureList edam:operation_0291, edam:operation_0337, edam:operation_0553, edam:operation_2404, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "GreenPhylDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v4" ; sc:url "http://www.greenphyl.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0780, edam:topic_3169, edam:topic_3179 ; sc:citation , "pubmed:36124976" ; sc:description "A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data." ; sc:featureList edam:operation_3192, edam:operation_3215, edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "greenscreen" ; sc:url "https://github.com/sklasfeld/GreenscreenProject" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC7018612", "pubmed:32055858" ; sc:description """GREG-studying transcriptional regulation using integrative graph databases. Scripts related to GREG (Gene Regulation Graph Database) and its papers. Use GREG at: http://www.moralab.science/GREG/. (The Gene Regulation Graph Database).""" ; sc:featureList edam:operation_0224, edam:operation_1781, edam:operation_2437 ; sc:name "GREG" ; sc:url "https://mora-lab.github.io/projects/greg.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3173, edam:topic_3517 ; sc:citation "pubmed:25886982" ; sc:description "Tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features." ; sc:featureList edam:operation_3501 ; sc:name "GREGOR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://csg.sph.umich.edu/GREGOR/index.php/site/index" ; biotools:primaryContact "Cristen Willer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation , "pubmed:32399550" ; sc:description """Modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem. GREMA (Gene networks Reconstruction using Evolutionary Modelling Algorithm) is a program for inferring a novel type of gene regulatory network (GRN) with confidence levels for every inferred regulation, which is emulated GRN (eGRN). The higher the confidence level, the more accurate the inferred regulation. GREMA gradually determines the regulations of an eGRN with confidence levels in descending order using either an S-system or a Hill function-based ordinary differential equation model. It makes use of an evolutionary modelling algorithm (EMA) that is based on evolutionary intelligence, including both crowd wisdom and an evolutionary strategy, to cope with the underdetermined problem. 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GRMT is able to efficiently recover the chronological order of mutations and scale well to large datasets. 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For each group a weight is estimated from the observed test statistics within the group." ; sc:featureList edam:operation_2238 ; sc:name "Grouped FDR" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://wpicr.wpic.pitt.edu/WPICCompGen/GroupedFDR/" ; biotools:primaryContact "Bernie Devlin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3308 ; sc:citation ; sc:description "Graph-based clustering and annotation for improved de novo transcriptome analysis." ; sc:featureList edam:operation_0291, edam:operation_0361 ; sc:name "Grouper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/COMBINE-lab/grouper" ; biotools:primaryContact "Rob Patro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3318, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:33412539" ; sc:description "A groupwise one-shot deep learning-based 4D image registration method." ; sc:featureList edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "GroupRegNet" ; sc:url "https://github.com/vincentme/GroupRegNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3474 ; sc:citation ; sc:description "A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data." ; sc:featureList edam:operation_1781 ; sc:name "GRRANN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kangtianyu/GRRANN" ; biotools:primaryContact "Kourosh Zarringhalam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation ; sc:description "This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC." ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_2990, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "GRridge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GRridge.html" ; biotools:primaryContact "Mark A. van de Wiel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation "pubmed:21266471" ; sc:description "Reference-based data compression for storage of resequencing data." ; sc:featureList edam:operation_0335 ; sc:name "GRS" ; sc:operatingSystem "Linux" ; sc:url "http://gmdd.shgmo.org/Computational-Biology/GRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2815, edam:topic_3419 ; sc:citation , "pmcid:PMC5440596", "pubmed:28588513" ; sc:description "Analysis of perceptual independence using general recognition theory." ; sc:featureList edam:operation_2238 ; sc:name "grtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fsotoc/grtools" ; biotools:primaryContact "Fabian A. Soto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3375 ; sc:citation , "pubmed:32369561" ; sc:description """Interactive multiparameter optimization of molecules in a continuous vector space. gruenif.ai is a web application for interactive multi-parameter optimization of molecules in a continous vector space. A web application is best explained through a live demo. Please watch our video for a detailed explanation of the functionality: Showcase. In its current form grünifai is commposed of multiple microservices. We recommend the use of Docker to compose all microservises into one running environment.""" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "grunifai" ; sc:url "https://github.com/jrwnter/gruenifai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0152 ; sc:citation "pubmed:25819445", "pubmed:25857669" ; sc:description "GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent." ; sc:featureList edam:operation_0295, edam:operation_2483 ; sc:name "GS-align" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.glycanstructure.org/gsalign" ; biotools:primaryContact "Ilya Vakser", "Sandor Vajda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Developed for aligning genomic sequences and uses bit-level operations. It is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements. It is suitable for aligning fairly divergent sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment." ; sc:featureList edam:operation_0292, edam:operation_0491, edam:operation_0495, edam:operation_2421 ; sc:name "GS-Aligner" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://biocomp.iis.sinica.edu.tw/new/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3489 ; sc:citation ; sc:description "GS-LAGE (Gene Specific Large-scale Analysis of Gene Expression) is a global analysis strategy for large-scale microarray datasets integrated from public databases such as NCBI GEO." ; sc:featureList edam:operation_2495 ; sc:name "GS-LAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lage.sookmyung.ac.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """Containerized GUIDE-seq Data Analysis Tools with Diverse Sequencer Compatibility. GS-Preprocess is a one-line, 6-argument pipeline that generates input data for the GUIDEseq Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.GUIDEseq) from raw Illumina sequencer output. For off-target profiling, Bioconductor GUIDEseq only requires a 2-line guideRNA fasta, demultiplexed BAM files of "plus"- and "minus"-strands, and Unique Molecular Index (UMI) references for each read. Expected Runtime and Resource Usage. Sample Bioconductor GUIDEseq Input.""" ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3933 ; sc:name "GS-Preprocess" ; sc:url "http://github.com/umasstr/GS-Preprocess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:description "GS3 (Genomic Selection / Gibbs Sampling / Gauss Seidel) is a program that estimates fixed and random effects, breeding values and SNP effects for genomic selection. It includes normal, mixture, or double exponential distributions for SNP effects, i.e. GBLUP, the so-called BayesCPi, and the Bayesian Lasso. It allows estimation of the variances and effects of SNPs, polygenic and environmental effects, and also the inclusion of heterogeneous variances as for the analysis of DYD’s" ; sc:featureList edam:operation_2238, edam:operation_2945 ; sc:name "GS3" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.3" ; sc:url "https://github.com/alegarra/gs3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0176, edam:topic_0199, edam:topic_0736 ; sc:citation , "pmcid:PMC10320170", "pubmed:37207343" ; sc:description "GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3192, edam:operation_3890 ; sc:isAccessibleForFree true ; sc:name "GS-SMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gs-smd.biomodellab.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3053, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:20501604" ; sc:description "Perform gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3224 ; sc:name "GSA-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , ; sc:url "http://gsa.muldas.org" ; biotools:primaryContact "Prof. Sangsoo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3941 ; sc:citation , "pmcid:PMC9403262", "pubmed:36035404" ; sc:description "A web platform to perform, learn, and discuss gene set analysis" ; sc:featureList edam:operation_2421, edam:operation_2436, edam:operation_3928 ; sc:license "Other" ; sc:name "GSA Central" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gsa-central.github.io/education.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3170 ; sc:citation "pubmed:25213199" ; sc:description "Computational method that integrates gene expression analysis with genome wide association studies to determine whether an a priori defined sets of genes shows statistically significant, concordant differences with respect to gene expression profiles and genotypes between two biological states. Gene sets are generally a group of genes that are putatively functionally related, co-regulated, or tightly linked on the same chromosome." ; sc:featureList edam:operation_2495 ; sc:name "GSAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gsaa.unc.edu/" ; biotools:primaryContact "qxiong@email.unc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_0625, edam:topic_0780, edam:topic_2885 ; sc:citation , "pmcid:PMC6790504", "pubmed:31608375" ; sc:description """Progress in the study of genome size evolution in Asteraceae. Genome Size in Asteraceae database.""" ; sc:featureList edam:operation_0327, edam:operation_0544, edam:operation_3478 ; sc:name "GSAD" ; sc:url "http://www.asteraceaegenomesize.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3321 ; sc:citation ; sc:description "Provides a fast implementation of permutation-based gene set analysis for two-sample problems. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation." ; sc:featureList edam:operation_2495, edam:operation_3224 ; sc:license "GPL-2.0" ; sc:name "GSALightning" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSALightning.html" ; biotools:primaryContact "Billy Heung Wing Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0081, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7041101", "pubmed:32093618" ; sc:description """An efficient sequence alignment tool for intra-species genomes. GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison. Developers: Dr. Hsin-Nan Lin and Dr. Wen-Lian Hsu Institute of Information Science, Academia Sinica, Taiwan. Personal genomics and comparative genomics are two fields that are more and more important in clinical practices and genome researches.""" ; sc:featureList edam:operation_0259, edam:operation_0292, edam:operation_0452, edam:operation_3209, edam:operation_3211 ; sc:license "MIT" ; sc:name "GSAlign" ; sc:url "https://github.com/hsinnan75/GSAlign" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC3509490", "pubmed:23044539" ; sc:description "Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure." ; sc:featureList edam:operation_3223, edam:operation_3463 ; sc:license "GPL-2.0" ; sc:name "GSAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSAR.html" ; biotools:primaryContact "Galina Glazko", "Yasir Rahmatallah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3421, edam:topic_3474 ; sc:citation , "pubmed:31586211" ; sc:description """An Online Calculator for the Prediction of Survival in Glioblastoma Patients Using Classical Statistics and Machine Learning. BACKGROUND:Although survival statistics in patients with glioblastoma multiforme (GBM) are well-defined at the group level, predicting individual patient survival remains challenging because of significant variation within strata. OBJECTIVE:To compare statistical and machine learning algorithms in their ability to predict survival in GBM patients and deploy the best performing model as an online survival calculator. METHODS:Patients undergoing an operation for a histopathologically confirmed GBM were extracted from the Surveillance Epidemiology and End Results (SEER) database (2005-2015) and split into a training and hold-out test set in an 80 20 ratio""" ; sc:featureList edam:operation_0417, edam:operation_3503, edam:operation_3659 ; sc:name "GSC" ; sc:url "https://cnoc-bwh.shinyapps.io/gbmsurvivalpredictor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Genotype Sparse Compression (GSC) is an advanced tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in a compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. In our study, we successfully compressed the VCF files from the 1000 Genomes Project (1000Gpip3), consisting of 2504 samples and 80 million variants, from an uncompressed VCF file of 803.70GB to approximately 1GB." ; sc:name "GSC (Genotype Sparse Compression)" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/luo-xiaolong/GSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3321 ; sc:citation , "pmcid:PMC4705686", "pubmed:26350211" ; sc:description "This tool takes as input several lists of activated and repressed genes. It then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. Finally, it provides both traditional R functions and an interactive, user-friendly interface." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:license "GPL-2.0" ; sc:name "GSCA" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSCA.html" ; biotools:primaryContact "Zhicheng Ji" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0208, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:36549921" ; sc:description "An integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels." ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "GSCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.life.hust.edu.cn/GSCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3379 ; sc:citation , "pmcid:PMC8059024", "pubmed:33882829" ; sc:description "Gene-set Distance Analysis (GSDA) is a R library for gene-set association analysis." ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "GSDA" ; sc:softwareHelp , ; sc:url "https://CRAN.R-project.org/package=GSDA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0122, edam:topic_0654, edam:topic_3474, edam:topic_3940 ; sc:citation , "pmcid:PMC7405446", "pubmed:32758136" ; sc:description """A database of 3D chromosome and genome structures reconstructed from Hi-C data. Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory,. GSDB : Genome Structure Database.""" ; sc:featureList edam:operation_0474, edam:operation_0531, edam:operation_3891 ; sc:name "GSDB" ; sc:url "http://sysbio.rnet.missouri.edu/3dgenome/GSDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3053, edam:topic_3321 ; sc:citation "pubmed:25504850" ; sc:description "Designed for the visualization of annotated features for genes, and the generation of high-quality figures for publication." ; sc:featureList edam:operation_0337 ; sc:name "GSDS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gsds.cbi.pku.edu.cn/" ; biotools:primaryContact "Hu Bo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3169, edam:topic_3321 ; sc:citation "pubmed:18229714" ; sc:description "Database for storing, visualizing, and analyzing ChIP-based transcription factor binding data and gene expression data." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "GSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://groups.csail.mit.edu/cgs/gse.html" ; biotools:primaryContact "Alex Rolfe", "Tim Danford" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , "pmcid:PMC1239896", "pubmed:12808457", "pubmed:16199517" ; sc:description "Computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes)." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3463 ; sc:name "GSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/gsea/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3053 ; sc:description "Gene Set Enrichment Analysis (GSEA) for 2 complementary gene sets" ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:name "GSEA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/33599-gsea2" ; biotools:primaryContact "Wei Keat Lim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA)." ; sc:featureList edam:operation_3224 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "GSEABase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSEABase.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3518 ; sc:description "It implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia using parallel computation on standard workstations and institutional computer grids." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3223 ; sc:license "Artistic-2.0" ; sc:name "GSEABenchmarkeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSEABenchmarkeR.html" ; biotools:primaryContact "Ludwig Geistlinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3321 ; sc:citation ; sc:description "Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics." ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:license "Artistic-2.0" ; sc:name "GSEAlm" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GSEAlm.html" ; biotools:primaryContact "Assaf Oron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:description "This package is aimed to integrate the gene expression and biological network. 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The novel feature of GSP4PDB is that a protein-ligand structural pattern is graphically represented as a graph such that the nodes represent protein’s components (amino acids and ligands) and the edges represent structural relationships (e.g. distance relationships). 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The code is the implementation of GTB-PPI method “Prediction of Protein-Protein Interactions Based on L1-Regularized Logistic Regression and Gradient Tree Boosting”. The dataset file contains the S. cerevisiae, H. pylori ,the indepedent data set and PPIs network (one-core network and crossover network).""" ; sc:featureList edam:operation_2492, edam:operation_3659, edam:operation_3937 ; sc:name "GTB-PPI" ; sc:url "https://github.com/QUST-AIBBDRC/GTB-PPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3056, edam:topic_3574 ; sc:citation "pubmed:25568282" ; sc:description "Implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data." ; sc:featureList edam:operation_3436 ; sc:name "gTDT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/GTDT" ; biotools:primaryContact "Bingshan Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0605, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC7133423", "pubmed:32058803" ; sc:description """Graph Traversal Edit Distance and Extensions. Graph Traversal Edit Distance.""" ; sc:featureList edam:operation_0337, edam:operation_0524, edam:operation_3096 ; sc:license "MIT" ; sc:name "GTED" ; sc:url "https://github.com/Ali-E/GTED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3325, edam:topic_3337 ; sc:citation , "pmcid:PMC4010069", "pubmed:23715323" ; sc:description "Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues." ; sc:featureList edam:operation_2422, edam:operation_2495, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "GTEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.gtexportal.org/home/" ; biotools:primaryContact "GTEx contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_3678 ; sc:citation , "pmcid:PMC10196670", "pubmed:37154702" ; sc:description "Web platform for supporting ageing studies." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GTExVisualizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://gtexvisualizer.herokuapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation ; sc:description "GTfold is a fast, scalable multicore code for predicting RNA secondary structure that is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction." ; sc:featureList edam:operation_0271, edam:operation_0278, edam:operation_2423 ; sc:name "GTfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://gtfold.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2306 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3011 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "convert a GTF file to a genePred" ; sc:featureList edam:operation_3267 ; sc:name "gtftogenepred" ; sc:softwareVersion "377" ; sc:url "https://github.com/ENCODE-DCC/kentUtils/blob/master/src/hg/utils/gtfToGenePred/gtfToGenePred.c" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:36000853" ; sc:description "A software package for analyzing various features of gene models." ; sc:featureList edam:operation_2499, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GTFtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genemine.org/gtftools.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation , "pmcid:PMC10436670", "pubmed:37596691" ; sc:description "Guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GTM-decon" ; sc:url "https://github.com/li-lab-mcgill/gtm-decon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3056 ; sc:citation , "pmcid:PMC7355278", "pubmed:32657366" ; sc:description """Inference of population admixture network from local gene genealogies. Inference of population admixture network from local gene genealogies under coalescent theory. GTmix is a computer program for inferring population admixture networks from inferred local gene genealogies. If you use GTmix, please cite:. The key feature of GTmix is that it works with local gene genealogies inferred from haplotypes.""" ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "GTmix" ; sc:url "https://github.com/yufengwudcs/GTmix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Context-aware non negative matrix factorization clustering" ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "GTNMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/61729-xwasco-gtnmf" ; biotools:primaryContact "Sebastiano Vascon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """A toolkit to unify pipelines in genomic and proteomic research. GTO is a toolkit to unify pipelines in genomic and proteomic research. GTO is a toolkit for genomics and proteomics, namely for FASTQ, FASTA and SEQ formats, with many complementary tools. The toolkit is for Unix-based systems, built for ultra-fast computations. GTO supports pipes for easy integration with the sub-programs belonging to GTO as well as external tools. GTO works as LEGOs, since it allows the construction of multiple pipelines with many combinations.""" ; sc:featureList edam:operation_3096, edam:operation_3198 ; sc:license "MIT" ; sc:name "GTO" ; sc:url "http://bioinformatics.ua.pt/gto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "Efficient implementation of the Generalized Topological Overlaping Measure (GTOM)" ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "GTOM - Generalized Topological Overlaping Measure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/17668-gtom-generalized-topological-overlaping-measure" ; biotools:primaryContact "Joaquín Goñi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3516 ; sc:description "Program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE." ; sc:featureList edam:operation_0335 ; sc:license "Other" ; sc:name "GTOOL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:31849005" ; sc:description """Performing QTL and eQTL Analyses with the R-Package GenomicTools. This Package is the continuation of the genomic analysis tools part of the GeneticTools package. Website accompanying the R-package 'GenomicTools'. Today the versions 0.2.8 for GenomicTools and 0.1.4 for GenomicTools.fileHandler have been released with a couple of bugfixes and a list of new features.""" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3435 ; sc:name "GTools" ; sc:url "http://genomictools.danielfischer.name" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Guanosine-5'-triphosphate (GTP) is a purine nucleotide. GTP is involved in energy transfer or an activator of substrates in biochemical reactions. GTP Binding proteins are regulatory proteins which becomes activated when bound to GTP and is involved in signal transduction." ; sc:featureList edam:operation_2945 ; sc:name "gtpbinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/gtpbinder/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3517, edam:topic_3518, edam:topic_3676 ; sc:citation , "pmcid:PMC8922302", "pubmed:35300047" ; sc:description "R package GTQC streamlines a majority of the quality control steps and produces a detailed HTML report on a plethora of quality control metrics, thus enabling a swift and rigorous data quality inspection prior to downstream GWAS and related analyses" ; sc:featureList edam:operation_0484, edam:operation_2428, edam:operation_3196 ; sc:license "Not licensed" ; sc:name "GTQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/slzhao/GTQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33231677" ; sc:description """An integrated view of transcription regulation. ChIP-seq experiment information were collected in semi-automated way from literature, GEO and ENCODE. Raw ChIP-seq data in the form of fastq and SRA files were fetched from ENCODE and SRA databases. Clusters for the same TF revealed by different peak calling methods were joined into metaclusters. Metaclusters represent non-redundant set of transcription factor binding sites. The clustering algorithm used in GTRD is described in the main GTRD paper [6].""" ; sc:featureList edam:operation_0444, edam:operation_3222, edam:operation_3431, edam:operation_3432 ; sc:name "GTRD" ; sc:url "http://gtrd.biouml.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32844332" ; sc:description """An Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population. Global Tree Reconstruction System (GTree) software is a open source software for neuron tracing. GTree is written in C++, and freely available for academic research using. GTree is used to reconstruct neurons in single images and reconstruct neuronal population from brain-wide image stacks.""" ; sc:featureList edam:operation_3435, edam:operation_3450, edam:operation_3478 ; sc:license "MIT" ; sc:name "GTree" ; sc:url "https://github.com/GTreeSoftware/GTree" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1017 ; sc:encodingFormat edam:format_2078 ; sc:name "Sequence range" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2919 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3391 ; sc:author ; sc:citation , "pmcid:PMC4835841", "pubmed:27089965" ; sc:description "Visualize genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot." ; sc:featureList edam:operation_0362, edam:operation_3208 ; sc:license "GPL-2.0" ; sc:name "gtrellis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gtrellis.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "Genotyping-in-thousands by sequencing (GT-seq) of non-invasive fecal and degraded samples. Genetic monitoring using non-invasive samples provides a complement or alternative to traditional population monitoring methods. However, Next Generation Sequencing approaches to monitoring typically require high quality DNA and the use of non-invasive samples (e.g. scat) is often challenged by poor DNA quality and contamination by non-target species. One promising solution is a highly multiplexed sequencing approach called Genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on non-invasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from non-invasively collected fecal samples" ; sc:featureList edam:operation_2428, edam:operation_3196 ; sc:name "GTseq-Pipeline" ; sc:url "https://github.com/GTseq/GTseq-Pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0152, edam:topic_0623, edam:topic_3292, edam:topic_3576 ; sc:citation , "pubmed:34351427" ; sc:description "GTXplorer provides an interactive platform for users to access, navigate, download and visualize the evolutionary information from primary protein sequences of the GT-A fold families." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "GTXplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vulcan.cs.uga.edu/gtxplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "A fast compression and cloud transmission tool optimized for FASTQ files." ; sc:featureList edam:operation_0335 ; sc:name "GTZ" ; sc:softwareHelp ; sc:url "https://github.com/Genetalks/gtz" ; biotools:primaryContact "Chengkun Wu", "Zhuo Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0176, edam:topic_0593, edam:topic_0659 ; sc:citation "pubmed:22160811" ; sc:description "Tool designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data." ; sc:featureList edam:operation_2945 ; sc:name "GUARDD" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://research.cbc.osu.edu/foster.281/software/#GUARDD" ; biotools:primaryContact "Mark P. Foster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3673 ; sc:citation , "pmcid:PMC4330336", "pubmed:25414349" ; sc:description "Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences." ; sc:featureList edam:operation_0323, edam:operation_3196, edam:operation_3745 ; sc:license "GPL-2.0" ; sc:name "Gubbins" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/nickjcroucher/gubbins" ; biotools:primaryContact "Simon R. Harris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "GUESS is a computationally optimised C++ implementation of a fully Bayesian variable selection approach that can analyse, in a genome-wide context, single and multiple responses in an integrated way." ; sc:featureList edam:operation_2409, edam:operation_2421 ; sc:name "GUESS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://bgx.org.uk/software/guess.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "Build Detection and Diagnosis Tools of Covid-19 on Chest Radiographs. Everything is in GUI." ; sc:isAccessibleForFree true ; sc:name "GUI-fying to build DL Model (Classification)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75166-gui-fying-to-build-dl-model-classification" ; biotools:primaryContact "Kevin Chng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "The GUI is easy to access and reduces the load of ophthalmologists in analyzing the retinal profile." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Graphical User Interface for Retinal Blood Vessel Extraction from Fundus Images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63118-graphical-user-interface-for-retinal-blood-vessel-extraction-from-fundus-images" ; biotools:primaryContact "Jemima Jeba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3374, edam:topic_3576 ; sc:description "A GUI for solving a set of delay differential equations (DDEs) and local search for best solutions" ; sc:featureList edam:operation_2426, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Graphical User Interface for Solving Delay Differential Equations and doing Local Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/37044-a-graphical-user-interface-for-solving-delay-differential-equations-and-doing-local-search" ; biotools:primaryContact "Dr. Soumya Banerjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation "pubmed:20497997" ; sc:description "Assess alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences, output is a graphic visualization of the alignment with confidence scores at each residue." ; sc:featureList edam:operation_0292, edam:operation_2233 ; sc:name "GUIDANCE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://guidance.tau.ac.il" ; biotools:primaryContact "GUIDANCE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3168, edam:topic_3572 ; sc:citation , "pmcid:PMC4489236", "pubmed:25883146" ; sc:description "Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters." ; sc:featureList edam:operation_0258 ; sc:name "GUIDANCE2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://guidance.tau.ac.il/ver2/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation ; sc:description "Guide (Genome Informatics Data Explorer) is a desktop application designed for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules. It also integrates useful data from multiple sources, such as gene annotation and orthologue data, and enables editing of R commands to customise the analyses for advanced users." ; sc:featureList edam:operation_0226, edam:operation_2495, edam:operation_3096 ; sc:name "Guide" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://guide.wehi.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:21685050" ; sc:description "An R package for the joint analysis of clinical microarray profiles and additional per gene measurements." ; sc:featureList edam:operation_0313, edam:operation_2495 ; sc:name "GuidedClustering" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://compdiag.uni-regensburg.de/software/guidedClustering.shtml" ; biotools:primaryContact "Claudio Lottaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0632, edam:topic_3512, edam:topic_3697 ; sc:citation , "pmcid:PMC7021469", "pubmed:32051236" ; sc:description """A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes. Pan-bacterial, genome-wide guide designer.""" ; sc:featureList edam:operation_0362, edam:operation_3096, edam:operation_3219 ; sc:name "GuideFinder" ; sc:url "https://github.com/ohlab/Guide-Finder" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_2205 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3752 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "Software to design CRISPR-Cas guide RNA pools in non-model genomes." ; sc:featureList edam:operation_2419 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "GuideMaker" ; sc:softwareHelp ; sc:softwareVersion "v0.3.1", "v0.3.4" ; sc:url "https://guidemaker.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0625, edam:topic_3474 ; sc:citation ; sc:description """A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. GuidePro:A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. GuidePro is a two-layer ensemble predictor that enables the integration of multiple predictive methods and feature sets to predict sgRNA efficiency for the CRISPR Cas9 protein knockouts.""" ; sc:featureList edam:operation_3092 ; sc:name "GuidePro" ; sc:url "https://bioinformatics.mdanderson.org/apps/GuidePro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:encodingFormat edam:format_2330 ; sc:name "Database ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_2032 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_1775, edam:topic_3678 ; sc:citation ; sc:description "Graphical User Interface for DNA Editing Screens (GUIDES) is a web application that designs CRISPR knockout libraries to target custom subsets of genes in the human or mouse genome" ; sc:featureList edam:operation_2419, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "GUIDES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://guides.sanjanalab.org/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0099, edam:topic_3297, edam:topic_3371 ; sc:citation ; sc:description "A generalized CRISPR guideRNA design tool." ; sc:featureList edam:operation_3095 ; sc:name "GuideScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.guidescan.com/" ; biotools:primaryContact "Andrea Ventura", "Christina Leslie", "Developers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3511 ; sc:citation ; sc:description "The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites." ; sc:featureList edam:operation_0415 ; sc:license "GPL-2.0" ; sc:name "GUIDEseq" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GUIDEseq.html" ; biotools:primaryContact "Lihua Julie Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3295, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "GUIdEStaR (G-quadruplex, uORF, IRES, Epigenetics, Small RNA, Repeats) is the integrated metadatabase in conjunction with neural network methods." ; sc:featureList edam:operation_2422 ; sc:name "GUIdEStaR" ; sc:url "http://www.guidestar.kr" ; biotools:primaryContact "Jee Eun Kang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0219, edam:topic_3336 ; sc:citation , "pmcid:PMC3965070", "pubmed:24234439" ; sc:contributor "British Pharmacological Society (BPS)", "International Union of Basic and Clinical Pharmacology (IUPHAR)", "Wellcome Trust" ; sc:description "An expert-curated pharmacological database of drug targets and their ligands." ; sc:featureList edam:operation_2421, edam:operation_3760 ; sc:funder "British Pharmacological Society (BPS)", "International Union of Basic and Clinical Pharmacology (IUPHAR)", "Wellcome Trust" ; sc:license "CC-BY-SA-3.0" ; sc:name "IUPHAR BPS Guide to PHARMACOLOGY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "The University of Edinburgh", "ed.ac.uk" ; sc:softwareHelp ; sc:url "http://www.guidetopharmacology.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3125, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description """revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization. GuidingNet is a method to reveal transcriptional cofactor and predict binding for DNA methyltransferase by network regularization.""" ; sc:featureList edam:operation_0239, edam:operation_0417, edam:operation_0445, edam:operation_2492 ; sc:name "GuidingNet" ; sc:url "https://github.com/AMSSwanglab/GuidingNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pmcid:PMC4821530", "pubmed:27045593" ; sc:description "GUIdock allows for the facile distribution of a systems biology application along with its graphics environment." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "GUIdock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/WebDataScience/GUIdock" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3053, edam:topic_3372 ; sc:citation ; sc:description "Using a graphical desktop sharing system to provide a browser-based interface for containerized software." ; sc:featureList edam:operation_3762 ; sc:license "MIT" ; sc:name "GUIdock-VNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioDepot/GUIdock-VNC" ; biotools:primaryContact "Ka Yee Yeung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3396 ; sc:author ; sc:citation , "pmcid:PMC3448640", "pubmed:23028459" ; sc:description "Framework built for the prioritization of disease candidate genes using a priori gene-disease associations and protein interactions. It consists of implementations of 8 algorithms: NetScore, NetZcore, NetShort, NetCombo, fFlow, NetRank, NetWalk and NetProp." ; sc:featureList edam:operation_3501 ; sc:name "GUILD" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://sbi.imim.es/web/index.php/research/software/guildsoftware" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2339 ; sc:encodingFormat edam:format_1963 ; sc:name "Ontology concept name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3619 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3396 ; sc:author ; sc:citation , "pubmed:23028459", "pubmed:24532728" ; sc:contributor "Javier Garcia-Garcia", "MICINN/MINECO & FEBS BIO2011-22568" ; sc:description "Uses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. These gene products are fed to a species-specific interaction network as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm." ; sc:featureList edam:operation_3501 ; sc:funder "MICINN/MINECO & FEBS BIO2011-22568" ; sc:name "GUILDify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UPF", "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://sbi.imim.es/web/GUILDify.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_3170, edam:topic_3377, edam:topic_3474 ; sc:citation , "pmcid:PMC10156718", "pubmed:37137934" ; sc:description "A machine learning method for the identification and characterization of novel COVID-19 drug targets." ; sc:featureList edam:operation_0282, edam:operation_3223, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "GuiltyTargets-COVID-19" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://guiltytargets-covid.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3379 ; sc:citation , "pmcid:PMC7469913", "pubmed:32580715" ; sc:description """a R package for dose escalation strategies in phase I cancer clinical trials. Graphical User Interfaces for Phase I Designs.""" ; sc:featureList edam:operation_2426, edam:operation_3454, edam:operation_3659 ; sc:name "GUIP1" ; sc:url "https://github.com/ddinart/GUIP1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_2573, edam:format_3586 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3170 ; sc:citation , "pmcid:PMC4864564", "pubmed:27239475" ; sc:description "The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "Guitar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Guitar.html" ; biotools:primaryContact "Jia Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_3168, edam:topic_3301 ; sc:citation ; sc:description """Detection of Chimerism and Contamination in Prokaryotic Genomes. Python package for detection of chimerism and contamination in prokaryotic genomes.""" ; sc:featureList edam:operation_0310, edam:operation_0450, edam:operation_3918 ; sc:license "GPL-3.0" ; sc:name "GUNC" ; sc:url "https://github.com/grp-bork/gunc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3301, edam:topic_3697 ; sc:citation "pubmed:22711789" ; sc:description "Software which implements a generalized UniFrac distance for analysis of microbiome data." ; sc:featureList edam:operation_0324 ; sc:name "GUniFrac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/GUniFrac/index.html" ; biotools:primaryContact "Hongzhe Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:15706530" ; sc:description "Program to visualize sequence annotation data of the genetic sequence data with graphical layout. This highly interactive program allows scrolling and zooming from the genomic landscape to discrete nucleic acid sequences. Its main function is quick rendering of data on a standalone personal computer to save the layout as a parsonal file. With optional link to the internet resources, and printing support, this program tries to make more greater use of computational media in research actitiviy." ; sc:featureList edam:operation_0564 ; sc:name "GUPPY" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://staff.aist.go.jp/yutaka.ueno/guppy/" ; biotools:primaryContact "Yutaka Ueno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "Python toolbox for the analysis of fiber photometry data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "GuPPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LernerLab/GuPPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0623, edam:topic_3407 ; sc:citation , "pmcid:PMC9039005", "pubmed:35495163" ; sc:description "A platform for gene function analysis in G. uralensis" ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3672 ; sc:license "Not licensed" ; sc:name "GURFAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.gzybioinformatics.cn/GURFAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC7703750", "pubmed:32176769" ; sc:description """Somatic selection distinguishes oncogenes and tumor suppressor genes. GUST - Genes Under Selection in Tumors. GUST predicts oncogenes (OGs), tumor suppressor gens (TSGs) and passenger genes (PGs) using somatic SNVs detected in a collection of tumors. It can classify single genes from targetted sequencing or multiple genes from whole-exome sequencing.""" ; sc:featureList edam:operation_2454, edam:operation_3227, edam:operation_3436 ; sc:name "GUST" ; sc:url "https://github.com/liliulab/gust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3068, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation , "pubmed:31584099" ; sc:description """a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. gutMDisorder (http: bio-annotation.cn gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in disorders and interventions. Alterations in the composition of the gut microbial community play crucial roles in the development of chronic disorders. And the beneficial effects of drugs, foods and other intervention measures on disorders could be microbially mediated. The current version of gutMDisorder documents 2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3799 ; sc:name "gutMDisorder" ; sc:url "http://bio-annotation.cn/gutMDisorder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3174, edam:topic_3360, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:33515036" ; sc:description """A server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. The compositionality of the microbiome data is well-known but often neglected. The compositional transformation pertains to the supervised learning of microbiome data and is a critical step that decides the performance and reliability of the disease classifiers. We value the excellent performance of the distal discriminative balance analysis (DBA) method, which selects distal balances of pairs and trios of bacteria, in addressing the classification of high-dimensional microbiome data. By applying this method to the species-level abundances of all the disease phenotypes in the GMrepo database, we build a balance-based model repository for the classification of human gut microbiome-related diseases. The model repository supports the prediction of disease risks for new sample(s)""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3659 ; sc:name "GutBalance" ; sc:url "http://lab.malab.cn/soft/GutBalance" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3375, edam:topic_3407, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:37356904" ; sc:description "Tool for prediction of human gut bacteria-mediated biotransformation of biotic and xenobiotic molecules using machine learning." ; sc:featureList edam:operation_3660, edam:operation_3929, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "GutBug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://metabiosys.iiserb.ac.in/gutbug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3174, edam:topic_3419, edam:topic_3697 ; sc:citation , "pubmed:32496513" ; sc:description """a database of the human gut MEtaGenome Atlas. Recently numerous studies have identified that the perturbations in the gut microbiome were associated with human health, including diseases and cancers, even mental health. The recent development of high-throughput sequencing based metagenomics technologies such as 16S ribosomal RNA gene amplicon-based and genome-centric approaches have burst the profiling of the landscape for gut microbiome and the identification of human health related microbes. Here, we presented the gutMEGA database, which hosted the results of metagenomics studies.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3799 ; sc:name "gutMEGA" ; sc:url "http://gutmega.omicsbio.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:34500458" ; sc:description "A comprehensive database for target genes of gut microbes and microbial metabolites." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "gutMGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-annotation.cn/gutmgene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3382, edam:topic_3407, edam:topic_3697 ; sc:citation ; sc:description "An interactive platform for gut microbiome interaction exploration." ; sc:featureList edam:operation_0276, edam:operation_3463, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "GutMicroNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gutmicro.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3697 ; sc:citation , "pubmed:34019648" ; sc:description "gutSMASH web server is an automated identification of primary metabolic gene clusters from the gut microbiota. It is an approach to functionally profile the human microbiome for specialized primary metabolic gene clusters." ; sc:featureList edam:operation_3432, edam:operation_3660, edam:operation_3929 ; sc:license "AGPL-3.0" ; sc:name "gutSMASH" ; sc:softwareHelp ; sc:url "https://gutsmash.bioinformatics.nl/" ; biotools:primaryContact , "Michael A Fischbach" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1211, edam:format_1216, edam:format_1925, edam:format_1927, edam:format_1929, edam:format_1930, edam:format_1942, edam:format_1948, edam:format_2330, edam:format_2332 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0097 ; sc:author "Wolfgang Gerlach" ; sc:citation ; sc:description "RNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length." ; sc:featureList edam:operation_0239, edam:operation_0338 ; sc:isAccessibleForFree true ; sc:name "GUUGle" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://bibiserv.cebitec.uni-bielefeld.de/guugle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3517 ; sc:citation , "pmcid:PMC10044409", "pubmed:36978010" ; sc:description "Efficient random access compression for gene sequence variations." ; sc:featureList edam:operation_3196, edam:operation_3211, edam:operation_3227, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "GVC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sXperfect/gvc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0797 ; sc:citation ; sc:description "A novel implementation that incorporates most features of the VISTA family—fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers." ; sc:featureList edam:operation_0448, edam:operation_0564 ; sc:license "Not licensed" ; sc:name "gVISTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.lbl.gov/cgi-bin/GenomeVista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622 ; sc:citation "pubmed:27272860" ; sc:description "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. This package uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data." ; sc:featureList edam:operation_0564 ; sc:license "Artistic-2.0" ; sc:name "Gviz" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Gviz.html" ; biotools:primaryContact "Florian Hahne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC8235866", "pubmed:34174938" ; sc:description "GVViZ: A tool for visualizing genes with disease causing variants." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "GVViZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/drzeeshanahmed/GVViZ-Public" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC5423544", "pubmed:28299468" ; sc:description "A Statistical Package to Conduct Genome-Wide Structural Equation Modeling." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "GW-SEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.people.vcu.edu/~bverhulst/GW-SEM/GW-SEM.R" ; biotools:primaryContact "Brad Verhulst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3055 ; sc:citation , "pmcid:PMC2893603", "pubmed:20509871" ; sc:description "Genome-Wide Association Meta Analysis software performs meta-analysis of the results of GWA studies of binary or quantitative phenotypes. Fixed- and random-effect meta-analyses are performed for both directly genotyped and imputed SNPs using estimates of the allelic odds ratio and 95% confidence interval for binary traits, and estimates of the allelic effect size and standard error for quantitative phenotypes." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "GWAMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.2.2" ; sc:url "https://www.geenivaramu.ee/en/tools/gwama" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "GWAPP enables reseachers working with Arabidopsis thaliana to do Genome Wide Association Mapping (GWAS) on their phenotypes." ; sc:featureList edam:operation_2429 ; sc:license "Not licensed" ; sc:name "GWAPP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gwapp.gmi.oeaw.ac.at/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:28108451" ; sc:description "Robust Analysis and Meta-Analysis of Genome-Wide Association Studies." ; sc:featureList edam:operation_0224 ; sc:name "GWAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.compgen.org/tools/GWAR" ; biotools:primaryContact "Pantelis Bagos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """an R shiny web application for visualizing genome-wide association studies data. an R shiny web application for visualizing genome-wide association studies (GWAS) data using the following plots:. The application is hosted at gwaRs.""" ; sc:featureList edam:operation_2939, edam:operation_3661, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "gwaRs" ; sc:url "https://gwasviz.shinyapps.io/gwaRs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description """The Parkinson’s Disease GWAS Locus Browser. The NHGRI-EBI GWAS Catalog: a curated collection of all human genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI. Summary Statistics from Other GWASes:.""" ; sc:featureList edam:operation_0305, edam:operation_0337, edam:operation_3226, edam:operation_3791 ; sc:name "GWAS" ; sc:url "https://pdgenetics.shinyapps.io/GWASBrowser/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC6943065", "pubmed:31566222" ; sc:description "A curated resource of genome-wide variant-trait associations in plants and animals | a curated resource of genome-wide variant-trait associations | e.g. plant; plant height; Zm00001d021954; chr1:14702150-37601000 | GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2019. [PMID=31566222]" ; sc:featureList edam:operation_0279, edam:operation_3095, edam:operation_3559 ; sc:name "GWAS Atlas" ; sc:url "https://bigd.big.ac.cn/gwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3316, edam:topic_3517 ; sc:citation ; sc:description """The variant call format provides efficient and robust storage of GWAS summary statistics. VCF vs plain text GWAS storage formats.""" ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3791 ; sc:license "MIT" ; sc:name "GWAS-VCF" ; sc:url "https://gwas.mrcieu.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3168, edam:topic_3295, edam:topic_3517 ; sc:citation "pubmed:23723249" ; sc:description "GWAS3D web server computes the probability of genetics variants affecting regulatory pathways and underlying disease/trait associations by integrating chromatin state, functional genomics, sequence motif, and conservation information when given GWAS data or variant list. GWAS3D also provides comprehensive annotations and visualizations to help users interpreting the results." ; sc:featureList edam:operation_0487, edam:operation_2436, edam:operation_3197, edam:operation_3227 ; sc:name "GWAS3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jjwanglab.org/gwas3d" ; biotools:primaryContact "GWAS3 Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3173, edam:topic_3517 ; sc:citation ; sc:description "Systematically evaluates GWAS signals and identifies context-specific regulatory variants. The updated web server includes six major features: (i) updates the regulatory variant prioritization method with our new algorithm; (ii) incorporates 127 tissue/cell type-specific epigenomes data; (iii) integrates motifs of 1480 transcriptional regulators from 13 public resources; (iv) uniformly processes Hi-C data and generates significant interactions at 5 kb resolution across 60 tissues/cell types; (v) adds comprehensive non-coding variant functional annotations; (vi) equips a highly interactive visualization function for SNP-target interaction." ; sc:featureList edam:operation_0438, edam:operation_3196, edam:operation_3227 ; sc:name "GWAS4D" ; sc:softwareHelp ; sc:url "http://mulinlab.tmu.edu.cn/gwas4d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3325, edam:topic_3366, edam:topic_3517 ; sc:citation , , , "pmcid:PMC3965119", "pmcid:PMC6323933", "pubmed:24316577", "pubmed:27899670", "pubmed:30445434" ; sc:description "A catalogue that provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5." ; sc:featureList edam:operation_0484, edam:operation_2421, edam:operation_2429, edam:operation_3459 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "GWAS catalog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.ebi.ac.uk/gwas/" ; biotools:primaryContact "GWAS Catalog Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3517 ; sc:citation ; sc:description "Represent and model data in the EMBL-EBI GWAS catalog." ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:license "Artistic-2.0" ; sc:name "gwascat" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/gwascat.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3517 ; sc:citation "pubmed:22139925" ; sc:description "Database for human genetic variants (GV) identified by genome-wide association studies. Contains twenty times more data than the NHGRI GWAS Catalog, manually curated from literature. Also has annotations for each GV." ; sc:featureList edam:operation_0282, edam:operation_0487, edam:operation_2436, edam:operation_3197 ; sc:name "GWASdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jjwanglab.org:8080/gwasdb/" ; biotools:primaryContact "For general questions", "For technical support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:34814627" ; sc:description "An R script to filter genome-wide association study" ; sc:featureList edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "gwasfilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lab319/gwas_filter" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3003, edam:format_3288 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3517 ; sc:author "Arcadi Navarro Cuartiellas", "Fernando Muñiz Fernando" ; sc:citation , "pubmed:21586520" ; sc:contributor "Angel Carreño Torres", "Carlos Morcillo Suarez" ; sc:description "User-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware. GWASpi aims to be a start-to-finish GWAS management application, from raw data to results, containing the most common analysis tools." ; sc:featureList edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "Genome Wide Association Study pipeline (GWASpi)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UPF", "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.gwaspi.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3517 ; sc:citation , "pubmed:31373609" ; sc:description "Package to query, download and wrangle GWAS Catalog data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "gwasrapidd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ramiromagno/gwasrapidd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , "pmcid:PMC3519456", "pubmed:23052040" ; sc:description "Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis." ; sc:featureList edam:operation_0226, edam:operation_2945, edam:operation_3431 ; sc:license "Artistic-2.0" ; sc:name "GWASTools" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/GWASTools.html" ; biotools:primaryContact , "Adrienne Stilp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:30395168" ; sc:description "R package for genome-wide survival analysis." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "gwasurvivr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/gwasurvivr" ; biotools:primaryContact "Abbas Rizvi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3678 ; sc:citation ; sc:description "GWAtoolbox is an R-package for fast quality control and data handling of multiple data files obtained from genome-wide association studies (GWAS)." ; sc:featureList edam:operation_2409, edam:operation_2428, edam:operation_2945 ; sc:name "GWAtoolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.4-7" ; sc:url "http://www.eurac.edu/en/research/health/biomed/services/Pages/GWAtoolbox.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description """Gene Co-expression Networks Analysis and Extended Modules Characterization in a Single Bioconductor Package. Pipeline for augmented co-expression analysis.""" ; sc:featureList edam:operation_3463, edam:operation_3766, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "GWENA" ; sc:url "https://bioconductor.org/packages/release/bioc/html/GWENA.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0219, edam:topic_0654 ; sc:citation "pubmed:12238765" ; sc:description "Allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search" ; sc:featureList edam:operation_0346, edam:operation_2451 ; sc:name "GWFASTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/gwfasta/" ; biotools:primaryContact "Dr.G.P.S.Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_0781 ; sc:citation "pubmed:19900970" ; sc:description "Integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions." ; sc:featureList edam:operation_0339, edam:operation_0477, edam:operation_0478, edam:operation_0482, edam:operation_2464 ; sc:name "GWIDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gwidd.bioinformatics.ku.edu" ; biotools:primaryContact "GWIDD Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0769, edam:topic_3293, edam:topic_3945 ; sc:citation , "pmcid:PMC7718741", "pubmed:33093185" ; sc:description """A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level. GWideCodeML is a Python package that provides support for testing evolutionary hypothesis using codeml (from the PAML package) in a genome-wide framework.""" ; sc:featureList edam:operation_0324, edam:operation_2238, edam:operation_2479 ; sc:license "GPL-3.0" ; sc:name "GWideCodeML" ; sc:url "https://github.com/lauguma/gwidecodeml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203 ; sc:author "Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM" ; sc:citation , "pmcid:PMC3965066", "pubmed:24185699", "pubmed:25736862" ; sc:contributor "Science Foundation Ireland" ; sc:description "Specialized ribosome profiling (ribo-seq) browser providing free access to the genomic alignments of ribo-seq reads in conjunction with mRNA-seq controls along with relevant annotation tracks. Based on the UCSC Genome Browser, the tool’s ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes while the separate tracks for each ribo-seq study enables cross-study comparisons." ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:funder "Science Foundation Ireland" ; sc:isAccessibleForFree true ; sc:name "GWIPS-viz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "School of Biochemistry & Cell Biology, University College Cork", "ucc.ie" ; sc:softwareHelp , ; sc:url "http://gwips.ucc.ie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:21829371" ; sc:description "Use greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal." ; sc:featureList edam:operation_3664 ; sc:name "GWiS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/baderlab/gwis" ; biotools:primaryContact "Joel S. Bader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2275, edam:topic_3343 ; sc:citation , "pubmed:32679606" ; sc:description """A grey wolf optimization approach to rigid and flexible receptor docking. Computational Biology and Bioinformatics Lab (CBBio). Department of Computer and Information Science. 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HAMAP signatures are also integrated into InterPro and the HAMAP rules into UniRule, the core part of the UniProt automatic annotation pipeline.""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_2995 ; sc:license "CC0-1.0" ; sc:name "HAMAP_SPARQL" ; sc:url "https://hamap.expasy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2258, edam:topic_2815 ; sc:citation ; sc:description "Database of human autophagy modulators with specific pathway and disease information." ; sc:featureList edam:operation_2421 ; sc:license "CC-BY-4.0" ; sc:name "HAMdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hamdb.scbdd.com/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0154, edam:topic_0199, edam:topic_0602, edam:topic_2830 ; sc:citation ; sc:description "A Bayesian regression model that integrates information to detect HLA-associated mutations." ; sc:featureList edam:operation_0324, edam:operation_0416, edam:operation_0479, edam:operation_3227, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HAMdetector" ; sc:url "https://github.com/HAMdetector/Escape.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269 ; sc:citation ; sc:description """A fast and simple package for calculating Hamming distance from multiple sequence data for heatmap visualization. Hamming distance calculation from multiple sequence data for heatmap visualization.""" ; sc:featureList edam:operation_0289, edam:operation_0337, edam:operation_2950 ; sc:license "MIT" ; sc:name "HamHeat" ; sc:url "https://github.com/alexeyrakov/HamHeat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0797, edam:topic_2269 ; sc:citation "pubmed:27177143" ; sc:description "Fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration." ; sc:featureList edam:operation_2409, edam:operation_3664 ; sc:name "HaMMLET" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.rutgers.edu/Software/HaMMLET/" ; biotools:primaryContact "John Wiedenhoeft" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3510 ; sc:citation "pubmed:26342231" ; sc:description "Tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs." ; sc:featureList edam:operation_0291 ; sc:name "Hammock" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.recamo.cz/en/software/hammock-cluster-peptides/" ; biotools:primaryContact "Adam Krejci" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3174, edam:topic_3277, edam:topic_3305 ; sc:citation ; sc:description "Benchmarking software to predict antibiotic resistance phenotypes in shotgun metagenomes using simulated data." ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "hAMRoaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ewissel/hAMRoaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3301, edam:topic_3305 ; sc:description "Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure" ; sc:featureList edam:operation_1812, edam:operation_2409, edam:operation_3482 ; sc:name "hAMRonization" ; sc:url "https://github.com/pha4ge/hAMRonization" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:19925686" ; sc:description "Tool for depicting experiments in a microarray data set as a set of minimum spanning trees." ; sc:featureList edam:operation_2495 ; sc:name "HAMSTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rwanwork/Hamster" ; biotools:primaryContact "Raymond Wan" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3303 ; sc:author "Daniel Georgiev", "Lucie Houdová", "Miloš Fetter" ; sc:contributor "TA CR" ; sc:description "Haplotype analyzer for the Czech population." ; sc:featureList edam:operation_0337 ; sc:funder "TA CR" ; sc:name "HANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of West Bohemia, Czech Republic" ; sc:softwareVersion "1" ; sc:url "https://cds-hana.zcu.cz/" ; biotools:primaryContact "Daniel Georgiev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3071, edam:topic_3406 ; sc:citation , "pubmed:32891434" ; sc:description """A dedicated quality of life resource following the diagnosis and treatment of head and neck cancer. A unique online database of papers published on quality of life in head and neck cancer. HANDLE-ON-QOL is a unique online searchable database of all papers published from 1982 to present on quality of life in head and neck cancer that have used questionnaires. This website uses cookies. By continuing to browse the site you are agreeing to our use of cookies. Accept More info.""" ; sc:featureList edam:operation_2421 ; sc:name "Handle-On-QOL" ; sc:url "http://www.handle-on-qol.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3068, edam:topic_3958 ; sc:citation ; sc:description "HandyCNV is an R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3661, edam:operation_3961 ; sc:license "GPL-3.0" ; sc:name "HandyCNV" ; sc:softwareHelp ; sc:url "https://github.com/JH-Zhou/HandyCNV" ; biotools:primaryContact "Yuangang Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2533, edam:topic_3053 ; sc:citation "pubmed:22045683" ; sc:description "Tool to predict the deleterious effects of a mutation by using 10 Neutral- Disease Mis-Sense Mutation Discriminatory (NDMSMD) features." ; sc:featureList edam:operation_2423, edam:operation_2479, edam:operation_3197 ; sc:name "Hansa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hansa.cdfd.org.in:8080/" ; biotools:primaryContact "H.A.Nagarajaram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3305, edam:topic_3379, edam:topic_3421 ; sc:citation , "pmcid:PMC8573013", "pubmed:34754431" ; sc:description "HantaReg is a registry for epidemiological studies, outbreaks and clinical studies on hantavirus disease. Frequent outbreaks around the globe and endemic appearance in different parts of the world emphasize the substantial risk of hantavirus diseases. Increasing incidence rates, trends of changing distribution of hantavirus species and new insights into clinical courses of hantavirus diseases call for multinational surveillance. Furthermore, evidence-based guidelines for the management of hantavirus diseases and scoring systems, which allow stratification of patients into risk categories, are lacking." ; sc:featureList edam:operation_3907 ; sc:name "HantaReg" ; sc:url "http://clinicalsurveys.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0654, edam:topic_3337 ; sc:citation , "pmcid:PMC7118582", "pubmed:32169169" ; sc:description """A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data. The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3211, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "hap-IBD" ; sc:url "https://github.com/browning-lab/hap-ibd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3500 ; sc:citation , "pmcid:PMC7302376", "pubmed:32552661" ; sc:description """Reconstructing accurate and long polyploid haplotypes using linked reads. We are providing ful support for this package. Feel free to ask your questions through email (sina.majidian@gmail.com) or Github's issue.""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3198, edam:operation_3227, edam:operation_3432 ; sc:name "Hap10" ; sc:url "https://sourceforge.net/projects/SDhaP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "software for combining haplotype estimates and SNP array data for identifying somatic segmental copy number and copy-neutral mutations." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "hapLOH" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://haploh.scheetlabsoftware.org/" ; biotools:primaryContact "Selina Vattathil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3053 ; sc:citation ; sc:description "R code for mapping HAPlotype-haplotype interactions with Adaptive Lasso." ; sc:featureList edam:operation_2429 ; sc:name "HAPAL" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.stt.msu.edu/~cui/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "An approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model." ; sc:featureList edam:operation_0310 ; sc:name "hapAssembly" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://rnc.r.dendai.ac.jp/hapAssembly.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:15583426" ; sc:description "R package implementing methods described in Burkett et al. (2004) for likelihood inference of trait associations with SNP haplotypes and other attributes using the EM Algorithm." ; sc:featureList edam:operation_0487, edam:operation_2426 ; sc:name "hapassoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stat.sfu.ca/statgen/research/hapassoc.html" ; biotools:primaryContact "Brad McNeney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "This method leverages the long-range information of sequencing reads that allows to obtain assembled haplotypes fragmented in a lower number of unphased haplotype blocks. At the same time, this method is also able to deal with higher coverages to better correct the errors in the original reads and to obtain more accurate haplotypes as a result." ; sc:featureList edam:operation_0487 ; sc:license "GPL-3.0" ; sc:name "HapCHAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hapchat.algolab.eu" ; biotools:primaryContact "Murray D. Patterson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "A software package for association mapping." ; sc:featureList edam:operation_0282 ; sc:name "HapCluster" ; sc:operatingSystem "Linux" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "2.3.0" ; sc:url "http://www.daimi.au.dk/~mailund/HapCluster/" ; biotools:primaryContact "Thomas Mailund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "A fast and memory-efficient method for haplotype assembly from long gapless reads, like those produced by SMRT sequencing technologies (PacBio RS II) and Oxford Nanopore flow cell technologies (MinION)." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "HapCol" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-BICOCCA" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "http://hapcol.algolab.eu/" ; biotools:primaryContact "Bonizzoni Paola" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1863 ; sc:encodingFormat edam:format_1964 ; sc:name "Haplotype map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies. The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md""" ; sc:featureList edam:operation_0487, edam:operation_3225 ; sc:name "HapCUT2" ; sc:softwareVersion "1.0", "1.1", "1.2", "1.3", "1.3.1" ; sc:url "https://github.com/vibansal/HapCUT2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3056, edam:topic_3796 ; sc:citation , "pubmed:35482481" ; sc:description "A package containing algorithms, exKING-robust and KIMGENS, to estimate kinship in haploid-diploid mixed populations." ; sc:featureList edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HapDipKinship" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YenWenWang/HapDipKinship" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0634, edam:topic_3168 ; sc:citation , "pmcid:PMC3125762", "pubmed:21576217" ; sc:description "Tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible." ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_0525, edam:operation_3096 ; sc:name "HapEdit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://embio.yonsei.ac.kr/hapedit" ; biotools:primaryContact "Sanghyun Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_3053 ; sc:description "HapEvolution is a cooperative coevolutionary algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes." ; sc:featureList edam:operation_3454 ; sc:name "HapEvolution" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.med.mun.ca/PTRG/What-We-Do/Research/PTRG-Research/HapEvolution.aspx" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330, edam:format_3475, edam:format_3508, edam:format_3547 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1863 ; sc:encodingFormat edam:format_2330, edam:format_3475, edam:format_3508, edam:format_3547 ; sc:name "Haplotype map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3475, edam:format_3508, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3475, edam:format_3508, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625 ; sc:citation , "pmcid:PMC3905877", "pubmed:24174545" ; sc:description "Package to identify very short IBD segments in large sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats." ; sc:featureList edam:operation_0487 ; sc:license "GPL-2.0" ; sc:name "hapFabia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hapFabia.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3056, edam:topic_3516 ; sc:citation ; sc:description "Software for the detection of selection signatures based on multiple population genotyping data." ; sc:featureList edam:operation_0253, edam:operation_3196 ; sc:name "hapFLK" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "https://forge-dga.jouy.inra.fr/projects/hapflk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:26449930" ; sc:description "Python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify." ; sc:featureList edam:operation_0337, edam:operation_2403, edam:operation_3225 ; sc:name "HapFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://mjsull.github.io/HapFlow/" ; biotools:primaryContact "Issue reporting", "Mitchell J Sullivan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0196, edam:topic_0781, edam:topic_3168 ; sc:citation , "pmcid:PMC7412389", "pubmed:32674515" ; sc:description """Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics""" ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_3180, edam:operation_3227, edam:operation_3644 ; sc:name "HAPHPIPE" ; sc:url "https://gwcbi.github.io/haphpipe_docs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families." ; sc:featureList edam:operation_0487 ; sc:name "Hapi" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.03" ; sc:url "http://hapi.csail.mit.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3277 ; sc:citation ; sc:description "HAPI-UR is a program for inferring phased haplotypes from unphased genotypes" ; sc:featureList edam:operation_0487 ; sc:name "HAPI-UR" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.01" ; sc:url "http://code.google.com/p/hapi-ur/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3421 ; sc:citation , "pubmed:34799151" ; sc:description "Graphical user interface for the haplotype frequency estimation software Hapl-o-Mat." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Hapl-o-Mat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DKMS/hapl-o-Mat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3053 ; sc:citation "pubmed:22537299" ; sc:description "Tool for assembling robust haplotype regions given alignments (from de-novo assembly or mapping to a reference) of genetically diverse sequence data. It compares each sequence to every other, and groups sequences together into sets that don’t have any conflicts (minimum coloring of the sequence ‘conflict graph’)." ; sc:featureList edam:operation_0310, edam:operation_0492, edam:operation_2995 ; sc:name "Hapler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cse.nd.edu/~biocmp/hapler/" ; biotools:primaryContact "Scott J. Emrich", "Shawn O'Neil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0780, edam:topic_3293, edam:topic_3673 ; sc:citation ; sc:description """Whole-Genome Sequence Typing shows extensive diversity of Listeria monocytogenes in the outdoor environment and poultry processing plants. Haploid Sequence-Typer (Haplo-ST). Haplo-ST is a pipeline for performing standardized whole-genome multi-locus sequence typing (wgMLST) of Listeria monocytogenes (Lm) isolates from whole-genome sequencing (WGS) data. Along with wgMLST profiles, this pipeline also generates assembled allele sequences and identifies paralogous genes for each Lm isolate.""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3227, edam:operation_3478, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Haplo-ST" ; sc:url "https://github.com/swarnalilouha/Haplo-ST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3053, edam:topic_3678 ; sc:citation ; sc:description "HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core." ; sc:featureList edam:operation_2429, edam:operation_3454 ; sc:name "HaploBlock" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.cs.technion.ac.il/labs/cbl/haploblock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0622, edam:topic_0769, edam:topic_3673 ; sc:citation ; sc:description """Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies. Haplocheck detects contamination in mtDNA AND WGS sequencing studies by analyzing only the mitchondrial DNA. You can use our cloud web service or install it locally.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3233 ; sc:license "MIT" ; sc:name "haplocheck" ; sc:url "https://github.com/genepi/haplocheck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description "Computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples." ; sc:featureList edam:operation_0310 ; sc:name "HaploClique" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://github.com/cbg-ethz/haploclique" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3056 ; sc:citation "pubmed:16362347" ; sc:description "Program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD." ; sc:featureList edam:operation_0487 ; sc:name "Haploclusters" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinf.wehi.edu.au/folders/melanie/haploclusters.html" ; biotools:primaryContact "Melanie Bahlo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:15654103" ; sc:description "Program that can be used to implement tests of neutrality based on the frequency distribution of haplotypes in a sample of DNA sequences (the “haplotype configuration”) and the number of segregating sites. The neutrality tests can be performed conditional on the standard neutral coalescent model with or without recombination, exponential population growth, or island migration." ; sc:featureList edam:operation_0487, edam:operation_2238 ; sc:name "haploconfig" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.stanford.edu/group/rosenberglab/haploconfig.html" ; biotools:primaryContact "Noah Rosenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0089, edam:topic_0196, edam:topic_0622, edam:topic_3305 ; sc:citation , "pmcid:PMC10122080", "pubmed:37087497" ; sc:description "Unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "HaploCoV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/matteo14c/HaploCoV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_3168, edam:topic_3299 ; sc:citation , "pubmed:36308467" ; sc:description "Viral Haplotype reconstruction from long reads via Deep Matrix Factorization." ; sc:featureList edam:operation_0487, edam:operation_3198, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HaploDMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dhcai21/HaploDMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0622, edam:topic_2533, edam:topic_2885, edam:topic_3053, edam:topic_3071, edam:topic_3474, edam:topic_3517, edam:topic_3678 ; sc:description "The HaploDX library provides a collection of functions to generate simulated population-specific genomic data in VCF format. The library includes parameters and functions to control mutation rates, linkage disequilibrium strength and block lengths, and number of individuals. To generate genomic data, the HaploDX framework offers a pipeline of functions that can be used to simulate: (1) the allele frequency spectra of different populations; (2) the Hardy-Weinberg principle for genotypes and haplotypes; (3) linkage disequilibrium across different populations." ; sc:featureList edam:operation_2426, edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HaploDX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2-beta.4" ; sc:url "https://github.com/remytuyeras/HaploDynamics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:27084951" ; sc:description "Web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree)." ; sc:featureList edam:operation_0323, edam:operation_2995 ; sc:name "HaploGrep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://haplogrep.uibk.ac.at/" ; biotools:primaryContact "Florian Kronenberg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_3016 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1863 ; sc:name "Haplotype map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2229, edam:topic_3518 ; sc:citation , "pmcid:PMC10320078", "pubmed:37070190" ; sc:description "Interactive haplogroup classification and analysis platform." ; sc:featureList edam:operation_0323, edam:operation_0557, edam:operation_0558 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Haplogrep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://haplogrep.i-med.ac.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_2885 ; sc:citation "pubmed:27288500" ; sc:description "Identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample." ; sc:featureList edam:operation_2478 ; sc:name "hapLOHseq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/integrativecancergenomics/software/haplohseq" ; biotools:primaryContact "Paul Scheet' lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Haploi is a haplotype inference program for multi-population data. Underlying Haploi is a new haplotype distribution model based on a nonparametric Bayesian model known as the hierarchical Dirichlet process, which represents a tractable surrogate to the coalescent process. It offers a well-founded statistical framework for posterior inference of individual haplotypes, and the size and configuration of haplotype ancestor pools given genotype data." ; sc:featureList edam:operation_0487 ; sc:name "Haploi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=475" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Haplotype assembly of diploid genomes using paired-end or PacBio reads" ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "HaploMaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/mfruzan/HaploMaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2885, edam:topic_3068, edam:topic_3325 ; sc:citation , "pubmed:15377505" ; sc:description "A tool for drawing pedigrees with special features for easy visualization of complex haplotype information." ; sc:featureList edam:operation_0282, edam:operation_0487, edam:operation_0488, edam:operation_0573 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "HaploPainter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://haplopainter.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "Query web based genome annotation tools HaploReg and RegulomeDB. It gathers information in a data frame which is suitable for downstream bioinformatic analyses. This will facilitate post-genome wide association studies streamline analysis for rapid discovery and interpretation of genetic associations." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3232 ; sc:license "GPL-3.0" ; sc:name "haploR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0.6" ; sc:url "https://github.com/izhbannikov/haploR" ; biotools:primaryContact "Ilya Y. Zhbannikov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. It is especially suitable for data sets with a large number of subjects and a large number of possibly sparsely located markers." ; sc:featureList edam:operation_3454 ; sc:license "Proprietary" ; sc:name "HaploRec" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.cs.helsinki.fi/group/genetics/haplotyping.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:21855840" ; sc:description "Software package that uses Whole Genome Next Generation Sequencing data from a nuclear family to phase the genomic data into haplotypes spanning entire chromosomes." ; sc:featureList edam:operation_0487, edam:operation_3454 ; sc:name "Haploscribe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://familygenomics.systemsbiology.net/node/376" ; biotools:primaryContact "Gustavo Glusman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:21059407" ; sc:description "Tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets." ; sc:name "HaploSearch" ; sc:url "http://www.haplosite.com/haplosearch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:19479748" ; sc:description "Collection of R codes, including HAPLOSIM and HAPVISUAL, for the purpose of clustering haplotypes and haplotype visualization" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "Haplosuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.statgen.nus.edu.sg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654, edam:topic_0780, edam:topic_3500 ; sc:citation ; sc:description "Tools for haplotype-wise reconstruction of pseudomolecules" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HaploSync" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andreaminio/haplosync" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0632, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description """A web application for simple and accurate mitochondrial haplogrouping using short DNA fragments. Using fragment variant profiles. Haplotracker is a mtDNA haplogroup (HG) tracking application specifically designed for fragmented DNA samples, such as degraded DNA, commonly found in forensic specimens or human remains and difficult to obtain large DNA sequences. For primer/probe design for mtDNA.""" ; sc:featureList edam:operation_0308, edam:operation_3218, edam:operation_3227 ; sc:name "Haplotracker" ; sc:url "https://haplotracker.cau.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """An infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic. HaplotypeExplorer is an interactive haplotype network viewer for spatiotemporal dissection of multimodal epidemic spectra.""" ; sc:featureList edam:operation_0487, edam:operation_1812, edam:operation_3432, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "Haplotype Explorer" ; sc:url "https://github.com/TKSjp/HaplotypeExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3056 ; sc:description "This pipeline prepares the population genotypes ped/map files, runs them on SHAPEIT, optionally uses the results as input for IMPUTE2 using the 1000G phase III reference panel, and finally converts them to Chromopainter_v2 formats in order to perform with fineSTRUCTURE fs 2.0.7 two clusterings of donors and recipients respectively, and with Chromopainter_v2 a painting of the resulting recipient clusters out of the donor clusters." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "haplotypeAnalysisPipeline" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/BiodataAnalysisGroup/haplotypeAnalysisPipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "Genotype Transposer is an excel macro that will format data from an Excel spreadsheet to a format ready to be used by the program “Arlequin“. After which, other macros will extract the haplotype information, calculate linkage disequilibrium between markers, and prepare an input sheet for the “GOLD” program. Then, a last macro can reconstruct the haplotypes of each individual in the population,using a maximum likelihood method and the haplotypes present in the population as proposed by Arlequin." ; sc:featureList edam:operation_0335 ; sc:name "Haplotyper" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.bioinformatics.org/macroshack/programs/haplotyper/description.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3127, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC8607637", "pubmed:34809571" ; sc:description "A toolkit for accurately identifying recombination and recombinant genotypes." ; sc:featureList edam:operation_0451, edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HaplotypeTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rhysf/HaplotypeTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "Designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently supports the following functionalities: LD and haplotype analysis, estimation of haplotype frequencies, single SNP and haplotype tests, permutation teststing and visualization and plotting of PLINK whole genome association results." ; sc:featureList edam:operation_3197 ; sc:license "MIT" ; sc:name "HaploView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.broadinstitute.org/haploview/haploview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:19561337" ; sc:description "Comparative haplotype browser for personal genome and metagenome." ; sc:featureList edam:operation_0337, edam:operation_0487 ; sc:license "GPL-3.0" ; sc:name "Haplowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://haplowser-free-download.softwares7.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3053 ; sc:citation "pubmed:25123903" ; sc:description "Somatic mutation caller, which can utilize the information of heterozygous germline variants near candidate mutations." ; sc:featureList edam:operation_3202 ; sc:name "HapMuC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/usuyama/hapmuc" ; biotools:primaryContact "Naoto Usuyama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC10493177", "pubmed:37647640" ; sc:description "Large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "HAPNEST" ; sc:url "https://github.com/intervene-EU-H2020/synthetic_data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes." ; sc:featureList edam:operation_0525, edam:operation_2425 ; sc:license "CECILL-2.1" ; sc:name "Hapo-G" ; sc:softwareVersion "1.3.7" ; sc:url "https://github.com/institut-de-genomique/HAPO-G" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269 ; sc:citation ; sc:description "A Standardized Processing Pipeline for Event-Related Potential Analyses." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HAPPE+ER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PINE-Lab/HAPPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """Holistic Analysis with Pre and Post Integration GWAS. HAPPI GWAS is a genome-wide association study (GWAS) tool written in R.""" ; sc:featureList edam:operation_3791 ; sc:name "HAPPI_GWAS" ; sc:url "https://github.com/Angelovici-Lab/HAPPI.GWAS.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3572 ; sc:citation ; sc:description "The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HAPPILEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PINE-Lab/HAPPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:15637718" ; sc:description "Estimates haplotype-specific odds ratios from genotype data on unrelated cases and controls using unconditional logistic regression. 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HARE: Highlighting Annotator for Ranking and Exploration. This open-source software package implements two components of a pipeline for identifying information relevant to a specific topic in text documents:.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3778 ; sc:name "HARE" ; sc:url "https://github.com/OSU-slatelab/HARE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_2828, edam:topic_3047 ; sc:citation , "pubmed:35799352" ; sc:description "A curated database of RNA-small molecules structures to aid rational drug design." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "HARIBOSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hariboss.pasteur.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3572 ; sc:citation , "pmcid:PMC5009651", "pubmed:27585881" ; sc:description "PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user." ; sc:featureList edam:operation_2409, edam:operation_2939 ; sc:license "GPL-3.0" ; sc:name "Harman" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Harman.html" ; biotools:primaryContact "Jason Ross" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description """A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity. This is the Github page for the code used in manuscript S. Jiang et al 2019. HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity (https://www.frontiersin.org/articles/10.3389/fgene.2020.00445/full).""" ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3927 ; sc:name "HARMONIES" ; sc:url "https://github.com/shuangj00/HARMONIES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description """Harmonization of diffusion MRI datasets with adaptive dictionary learning. Harmonization of diffusion MRI datasets across scanners.""" ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "Harmonization" ; sc:url "http://github.com/samuelstjean/harmonization" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_1317, edam:topic_2814 ; sc:citation "pubmed:16844999" ; sc:description "Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0394, edam:operation_0474, edam:operation_0477 ; sc:name "Harmony" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/harmony/" ; biotools:primaryContact "Dr.N. Srinivasn", "Dr.R. Sowdhamini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6884693", "pubmed:31740819" ; sc:description """Fast, sensitive and accurate integration of single-cell data with Harmony. Scalable integration of single cell RNAseq data for batch correction and meta analysis. Check out the latest preprint of Harmony on bioRxiv. Harmony has been tested on R versions >= 3.4. Please consult the DESCRIPTION file for more details on required R packages. 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HARP (a database of Hansen's Disease Antimicrobial Resistance Profiles) is an integrated web-resource with predicted structural implications of systematic mis-sense mutations in known drug targets of Mycobacterium leprae.""" ; sc:featureList edam:operation_0224, edam:operation_0279, edam:operation_0331, edam:operation_0478, edam:operation_3482 ; sc:name "HARP" ; sc:url "https://harp-leprosy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description "HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method." ; sc:featureList edam:operation_0487 ; sc:name "HARSH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.21" ; sc:url "http://genetics.cs.ucla.edu/harsh/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3321, edam:topic_3518 ; sc:citation ; sc:description "The package is used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Harshlight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Harshlight.html" ; biotools:primaryContact "Maurizio Pellegrino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "HARU is a heterogenous compute solution for Oxford Nanopore Technologies' adaptive sampling (also known as selective sequencing and Read Until). Read Until allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to a genomic region of 'interest'. 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Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI." ; sc:featureList edam:operation_1777, edam:operation_2421, edam:operation_3092 ; sc:name "Harvester" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://harvester.fzk.de/harvester/" ; biotools:primaryContact "Urban Liebel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """A framework for hierarchical feature learning and selection from whole genome sequencing data. 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This has been initially developed for Clostridium difficile, but could be adpated to other bacteria. Singularity - instructions can be found here https://github.com/sylabs/singularity/blob/master/INSTALL.md. This workflow will run on systems that support the dependencies above. It has been tested on MacOS, Ubuntu and CentOS. Minimal system resources are required to generate hash-cgMLST profiles alone, however generating assemblies using SPAdes is the main resource constraint for the whole pipeline, the amount of memory to use per core can be set in the nextflow.config file, e.g. 8 Gb. Java version 8 or later (required for nextflow).""" ; sc:featureList edam:operation_0310, edam:operation_3211, edam:operation_3840 ; sc:name "hash-cgMLST" ; sc:url "https://github.com/davideyre/hash-cgmlst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_2885, edam:topic_3170, edam:topic_3697 ; sc:citation , "pmcid:PMC8577285", "pubmed:34751586" ; sc:description "HashSeq infers true biological 16S rRNA sequence variants from sequence errors generated from an Illumina sequencing instrument." ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3435, edam:operation_3659, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HashSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FarnazFouladi/HashSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description """Fast Hybrid Assembly of Long Reads. HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. HASLR is capable of assembling large genomes on a single computing node. Our experiments show that it can assemble a CHM1 human dataset in less than 10 hours using 64 CPU threads.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "HASLR" ; sc:url "https://github.com/vpc-ccg/haslr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0804, edam:topic_2275, edam:topic_2830, edam:topic_3292, edam:topic_3293 ; sc:citation "pubmed:23777206" ; sc:description "Server designed as a scientific tool for researchers to visualize their phylogenetic, biochemical, and immunological HA data in the three-dimensional context of the HA structure, in the hopes that the context may help researchers better interpret their data and generate new hypotheses." ; sc:featureList edam:operation_0474, edam:operation_0477 ; sc:name "HASP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://exon.niaid.nih.gov/HASP.html" ; biotools:primaryContact "Support page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_3168 ; sc:citation , "pubmed:33538292" ; sc:description """Accurate Haplotype-Resolved Assembly Reveals The Origin Of Structural Variants For Human Trios. Partition stLFR reads based on trio-binning algorithm using parentally unique markers.""" ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "HAST" ; sc:url "https://github.com/BGI-Qingdao/HAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0769, edam:topic_3292, edam:topic_3474 ; sc:citation ; sc:description """Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit. Client for the HASTE Storage Engine. Smart middleware for working with a variety of storage media with Scientific Computing datasets. Supports Python 2.7 and Python 3.*.""" ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "HASTE" ; sc:softwareHelp ; sc:url "http://haste.research.it.uu.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3316 ; sc:author "Ben Blamey" ; sc:description "A collection of software components that can be used to build intelligent streaming pipelines for scientific data streams." ; sc:featureList edam:operation_3695 ; sc:name "HASTE Toolkit" ; sc:url "https://github.com/HASTE-project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3068, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:34060239" ; sc:description """HASTEN is a tool that makes it easier to run machine learning boosted virtual screening workflows. It is written in very general Python without relying in non-standard libraries so it is easy to run in any Python environment Currently only chemprop is supported as machine learning method, but it is easy to write Shell-scripts to plug-in your own methods. Glide from Schrodinger is supported in this version, but the same applies here: it should be easy to plug-in your own docking program. Do note that the HASTEN assumes that the smaller the docking score, the better the score. There is also simulation mode, which allows you to run benchmarks using existing docking_scores without in reality doing anything in 3D. This mode can be useful when adjusting the machine learning parameters.""" ; sc:featureList edam:operation_3359, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HASTEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TuomoKalliokoski/HASTEN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3315, edam:topic_3940 ; sc:citation , "pmcid:PMC10270569", "pubmed:37276238" ; sc:description "Hypergraph analysis toolbox." ; sc:featureList edam:operation_0250, edam:operation_0337, edam:operation_0455 ; sc:isAccessibleForFree true ; sc:name "HAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hypergraph-analysis-toolbox.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0634, edam:topic_2830, edam:topic_2885 ; sc:citation , "pubmed:32735319" ; sc:description "HATK(HLA Analysis Tool-Kit) is a collection of tools and modules to perform HLA fine-mapping analysis, which is to identify which HLA allele or amino acid position of the HLA gene is driving the disease. HLA fine-mapping analysis is an indispensable analysis in studies of autoimmune diseases." ; sc:featureList edam:operation_0337, edam:operation_3557, edam:operation_3659 ; sc:name "HATK" ; sc:url "https://github.com/WansonChoi/HATK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:24187504" ; sc:description "Increased specificity for analysis of tiling-array data in comparison with alternative methods, and that it accurately detected regions-of-interest in different applications of tiling-arrays." ; sc:featureList edam:operation_2495 ; sc:name "HATSEQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://hema13.erasmusmc.nl/index.php/Hypergeometric_Analysis_of_Tiling-arrays" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3511 ; sc:citation "pubmed:27428829" ; sc:description "C-program for the identification of attC sites in any type of DNA data. It uses a hidden Markov model (HMM) to describe each part of the attC site in a probabilistic manner." ; sc:featureList edam:operation_0415 ; sc:name "HattCI" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://bioinformatics.math.chalmers.se/HattCI" ; biotools:primaryContact "Marina Pereira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_0769 ; sc:citation ; sc:description """Bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. HAVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples.The pipeline is ideal for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks.""" ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_0310, edam:operation_3227 ; sc:name "HaVoC" ; sc:url "https://www.helsinki.fi/en/projects/havoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:17349036" ; sc:description "An interactive visual analytics tool for genome assemblies." ; sc:featureList edam:operation_3184 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "HawkEye" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://amos.sourceforge.net/wiki/index.php?title=Hawkeye" ; biotools:primaryContact "Michael Schatz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline." ; sc:featureList edam:operation_0438, edam:operation_0441 ; sc:license "AGPL-3.0" ; sc:name "Haystack" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.5.3" ; sc:url "https://github.com/pinellolab/haystack_bio" ; biotools:primaryContact "Guo-Cheng Yuan", "Luca Pinello" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3295, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7358203", "pubmed:32660516" ; sc:description """Accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis. Hierarchical Bayesian Analysis of Differential Expression and ALternative Splicing (HBA-DEALS).""" ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0440, edam:operation_2495, edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "HBA-DEALS" ; sc:url "https://github.com/TheJacksonLaboratory/HBA-DEALS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation "pubmed:18467777" ; sc:description "Tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph)." ; sc:featureList edam:operation_2406 ; sc:name "HBAT" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/hbat/" ; biotools:primaryContact "Abhishek Tiwari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3419, edam:topic_3444 ; sc:citation , "pmcid:PMC5869013", "pubmed:29601060" ; sc:description "hBayesDM (hierarchical Bayesian modeling of Decision-Making tasks), which offers computational modeling of an array of reinforcement learning and decision-making tasks and social exchange games." ; sc:featureList edam:operation_3664 ; sc:license "Other" ; sc:name "hBayesDM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.0" ; sc:url "https://github.com/CCS-Lab/hBayesDM" ; biotools:primaryContact "Woo-Young Ahn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3542 ; sc:citation "pubmed:9351466" ; sc:description "The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures." ; sc:featureList edam:operation_0405 ; sc:name "HCA (hydrophobic cluster analysis)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::HCA" ; biotools:primaryContact "Isabelle Callebaut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3336 ; sc:citation , "pubmed:20855562" ; sc:description "HCA-Vision is an automated image analysis software package developed by CSIRO that rapidly and reproducibly measures and reports on important cell features for drug discovery." ; sc:featureList edam:operation_3443 ; sc:name "HCA-Vision" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.6" ; sc:url "http://www.hca-vision.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3047, edam:topic_3303, edam:topic_3343 ; sc:citation ; sc:description """Hilbert-Curve Assisted Structure Embedding Method. Hilbert-Curve Assisted Structure Embedding (HCASE) Method. This repository contains source code of the Hilbert-Curve Assisted Structure Embedding (HCASE) method. The method and a proof-of-concept study has been published as a preprint and can be accessed here: https://chemrxiv.org/articles/Hilbert-Curve_Assisted_Structure_Embedding_Method/11911296 .""" ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3432, edam:operation_3935 ; sc:license "MIT" ; sc:name "HCASE" ; sc:url "https://github.com/ncats/hcase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3336, edam:topic_3373, edam:topic_3377 ; sc:citation , "pmcid:PMC9684616", "pubmed:36420558" ; sc:description "HCDT (Highly Confident Drug-Target Database) is a combined database that provides validated associations between drugs and target genes." ; sc:featureList edam:operation_2421, edam:operation_3928, edam:operation_3938 ; sc:license "Other" ; sc:name "HCDT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hainmu-biobigdata.com/hcdt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3577 ; sc:citation , "pubmed:32500221" ; sc:description """Validation of an online tool for early prediction of the failure-risk in gestational trophoblastic neoplasia patients treated with methotrexate. hCG trophoblastic tumor or neoplasia.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3659 ; sc:name "hCGres" ; sc:url "https://www.biomarker-kinetics.org/hCG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3298, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC9645610", "pubmed:36350801" ; sc:description """A novel statistical method for phenome-wide association studies. We derived a novel and powerful multivariate method, which we referred to as HCLC-FC (Hierarchical Clustering Linear Combination with False discovery rate Control), to test the association between a genetic variant with multiple phenotypes for each phenotypic category in phenome-wide association studies (PheWAS). The R package HCLCFC is a novel tool that allows users to partition a large number of phenotypes into disjoint clusters; applicable to electronic medical records (EMR)-based PheWAS.""" ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HCLC-FC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/XiaoyuLiang/HCLCFC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301 ; sc:contributor "Francesco Asnicar", "Francesco Beghini" ; sc:description "Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication." ; sc:featureList edam:operation_0337, edam:operation_0531, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Hclust2" ; sc:softwareHelp ; sc:url "https://github.com/SegataLab/hclust2" ; biotools:primaryContact "Segata Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_3940 ; sc:citation , "pmcid:PMC8120939", "pubmed:34025950" ; sc:description "Hi-C Matrix Balancin (HCMB) is a Python package for processing the normalization of highly sparse Hi-C contact data." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "HCMB" ; sc:url "https://github.com/HUST-DataMan/HCMB" ; biotools:primaryContact , "Ke Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:36018233" ; sc:description "hCoCena is an R-package that allows you to integrate and jointly analyse multiple transcriptomic datasets or simply analyse a single dataset if you don't want to do any data integration." ; sc:featureList edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "hCoCena" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MarieOestreich/hCoCena" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2830, edam:topic_3930, edam:topic_3966 ; sc:citation , "pubmed:35348639" ; sc:description "A genetic and proteomic database for the SARS-CoV, MERS-CoV, and SARS-COV-2." ; sc:featureList edam:operation_0416, edam:operation_2421, edam:operation_2422 ; sc:license "Apache-2.0" ; sc:name "hCoronavirusesDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hcoronaviruses.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_2830, edam:topic_3336 ; sc:citation , "pubmed:36573474" ; sc:description "An efficient docking method for modeling covalent protein-ligand interactions." ; sc:featureList edam:operation_0394, edam:operation_0480, edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "HCovDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://huanglab.phys.hust.edu.cn/hcovdock/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640 ; sc:citation ; sc:description "Decompose given hierarchical clustering tree into non-overlapping clusters in a semi-supervised way by using available patients follow-up information as guidance. Contains functions for snipping HC tree, various cluster quality evaluation criteria, assigning new patients to one of the two given HC trees, testing the significance of clusters with permutation argument and clusters visualization using sample's molecular entropy." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "HCsnip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HCsnip.html" ; biotools:primaryContact "Askar Obulkasim" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:name "Database ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781, edam:topic_1317 ; sc:citation ; sc:description "A specialized and medically-oriented database of published variations observed within the internal ribosome entry site (IRES) variants in hepatitis C virus." ; sc:featureList edam:operation_0349 ; sc:isAccessibleForFree true ; sc:name "HCVIVdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ" ; sc:softwareHelp ; sc:softwareVersion "0.7" ; sc:url "http://www.hcvivdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2269, edam:topic_3047 ; sc:citation , "pubmed:32449536" ; sc:description """A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. A web server for predicting the bioactivity of HCV NS5B inhibitors. Enter your input molecule(s) in SMILES notation Insert example data.""" ; sc:featureList edam:operation_2939, edam:operation_2943, edam:operation_3891, edam:operation_3938 ; sc:name "HCVpred" ; sc:url "http://codes.bio/hcvpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3361, edam:topic_3382 ; sc:citation , "pubmed:33079991" ; sc:description """Visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering. Please select ONE file to upload. 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In ad….""" ; sc:featureList edam:operation_2428, edam:operation_2949, edam:operation_3659 ; sc:name "HDMAC" ; sc:url "https://github.com/chung-R/HD-MAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:34864918" ; sc:description "HDMC (Hierarchical Distribution Matching and Contrastive learning) is a novel deep learning based framework for batch effect removal in scRNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HDMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhanglabNKU/HDMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_2275 ; sc:citation , "pmcid:PMC5793843", "pubmed:28521030" ; sc:description "Protein-protein and protein-DNA/RNA docking based on a hybrid algorithm of template-based modeling and ab initio free docking." ; sc:featureList edam:operation_0476, edam:operation_0478, edam:operation_2575 ; sc:name "HDOCK" ; sc:softwareHelp , ; sc:url "http://hdock.phys.hust.edu.cn/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3308 ; sc:citation , "pmcid:PMC4937203", "pubmed:27266441" ; sc:description "Characterization of intra-individual variability generates physiology-measurement data that can be written as a matrix with the different subsamples in the columns and the different phenotypic units in the rows. 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Welcome to Hepatitis Delta Virus Database (HDVdb). The Hepatitis D Virus (HDV) Database, HDVdb contains comprehensive data on HDV genetic sequences that allows the researchers to investigate the genetic variability of the virus. 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Many functions are also provided for investigating sequence features." ; sc:featureList edam:operation_0337, edam:operation_2928 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "heatmaps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/heatmaps.html" ; biotools:primaryContact "Malcolm Perry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot." ; sc:featureList edam:operation_0531 ; sc:license "GPL-2.0" ; sc:name "Heatplus" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Heatplus.html" ; biotools:primaryContact "Alexander Ploner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3053, edam:topic_3056, edam:topic_3697 ; sc:citation "pubmed:18415976" ; sc:description "Tool for simulation of bacterial (more exactly prokaryotic) communities. 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Kintsakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "RHermes is a broad-scoped targeted metabolomics software designed to analyse LC-MS and LC-MS/MS data to identify compounds in biological or environmental samples." ; sc:featureList edam:operation_0224, edam:operation_3215, edam:operation_3803 ; sc:name "HERMES" ; sc:url "https://github.com/RogerGinBer/RHermes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2711 ; sc:encodingFormat edam:format_1929 ; sc:name "Genome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0781, edam:topic_3511 ; sc:author "Jan Pačes", "Ondřej Moravčík" ; sc:citation , "pmcid:PMC308809", "pubmed:14681356" ; sc:contributor "Adam Pavlí­ček", "Eva Prysiazhniuk", "Lucie Studená", "Mirka Famfulí­ková", "Radek Zí­ka" ; sc:description "Human endogenous retroviruses database." ; sc:featureList edam:operation_0361, edam:operation_0362, edam:operation_0415, edam:operation_2478, edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "HERVd" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-CZ", "Institute of Molecular Genetics, AS CR" ; sc:softwareHelp , ; sc:url "https://herv.img.cas.cz" ; biotools:primaryContact "Jan Pačes", "Ondřej Moravčík" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0637, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC8734250", "pubmed:34991460" ; sc:description "HESML is an efficient, scalable and large Java software library of ontology-based semantic similarity measures and Information Content (IC) models based on WordNet, SNOMED-CT, MeSH or any other OBO-based ontology." ; sc:featureList edam:operation_0306, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "HESML" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://hesml.lsi.uned.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3382, edam:topic_3794 ; sc:citation , "pubmed:33638346" ; sc:description """An R package for Gaussian graphical model-based heterogeneity analysis. 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Few-shot semantic segmentation remains an open problem because limited support (training) images are insufficient to represent the diverse semantics within target categories.""" ; sc:featureList edam:operation_0224 ; sc:name "HFA" ; sc:url "https://github.com/Bibikiller/HFA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3479 ; sc:name "Gene order" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:name "Position frequency matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3510 ; sc:author "Oren Tzfadia" ; sc:citation , "pmcid:PMC4854547", "pubmed:27071037" ; sc:description "A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms." ; sc:featureList edam:operation_0240, edam:operation_3092 ; sc:name "hfAIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/hfAIM/" ; biotools:primaryContact "Oren Tzfadia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3335, edam:topic_3360, edam:topic_3577 ; sc:citation , "pubmed:34164644" ; sc:description "A biomarker knowledge database for heart failure heterogeneity and personalized applications." ; sc:isAccessibleForFree true ; sc:name "HFBD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sysbio.org.cn/HFBD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3335, edam:topic_3423, edam:topic_3577 ; sc:citation , "pmcid:PMC8607296", "pubmed:34791105" ; sc:description "Heart Failure Integrated Platform (HFIP) is an integrated multi-omics data and knowledge platform for the precision medicine of heart failure." ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_2421 ; sc:name "HFIP" ; sc:url "http://heartfailure.medical-bigdata.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3360, edam:topic_3421 ; sc:citation , "pmcid:PMC8503963", "pubmed:34544760" ; sc:description "A MATLAB-based graphic user interface for high frequency oscillations marking." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HFOApp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zelanolab/hfoapp.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0634, edam:topic_0781 ; sc:citation "pubmed:22064861" ; sc:description "The LANL hemmorhagic fever virus database, a new platform for analyzing biothreat viruses." ; sc:featureList edam:operation_0338, edam:operation_2422, edam:operation_2478, edam:operation_3431 ; sc:name "HFV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hfv.lanl.gov/content/index" ; biotools:primaryContact "HFV Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229 ; sc:citation ; sc:description """Fast hierarchical clustering for large-scale single-cell data. The core function of HGC takes a graph G as the input. Here G is the adjacency matrix of a graph of cells, where the element in G are the weights of edges in the graph, and zero means no link between the corresponding node pairs. G should be a dgCMatrix supported by the R package Matrix.""" ; sc:featureList edam:operation_2938, edam:operation_2942, edam:operation_3432 ; sc:name "HGC" ; sc:url "https://www.github.com/XuegongLab/HGC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2298 ; sc:name "Gene ID (HGNC)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3271 ; sc:name "Gene tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation , , , "pmcid:PMC3441226", "pmcid:PMC9312353", "pubmed:22672625", "pubmed:36101400" ; sc:description "The Human Gene Coexpression Analysis tool (HGCA) is based on the coexpression analysis of 55431 Human genes from gene pair correlation data of 3500 RNASeq samples from the GTEx Project" ; sc:featureList edam:operation_2938 ; sc:isAccessibleForFree true ; sc:name "Human Gene Correlation Analysis (HGCA)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://www.michalopoulos.net/hgca2.0/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053 ; sc:citation , "pmcid:PMC4051124", "pubmed:24694260" ; sc:description "Prioritizing disease-causing gene variants by biological distance." ; sc:featureList edam:operation_3197, edam:operation_3226 ; sc:name "HGCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hgc.rockefeller.edu/" ; biotools:primaryContact "Yuval Itan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0622, edam:topic_3489, edam:topic_3512 ; sc:citation , "pmcid:PMC3013718", "pubmed:21071397" ; sc:description "The Hymenoptera Genome Database is a comprehensive model organism database for insect species of the order Hymenoptera. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "The Hymenoptera Genome Database (HGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://HymenopteraGenome.org" ; biotools:primaryContact "HGD Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0203, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC9825607", "pubmed:36318261" ; sc:description "An integrated homologous gene database across multiple species." ; sc:featureList edam:operation_2422, edam:operation_3625, edam:operation_3663, edam:operation_3672, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "HGD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/hgd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0625, edam:topic_0821, edam:topic_3474 ; sc:citation ; sc:description "HGDiscovery is an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase." ; sc:featureList edam:operation_0331, edam:operation_0477, edam:operation_3501 ; sc:name "HGDiscovery" ; sc:url "http://biosig.unimelb.edu.au/hgdiscovery/" ; biotools:primaryContact "David B. Ascher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3169, edam:topic_3512 ; sc:citation , "pubmed:35266510" ; sc:description "A heterogeneous graph embedding model for predicting interactions between transcription factor and target gene." ; sc:featureList edam:operation_2437, edam:operation_2454, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HGETGI" ; sc:url "https://github.com/PGTSING/HGETGI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885, edam:topic_3071, edam:topic_3500 ; sc:citation , "pmcid:PMC7792568", "pubmed:33417691" ; sc:description """A collective database of helmeted guinea fowl genomics. Helmeted guinea fowl (HGF; Numida meleagris) is vigorous, hardy, and mostly disease-free game birds. The rearing of HGF is a potential alternative poultry system. Because of the characteristics of the HGF, the study of HGF is valuable, so we conduct an improved domesticated HGF genome de novo assembly generated by long and short read sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds including domesticated animals, wild progenitors, and closely related wild species. The data are important to provide valuable genetic resources for researchers and breeders to improve production in this species. For this purpose, we have developed a comprehensive and easy-to-use web-based database, HGFDB.""" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3227, edam:operation_3891 ; sc:name "HGFDB" ; sc:url "http://hgfdb.ynau.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_3382 ; sc:citation , "pmcid:PMC9077837", "pubmed:35525918" ; sc:description "Hierarchical Guided Genome Assembler (HGGA) a framework to guide genome assembly with additional data." ; sc:featureList edam:operation_0282, edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HGGA" ; sc:url "https://github.com/rikuu/hgga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3377, edam:topic_3379 ; sc:citation , "pubmed:33331887" ; sc:description """Heterogeneous graph inference with matrix completion for computational drug repositioning. Inspired by the low-rank completion of BNNR and the guilt-by-association principle of HGBI, we propose a heterogeneous graph inference with matrix completion (HGIMC) method to predict potential indications for drugs. Overview This repository contains data and code for HGIMC method, which is based on the model at https: github.com BioinformaticsCSU HGIMC. November 23, 2020 Software Open Access.""" ; sc:featureList edam:operation_3435 ; sc:name "HGIMC" ; sc:url "http://doi.org/10.5281/zenodo.4285640" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2815, edam:topic_3325, edam:topic_3366 ; sc:citation , , , , , "pmcid:PMC3898141", "pubmed:12754702", "pubmed:18245393", "pubmed:19348700", "pubmed:24077912", "pubmed:28349240" ; sc:description "The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. 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It incorporates 43 location-specific histone modifications in human. The database can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. 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Software tool for Hi-C HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework""" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3659 ; sc:name "HiC-DCplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/leslielab/hicdcplus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_0654, edam:topic_0769 ; sc:citation , "pmcid:PMC7672694", "pubmed:32369554" ; sc:description """A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C. This will install the python package (and its cli command) hic_hiker.""" ; sc:featureList edam:operation_0525, edam:operation_1812, edam:operation_3216 ; sc:license "BSD-3-Clause" ; sc:name "HiC-Hiker" ; sc:url "https://github.com/ryought/hic_hiker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:author ; sc:citation , "pmcid:PMC4665391", "pubmed:26619908" ; sc:description "This tool was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, it can analyze data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C. The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster using the PBS-Torque scheduler." ; sc:featureList edam:operation_2945 ; sc:name "HiC-Pro" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut Curie", "curie.fr" ; sc:softwareHelp , , ; sc:softwareVersion "2.7.8" ; sc:url "https://github.com/nservant/HiC-Pro" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_3168 ; sc:citation , "pubmed:35781332" ; sc:description "A computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization." ; sc:featureList edam:operation_0531, edam:operation_3198, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HiC-TE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.fi.muni.cz/lexa/hic-te/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3169, edam:topic_3173, edam:topic_3940 ; sc:citation , "pmcid:PMC8769930", "pubmed:34850813" ; sc:description "Framework to extract various one-dimensional features from chromosome structure data." ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HiC1Dmetrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hic1d.herokuapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC10516390", "pubmed:37478379" ; sc:description "HiC4D is a tool for forecasting spatiotemporal Hi-C data with residual ConvLSTM (ResConvLSTM)." ; sc:featureList edam:operation_0272, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "HiC4D" ; sc:url "http://dna.cs.miami.edu/HiC4D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC6612845", "pubmed:31510693" ; sc:description "hicGAN infers super resolution Hi-C data with generative adversarial networks | Hi-C data super-resolution with generative adversarial networks | We proposed hicGAN, an open-sourced framework, for inferring high resolution Hi-C data from low resolution Hi-C data with generative adversarial networks (GANs)" ; sc:license "MIT" ; sc:name "hicGAN" ; sc:url "https://github.com/kimmo1019/hicGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_2830 ; sc:citation ; sc:description """Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Koren N, Walenz BP, Rhie A, Vollger M, Grothe R, Logsdon GA, Eichler EE, Phillippy AM, Koren S. HiCanu: precise assembly of segmental duplications and haplotypes using high-fidelity long reads. Biorxiv. (2020). Canu is a hierarchical assembly pipeline which runs in four steps:. Detect overlaps in high-noise sequences using MHAP.""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3192, edam:operation_3472 ; sc:name "HiCanu" ; sc:url "https://github.com/marbl/canu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0632 ; sc:citation ; sc:description "Probe design and proximity detection for targeted chromosome conformation capture applications." ; sc:featureList edam:operation_2419 ; sc:name "HiCapTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sahlenlab/HiCapTools" ; biotools:primaryContact "Pelin Sahlén" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3382, edam:topic_3474, edam:topic_3940 ; sc:citation , "pmcid:PMC9048669", "pubmed:35274679" ; sc:description "HiCARN: Resolution Enhancement of Hi-C Data Using Cascading Residual Networks" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HiCARN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OluwadareLab/HiCARN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0097, edam:topic_0654, edam:topic_1317 ; sc:citation "pubmed:25132176" ; sc:description "Hi-C data analysis tool. Importantly, HiCat is focussed on analysis of larger structural features of chromosomes and on comparative studies." ; sc:featureList edam:operation_2480, edam:operation_2483 ; sc:name "HiCat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.botinst.uzh.ch/research/development/grossnik/HiCat.html" ; biotools:primaryContact "Dr. Célia Baroux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0769, edam:topic_3174, edam:topic_3940 ; sc:citation ; sc:description "HiCBin is a new open-source metagenomic Hi-C-based binning pipeline to recover high-quality MAGs. 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It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources." ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "HiCcompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HiCcompare.html" ; biotools:primaryContact "John Stansfield" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0654, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC8083178", "pubmed:33981483" ; sc:description """identifying long range chromosomal contacts in Hi-C data. Scripts for prediction of long-range interactions between regions/domains based on Hi-C maps. Establish contact!. HiCEnterprise takes a list of regions/domains and searches for their significant interactions on given Hi-C maps. Package consists of two types of analyses: regions and domains. HiCEnterprise is a software tool for identification of long-range chromatin contacts based on the Hi-C experiments.""" ; sc:featureList edam:operation_0303, edam:operation_2238, edam:operation_3891 ; sc:license "MIT" ; sc:name "HiCEnterprise" ; sc:url "http://regulomics.mimuw.edu.pl/wp/hicenterprise" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3169, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC7319437", "pubmed:32301980" ; sc:description """A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. HiCExplorer — HiCExplorer 3.6 documentation. scHiCExplorer — scHiCExplorer 7 documentation. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3435 ; sc:name "HiCExplorer" ; sc:softwareHelp , ; sc:url "https://hicexplorer.usegalaxy.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3169 ; sc:citation , "pmcid:PMC7590616", "pubmed:33109075" ; sc:description """a package to correct and analyze the diploid Hi-C data. An integrated package to process diploid Hi-C data. HiCHap is a Python package designed to process and analyze Hi-C data, primarily the diploid Hi-C data for phased haplotypes.""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "HiCHap" ; sc:url "https://pypi.org/project/HiCHap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3173, edam:topic_3179, edam:topic_3517 ; sc:citation , "pubmed:36215037" ; sc:description "A comprehensive database of HiChIP regulatory interactions." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "HiChIPdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://health.tsinghua.edu.cn/hichipdb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_3750 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:name "Structural profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0607, edam:topic_3656 ; sc:citation ; sc:description "A Python package for HiChIP data processing and quality control pipeline." ; sc:featureList edam:operation_0279, edam:operation_0570, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "hichipper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://aryee.mgh.harvard.edu/hichipper/" ; biotools:primaryContact "Caleb Lareau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3940 ; sc:citation , "pmcid:PMC9232133", "pubmed:35696429" ; sc:description "A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HiCImpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sl-lin/HiCImpute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "HiCNorm is a parametric model to remove systematic biases in the raw Hi-C contact maps. It relates chromatin interactions and systemic biases at the desired resolution level,resulting in a simple, yet accurate normalization procedure. Compared to the exiting Hi-C normalization method, our model has only a few parameters, is much easier to implement, can be interpreted intuitively, and achieves higher reproducibility in real Hi-C data" ; sc:featureList edam:operation_3659 ; sc:name "HiCNorm" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.people.fas.harvard.edu/~junliu/HiCNorm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_2269 ; sc:citation "pubmed:26392354" ; sc:description "Python data visualization tool for integrating different data types with interaction matrixes." ; sc:featureList edam:operation_0337 ; sc:name "HiCPlotter Beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kcakdemir/HiCPlotter" ; biotools:primaryContact "Kadir Akdemir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "hicrep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hicrep.html" ; biotools:primaryContact "Tao Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654 ; sc:citation , "pubmed:33576390" ; sc:description """Fast comparison of Hi-C contact matrices in Python. A fast implementation of the HiCRep algorithm for computing similarities between pairs of Hi-C matrices. This repository is temporarily located at https://github.com/dejunlin/hicrep.""" ; sc:license "GPL-2.0" ; sc:name "HiCRep-py" ; sc:url "https://github.com/Noble-Lab/hicrep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3315, edam:topic_3794, edam:topic_3940 ; sc:citation ; sc:description """a computational method to estimate and predict the resolution of HiC libraries. Estimating and predicting HiC library resolution. The purpose of this container is to estimate the resolution of your HiC library and to predict the resolution the same library will reach when sequenced at deeper level. There are two main functionality to use HiCRes: you can either start from your analyzed library by providing a bam file containing the valid read pairs and the genome index you used (much faster option) or you can start from your raw sequencing data by providing the 2 fastq files, the enzyme you used, and the species (much slower, limited to human and mouse for now, and MboI, HindIII or Arima digestions).""" ; sc:featureList edam:operation_0365, edam:operation_3198, edam:operation_3219 ; sc:name "HiCRes" ; sc:url "http://github.com/ClaireMarchal/HiCRes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """a Hi-C super-resolution framework for producing highly realistic contact maps. Implementation of HiCSR framework described in this paper:. HiCSR is a Hi-C super-resolution framework written in python capable of producing enhanced contact maps which are both accurate and realistic. The HiCSR framework optimizes for a weighted combination of adversarial loss, pixel-wise L1 loss, and a feature reconstruction loss obtained from the latent representation of a task specific denoising autoencoder.""" ; sc:featureList edam:operation_2429, edam:operation_3359, edam:operation_3435 ; sc:license "MIT" ; sc:name "HiCSR" ; sc:url "https://github.com/PSI-Lab/HiCSR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654, edam:topic_0769, edam:topic_3382 ; sc:author , "Amaury Bignaud" ; sc:citation , "pubmed:34415528" ; sc:contributor ; sc:description "A lightweight library that generates and handles Hi-C contact maps in either cooler-compatible 2Dbedgraph or instaGRAAL format." ; sc:featureList edam:operation_2429, edam:operation_3435, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "hicstuff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/koszullab/hicstuff" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091 ; sc:citation ; sc:description "Blazing fast toolkit to work with .hic and .cool files" ; sc:license "MIT" ; sc:name "hictk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1", "0.0.10", "0.0.11", "0.0.2", "0.0.3", "0.0.4", "0.0.5", "0.0.6", "0.0.7", "0.0.8", "0.0.9" ; sc:url "https://github.com/paulsengroup/hictk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_3169 ; sc:citation , "pmcid:PMC10081873", "pubmed:36961339" ; sc:description "Interactive visualization of multiscale and multimodal Hi-C and 3D genome data." ; sc:featureList edam:operation_0337, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:name "HiCube" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wmalab/HiCube" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3173 ; sc:citation ; sc:description "A mapping pipeline for HiC interaction data. Performs independent mapping on each end of the interaction pair and removes commonly found artefacts." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "HiCUP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.babraham.ac.uk/projects/hicup/" ; biotools:primaryContact "Steven Wingett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3837, edam:topic_3940 ; sc:citation ; sc:description "HiCzin is a tool for normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_0487, edam:operation_3435, edam:operation_3659 ; sc:license "MIT" ; sc:name "HiCzin" ; sc:url "https://github.com/dyxstat/HiCzin" ; biotools:primaryContact "Fengzhu Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3390, edam:topic_3474 ; sc:citation ; sc:description """a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data. Time-series hidden state visualization toolkit based on JavaScript, Python and ECharts framework.""" ; sc:featureList edam:operation_0337 ; sc:name "HiddenVis" ; sc:url "https://github.com/jyan97/HiddenVis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:23335015" ; sc:description "Software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species. It takes as input a collection of unrooted gene trees along with a rooted species tree." ; sc:featureList edam:operation_3625 ; sc:name "HiDe" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/hide/" ; biotools:primaryContact "Guy Banay", "Mukul Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2259, edam:topic_3308, edam:topic_3315, edam:topic_3697 ; sc:citation , "pmcid:PMC7789082", "pubmed:33413539" ; sc:description """HiDeF (Hierarchical community Decoding Framework). 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The tree hierarchy provides a natural structure in multi-species ortholog groups, and the aggregation of multiple sequences allows for multiple alignment similarity searching techniques." ; sc:featureList edam:operation_2421, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "Hieranoid" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2" ; sc:url "http://hieranoidb.sbc.su.se/" ; biotools:primaryContact "Mateusz Kaduk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "It is an implementation of hierarchical (a.k.a. multi-scale) Kalman filter using belief propagation." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:name "Hierarchical Kalman Filter for clinical time series prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/39707-hierarchical-kalman-filter-for-clinical-time-series-prediction" ; biotools:primaryContact "Shuang Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "We developed an algorithm that deals with Hierarchical Feature Spaces, with focus on relative abundances of microbial communities but with the potential to be expanded to a wide range of Machine Learning tasks were features have an underlying hierarchical structure." ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Hierarchical Feature Engineering" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HenschelLab/HierarchicalFeatureEngineering" ; biotools:primaryContact "Andreas Henschel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0108, edam:topic_0203, edam:topic_0625, edam:topic_3170 ; sc:citation , "pmcid:PMC8088563", "pubmed:33932993" ; sc:description "Hierarchicell is an R-package for estimating power for tests of differential expression with single-cell data." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3659 ; sc:name "Hierarchicell" ; sc:url "https://github.com/kdzimm/hierarchicell" ; biotools:primaryContact , "Carl D. Langefeld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "REST Web service to get parents, children or siblings of an ontology term from a BioPortal ontology." ; sc:featureList edam:operation_2422 ; sc:name "Hierarchy Web services" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://data.bioontology.org/documentation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3324, edam:topic_3796 ; sc:citation ; sc:description """A multi-level clustering scheme for population assignments based on core genome MLST. HierCC (Hierarchical clustering of cgMLST). HierCC is a multi-level clustering scheme for population assignments based on core genome Multi-Locus Sequence Types (cgMLSTs). HierCC has been implemented in EnteroBase since 2018.""" ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_3432, edam:operation_3478, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "HierCC" ; sc:softwareHelp ; sc:url "http://enterobase.warwick.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Hierarchical Random Forest for Information Transfer. Release First release of HieRFIT. There is an increasing demand for data integration and cross-comparison in the single cell genomics field. This release is a working version of HieRFIT with full functionalities.""" ; sc:featureList edam:operation_0451, edam:operation_0452, edam:operation_3435 ; sc:name "HieRFIT" ; sc:url "https://github.com/yasinkaymaz/HieRFIT/releases/tag/v1.0.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers." ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "hierGWAS" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hierGWAS.html" ; biotools:primaryContact "Laura Buzdugan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0632, edam:topic_0659, edam:topic_3320 ; sc:citation , "pubmed:36243969" ; sc:description "High-throughput FISH detection of endogenous pre-mRNA splicing isoforms." ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_0433, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HiFENS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CBIIT/mistelilab-hifens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3169, edam:topic_3382, edam:topic_3940 ; sc:citation , "pmcid:PMC6961295", "pubmed:31937349" ; sc:description """Estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution. A tool for high-resolution estimation of DNA-DNA interaction frequency from Hi-C data. HIFI is a set of tools to infer true intra-chromosomal interaction frequencies at restriction fragment (RF) resolution from Hi-C data. It uses adaptive kernel density estimation and Markov Random Field approaches to provide accurate estimates of interaction frequency matrices from sparse read-count matrices.""" ; sc:featureList edam:operation_0365, edam:operation_2429, edam:operation_3435 ; sc:name "HIFI" ; sc:url "https://github.com/BlanchetteLab/HIFI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0637, edam:topic_3050, edam:topic_3168 ; sc:citation , "pmcid:PMC7716423", "pubmed:33276723" ; sc:description """Efficient COI barcoding using high throughput single-end 400 bp sequencing. The BGISEQ-500 platform has launched a new test sequencing kits capable of single-end 400 bp sequencing (SE400), which offers a simple and reliable way to achieve DNA barcodes efficiently. In this study, we explored the potential of the BGISEQ-500 SE400 sequencing in DNA barcode reference construction, meanwhile provided an updated HIFI-Barcode software package that can generate COI barcode assemblies using HTS reads of length >= 400 bp.""" ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3192, edam:operation_3200, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "HIFI-SE" ; sc:url "https://pypi.org/project/HIFI-SE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3673, edam:topic_3810 ; sc:citation , "pmcid:PMC8864876", "pubmed:35193521" ; sc:description "Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz)." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HiFiAdapterFilt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0" ; sc:url "https://github.com/sheinasim/HiFiAdapterFilt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Hifiasm: a haplotype-resolved assembler for accurate Hifi reads" ; sc:featureList edam:operation_0524, edam:operation_0525 ; sc:license "MIT" ; sc:name "Hifiasm" ; sc:softwareHelp ; sc:softwareVersion "0.16.1" ; sc:url "https://github.com/chhylp123/hifiasm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174 ; sc:description "Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads." ; sc:featureList edam:operation_0310 ; sc:license "MIT" ; sc:name "Hifiasm-meta" ; sc:url "https://github.com/xfengnefx/hifiasm-meta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3174 ; sc:citation , "pubmed:35482530" ; sc:description "Integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs." ; sc:featureList edam:operation_0310, edam:operation_3731, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "HiFine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dyxstat/HiFine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "The software package HiFiX implements the novel algorithm for HIgh FIdelity Clustering of Sequences." ; sc:featureList edam:operation_0291, edam:operation_3432 ; sc:name "HiFiX" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.5" ; sc:url "http://lbbe.univ-lyon1.fr/-HiFiX-.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_3374, edam:topic_3954 ; sc:citation , "pubmed:33877971" ; sc:description "HIFU-beam is a free open source software with graphical user interface for modeling nonlinear axially symmetric focused ultrasound beams with account for possible formation of shock fronts." ; sc:featureList edam:operation_2426, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "HIFU beam" ; sc:url "http://limu.msu.ru/node/3555?language=en" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_1775, edam:topic_3174, edam:topic_3941 ; sc:citation , "pubmed:37649370" ; sc:description "Homology independent protein function prediction by a novel protein-language self-attention model." ; sc:featureList edam:operation_0477, edam:operation_1777, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "HiFun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.unimd.org/HiFun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0621, edam:topic_3053, edam:topic_3474 ; sc:citation ; sc:description """Hierarchical Representations of Gene Ontology and Genes in the Poincaré Ball. Preprint version available here https://www.biorxiv.org/content/10.1101/2020.07.14.195750v1. git clone https://github.com/JaesikKim/HiG2Vec.git. Simply clone this repository via.""" ; sc:featureList edam:operation_2454, edam:operation_2492, edam:operation_3672 ; sc:name "HiG2Vec" ; sc:url "https://github.com/JaesikKim/HiG2Vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3301 ; sc:citation , "pubmed:25450223" ; sc:description "Bacteriological, clinical, genomic and proteomic database of H. influenzae." ; sc:featureList edam:operation_0226, edam:operation_2403, edam:operation_2406 ; sc:name "HIGDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioserver1.physics.iisc.ernet.in/HIGDB/" ; biotools:primaryContact "Dr. Anand Anbarasu", "Dr. K. Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344, edam:topic_3954 ; sc:description "Simulates high intensity focused ultrasound beams and heating effects in layered media" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "High intensity focused ultrasound simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/30886-high-intensity-focused-ultrasound-simulator" ; biotools:primaryContact "Josh Soneson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0605, edam:topic_3474, edam:topic_3957 ; sc:citation , "pmcid:PMC9968329", "pubmed:36841846" ; sc:description "A double-viewed hierarchical graph learning model, HIGH-PPI, to predict PPIs and extrapolate the molecular details involved." ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HIGH-PPI" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/zqgao22/HIGH-PPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0634, edam:topic_3300, edam:topic_3360 ; sc:citation ; sc:description """An integrated resource for High-Altitude associated genes and proteins, interacting networks and semantic-similarities. 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This software utilized maximum likelihood and smooth algorithm, and could deal with ten thousand markers that make map distance more stably." ; sc:featureList edam:operation_0282 ; sc:name "HighMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://highmap.biomarker.com.cn/" ; biotools:primaryContact "Biomarker group", "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:36519623" ; sc:description "A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention." ; sc:featureList edam:operation_3454, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HiGNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/idruglab/hignn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:32502244" ; sc:description """How to compute longitudinal GWAS data in population designs. Implementing Lasso methods to identify significant SNPs and estimate joint genetic effects for non-longitudinal traits or longitudinal traits in GWAS. The HiGWAS package is developed to identify significant SNPs that control phenotypic variation and estimate their additive and dominant genetic effects based on the Bayesian Lasso or Group Lasso model. The package provides two statistical models, BLS can detect the association using one single time measured phenotypc and GLS solve the association based on the longitudinal phenotype. [1]. Li, J., Das, K., Fu, G., Li, R., & Wu, R. (2011). The Bayesian lasso for genome-wide association studies. Bioinformatics, 27(4), 516-523. [2]. Li. J., Wang, Z., Li, R., Wu, R.(2015).Bayesian Group Lasso for nonparametric varying-coefficient models with application to functional genome-wide association studies. The Annals of Applied Statistics. 9(1).""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659, edam:operation_3935 ; sc:name "HiGwas" ; sc:url "https://github.com/wzhy2000/higwas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_3053, edam:topic_3295 ; sc:citation "pubmed:25725496" ; sc:description "New Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different cell types, developmental stages, even multiple species) using genome-wide histone modification data." ; sc:featureList edam:operation_2520 ; sc:name "hiHMM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.00" ; sc:url "https://sites.google.com/site/kasohn/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0781, edam:topic_3324 ; sc:citation ; sc:description "HIV-1 incidence and infection time estimator, which processes envelope gene sequences using hierarchical clustering algorithms and informs the stage of infection, along with time since infection for incident cases." ; sc:featureList edam:operation_3461 ; sc:name "HIITE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://p512.usc.edu/request/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1017 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence range" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1279 ; sc:encodingFormat edam:format_2060 ; sc:name "Sequence map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:author ; sc:citation , "pubmed:27153599" ; sc:description "Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve." ; sc:featureList edam:operation_0573 ; sc:license "GPL-2.0" ; sc:name "HilbertCurve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HilbertCurve.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3315 ; sc:citation ; sc:description "Functions to visualize long vectors of integer data by means of Hilbert curves." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "HilbertVis" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HilbertVis.html" ; biotools:primaryContact "Simon Anders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "An interactive tool to visualize long vectors of integer data by means of Hilbert curves." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "HilbertVisGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HilbertVisGUI.html" ; biotools:primaryContact "Simon Anders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_2229, edam:topic_3315 ; sc:citation , "pmcid:PMC8489061", "pubmed:34607562" ; sc:description "Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks." ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_3799, edam:operation_3891, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HiLoop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BenNordick/HiLoop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:17847101" ; sc:description "Web server for predicting rigid protein parts and the flexible hinge regions connecting them in the native topology of protein chains by employing elastic network (EN) models." ; sc:featureList edam:operation_0474 ; sc:name "HingeProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.prc.boun.edu.tr/appserv/prc/hingeprot/" ; biotools:primaryContact "Polymer Research Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3173 ; sc:citation "pubmed:25086003" ; sc:description "HMM-based Identification of TF Footprints" ; sc:featureList edam:operation_0415, edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "HINT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hint.yulab.org/" ; biotools:primaryContact "Haiyuan Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:22123737" ; sc:description "human integrated Pathway DataBase with facile visualiztion: an integrated pathway databasethat combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta, and KEGG." ; sc:featureList edam:operation_0335, edam:operation_2497, edam:operation_3083, edam:operation_3439, edam:operation_3562 ; sc:name "hiPathDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hipathdb.kobic.re.kr/" ; biotools:primaryContact "hiPathDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602 ; sc:citation , "pmcid:PMC5354899", "pubmed:28042959" ; sc:description "Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway." ; sc:featureList edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "hipathia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hipathia.html" ; biotools:primaryContact "Marta R. Hidalgo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3518 ; sc:citation , "pmcid:PMC6908734", "pubmed:31831811" ; sc:description """Using mechanistic models for the clinical interpretation of complex genomic variation. The sustained generation of genomic data in the last decade has increased the knowledge on the causal mutations of a large number of diseases, especially for highly penetrant Mendelian diseases, typically caused by a unique or a few genes. However, the discovery of causal genes in complex diseases has been far less successful. Many complex diseases are actually a consequence of the failure of complex biological modules, composed by interrelated proteins, which can happen in many different ways, which conferring a multigenic nature to the condition that can hardly be attributed to one or a few genes.""" ; sc:featureList edam:operation_0331, edam:operation_0533, edam:operation_3562 ; sc:name "Hipathia-genomics" ; sc:url "http://hipathia.babelomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:33750003" ; sc:description "hiphop is an R package for paternity assignment among close relatives using a simple exclusion method for biallelic markers." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3894 ; sc:license "GPL-2.0" ; sc:name "hiphop" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=hiphop" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Make NGS data analysis quick and easy with high performance pipelines and intuitive web GUI." ; sc:featureList edam:operation_3198, edam:operation_3227 ; sc:name "HiPipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hipipe.ncgm.sinica.edu.tw/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , "pubmed:35788820" ; sc:description """Hiplot (https://hiplot.org) provides concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Hiplot (ORG) is maintained and updated by the Openbiox open-source community.""" ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Hiplot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hiplot.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation "pubmed:29315405" ; sc:description "HipMCL: A High-Performance Parallel Algorithm for Large-Scale Network Clustering" ; sc:license "Other" ; sc:name "HipMCL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/azadcse/hipmcl/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0749, edam:topic_3295 ; sc:citation "pubmed:25480377" ; sc:description "Workflow for analyzing Hi-C paired-end reads in FASTQ format and predict enhancer–target gene interactions. HIPPIE streamlines the entire processing phase including reads mapping, quality control and enhancer–target gene prediction as well as characterizing the interactions." ; sc:featureList edam:operation_2520, edam:operation_3439 ; sc:name "HIPPIE" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://wanglab.pcbi.upenn.edu/hippie/" ; biotools:primaryContact "Wang Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3304, edam:topic_3306 ; sc:citation ; sc:description """A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. This package contains validation tests for models of hippocampus, based on the SciUnit framework and the NeuronUnit package. The purpose of this repository is to provide examples on how to run the validation tests of HippoUnit on models of the hippocampal CA1 pyramidal cell available in the literature and on ModelDB. Current tests cover somatic behavior and signal propagation and integration in apical dendrites of hippocampal CA1 pyramidal cell models. Feature errors: Z-score (the difference of model feature value from the exerimental mean feature value in the unit of the experimental SD.). git clone https://github.com/KaliLab/hippounit.git.""" ; sc:featureList edam:operation_2428, edam:operation_3450, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "HippoUnit" ; sc:softwareHelp ; sc:url "https://github.com/KaliLab/hippounit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Hipsec is a tool for predicting high-level protein production in Aspergillus niger. The software predicts if gene overexpression of an extracellular protein will lead to successful high-level production in Aspergillus niger. The prediction is based on a protein’s amino acid sequence. One or more protein sequences can be pasted into the the text area (fasta format) or uploaded as a fasta file." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "Hipsec" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://helix.ewi.tudelft.nl/hipsec/home.py" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence features metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "Haplotype inference and phasing for Short Tandem Repeats (hipSTR) is a haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data. It also enables genome-wide analysis and validation of de novo STR mutations." ; sc:featureList edam:operation_0237, edam:operation_3218, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "hipSTR" ; sc:softwareHelp ; sc:url "https://hipstr-tool.github.io/HipSTR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168, edam:topic_3519 ; sc:citation ; sc:description "Contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification." ; sc:featureList edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "hiReadsProcessor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hiReadsProcessor.html" ; biotools:primaryContact "Nirav V Malani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC4772016", "pubmed:26848124" ; sc:description "HiRise is a software pipeline that can identify poor quality joins and produce accurate, long-range sequence scaffolds." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HiRise" ; sc:url "https://github.com/DovetailGenomics/HiRise_July2015_GR" ; biotools:primaryContact "Dovetail Genomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , , , "pmcid:PMC4655817", "pmcid:PMC5032908", "pmcid:PMC5792058", "pubmed:25751142", "pubmed:27560171", "pubmed:27941783" ; sc:description "Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)." ; sc:featureList edam:operation_0292 ; sc:license "GPL-3.0" ; sc:name "HISAT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/hisat2/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_2269 ; sc:citation , "pubmed:32931549" ; sc:description """leveraging higher-order structures for clustering analysis in biological networks. MOTIVATION:Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into the understanding of complex biological systems. Existing clustering techniques make use of lower-order connectivity patterns at the level of individual biological entities and their connections, but few of them can take into account of higher-order connectivity patterns at the level of small network motifs. RESULTS:Here, we present a novel clustering framework, namely HiSCF, to identify functional modules based on the higher-order structure information available in a biological network. Taking advantage of higher-order Markov stochastic process, HiSCF is able to perform the clustering analysis by exploiting a variety of network motifs""" ; sc:featureList edam:operation_2844, edam:operation_3927, edam:operation_3928 ; sc:name "HiSCF" ; sc:url "https://github.com/allenv5/HiSCF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Hierarchical Structured Component analysis of microRNA-mRNA integration model is a novel statistical method to find biological relationship, efficiently study and identify such integrated markers. It could use subgroup information, it yelded more results, as related to phenotypes, than those of other existing methods that lack network information. It can be easily applied to other cancer studies to identify miRNA-mRNA integration sets for early diagnosis and prognosis." ; sc:featureList edam:operation_2426 ; sc:name "HisCoM-mimi" ; sc:url "http://statgen.snu.ac.kr/software/hiscom-mimi/" ; biotools:primaryContact "Sungyoung Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Efficient all-vs-all long read aligner for SMRT sequencing data." ; sc:featureList edam:operation_0525 ; sc:license "Other" ; sc:name "HISEA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/lucian-ilie/HISEA" ; biotools:primaryContact "Lucian Ilie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3169, edam:topic_3452, edam:topic_3940 ; sc:citation , "pmcid:PMC7425017", "pubmed:32787954" ; sc:description """Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. HiSIF - HiC Significant Interacting Fragments. HiSIF was implemented by using C++/C with parallel processing being written in C. It has been compiled and run exclusively on Linux operating systems. This tool only requires the g++ compiler and a reference genome for HG19. Standalone CERN ROOT C++ framework is used to extract fit parameters of the CTS interactions. A small C tool is provided to process the initial data from NCBI. HiSIF supports all of the available three Hi-C protocols (Hi-C, TCC and in situ Hi-C). The tool is named from the fact that it is designed to find the significant interactions from a given sample of Hi-C reads.""" ; sc:featureList edam:operation_0481, edam:operation_3431, edam:operation_3435 ; sc:name "HiSIF" ; sc:url "https://github.com/yufanzhouonline/HiSIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0128, edam:topic_0154, edam:topic_0176, edam:topic_3175 ; sc:citation , "pmcid:PMC7929440", "pubmed:33406224" ; sc:description """A bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. Protein and nucleic acid interactions play a vital role in many biological processes such as DNA replication, repair and processing, as well as RNA processing and translocation.""" ; sc:featureList edam:operation_0279, edam:operation_0420, edam:operation_2476, edam:operation_3891, edam:operation_4009 ; sc:name "HISNAPI" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/HISNAPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0621, edam:topic_2229, edam:topic_3068 ; sc:citation , "pubmed:33984507" ; sc:description "HisPhosSite is a comprehensive database of histidine phosphorylated proteins and sites." ; sc:featureList edam:operation_0417, edam:operation_2421, edam:operation_3755 ; sc:name "HisPhosSite" ; sc:url "http://reprod.njmu.edu.cn/cgi-bin/HisPhosSite/HisPhosSite.php" ; biotools:primaryContact "Xiaofeng Song", "Xuejiang Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC10193785", "pubmed:37198529" ; sc:description "Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes." ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HISS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SwiftSeal/HISS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "A user-friendly tool for cloud-based whole slide image segmentation. Histo-cloud (HistomicsTK-deeplab) is a modified version of HistomicsTK by Brendon Lutnick. HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI." ; sc:featureList edam:operation_3443, edam:operation_3629, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Histo-Cloud" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/SarderLab/Histo-cloud" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2032 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3383 ; sc:citation ; sc:description "Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively." ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "histoCAT" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bodenmillerlab.org/research-2/histoCAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3383, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc:description "Open-source Software for Histological Image Pre-processing and Augmentation to Improve Development of Robust Convolutional Neural Networks." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "HistoClean" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HistoCleanQUB/HistoClean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3263, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC9340569", "pubmed:34911013" ; sc:description "Federated learning for computational pathology on gigapixel whole slide images." ; sc:featureList edam:operation_3359, edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HistoFL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/mahmoodlab/HistoFL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0634, edam:topic_0821, edam:topic_2815, edam:topic_3295 ; sc:citation "pubmed:22140112" ; sc:description "A browsable, manually curated, and relational database of human histone proteins and histone modifying enzymes. It contains 55 human histone proteins, 106 distinct sites of their post-translational modifications (PTMs) and 152 histone-modifying enzymes. Entries have been grouped into 5 types of histones, 8 types of post-translational modifications and 14 types of enzymes that catalyze addition and removal of these modifications." ; sc:featureList edam:operation_0417, edam:operation_2409, edam:operation_2422, edam:operation_3645, edam:operation_3755 ; sc:name "HIstome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iiserpune.ac.in/~coee/histome/" ; biotools:primaryContact "Sanjay Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3382, edam:topic_3474 ; sc:description "HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI." ; sc:featureList edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "HistomicsTK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DigitalSlideArchive/HistomicsTK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3383, edam:topic_3474 ; sc:citation , "pmcid:PMC10583115", "pubmed:37860768" ; sc:description "Python package for training Multiple Instance Learning models on histopathology slides." ; sc:featureList edam:operation_0479, edam:operation_3435, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HistoMIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/secrierlab/HistoMIL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2332 ; sc:name "Sequence search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation , "pubmed:25073878" ; sc:description "Count the number of MS/MS ions in a given spectrum to determine the unambiguous localization of a post-translational modification (PTM). The software lists number and type of site determining ions found between the assigned PTM localization by Mascot (Matrix Science) and the closest other amino acids which can host the modification. The PTMs included in the script are phosphorylation (S,T,Y), acetylation (K), mono- and dimethylation (K,R) and trimethylation (K)." ; sc:featureList edam:operation_0226, edam:operation_0417 ; sc:name "Histone Coder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bmb.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/middle-down/Software" ; biotools:primaryContact "Simone Sidoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0122, edam:topic_0154, edam:topic_0166, edam:topic_3295 ; sc:citation "pubmed:20739309" ; sc:description "The structural genomics of histone tail recognition web server is an open access resource that presents within mini articles all publicly available experimental structures of histone tails in complex with human proteins. Each article is composed of interactive 3D slides that dissect the structural mechanism underlying the recognition of specific sequences and histone marks." ; sc:featureList edam:operation_0245, edam:operation_0246, edam:operation_3092 ; sc:name "Structural Genomics of Histone Tail Recognition" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apps.thesgc.org/resources/histone_tails/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3169, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC4347972", "pubmed:25884684" ; sc:description "Analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples." ; sc:featureList edam:operation_3222, edam:operation_3223, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "histoneHMM" ; sc:softwareHelp ; sc:softwareVersion "1.7" ; sc:url "https://github.com/matthiasheinig/histoneHMM" ; biotools:primaryContact "Matthias Heinig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3056, edam:topic_3299 ; sc:citation ; sc:description "Accurate reconstruction of ancestral sequences and evolutionary rates." ; sc:featureList edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "Historian" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/evoldoers/historian" ; biotools:primaryContact "Ian H. Holmes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0749, edam:topic_3169, edam:topic_3176, edam:topic_3295 ; sc:citation ; sc:description """A Tool to Identify Nucleosome Free Regions from ChIP-Seq of Histone Post-Translational Modifications. A Tool to Identify Nucleosome Free Regions from ChIP-Seq Against Histone Modifications. USAGE: perl HISTRADER.pl --bedGraph ChIP.bedGraph --peaks ChIP.bed.""" ; sc:featureList edam:operation_0432, edam:operation_3192, edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "HisTrader" ; sc:url "https://github.com/SvenBaileyLab/Histrader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0140, edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation "pubmed:21097881" ; sc:description "A comprehensive and fully curated database for Herb Ingredients’ Targets. Molecular target information involves those proteins being directly/indirectly activated/inhibited, protein binders and enzymes whose substrates or products are those compounds. Those up/down regulated genes are included under the treatment of individual ingredients. The experimental condition, observed bioactivity and various references are provided. The database can be queried via keyword or similarity search." ; sc:featureList edam:operation_0224, edam:operation_0360, edam:operation_2421, edam:operation_2422, edam:operation_2489 ; sc:name "HIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lifecenter.sgst.cn/hit/" ; biotools:primaryContact "Zhiwei Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3697 ; sc:citation ; sc:description """Hierarchical Taxonomic Classification of Fungal ITS Sequences. Abstract Motivation Fungi are key elements in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human microbiome and can be causative agents of human infections. An accurate and robust method for fungal ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight of the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them consider the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors""" ; sc:featureList edam:operation_3460 ; sc:name "HiTaC" ; sc:url "https://gitlab.com/dacs-hpi/hitac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097 ; sc:citation , "pmcid:PMC3476334", "pubmed:22923296" ; sc:description "This package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3435 ; sc:license "Artistic-2.0" ; sc:name "HiTC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HiTC.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3175, edam:topic_3673, edam:topic_3794 ; sc:citation ; sc:description """A computational pipeline to identify non-reference transposable element insertions in Hi-C data. computational tool to identify trasposable element insertions using Hi-C data. HiTea (Hi-C based Transposable Element Analyzer) is geared to idenify non-reference transposable elemenet insertions from the Hi-C data. It uses split Hi-C read information and read coverage to detect insertions of three major classes of active human transposable elements (TE) - Alu (SINE), L1HS(LINE) and SVA.""" ; sc:featureList edam:operation_0525, edam:operation_3196, edam:operation_3359 ; sc:license "MIT" ; sc:name "HiTea" ; sc:url "https://github.com/parklab/HiTea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:21115437" ; sc:description "An algorithm for correcting reads produced by high-throughput sequencing methods." ; sc:featureList edam:operation_2425, edam:operation_3195, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "HiTEC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.csd.uwo.ca/%7Eilie/HiTEC/" ; biotools:primaryContact "Lucian Ilie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_3557 ; sc:citation "pubmed:20947562" ; sc:description "HitPredict is a database with quality assessed PPIs in nine species. HitPredict assigns a confidence level to interactions based on a reliability score that is computed using evidence from sequence, structure and functional annotations of the interacting proteins." ; sc:featureList edam:operation_0277, edam:operation_2464, edam:operation_2492, edam:operation_2949, edam:operation_3439 ; sc:name "HitPredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hintdb.hgc.jp/htp/" ; biotools:primaryContact "HitPredict Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23761448" ; sc:description "HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis) web server uses command line MATLAB scripts to analyze input high throughput capillary electrophoresis data." ; sc:featureList edam:operation_2429, edam:operation_2520, edam:operation_3642 ; sc:name "HiTRACE-Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hitrace.org" ; biotools:primaryContact "Pablo Cordero (Site admin)", "Rhiju Das (PI)", "Site admins: Hanjoo Kim (Site admin)", "Sungroh Yoon (PI)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602, edam:topic_2269, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25428347" ; sc:description "Software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. It provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis." ; sc:featureList edam:operation_2403 ; sc:name "HiTSelect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/diazlab/HiTSelect" ; biotools:primaryContact "Aaron Diaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_3053, edam:topic_3303 ; sc:citation "pubmed:26708334" ; sc:description "Prioritizes patient variants relative to their weighted proximity to functional assay results in a protein-protein interaction network. It is highly extensible, allowing incorporation of diverse data types to refine prioritization." ; sc:featureList edam:operation_3226 ; sc:name "HitWalker2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biodev/HitWalker2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3464 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file." ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HIV-TRACE" ; sc:softwareVersion "0.1.7" ; sc:url "https://github.com/veg/hivtrace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "The HIVbio is the home page of various informations that are provided here for Human Immunodefeciency Virus (HIV) life cycle and Infection." ; sc:featureList edam:operation_2945 ; sc:name "hivbio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hivbio/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0781, edam:topic_3510 ; sc:citation "pubmed:18249180" ; sc:description "Web-server for predicting HIV protease cleavage sites in proteins." ; sc:featureList edam:operation_3092 ; sc:name "HIVcleave" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/HIV/" ; biotools:primaryContact "Hong-Bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3626595", "pubmed:23596523" ; sc:description "HIVcoPRED: is a web server developed for predicting the coreceptor usage by HIV-1. It takes amino acid sequences of Variable loop (V3) of gp120 protein of HIV and predicts the coreceptor used by the HIV strain." ; sc:featureList edam:operation_2945 ; sc:name "hivcopred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hivcopred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3571 ; sc:citation , "pmcid:PMC4795927", "pubmed:26989153" ; sc:description "High-performance integrated virtual environment: a robust infrastructure for next-generation sequence data analysis." ; sc:featureList edam:operation_2403 ; sc:name "HIVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hive.biochemistry.gwu.edu/home" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168, edam:topic_3697 ; sc:citation , "pubmed:32717050" ; sc:description """An interactive network visualization tool. Update: Interactive hive panels can be easily built using different data formats. A wiki tutorial will be up soon. Stay tuned!. Welcome to the Hive Panel Explorer wiki!. Hive Panel Explorer is a Python script that takes a network and creates a static HTML page with interactive SVG graphics in D3. The visualization produced is a matrix of hive plots plotted using attributes of the nodes and edges (such as degree and centrality). The interactive features let users explore their network and discover patterns in their network. For more information on the design of the tool and on the kind of patterns it can reveal, check out Sarah Perez's Master Thesis.""" ; sc:featureList edam:operation_3925 ; sc:name "Hive_Panel_Explorer" ; sc:softwareHelp ; sc:url "https://github.com/hallamlab/HivePanelExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3673 ; sc:citation , "pubmed:33453108" ; sc:description """An accurate tool to detect virus integrations in the host genome. After obtaining the integration sites, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations.""" ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3359, edam:operation_3695 ; sc:name "HIVID2" ; sc:url "https://github.com/zengxi-hada/HIVID2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:26969411" ; sc:description "First integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. It is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation." ; sc:featureList edam:operation_3208 ; sc:name "HiView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.unc.edu/~yunmli/HiView/" ; biotools:primaryContact "Li Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "The Human Immunodeficiency Virus is a retrovirus and has a genome size of about 9.5 Kb with repertoire of only 15-20 proteins." ; sc:featureList edam:operation_2945 ; sc:name "hivint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hivint/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC8237426", "pubmed:34176496" ; sc:description "A python-based tool for HIV-1 genome intactness inference." ; sc:featureList edam:operation_0337, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HIVIntact" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ramics/HIVIntact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "João Carneiro" ; sc:citation ; sc:description "The HIVoligoDB is a comprehensive on-line resource with curated datasets of oligonucleotides for the human immunodeficiency virus (HIV). The database provides a curated and regularly updated list of oligonucleotides and a description of the genetic diversity across the HIV-1 and HIV-2 genomes to facilitate the design of accurate diagnostic methods and therapeutic approaches." ; sc:isAccessibleForFree true ; sc:name "HIVoligoDB - The HIV oligonucleotide database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://portugene.com/HIVoligoDB/cgi-bin/HIVoligoDB_home.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0821, edam:topic_2258 ; sc:citation ; sc:description "In this server, user can predict the IC50/Percent inhibition of given compounds against three HIV proteins namely reverse transcriptase, protease and integrase." ; sc:featureList edam:operation_2492 ; sc:license "GPL-3.0" ; sc:name "HIVprotI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.imtech.res.in/manojk/hivproti/" ; biotools:primaryContact "Dr. Manoj Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2640 ; sc:citation , "pmcid:PMC7397777", "pubmed:32667823" ; sc:description """A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. A customizable environment for the structural modeling and analysis of peptide-HLA complexes.""" ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:name "HLA-Arena" ; sc:url "https://github.com/KavrakiLab/hla-arena" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2830, edam:topic_3421, edam:topic_3930 ; sc:citation , "pmcid:PMC7317360", "pubmed:32227681" ; sc:description """A user-friendly tool to analyse HLA class I and class II compatibility on the amino acid level. HLA-EMMA is a software package designed to perform HLA class I and class II compatibility analysis on the amino acid level. HLA-EMMA predicts & analyses HLA antibody formation.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3196 ; sc:name "HLA-EMMA" ; sc:url "http://www.HLA-EMMA.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0804, edam:topic_3421 ; sc:citation , "pubmed:34862850" ; sc:description "A new EPIsode in exploring donor/recipient epitopic compatibilities." ; sc:featureList edam:operation_0416, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "HLA-Epi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hla.univ-nantes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3056, edam:topic_3168 ; sc:citation , "pubmed:31742916" ; sc:description """Distribution of the HLA-DPB1 alleles in a Russian population living in the Chelyabinsk region (South Ural of Russia). Tools for handling and analysing data with ambiguities. These programs expect plain text files in UNIFORMAT v3 as input. A download link to the results file is provided once the execution is completed (on screen and/or by email). Read more about these tools (and see examples of input files) in the usage overview.""" ; sc:featureList edam:operation_0487 ; sc:name "hla-net" ; sc:url "https://hla-net.eu/tools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_2885, edam:topic_3360 ; sc:citation ; sc:description """A Natural Language Processing based resource for curating HLA association from PubMed abstracts. HLA Web Resource for SNPs, Populations, Resources, ADRs, Diseases.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3280 ; sc:name "HLA-SPREAD" ; sc:url "http://hla-spread.igib.res.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2830, edam:topic_3421, edam:topic_3930 ; sc:citation , "pmcid:PMC9116210", "pubmed:35289353" ; sc:description "An integrated structure-based computational toolkit for immunotherapy." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_0479 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HLA3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.hla3d.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3125, edam:topic_3534 ; sc:citation "pubmed:8254189" ; sc:description "Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature." ; sc:featureList edam:operation_0252, edam:operation_0420, edam:operation_0465, edam:operation_2575 ; sc:name "Bimas HLA Peptide Binding Predictions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-bimas.cit.nih.gov/molbio/hla_bind/" ; biotools:primaryContact "Kenneth Parker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC10169335", "pubmed:37161375" ; sc:description "HLA class I clustering based on 3D structure." ; sc:featureList edam:operation_0252, edam:operation_0480, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HLA-Clus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yshen25/HLA-Clus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0769, edam:topic_2830 ; sc:citation , "pmcid:PMC10258777", "pubmed:37308510" ; sc:description "Unraveling the glycosylated immunopeptidome with HLA-Glyco." ; sc:featureList edam:operation_0416, edam:operation_0417, edam:operation_3637, edam:operation_3649 ; sc:isAccessibleForFree true ; sc:name "HLA-Glyco" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hla-glyco.nesvilab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:14960470" ; sc:description "TheHLA-DR4Pred is an SVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction method. The accuracy of the SVM and ANN based methods is ~86% and ~78% respectively." ; sc:featureList edam:operation_2945 ; sc:name "hladr4pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hladr4pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "HLA-DR4Pred 2.0 is the update of the older version HLA-DR4Pred, which was a SVM and ANN based method to predict the HLA-DRB1*04:01 bindind peptides." ; sc:featureList edam:operation_2945 ; sc:name "hladr4pred2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hladr4pred2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:35580839" ; sc:description "HLAncPred is a webserver for the prediction of promiscuous binders of non-classical HLA-G and HLA-E alleles (HLA-G*01:01, HLA-G*01:03, HLA-G*01:04, HLA-E*01:01 and HLA-E*01:03)." ; sc:featureList edam:operation_2945 ; sc:name "hlancpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hlancpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3930 ; sc:citation , "pubmed:32124314" ; sc:description """HLA Typing and Quantification of Expression with Personalized Index. HLApers integrates software such as kallisto, Salmon and STAR. Before using it, please read the license notices here. The first step is to use hlapers prepare-ref to build an index composed of Gencode transcripts, where we replace the HLA transcripts with IMGT HLA allele sequences.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227, edam:operation_3799 ; sc:name "HLApers" ; sc:url "https://github.com/genevol-usp/HLApers.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "HLAreporter (HLA reporter) is a novel tool  for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads." ; sc:featureList edam:operation_0310, edam:operation_2429, edam:operation_3429 ; sc:name "HLAreporter" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "1.03" ; sc:url "http://paed.hku.hk/genome/software.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pubmed:21079948" ; sc:description "Patient-specific predictions of HLA restriction elements and optimal epitopes within peptides." ; sc:featureList edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HLArestrictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://cbs.dtu.dk/services/HLArestrictor/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315 ; sc:description "A MATLAB code for Human Learning Optimization(HLO) algorithm" ; sc:isAccessibleForFree true ; sc:name "Human Learning Optimization(HLO) algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65577-human-learning-optimization-hlo-algorithm" ; biotools:primaryContact "Ling Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC4150950", "pubmed:25141912" ; sc:description "HLP is a server developed for predicting half-life of peptides in intestine like environment. It generates all possible mutants (single mutation at each position per cycle) for a peptide and predict/calculate half-life and physicochemical properties (e.g. charge, polarity, hydrophobicity, volume, pK) of mutant peptides." ; sc:featureList edam:operation_2945 ; sc:name "hlp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hlp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3379, edam:topic_3474, edam:topic_3948 ; sc:citation , "pubmed:32145017" ; sc:description """Improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. Welcome to the Home Page of HLPpred-Fuse. HLPpred-Fuse could be established according to the following steps: (i) feature representation scheme was employed to generate 54 probabilistic features derived from 54 prediction models that utilized nine different types of peptide features, i.e. AAC, DPC, amino acid index (AAI), binary profile (BPF), composition-transition-distribution (CTD), conjoint triad (CTF), quasi-sequence order (QSO), grouped dipeptide composition (GDPC), and grouped tripeptide composition (GTPC), and six ML classifiers, i.e. SVM, RF, gradient boosting (GB), extremely randomized tree (ERT), k-nearest neighbor (KNN), and AdaBoost (AB); and (ii) those 54 probabilistic features were fused and inputted to ERT to develop a final predictor separately for both layers. For a given peptide sequence, HLPpred-Fuse predicts HLPs activity and probability values.""" ; sc:featureList edam:operation_3631 ; sc:name "HLPpred-Fuse" ; sc:url "http://thegleelab.org/HLPpred-Fuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3295 ; sc:citation "pubmed:19900972" ; sc:description "Database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, 2585 genes and 212 miRNA have been collected with the experimental evidences involved in the different stages of lung carcinogenesis through text mining. The results from analysis of transcription factor-binding motifs, the promoters and the SNP sites for each gene are also included. Genes with epigenetic regulation were also included." ; sc:featureList edam:operation_0306, edam:operation_0314, edam:operation_1781, edam:operation_3439, edam:operation_3501 ; sc:name "HLungDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.megabionet.org/bio/hlung/" ; biotools:primaryContact "Tieliu Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3169, edam:topic_3295 ; sc:citation "pubmed:24021381" ; sc:description "Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction." ; sc:featureList edam:operation_3227 ; sc:name "HMCan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cbrc.kaust.edu.sa/hmcan/" ; biotools:primaryContact "Haitham Ashoor", "Valentina Boeva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0623, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC7871585", "pubmed:33557954" ; sc:description "Hierarchical multi-task deep learning for annotating antibiotic resistance genes." ; sc:featureList edam:operation_0224, edam:operation_3092, edam:operation_3482 ; sc:name "HMD-ARG" ; sc:url "http://www.cbrc.kaust.edu.sa/HMDARG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3421, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:35701681" ; sc:description "Head-mounted display-based egocentric marker-less tool and hand pose estimation for augmented surgical guidance." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HMD-EgoPose" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/doughtmw/hmd-ego-pose" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "Human microbe-disease association prediction using network consistency projection." ; sc:featureList edam:operation_3439 ; sc:name "Human Microbe-Disease Association Database (HMDAD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cuilab.cn/hmdad" ; biotools:primaryContact "De-Shuang Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0621, edam:topic_3172, edam:topic_3421 ; sc:citation "pubmed:16302993", "pubmed:17202168", "pubmed:18953024" ; sc:description "Freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches." ; sc:featureList edam:operation_0224, edam:operation_0339, edam:operation_0360, edam:operation_2421, edam:operation_3431 ; sc:name "HMDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hmdb.ca/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3053, edam:topic_3174 ; sc:citation , "pubmed:37639797" ; sc:description "A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background." ; sc:featureList edam:operation_0224, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:name "HMDB" ; sc:url "http://www.orgene.net/HMDB/" ; biotools:primaryContact "Ting Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease)." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "hmdbQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hmdbQuery.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3063, edam:topic_3303 ; sc:citation , "pmcid:PMC6323994", "pubmed:37650649" ; sc:description "Database for experimentally supported human microRNA-disease associations." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "HMDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cuilab.cn/hmdd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0166, edam:topic_0621 ; sc:citation , "pmcid:PMC7261632", "pubmed:32061934" ; sc:description """A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry. Upload a list of template interfaces. TM-align Score Threshold (0 to 1):.""" ; sc:featureList edam:operation_0477, edam:operation_2464, edam:operation_2492 ; sc:name "HMI-PRED" ; sc:url "https://interactome.ku.edu.tr/hmi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3473 ; sc:citation "pubmed:27046867" ; sc:description "Algorithm which uses distribution and centroid information to cluster a sample and was applied to biological data." ; sc:featureList edam:operation_3432 ; sc:name "HML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://emu.src.riken.jp/HML/" ; biotools:primaryContact "Tatsuhiko Tsunoda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0736, edam:topic_3168 ; sc:citation "pubmed:21609463" ; sc:description "Protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. It corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors." ; sc:featureList edam:operation_0246, edam:operation_2995 ; sc:name "HMM-FRAME" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/hmm-frame/" ; biotools:primaryContact "Yanni Sun", "Yuan Zhang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1964 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820 ; sc:citation , "pmcid:PMC1523218", "pubmed:16597327" ; sc:description "HMM-TM is a tool that takes a protein sequence as input and predicts the transmembrane regions of alpha-helical" ; sc:featureList edam:operation_0269, edam:operation_0270, edam:operation_2423 ; sc:name "HMM-TM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.compgen.org/tools/HMM-TM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Align sequences to a profile HMM." ; sc:featureList edam:operation_2403 ; sc:name "hmmalign (genouest)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webservices.genouest.org/opal2/dashboard?command=docs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Profile HMM construction from multiple sequence alignments." ; sc:featureList edam:operation_0492 ; sc:name "hmmbuild (genouest)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webservices.genouest.org/opal2/dashboard?command=docs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Convert between profile HMM file formats." ; sc:featureList edam:operation_2403 ; sc:name "hmmconvert (genouest)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webservices.genouest.org/opal2/dashboard?command=docs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3572 ; sc:citation ; sc:description "Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for further analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples." ; sc:featureList edam:operation_3195 ; sc:license "GPL-3.0" ; sc:name "HMMcopy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HMMcopy.html" ; biotools:primaryContact "Daniel Lai", "Sohrab Shah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Sample sequence(s) from a profile HMM." ; sc:featureList edam:operation_2403 ; sc:name "hmmemit (genouest)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webservices.genouest.org/opal2/dashboard?command=docs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:encodingFormat edam:format_1370 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:encodingFormat edam:format_3329 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; 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sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623 ; sc:citation , , , , "pmcid:PMC3125773", "pmcid:PMC3197634", "pmcid:PMC3695513", "pubmed:21593126", "pubmed:22039361", "pubmed:23598997", "pubmed:29905871" ; sc:description "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search." ; sc:featureList edam:operation_0230, edam:operation_0296, edam:operation_0335, edam:operation_0336, edam:operation_0338, edam:operation_0492, edam:operation_2238, edam:operation_2421, edam:operation_2422, edam:operation_3434, edam:operation_3481 ; sc:license "Other" ; sc:name "HMMER3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.1b1" ; sc:url "http://hmmer.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2066 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623 ; sc:author "Sean Eddy" ; sc:citation , ; sc:description "HMMER3 hmmscan is used to search sequences against collections of profiles." ; sc:featureList edam:operation_0338 ; sc:name "HMMER hmmscan (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscan" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2066 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623 ; sc:author "Sean Eddy" ; sc:citation , ; sc:description "HMMER3 phmmer is used to search one or more sequences against a sequence database." ; sc:featureList edam:operation_0338 ; sc:name "HMMER phmmer (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_phmmer" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation ; sc:description "Supervised classification of superfamily protein sequences with a reliable cut-off threshold." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:name "HMMERCTTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BBCMdP/HMMERCTTER" ; biotools:primaryContact "Arjen ten Have" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3299 ; sc:citation , "pmcid:PMC10148686", "pubmed:37128578" ; sc:description "An ensemble method for multiple sequence alignment." ; sc:featureList edam:operation_0300, edam:operation_0479, edam:operation_0492, edam:operation_0496, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "HMMerge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MinhyukPark/HMMerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Retrieve profile HMM(s) from a file." ; sc:featureList edam:operation_2403 ; sc:name "hmmfetch (genouest)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webservices.genouest.org/opal2/dashboard?command=docs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2305 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , "pubmed:12783628", "pubmed:16249266" ; sc:description "Prediction of vertebrate and C. elegans genes." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "HMMgene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://cbs.dtu.dk/services/HMMgene/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3474 ; sc:citation , "pmcid:PMC5952413", "pubmed:29764422" ; sc:description "A hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "hmmIBD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/glipsnort/hmmIBD" ; biotools:primaryContact "Stephen F. Schaffner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:24225132" ; sc:description "Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "HMMpTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://aias.biol.uoa.gr/HMMpTM/" ; biotools:primaryContact "Biophysics & Bioinformatics Laboratory" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ], [ a bsct:FormalParameter ; 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sc:applicationSubCategory edam:topic_2814 ; sc:author ; sc:citation , "pmcid:PMC8896651", "pubmed:34954790" ; sc:description "A unified and modular interface to homology modelling software" ; sc:featureList edam:operation_0321, edam:operation_0477 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "homelette" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PhilippJunk/homelette" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:24564644" ; sc:description "Fast and effective solution to disentangle homologous sequences based on a maximum likelihood optimization." ; sc:featureList edam:operation_2995 ; sc:name "HomeoSplitter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioweb.supagro.inra.fr/homeoSplitter/" ; biotools:primaryContact "Vincent Ranwez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem." ; sc:featureList edam:operation_0238 ; sc:name "homer" ; sc:softwareVersion "4.9.1" ; sc:url "http://homer.ucsd.edu/homer/motif/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "A comparative modelling server for protein structure prediction. Automatic template selection." ; sc:featureList edam:operation_0477 ; sc:name "HOMER-A" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://protein.bio.unipd.it/homer/auto.html" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "A comparative modelling server for protein structure prediction. Manual template selection." ; sc:featureList edam:operation_0477 ; sc:name "HOMER-M" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://protein.bio.unipd.it/homer/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:19534752" ; sc:description "Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system." ; sc:featureList edam:operation_0324, edam:operation_2403, edam:operation_2409 ; sc:name "HOMOLENS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pbil.univ-lyon1.fr/databases/homolens.php" ; biotools:primaryContact "Guy Perrière" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3332, edam:topic_3520 ; sc:citation ; sc:description "Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data." ; sc:featureList edam:operation_3214 ; sc:name "Homologous Series Detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.envihomolog.eawag.ch/" ; biotools:primaryContact "Martin Loos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:description "This is a command line tool for sampling related sequences from Ensembl. It requires PyCogent, Numpy, SQLAlchemy, PyMysql, Click and SciTrack. At present, this tool provides capabilities to support sampling one-to-one orthologs from protein coding genes stored in an Ensembl MySQl database. It can either write out the protein coding sequences from the canonical CDS, or it can write out the Ensembl multiple sequence alignment of the entire gene with annotated features masked." ; sc:featureList edam:operation_2945 ; sc:name "HomoloSampler" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bitbucket.org/pycogent3/homologsampler" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0820, edam:topic_2275, edam:topic_3047 ; sc:citation , "pmcid:PMC7319549", "pubmed:32484557" ; sc:description """A web server tool to incorporate 'homologous' water molecules into GPCR structures. Program to incorporate internal water molecules to GPCR models. A free access tool to incorporate internal water molecules to GPCR structures. available at http://lmc.uab.cat/homolwat.""" ; sc:featureList edam:operation_0269, edam:operation_0477, edam:operation_0478, edam:operation_2476, edam:operation_2995 ; sc:name "HomolWat" ; sc:url "http://lmc.uab.es/homolwat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC8011154", "pubmed:33789731" ; sc:description "Homopolish is a method for the removal of systematic errors in nanopore sequencing by homologous polishing." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "Homopolish" ; sc:url "https://github.com/ythuang0522/homopolish" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3325, edam:topic_3500 ; sc:citation "pubmed:19465395", "pubmed:22669902" ; sc:description "A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable." ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_2429, edam:operation_3196, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "HomozygosityMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.homozygositymapper.org" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC10323168", "pubmed:37369033" ; sc:description "Accelerating open modification spectral library searching on tensor core in high-dimensional space." ; sc:featureList edam:operation_3649, edam:operation_3755, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "HOMS-TC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tycheyoung/homs-tc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3299 ; sc:citation "pubmed:24307702" ; sc:description "Homozygous stretch identifier from next-generation sequencing data." ; sc:featureList edam:operation_2403 ; sc:name "HomSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/" ; biotools:primaryContact "İGBAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3300, edam:topic_3304, edam:topic_3419 ; sc:citation , "pubmed:34320125" ; sc:description "A template for reproducible psychophysiological tasks for clinic, laboratory, and home use." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Honeycomb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://brown-ccv.github.io/honeycomb-docs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0654 ; sc:citation , "pmcid:PMC9805585", "pubmed:36440918" ; sc:description "A tool designed for assessing and measuring homophily in networks whose nodes have categorical attributes, namely when the nodes of networks come partitioned into classes." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "honto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cumbof/honto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:33260110" ; sc:description """Multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images. A platform for end-to-end development of machine learning solutions in biomedical imaging. Upload medical imaging data easily and securely.""" ; sc:featureList edam:operation_3436 ; sc:name "HookNet" ; sc:url "http://grand-challenge.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3365 ; sc:citation ; sc:description "This algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. It uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "hopach" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hopach.html" ; biotools:primaryContact "Katherine S. Pollard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "HoPhage (Host of Phage) is a computational tool that integrates two modules respectively using the deep learning and the Markov chain model to identify the host of a given phage fragment from metagenome or metavirome data at the genus level. HoP demonstrates a superior performance on short fragments within a wide candidate host range at every taxonomic level when testing on the artificial benchmark dataset of artificial phage contigs and the real virome data." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_2454 ; sc:name "HoPhage" ; sc:url "http://cqb.pku.edu.cn/ZhuLab/HoPhage/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_0611, edam:topic_2275, edam:topic_2828 ; sc:citation ; sc:description """Boosting protein functional dynamics with colored contact maps. A tool to boost protein functonal dynamics with colored contact maps. HOPMA is intended to help to define elastic network representations of protein structures. NOn-Linear rigid Block NMA approach (NOLB) a new conceptually simple and computationally efficient method for non-linear normal mode analysis.""" ; sc:featureList edam:operation_2426, edam:operation_2476 ; sc:license "MIT" ; sc:name "HOPMA" ; sc:url "https://team.inria.fr/nano-d/software/nolb-normal-modes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "A webserver to predict peptide hormones" ; sc:featureList edam:operation_2945 ; sc:name "hoppred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/hoppred/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3324 ; sc:citation , "pmcid:PMC6913047", "pubmed:31842945" ; sc:description """Automated detection and authentication of pathogen DNA in archaeological remains. HOPS is a java pipeline which focuses on screening MALT data (see Table of Contents) for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison. To use HOPS you will need a config file, which specifies some key parameters for MALT and MaltExtract. You can have multiple config files to quickly redo a previous analysis or archive them to remember parameters you used in an analysis. HOPS will in every case create a log that tells you which command was sent to Slurm, in case you encounter problems, that log file is a very good place to start looking for the problem""" ; sc:featureList edam:operation_2422, edam:operation_3198, edam:operation_3431, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "HOPS_MALT" ; sc:url "https://github.com/rhuebler/HOPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3277, edam:topic_3520 ; sc:citation , "pubmed:33045081" ; sc:description """High-performance library for (non-)uniform sampling of convex-constrained models. The Highly Optimized Polytope Sampling toolbox is an open-source C++17 library for efficient and scalable MCMC algorithms for sampling convex-constrained spaces possibly equipped with arbitrary target functions.""" ; sc:featureList edam:operation_1812, edam:operation_3938 ; sc:license "MIT" ; sc:name "HOPS_tk" ; sc:url "https://github.com/modsim/hops/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:19417074" ; sc:description "HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures." ; sc:featureList edam:operation_0245, edam:operation_0346, edam:operation_0360, edam:operation_0477, edam:operation_2487 ; sc:name "HorA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/horaserver/" ; biotools:primaryContact "N. Grishin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2099 ; sc:name "Name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0780, edam:topic_3300, edam:topic_3500 ; sc:citation , "pmcid:PMC9039076", "pubmed:35469024" ; sc:description "HORDB a comprehensive database of peptide hormones." ; sc:featureList edam:operation_0418, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:name "HORDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hordb.cpu-bioinfor.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3292, edam:topic_3316 ; sc:citation ; sc:description "HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in vertabrates. ORs are G-Coupled Protein Receptors with a 7-transmembrane structure. The ORs are responsible for triggering the olfactory signal transduction pathway. You will find here information on the entire human OR repertoire, including a rich annotation on genomic variations, classification, orthologs and other features. Also available are OR repertoires of other mammalian species." ; sc:name "The Human Olfactory Data Explorer (HORDE)" ; sc:url "https://genome.weizmann.ac.il/horde/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3474 ; sc:description "Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use." ; sc:license "Apache-2.0" ; sc:name "Horovod" ; sc:softwareHelp ; sc:url "https://github.com/horovod/horovod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2815, edam:topic_3174 ; sc:citation , "pmcid:PMC10749771", "pubmed:38039142" ; sc:description "Hostile removes host sequences from short and long reads, consuming paired or unpaired fastq[.gz] input." ; sc:featureList edam:operation_0524, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Hostile" ; sc:url "https://github.com/bede/hostile" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3305, edam:topic_3337, edam:topic_3673 ; sc:citation , "pmcid:PMC10152008", "pubmed:37131148" ; sc:description "Canadian whole genome sequencing and clinical data resource." ; sc:featureList edam:operation_3196, edam:operation_3436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "HostSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.cgen.ca/hostseq-studies-2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1931 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3697 ; sc:description "A versatile pipeline to remove host contaminants from metagenomics raw datasets, using BBMap and Kraken2." ; sc:featureList edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "hostzap" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/quadram-institute-bioscience/hostzap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:24860160" ; sc:description "Free software to detect genomic regions unusually rich (hotspot) in a given pattern via scan statistics." ; sc:featureList edam:operation_0239 ; sc:name "hot_scan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/itojal/hot_scan" ; biotools:primaryContact "Rafael Rosales" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0601, edam:topic_0736, edam:topic_0769, edam:topic_3538 ; sc:citation , "pmcid:PMC10278204", "pubmed:37167423" ; sc:description "Pipeline for transferring annotations between proteins beyond globular domains." ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_2422, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "HoTIDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hotidp.leloir.org.ar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:21385051" ; sc:description "Algorithm for finding significanlty altered subnetworks in a large gene interaction network." ; sc:featureList edam:operation_1781 ; sc:name "HotNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://compbio.cs.brown.edu/projects/hotnet/" ; biotools:primaryContact "Ben Raphael" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360 ; sc:citation ; sc:description "A tool identifies significantly mutated groups of interacting genes from large cancer sequencing studies." ; sc:featureList edam:operation_2497 ; sc:name "HotNet2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "imada.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://github.com/raphael-group/hotnet2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0130, edam:topic_0166, edam:topic_0602 ; sc:citation "pubmed:20444871" ; sc:description "HotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface, output includes an interactive 3D visualization of the hot spots." ; sc:featureList edam:operation_0331, edam:operation_2464, edam:operation_2492 ; sc:name "HotPoint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prism.ccbb.ku.edu.tr/hotpoint" ; biotools:primaryContact "HotPOINT Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0166, edam:topic_3534 ; sc:citation "pubmed:22080558" ; sc:description "Database of predicted hot spot clusters. Hot spots are energetically important residues at protein interfaces, clustered across the interface. HotRegion provides the hot region information of the interfaces by using predicted hot spot resides, and structural properties." ; sc:featureList edam:operation_0272, edam:operation_0387, edam:operation_2575, edam:operation_3432 ; sc:name "HotRegion" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prism.ccbb.ku.edu.tr/hotregion/" ; biotools:primaryContact "Engin Cukuroglu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "HotSpot is a software of prediction of hot spot residues through physicochemical characteristics of amino acid sequences" ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "HotSpot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sfb.kaust.edu.sa/Pages/Software.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_2814 ; sc:citation , "pubmed:32315389" ; sc:description """An integrated resource for mutation analysis in protein 3D structures. Analyse Mutations in Protein 3D Structures. Analysing Your Own Mutation Data for Clusters. No need to screen for mutation types provided. Any variant classifications can for HotSpot3D, not just missense mutation.""" ; sc:featureList edam:operation_0570, edam:operation_3225, edam:operation_3432 ; sc:name "HotSpot3D" ; sc:url "http://niulab.scgrid.cn/HotSpot3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0632, edam:topic_2885 ; sc:citation ; sc:description "Software to support sperm-typing for investigating recombination hotspots." ; sc:featureList edam:operation_0308, edam:operation_0451, edam:operation_0484 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "hotspot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://github.com/evolbioinf/hotspot/" ; biotools:primaryContact "Bernhard Haubold" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196, edam:format_1476 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1929, edam:format_2331 ; sc:name "DNA sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2332 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_2814 ; sc:author , , , "Antonin Pavelka", "Lenka Sumbalova" ; sc:citation ; sc:contributor , , "European Commission", "Eva Sebestova", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic", "Ondrej Vavra" ; sc:description "An automated design of mutations and smart libraries for engineering of protein function and stability and annotation of protein structures." ; sc:featureList edam:operation_0244, edam:operation_0249, edam:operation_0319, edam:operation_0331, edam:operation_0384, edam:operation_0449, edam:operation_0482, edam:operation_0492, edam:operation_0570, edam:operation_3092 ; sc:funder "European Commission", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "HotSpot Wizard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp ; sc:softwareVersion "3.1" ; sc:url "https://loschmidt.chemi.muni.cz/hotspotwizard/" ; biotools:primaryContact "HotSpot Wizard team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3071 ; sc:citation , "pmcid:PMC7211031", "pubmed:32386297" ; sc:description """Database for hotspot mutations and annotations in cancer. Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes like BRAF, IDH1, KRAS and NRAS among many other genes. Hotspots are attractive because provide opportunities for biomedical research and novel treatments. Nevertheless, recent evidence, such as DNA hairpins for APOBEC3A, suggests that a considerable fraction of hotspots seem to be passengers rather than drivers. To document hotspots, the database HotSpotsAnnotations is proposed. For this, a statistical model was implemented to detect putative hotspots, which was applied to TCGA cancer datasets covering 33 cancer types, 10 182 patients and 3 175 929 mutations""" ; sc:featureList edam:operation_3227, edam:operation_3435 ; sc:name "HotSpotAnnotations" ; sc:url "http://bioinformatica.mty.itesm.mx/HotSpotAnnotations" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pmcid:PMC1462870", "pubmed:14704198" ; sc:description "Software for identifying recombination hotspots from population SNP data." ; sc:featureList edam:operation_0451 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HOTSPOTTER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://stephenslab.uchicago.edu/software.html#hotspotter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:26365245" ; sc:description "Web server to predict the host spots in RNA binding proteins (RBPs)" ; sc:featureList edam:operation_2492 ; sc:name "HotSPRing" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.csb.iitkgp.ernet.in/applications/HotSPRing/main.php" ; biotools:primaryContact "Ranjit Prasad Bahadur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0593, edam:topic_2828, edam:topic_3047, edam:topic_3534 ; sc:citation ; sc:description """Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data. The program uses a residual deep learning model to predict water hot-spots on the surface of proteins. Supply a pdb file (or just the accession code) and rank the water molecules within it or scan the surface of the whole protein for most likely water hot spots. Note: This tool relies on EDTSurf, therefore runs only on Linux. If you have a linux system, install via pip from PyPi (recommended):.""" ; sc:featureList edam:operation_0321, edam:operation_0387, edam:operation_2422, edam:operation_2476, edam:operation_2575 ; sc:license "MIT" ; sc:name "hotWater" ; sc:url "https://pypi.org/project/hotWater/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2331 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_0623, edam:topic_0797, edam:topic_3293 ; sc:citation ; sc:description "This database allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family." ; sc:featureList edam:operation_0224 ; sc:name "Homologous vertebrate genes database (HOVERGEN)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pbil.univ-lyon1.fr/databases/hovergen.html" ; biotools:primaryContact "Laurent Duret" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8783475", "pubmed:35065593" ; sc:description "Python package for testing strandedness of RNA-Seq fastq files." ; sc:featureList edam:operation_2428, edam:operation_3258, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "how_are_we_stranded_here" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/betsig/how_are_we_stranded_here" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3263, edam:topic_3318, edam:topic_3403 ; sc:citation , "pmcid:PMC8311505", "pubmed:34291683" ; sc:description "Developing an Innovative System of Open and Flexible, Patient-Family-Centered, Virtual Visiting in ICU During the COVID-19 Pandemic." ; sc:isAccessibleForFree true ; sc:name "HowRU" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://www.taleka.com/howru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623 ; sc:citation ; sc:description "A simple interface to and data from the Human Protein Atlas project." ; sc:featureList edam:operation_0337, edam:operation_3431 ; sc:license "Artistic-2.0" ; sc:name "hpar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/hpar.html" ; biotools:primaryContact "Laurent Gatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0203, edam:topic_0625, edam:topic_2229 ; sc:citation ; sc:description """A Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas. HPAStainR package to be submitted to Bioconductor. HPAStain.R is an R package/Shiny app used to query the Human Protein Atlas for staining data. The purpose of this tool is to test if a list of proteins/genes is associated with a certain cell type in a HPA tested tissue. E.g. you have a list of protein coding genes from a differential expression single cell analysis and want to see if these proteins are associated with a known cell type. Instead of querying HPA multiple times you can load your list in HPAStainR which will return a ranked table of the cell types with the most protein staining.""" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3629 ; sc:name "HPAStainR" ; sc:url "https://32tim32.shinyapps.io/HPAStainR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3316, edam:topic_3520 ; sc:citation ; sc:description """A Novel HPC-aware Tool for Improved Large Scale RNA-editing Analysis. REDItools2 is the optimized, parallel multi-node version of REDItools. REDItools takes in input a RNA-Seq (or DNA-Seq BAM) file and outputs a table of RNA-Seq editing events. Here is an example of REDItools's output:. The following image explains the high-level architecture.""" ; sc:featureList edam:operation_3096, edam:operation_3196, edam:operation_3359 ; sc:name "HPC-REDItools" ; sc:url "https://github.com/BioinfoUNIBA/REDItools2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0654, edam:topic_3169, edam:topic_3511 ; sc:citation "pubmed:20598134" ; sc:description "Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-seq data to identify protein-interacting genomic regions." ; sc:featureList edam:operation_3222 ; sc:name "HPeak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cauyrd/HPeak" ; biotools:primaryContact "Z.S.Qin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7641121", "pubmed:33193666" ; sc:description """Co-expression Network Database for de novo Transcriptome Assembly of Paeonia lactiflora Pall. Paeonia lactiflora Pall., commonly known as the herbaceous peony, is an ornamental flowering plant known around the world. Its oil contains a high proportion of polyunsaturated fatty acids (PUFAs). We produced 40 in-house RNA-seq datasets from 10 different tissues and performed de novo transcriptome assembly to obtain a complete transcriptome. Moreover,we had constructed the co-expression network database, HpeNet, which contains transcriptome data, gene information, the co-expression network, and so forth. Furthermore some analytical tools, such as blast, gene expression profiling analysis and gene set enrichment analysis (GSEA), were supported for network analysis and functional annotation. We hope that the HpeNet database will be beneficial to future work on Paeonia lactiflora Pall.""" ; sc:featureList edam:operation_0524, edam:operation_2436, edam:operation_3258, edam:operation_3431, edam:operation_3463 ; sc:name "HpeNet" ; sc:url "http://bioinformatics.cau.edu.cn/HpeNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2275 ; sc:citation ; sc:description "Blind protein–peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, it considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program." ; sc:featureList edam:operation_0477, edam:operation_0478, edam:operation_3647 ; sc:name "HPEPDOCK" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/hpepdock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_3295, edam:topic_3315, edam:topic_3674 ; sc:citation , "pmcid:PMC7336418", "pubmed:32631226" ; sc:description """An ultrafast, friendly tool for DMR detection and visualization. If you want to use this tool just now, there is an executable file for Linux x86_64 systems. This compressed file is available at releases page. But, previously, CUDA and Nvidia drivers must be installed in your system. For that, you can go to System requirements section. HPG-Dhunter is an interactive tool for detecting Differentially Methylathed Regions (DMRs) and visualizing DNA methylation signals. It is based on building a methylation signal from the information yielded by HPG-HMapper, and using a NVidia GPU and the CUDA programming model to compute the Discrete Wavelet Transform (DWT) of this methylation signal. The transformation of the signals in turn allows the comparison of different signals at low resolution levels, easily identifying DMRs with a low workload, when compared to other strategies. HPG-Dhunter is part of the HPG-MSuite.""" ; sc:featureList edam:operation_0337, edam:operation_3206, edam:operation_3809 ; sc:license "LGPL-3.0" ; sc:name "HPG-DHunter" ; sc:url "https://github.com/grev-uv/hpg-dhunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0654, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:25143289" ; sc:description "Ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping." ; sc:featureList edam:operation_2429, edam:operation_2928 ; sc:name "HPG Aligner" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://docs.bioinfo.cipf.es/projects/hpg-aligner/wiki" ; biotools:primaryContact "Ignacio Medina", "Joaquín Dopazo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26921234" ; sc:description "Toolkit to explore and analyze nanopore sequencing data that can run both on a single computer and on the Hadoop distributed computing framework." ; sc:featureList edam:operation_2403 ; sc:name "HPG pore" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/opencb/hpg-pore/wiki" ; biotools:primaryContact "Joaquín Dopazo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_3324, edam:topic_3474 ; sc:citation , "pmcid:PMC9154073", "pubmed:35669347" ; sc:description "An R/Bioconductor package for predicting host-pathogen protein-protein interactions from protein sequences using ensemble machine learning approach." ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HPiP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BabuLab-UofR/HPiP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0625, edam:topic_3957 ; sc:citation , "pmcid:PMC9718936", "pubmed:36514317" ; sc:description "Host-pathogen interactome prediction with phenotypic scoring." ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HPIPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SysBioUAB/hpi_predictor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3370 ; sc:citation ; sc:description "A general tool for simulating and optimizing HPLC gradients." ; sc:featureList edam:operation_3633 ; sc:name "hplcsimulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hplcsimulator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0154, edam:topic_0176, edam:topic_2275 ; sc:citation "pubmed:15980491", "pubmed:22570416" ; sc:description "Automated tool for computing pK values of ionizable groups in macromolecules and adding missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties." ; sc:featureList edam:operation_0475, edam:operation_0477, edam:operation_0480, edam:operation_2426, edam:operation_2476 ; sc:name "H++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://biophysics.cs.vt.edu/H++" ; biotools:primaryContact "Ramu Anandakrishnan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation , "pubmed:15073379" ; sc:description "HPM (Haplotype Pattern Mining) is a program for gene mapping in case-control haplotype data." ; sc:featureList edam:operation_2429, edam:operation_2945 ; sc:name "HPM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.helsinki.fi/group/genetics/hpm.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_2815, edam:topic_3068, edam:topic_3325 ; sc:citation , "pmcid:PMC3965098", "pubmed:24217912" ; sc:description "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. It can be used for clinical diagnostics in human genetics, bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes and for providing a standardized vocabulary for clinical databases. All the data is available for download and can be browsed online." ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:name "HPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hpo.jax.org/app/" ; biotools:primaryContact "Melissa Haendel", "Peter Robinson", "Sebastian Köhler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2229 ; sc:citation , "pubmed:34672333" ; sc:description "Deep graph convolutional networks for predicting human protein-phenotype associations." ; sc:featureList edam:operation_1777, edam:operation_3092, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HPODNets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liulizhi1996/HPODNets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0625, edam:topic_0634 ; sc:citation , "pubmed:33822886" ; sc:description "HPOFiller is a tool for identifying missing protein-phenotype associations by graph convolutional network." ; sc:featureList edam:operation_3094, edam:operation_3359, edam:operation_3435 ; sc:name "HPOFiller" ; sc:url "https://github.com/liulizhi1996/HPOFiller" ; biotools:primaryContact "Shanfeng Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0625 ; sc:citation , "pubmed:32379868" ; sc:description """Improving prediction of human protein-phenotype associations by learning to rank. Predict human protein-HPO term associations using Learning to Rank.""" ; sc:featureList edam:operation_0303, edam:operation_3659, edam:operation_3778 ; sc:name "HPOLabeler" ; sc:url "http://issubmission.sjtu.edu.cn/hpolabeler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0128, edam:topic_0602, edam:topic_2815 ; sc:citation "pubmed:14525934", "pubmed:14681466" ; sc:description "Centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in it is curated by experts, who manually extract it from published literature." ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0417, edam:operation_2492, edam:operation_2949 ; sc:name "The Human Protein Reference Database (HPRD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hprd.org/" ; biotools:primaryContact "Suraj Peri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0634, edam:topic_2815 ; sc:citation , "pubmed:33136065" ; sc:description """A comprehensive database for human proteome repeats. Human Proteome Repeats Database. HPREP : HUMAN PROTEOME REPEATS.""" ; sc:featureList edam:operation_0379, edam:operation_2421, edam:operation_2575 ; sc:name "HPREP" ; sc:url "http://bioinfo.bdu.ac.in/hprep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:36243970" ; sc:description "An online database for ligand binding sites in human proteome." ; sc:featureList edam:operation_0303, edam:operation_0482, edam:operation_2492, edam:operation_2575, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "HProteome-BSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://galaxy.seoklab.org/hproteome-bsite/database/domains/39056" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3379, edam:topic_3395 ; sc:citation , , , ; sc:description "hPSCreg is a global registry for human pluripotent stem cell lines (hPSC lines). It aims to provide to the community: 1) a central and searchable hub for available hPSC lines; 2) a central registry of clinical studies based on hPSC-lines; 3) a standardized identifier for hPSC lines and register of these standard names; 4) a trustworthy data source for hPSC lines by verifying the ethical and biological conformity of registered lines based on community standards; 5) comparability of quality standards in hPSC research; 5) certification of quality and ethical provenance of hPSC lines; 6) a platform where any scientist or institution generating or working with human PSC lines can register their cell lines, projects or clinical studies" ; sc:name "hPSCreg" ; sc:softwareHelp ; sc:url "https://hpscreg.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3299, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description "HPTT is a a visualized and expandable webtool for whole-genome-based Helicobacter pylori geographic surveillance. HPTT is a genomic typing tool based on SNP (single nucleotide polymorphism) of bacterial pathogens, which can facilitate not only H. pylori isolates, but also other pathogens that highly related to the public health." ; sc:featureList edam:operation_0224, edam:operation_0525, edam:operation_3431, edam:operation_3840 ; sc:name "HPTT" ; sc:url "https://db.cngb.org/HPTT/" ; biotools:primaryContact "Hongdong Tan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3064, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:33074547" ; sc:description """Usage of the Sea Urchin Hemicentrotus pulcherrimus Database, HpBase. Hemicentrotus pulcherrimus Genome Resources. Hemicentrotus pulcherrimus Genome and Transcriptome database. Hemicentrotus pulcherrimus (A. Agassiz, 1863) (Animaria: Echinodermata: Echinoidea: Echinoida: Strongylocentrotiae: Hemicentrotus) is the most widely distributed sea urchin in Japan and important marine food resources in eastern Asia. This species has a long history as a model organism in the field of developmental and cell biology since the mid 1900s. The web site provides information on H. pulcherrimus genome and transcriptome for a wide range of biologists. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/insdc (NIG.AC.JP), bio.tools/dfast (NIG.AC.JP), bio.tools/ddbj (NIG.AC.JP), bio.tools/cibex (NIG.AC.JP) ||| CORRECT NAME OF TOOL COULD ALSO BE 'H pulcherrimus'""" ; sc:featureList edam:operation_2421, edam:operation_3208, edam:operation_3258 ; sc:name "Hpul" ; sc:url "http://cell-innovation.nig.ac.jp/Hpul/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0781, edam:topic_2815, edam:topic_3174 ; sc:citation ; sc:description "Sensitive and specific genotyping of human papillomavirus in metagenomic DNA." ; sc:featureList edam:operation_3196 ; sc:name "HPViewer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/yuhanH/HPViewer/" ; biotools:primaryContact "Zhiheng Pei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3172, edam:topic_3300, edam:topic_3337 ; sc:citation , "pmcid:PMC9747802", "pubmed:36513738" ; sc:description "Tissue registration and exploration user interfaces in support of a human reference atlas." ; sc:featureList edam:operation_0337, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cns-iu.github.io/HRA-supporting-information/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2885, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC8024315", "pubmed:33824393" ; sc:description "hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3196, edam:operation_3661 ; sc:name "hReg-CNCC" ; sc:url "https://github.com/AMSSwanglab/hReg-CNCC" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3474 ; sc:citation , "pubmed:35042156" ; sc:description "Filter pruning based on High Relevance between activation maps and class labels." ; sc:featureList edam:operation_0337, edam:operation_0455, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "HRel" ; sc:url "https://github.com/sarvanichinthapalli/HRel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3300, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:33866354" ; sc:description "Hyperbolic relational graph convolution networks plus (HRGCN+) is a simple but highly efficient QSAR-modeling web application." ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3799, edam:operation_4009 ; sc:name "HRGCN+" ; sc:url "https://quantum.tencent.com/hrgcn/" ; biotools:primaryContact "Dongsheng Cao", "Tingjun Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """High-throughput analysis of bacterial ribosome profiling data. High-throughput annotation by Ribo-seq. We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.""" ; sc:featureList edam:operation_0436, edam:operation_2422, edam:operation_2428, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "HRIBO" ; sc:softwareHelp ; sc:url "https://github.com/RickGelhausen/HRIBO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0602, edam:topic_2259, edam:topic_2269, edam:topic_3321 ; sc:citation "pubmed:23407360" ; sc:description "General statistical inference framework for stochastic transcription-translation networks." ; sc:featureList edam:operation_3658 ; sc:name "HRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://homepages.inf.ed.ac.uk/gsanguin/software.html" ; biotools:primaryContact "Andrea Ocone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34570169" ; sc:description "Perform differential expression tests for RNASeq at scale with a configurable interface and visualize results with tunable control over p-value thresholds." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3223, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SD2E/omics_tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32248092" ; sc:description """Deep High-Resolution Representation Learning for Visual Recognition. HigherHRNet-Human-Pose-Estimation.""" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3659 ; sc:name "HRNet" ; sc:url "https://github.com/HRNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC7658224", "pubmed:33177631" ; sc:description """A manually-curated database about the regulatory relationship between HPV and host RNA. 2.HRRD contains the map of HPVs, the regulation relationship between HPV and RNA. 1.The relationship between HPV and host RNA has been identified with biological function.""" ; sc:featureList edam:operation_2422, edam:operation_2429, edam:operation_3196 ; sc:name "HRRD" ; sc:url "http://www.hmuhrrd.com/HRRD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3125, edam:topic_3407, edam:topic_3511 ; sc:citation "pubmed:19773424" ; sc:description "The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding motifs and cis-regulatory modules for the co-occurring transcription factor binding motifs, which are within a binding locus. It also contains individual binding sites whose regulatory action has been verified by in vitro experiments." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575 ; sc:name "HRTBLDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.uthscsa.edu/hrtbldb/" ; biotools:primaryContact "Victor Jin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3077, edam:topic_3172 ; sc:citation ; sc:description """Hierarchical approach to removal of unwanted variation for large-scale metabolomics data. hRUV is a package for normalisation of multiple batches of metabolomics data in a hierarchical strategy with use of samples replicates in a large-scale studies. The tool utilises 2 types of replicates: intra-batch and inter-batch replicates to estimate the unwatned variation within and between batches with RUV-III.""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3891 ; sc:name "hRUV" ; sc:url "https://shiny.maths.usyd.edu.au/hRUV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335 ; sc:citation , "pmcid:PMC5118625", "pubmed:27920726" ; sc:description "HRVanalysis is a free software that can be used to analyze cardiac autonomic activity." ; sc:featureList edam:operation_3443 ; sc:license "Other" ; sc:name "HRVanalysis" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://anslabtools.univ-st-etienne.fr/en/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_2640, edam:topic_3373 ; sc:citation ; sc:description "Predicting Potential Efficacious Drug Combination Based on Hypergraph Random Walk with Restart." ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:name "HRWR" ; sc:url "https://github.com/wangqi27/HRWR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0654 ; sc:citation "pubmed:26250111" ; sc:description "Nucleotide-Nucleotide aligner that searches nucleotide queries against a large nucleotide database." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "HS-BLASTN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/chenying2016/queries" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3321 ; sc:citation "pubmed:12929082" ; sc:description "Software of testing association using tightly linked markers in nuclear pedigrees." ; sc:featureList edam:operation_3224 ; sc:name "HS-TDT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.math.mtu.edu/~shuzhang/software.html" ; biotools:primaryContact "Shuanglin Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_2275, edam:topic_3175 ; sc:citation "pubmed:26936376" ; sc:description "Fexible tool that can jointly analyze multiple contact maps from Hi-C experiments to infer the 3D chromatin structure of the genome." ; sc:featureList edam:operation_0392, edam:operation_2442 ; sc:name "HSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ouyanglab.jax.org/hsa/" ; biotools:primaryContact "Zhengqing Ouyang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0219, edam:topic_0621, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC9547538", "pubmed:36208223" ; sc:description "Database of highly similar duplicate genes from plants, animals, and algae." ; sc:featureList edam:operation_2421, edam:operation_3208, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "HSDatabase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hsdfinder.com/database/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2229, edam:topic_3299, edam:topic_3512 ; sc:citation , "pmcid:PMC9580922", "pubmed:36303740" ; sc:description """An integrated tool for predicting highly similar duplicates (HSDs) in eukaryotic genomes. HSDFinder aims to become a useful platform for the identification and analysis of HSDs in the eukaryotic genomes, which deepen our insights into the gene duplication mechanisms driving the genome adaptation.""" ; sc:featureList edam:operation_0531, edam:operation_3208, edam:operation_3963 ; sc:isAccessibleForFree true ; sc:name "HSDFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hsdfinder.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2814 ; sc:citation ; sc:description "HSEpred is a web server to predict the HSE(Half-Sphere Exposure) measures and infer residue contact numbers using the predicted HSE values, based on a well-prepared non-homologous protein structure dataset." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "HSEpred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/hse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0157, edam:topic_2229 ; sc:citation "pubmed:15647269" ; sc:description "Allows predicting the subcellular localization of human proteins. This is based on various type of residue composition of proteins using SVM technique." ; sc:featureList edam:operation_2479, edam:operation_2489 ; sc:name "HSLpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://webs.iiitd.edu.in/raghava/hslpred/" ; biotools:primaryContact "Dr. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3295, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:33446014" ; sc:description """A high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching. HSM6AP is a machine-learning framework to predict m6A based on Sequence and Gnomic coordinates. DNA methylation is an important epigenetic modification, which is closely related to the development and progression of cancer. As a cancer-related biomarker, the effective identification of DNA methylation sites has import implications in understanding the pathogenesis of cancer, cancer diagnosis and drug development.""" ; sc:featureList edam:operation_0253, edam:operation_0417, edam:operation_3937 ; sc:name "HSM6AP" ; sc:url "http://lab.malab.cn/~lijing/HSM6AP.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0203, edam:topic_0601, edam:topic_3518 ; sc:citation , "pubmed:35771633" ; sc:description "Identification of motifs in sequences composed of non-single-letter elements." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0337, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HSMotifDiscover" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hsmotifdiscover.shinyapps.io/HSMotifDiscover_ShinyApp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36257278" ; sc:description "A hybrid semantic network for polyp segmentation." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HSNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/baiboat/HSNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3336, edam:topic_3379, edam:topic_3500 ; sc:citation , "pmcid:PMC7043294", "pubmed:32090260" ; sc:description """A computational repository of heat shock protein modulators. A bird's-eye view of Heat Shock Proteins. HSPMdb will assist the scientific community working in the area of chaperone biology for designing novel inhibitors. It will also be useful for creating datasets for developing novel scaffold using in silico prediction algorithms.""" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3431 ; sc:name "HSPMdb" ; sc:url "http://bioinfo.imtech.res.in/bvs/hspmdb/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation ; sc:description "Homology-derived secondary structure of proteins database." ; sc:featureList edam:operation_0224 ; sc:name "HSSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://swift.cmbi.ru.nl/gv/hssp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3300, edam:topic_3315 ; sc:citation ; sc:description """Framework to determine optimal parameter selection for a generic spike sorting algorithm. Heuristic Spike Sort Tuner Readme. Novel paradigm for optimal parameter selection of a generic spike sorting algorithm. Full code base written for Matlab 2018a is available here. Full documentation along with a getting started guide is in the HSST Manual.pdf.""" ; sc:featureList edam:operation_3435, edam:operation_3802 ; sc:name "HSST" ; sc:url "http://www.github.com/davidbjanes/HSST" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1476, edam:format_2200 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation , "pubmed:29846641" ; sc:description "Symmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule." ; sc:featureList edam:operation_0478 ; sc:name "HSYMDOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2018-06-02" ; sc:url "http://huanglab.phys.hust.edu.cn/hsymdock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3444 ; sc:citation , , "pmcid:PMC8392551", "pmcid:PMC8598444", "pubmed:34358288", "pubmed:34444597" ; sc:description "Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging." ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alonalj/hta" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_3168, edam:topic_3577 ; sc:citation , "pubmed:36194209" ; sc:description "Aggregation and fully automated clinical interpretation of genetic variants in heritable thoracic aortic aneurysm and dissection." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "HTAADVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://htaadvar.fwgenetics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3071, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:36130266" ; sc:description "HTCA is an interactive web-based healthy human single-cell transcriptome landscape, containing 19 adult tissues and their matching fetal tissues, demonstrating diverse and in-depth transcriptomics profiles of all cell types across tissues." ; sc:featureList edam:operation_0224, edam:operation_0313, edam:operation_0314 ; sc:license "GPL-3.0" ; sc:name "HTCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.htcatlas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pubmed:34780326" ; sc:description "Heterogeneous Task Decoupling for Two-Stage Object Detection." ; sc:featureList edam:operation_3436, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "HTD" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/CityU-AIM-Group/HTD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3489 ; sc:citation , "pmcid:PMC8672147", "pubmed:34950901" ; sc:description "High Throughput Experimental Materials Database" ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "HTEM-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://htem.nrel.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3572 ; sc:citation , "pmcid:PMC10027062", "pubmed:36950141" ; sc:description "R package and shinyR application for quality controls of HTG EDGE-seq protocols." ; sc:featureList edam:operation_0314, edam:operation_2428, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HTGQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lodovico.shinyapps.io/shinyHTGQC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749 ; sc:citation ; sc:description "HTHmotif is a novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes" ; sc:featureList edam:operation_0238 ; sc:name "HTHmotif" ; sc:operatingSystem "Linux" ; sc:url "http://stormo.wustl.edu/HTHmotif" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_0820 ; sc:citation ; sc:description "HTM-ONE takes single amino acid sequence as input and returns residue-wise prediction of several one-dimensional structural properties of helical transmembrane regions." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "HTM-ONE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mizuguchilab.org/netasa/htmone/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Create a html report from a blast result." ; sc:featureList edam:operation_0335 ; sc:name "html4blast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7a" ; sc:url "https://bioweb.pasteur.fr/packages/pack@html4blast@1.7a" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3365 ; sc:citation "pubmed:24849578" ; sc:description "Novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "HTML5 PivotViewer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cbrg.ox.ac.uk/data/pivotviewer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC9284292", "pubmed:35643087" ; sc:description "Exploiting maize haplotype-tag polymorphisms for germplasm resource analyses and genomics-informed breeding." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3894 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "HTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://htp.plantdna.site/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0632, edam:topic_3321, edam:topic_3519 ; sc:citation "pubmed:26540331" ; sc:description "Created to provide the scientific community with a simple and intuitive online primer design tool for both laboratory-scale and high-throughput projects of sequence-independent gene cloning and site-directed mutagenesis and a Tm calculator for quick queries." ; sc:featureList edam:operation_0308 ; sc:name "HTP-OligoDesigner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ifsc.usp.br/htpoligo/" ; biotools:primaryContact "Gustavo Machado Alvares de Lima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780 ; sc:citation ; sc:description "HTPheno is a software for high-throughput plant phenotyping is presented. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening." ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:name "HTPheno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://htpheno.ipk-gatersleben.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3519 ; sc:citation , "pmcid:PMC2788924", "pubmed:19808880" ; sc:description "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science, etc. It handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features." ; sc:featureList edam:operation_2478 ; sc:license "Artistic-2.0" ; sc:name "HTqPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HTqPCR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:12037407" ; sc:description "Haplotype/Trait Association Software." ; sc:featureList edam:operation_0487, edam:operation_3658 ; sc:name "HTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://statgen.ncsu.edu/zaykin/htr.html" ; biotools:primaryContact "Dmitri Zaykin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3263, edam:topic_3305, edam:topic_3372 ; sc:citation , "pubmed:33320896" ; sc:description """A new tool to facilitate public health field visits and electronic data capture. HTrack (Household Tracking) is an application built in R-Shiny for use on encrypted Android devices. This app was created to allow for offline data collection in studies where stringent data-security requirements must be met (see https://doi.org/10.1371/journal.pone.0244028), though it can also be run online if needed. The application allows for field navigation and secure field-level data capture. It also serves as a bridge to an alternate software, like EpiInfo, to collect participant-level questionnaire data. This repository houses:.""" ; sc:featureList edam:operation_3096 ; sc:name "HTrack" ; sc:url "https://github.com/dmrodz/htrack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC10074024", "pubmed:37033465" ; sc:description "An R package for learning non-contiguous haplotypes associated with a phenotype." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "HTRX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YaolingYang/HTRX" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602, edam:topic_3523 ; sc:citation , "pmcid:PMC3051329", "pubmed:21258062" ; sc:description "This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3224 ; sc:license "Artistic-2.0" ; sc:name "HTSanalyzeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HTSanalyzeR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0623, edam:topic_2269, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25563332" ; sc:description "Implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters)." ; sc:featureList edam:operation_2426, edam:operation_3432 ; sc:name "HTSCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/HTSCluster/index.html" ; biotools:primaryContact "Andrea Rau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_2269 ; sc:citation , "pmcid:PMC8896640", "pubmed:34999766" ; sc:description "Custom compression for CRAM and others." ; sc:featureList edam:operation_0335, edam:operation_3435, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "HTScodecs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/samtools/htscodecs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Python framework to process and analyse high-throughput sequencing (HTS) data" ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "HTSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://htseq.readthedocs.io/en/release_0.9.1/" ; biotools:primaryContact "Simon Anders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3308, edam:topic_3534, edam:topic_3794 ; sc:citation , "pmcid:PMC9825771", "pubmed:36394253" ; sc:description "htseq-clip, a python package developed for preprocessing, extracting and summarizing crosslink site counts from i/eCLIP experimental data." ; sc:featureList edam:operation_3695, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "htseq-clip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EMBL-Hentze-group/htseq-clip" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , , ; sc:description "This script takes an alignment file in SAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it." ; sc:featureList edam:operation_0236 ; sc:name "htseqcount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.1p1" ; sc:url "https://htseq.readthedocs.io/en/release_0.9.1/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "Libraries to perform NGS analysis." ; sc:featureList edam:operation_2945 ; sc:license "Artistic-2.0" ; sc:name "HTSeqGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HTSeqGenie.html" ; biotools:primaryContact "Jens Reeder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3168, edam:topic_3382 ; sc:citation ; sc:description """A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. Quality control analysis for high-throughput sequencing data (HTS). HTSeqQC Quick Start — HTSeqQC Quick Start documentation. The Open Science Workspace for Collaborative Data-driven Discovery.""" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3695 ; sc:license "MIT" ; sc:name "HTSeqQC" ; sc:softwareHelp ; sc:url "https://reneshbedre.github.io/blog/htseqqc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "htSeqTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/htSeqTools.html" ; biotools:primaryContact "Oscar Reina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC3740625", "pubmed:23821648" ; sc:description "This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions." ; sc:featureList edam:operation_3695 ; sc:license "Artistic-2.0" ; sc:name "HTSFilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HTSFilter.html" ; biotools:primaryContact "Andrea Rau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_1775, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:26399714" ; sc:description "Python package used to create gene sets for the study of high-throughput sequencing data." ; sc:featureList edam:operation_3459 ; sc:name "htsint" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://ajrichards.github.io/htsint/" ; biotools:primaryContact "Adam J Richards" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , "pmcid:PMC7931820", "pubmed:33594436" ; sc:description "The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). 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It is utilized and incorporated into both SAMtools and BCFtools." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HTSlib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Wellcome Sanger Institute" ; sc:softwareHelp ; sc:softwareVersion "1.0", "1.1", "1.10", "1.10.1", "1.10.2", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.17", "1.18", "1.19", "1.2", "1.2.1", "1.3", "1.3.1", "1.3.2", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Wellcome Sanger Institute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3277 ; sc:citation "pubmed:21685046" ; sc:description "Represents the structure of signals in the screen using linear mixed models, normalizes and summarizes the phenotypes to make them comparable across samples, and outputs a list of hits while controlling the False Discovery Rate. 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Boutros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0203 ; sc:citation ; sc:description "Exploratory data analysis and visualization of arrayed high-throughput screens." ; sc:featureList edam:operation_0571, edam:operation_2495 ; sc:name "HTSvis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://htsvis.dkfz.de/HTSvis/" ; biotools:primaryContact "Michael Boutros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3334, edam:topic_3520 ; sc:citation , "pubmed:35932982" ; sc:description "HTT-OMNI (HTT OMics and Network Integration) a web-based application for HIP network analysis, visualization, and omics data exploration." ; 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sc:url "https://huarc.net/database" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0634, edam:topic_3557 ; sc:citation "pubmed:18503085" ; sc:description "Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_2422, edam:operation_3083, edam:operation_3439 ; sc:name "Hubba" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hub.iis.sinica.edu.tw/Hubba" ; biotools:primaryContact "Chia-Hao Chin", "Chin-Wen Ho", "Chung-Yen Lin", "Hsin-Hung Wu", "Shu-Hwa Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0637, edam:topic_3168, edam:topic_3174, edam:topic_3512 ; 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dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3068, edam:topic_3303, edam:topic_3344 ; sc:citation "pubmed:16845111" ; sc:description "This tool uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature." ; sc:featureList edam:operation_0224, edam:operation_0305, edam:operation_2422, edam:operation_3778 ; sc:name "HubMed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.hubmed.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_3170 ; sc:citation , "pmcid:PMC7402588", "pubmed:32753773" ; sc:description """A Novel Tool for Hub-centric Visualization. hubViz (a novel tool for hub-centric Visualization) is a novel tool for hub-centric visualization which is based on a latent space joint model (LSJM) for visualization. ‘hubviz’ package provides computationally efficient and user friendly interface to fit the hubViz models. The following help pages provide a good start point for the genetic analysis using the ‘hubviz’ package, including the overview of ‘hubviz’ package and the example command lines:.""" ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_3927 ; sc:name "hubViz" ; sc:url "https://dongjunchung.github.io/hubviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2229, edam:topic_3303, edam:topic_3374, edam:topic_3957 ; sc:citation , "pmcid:PMC9962590", "pubmed:36851706" ; sc:description "The HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus." ; sc:featureList edam:operation_0478, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HuCoPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.usu.edu/hucopia/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3065 ; sc:citation , "pmcid:PMC2967454", "pubmed:20979583" ; sc:description "Atlas pages that are unique in containing digital 3D models of human developmental stages, organ specific gene expression datasets as well as annotated histology sections." ; sc:featureList edam:operation_3553 ; sc:name "HuDSeN atlas and spatial gene expression database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hudsen.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3298, edam:topic_3382, edam:topic_3517 ; sc:citation ; sc:description "An R package for creating mirrored Manhattan plots" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "hudson" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RitchieLab/hudson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_3510 ; sc:citation "pubmed:23427990" ; sc:description "HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences." ; sc:featureList edam:operation_0245, edam:operation_0474 ; sc:name "HUF-ZINC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2393 ; sc:name "mFLJ/mKIAA number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3512 ; sc:citation ; sc:description "Database of the human cDNA project at the Kazusa DNA Research Institute, covering various sets of large human proteins of hitherto unidentified functions." ; sc:featureList edam:operation_0224 ; sc:name "HUGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kazusa.or.jp/huge/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3179, edam:topic_3474, edam:topic_3957 ; sc:citation , "pubmed:35021191" ; sc:description "Reconstruction of human protein-coding gene functional association network based on machine learning." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "HuGFAN" ; sc:url "https://github.com/xthuang226/HuGFAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3068, edam:topic_3577 ; sc:citation , "pubmed:33439542" ; sc:description """An international, open and dynamic library for up-to-date clinical information. Collect information about clinic management and research projects.""" ; sc:featureList edam:operation_2422, edam:operation_3196 ; sc:name "Human-Disease-Genes" ; sc:url "http://www.humandiseasegenes.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0202, edam:topic_3047, edam:topic_3396 ; sc:citation ; sc:description "Human-gpDB is a publicly accessible, relational database of human G-Proteins and their interactions with human GPCRs and Effectors. The database currently holds information about 713 human GPCRs, 36 human G-Proteins and 99 human Effectors. The collection of the information about the interactions between these molecules was done manually and the current status of Human-gpDB reveals information about 1663 connections between GPCRs and G-Proteins and 1618 connections between G-Proteins and Effectors. The sequences of G-Proteins and GPCRs are classified according to a hierarchy of different classes, families and sub-families, whereas the Effectors sequences are classified in families, subfamilies and types, based on extensive literature search. The classification of GPCRs follows the IUPHAR classification, while the Effectors classification is a unique feature and is based on their function." ; sc:name "human-gpDB" ; sc:url "https://human-gpdb.lcsb.uni.lu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3300, edam:topic_3512 ; sc:citation , "pmcid:PMC8094437", "pubmed:33942874" ; sc:description "Human IRES Atlas is an integrative platform for studying IRES-driven translational regulation in humans." ; sc:featureList edam:operation_0438, edam:operation_0439, edam:operation_2421 ; sc:name "Human IRES Atlas" ; sc:url "http://cobishss0.im.nuk.edu.tw/Human_IRES_Atlas/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_2815, edam:topic_3325, edam:topic_3577 ; sc:citation , "pubmed:29995249" ; sc:description "Human Phenotype Ontology, a standardized vocabulary of phenotypic abnormalities encountered in human disease. With unmatched depth it enables clinicians to record and analyse data with extremely accurate computer interpretable ontology terms. Developed by The Monarch Initiative." ; sc:featureList edam:operation_2422, edam:operation_3196 ; sc:name "Human Phenotype Ontology" ; sc:url "http://www.human-phenotype-ontology.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_2229, edam:topic_3324, edam:topic_3957 ; sc:citation , "pmcid:PMC8924640", "pubmed:35356543" ; sc:description "Comprehensive characterization of human-virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs." ; sc:featureList edam:operation_0306, edam:operation_2436, edam:operation_2949, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "human-virus PPIs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/HVPPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2815, edam:topic_3071 ; sc:citation , "pmcid:PMC10320146", "pubmed:37216609" ; sc:description "Interactive spatio-temporal visualization and database of human archeogenomics." ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Human AGEs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://archeogenomics.eu/en/home" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815, edam:topic_3170, edam:topic_3308, edam:topic_3337 ; sc:citation , "pubmed:35124170" ; sc:description "A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue." ; sc:featureList edam:operation_2422, edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "Human Eye Transcriptome Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.eye-transcriptome.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3063, edam:topic_3320, edam:topic_3325, edam:topic_3512, edam:topic_3571 ; sc:citation ; sc:description "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS)." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_2421, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "Human Splicing Finder" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.umd.be/HSF3/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3277, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:33221926" ; sc:description """A public repository of curated and standardized metadata for human metagenomes. Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes""" ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_3435 ; sc:name "HumanMetagenomeDB" ; sc:url "https://webapp.ufz.de/hmgdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3174 ; sc:author "Curtis Huttenhower" ; sc:citation ; sc:description "HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”" ; sc:featureList edam:operation_0324, edam:operation_3221, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "humann" ; sc:softwareHelp ; sc:softwareVersion "3.0-3.6.1" ; sc:url "https://huttenhower.sph.harvard.edu/humann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "HUMAnN 2.0 is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or capable of doing)?”" ; sc:featureList edam:operation_3929 ; sc:name "HUMAnN2" ; sc:url "http://huttenhower.sph.harvard.edu/humann2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_3053, edam:topic_3318, edam:topic_3517 ; sc:citation , "pmcid:PMC8728227", "pubmed:34747468" ; sc:description "An improved database of human gene networks for disease research." ; sc:featureList edam:operation_2421, edam:operation_2454, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "HumanNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3" ; sc:url "https://www.inetbio.org/humannet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_0769, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC7699549", "pubmed:33233537" ; sc:description """Web Services, Tools and Databases for Exploring Human microRNA Data. The Chair for Clinical Bioinformatics at Saarland University has developed numerous tools to aid microRNA researchers. HumiR is here to match you with the perfect tool for all your miRNA analysis needs.""" ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3792, edam:operation_3799 ; sc:name "HumiR" ; sc:url "https://www.ccb.uni-saarland.de/humir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316 ; sc:citation , "pubmed:33693476" ; sc:description "Hummingbird is a Python framework that gives a variety of optimum instance configurations to run your favorite genomics pipeline on cloud platforms." ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3096 ; sc:license "Apache-2.0" ; sc:name "Hummingbird" ; sc:url "https://github.com/StanfordBioinformatics/Hummingbird" ; biotools:primaryContact "Cuiping Pan", "Michael P Snyder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3292, edam:topic_3520 ; sc:citation , "pubmed:32813527" ; sc:description "HUMOS (How to Understand My Orbitrap Spectrum?) is a web application based on Dash framework. It helps to teach and learn more about Orbitraps and shotgun proteomics." ; sc:featureList edam:operation_3215, edam:operation_3631, edam:operation_3694, edam:operation_3799, edam:operation_3860 ; sc:license "Apache-2.0" ; sc:name "HUMOS" ; sc:url "http://humos.bmb.sdu.dk" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_3303 ; sc:citation , "pubmed:33508086" ; sc:description """An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition. A very simple framework for state-of-the-art NLP. Developed by Humboldt University of Berlin and friends. A powerful NLP library. Flair allows you to apply our state-of-the-art natural language processing (NLP) models to your text, such as named entity recognition (NER), part-of-speech tagging (PoS), special support for biomedical data, sense disambiguation and classification, with support for a rapidly growing number of languages.""" ; sc:featureList edam:operation_1812, edam:operation_3280 ; sc:license "MIT" ; sc:name "HunFlair" ; sc:url "https://github.com/flairNLP/flair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Hungarian algorithm for linear sum assignment. Works for square and rectangular cost matrices." ; sc:isAccessibleForFree true ; sc:name "Hungarian Algorithm for Linear Sum Assignment Problem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/62970-hungarian-algorithm-for-linear-sum-assignment-problem" ; biotools:primaryContact "ondrejdee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3071 ; sc:author "Alberto Calderone", "Susanna Liberti" ; sc:citation , "pubmed:22804825" ; sc:contributor "Francesca Sacco", "Livia Perfetto", "Marta Iannuccelli" ; sc:description "Online web resource for recovering information about human phosphatases." ; sc:featureList edam:operation_2421 ; sc:name "Hupho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA", "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://hupho.uniroma2.it" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9825509", "pubmed:36318258" ; sc:description "An integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses." ; sc:featureList edam:operation_0313, edam:operation_0571, edam:operation_2428, edam:operation_2436, edam:operation_3431 ; sc:license "Not licensed" ; sc:name "HUSCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://husch.comp-genomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3068, edam:topic_3071, edam:topic_3374 ; sc:citation , "pmcid:PMC7708619", "pubmed:33262341" ; sc:description """Database for skin permeation of xenobiotics. Jupyter Notebook which leads through the code used to create huskinDB publication Figures. huskinDB is a human skin permeation database containing information on experimental protocols used. It provides an interactive access to the data, filtering options and a possibility to search for structures.""" ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3695 ; sc:name "HuskinDB" ; sc:url "https://huskindb.drug-design.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2815, edam:topic_3382 ; sc:citation , "pmcid:PMC8116600", "pubmed:33996848" ; sc:description "Python module for Humphrey Visual Field (HVF) report data extraction. The package can taken in HVF single field analysis report images (from HFA2 or HFA3), and using OCR (tesseract) and image processing techniques (openCV), extracts data into an object oriented format for further processing." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3443, edam:operation_3907 ; sc:license "GPL-3.0" ; sc:name "hvf_extraction_script" ; sc:url "https://github.com/msaifee786/hvf_extraction_script" ; biotools:primaryContact "Ying Han" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3324, edam:topic_3518, edam:topic_3957 ; sc:citation , "pubmed:33515030" ; sc:description """A comprehensive database for human-virus protein-protein interactions. Here, we introduce a comprehensive human-virus PPI database, HVIDB (http://zzdlab.com/hvidb/), which is based on (i) multiple data resources associated with human-virus PPIs and provides (ii) an integrative, computational platform to predict interactions between human and virus proteins.""" ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3223, edam:operation_3431 ; sc:name "HVIDB" ; sc:url "http://zzdlab.com/hvidb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2269 ; sc:citation ; sc:description "Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction." ; sc:featureList edam:operation_0487, edam:operation_2238, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "hwep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dcgerard/hwep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3374 ; sc:description "Test if a locus is under Hardy Weinberg Proportion" ; sc:isAccessibleForFree true ; sc:name "HWEtest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/14425-hwetest" ; biotools:primaryContact "Giuseppe Cardillo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:author "D Weis" ; sc:citation , , "pmcid:PMC3855366", "pubmed:16931036", "pubmed:24018862" ; sc:description "An Excel spreadsheet for analysis of H/D exchange mass spectra." ; sc:featureList edam:operation_0404 ; sc:license "GPL-2.0" ; sc:name "HX-Express" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v2" ; sc:url "http://www.hxms.com/HXExpress/" ; biotools:primaryContact "J Engen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0769 ; sc:citation ; sc:description "hyb is a bioinformatics pipeline for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "hyb" ; sc:url "https://github.com/gkudla/hyb" ; biotools:primaryContact "Grzegorz Kudla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0798, edam:topic_3168, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC9241225", "pubmed:35768759" ; sc:description "A hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Hyb4mC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YingLiangjxau/Hyb4mC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0632, edam:topic_0769, edam:topic_3293 ; sc:citation ; sc:description "A workflow for the detection and phasing of hybrids in target capture datasets." ; sc:featureList edam:operation_0310, edam:operation_0324, edam:operation_0487, edam:operation_3454 ; sc:name "HybPhaser" ; sc:url "https://github.com/LarsNauheimer/HybPhaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3293, edam:topic_3316, edam:topic_3512 ; sc:citation ; sc:description "Containerization and additional options for assembly and paralog detection in target enrichment data." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3192, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "hybpiper-rbgv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/chrisjackson-pellicle/HybPiper-RBGV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3293 ; sc:citation ; sc:description "De novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs." ; sc:featureList edam:operation_0232, edam:operation_0323 ; sc:license "BSD-2-Clause" ; sc:name "Hybrid-denovo" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformaticstools.mayo.edu/research/hybrid-denovo/" ; biotools:primaryContact "Chen Xianfeng", "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:20378555" ; sc:description "An algorithm for error correction of the reads from various DNA sequencing platforms" ; sc:featureList edam:operation_2425, edam:operation_3195, edam:operation_3218 ; sc:name "Hybrid-SHREC" ; sc:url "http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/" ; biotools:primaryContact "Leena Salmela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382, edam:topic_3404 ; sc:description "MATLAB script for Hybrid Skin Lesion Segmentation Tool using PCA and Iterative Canny Edge." ; sc:featureList edam:operation_3443, edam:operation_3891, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Hybrid Skin Lesion Segmentation Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50698-a-hybrid-skin-lesion-segmentation-tool-using-pca-and-iterative-canny-edge" ; biotools:primaryContact "Tyler Coye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0202, edam:topic_0605, edam:topic_2275 ; sc:citation , "pmcid:PMC7500467", "pubmed:33102525" ; sc:description """Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. Automatic set up of Molecular Mechanics/Coarse-Grained (MM/CG) simulations for human G Protein-Coupled Receptor (GPCR)/ligand complexes.""" ; sc:featureList edam:operation_0269, edam:operation_2476, edam:operation_3893, edam:operation_3938 ; sc:name "Hybrid MM CG" ; sc:url "http://mmcg.grs.kfa-juelich.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0654, edam:topic_3053, edam:topic_3127 ; sc:citation "pubmed:26394708" ; sc:description "Software package to visualise the recombination signal in large DNA sequence dataset, and it can be used to analyse recombination, genetic introgression, hybridisation and horizontal gene transfer." ; sc:featureList edam:operation_0337, edam:operation_0564 ; sc:name "HybridCheck" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/BenJWard/HybridCheck" ; biotools:primaryContact "Ben J. Ward", "Dr. Cock van Oosterhout" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0769, edam:topic_3297, edam:topic_3500 ; sc:citation ; sc:description """Pipeline for allele inheritance and gene copy number prediction in industrial yeast hybrids. Fast and accurate parental allele inheritance prediction tool for hybrid species.""" ; sc:featureList edam:operation_0362, edam:operation_0436, edam:operation_2421 ; sc:license "MIT" ; sc:name "HybridMine" ; sc:url "https://github.com/Sookie-S/HybridMine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3678 ; sc:citation ; sc:description "Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "HybridMTest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/HybridMTest.html" ; biotools:primaryContact "Demba Fofana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_3538 ; sc:citation , "pubmed:32860044" ; sc:description """Dichotomy of sequence-based methods developed using structured complexes versus disordered proteins. hybridPBRpred - web server from Biomine lab. HybridPBRpred combines prediction of protein-binding residues generated by SCRIBER (predictor that was trained using structures of protein-protein complexes) and DisoRDPbind (predictor that was trained using disordered protein-binding residues), with the underlying goal to produce complete set of the protein-binding residues.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0474, edam:operation_3904 ; sc:name "hybridPBRpred" ; sc:url "http://biomine.cs.vcu.edu/servers/hybridPBRpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_2640, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC7647696", "pubmed:32861878" ; sc:description """A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. a hybrid-learning architecture for succinylation site prediction.""" ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0418 ; sc:name "HybridSucc" ; sc:url "http://hybridsucc.biocuckoo.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "Improved blood velocity measurements with a hybrid image filtering and iterative Radon transform" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "HybridVel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42019-hybridvel" ; biotools:primaryContact "Pratik Chhatbar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3382 ; sc:citation ; sc:description "A hybrid single particle tracking software using manual and automatic detection of dim signals." ; sc:featureList edam:operation_2476, edam:operation_3443 ; sc:name "HybTrack" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bhlee1117/HybTrack" ; biotools:primaryContact "Byung Hun Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_2814, edam:topic_3538 ; sc:citation "pubmed:25505088" ; sc:description "Python-based program for prediction of rotational correlation time of folded protein domains in the context of flexible multidomain proteins and protein complexes with long disordered tails and/or interdomain linkers as well as intrinsically disordered proteins." ; sc:featureList edam:operation_2479 ; sc:name "HYCUD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_hycud.html" ; biotools:primaryContact "Markus Zweckstetter" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:27670643" ; sc:description "Provides access to an accurate classifier for hydrogenase sequences and a curated database of hydrogenases by known type." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "HydDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://services.birc.au.dk/hyddb" ; biotools:primaryContact "Dan Søndergaard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0632, edam:topic_0654, edam:topic_3519 ; sc:citation "pubmed:17951798" ; sc:description "Program for designing pairs of degenerate primers for a given set of DNA sequences. HYDEN works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp)." ; sc:featureList edam:operation_2419 ; sc:name "HYDEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/hyden/HYDEN.htm" ; biotools:primaryContact "Chaim Linhart", "Ron Shamir" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3510, edam:topic_3574 ; sc:citation , "pubmed:26661679" ; sc:description "Novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease." ; sc:featureList edam:operation_3092 ; sc:name "HydPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lishuyan.lzu.edu.cn/hydpred/" ; biotools:primaryContact "Shuyan Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3071 ; sc:citation "pubmed:25411330" ; sc:description "New approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques." ; sc:featureList edam:operation_3436 ; sc:name "HyDRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web.engr.illinois.edu/~mkim158/" ; biotools:primaryContact "Minji Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0593, edam:topic_0736, edam:topic_3315 ; sc:citation , "pmcid:PMC8114120", "pubmed:34025944" ; sc:description "HYDRA is a multi-objective optimization-based de novo protein design method, which is implemented in a new quantified and continuous sequence space.We use two different energy functions to evaluate the decoy sequences simultaneously, and aided by the prior information collected from DSSP and PDB data base, a space transformation procedure is conducted in each iteration.In the new ordered sequence space, the searching process will be boosted dramatically." ; sc:featureList edam:operation_0320, edam:operation_0476, edam:operation_2421, edam:operation_3644, edam:operation_4008 ; sc:name "Hydra" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/HYDRA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3930 ; sc:citation , "pmcid:PMC7176284", "pubmed:32275708" ; sc:description """A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. There is a need for more flexible gene expression analyses for precision oncology applications. We developed an unsupervised clustering approach for identifying clinically relevant expression patterns. The hydra analysis framework uses state-of-the-art Bayesian non-parametric statistics to learn which genes are differentially expressed without the need for matched normal expression data. This is very useful in the pediatric oncology setting where matched normal tissue is usually not available. ||| NAME (hydra) SIMILAR TO (PUB. DIFFERENT) bio.tools/hydra (HyDRA), bio.tools/hydra_sv (Hydra)""" ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_3223, edam:operation_3463, edam:operation_3891 ; sc:name "hydra_bnpy" ; sc:url "http://www.github.com/jpfeil/hydra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0654, edam:topic_3175 ; sc:citation "pubmed:25527832" ; sc:description "Detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. It can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments." ; sc:featureList edam:operation_2429, edam:operation_3228, edam:operation_3432 ; sc:name "Hydra" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cphg.virginia.edu/quinlan/?page_id=30" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3315, edam:topic_3421, edam:topic_3534 ; sc:citation , "pubmed:32401510" ; sc:description """Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. Predict potential water molecules in the protein binding pocket. HydraMap V1.0 - Automatic Tailoring and Transplanting. We developed an empirical method for predicting the favorable hydration sites in a protein binding pocket.""" ; sc:featureList edam:operation_2575, edam:operation_2929, edam:operation_3454, edam:operation_3891, edam:operation_3938 ; sc:name "HydraMap" ; sc:url "http://www.sioc-ccbg.ac.cn/software/hydramap/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1546 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "PyMOL script for retrieving hydrogen bond characteristics from protein structures." ; sc:featureList edam:operation_0391 ; sc:license "MIT" ; sc:name "hydrogen_bondifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jtprince/hydrogen_bondifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc:description """Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomes. Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein co-translational folding. In this work, we explore how codon variants affect the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA. By analyzing over 14,000 bacterial, archaeal, and fungal ORFeomes, we found that Bacteria and Archaea exhibit an exponential ramp of hydrogen bonding at the 5′-end of CDSs, while a similar ramp was not found in Fungi. The ramp develops within the first 20 codon positions in prokaryotes, eventually reaching a steady carrying capacity of hydrogen bonding that does not differ from Fungi""" ; sc:featureList edam:operation_0284, edam:operation_0394, edam:operation_2962 ; sc:name "Hydrogen bonding does" ; sc:url "https://juanvillada.shinyapps.io/hbonds/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3307 ; sc:citation "pubmed:7108955" ; sc:description "Hydrophobicity Grapher graphs the hydrophobicity/hydrophilicity of a sequence of amino acids, using a sliding window. The window size can be specified by the user, and several hydrophobicity scales can be used to determine the plot." ; sc:featureList edam:operation_2479 ; sc:name "Hydrophobicity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://athena.bioc.uvic.ca/virology-ca-tools/hydrophobicity/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3365 ; sc:citation , "pubmed:35876159" ; sc:description "A open-source architecture which is inspired by previously reported DEFactor architecture and based on hydrogen labeled graphs." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "HyFactor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Laboratoire-de-Chemoinformatique/HyFactor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Identifies primer and microarray probe binding sites in genomic DNA." ; sc:featureList edam:operation_2421 ; sc:name "hyfi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hyfi.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_2640, edam:topic_3168 ; sc:citation ; sc:description "A Hybrid approach for Detection of Insertions and Deletions." ; sc:featureList edam:operation_0452, edam:operation_3199, edam:operation_3962 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "HyINDEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alok123t/HyINDEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0769, edam:topic_0780, edam:topic_3382 ; sc:citation , "pubmed:32300867" ; sc:description """A semi-automated digital image analysis tool for measuring the length of roots and fungal hyphae of dense mycelia. 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sc:softwareHelp ; sc:url "http://bioimaging.usc.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:34214695" ; sc:description "A processing tool for scanning probe microscopy and other n-dimensional datasets." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Hystorian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.unige.ch/paruch-group/hystorian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:21396103" ; sc:description "New R package that we have developed for detection, quantification, and visualization of homozygous segments/ROH in high-density SNP datasets." ; sc:featureList edam:operation_0337, edam:operation_2423, edam:operation_3799 ; sc:name "hzAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://emu.src.riken.jp/hzAnalyzer/" ; biotools:primaryContact "Tatsuhiko Tsunoda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3383 ; sc:citation ; sc:description "Semi-Automatic Analysis of Invasion and Migration Transwell Assays." ; sc:featureList edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "I-AbACUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.marilisacortesi.com/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0868 ; sc:name "Profile-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797 ; sc:citation ; sc:description "A highly sensitive software tool to detect degenerated homology relations within and between different genomes." ; sc:featureList edam:operation_2451 ; sc:name "i-ADHoRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/i--ADHoRe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2885, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:20435672" ; sc:description "Web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS)." ; sc:featureList edam:operation_2436, edam:operation_2497, edam:operation_3224 ; sc:name "i-GSEA4GWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gsea4gwas.psych.ac.cn" ; biotools:primaryContact "i-GSEA4GWAS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081 ; sc:citation , "pubmed:32622978" ; sc:description """Identification of ligand-binding residues using protein sequence profile alignment and query-specific support vector machine model. Information embedded in ligand-binding residues (LBRs) of proteins is important for understanding protein functions. How to accurately identify the potential ligand-binding residues is still a challenging problem, especially only protein sequence is given. In this paper, we establish a new query-specific computational method, named I-LBR, for the identification of LBRs without directly using the information of protein 3D structure. I-LBR includes two modes, named as I-LBRGP and I-LBRLS, for the general-purpose and ligand-specific LBR identification""" ; sc:featureList edam:operation_0300, edam:operation_2495, edam:operation_3767 ; sc:name "I-LBR" ; sc:url "https://jun-csbio.github.io/I-LBR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1467 ; sc:name "Protein chain" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1742 ; sc:name "PDB residue number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2885 ; sc:citation ; sc:description "Neural Network based Predictor of Protein stability Changes upon Single Point Mutation from the Protein Structure." ; sc:featureList edam:operation_2406 ; sc:name "I-MUTANT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://folding.biofold.org/i-mutant/i-mutant2.0.html" ; biotools:primaryContact "Emidio Capriotti" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1467 ; sc:name "Protein chain" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1742 ; sc:name "PDB residue number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0199, edam:topic_2814, edam:topic_2885 ; sc:citation "pubmed:15980478" ; sc:description "Predictor of effects of single point protein mutation on its stability from protein sequences or structures." ; sc:featureList edam:operation_0250, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "I-MUTANT Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi" ; biotools:primaryContact "Emidio Capriotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_0199 ; sc:citation "pubmed:26454277" ; sc:description "Software that uses Circos to render interactive images for protein sequence visualization." ; sc:featureList edam:operation_0337, edam:operation_2479 ; sc:name "I-PV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.i-pv.org/" ; biotools:primaryContact "Ibrahim Tanyalcin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0166, edam:topic_0736 ; sc:citation "pubmed:9698570" ; sc:description "Method for predicting initiation sites of folding protein sequences." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "I-sites" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.bioinfo.rpi.edu/bystrc/Isites2/" ; biotools:primaryContact "Chris Bystroff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_1775, edam:topic_2275, edam:topic_2814 ; sc:citation , , , , "pmcid:PMC2849174", "pmcid:PMC4428668", "pmcid:PMC4489253", "pmcid:PMC8336924", "pubmed:20360767", "pubmed:25549265", "pubmed:25883148", "pubmed:34355210" ; sc:description "Best in tertiary structure prediction (as ‘Zhang-Server’) in the community-wide blind benchmarks CASP7 and CASP8. It uses mainly profile-profile comparison to identify templates and alignments for deriving distance constraints. Its power lies in how it combines the distance constraints from up to the 50 best-ranked templates. It performs some knowledge-based free modelling in regions without any template-based information." ; sc:featureList edam:operation_0310, edam:operation_0474 ; sc:name "I-TASSER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/I-TASSER/" ; biotools:primaryContact "Yang Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2828 ; sc:citation , "pmcid:PMC5793832", "pubmed:28472524" ; sc:description "Automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation" ; sc:featureList edam:operation_0477, edam:operation_3454, edam:operation_3455 ; sc:name "I-TASSER-MR" ; sc:softwareHelp , ; sc:url "http://zhanglab.ccmb.med.umich.edu/I-TASSER-MR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "For quantitative proteomics using iTRAQ." ; sc:featureList edam:operation_3631 ; sc:license "GPL-1.0" ; sc:name "i-Tracker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bessantlab.org/software/i-tracker/" ; biotools:primaryContact "Ian Shadforth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC7063232", "pubmed:32181151" ; sc:description """An open source, freeware tool to simulate river water temperature coupled with HEC-RAS. This method paper explains the i-Tree Cool River model algorithms for simulating the response of river water temperature to urban greening. The model captures the warming and cooling impacts of urban development and restoration through a water and energy budget. The water budget includes river inflows from urban storm sewers and reservoirs, and the associated water temperatures. The energy budget adjusts radiation fluxes due to riparian shading and evapotranspiration, and propagates temperature downstream. Restorative cooling of the river can be simulated through algorithms for cool groundwater, either as direct inflows or by river water replacement called hyporheic exchange""" ; sc:featureList edam:operation_0387, edam:operation_2426 ; sc:name "i-Tree Cool River" ; sc:url "https://www.itreetools.org/tools/research-suite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC9091563", "pubmed:35571057" ; sc:description "a computational approach called i2APP that can identify APPs using a two-step machine learning framework" ; sc:featureList edam:operation_3631, edam:operation_3936, edam:operation_3937 ; sc:license "Not licensed" ; sc:name "i2APP" ; sc:url "https://github.com/greyspring/i2APP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3063, edam:topic_3382 ; sc:citation , "pubmed:36053173" ; sc:description "i2b2-etl provides a command line interface and api interface to import, delete concepts and facts and encounters." ; sc:featureList edam:operation_0224, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "i2b2-etl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/i2b2/i2b2-etl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_2815, edam:topic_3557 ; sc:citation "pubmed:15657099", "pubmed:17535438" ; sc:description "To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_2492, edam:operation_3083, edam:operation_3439 ; sc:name "I2D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ophid.utoronto.ca/ophidv2.204/" ; biotools:primaryContact "Igor Jurisica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3382 ; sc:citation , "pubmed:33244599" ; sc:description """An R package for simulating data from images and the implications in biomedical research. The R package i2d is a novel tool that allows users to transform an image into a simulated dataset that can be used to extract and analyze the complex information in biomedical and biological research. The package also includes three novel and efficient methods for image clustering based on finding minimum spanning tree by Prim's algorithm, detecting communities by modularity optimization, and finding the branches of the backbone of minimum spanning tree.""" ; sc:featureList edam:operation_3432, edam:operation_3443, edam:operation_3799 ; sc:name "i2d_R" ; sc:url "http://github.com/XiaoyuLiang/i2d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3382 ; sc:citation ; sc:description """Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results. Interactive & iterative dashboards in R. Iterative and Interactive Dashboards.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3436 ; sc:license "MIT" ; sc:name "i2dash" ; sc:url "https://gitlab.gwdg.de/loosolab/container/i2dash.deployment" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0166, edam:topic_0736, edam:topic_3534 ; sc:citation "pubmed:15215437", "pubmed:15980484" ; sc:description "Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces." ; sc:featureList edam:operation_0303, edam:operation_2464, edam:operation_2487, edam:operation_2575 ; sc:name "I2I-SiteEngine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/" ; biotools:primaryContact "I2I-SiteEngine Administrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814, edam:topic_3318 ; sc:citation "pubmed:27131371" ; sc:description "Completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique." ; sc:featureList edam:operation_0322 ; sc:name "i3Drefine" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://sysbio.rnet.missouri.edu/multicom_toolbox/tools.html" ; biotools:primaryContact "Jianlin Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0659, edam:topic_0749, edam:topic_3169, edam:topic_3306 ; sc:citation , "pmcid:PMC10236371", "pubmed:37273849" ; sc:description "3plex enables deep computational investigation of triplex forming lncRNAs." ; sc:featureList edam:operation_0278, edam:operation_2441, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "i3plex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/molinerisLab/3plex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:31805335" ; sc:description """Bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome. i4mC-ROSE is available for public""" ; sc:featureList edam:operation_3659 ; sc:name "i4mC-ROSE" ; sc:url "http://kurata14.bio.kyutech.ac.jp/i4mC-ROSE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC7168350", "pubmed:32322372" ; sc:description """Improved identification of DNA N4-methylcytosine sites in the mouse genome using multiple encoding schemes. i4mC-Mouse is available for public.""" ; sc:featureList edam:operation_3936 ; sc:name "i4mC-Mouse" ; sc:url "http://kurata14.bio.kyutech.ac.jp/i4mC-Mouse/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_0780, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:35771648" ; sc:description "A CapsuleNet-based framework for identifying DNA N6-methyladenine sites." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "i6mA-Caps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nsclbio.jbnu.ac.kr/tools/i6mA-Caps/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3318 ; sc:description "i6mA-DNCP is a computational tool for identifying 6mA sites in rice genome." ; sc:isAccessibleForFree true ; sc:name "i6mA-DNCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/72549-i6ma-dncp" ; biotools:primaryContact "Liang Kong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:33010390" ; sc:description """A stacking ensemble-based computational prediction of DNA N6-methyladenine (6mA) sites in the Rosaceae genome. Welcome to Our Bioinformatics Lab!.""" ; sc:name "i6mA-stack" ; sc:url "http://nsclbio.jbnu.ac.kr/tools/i6mA-stack/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0780, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:33834381" ; sc:description "i6mA-VC is a multi-classifier voting method for the computational identification of DNA N6-methyladenine sites." ; sc:featureList edam:operation_0224, edam:operation_3936, edam:operation_3937 ; sc:name "i6mA-VC" ; sc:url "http://www.zhanglab.site/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0605, edam:topic_0736, edam:topic_3520 ; sc:citation , "pmcid:PMC6908504", "pubmed:31867311" ; sc:description """Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. iAcetyP : Identify acetylation protein via Chou's 5-steps rule and general pseudo components : Read Me : Supporting Information : Citation :. Enter the sequences of query proteins in FASTA format (Example), and select Submit button for identifying acetylation protein. The number of proteins is limited at 5 or less for each submission""" ; sc:featureList edam:operation_0417, edam:operation_2489, edam:operation_3755 ; sc:name "iACetyP" ; sc:url "http://www.jci-bioinfo.cn/iAcetyP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3374 ; sc:citation , "pubmed:31593226" ; sc:description """An efficient multi-label classifier for recognizing anatomical therapeutic chemical (ATC) classes of drugs. Recognizing the Anatomical Therapeutic Chemical (ATC) classes of first level for given drugs. Functions : Recognizing the Anatomical Therapeutic Chemical (ATC) classes of first level for given drugs.""" ; sc:license "MIT" ; sc:name "iATC-NRAKEL" ; sc:url "https://github.com/zhou256/iATC-NRAKEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3384, edam:topic_3452 ; sc:citation , "pubmed:31845123" ; sc:description """Modular Open-Source Software for Digital Radiography. A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices.""" ; sc:featureList edam:operation_3443 ; sc:name "iBEX" ; sc:url "https://github.com/altaybrusan/ibex/tree/FastDev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3303, edam:topic_3379, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC6786512", "pubmed:31600197" ; sc:description """A public access, broad coverage resource. NIH Office of Portfolio Analysis. iCite is a tool to access a dashboard of bibliometrics for papers associated with a portfolio. Users type in a PubMed query or upload the PubMed IDs of articles of interest. iCite has three modules: Influence, Translation, and Open Citations. iCite: Influence delivers metrics of scientific influence such as the Relative Citation Ratio (RCR), which is field- and time-adjusted, and benchmarked to NIH publications as the baseline. Read about how RCR is calculated at PLOS Biology. Bulk data can be accessed at the iCite database snapshot repository""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3436 ; sc:license "Proprietary" ; sc:name "iCite" ; sc:softwareHelp ; sc:url "https://icite.od.nih.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3168, edam:topic_3379, edam:topic_3577 ; sc:citation ; sc:description """Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts. Solution to iDASH'19 challenge track 1.""" ; sc:featureList edam:operation_0224, edam:operation_3283 ; sc:name "iDASH" ; sc:url "https://github.com/gersteinlab/iDASH19bc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0157, edam:topic_0780 ; sc:citation , "pmcid:PMC6669840", "pubmed:31391777" ; sc:description "Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor | Defensins as 1 of major classes of host defense peptides play a significant role in the innate immunity, which are extremely evolved in almost all living organisms. Developing high-throughput computational methods can accurately help in designing drugs or medical means to defense against pathogens. To take up such a challenge, an up-to-date server based on rigorous benchmark dataset, referred to as iDEF-PseRAAC, was designed for predicting the defensin family in this study. By extracting primary sequence compositions based on different types of reduced amino acid alphabet, it was calculated that the best overall accuracy of the selected feature subset was achieved to 92.38%" ; sc:name "iDEF-PseRAAC" ; sc:url "http://bioinfor.imu.edu.cn/idpf/public/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6299935", "pubmed:30567491" ; sc:description "Integrated web application for differential expression and pathway analysis of RNA-Seq." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iDEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.sdstate.edu/idep/" ; biotools:primaryContact "X. Ge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168 ; sc:citation , "pubmed:31117818" ; sc:description "Identifying DNase I hypersensitive sites with balanced dinucleotide-based detrending moving-average cross-correlation coefficient." ; sc:featureList edam:operation_0438 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iDHS-DMCAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shengli0201/Datasets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169 ; sc:citation , "pubmed:29360500" ; sc:description "Identification of DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC." ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iDNA6mA-PseKNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lin-group.cn/server/iDNA6mA-PseKNC" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3295 ; sc:citation , "pmcid:PMC6746913", "pubmed:31552096" ; sc:description "A Computational Tool for Detecting N6-Methyladenine Sites in Rice | Home About us Web-Server Contact us Download Citation | 6mA is formed by transferring methyl groups to the 6th position of the adenine ring catalyzed by methyl-transferases. It is a non-canonical DNA modification that is present at low levels in different eukaryotes. 6mA possesses similar characteristics between prokaryotes and eukaryotes. Its functions display diversity, such as guiding the discrimination between original and newly synthesized DNA strand after replication, regulating gene transcription and repressing transposable elements; in the cell cycle, reducing the stability of base pairings for opening DNA duplexes. Strikingly, the protection from methylation is an inherited state that, however, can be modified by environmental conditions" ; sc:featureList edam:operation_0438 ; sc:name "iDNA6mA-Rice" ; sc:url "http://lin-group.cn/server/iDNA6mA-Rice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3398, edam:topic_3399, edam:topic_3404 ; sc:citation , "pubmed:31465600" ; sc:description "Validation of an integrated dermoscopic scoring method in an European teledermoscopy web platform | EADV-iDScore project “European web platform for the development of a Scoring Classifier for Early Melanoma detection” (EADV PPRC project number 2016-012)" ; sc:name "iDScore" ; sc:url "http://eadv-idscore.dbm.unisi.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3173 ; sc:citation , "pmcid:PMC6858347", "pubmed:31729402" ; sc:description """Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. integrative analysis of (epi-)DNA and gene expression data for the identification of candidate cancer drivers. iEDGE is an R-package for performing integrative analysis of (epi-)DNA and gene expression data that builds upon, and significantly expands, the methodology first described in Monti, Chapuy, et. al., Cancer Cell (2012). This package provides the generalized pipeline to perform integrative analysis of epi-genomic data (methylation, copy number alteration, mutation, microRNA, etc.) and gene-expression data from paired samples, and consists of 3 major modules:. Integrative analysis of (Epi-)DNA and Gene Expression Data.""" ; sc:featureList edam:operation_2495, edam:operation_3200, edam:operation_3223, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "iEDGE" ; sc:url "https://montilab.bu.edu/iEDGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3444 ; sc:citation , "pubmed:31658449" ; sc:description """An open-source multifunction GUI-based Matlab toolbox for localization and visualization of human intracranial electrodes. Localization and Visualization of Intracranial Electrodes.""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "iEEGview" ; sc:url "https://github.com/GuangyeLiGit/iEEGview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0654, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC6929481", "pubmed:31874637" ; sc:description """Identifying enhancers and their strength using ensembles of convolutional neural networks. BACKGROUND:Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength.""" ; sc:name "iEnhancer-ECNN" ; sc:url "https://github.com/ngphubinh/enhancers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3376 ; sc:citation , "pmcid:PMC6607226", "pubmed:31565348" ; sc:description "Developing Evidence to Decision Frameworks and an Interactive Evidence to Decision Tool for Making and Using Decisions and Recommendations in Health Care | Evidence-informed health care decisions and recommendations need to be made systematically and transparently. Mediating technology can help manage boundaries between groups making decisions and target audiences, enhancing salience, credibility, and legitimacy for all. This article describes the development of the Evidence to Decision (EtD) framework and an interactive tool to create and use frameworks (iEtD) to support communication in decision making. Methods: Using a human-centered design approach, we created prototypes employing a broad range of methods to iteratively develop EtD framework content and iEtD tool functionality" ; sc:name "iEtD" ; sc:url "https://ietd.epistemonikos.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3053, edam:topic_3379, edam:topic_3577 ; sc:citation ; sc:description """An integrative resource for investigating genetic model of drug response in cancer. An integrative database for investigating genetic model of drug response in cancer. iGMDR database collects predictive models of response for anti-cancer drugs. The efficacy of anticancer drugs usually varies from individual to individual, mainly due to genetic heterogeneity""" ; sc:featureList edam:operation_2454, edam:operation_3435 ; sc:name "iGMDR" ; sc:url "https://igmdr.modellab.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3534 ; sc:citation , "pmcid:PMC6337799", "pubmed:30654827" ; sc:description "Improved pipeline for analyzing CRISPR cleavage specificity." ; sc:featureList edam:operation_0308, edam:operation_3216, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iGUIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cnobles/iGUIDE" ; biotools:primaryContact "Chris Nobles" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0208, edam:topic_0634, edam:topic_0769, edam:topic_3375 ; sc:citation ; sc:description """Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS. This repository consists of set of exeamples to showcase the ways of interacting with iLINCS API. The examples are implemented in the RStudio notebook usingIlincsApis.Rmd and the "knitted" html output of the notebook is provided in usingIlincsApis.html.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_2497 ; sc:name "iLINCS" ; sc:url "http://ilincs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0091, edam:topic_3474 ; sc:citation , "pubmed:31067315" ; sc:description "Integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data." ; sc:featureList edam:operation_0279, edam:operation_0303, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iLearn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ilearn.erc.monash.edu/" ; biotools:primaryContact "Jiangning Song", "Zhen Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pubmed:31619811" ; sc:description """Mapping RNA-chromatin interactions by sequencing with iMARGI. Overview — iMARGI Pipeline 1.1 documentation.""" ; sc:featureList edam:operation_2429 ; sc:name "iMARGI" ; sc:url "https://sysbio.ucsd.edu/imargi_pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3419, edam:topic_3676 ; sc:citation , "pmcid:PMC6309067", "pubmed:30591030" ; sc:description "Integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iMEGES" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/WGLab/iMEGES" ; biotools:primaryContact "Atlas Khan", "Kai Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3175 ; sc:citation , "pmcid:PMC6299635", "pubmed:30563451" ; sc:description "Program to identify novel mobile genetic elements inserted in individual genomes." ; sc:featureList edam:operation_3192, edam:operation_3199 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iMGEins" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/DMnBI/iMGEins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0659, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:31860075" ; sc:description """An R package to impute microRNA expression using protein-coding genes. imputed miRNA activity from gene expression (Title Case). iMIRAGE: imputed microRNA activity from gene expression. As the name stands, iMIRAGE a set of tools that facilitates imputation of microRNA or miRNA expression using protein-coding genes. With a growing repertoire of publicly available transcriptomic data, it is now possible to study miRNA expression in several phenotypes""" ; sc:featureList edam:operation_0463, edam:operation_3557, edam:operation_3792 ; sc:name "iMIRAGE" ; sc:url "https://aritronath.github.io/iMIRAGE/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3127, edam:topic_3174 ; sc:citation , "pmcid:PMC6602517", "pubmed:31081014" ; sc:description "integrative McDonald and Kreitman test." ; sc:featureList edam:operation_0310, edam:operation_0451, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iMKT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://imkt.uab.cat" ; biotools:primaryContact , "Jesús Murga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0780, edam:topic_3050 ; sc:citation ; sc:description "Methods for broad-scale plant phenology assessments using citizen scientists’ photographs | iNaturalist.org is a joint initiative of the California Academy of Sciences and the National Geographic Society | Explore and share your observations from the natural world" ; sc:name "iNaturalist" ; sc:url "http://www.inaturalist.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_2814 ; sc:citation , "pmcid:PMC6825713", "pubmed:31700529" ; sc:description """A PyMOL plugin for an efficient 3D protein structure superimposition approach. Background:Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures. Results:We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles.""" ; sc:featureList edam:operation_0295, edam:operation_0337, edam:operation_2487 ; sc:name "iPBAvizu" ; sc:url "https://www.dsimb.inserm.fr/dsimb_tools/iPBAVizu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474, edam:topic_3794 ; sc:citation ; sc:description """A deep learning framework for improving protein interaction prediction using sequence properties. Abstract Motivation Almost all critical functions and processes in cells are sustained by the cellular networks of protein-protein interactions (PPIs), understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack high-quality PPI data for constructing the networks, which makes it challenging to study the functions of association of proteins. High-throughput experimental techniques have produced abundant data for systematically studying the cellular networks of a biological system and the development of computational method for PPI identification.""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3439 ; sc:name "iPPI-deepL" ; sc:url "https://github.com/model-lab/deeplearning.ppi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3794 ; sc:citation , "pubmed:30187132" ; sc:description "Identification of Sigma70 promoters using multiple windowing and minimal features." ; sc:featureList edam:operation_0440 ; sc:isAccessibleForFree true ; sc:name "iPro70-FMWin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ipro70.pythonanywhere.com/" ; biotools:primaryContact "Siddiqur Rahman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_2269, edam:topic_3169, edam:topic_3474 ; sc:citation , "pmcid:PMC6933727", "pubmed:31881828" ; sc:description """Identifying protein-DNA binding residues using capsule neural networks. Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of post-genomic where data on protein sequences have expanded very fast. In this study, we propose iProDNA-CapsNet -- a new prediction model identifying protein-DNA binding residues using an ensemble of Capsule Neural Networks (CapsNets) on position specific scoring matrix (PSMM) profiles. The use of CapsNets promises an innovative approach to determine the location of DNA-binding residues. In this study, the benchmark datasets introduced by Hu et al. (2017), i.e., PDNA-543 and PDNA-TEST, were used to train and evaluate the model, respectively. To fairly assess the model performance, comparative analysis between iProDNA-CapsNet and existing state-of-the-art methods was done""" ; sc:featureList edam:operation_0480, edam:operation_3092, edam:operation_3900 ; sc:name "iProDNA-CapsNet" ; sc:url "https://github.com/ngphubinh/iProDNA-CapsNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3534 ; sc:citation , "pmcid:PMC6556904", "pubmed:29897410" ; sc:description "Integrated feature-based webserver in silico prediction of protease substrates and their cleavage sites for 38 different protease types, covering four major protease families: Aspartic (A), Cysteine (C), Metallo (M) and Serine (S)." ; sc:featureList edam:operation_0267, edam:operation_0418, edam:operation_0422 ; sc:name "iProt-Sub" ; sc:softwareHelp ; sc:url "http://iprot-sub.erc.monash.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:31861928" ; sc:description """A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties. A sequence-based tool for the prediction and analysis of quorum sensing peptides using informative physicochemical properties. Enter your input sequence(s) in FASTA format Insert example data""" ; sc:featureList edam:operation_0417, edam:operation_2489, edam:operation_3631 ; sc:name "iQSP" ; sc:url "http://codes.bio/iqsp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6796771", "pubmed:31581049" ; sc:description """Identifying N2-methylguanosine Sites Based on Sequence-Derived Information. iRNA-m2G: identifying N2-methylguanosine sites. The benchmark datasets that uesed to train and test the proposed model are provided on this page. Benchmark dataset S1 contains 143 m2G site containing sequences and 143 non-m2G site containing sequences from H. sapiens, M. musculus and S. cerevisiae, respectively. Benchmark dataset S2 contains 143 non-m2G site containing sequences (same as dataset S1) and 1246 non-m2G site containing sequences from H. sapiens, M. musculus and S. cerevisiae, respectively""" ; sc:featureList edam:operation_0224 ; sc:name "iRNA-m2G" ; sc:url "http://lin-group.cn/server/iRNA-m2G.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC6796804", "pubmed:31581051" ; sc:description """Identifying N7-methylguanosine Sites by Fusing Multiple Features. N7-methylguanosine (m7G) is an essential RNA modification and participates in a series of biological processes. However, our knowledge about its biological functions is very limited. In order to reveal its new functions, it is necessary to develop various methods to identify m7G sites. Since experimental methods to detect m7G sites are still expensive, we proposed the first computational method, called iRNA-m7G, to detect m7G sites in Homo Sapiens. iRNA-m7G is developed by fusing multiple features, i.e., nucleotide property & frequency, pseudo dinucleotide composition, and secondary structure composition. The framework of iRNA-m7G is shown as following""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:name "iRNA-m7G" ; sc:url "http://lin-group.cn/server/iRNA-m7G/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3170 ; sc:citation ; sc:description "Computational tool for identifying D modification sites in RNA sequence." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "iRNAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin-group.cn/server/iRNAD" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654 ; sc:citation , "pmcid:PMC6759546", "pubmed:31620165" ; sc:description """Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition. : Server : ReadMe : Supporting Information : Citation : Contact Us :""" ; sc:featureList edam:operation_0224, edam:operation_3435 ; sc:name "iRO-PsekGCC" ; sc:url "http://bliulab.net/iRO-PsekGCC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3263 ; sc:citation , "pmcid:PMC6334444", "pubmed:30646845" ; sc:description "Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "iRODS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "4.2.5" ; sc:url "https://irods.org/" ; biotools:primaryContact "iRODS Consortium Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "iS-CellR (Interactive platform for Single-cell RNAseq) is a web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data." ; sc:featureList edam:operation_0337, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iS-CellR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/immcore/iS-CellR" ; biotools:primaryContact "Mitulkumar V. Patel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC6819733", "pubmed:31662430" ; sc:description """Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. Streptococcus mutans is a Gram-positive bacterium that thrives under acidic conditions and is a primary cause of tooth decay (dental caries). To better understand the metabolism of S. mutans on a systematic level, we manually constructed a genome-scale metabolic model of the S. mutans type strain UA159. The model, called iSMU, contains 675 reactions involving 429 metabolites and the products of 493 genes. We validated iSMU by comparing simulations with growth experiments in defined medium. The model simulations matched experimental results for 17 of 18 carbon source utilization assays and 47 of 49 nutrient depletion assays. We also simulated the effects of single gene deletions. The model's predictions agreed with 78.1% and 84.4% of the gene essentiality predictions from two experimental data sets.""" ; sc:featureList edam:operation_0533, edam:operation_3660 ; sc:name "iSMU" ; sc:url "http://jensenlab.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3314 ; sc:citation , "pubmed:31597209" ; sc:description """A National-Scale Framework for Visualizing Riverine Concentrations of Microplastics Released from Municipal Wastewater Treatment Incorporating Generalized Instream Losses. iSTREEM® is an in-stream environmental exposure model which predicts the concentration of a chemical used in "down-the-drain" products. It is a tool to promote product stewardship and regulatory compliance for chemical suppliers and manufacturers of formulated products of all sizes across commodity groups. Predicted environmental concentrations are calculated for the continental United States and several watersheds in Canada:.""" ; sc:name "iSTREEM" ; sc:url "https://www.istreem.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0769, edam:topic_2275 ; sc:citation ; sc:description """An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. Support Vector Machine and Random walk Graph Kernel for Protein Interface Scoring. Welcome to iScore’s documentation! — iScore documentation. Support Vector Machine on Graph kernel for protein-protein conformation ranking. Install iScore using pip install iScore. Minimal information to install the module. iScore offers simple solutions to classify protein-protein interfaces using a support vector machine approach on graph kernels. The simplest way to use iScore is through dedicated binaries that hide the complexity of the approach and allows access to the code with simple command line interfaces. The two binaries are iscore.train and iscore.predict that respectively train a model using a trainging set and use this model to predict the near-native character of unkown conformations. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_0337, edam:operation_3899 ; sc:license "Apache-2.0" ; sc:name "iScore" ; sc:softwareHelp ; sc:url "https://github.com/DeepRank/iScore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "A Tool for Expression-Based Quality Control in RNA Sequencing | A Quality control analysis tool for NGS technologies | iSeqQC: An Expression based Quality Control tool | 'American Typewriter'; color:#081d58\">iSeqQC- An Expression based Quality Control tool | Please wait while the server is working.. | iSeqQC- An Expression based Quality Control tool | iSeqQC displays the results in a form of a summary table and several plots: Summary statistics, counts distribution, Mapped read density, Housekeeping gene expression, Principal Component variances, Hierarchical relationship between samples and correlations (Pearson and Spearman)" ; sc:featureList edam:operation_3218, edam:operation_3891 ; sc:name "iSeqQC" ; sc:url "http://cancerwebpa.jefferson.edu/iSeqQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0121, edam:topic_0634, edam:topic_3520 ; sc:citation , "pubmed:31797049" ; sc:description """MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery. A free resource for expression-based gene discovery in the eye""" ; sc:featureList edam:operation_2495, edam:operation_3637, edam:operation_3741, edam:operation_3767 ; sc:name "iSyTE" ; sc:url "https://research.bioinformatics.udel.edu/iSyTE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_3292 ; sc:citation ; sc:description "Sequence-based tool for predicting bacterial transcriptional terminators." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "iTerm-PseKNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin-group.cn/server/iTerm-PseKNC/" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3473 ; sc:citation , "pmcid:PMC6301332", "pubmed:30576489" ; sc:description "Integrated text-mining system for large-scale knowledge extraction from the literature." ; sc:featureList edam:operation_3280, edam:operation_3501, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "iTextMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://research.bioinformatics.udel.edu/itextmine/integrate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_3168 ; sc:citation , "pubmed:30747482" ; sc:description "Web-based application that provides variant assessment, interactive pathway impact analysis of genetic variants, as well as a unique Gene Ontology (GO) analysis." ; sc:featureList edam:operation_3197, edam:operation_3501, edam:operation_3675 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "iVariantGuide" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://advaitabio.com/ivariantguide/" ; biotools:primaryContact "ADVAITA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3170, edam:topic_3305, edam:topic_3308 ; sc:citation , "pmcid:PMC9235372", "pubmed:35758882" ; sc:description "A transcriptome atlas and interactive analysis platform for autoimmune disease." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "IAAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://galaxy.ustc.edu.cn/IAAA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0202, edam:topic_2640, edam:topic_3376 ; sc:citation "pubmed:26942877" ; sc:description "This web-server was developed to identify the anticancer peptides based on the sequence information." ; sc:featureList edam:operation_2479, edam:operation_3631 ; sc:name "iACP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/iACP" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:33529337" ; sc:description """Anticancer peptides prediction with deep representation learning features. Anti-Cancer Peptide Prediction with Deep Representation Learning Features. This repository contains the source code and links to the data and pretrained embedding models accompanying the iACP-DRLF paper: Anti-Cancer Peptide Prediction with Deep Representation Learning Features.""" ; sc:featureList edam:operation_3211, edam:operation_3631, edam:operation_3936, edam:operation_3937 ; sc:license "MIT" ; sc:name "iACP-DRLF" ; sc:url "http://public.aibiochem.net/iACP-DRLF/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:35772910" ; sc:description "Computational prediction of anticoronavirus peptides (ACVPs) using their sequences." ; sc:featureList edam:operation_0224, edam:operation_3092, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "iACVP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://kurata35.bio.kyutech.ac.jp/iACVP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3168, edam:topic_3516, edam:topic_3676 ; sc:citation ; sc:description "Program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)" ; sc:featureList edam:operation_3196 ; sc:name "iAdmix" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://bansal-lab.github.io/software/iadmix.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC9670693", "pubmed:36406571" ; sc:description """A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides. Welcome to the Home Page of iAMAP-SCM.""" ; sc:featureList edam:operation_0321, edam:operation_0478, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "iAMAP-SCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/iAMAP-SCM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0202, edam:topic_0610, edam:topic_3301 ; sc:citation "pubmed:23395824" ; sc:description "This web-server is a two-level multi-label predictor. It can be used to identify an uncharacterized peptide as antimicrobial peptide (AMP) or non-AMP according to its sequences information alone." ; sc:featureList edam:operation_2479, edam:operation_3631 ; sc:name "iAMP-2L" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iAMP-2L" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "Iamxt is an array-based max-tree toolbox implemented in Python using the NumPy library for array processing. It can be used in mathematical morphology research and image processing." ; sc:featureList edam:operation_3443 ; sc:license "BSD-2-Clause" ; sc:name "iamxt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v0.1" ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX-D-15-00049" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3306, edam:topic_3474 ; sc:citation , "pubmed:33017626" ; sc:description """Improved prediction and analysis of amyloid proteins using a scoring card method with propensity scores of dipeptides. This is the website for predicting Amyloid Proteins from the publication called ... iAMY-SCM: Improved Prediction and Analysis of Amyloid Proteins Using Scoring Card Method.""" ; sc:featureList edam:operation_3767 ; sc:name "iAMY-SCM" ; sc:url "http://camt.pythonanywhere.com/iAMY-SCM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1176 ; sc:name "GO concept ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3173, edam:topic_3298, edam:topic_3673 ; sc:citation , "pubmed:36300629" ; sc:description "A cross-species omics knowledgebase for animals." ; sc:featureList edam:operation_0224, edam:operation_1781, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "IAnimal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ianimal.pro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9549785", "pubmed:36225530" ; sc:description "A neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics." ; sc:featureList edam:operation_0314, edam:operation_3359, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iAntiSplodge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HealthML/AntiSplodge/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9834665", "pubmed:36609432" ; sc:description "Curated atlas of the biogenesis of spliceosome machinery during RNA splicing." ; sc:featureList edam:operation_0337, edam:operation_2499 ; sc:isAccessibleForFree true ; sc:name "IARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pucpr-bioinformatics.github.io/atlas/atlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC10268951", "pubmed:37235532" ; sc:description "A web server for machine learning-based prediction of protein-protein and antibody-protein antigen binding affinities." ; sc:featureList edam:operation_0252, edam:operation_0272, edam:operation_0477, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "iAREA-AFFINITY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://affinity.cuhk.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3299 ; sc:citation "pubmed:20583925" ; sc:description "Collection of tools to reconstruct evolutionary histories which include recombination and back/recurrent mutation events." ; sc:featureList edam:operation_0451 ; sc:name "iARG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.brown.edu/Research/Istrail_Lab/iarg.php" ; biotools:primaryContact "Sorin Istrail" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3444 ; sc:citation , "pubmed:34494276" ; sc:description "Joint intraclassly adaptive GAN and segmentation network for unsupervised cross-domain in neonatal brain MRI segmentation." ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IAS-NET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lb-whu/RAS-NET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3360, edam:topic_3379, edam:topic_3399, edam:topic_3452 ; sc:citation , "pmcid:PMC8680857" ; sc:description "The Integrated Aging Studies Databank and Repository (IASDR) IASDR serves as a resource for the scientific community to foster new scientific questions and analyses" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IASDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.peppercenter.org/public/dspIASDR.cfm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies." ; sc:featureList edam:operation_3465 ; sc:license "GPL-2.0" ; sc:name "iASeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iASeq.html" ; biotools:primaryContact "Yingying Wei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3308 ; sc:citation ; sc:description "Standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs." ; sc:featureList edam:operation_0310 ; sc:name "iAssembler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3.2" ; 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Panchenko", "Thomas Madej" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC8396555", "pubmed:34445663" ; sc:description "Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features" ; sc:featureList edam:operation_3631, edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iBitter-Fuse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://camt.pythonanywhere.com/iBitter-Fuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3306, edam:topic_3390, edam:topic_3474 ; sc:citation , "pubmed:32234434" ; sc:description """Identification and characterization of bitter peptides using a scoring card method with propensity scores of dipeptides. 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The role of this page is a brief introduction to iBLP. Bioluminescent proteins are a class of proteins that widely distributed in many living organisms with various mechanisms of light emission including bioluminescence and chemiluminescence from luminous organisms.""" ; sc:featureList edam:operation_0303, edam:operation_2409, edam:operation_3937 ; sc:name "iBLP" ; sc:url "http://lin-group.cn/server/iBLP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Predict outcomes faster using a platform built with data fabric architecture. Collect, organize and analyze data, no matter where it resides." ; sc:featureList edam:operation_2409 ; sc:license "Proprietary" ; sc:name "IBM Cloud Data Pak" ; sc:softwareHelp ; sc:url "https://www.ibm.com/products/cloud-pak-for-data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623, edam:topic_0654, edam:topic_3510 ; sc:citation "pubmed:10786305", "pubmed:11056059", "pubmed:12060689", "pubmed:12202776", "pubmed:12824385", "pubmed:15215340", "pubmed:9520502" ; sc:description "Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools." ; sc:featureList edam:operation_0238, edam:operation_0452, edam:operation_0492, edam:operation_2479, edam:operation_3761 ; sc:name "IBM Bioinformatics and Pattern Discovery Group" ; sc:url "http://cbcsrv.watson.ibm.com/Tspd.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2840 ; sc:citation , "pmcid:PMC7750002", "pubmed:33362981" ; sc:description """An R package for benchmark dose estimation. The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper's objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "ibmd" ; sc:url "https://shiny-efsa.openanalytics.eu/app/bmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation , "pmcid:PMC4627701", "pubmed:22850063" ; sc:contributor ; sc:description "Integrated Bayesian Modeling of eQTL data." ; sc:featureList edam:operation_2426 ; sc:license "Artistic-2.0" ; sc:name "iBMQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iBMQ.html" ; biotools:primaryContact "Greg Imholte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3047 ; sc:citation , "pmcid:PMC9474292", "pubmed:36147670" ; sc:description "A sequence-based predictor package for identifying ion binding protein in phage." ; sc:featureList edam:operation_0303, edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IBPred" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/ShishiYuan/IBPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10025434", "pubmed:36847692" ; sc:description "Integrated Benchmarking Single-cell RNA-sequencing Analytical Pipeline." ; sc:featureList edam:operation_3435, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IBRAP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/connorhknight/IBRAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "IBRENA (Insilico Biochemical REaction Network Analysis) is a software to aid the analysis of complex biological reaction networks. In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis." ; sc:featureList edam:operation_2497 ; sc:name "IBRENA" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.eng.buffalo.edu/~neel/ibrena/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080, edam:topic_0092 ; sc:citation "pubmed:26069263" ; sc:description "Software package that can be used for representing the organization of either protein or nucleotide sequences, in a convenient, efficient and precise manner." ; sc:featureList edam:operation_0337 ; sc:name "IBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibs.biocuckoo.org/" ; biotools:primaryContact "Jian Ren", "Yu Xue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_2640, edam:topic_3500 ; sc:citation "pubmed:20484374" ; sc:description "The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS." ; sc:featureList edam:operation_0224, edam:operation_2422, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:name "IBWS: IST Bioinformatics Web Services" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.hsanmartino.it/ibws/" ; biotools:primaryContact "Paolo Romano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_1317 ; sc:citation "pubmed:19395593" ; sc:description "A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands." ; 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sc:description "A Web Server for Predicting Cardiotoxicity of Small Molecules." ; sc:featureList edam:operation_3799, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "icardioToxCSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biosig.lab.uq.edu.au/cardiotoxcsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "An R package to compute Individualized Coherent Absolute Risk Estimators." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "iCARE" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iCARE.html" ; biotools:primaryContact "Bill Wheeler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; 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High throughput sequencing of immune cell receptor sequences presents a unique opportunity to inform our understanding of immunological response to infection and how we can detect it. iCAT is a user-friendly, graphical-interface software that takes exposed and non-exposed samples of T-cell receptor (TCR) clonotypes as input and identifies pathogen-specific TCR sequences. 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With the assistance of FKNN, the highlight of this tool is to employ amino acid sequence features extracted by incorporating the sequence evolution information into PseAAC via a grey system model (Grey-PSSM)." ; sc:featureList edam:operation_3092 ; sc:name "iCataly-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iCataly-PseAAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3293 ; sc:citation , "pmcid:PMC8725190", "pubmed:34907423" ; sc:description "An integrative database of cancer-associated viruses." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "iCAV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://icav.omicsbio.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_0634, edam:topic_3376 ; sc:citation ; sc:description "Visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D." ; sc:featureList edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "iCAVE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://research.mssm.edu/gumuslab/software.html" ; biotools:primaryContact "Zeynep H Gümüş" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36095221" ; sc:description "Immune Checkpoint Blockade therapy Atlas (ICBatlas) is a database providing comprehensive expression resources and functional analysis for patients with ICB therapy. 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ICBM-Webmaster (Stand: 21.08.2020).""" ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3860 ; sc:name "ICBM-OCEAN" ; sc:url "http://www.icbm.de/icbm-ocean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:21291413" ; sc:description "R package that implements algorithms for parameter estimation and model selection for Isotonic Conjunctive Bayesian Network (I-CBN) models. It combines isotonic regression on a partially ordered set with CBNs for estimating order constraints among events. 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IceBear is a research data management tool for structural biology. It currently covers crystallization trials, crystal fishing and shipping, as well as linking crystals, datasets, and PDB depositions for full chain of custody. It gives you a highly task-focused interface and a flexible access rights system. And it's FREE to download and install in your lab.""" ; sc:featureList edam:operation_2409, edam:operation_2475, edam:operation_3200, edam:operation_3431 ; sc:name "IceBear" ; sc:url "https://icebear.fi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654, edam:topic_0749, edam:topic_0798 ; sc:citation "pubmed:22009673" ; sc:description "Web-based resource for integrative and conjugative elements (ICEs) found in bacteria." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_2423 ; sc:name "ICEberg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://db-mml.sjtu.edu.cn/ICEberg/" ; biotools:primaryContact "Hong-Yu OU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821 ; sc:citation , "pmcid:PMC7222511", "pubmed:32410570" ; sc:description """An interactive online tool for calculating initial rates from continuous enzyme kinetic traces. An Interactive Continuous Enzyme Kinetics Analysis Tool (ICEKAT) was developed for semi-automated calculation of initial rates from continuous enzyme kinetic traces with particular application to the evaluation of Michaelis-Menten and EC50/IC50 kinetic parameters, as well as the results of high-throughput screening assays. ICEKAT allows users to interactively fit kinetic traces using convenient browser-based selection tools, ameliorating tedious steps involved in defining ranges to fit in general purpose programs like Microsoft Excel and Graphpad Prism, while still maintaining simplicity in determining initial rates. As a test case, we quickly analyzed over 500 continuous enzyme kinetic traces resulting from experimental data on the response of the protein lysine deacetylase Sirt1 to small-molecule activators.""" ; sc:featureList edam:operation_0334 ; sc:license "MIT" ; sc:name "ICEKAT" ; sc:url "https://icekat.herokuapp.com/icekat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3934 ; sc:citation ; sc:description """a transcriptome-based framework to dissect intercellular communication. Floriane Noël and Lucile Massenet-Regad. To install it, the easiest way is to use the R package devtools and its function install_github. 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If you would like to reference chespa in an academic paper, we ask you include the following:. chespa, version 1.0.0 http://github.com/pnnl/chespa (accessed MMM YYYY).""" ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3803 ; sc:name "ichespa" ; sc:url "http://github.com/pnnl/chespa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0769, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC8244591", "pubmed:34220740" ; sc:description "ChewieSnake is an end-to-end cgMLST based workflow for analyzing a set of assemblies (or reads) and obtaining an easy-to-interpret cgMLST report." ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ichewieSnake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/bfr_bioinformatics/chewieSnake" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169 ; sc:citation ; sc:description "This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. 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The tool is developed for circRNA-RBP interaction sites identification using deep hierarchical network. 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Potential lncRNA-disease association prediction. 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Bishop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_2640, edam:topic_3170, edam:topic_3173 ; sc:citation , "pubmed:33508087" ; sc:description """Extracting interconnected communities in gene Co-expression networks. This is an implementation of ICN detection for gene co-expression network (GCN) in Matlab. In constrast to the community structure, we consider a pair of communities be interconnected if a subset of genes from one community is correlated with a subset of genes from another community. Please refer to the paper "Extracting Interconnected Communities in Gene co-expression Networks" for details.""" ; sc:featureList edam:operation_1781, edam:operation_3463, edam:operation_3766 ; sc:name "ICN" ; sc:url "https://figshare.com/articles/software/ICN-package/13229093" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0166, edam:topic_3382, edam:topic_3542 ; sc:citation , "pmcid:PMC8892267", "pubmed:35252351" ; sc:description "From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode." ; sc:featureList edam:operation_0295, edam:operation_0302, edam:operation_0320, edam:operation_0570, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iCn3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/Structure/icn3d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "Integrative copy number variation (CNV) detection from multiple platform and experimental design." ; sc:featureList edam:operation_3233 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "iCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iCNV.html" ; biotools:primaryContact "Zilu Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605 ; sc:citation , "pubmed:27027585" ; sc:description "This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results." ; sc:featureList edam:operation_0337, edam:operation_2990, edam:operation_3438 ; sc:license "GPL-2.0" ; sc:name "iCOBRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iCOBRA.html" ; biotools:primaryContact "Charlotte Soneson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3297, edam:topic_3512 ; sc:citation ; sc:description "iCodon is a tool for ideal codon design for customized gene expression." ; sc:featureList edam:operation_0314, edam:operation_0441, edam:operation_3095 ; sc:name "iCodon" ; sc:url "https://bazzinilab.shinyapps.io/icodon/" ; biotools:primaryContact "Ariel Alejandro Bazzini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0769, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:36073898" ; sc:description "The Icolos tool is a workflow manager for structure-based workflows in computational chemistry, that abstracts execution logic from implementation as much as possible." ; sc:featureList edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Icolos" ; sc:softwareHelp ; sc:url "https://github.com/MolecularAI/Icolos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2640, edam:topic_3170, edam:topic_3676 ; sc:citation ; sc:description "iCOMIC is an open source genomic data analysis tool characterized by a user friendly GUI. It integrates many independent core workflows for Whole Genome/Exome Sequencing and RNA-Seq data analysis along with Machine Learning tools, cTaG and NBDriver for cancer related data analysis." ; sc:featureList edam:operation_3223, edam:operation_3227, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "iCOMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RamanLab/iCOMIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3071, edam:topic_3169 ; sc:citation "pubmed:25881165" ; sc:description "Allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool)." ; sc:featureList edam:operation_0335 ; sc:name "iConvert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.tecnoparco.org/SNPchimp/index.php/links" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:20562415" ; sc:description "Iteratively align deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy." ; sc:featureList edam:operation_0310, edam:operation_3218 ; sc:name "ICORN" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "1", "2" ; sc:url "http://icorn.sourceforge.net/" ; biotools:primaryContact "T. D. Otto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0176, edam:topic_3382 ; sc:citation , "pubmed:34652149" ; sc:description "A Python package to calculate, visualize and analyze correlation maps of proteins." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "icorrelationplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tekpinar/correlationplus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3174 ; sc:citation , "pmcid:PMC5414344", "pubmed:28464793" ; sc:description "The Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins." ; sc:featureList edam:operation_3744 ; sc:name "ICoVeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://git.list.lu/eScience/ICoVeR" ; biotools:primaryContact "Magdalena Calusinska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3360, edam:topic_3517 ; sc:citation , "pmcid:PMC8127495", "pubmed:34001247" ; sc:description "iCPAGdb is an atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility." ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3791 ; sc:name "iCPAGdb" ; sc:url "http://cpag.oit.duke.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3651 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:23454610" ; sc:description "Tool for processing and analyzing ICPL LC-MS/MS (ESI) data." ; sc:featureList edam:operation_3203, edam:operation_3215, edam:operation_3629, edam:operation_3630, edam:operation_3631, edam:operation_3635, edam:operation_3636, edam:operation_3705 ; sc:name "ICPL_ESIQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.biochem.mpg.de/en/rg/lottspeich/technologies/ICPLQuant" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3468 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:19953540" ; sc:description "Tool for processing and analyzing ICPL LC-MALDI data." ; sc:featureList edam:operation_2421, edam:operation_3203, edam:operation_3629, edam:operation_3630, edam:operation_3635, edam:operation_3649, edam:operation_3705, edam:operation_3767, edam:operation_3799 ; sc:name "ICPLQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.biochem.mpg.de/en/rg/lottspeich/technologies/ICPLQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15215402", "pubmed:16845075" ; sc:description "Predict regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. It reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes." ; sc:featureList edam:operation_0438, edam:operation_0441, edam:operation_0445, edam:operation_2575 ; sc:name "iCR" ; sc:url "http://210.212.215.199/icr/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_0769, edam:topic_3452 ; sc:citation , "pmcid:PMC7291075", "pubmed:32566137" ; sc:description """Generating interoperable electronic case report forms using online codebooks. Semantic interoperability of clinical data requires the use of a common vocabulary, such as SNOMED-CT. Unfortunately, mapping data to such a terminology is time-consuming and requires expert knowledge of both the dataset and the terminology. A viable alternative can be the reuse of codebooks - published dataset definitions which, in some cases, have already been mapped to a terminology. We designed the iCRF Generator, a tool which makes it easy to generate interoperable electronic Case Report Forms for (currently) three major EDCs: OpenClinica 3, Castor and REDCap. The tool currently provides access to several codebooks stored online in Art-Decor, such as:.""" ; sc:featureList edam:operation_1812, edam:operation_3096, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "iCRF Generator" ; sc:url "https://github.com/aderidder/iCRFGenerator/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:34905767" ; sc:description "An integrative analysis of CRISPR screen by reducing false positive hits." ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "iCRISEE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.icrisee.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3304, edam:topic_3444 ; sc:citation , "pmcid:PMC7200822", "pubmed:32371990" ; sc:description """Iterative consensus spectral clustering improves detection of subject and group level brain functional modules. Iterative consensus spectral clustering for brain functional modules. The code repo for the iterative consensus spectral clustering that performs detection of subject and group level brain functional modules. We obtained the following group level modularizations for normal healthy samples:. The proposed algorithm can also be used to obtain subject-level modules from multiple scans (of the same subject). For more details refer to the paper.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3927 ; sc:name "ICSC" ; sc:url "https://github.com/SCSE-Biomedical-Computing-Group/ICSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3173, edam:topic_3303, edam:topic_3395 ; sc:citation , ; sc:description """Data portal for standardized stem cell information. ICSCB is operated by CiRA,Kyoto University. It is an Intergerated Collection of Stem Cell Bank data by miacarm, standard data format for all the stem cell lines with minimum necessary information for research in regenerative medicine. Searching fields (16641 cell lines). All SKIP ( 5615 ) RIKEN BRC ( 4111 ) eagle-i ( 3548 ) hPSCreg ( 3367 ).""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3435 ; sc:name "ICSCB" ; sc:url "http://icscb.stemcellinformatics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125 ; sc:citation "pubmed:16362906" ; sc:description "Identify conserved structural features at sequentially degenerate locations in transcription factor binding sites. ICSF uses base-pair step parameters obtained from a collection of high-resolution DNA crystal structures to discover structural conservation that exists in the sequentially degenerate areas within a binding site and produce profiles of the structural features along the entire site." ; sc:featureList edam:operation_0415 ; sc:name "ICSF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zlab.bu.edu/ICSF/" ; biotools:primaryContact "Zhiping Weng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2885, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:21622953" ; sc:description "ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functional SNP annotation and pathway based analysis to identify these SNPs and pathways." ; sc:featureList edam:operation_0283, edam:operation_0484, edam:operation_0488, edam:operation_2497, edam:operation_3661 ; sc:name "ICSNPathway" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://icsnpathway.psych.ac.cn/" ; biotools:primaryContact "ICSNPathway Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3303 ; sc:citation , "pubmed:32950852" ; sc:description """An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors. Identifying the ion channel-targeted conotoxins using reduced amino acid alphabet composition. Conotoxins are small peptide toxins which are rich in disulfide and have the unique diversity of sequences.""" ; sc:featureList edam:operation_3432, edam:operation_3936, edam:operation_3937 ; sc:name "ICTC-RAAC" ; sc:url "http://bioinfor.imu.edu.cn/ictcraac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602 ; sc:citation , "pmcid:PMC4706053", "pubmed:26834985" ; sc:description "Integrated Complex Traits Networks. Database that allows researchers to build heterogeneous networks by integrating a variety of biological interactions, thus offering a systems-level view of human complex traits." ; sc:featureList edam:operation_2409, edam:operation_3216, edam:operation_3501 ; sc:license "MIT" ; sc:name "iCTNet2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://apps.cytoscape.org/apps/ictnet2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0781 ; sc:citation , , "pmcid:PMC10227694", "pubmed:37141106" ; sc:description "Committee for developing, refining, and maintaining a universal virus taxonomy. The goal is to categorize the multitude of known viruses into a single classification scheme that reflects their evolutionary relationships, i.e. their individual phylogenies." ; sc:featureList edam:operation_2421, edam:operation_3460 ; sc:name "ICTV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "rki.de" ; sc:softwareHelp ; sc:url "http://www.ictvonline.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation ; sc:description "Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs." ; sc:featureList edam:operation_3435 ; sc:name "ICV" ; sc:url "https://icvmapp3r.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3382 ; sc:description "Icy provides the software resources to visualize, annotate and quantify bioimaging data." ; sc:featureList edam:operation_3443 ; sc:name "Icy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.1.1" ; sc:url "http://www.icy.bioimageanalysis.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3336, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:34672553" ; sc:description "Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding." ; sc:featureList edam:operation_0440, edam:operation_2238, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iCYP-MFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://103.130.219.193:5002" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3293 ; sc:citation ; sc:description "Rapid browser-based visualization for phylogenetic trees and networks." ; sc:featureList edam:operation_0567, edam:operation_3083 ; sc:name "IcyTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://icytree.org/" ; biotools:primaryContact "Timothy G. Vaughan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3475 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3620 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3620 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Aligns metabolite data from multiple files to single spreadsheet." ; sc:featureList edam:operation_3628 ; sc:name "ID-Align" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ce4csb.org/applications/idalign/idalign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0154, edam:topic_0637, edam:topic_0821 ; sc:citation , "pubmed:32031718" ; sc:description """Metastable decomposition at the peptide C-terminus. "iD-plus" MS-based search engine for protein identification. Copyright© 2017-2020,IPR Osaka Univ.""" ; sc:featureList edam:operation_2929, edam:operation_3644, edam:operation_3646, edam:operation_3767 ; sc:name "iD-plus" ; sc:url "http://coco.protein.osaka-u.ac.jp/id-plus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0610, edam:topic_0637, edam:topic_0659, edam:topic_3168 ; sc:citation ; sc:description """Integration of ecological responses to a soil bacterial 16S rRNA gene database. Abstract High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalising syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterise taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from the survey metadata.""" ; sc:featureList edam:operation_0224, edam:operation_3200, edam:operation_3659 ; sc:name "ID-TaxER" ; sc:url "https://shiny-apps.ceh.ac.uk/ID-TaxER/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3345 ; sc:citation ; sc:description "Convert a set of Ensembl IDs from a previous release into their current equivalents." ; sc:featureList edam:operation_3282 ; sc:name "ID History converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "Sanger Institute" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ensembl.org/Homo_sapiens/UserData/UploadStableIDs" ; biotools:primaryContact "Andrew Yates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC8245499", "pubmed:34193950" ; sc:description "Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties." ; sc:featureList edam:operation_0267, edam:operation_0418, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDACP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mer.hc.mmh.org.tw/iDACP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3174, edam:topic_3315, edam:topic_3360, edam:topic_3941 ; sc:citation ; sc:description "IDAM provides a framework for the identification of microbial disease-associated biomarkers based on metagenomic and metatranscriptomic data. The raw sequencing data (matched metagenomic and metatranscriptomic data) or the expression matrix is required. The output is gene modules consisting of gene and sample subsets." ; sc:featureList edam:operation_0323, edam:operation_2495, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IDAM" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/OSU-BMBL/IDAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "IDBA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://i.cs.hku.hk/%7Ealse/idba" ; biotools:primaryContact "Yu Peng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:name "Sequence accession (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation , "pubmed:17004234" ; sc:description "Locus-specific databases for immunodeficiency-causing mutations." ; sc:featureList edam:operation_0224 ; sc:name "Immunodeficiency mutation databases (IDbases)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://structure.bmc.lu.se/idbase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_1317, edam:topic_3125 ; sc:citation ; sc:description "A server for the identification of DNA binding proteins." ; sc:featureList edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "iDBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://idbps.tau.ac.il/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0204 ; sc:citation , "pubmed:32144887" ; sc:description """Sequence-based Detection of DNA-binding Proteins using Multiple-view Features Allied with Feature Selection. DNA-binding proteins play essential roles in many molecular functions and gene regulation. Therefore, it becomes highly desirable to develop effective computational techniques for detecting DNA-binding proteins. In this paper, we proposed a new method, iDBP-DEP, which performs DNA-binding prediction by using the discriminative feature derived from multi-view feature sources including evolutionary profile, dipeptide composition, and physicochemical properties with feature selection. We evaluated iDBP-DEP on two benchmark datasets, i. e., PDB1075 and PDB594 by rigorous Jackknife test. Compared with the state-of-the-art sequence-based DNA-binding predictors, the proposed iDBP-DEP achieved 1.8 % and 3.0 % improvements of accuracy (Acc) and Mathew's Correlation Coefficient (MCC), respectively, on PDB1075 dataset; 7.4 % and 14.8 % improvements of Acc and MCC, respectively, on PDB594""" ; sc:featureList edam:operation_3900, edam:operation_3901, edam:operation_3903 ; sc:name "iDBP-DEP" ; sc:url "https://github.com/Zll-codeside/iDBP-DEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0654, edam:topic_2814, edam:topic_3125 ; sc:citation "pubmed:20089514" ; sc:description "This tool was developed for the identification of DNA binding proteins (DBPs) for proteins with known three-dimensional structure" ; sc:featureList edam:operation_0420 ; sc:name "iDBPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://idbps.tau.ac.il/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_3299 ; sc:citation , "pmcid:PMC8710592", "pubmed:34966754" ; sc:description "An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution." ; sc:featureList edam:operation_3208, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "IDbSV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://IDbSV.medbiotech-lab.ma" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1857 ; sc:encodingFormat edam:format_2035 ; sc:name "Atomic occupancy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2571 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Isotope distribution and theoretical spectrum calculation with GUI." ; sc:featureList edam:operation_2238, edam:operation_3441, edam:operation_3632 ; sc:name "IDCalc" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://proteome.gs.washington.edu/software/IDCalc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247, edam:format_3655, edam:format_3747 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247, edam:format_3655 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "A converter between pepXML and mzIdentML formats for peptide identifications from tandem mass spectrometry. Developed by the ProteoWizard team." ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "idconvert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "lumc.nl" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://proteowizard.sourceforge.net/tools/idconvert.html" ; biotools:primaryContact "SourceForge team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3316 ; sc:citation ; sc:description """A pipeline for quick clade identification of SARS-CoV-2 isolates. idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud.""" ; sc:featureList edam:operation_3198 ; sc:name "idCOV" ; sc:softwareHelp ; sc:url "https://github.com/xz-stjude/idcov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3420 ; sc:citation , "pubmed:32941628" ; sc:description """A comprehensive resource featuring genes, variants and characteristics associated with infertility. Infertility Disease DataBase (IDDB) provides a versatile resource for genes, experiments and clinical records related with the infertility diseases, data in IDDB is annually updated and freely served for biologists and doctors interested in reproduction and infertility.""" ; sc:featureList edam:operation_0533, edam:operation_2422, edam:operation_2436 ; sc:name "IDDB" ; sc:url "http://mdl.shsmu.edu.cn/IDDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3047, edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:33657650" ; sc:description "IDDRRA is a software that allows the user to design and model a DNA molecule, irradiate it with various types of radiation included in the Geant4 physics models, and then analyze the simulation outcome in terms of Single Strand Breaks (SSB), Double Strand Breaks (DSB), Cluster Damage Sites (CDS) and energy deposition. IDDRRA, combines powerful tools in a single platform, providing the ability to quantify DNA damage and DNA damage repair using MC forecast algorithms." ; sc:featureList edam:operation_2476, edam:operation_3431, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "IDDRRA" ; sc:url "https://3dmi.upatras.gr/IDDRRA" ; biotools:primaryContact "George C. Kagadis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC8557387", "pubmed:34729472" ; sc:description "A decision tree-based method for the refinement of variants in FFPE DNA sequencing data." ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Ideafix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mmaitenat/ideafix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601, edam:topic_0736, edam:topic_3534, edam:topic_3538 ; sc:citation "pubmed:22067451" ; sc:description "Collection of experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). Manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites." ; sc:featureList edam:operation_0417, edam:operation_0470, edam:operation_3092, edam:operation_3778 ; sc:name "IDEAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/" ; biotools:primaryContact "Satoshi Fukuchi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:description "This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ideal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ideal.html" ; biotools:primaryContact "Federico Marini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:description "This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ideal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ideal.html" ; biotools:primaryContact "Federico Marini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC8784862", "pubmed:35073995" ; sc:description "IDEAS (Individual level Differential Expression Analysis for Single cells) an R package for differential expression analysis using single cell RNA-seq data of multiple individuals." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IDEAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Sun-lab/ideas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:34297803" ; sc:description "Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network." ; sc:featureList edam:operation_0278, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDeepC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hehew321/iDeepC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3474 ; sc:citation , "pubmed:32808039" ; sc:description """RNA-binding protein recognition based on multi-view deep feature and multi-label learning. RNA-binding protein (RBP) is a class of proteins that bind to and accompany RNAs in regulating biological processes. An RBP may have multiple target RNAs, and its aberrant expression can cause multiple diseases. Methods have been designed to predict whether a specific RBP can bind to an RNA and the position of the binding site using binary classification model. However, most of the existing methods do not take into account the binding similarity and correlation between different RBPs. While methods employing multiple labels and Long Short Term Memory Network (LSTM) are proposed to consider binding similarity between different RBPs, the accuracy remains low due to insufficient feature learning and multi-label learning on RNA sequences""" ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_3901, edam:operation_3902, edam:operation_3937 ; sc:name "iDeepMV" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/iDeepMV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:34337657" ; sc:description "identification of protein submitochondrial localization with deep learning." ; sc:featureList edam:operation_0267, edam:operation_2489, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDeepSubMito" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/houzl3416/iDeepSubMito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3168, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC10483029", "pubmed:37589603" ; sc:description "Deep learning interactive tool for alignment-free clustering of DNA sequences." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iDeLUCS" ; sc:url "https://github.com/Kari-Genomics-Lab/iDeLUCS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3071 ; sc:citation , "pubmed:35679537" ; sc:description "Aa ranking framework for miRNA-disease association identification." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "idenMD-NRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bliulab.net/idenMD-NRF/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3361, edam:topic_3678 ; sc:citation , "pmcid:PMC7355299", "pubmed:32657359" ; sc:description """Identifiability and experimental design in perturbation studies. Interaction strengths between nodes in directed networks can be quantified from observations of the network's response to perturbations. This package reveals the identifiability of the inferred network parameters and optimizes experimental design for network perturbation studies. See our publication for details. You can install the IdentiFlow package with pip:.""" ; sc:featureList edam:operation_0337, edam:operation_3927 ; sc:license "MIT" ; sc:name "IdentiFlow" ; sc:url "http://github.com/GrossTor/IdentiFlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3361, edam:topic_3678 ; sc:citation ; sc:description """Identifiability and experimental design in perturbation studies. Interaction strengths between nodes in directed networks can be quantified from observations of the network's response to perturbations. This package reveals the identifiability of the inferred network parameters and optimizes experimental design for network perturbation studies. See our publication for details. You can install the IdentiFlow package with pip:. The package is easy to use and we demonstrate its most relevant features in the example below. You find the example script in identiflow/examples. This folder also contains the scripts that were used to analyse the KEGG pathways, as described in our paper.""" ; sc:featureList edam:operation_0337, edam:operation_3927 ; sc:license "MIT" ; sc:name "IdentiFlow-P" ; sc:url "http://github.com/GrossTor/IdentiFlow" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0780, edam:topic_2229, edam:topic_3293 ; sc:citation , "pmcid:PMC8351581", "pubmed:34434652" ; sc:description "IdentPMP is a web application that predict plant moonlighting protein." ; sc:featureList edam:operation_3092, edam:operation_3767, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IdentPMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://identpmp.aielab.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622 ; sc:citation ; sc:description "Plots data associated with arbitrary genomic intervals along chromosomal ideogram." ; sc:featureList edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "IdeoViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IdeoViz.html" ; biotools:primaryContact "Shraddha Pai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_0781, edam:topic_3297 ; sc:citation , "pmcid:PMC4177671", "pubmed:25254639" ; sc:description "Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform." ; sc:featureList edam:operation_0416 ; sc:license "GPL-3.0" ; sc:name "IDEPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/veg/idepi" ; biotools:primaryContact "Sergei L. Kosakovsky Pond" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation , "pmcid:PMC10463720", "pubmed:37608264" ; sc:description "The goal of iDESC is to identify differential expressed gene signatures between two groups in single cell RNA-seq considering subject effect with zero-inflated negative binomial mixed model." ; sc:featureList edam:operation_3197, edam:operation_3223, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "iDESC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yl883/iDESC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3315 ; sc:citation , "pubmed:33295914" ; sc:description """identifying DNase I hypersensitive sites based on LASSO and stacking learning. Enter the query DNA sequences in FASTA format (Example):.""" ; sc:featureList edam:operation_0224, edam:operation_3937 ; sc:name "iDHS-DASTS" ; sc:url "http://www.xdu-duan.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0821, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:33751027" ; sc:description "iDHS-Deep is an integrated tool for predicting DNase I hypersensitive sites by deep neural network." ; sc:featureList edam:operation_0327, edam:operation_0438, edam:operation_3222 ; sc:name "iDHS-Deep" ; sc:url "http://lin-group.cn/server/iDHS-Deep/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3756 ; sc:name "Localisation score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0621, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC10064468", "pubmed:37009307" ; sc:description "Identification of dihydrouridine sites through ensemble learning models." ; sc:featureList edam:operation_0417, edam:operation_0464, edam:operation_3935 ; sc:name "iDHU-Ensem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://taseersuleman-idhu-ensem-idhu-ensem.streamlit.app/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC10077956", "pubmed:37034305" ; sc:description "An integrative signal extractor for data-independent acquisition proteomics." ; sc:featureList edam:operation_3646, edam:operation_3695, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IDIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Biocomputing-Research-Group/IDIA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3442 ; sc:name "MRI image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC10089090", "pubmed:36807461" ; sc:description "A pipeline for automated configuration and processing of diffusion MRI data. iDIO is a software toolkit for processing diffusion-weighted MRI data. It integrates the functionalities of modern MRI software packages to constitute a complete data processing pipeline for structural connectivity analysis of the human brain." ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "iDIO" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/iDIO4dMRI/iDIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0622 ; sc:citation ; sc:description "A package for plotting genomic data by chromosomal location." ; sc:featureList edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "idiogram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/idiogram.html" ; biotools:primaryContact "Karl J. Dykema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654, edam:topic_2815, edam:topic_3500 ; sc:citation "pubmed:17893084" ; sc:description "Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface." ; sc:featureList edam:operation_0337, edam:operation_0573, edam:operation_2429 ; sc:name "Idiographica" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rtools.cbrc.jp/idiographica/" ; biotools:primaryContact "Kin T." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2259, edam:topic_3315, edam:topic_3697 ; sc:citation , "pmcid:PMC8764688", "pubmed:34992138" ; sc:description "iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3629, edam:operation_3925, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "iDIRECT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nxiao6gt/iDIRECT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9580925", "pubmed:36304260" ; sc:description "An Integrated Application for Differential Splicing Analysis and Visualization." ; sc:featureList edam:operation_0264, edam:operation_3223, edam:operation_3463, edam:operation_3766, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iDJExpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MauerLab/DJExpress" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071 ; sc:citation ; sc:description "Identifier mapping performance analysis." ; sc:featureList edam:operation_3282 ; sc:license "GPL-2.0" ; sc:name "IdMappingAnalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IdMappingAnalysis.html" ; biotools:primaryContact "Alex Lisovich", "Roger Day" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3070 ; sc:citation ; sc:description "Data retrieval for identifier mapping performance analysis." ; sc:featureList edam:operation_2422, edam:operation_3282 ; sc:license "GPL-2.0" ; sc:name "IdMappingRetrieval" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IdMappingRetrieval.html" ; biotools:primaryContact "Alex Lisovich", "Roger Day" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3344, edam:topic_3517, edam:topic_3574 ; sc:citation , "pmcid:PMC10387571", "pubmed:37529100" ; sc:description "Federated generalized linear mixed models for collaborative genome-wide association studies." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "idMEGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Li-Wentao/dMEGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0593, edam:topic_2640, edam:topic_3172 ; sc:citation , "pmcid:PMC9706903", "pubmed:36443658" ; sc:description "Network-based approach for integrating differential analysis of cancer metabolomics." ; sc:featureList edam:operation_0314, edam:operation_3802, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDMET" ; sc:url "https://github.com/riramatsuta/iDMET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3577, edam:topic_3697, edam:topic_3810 ; sc:citation , "pmcid:PMC7355246", "pubmed:32657370" ; sc:description "An alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "IDMIL" ; sc:url "https://github.com/mrahma23/IDMIL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC7019181", "pubmed:32117926" ; sc:description """Gene-Focused Networks Underlying Phenotypic Convergence in a Systematically Phenotyped Cohort With Heterogeneous Intellectual Disability. The broad spectrum of intellectual disability (ID) patients' clinical manifestations, the heterogeneity of ID genetic variation, and the diversity of the phenotypic variation represent major challenges for ID diagnosis. By exploiting a manually curated systematic phenotyping cohort of 3803 patients harboring ID, we identified 704 pathogenic genes, 3848 pathogenic sites, and 2075 standard phenotypes for underlying molecular perturbations and their phenotypic impact. We found the positive correlation between the number of phenotypes and that of patients that revealed their extreme heterogeneities, and the relative contribution of multiple determinants to the heterogeneity of ID phenotypes""" ; sc:featureList edam:operation_2454, edam:operation_3461, edam:operation_3463 ; sc:name "IDminer" ; sc:url "http://218.4.234.74:3100/IDminer/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0654, edam:topic_3169, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC9575223", "pubmed:36253864" ; sc:description "Multi-scale deep biological language learning model for the interpretable prediction of DNA methylations." ; sc:featureList edam:operation_0417, edam:operation_3206, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDNA-ABF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://inner.wei-group.net/idnaabf/#/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:34601568" ; sc:description "A generic webserver for predicting DNA methylation sites" ; sc:featureList edam:operation_0308, edam:operation_0417, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iDNA-ABT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://server.wei-group.net/iDNA_ABT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3295, edam:topic_3572 ; sc:citation "pubmed:25596338" ; sc:description "This web-server is according to its genetic codes by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample. And by means of the approach of optimizing training datasets for predicting DNA methylation sites. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed their counterparts in the existing prediction methods." ; sc:featureList edam:operation_3204 ; sc:name "iDNA-Methyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iDNA-Methyl" ; biotools:primaryContact "Xuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3295, edam:topic_3511 ; sc:citation ; sc:description "Identifying DNA 4-methylcytosine sites." ; sc:featureList edam:operation_0415 ; sc:name "iDNA4mC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/iDNA4mC" ; biotools:primaryContact "Hao Lin", "Wei Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:34291710" ; sc:description "iDNA6mA-Rice-DL is a local web server for identifying DNA N6-methyladenine sites in rice genome by deep learning method. Accurate detection of N6-methyladenine (6mA) sites by biochemical experiments will help to reveal their biological functions, still, these wet experiments are laborious and expensive. Therefore, it is necessary to introduce a powerful computational model to identify the 6mA sites on a genomic scale, especially for plant genomes. In view of this, we proposed a model called iDNA6mA-Rice-DL for the effective identification of 6mA sites in rice genome, which is an intelligent computing model based on deep learning method. Traditional machine learning methods assume the preparation of the features for analysis. However, our proposed model automatically encodes and extracts key DNA features through an embedded layer and several groups of dense layers." ; sc:name "iDNA6mA-Rice-DL" ; sc:url "https://hub.docker.com/r/his1server/idna6ma-rice-dl" ; biotools:primaryContact , "Liang Kong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0160, edam:topic_0623, edam:topic_3293, edam:topic_3810 ; sc:citation , "pmcid:PMC8279765", "pubmed:34276598" ; sc:description "\"IDOPS IDentification of Pesticidal Proteins\", a profile HMM-based tool to detect pesticidal sequences and compare their genetic context" ; sc:featureList edam:operation_0479, edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IDOPS" ; sc:operatingSystem "Linux" ; sc:url "https://anaconda.org/GAMB-GO/idops" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0218, edam:topic_3474, edam:topic_3538 ; sc:citation , "pubmed:32702119" ; sc:description """Identification of Intrinsically Disordered Regions based on Sequence to Sequence Learning. Identification of Intrinsically Disordered Proteins and Regions. based on Sequence to Sequence Learning. The datasets used in this study can be downloaded from below links:.""" ; sc:featureList edam:operation_0272, edam:operation_0470, edam:operation_3904 ; sc:name "IDP-Seq2Seq" ; sc:url "http://bliulab.net/IDP-Seq2Seq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_3474, edam:topic_3538, edam:topic_3542 ; sc:citation , "pmcid:PMC9465686", "pubmed:36030416" ; sc:description "A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States." ; sc:featureList edam:operation_0470, edam:operation_2476, edam:operation_2488, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "IDPConformerGenerator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/julie-forman-kay-lab/IDPConformerGenerator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0601, edam:topic_3407 ; sc:citation ; sc:description """Characterization and Identification of Lysine Phosphoglycerylation Sites Based on Sequence-Based Features. iDPGK is a web server for identifying phosphoglycerylation sites. Protein phosphoglycerylation is the reaction in which a 1,3-bisphosphoglyceric acid (1,3-BPG) is attached to a lysine residue of a protein molecule, and thus to form a 3-phosphoglyceryl-lysine (pgK). Phosphoglycerylation is a reversible and non-enzymatic post-translational modification (PTM). It has been shown that the process of lysine phosphoglycerylation plays important regulatory roles in glucose metabolism and glycolytic process. However, studies in this field have been limited by the difficulty of experimentally identifying modified site specificity in lysine phosphoglycerylation (PGK). To facilitate this process, several tools have been proposed for the computational identification of PGK sites.""" ; sc:featureList edam:operation_0321, edam:operation_0417, edam:operation_3755 ; sc:name "iDPGK" ; sc:url "http://mer.hc.mmh.org.tw/iDPGK/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_3538 ; sc:citation , , , "pubmed:27899601", "pubmed:31713636", "pubmed:34850135" ; sc:description "Ontology used to describe disordered regions in intrinsically disordered proteins." ; sc:featureList edam:operation_3092 ; sc:license "CC-BY-4.0" ; sc:name "IDP ontology" ; sc:provider "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp ; sc:url "https://disprot.org/ontology" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:32897718" ; sc:description "A Sequence-Based Predictor for Identifying and Analyzing Dipeptidyl Peptidase IV (DPP-IV) Inhibitory Peptides Using a Scoring Card Method." ; sc:featureList edam:operation_0407, edam:operation_0418, edam:operation_3631 ; sc:name "iDPPIV-SCM" ; sc:url "http://camt.pythonanywhere.com/iDPPIV-SCM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0154, edam:topic_0736, edam:topic_3538 ; sc:citation , "pmcid:PMC9015136", "pubmed:35436286" ; sc:description "A package for profiling and analyzing Intrinsically Disordered Proteins in R." ; sc:featureList edam:operation_0470, edam:operation_0474, edam:operation_2574, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "idpr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/idpr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3300, edam:topic_3407, edam:topic_3534, edam:topic_3538 ; sc:citation , "pmcid:PMC9327236", "pubmed:35883018" ; sc:description "A repository of binding sites for intrinsically disordered proteins complexes with known 3D structures." ; sc:featureList edam:operation_0470, edam:operation_2464, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "IDPsBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.s-bioinformatics.cn/idpsbind/home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility." ; sc:featureList edam:operation_2238, edam:operation_3463 ; sc:name "IDR" ; sc:url "https://github.com/nboley/idr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0654, edam:topic_3169 ; sc:citation , "pmcid:PMC7102997", "pubmed:32009147" ; sc:description """IDR2D identifies reproducible genomic interactions. Chromatin interaction data from protocols such as ChIA-PET, HiChIP and Hi-C provide valuable insights into genome organization and gene regulation, but can include spurious interactions that do not reflect underlying genome biology. We introduce an extension of the Irreproducible Discovery Rate (IDR) method called IDR2D that identifies replicable interactions shared by chromatin interaction experiments. IDR2D provides a principled set of interactions and eliminates artifacts from single experiments. The method is available as a Bioconductor package for the R community, as well as an online service at https: idr2d.mit.edu""" ; sc:featureList edam:operation_3222 ; sc:name "IDR2D" ; sc:url "https://idr2d.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0654, edam:topic_3474 ; sc:citation , "pubmed:36044786" ; sc:description "Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework." ; sc:featureList edam:operation_3900, edam:operation_3901, edam:operation_3902 ; sc:license "Other" ; sc:name "iDRBP-ECHF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/iDRBP-ECHF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_3474 ; sc:citation , "pubmed:34932484" ; sc:description "Identifying DNA- and RNA- binding proteins based on hierarchical ensemble learning." ; sc:featureList edam:operation_0420, edam:operation_3900, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "iDRBP-EL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/iDRBP-EL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0203, edam:topic_3125 ; sc:citation , "pubmed:33780341" ; sc:description "IDRBP-PPCT is a web application for identifying nucleic acid-binding proteins based on position-specific score matrix and position-specific frequency matrix cross transformation." ; sc:featureList edam:operation_0420, edam:operation_3900, edam:operation_3901 ; sc:name "IDRBP-PPCT" ; sc:url "http://bliulab.net/IDRBP-PPCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_3474 ; sc:citation , "pubmed:32920048" ; sc:description """Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network. A new sequence-based computational predictor for identifying DNA-binding proteins and RNA-binding proteins. In which, multi-label learning and a novel motif-based convolution neural network were employed. It reduced the cross prediction between DNA-binding proteins and RNA-binding proteins and improved the predictive perfermance for identification of DNA-binding proteins and RNA-binding proteins. It is a useful tool for nucleic acid binding protein prediction. The framework and working process of iDRBP_MMC are shown in Fig.1.""" ; sc:featureList edam:operation_0420, edam:operation_3900, edam:operation_3901 ; sc:name "iDRBP_MMC" ; sc:url "http://bliulab.net/iDRBP_MMC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3033 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_3326 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3033, edam:format_3475 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3033, edam:format_3617 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_1775, edam:topic_3473 ; sc:citation ; sc:description "An interactive version of DREM software, which enables to integrate static protein-DNA interaction data with different types of time series data for reconstructing dynamic regulatory networks. It also allows users to interactively visualize a gene, TF, path or model-centric view of each of these data types, their interactions and their impact on the resulting model." ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3664, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iDREM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/phoenixding/idrem" ; biotools:primaryContact "Jun Ding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC7755418", "pubmed:32756939" ; sc:description """Predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions. IDRMutPred is a specific and accurate computational approach to prioritizing disease-associated nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions (IDR). IDRMutPred is specifically trained on the IDR nsSNVs, and is specifically utilized to the IDR nsSNVs. IDRMutPred outperforms other general-purpose predictors for the IDR nsSNVs. This web server will serve as a valuable tool in the research community that focuses on the study of nsSNVs, especially those located in intrinsic disordered regions (Go to Predictor).""" ; sc:featureList edam:operation_0484, edam:operation_3226, edam:operation_3904 ; sc:name "IDRMutPred" ; sc:url "http://www.wdspdb.com/IDRMutPred" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0154, edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:35709747" ; sc:description "Identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework." ; sc:featureList edam:operation_0321, edam:operation_3901, edam:operation_3902, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "iDRNA-ITF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/iDRNA-ITF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3125, edam:topic_3474 ; sc:citation , "pubmed:37405873" ; sc:description "Identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers." ; sc:featureList edam:operation_0420, edam:operation_3900, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "iDRPro-SC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/iDRPro-SC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0659, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC7384678", "pubmed:32667925" ; sc:description """Integration of drug repositioning and drug-target prediction via cross-network embedding. iDrug is a computational pipeline to jointly predict novel drug-disease and drug-target interactions based on a heterogeneous network. iDrug adpots cross-network embedding to learn lower dimensional feature spaces for drugs, targets, and diseases in the heterogeneous network. A paper describing the approach is currently under review. A link to the paper will be added once it is published.""" ; sc:featureList edam:operation_0303, edam:operation_3625, edam:operation_3938 ; sc:name "iDrug" ; sc:url "https://github.com/Case-esaC/iDrug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0820, edam:topic_0821, edam:topic_3336 ; sc:citation "pubmed:25513722" ; sc:description "By means of the approach of optimizing training datasets, this webserver was developed for predicting drug-target interaction. It contains four predictors: iDrug-GPCR, iDrug-Chl, iDrug-Ezy, and iDrug-NR, specialized for indentying the interactions of drug compounds with GPCRs (G protein-coupled receptors), ion channels, enzymes, and NR (nuclear receptors), respectively." ; sc:featureList edam:operation_2492 ; sc:name "iDrug-Target" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iDrug-Target/" ; biotools:primaryContact "Xuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3295, edam:topic_3422 ; sc:citation ; sc:description """Multi-layered network-based pathway activity inference using directed random walks. iDRW is an integrative pathway activity inference method using directed random walks on graph. It integrates multiple genomic profiles and transfroms them into a single pathway profile using a pathway-based integrated gene-gene graph.""" ; sc:featureList edam:operation_2495, edam:operation_3094, edam:operation_3925, edam:operation_3928 ; sc:name "iDRW" ; sc:url "https://github.com/sykim122/iDRW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3293, edam:topic_3324, edam:topic_3837 ; sc:citation ; sc:description """IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring. Infectious Disease Sequencing Platform. IDseq is a hypothesis-free global software platform that helps scientists identify pathogens in metagenomic sequencing data.""" ; sc:featureList edam:operation_0363, edam:operation_0524, edam:operation_3192, edam:operation_3198, edam:operation_3431 ; sc:license "MIT" ; sc:name "IDseq" ; sc:softwareHelp ; sc:url "https://idseq.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9177784", "pubmed:35579321" ; sc:description "IDSL.IPA Characterizes the Organic Chemical Space in Untargeted LC/HRMS Data Sets." ; sc:featureList edam:operation_3215, edam:operation_3628, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IDSL-IPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ipa.idsl.me" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3370, edam:topic_3520 ; sc:citation , "pubmed:37311059" ; sc:description "Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3628, edam:operation_3629, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IDSL CSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=IDSL.CSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC7430881", "pubmed:32736513" ; sc:description """an lncRNA functional similarity calculation model based on an improved disease semantic similarity method. BACKGROUND:It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting lncRNA functions and identifying potential lncRNA-disease associations. Nevertheless, among them, little effort has been attempted to measure lncRNA functional similarity, which is an essential part of association prediction models. RESULTS:In this study, we presented an lncRNA functional similarity calculation model, IDSSIM for short, based on an improved disease semantic similarity method, highlight of which is the introduction of information content contribution factor into the semantic value calculation to take into account both the hierarchical structures of disease directed acyclic graphs and the disease specificities""" ; sc:featureList edam:operation_3435 ; sc:name "IDSSIM" ; sc:url "https://github.com/CDMB-lab/IDSSIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0632, edam:topic_0654, edam:topic_0659 ; sc:citation "pubmed:18440976" ; sc:description "Suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures." ; sc:featureList edam:operation_0308, edam:operation_0502, edam:operation_0570, edam:operation_2419, edam:operation_2439 ; sc:name "IDT SciTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.idtdna.com/SciTools/SciTools.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3343 ; sc:citation "pubmed:22649057" ; sc:description "idTarget is a web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. idTarget screens against protein structures in PDB." ; sc:featureList edam:operation_0245, edam:operation_0321, edam:operation_0478, edam:operation_0482, edam:operation_2489 ; sc:name "idTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://idtarget.rcas.sinica.edu.tw" ; biotools:primaryContact "Jung-Hsin Lin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:36215051" ; sc:description "iDVIP is a web server for identifying Viral integrase inhibitory peptides (VINIPs)." ; sc:featureList edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "iDVIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mer.hc.mmh.org.tw/iDVIP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3376 ; sc:citation , "pmcid:PMC8176530", "pubmed:34141876" ; sc:description """An R package for generating analysis-ready data from electronic health records-diagnoses and procedures. The proposed open-source dxpr package is a software tool aimed at expediting an integrated analysis of electronic health records (EHRs). The dxpr package provides mechanisms to integrate, analyze, and visualize clinical data, including diagnosis and procedure records.""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "idxpr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DHLab-TSENG/dxpr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC9130477", "pubmed:35645963" ; sc:description "Deep Learning-Based Segmentation of the Inner Ear's Total Fluid Space." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "IE-Vnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pydsgz/IEVNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_2830, edam:topic_3930 ; sc:citation , "pubmed:36099422" ; sc:description "an atlas of HLA-presented immune epitopes derived from non-coding regions." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2422 ; sc:license "Other" ; sc:name "IEAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/IEAtlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2830, edam:topic_3489 ; sc:citation "pubmed:19906713" ; sc:description "The Immune Epitope Database provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes." ; sc:featureList edam:operation_0224, edam:operation_0252, edam:operation_0416, edam:operation_2429, edam:operation_3431 ; sc:name "The Immune Epitope Database (IEDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.immuneepitope.org/" ; biotools:primaryContact "IEDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0621, edam:topic_0804, edam:topic_2830 ; sc:citation "pubmed:21030437" ; sc:description "The 3D structural component of the Immune Epitope Database (IEDB). It catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB)." ; sc:featureList edam:operation_0224, edam:operation_0250, edam:operation_0360, edam:operation_0416 ; sc:name "IEDB-3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iedb.org" ; biotools:primaryContact "Julia Ponomarenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0102, edam:topic_2830 ; sc:citation "pubmed:18515843", "pubmed:22610854" ; sc:description "The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools. peptide:MHC-I binding and T-cell epitope tools have been added, mapping of discontinuous epitopes onto 3D structures was also added." ; sc:featureList edam:operation_0416, edam:operation_2429 ; sc:name "IEDB-AR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.immuneepitope.org" ; biotools:primaryContact "IEDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3324, edam:topic_3360, edam:topic_3400, edam:topic_3421 ; sc:citation , "pmcid:PMC6877653", "pubmed:31803189" ; sc:description """Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens. Free epitope database and prediction resource. Free resource for searching and exporting immune epitopes. Includes more than 95% of all published infectious disease, allergy, autoimmune, and transplant epitope data.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2421 ; sc:name "IEDB" ; sc:url "http://www.iedb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2269, edam:topic_3305, edam:topic_3324, edam:topic_3400 ; sc:citation ; sc:description """a common data model for global HIV cohort collaboration. IeDEA International epidemiology Databases to Evaluate AIDS. REDCap Data Dictionaries for IeDEA. IeDEA is an international research consortium established in 2006 by the National Institute of Allergy and Infectious Diseases to provide a rich resource for globally diverse HIV/AIDS data.""" ; sc:featureList edam:operation_3435, edam:operation_3436 ; sc:name "IeDEA" ; sc:url "https://www.iedea.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0160, edam:topic_0602, edam:topic_0749 ; sc:citation "pubmed:22638578" ; sc:description "iELM webserver predicts the function and positional interface for short linear motifs important in protein-protein interactions." ; sc:featureList edam:operation_0272, edam:operation_2464, edam:operation_2492, edam:operation_3439 ; sc:name "iELM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://i.elm.eu.org" ; biotools:primaryContact "Peter Jehl", "Robert J. Weatheritt", "Toby J. Gibson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC5777932", "pubmed:27915398" ; sc:description "Interactive electrode localization utility (ielu) is a software package that provides a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "ielu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/aestrivex/ielu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3303, edam:topic_3325, edam:topic_3360 ; sc:citation , , "pmcid:PMC5763153", "pmcid:PMC5959948", "pubmed:28726811", "pubmed:29340838" ; sc:description "Inborn Errors of Metabolism Knowledgebase (IEMbase) accepts an array of biochemical and clinical symptoms from a user and returns a ranked list of possible IEM disorders that match the input profile. In addition, the system can explain the rationale of its results, suggest possible tests that would assist in narrowing down the differential diagnosis, and provide access to its database of biochemical, molecular, and clinical information if more evidence is desired." ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:name "IEMbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://iembase.org/" ; biotools:primaryContact "Prof. Dr. Nenad Blau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3169, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9664816", "pubmed:36376800" ; sc:description "A prediction method based on deep learning is proposed to identify enhancers and enhancer strength, called iEnhancer-DCLA" ; sc:featureList edam:operation_0372, edam:operation_0445, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iEnhancer-DCLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WamesM/iEnhancer-DCLA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3315, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC10014624", "pubmed:36936423" ; sc:description "Predicting enhancers and their strength based on DenseNet and improved convolutional block attention module." ; sc:featureList edam:operation_0303, edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "iEnhancer-DCSV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/leirufeng/iEnhancer-DCSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:33481715" ; sc:description """A novel two-layer predictor for identifying enhancer by position specific of nucleotide composition. An enhancer is a short region of DNA with the ability to recruit transcription factors and their complexes, thus increasing the likelihood of the transcription possibility. Considering the importance of enhancers, the enhancer identification was popular in computational biology. In this paper, we propose a two-layer enhancer predictor, called iEnhancer-KL. Kullback-Leibler (KL) divergence is taken into consideration to improve feature extraction method PSTNP. Furthermore, LASSO is used to reduce the dimension of features to get better prediction performance. Finally, the selected features are tested on several machine learning models to find the best model with great performance""" ; sc:featureList edam:operation_3937 ; sc:name "iEnhancer-KL" ; sc:url "https://github.com/Not-so-middle/iEnhancer-KL.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:34364858" ; sc:description "iEnhancer-RD:Identification of enhancers and their strength using RKPK features and deep neural networks" ; sc:featureList edam:operation_0438 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iEnhancer-RD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YangHuan639/iEnhancer-RD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:33119044" ; sc:description """Interpretable sequence-based enhancers and their strength predictor. The program is developed for enhaner prediction, including five individual feature-based models: spectrum profile, mismatch profile, subsequence profile, PSSM and PseDNC, and ensemble learning model. Before the prediction, please make sure your computer has installed the software: the python package: repDNA and shap. repDNA (http://bioinformatics.hitsz.edu.cn/repDNA/).""" ; sc:featureList edam:operation_2495, edam:operation_3937 ; sc:name "iEnhancer-XG" ; sc:url "https://github.com/jimmyrate/ienhancer-xg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Calculate the isoelectric point of proteins." ; sc:featureList edam:operation_0403 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/iep.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3173, edam:topic_3474, edam:topic_3674 ; sc:citation , "pmcid:PMC9763632", "pubmed:36582444" ; sc:description "Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning." ; sc:featureList edam:operation_0417, edam:operation_3096, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iEpiCas-DL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sunlab.fun:3838/EpiCas-DL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3305, edam:topic_3325, edam:topic_3518 ; sc:citation , "pmcid:PMC10327521", "pubmed:37409354" ; sc:description """Robust outlier identification for DNA methylation data. The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iepimutacions" ; sc:url "https://bioconductor.org/packages/release/bioc/html/epimutacions.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0634, edam:topic_2640, edam:topic_3168 ; sc:citation , "pubmed:36322906" ; sc:description "A package used as a classifier for determining the origin of a mutation, specifically for samples that have been preserved using formalin-fixation paraffin-embedding (FFPE)." ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:license "Not licensed" ; sc:name "iexcerno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jdavilal/excerno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10220493", "pubmed:37250782" ; sc:description "Visualizing gene expression changes in time, space, and single cells." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iexpressyouRcell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LabTranslationalArchitectomics/expressyouRcell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3318, edam:topic_3542 ; sc:citation ; sc:description "ABC (Artificial Bee Colony) and IF-ABC (Internal Geedback Artificial Bee Colony) are algorithms for protein structure optimization using off-lattice model." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:name "ABC and IF-ABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "9.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50863-codes-of-abc-and-if-abc-algorithms-for-protein-structure-optimization-using-off-lattice-model" ; biotools:primaryContact "Li Bai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3168, edam:topic_3474, edam:topic_3512, edam:topic_3958 ; sc:citation ; sc:description "A novel isolation-forest-based package to detect copy number variations from various NGS datasets." ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ifCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SimCab-CHU/ifCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7861262", "pubmed:33733166" ; sc:description "IFeaLiD is an interactive visualization for feature localization in deep neural networks." ; sc:featureList edam:operation_0573, edam:operation_3925, edam:operation_3926 ; sc:license "GPL-3.0" ; sc:name "IFeaLiD" ; sc:url "https://ifealid.cebitec.uni-bielefeld.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_2814 ; sc:citation ; sc:description "Python Toolkit and Web Server for Calculating a Wide Range of Structural and Physicochemical Feature Descriptors from Protein and Peptide Sequences." ; sc:featureList edam:operation_0250 ; sc:name "iFeature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ifeature.erc.monash.edu/" ; biotools:primaryContact "Jiangning Song", "Zhen Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2258, edam:topic_3047, edam:topic_3512 ; sc:citation , "pmcid:PMC9252729", "pubmed:35524557" ; sc:description "iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3891, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iFeatureOmega" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ifeatureomega.erc.monash.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2585 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC8343166", "pubmed:34353886" ; sc:description """findCPcli is a command line python-tool for the computation of chokepoint reactions in genome-scale metabolic models. The main purpose of the tool is to compute chokepoints by taking into account both the topology and the dynamic information of the network. In addition to the computation of chokepoints, findCPcli can compute and remove dead-end metabolites, find essential reactions and update the flux bounds of the reactions according to the results of Flux Variability Analysis. findCPcli takes as input an SBML files of genome-scale models, and provides as output a spreadsheet file with the results of the chokepoint computation.""" ; sc:featureList edam:operation_3660, edam:operation_3929, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ifindCPcli" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/findCP/findCPcli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821 ; sc:citation , "pubmed:35861063" ; sc:description "An automated web tool for determining enzyme-kinetic parameters based on the high-curvature region of progress curves." ; sc:featureList edam:operation_0334 ; sc:isAccessibleForFree true ; sc:name "iFIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.i-fit.si" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9607125", "pubmed:36287122" ; sc:description "Flnc is software that can accurately identify full-length long noncoding RNAs (lncRNAs) from human RNA-seq data. lncRNAs are linear transcripts of more than 200 nucleotides that do not encode proteins." ; sc:featureList edam:operation_0440, edam:operation_3216, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iFlnc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CZhouLab/Flnc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This web server is developed for users working in the field of vaccine design. This server allows users to predict and design IFN-gamma inducing peptides. It have following three modules." ; sc:featureList edam:operation_2945 ; sc:name "ifnepitope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ifnepitope/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0176, edam:topic_0659 ; sc:citation "pubmed:25910700" ; sc:description "Web portal for interactive RNA folding simulations." ; sc:featureList edam:operation_2439 ; sc:name "iFoldRNA" ; sc:softwareHelp ; sc:url "http://troll.med.unc.edu/ifoldrna.v2/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:citation , "pmcid:PMC5167396", "pubmed:27992540" ; sc:description "Incorporating Find Occurrence of Regulatory Motifs." ; sc:featureList edam:operation_0239 ; sc:name "iFORM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wenjiegroup/iFORM" ; biotools:primaryContact "Wenjie Shu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622, edam:topic_2640, edam:topic_3175, edam:topic_3673 ; sc:citation , "pubmed:23661695" ; sc:description "Integrated fusion gene explorer." ; sc:featureList edam:operation_0570 ; sc:name "iFUSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ifuse.erasmusmc.nl/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Fast, free, and highly customizable genome browser for viewing and exploring big genomic datasets." ; sc:featureList edam:operation_3208 ; sc:name "IGB" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://bioviz.org/igb/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_2830, edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:23671333" ; sc:description "Web tool can be used to view the matches to germline V(D)J gene segments, details at rearrangement junctions, the delineation of Ig sub-regions as well as other commonly sought information. Ithas the capacity to analyze both nucleotide and protein sequences." ; sc:featureList edam:operation_0310, edam:operation_2479, edam:operation_3192, edam:operation_3197 ; sc:name "IgBLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/igblast/" ; biotools:primaryContact "Contacts" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640 ; sc:citation , "pmcid:PMC5237550", "pubmed:28088185" ; sc:contributor ; sc:description "This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "iGC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iGC.html" ; biotools:primaryContact "Liang-Bo Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_2885 ; sc:citation ; sc:description """high-performance search for large-scale genomic interval datasets. IGD: A high-performance search engine for large-scale genomic interval datasets. Databases of large-scale genome projects now contain thousands of genomic interval datasets. These data are a critical resource for understanding the function of DNA. However, our ability to examine and integrate interval data of this scale is limited. Here, we introduce the integrated genome database (IGD), a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory. IGD uses a novel linear binning method that allows us to scale analysis to billions of genomic regions.""" ; sc:featureList edam:operation_2421, edam:operation_3359, edam:operation_3436 ; sc:license "MIT" ; sc:name "IGD" ; sc:url "https://github.com/databio/IGD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:21037256" ; sc:description "Integrated and curated repository of mutation data on common genetic diseases afflicting the Indian populations. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers." ; sc:featureList edam:operation_0331, edam:operation_2421, edam:operation_3196, edam:operation_3202, edam:operation_3431 ; sc:name "IGDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.igdd.iicb.res.in" ; biotools:primaryContact "Kunal Ray" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation ; sc:description "Analyzes antibody repertoires and discovers new V genes from high-throughput sequencing reads. Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)." ; sc:featureList edam:operation_0314, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IgDiscover" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.6.0" ; sc:url "http://igdiscover.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0769, edam:topic_3050, edam:topic_3174 ; sc:citation , "pubmed:36912756" ; sc:description "An integrated genome decontamination pipeline for wild ciliated microeukaryotes." ; sc:featureList edam:operation_0525, edam:operation_3187, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iGDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GWang2022/iGDP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3407, edam:topic_3955 ; sc:citation ; sc:description "IgemRNA is an open access toolbox for transcriptome data statistical and biochemical network topology-based analysis. IgemRNA was developed in the MATLAB environment in order to take advantage of the up-to-date and most commonly distributed GSM modelling tool Cobra Toolbox 3.0 and spreadsheet file capabilities." ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3501, edam:operation_3695, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IgemRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BigDataInSilicoBiologyGroup/IgemRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3517 ; sc:citation ; sc:description "Statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies." ; sc:featureList edam:operation_3196 ; sc:name "IGES" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/daviddaigithub/IGESS" ; biotools:primaryContact "Can Yang", "Xiang Wan", "Zongben X" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3678 ; sc:citation ; sc:description "IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well." ; sc:featureList edam:operation_3196 ; sc:name "IGG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://statgenpro.psychiatry.hku.hk/limx/igg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pmcid:PMC8593043", "pubmed:34795698" ; sc:description "An implementation of scale functions for setting axis breaks of a 'gg' plot." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "iggbreak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=ggbreak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3053 ; sc:citation , "pubmed:32163125" ; sc:description """Differential gene usage in immune repertoires. Decoding the properties of immune repertoires is key in understanding the response of adaptive immunity to challenges such as viral infection. One important task in immune repertoire profiling is the detection of biases in Ig gene usage between biological conditions. IgGeneUsage is a computational tool for the analysis of differential gene usage in immune repertoires. It employs Bayesian hierarchical models to fit complex gene usage data from immune repertoire sequencing experiments and quantifies Ig gene usage biases as probabilities.""" ; sc:featureList edam:operation_0252, edam:operation_3223, edam:operation_3799 ; sc:name "IgGeneUsage" ; sc:url "https://bioconductor.org/packages/IgGeneUsage/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2830, edam:topic_3168 ; sc:description "The Immunoglobulin Intraclonal Diversification Analysis tool (IgIDivA) offers the opportunity for an in-depth analysis of high-throughput sequencing data, with the scope of studying the intraclona diversification process through the identification of the somatic hypermutations that take place within the IGV gene region, the detailed characterization of their connections, the establishment of the mutational pathways and the calculation of metrics that allow the objective determination of the level of ID in a sample, together with statistical analysis for the comparison of different features of the ID level for different groups of samples." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IgIDivA" ; sc:softwareVersion "0.9" ; sc:url "https://github.com/laurazara/IgIDivA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:22355227" ; sc:description "Web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region." ; sc:featureList edam:operation_0415, edam:operation_0430 ; sc:name "IGIPT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.iiit.ac.in/IGIPT/" ; biotools:primaryContact "Dr.Nita Parekh", "Ruchi Jain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3173, edam:topic_3308, edam:topic_3474, edam:topic_3974 ; sc:citation , "pmcid:PMC8381510", "pubmed:34425860" ; sc:description "An integrative transcriptomic and epigenomic classifier for glioblastoma molecular subtypes." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iGlioSub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mensenyat/iGlioSub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description """Interpreting blood GLUcose data with R package iglu. iglu: Interpreting data from Continuous Glucose Monitors (CGMs). The R package ‘iglu’ provides functions for outputting relevant metrics for data collected from Continuous Glucose Monitors (CGM). For reference, see “Interpretation of continuous glucose monitoring data: glycemic variability and quality of glycemic control.” Rodbard (2009). For more information on the package, see package website. Interpreting Glucose Data from Continuous Glucose Monitors.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:name "iglu" ; sc:url "https://github.com/irinagain/iglu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description "IgMAT is a tool for the automatic discrimination and annotation of antibody sequences, specifically designed to be integrated into analysis pipelines or being used as a cli tool. IgMAT is highly customizable, allowing the addition of custom antibody sequences datasets and generating a range of output formats including a bed file of FR and CDR coordinates allowing simple downstream analysis on individual regions." ; sc:featureList edam:operation_0260, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IgMAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TPI-Immunogenetics/igmat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_3314 ; sc:citation , "pubmed:37177853" ; sc:description "A program to identify, characterize, and quantify molecular interactions." ; sc:featureList edam:operation_0272, edam:operation_0337, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "IGMPlot" ; sc:operatingSystem "Linux" ; sc:url "http://igmplot.univ-reims.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC9732676", "pubmed:36506593" ; sc:description "Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling." ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3443, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Igneous" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.12.0" ; sc:url "https://pypi.org/project/igneous-pipeline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_2269 ; sc:citation , "pmcid:PMC8061571", "pubmed:33976973" ; sc:description "ignomonicM is an R-package to estimate natural mortality throughout different life stages." ; sc:featureList edam:operation_3435, edam:operation_3503, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "ignomonicM" ; sc:softwareHelp , ; sc:url "https://cran.r-project.org/package=gnomonicM" ; biotools:primaryContact "Enrique Morales-Bojórquez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0202, edam:topic_0602, edam:topic_3343 ; sc:citation , "pmcid:PMC3754978", "pubmed:24015221" ; sc:description "Predicting interaction between GPCRs and drugs in the cellular networks." ; sc:featureList edam:operation_0276 ; sc:name "iGPCR-Drug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iGPCR-Drug/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623, edam:topic_0804, edam:topic_2830 ; sc:citation "pubmed:26883492" ; sc:description "The web-server IGPred was developed to identify the immunoglobulins (antibodies) based on the sequence information." ; sc:featureList edam:operation_2479, edam:operation_3767 ; sc:name "IGPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/IGPred" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0804, edam:topic_2830, edam:topic_3168, edam:topic_3324 ; sc:citation "pubmed:26072509" ; sc:description "Performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires." ; sc:featureList edam:operation_3195 ; sc:name "IgRepertoireConstructor" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://yana-safonova.github.io/ig_repertoire_constructor/" ; biotools:primaryContact "Yana Safonova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0804, edam:topic_2830 ; sc:citation "pubmed:26007226" ; sc:description "Tool for simulation of antibody repertoire and Ig-seq library. It is designed for testing and benchmarking tools for reconstruction of Ig repertoires." ; sc:featureList edam:operation_2426, edam:operation_2479 ; sc:name "IgSimulator" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://yana-safonova.github.io/ig_simulator/" ; biotools:primaryContact "Yana Safonova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:35514186" ; sc:description "Intermolecular Graph Transformer (IGT) employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture." ; sc:featureList edam:operation_2492, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IGT" ; sc:url "https://github.com/microsoft/IGT-Intermolecular-Graph-Transformer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_0821, edam:topic_3303, edam:topic_3336 ; sc:citation , "pubmed:36896476" ; sc:description """An integrative genome database of traditional Chinese medicine plants. An Integrative Genome Database of Traditional Chinese Medicines. IGTCM (An Integrative Genome Database of Traditional Chinese Medicines) is a comprehensive database of traditional Chinese medicine (TCM) genome and is also an integrative database of TCM with modern molecular biology. It contains six diverse components including herb, ingredient, gene, protein, rna and cds, which integrate TCM with modern molecular biology not only by internal molecular mechanism, also by enhanced understanding of secondary metabolic processes.""" ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "IGTCM" ; sc:url "http://yeyn.group:96/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3382, edam:topic_3409, edam:topic_3474 ; sc:citation ; sc:description "IGUANA is a graph neural network built for colon biopsy screening. IGUANA represents a whole-slide image (WSI) as a graph built with nodes on top of glands in the tissue, each node associated with a set of interpretable features. The output of the pipeline is explainable, indicating glands and features that contribute to a WSI being predicted as abnormal." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IGUANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iguana.dcs.warwick.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:citation , , "pmcid:PMC3603213", "pmcid:PMC9825295", "pubmed:21221095", "pubmed:36562559" ; sc:description "High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http." ; sc:featureList edam:operation_0337, edam:operation_3184 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "IGV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/igv/" ; biotools:primaryContact "IGV GitHub issues", "IGV help group", "IGV support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3320, edam:topic_3517 ; sc:citation ; sc:description """An embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). igv.js is an embeddable interactive genome visualization component developed by the Integrative Genomics Viewer (IGV) team. igv.js is an embeddable interactive genome visualization component written in JavaScript and CSS. It is based on the desktop Integrative Genomics Viewer (IGV), and developed by the same team. See the sidebar for detailed documentation.**. To create an igv.js browser supply a container div and an initial configuration defining the reference genome, initial tracks, and other state to the function igv.createBrowser(div, config). ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/igv ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/igvtools (GITHUB.COM/igvteam/igv) ||| CORRECT NAME OF TOOL COULD ALSO BE 'igv.js'""" ; sc:featureList edam:operation_0484, edam:operation_3198, edam:operation_3208 ; sc:license "MIT" ; sc:name "IGViewer" ; sc:softwareHelp ; sc:url "https://igv.org/app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070 ; sc:description "Access to igv.js, the Integrative Genomics Viewer running in a web browser." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "igvR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/igvR.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC3603213", "pubmed:22517427" ; sc:description "The igvtools utility provides a set of tools for pre-processing data files." ; sc:featureList edam:operation_0256, edam:operation_0335 ; sc:license "MIT" ; sc:name "IGVtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://software.broadinstitute.org/software/igv/igvtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3390, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:33486591" ; sc:description """A online platform for identifying human enzyme classes via reduced amino acid cluster strategy. Enzyme, as a kind of biocatalyst, dominates many catalytic processes such as metabolism, nutrition and energy conversion, and most of the reactions closely related to human life process are also enzyme catalytic reactions. Identifying the 2-level antimicrobial peptides using reduced acid amino composition.""" ; sc:featureList edam:operation_3092, edam:operation_3432, edam:operation_3937 ; sc:name "IHEC-RAAC" ; sc:url "http://bioinfor.imu.edu.cn/ihecraac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3473, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC10457689", "pubmed:37635767" ; sc:description "An interactive web server for large-scale and comprehensive discovery of genes of interest in hepatocellular carcinoma." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "IHGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.hccdatasph.cn/app/ihga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC10243898", "pubmed:37279783" ; sc:description "Curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis." ; sc:featureList edam:operation_3192, edam:operation_3460, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "IHM-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/khatriabhi2319/autoqii2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3125, edam:topic_3169, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:35809058" ; sc:description "Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence." ; sc:featureList edam:operation_0417, edam:operation_3903, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iHMnBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lennylv/iHMnBS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3300, edam:topic_3512 ; sc:citation , "pmcid:PMC7015864", "pubmed:32117916" ; sc:description """Inferring lncRNA Functional Similarity Based on Integrating Heterogeneous Network Data. Long non-coding RNAs (long ncRNAs, lncRNA) are one of great importance non-coding RNA with exceeding 200 nucleotides which are involved in human crucial biological processes. Improved evidences has proved that lncRNAs with similar expression patterns, expression profile and associated with similar diseases may share similar functions. Using the available data to build networks that are able to systematically and comprehensively infer the functional similarity of lncRNA. Determining the functional similarity of lncRNAs is beneficial to clarify the mechanism of their in life activities and complex diseases. IHNLncSim is a freely and reliable computational model can calculate functional similarity between lncRNAs, it will be advantageous to discover their functions which are ambiguous.""" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3925 ; sc:name "IHNLncSim" ; sc:url "http://www.lirmed.com/ihnlncsim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0218, edam:topic_0602, edam:topic_3068, edam:topic_3303 ; sc:citation "pubmed:15226743", "pubmed:16204114", "pubmed:17485473" ; sc:description "It allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, it reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. 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IHP-PING: Integrated Human Protein-Protein Interaction Network Generator. Maintainer: Gaston K. Mazandu 1,2,3 , Bioinformatics and Genomics Informatics Tools. IHP-PING provides a flexible python package, which extracts and integrates heterogeneous PPI datasets to generate a unified PPI network on-the-fly, which is stored locally for further potential user applications through three main steps starting from user input as shown in the figure (Part A) below, with basic statistics and properties: power-law and small-world (Part B).""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:name "IHP-PING" ; sc:url "http://web.cbio.uct.ac.za/ITGOM/post-analysis-tools/ihp-ping-dev/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_2640, edam:topic_3336 ; sc:citation ; sc:description "IHRW is an improved hypergraph random walk model for predicting triple drug therapy." ; sc:name "IHRW" ; sc:url "https://github.com/wangqi27/IHRW" ; biotools:primaryContact "Guiying Yan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC1382018", "pubmed:16494531" ; sc:description "The integrated haplotype Score is a measure of the amount of extended haplotype homozygosity at a given SNP along the ancestral allele relative to the derived allele. This measure is typically standardized empirically to the distribution of observed iHS scores over a range SNPs with similar derived allele frequencies. Extended homozygosity for haplotypes on a high frequency derived allele relative to the ancestral background is a signature of a positively selected sweep." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "iHS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://coruscant.itmat.upenn.edu/whamm/ihs.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0623 ; sc:citation "pubmed:23756733" ; sc:description "This web-server was developed to identify the family of heat shock proteins by using reduced amino acid alphabet." ; sc:featureList edam:operation_2479, edam:operation_3767 ; sc:name "iHSP-PseRAAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/iHSP-PseRAAAC" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3315, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "Iterative hard thresholding - a multiple regression approach to analyze data from a Genome Wide Association Studies (GWAS)." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IHT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/OpenMendel/MendelIHT.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:author ; sc:citation , "pmcid:PMC4930141", "pubmed:27240256" ; sc:description "Multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "IHW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/IHW/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:citation , , "pmcid:PMC4057693", "pubmed:24857907" ; sc:description "New predictor which was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition." ; sc:featureList edam:operation_2479 ; sc:name "iHyd-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://app.aporc.org/iHyd-PseAAC/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0601, edam:topic_0621, edam:topic_2640, edam:topic_3500 ; sc:citation ; sc:description "An integrative database of the expression dynamics of proteins in response to hypoxia in animals." ; sc:featureList edam:operation_0417, edam:operation_2476, edam:operation_3630 ; sc:isAccessibleForFree true ; sc:name "iHypoxia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ihypoxia.omicsbio.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:35801934" ; sc:description "Predicting drug-target interactions through interactive and independent features based on attention mechanism." ; sc:featureList edam:operation_0269, edam:operation_3937, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IIFDTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/czjczj/IIFDTI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC10088697", "pubmed:37041520" ; sc:description "Improved prediction of IL-13 inducing peptides using popular machine learning classifiers." ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_2428, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "iIL13Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.soodlab.com/iil13pred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pmcid:PMC7495796", "pubmed:34565935" ; sc:description "An R Package for Online Item Calibration, Scoring, Evaluation of Model Fit, and Useful Functions for Unidimensional IRT." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iirtplay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/cran/irtplay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_0602, edam:topic_3336 ; sc:citation , "pmcid:PMC4065059", "pubmed:24949626" ; sc:description "Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3672 ; sc:name "IIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo03.ibi.unicamp.br/lnbio/IIS2/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3315, edam:topic_3382 ; sc:citation , "pmcid:PMC9230243", "pubmed:35755841" ; sc:description "Dynamic Python-Based Method Provides Quantitative Analysis of Intercellular Junction Organization During S. pneumoniae Infection of the Respiratory Epithelium." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IJOQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DevonsMo/IJOQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0821 ; sc:citation "pubmed:26628587" ; sc:description "Heuristic framework for inference of kinase activities from Phosphoproteomics data." ; sc:featureList edam:operation_3658 ; sc:name "IKAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/marcel-mischnik/IKAP" ; biotools:primaryContact "Marcel Mischnik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6771546", "pubmed:31574155" ; sc:description """IKAP - Identifying K mAjor cell Population groups in single-cell RNA-seq analysis. IKAP – Identifying K mAjor cell Population groups in single-cell RNA-seq analysis. Note: IKAP will, by default, regress out the percentage of mitochondrial gene counts and total UMI counts and scale the expression matrix using Seurat ScaleData function. These two values should be save in Seurat metadata with column names 'percent.mito' and 'nUMI' respectively. If you want to regress out different confounding variables or use different column names, please save these variables in Seurat metadata and set 'confounders' (an IKAP parameter) as their column names in the Seurat metadata data frame.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3432, edam:operation_3659, edam:operation_3891 ; sc:name "IKAP_cells" ; sc:url "https://github.com/NHLBI-BCB/IKAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3068, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC7200062", "pubmed:32118530" ; sc:description """Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Kaptive reports information about surface polysaccharide loci for Klebsiella and Acinetobacter baumannii genome assemblies. You can also run a graphical version of Kaptive via this web interface (source code). Given a novel genome and a database of known loci (K, O or OC), Kaptive will help a user to decide whether their sample has a known or novel locus. It carries out the following for each input assembly:. Kaptive is a tool for bacterial surface polysaccharide locus typing and variant evaluation. BLAST for all known locus nucleotide sequences (using blastn) to identify the best match ('best' defined as having the highest coverage).""" ; sc:featureList edam:operation_0525, edam:operation_2422, edam:operation_3216, edam:operation_3431, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "iKaptive" ; sc:url "https://github.com/katholt/Kaptive" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3077, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC9694301", "pubmed:36430895" ; sc:description "Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of file formats containing genomic and transcriptomic sequence data." ; sc:featureList edam:operation_2422, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iKARAJ" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/GTP-programmers/KARAJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC7876079", "pubmed:33584612" ; sc:description """A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets. kernInt uses the kernel framework to unify supervised and unsupervised microbiome analyses, while paying special attention to spatial and temporal integration. If you find our package useful, please cite:.""" ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3659, edam:operation_3799, edam:operation_3891 ; sc:name "ikernInt" ; sc:url "https://github.com/elies-ramon/kernInt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3395, edam:topic_3500 ; sc:citation "pubmed:20929875", "pubmed:21930503" ; sc:description "The International Knockout Mouse Consortium database and web portal which serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for specific genes, and follow links to the respective repositories from which corresponding IKMC products can be ordered. Researchers can also use the web site to nominate genes for targeting, or to indicate that targeting of a gene should receive high priority." ; sc:featureList edam:operation_0314, edam:operation_2454, edam:operation_3431, edam:operation_3672 ; sc:name "IKMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.knockoutmouse.org" ; biotools:primaryContact "Martin Ringwald" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0659, edam:topic_3168, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC10098151", "pubmed:37065122" ; sc:description "High-throughput tool for alignment-free phylogenetics." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:name "iKsak" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/labxscut/ksak" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_3400 ; sc:citation ; sc:description "Prediction of Interleukin-13 inducing peptides." ; sc:featureList edam:operation_0252, edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IL-13Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/il13pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2269, edam:topic_3400, edam:topic_3474 ; sc:citation , "pmcid:PMC7665369", "pubmed:33034338" ; sc:description """Computer-aided prediction and design of IL-6 inducing peptides. 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Identification of Linear B-Cell Epitopes. Input your epitope sequence here. The sequence should be in FASTA format. Example. Please be patient after submitting and do not close this page. 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ILDGDB is a manually curated database that provides comprehensive experimentally supported associations between genes and interstitial lung diseases (ILDs). The current version of ILDGDB incorporates 20 ILDs and over 600 genes obtained from 3000 articles in four species. 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ILoReg is a novel tool for cell population identification from single-cell RNA-seq (scRNA-seq) data. 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Chow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "Package for integrative missing value estimation of microarray data sets with limited number of samples, high level of noise, or high rate of missing values. iMISS works by incorporating information from multiple reference microarray datasets to screen reliable neighbor genes used in basic local estimation algorithms such as the Local Least Squares (LLS) algorithm. In addition to the integrative algorithms, implementations of KNN and LLS based imputation algorithms are also provided." ; sc:featureList edam:operation_2495 ; sc:name "iMISS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://zhoulab.usc.edu/iMISS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0736, edam:topic_3301, edam:topic_3324 ; sc:citation ; sc:description "ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction." ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_3461, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "ImitateDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://imitatedb.sblab-nsit.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_2640, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description """A multivariate mixture model approach to integrative analysis of multiple types of omics data. R package for integrative genomics analysis using a multivariate mixture model framework. Ziqiao Wang and Peng Wei. IMIX: A multivariate mixture model approach to integrative analysis of multiple types of omics data. bioRxiv 2020.06.23.167312; doi: https://doi.org/10.1101/2020.06.23.167312.""" ; sc:featureList edam:operation_0282, edam:operation_2495, edam:operation_3206, edam:operation_3207 ; sc:name "IMIX" ; sc:url "https://github.com/ziqiaow/IMIX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3168, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC10013792", "pubmed:36930763" ; sc:description "Machine learning framework for identifying severity of tomato yellow leaf curl virus and their experimental validation." ; sc:featureList edam:operation_0308, edam:operation_2428, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:name "IML-TYLCVs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://balalab-skku.org/IML-TYLCVs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Displays 3D images." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "IMLOOK3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/4190-imlook3d" ; biotools:primaryContact "Omer Demirkaya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0780, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:34218542" ; sc:description "The imlp cli tool predicts iMTS-L propensity profiles for proteins of interest." ; sc:featureList edam:operation_0314, edam:operation_0418, edam:operation_2489 ; sc:license "MIT" ; sc:name "iMLP" ; sc:url "https://github.com/CSBiology/iMLP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2259, edam:topic_3168 ; sc:citation ; sc:description "Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable." ; sc:featureList edam:operation_2497 ; sc:license "Artistic-2.0" ; sc:name "IMMAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IMMAN.html" ; biotools:primaryContact "Minoo Ashtiani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3315, edam:topic_3452 ; sc:citation , "pmcid:PMC7818958", "pubmed:33520382" ; sc:description "Light transport modeling in highly complex tissues using the implicit mesh-based Monte Carlo algorithm." ; sc:featureList edam:operation_2426 ; sc:name "iMMC" ; sc:url "http://mcx.space/#mmc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "ImmCancer - Portal For Cancer Immunothrerapy Tools And Repositories" ; sc:featureList edam:operation_2945 ; sc:name "immcancer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/immcancer/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_3172, edam:topic_3308, edam:topic_3407 ; sc:citation , "pmcid:PMC9898792" ; sc:description "A user-friendly web-based platform to infer metabolic function from omics data." ; sc:featureList edam:operation_3435, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ImmCellFie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://immcellfie.renci.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3934 ; sc:citation ; sc:description """Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data with ImmClassifier. Knowledge-based and lineage-driven immune cell classification in single-cell RNA-Seq data. ImmClassifier (Immune cell classifier), a knowledge-based and lineage-driven immune cell classification algorithm with fine annotation granularity yet high prediction accuracy. ImmClassifer seamlessly integrates the biology of immune cell differentiation, the strength of heterogeneous reference datasets and the state-of-art machine learning models. ImmClassifier cascades a machine learning module and a deep learning module. Maintainer: Xuan Liu xuan.liu.1@uth.tmc.edu Sara Gosline sara.gosline@sagebase.org.""" ; sc:featureList edam:operation_2495 ; sc:name "ImmClassifier" ; sc:url "https://github.com/xliu-uth/ImmClassifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2885 ; sc:citation , "pmcid:PMC9805583", "pubmed:36413071" ; sc:description "Tool to merge VCF genotype files at scale" ; sc:featureList edam:operation_3196, edam:operation_3359, edam:operation_3436, edam:operation_3557, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IMMerge" ; sc:url "https://github.com/belowlab/IMMerge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3308, edam:topic_3385 ; sc:citation , "pmcid:PMC5167062", "pubmed:27531105" ; sc:description "ImmQuant is a software tool allowing immunologists to upload transcription profiles of multiple tissue samples, apply deconvolution methodology to predict differences in cell-type quantities between the samples, and then inspect the inferred cell-type alterations using convenient visualization tools." ; sc:featureList edam:operation_2403 ; sc:license "Other" ; sc:name "ImmQuant" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csgi.tau.ac.il/ImmQuant/" ; biotools:primaryContact "Irit Gat-Viks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0804, edam:topic_2640, edam:topic_3400 ; sc:citation , "pmcid:PMC8643631", "pubmed:34755873" ; sc:description "The regulon atlas of immune-related pathways across cancer types." ; sc:featureList edam:operation_0533, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "ImmReg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/ImmReg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation , "pmcid:PMC8349898", "pubmed:34127402" ; sc:description "An open resource for exploring immunotherapy-related multidimensional genomic profiles in melanoma." ; sc:isAccessibleForFree true ; sc:name "Immu-Mela" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.vanderbilt.edu/database/Immu-Mela/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0804, edam:topic_2229, edam:topic_3308, edam:topic_3934 ; sc:citation , "pubmed:34636837" ; sc:description "A tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction." ; sc:featureList edam:operation_0252, edam:operation_0314, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "ImmuCellAI-mouse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.life.hust.edu.cn/ImmuCellAI-mouse/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_3033 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2333 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation ; sc:description "R package designed to analyse T-cell receptor (TCR) and B-cell receptor (BCR) repertoires" ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "immunarch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , , ; sc:url "https://immunarch.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation ; sc:description "Tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking | The goal of the immuneSIM simulation is to in silico generate human and mouse B- and T-cell repertoires with user-defined properties to provide the user with custom native or aberrant immune receptor sequence repertoires to benchmark their repertoire analysis tools. The simulation algorithm implements an in silico VDJ recombination process with on-the-go annotation of the generated sequences and if enabled by the user somatic hypermutation (SHM) and motif implantation. With a wide range of user-modifiable parameters, a uniquely diverse set of repertoires can be created. The parameters include: Clone count distribution, Germline Gene Usage, Insertion and Deletion Occurrence, SHM likelihood and Motif Implantation" ; sc:license "GPL-3.0" ; sc:name "immuneSIM" ; sc:url "https://github.com/GreiffLab/immuneSIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2830, edam:topic_3306, edam:topic_3374, edam:topic_3930 ; sc:citation , "pmcid:PMC10227038", "pubmed:37248282" ; sc:description "Deep-learning models for predicting the structures of immune proteins." ; sc:featureList edam:operation_0252, edam:operation_0480, edam:operation_0481, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ImmuneBuilder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6612828", "pubmed:31510660" ; sc:description "Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology | Reproducible pipeline for \"Comprehensive evaluation of cell-type quantification methods for immuno-oncology\", Sturm et al. 2019, https://doi.org/10.1093/bioinformatics/btz363 | Comprehensive evaluation of cell-type quantification methods for immuno-oncology | A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) | immunedeconv - an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data | Sturm, G., Finotello, F., Petitprez, F., Zhang, J | The source code in this project can be used to reproduce the results described in the paper" ; sc:featureList edam:operation_3629, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "immunedeconv" ; sc:url "https://github.com/grst/immune_deconvolution_benchmark" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032, edam:format_3475 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3779 ; sc:encodingFormat edam:format_3750 ; sc:name "Annotated text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3750, edam:format_4003 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_3752 ; sc:name "Resource metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_3750, edam:format_3987 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2830, edam:topic_3474, edam:topic_3524, edam:topic_3948 ; sc:author , , , , "Sandve Research Group for Biomedical Informatics" ; sc:citation , "pmcid:PMC10312379", "pubmed:37396030" ; sc:contributor , , , , , , , , , , , , , , , , "Alexandre Almeida Costa", "Fabian L. M. Bernal", "Ivar Grytten", "Knut Rand", "Knut Waagan", "Nikolay Vazov", "Radmila Kompova" ; sc:description "immuneML is a flexible platform designed for machine learning-based analysis and classification of adaptive immune receptor repertoires (AIRR). The platform is available in several formats, including a command-line tool and a Galaxy web interface, and is accessible to a wide range of users from data scientists to clinicians. immuneML offers comprehensive functionality for exploratory analysis of datasets, training machine learning models for repertoire or receptor sequence classification, simulating immune events, and applying trained ML models to new datasets with unknown class labels. The platform also provides developer documentation for extending functionality with new components." ; sc:featureList edam:operation_0252, edam:operation_0337, edam:operation_0416, edam:operation_2426, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "immuneML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Oslo" ; sc:softwareHelp , ; sc:softwareVersion "1.1.2 - 1.1.4", "1.2.0 - 1.2.5", "2.0.0 - 2.0.6", "2.1.0 - 2.1.2", "2.2.0 - 2.2.5" ; sc:url "http://immuneml.uio.no" ; biotools:primaryContact , "Sandve Research Group for Biomedical Informatics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_2830, edam:topic_3063, edam:topic_3930 ; sc:citation , "pmcid:PMC9421535", "pubmed:36046619" ; sc:description "Reference-based comparison of adaptive immune receptor repertoires." ; sc:featureList edam:operation_0300, edam:operation_0491, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "immuneREF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GreiffLab/immuneREF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3071 ; sc:citation ; sc:description "Provides a convenient API for accessing data sets within ImmuneSpace, the data repository and analysis platform of the Human Immunology Project Consortium (HIPC)." ; sc:featureList edam:operation_2421 ; sc:license "GPL-2.0" ; sc:name "ImmuneSpaceR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ImmuneSpaceR.html" ; biotools:primaryContact "Renan Sauteraud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_2830, edam:topic_3930, edam:topic_3948 ; sc:citation ; sc:description """An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The SARS-CoV-2 Immunoanalytics platform is an online tool for the visulisation and analysis of multiple genomic and immunoinformatic meta-analyses. The tool combines an extensive epitope mapping and prediction meta-analysis, with an updated variant database (55,944 non-synonymous mutations) based on 16,087 whole genome sequences, and an analysis of human coronavirus homology, combined with up-to-date annotations from the UniProt database. With this tool and the data we have generated, we hope researchers can perform their own further research, whatever it may be.""" ; sc:featureList edam:operation_0416, edam:operation_3196, edam:operation_3227 ; sc:name "immuno-analytics" ; sc:url "http://genomics.lshtm.ac.uk/immuno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2229, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC8036970", "pubmed:33916145" ; sc:description "ImmunoAIzer is a deep learning-based computational framework to characterize cell distribution and gene mutation in tumor microenvironment." ; sc:featureList edam:operation_2454, edam:operation_3227, edam:operation_3927 ; sc:name "ImmunoAIzer" ; sc:url "https://github.com/BianChang/ImmunoAIzer" ; biotools:primaryContact "Jie Tian", "Yang Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3360, edam:topic_3361 ; sc:citation ; sc:description "Model based clustering and meta-clustering of Flow Cytometry Data." ; sc:featureList edam:operation_3432 ; sc:license "Artistic-2.0" ; sc:name "immunoClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/immunoClust.html" ; biotools:primaryContact "Till Soerensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3337, edam:topic_3360, edam:topic_3421, edam:topic_3934 ; sc:citation , , "pmcid:PMC8112868", "pubmed:33929322" ; sc:description """A computational framework for the non-specialist to profile cellular heterogeneity in cytometry datasets. The immunoCluster package uses the scDataViz bioconductor package’s vizualization tools and adaptation of the SingleCellExperiment data structure to build simple and flexible cytometry analysis workflows like those outlined in Nowicka et al. (2017) CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.""" ; sc:featureList edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:license "MIT" ; sc:name "ImmunoCluster" ; sc:url "https://github.com/kordastilab/ImmunoCluster" ; biotools:primaryContact , "James N. Arnold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_0622, edam:topic_0623, edam:topic_0736, edam:topic_0804, edam:topic_3299 ; sc:citation ; sc:description "A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families." ; sc:featureList edam:operation_2414, edam:operation_2423 ; sc:name "ImmunoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cegg.unige.ch/Insecta/immunodb" ; biotools:primaryContact "Robert M Waterhouse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2830, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC7430879", "pubmed:32778050" ; sc:description """Enabling systems immunology with a manually curated intercellular immune interaction network. ImmunoGlobe is a map of the immune network that describes how different parts of the immune system work together to drive immune responses. By structuring our knowledge of immune interactions into a directed graph, ImmunoGlobe makes it easy to explore the relationships between components of the immune system.""" ; sc:featureList edam:operation_0252, edam:operation_3094, edam:operation_3925 ; sc:name "ImmunoGlobe" ; sc:url "http://www.immunoglobe.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web service" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3400 ; sc:citation , "pmcid:PMC7648030", "pubmed:32810311" ; sc:description """A novel scoring method based on RNA-Seq immunograms describing individual cancer-immunity interactions. Because of the complexity of cancer-immune system interactions, combinations of biomarkers will be required for predicting individual patient responses to treatment and for monitoring combination strategies to overcome treatment resistance. To this end, the "immunogram" has been proposed as a comprehensive framework to capture all relevant immunological variables. Here, we developed a method to convert transcriptomic data into immunogram scores (IGS). This immunogram includes 10 molecular profiles, consisting of innate immunity, priming and activation, T cell response, interferon γ (IFNG) response, inhibitory molecules, regulatory T cells, myeloid-derived suppressor cells (MDSCs), recognition of tumor cells, proliferation, and glycolysis""" ; sc:featureList edam:operation_0252, edam:operation_2436, edam:operation_3435 ; sc:name "immunogram" ; sc:url "https://yamashige33.shinyapps.io/immunogram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0804, edam:topic_3297, edam:topic_3500 ; sc:citation , "pmcid:PMC7450168", "pubmed:32548865" ; sc:description """UK Veterinary Immunological Toolbox Website is promoting vaccine research by facilitating communication and removing reagent barriers. Colorized scanning electron micrograph of a B cell from a human donor [Credit: NIAID]. Welcome to the Immunological Toolbox, a repository of antibodies, other reagents and resources to promote veterinary immunology research. The Antibody Hub has been established with the aim of improving animal and human health globally.""" ; sc:featureList edam:operation_0560 ; sc:name "UK Veterinary Immunological Toolbox Website" ; sc:url "https://www.immunologicaltoolbox.co.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC9988424", "pubmed:36890882" ; sc:description "Web-based computational pipeline for analysing and mining immunopeptidomic data." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "Immunolyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://immunolyser.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_0804, edam:topic_3400 ; sc:citation , "pubmed:31844327" ; sc:description """High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Wellcome Trust Sanger Institute.""" ; sc:featureList edam:operation_0560, edam:operation_3196, edam:operation_3501 ; sc:name "immunophenotype" ; sc:url "http://www.immunophenotype.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC6367516", "pubmed:30753476" ; sc:description "ImmunoSPdb is a repository of experimentally validated peptides which suppress the immune system. 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Independent Component Analysis of Bacterial Transcriptomes. iModulonDB is maintained by the Systems Biology Research Group at the University of California, San Diego.""" ; sc:featureList edam:operation_0337, edam:operation_1781, edam:operation_2437 ; sc:name "iModulonDB" ; sc:url "http://imodulondb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3678 ; sc:citation "pubmed:26740524" ; sc:description "iMOMLogit provides improved performance in identifying true models and reducing estimation and prediction error in a number of simulation studies." ; sc:featureList edam:operation_2423 ; sc:name "iMOMLogit" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.stat.tamu.edu/~amir/code.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0208, edam:topic_2640, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC10400808", "pubmed:37547083" ; sc:description "A web server for interactive multiomics and pharmacological analyses of patient-derived cancer cell lines." ; sc:featureList edam:operation_0337, edam:operation_3463, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "IMOPAC" ; sc:url "http://www.hbpding.com/IMOPAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0166, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:15215459" ; sc:description "iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures." ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_0360, edam:operation_2949 ; sc:name "iMOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/imot/iMOTserver.html" ; biotools:primaryContact "Dr. R. Sowdhamini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_1775 ; sc:citation "pubmed:22684505" ; sc:description "Integrative Multi-species Prediction (IMP) is a webserver that enables biologists to analyze their experimental results in the functional context of gene networks from multiple organisms." ; sc:featureList edam:operation_2436, edam:operation_3439 ; sc:name "IMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imp.princeton.edu" ; biotools:primaryContact "Troyanskaya O. G." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3382, edam:topic_3892 ; sc:citation , "pubmed:31396911" ; sc:description "Modeling Biological Complexes Using Integrative Modeling Platform | Scripts to assess sampling convergence and exhaustiveness" ; sc:featureList edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "IMP-sampcon" ; sc:url "https://github.com/salilab/IMP-sampcon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0602, edam:topic_0611, edam:topic_2275, edam:topic_2828, edam:topic_3382 ; sc:citation "pubmed:21877292" ; sc:description "Integrative Modeling Platform broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies. Detailed structural characterization of assemblies is generally impossible by any single existing experimental or computational method. This barrier can be overcome by hybrid approaches that integrate data from diverse biochemical and biophysical experiments." ; sc:name "IMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.salilab.org/imp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:citation , "pmcid:PMC5159968", "pubmed:7986083" ; sc:description "Integrated Meta-omic Pipeline. Large-scale standardized integrated analysis of coupled metagenomic and metatranscriptomic data. Incorporates robust read preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations." ; sc:featureList edam:operation_0310, edam:operation_0314, edam:operation_0362 ; sc:license "MIT" ; sc:name "IMP" ; sc:softwareHelp , ; sc:softwareVersion "1.4" ; sc:url "http://r3lab.uni.lu/web/imp/" ; biotools:primaryContact "Shaman Narayanasamy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3510, edam:topic_3945 ; sc:citation ; sc:description "A Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. This software makes use of several known bioinformatics software, e.g., ConTest, Jmol, PhyML, ATV, etc." ; sc:featureList edam:operation_0492, edam:operation_0539, edam:operation_0570, edam:operation_2403, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IMPACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://impact-gui.sourceforge.net/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814, edam:topic_3071, edam:topic_3511, edam:topic_3945 ; sc:citation , "pubmed:25329307" ; sc:description "Java swing based Graphical User Interface program for analyzing and/or combining several selection results from programs like, PAML (codeml), Datamonkey, TreeSAAP. Provides 3D homology modeling through Swiss Model and 3D mapping of selection results through Jmol." ; sc:featureList edam:operation_0250, edam:operation_0539, edam:operation_0570, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IMPACT_S" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://impact-s.sourceforge.net/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2259, edam:topic_3172, edam:topic_3308 ; sc:citation ; sc:description "IMPaLA is a web tool for the joint pathway analysis of transcriptomics or proteomics and metabolomics data." ; sc:featureList edam:operation_2497 ; sc:name "IMPaLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "9" ; sc:url "http://impala.molgen.mpg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """Partial Annotations for Cell Instance Segmentation. Partial Annotations for MultiplexCell Instance Segmentation.""" ; sc:featureList edam:operation_3435, edam:operation_3553, edam:operation_3557 ; sc:name "ImPartial" ; sc:url "https://github.com/natalialmg/ImPartial" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "Genotype-phenotype annotations from knockout mouse strain for every protein coding gene in the mouse genome." ; sc:featureList edam:operation_2422 ; sc:name "IMPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.mousephenotype.org" ; biotools:primaryContact "Terry Meehan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Package contains methods for data retrieval from IMPC Database." ; sc:featureList edam:operation_2409, edam:operation_2422 ; sc:license "Other" ; sc:name "IMPCdata" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IMPCdata.html" ; biotools:primaryContact "Jeremy Mason" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3168 ; sc:citation , "pubmed:36892171" ; sc:description "Fast and comprehensive IMmune Paired-End Reads Merger for sequencing data." ; sc:featureList edam:operation_0232, edam:operation_0310, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IMperm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhangwei2015/IMperm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation "pubmed:24990607" ; sc:description "Software package implementing methods for imputation from summary statistics and accompanying data. The software takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants." ; sc:featureList edam:operation_2238, edam:operation_2403 ; sc:name "ImpG-Summary" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bogdan.bioinformatics.ucla.edu/software/impg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3407, edam:topic_3423, edam:topic_3895 ; sc:citation , "pmcid:PMC10767881", "pubmed:37870445" ; sc:description "Integrated medicinal plantomics is an integrated platform for organizing, analyzing, and sharing omics data of medicinal plantomics." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "IMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.bic.ac.cn/IMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pmcid:PMC7290057", "pubmed:32581646" ; sc:description """An Integrated Method for Predicting Potential Associations Between miRNAs and Diseases.

Background< h4>With the rapid development of biological research, microRNAs (miRNAs) have increasingly attracted worldwide attention. The increasing biological studies and scientific experiments have proven that miRNAs are related to the occurrence and development of a large number of key biological processes which cause complex human diseases. Thus, identifying the association between miRNAs and disease is helpful to diagnose the diseases. Although some studies have found considerable associations between miRNAs and diseases, there are still a lot of associations that need to be identified. Experimental methods to uncover miRNA-disease associations are time-consuming and expensive""" ; sc:featureList edam:operation_0463, edam:operation_3659, edam:operation_3792 ; sc:name "IMPMD" ; sc:url "https://github.com/Sunmile/IMPMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0199, edam:topic_3796 ; sc:citation , "pubmed:35976111" ; sc:description "McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level." ; sc:featureList edam:operation_3557 ; sc:license "Other" ; sc:name "impMKT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imkt.uab.cat" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1930 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0602, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "iMPP is a tool designed to predict and assemble peptides from short fragmentary reads. iMPP is written in C++ and has been tested on a 64-bit Linux system. The input for the software are FASTQ sequences, and the output comprises of 4 files: 1. predicted genes (nucl), 2. predicted peptides (prot), 3. gene predictions in gff format, 4. assembled peptide sequences (prot)." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3644, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iMPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Sirisha-t/iMPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2830, edam:topic_3056 ; sc:citation , "pmcid:PMC5095119", "pubmed:27867380" ; sc:description "Immune Germline Prediction (IMPre), a tool for predicting germline Variable/Joining genes and alleles using deep-sequencing data derived from T-cell receptor/B-cell receptor repertoires." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "IMPre" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/zhangwei2015/IMPre" ; biotools:primaryContact "Xiao Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3384, edam:topic_3444 ; sc:description "improj3 generates 3D projections from image stacks" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "improj3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/45800-improj3" ; biotools:primaryContact "Fang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description """A flexible software platform for adaptive neuroscience experiments. A flexible software platform for real-time and adaptive neuroscience experiments. improv is a streaming software platform designed to enable adaptive experiments. By analyzing data, such as 2-photon calcium images, as it comes in, we can obtain information about the current brain state in real time and use it to adaptively modify an experiment as data collection is ongoing.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3443 ; sc:license "MIT" ; sc:name "improv" ; sc:url "http://github.com/pearsonlab/improv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3334, edam:topic_3676 ; sc:citation , "pmcid:PMC9763511", "pubmed:36561149" ; sc:description "Integrating Multiple Phenotype Resources Optimises Variant Evaluation in genetically determined Developmental Disorders." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IMPROVE-DD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Stuart-Aitken/IMPROVE-DD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0820, edam:topic_1317, edam:topic_3168 ; sc:citation , "pmcid:PMC7495477", "pubmed:32938971" ; sc:description """The Integral Membrane Protein Stability Selector. Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites""" ; sc:featureList edam:operation_0269, edam:operation_0308, edam:operation_0331, edam:operation_3226, edam:operation_3795 ; sc:name "IMPROvER" ; sc:url "http://improver.ddns.net/IMPROvER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168 ; sc:citation ; sc:description "This tool captures single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. 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sc:softwareHelp ; sc:url "http://www.stanford.edu/group/rosenberglab/infocalc.html" ; biotools:primaryContact "Noah A Rosenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_3315 ; sc:citation ; sc:description """Identifying flow modules in ecological networks using Infomap. Network community detection using the Map Equation framework. A a package for running Infomap, inspired by ecological networks. Infomap finds important patterns in complex networks by optimizing the map equation, which exploits the information-theoretic duality between the problem of compressing data and detecting patterns. 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This folder contains a Python port of MiXeR, wrapping the same C/C++ core as we previously used from MATLAB. This is work in progress, but eventually it should singificantly improve user experience, as Python allows much simpler installation procedures, makes it less error prone, allows to implement well-documented command-line interface (python mixer.py --help), and provide visualization. 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Michael, and Newton, Michael A. Minimally-supervised, chemogenomic strategies for effective compound prioritization on kinases.\" | This repository implements two experiments described in the manuscript: | Training a single model for prediction on new kinases | Conducting leave-one-out cross-validation and outputing the final leave-one-out prediction on each input kinase" ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3891 ; sc:license "Unlicense" ; sc:name "Informer" ; sc:url "https://github.com/leepei/informer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:encodingFormat edam:format_1457 ; sc:name "RNA secondary structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3466, edam:format_3508, edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_3311 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author , "Anke Busch" ; sc:citation , "pmcid:PMC1933236", "pubmed:17452349" ; sc:description "RNA sequence design by inverse folding." ; sc:featureList edam:operation_3095 ; sc:isAccessibleForFree true ; sc:name "INFORNA Sequence Design" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "2.2.0" ; sc:url "http://rna.informatik.uni-freiburg.de/INFORNA/" ; biotools:primaryContact , "Anke Busch" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display basic information about sequences." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "infoseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/infoseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_3464 ; sc:name "Ontology concept" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:encodingFormat edam:format_2062, edam:format_3556 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_1775 ; sc:citation , "pmcid:PMC4489281", "pubmed:26019177" ; sc:description "Interaction Network GO Annotator protein function predictor." ; sc:featureList edam:operation_1777 ; sc:name "INGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA", "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://inga.bio.unipd.it/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:19880367" ; sc:description "Integrated platform for next-generation sequencing project, the core function of which is to detect SNPs and indels using a Bayesian algorithm.It does not have any read length restriction. 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Applying this method on polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points, recognizing causal mutations in mutant genomes or QTL loci. 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Redirecting to the new location... FluConvert and IniFlu (ver.1.0.0.0701).""" ; sc:featureList edam:operation_0292, edam:operation_2421, edam:operation_2422 ; sc:license "MIT" ; sc:name "IniFlu" ; sc:operatingSystem "Windows" ; sc:url "https://apps.flutures.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc:description "MATLAB based matched filter is implemented for an Intravascular Near-Infrared Fluorescence (iNIRF) imaging method." ; sc:featureList edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Intravascular Near-Infrared Fluorescence (iNIRF) Imaging" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47367-intravascular-near-infrared-fluorescence-inirf-imaging" ; biotools:primaryContact "Sam Nazari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510 ; sc:citation ; sc:description "New predictor was developed by incorporating the position-specific dipeptide propensity into the general pseudo amino acid composition for discriminating the nitrotyrosine sites from non-nitrotyrosine sites in proteins." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "iNitro-Tyr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://app.aporc.org/iNitro-Tyr/" ; biotools:primaryContact "Yan Xu Close" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7671370", "pubmed:33543123" ; sc:description """Prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution. The Individual Meta Random Forest (InMeRF) is a tool to predict the pathogenicity of nonsynonymous SNVs (nsSNVs) using 150 independent models that were individually generated for all possible amino acid (AA) substitutions. 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sc:url "http://inpsmd.biocomp.unibo.it" ; biotools:primaryContact , "Piero Fariselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0749, edam:topic_3303 ; sc:citation , "pmcid:PMC8933636", "pubmed:35356545" ; sc:description "An intelligent network pharmacology platform unique for traditional Chinese medicine." ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "INPUT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbcb.cdutcm.edu.cn/INPUT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123, edam:topic_0128, edam:topic_3510 ; sc:citation ; sc:description "Wwo-level predictor. It can be used to identify an uncharacterized protein as nuclear receptor (NR) or non-NR according to its sequences information alone." ; sc:featureList edam:operation_2479 ; sc:name "iNR-PhysChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iNR-PhysChem" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """Integrating millions of single cells using batch-aware triplet neural networks. INtegration of millions of Single Cells using batch-aware Triplet networks. insct is a deep learning algorithm which calculates an integrated embedding for scRNA-seq data. With insct, you can:. a, INSCT learns a data representation, which integrates cells across batches. 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It is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. It covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations." ; sc:featureList edam:operation_2422 ; sc:name "Nucleotide Sequence Database Collaboration" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Identifiers.org" ; sc:softwareHelp ; sc:url "http://identifiers.org/insdc/" ; biotools:primaryContact "ENA Contact details" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0749 ; sc:citation "pubmed:26656931" ; sc:description "Easy-to-use and powerful web server for biologists analysing genomic sequence data for in silico cis-regulatory modules prediction and analysis." ; sc:featureList edam:operation_1781 ; sc:name "INSECT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT2/" ; biotools:primaryContact "Dr. Patricio Yankilevich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_3168, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """InsectOR – webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. Insect Olfactory Receptor Genome Wide Survey. Prediction of odorant receptor genes from newly sequenced insect genomes is a difficult task in absence of antennal transcriptome data. This tool will make it easier for you.""" ; sc:featureList edam:operation_0433, edam:operation_3092, edam:operation_3663 ; sc:name "InsectOR" ; sc:url "http://caps.ncbs.res.in/insectOR/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2206, edam:format_3003 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0102, edam:topic_0160, edam:topic_0204, edam:topic_0749, edam:topic_3173 ; sc:citation , , , , "pmcid:PMC4344487", "pmcid:PMC5753247", "pmcid:PMC7145625", "pmcid:PMC8728178", "pubmed:25477382", "pubmed:29126285", "pubmed:31665499", "pubmed:34751401" ; sc:description "ReMap is a large scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Drosophila melanogaster and Arabidopsis thaliana transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA). ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers." ; sc:featureList edam:operation_0362, edam:operation_0527, edam:operation_3198, edam:operation_3222 ; sc:license "CC-BY-NC-4.0" ; sc:name "ReMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2014", "2018", "2020", "2022" ; sc:url "https://remap.univ-amu.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3343 ; sc:citation , "pmcid:PMC3850689", "pubmed:24090499" ; sc:description "A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data." ; sc:featureList edam:operation_2233 ; sc:name "InsertionMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/insertionmapper/" ; biotools:primaryContact "Chunguang Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_0780, edam:topic_0781, edam:topic_3500 ; sc:citation "pubmed:19417071" ; sc:description "Web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes." ; sc:featureList edam:operation_0239, edam:operation_0308, edam:operation_3196, edam:operation_3208, edam:operation_3695 ; sc:name "Insignia" ; sc:url "http://insignia.cbcb.umd.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3172 ; sc:citation ; sc:description "Comparative analysis of open source in silico fragmentation tools." ; sc:featureList edam:operation_3763 ; sc:name "In silico fragmentation evaluation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/insilico-fragmentation/" ; biotools:primaryContact "Oliver Fiehn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation "pubmed:14752001" ; sc:description "Provides tools for theoretical PCR amplification, AFLP-PCR and PFGE with all up-to-date public complete bacterial genomes (300+ genomes available)." ; sc:featureList edam:operation_0307, edam:operation_0308, edam:operation_0575, edam:operation_2429, edam:operation_3217 ; sc:name "In silico simulation of molbio experiments" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://insilico.ehu.es/" ; biotools:primaryContact "Bikandi J." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3365, edam:topic_3520 ; sc:citation "pubmed:16512677" ; sc:description "Proteomics open-source project, aimed at implementing recurrent computations that are necessary for proteomics data analysis." ; sc:featureList edam:operation_2479 ; sc:name "InSilicoSpectro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://search.cpan.org/~alexmass/InSilicoSpectro/" ; biotools:primaryContact "Alexandre Masselot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2229 ; sc:citation , "pubmed:36075505" ; sc:description "Incorporating Network Structure Information for Single-Cell Type Classification." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_2996 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "INSISTC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://hulab.ucf.edu/research/projects/INSISTC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3175, edam:topic_3474 ; sc:citation , "pmcid:PMC9990265", "pubmed:36879189" ; sc:description "Method for detecting insertions based on deep learning network." ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:name "INSnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eioyuou/INSnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3511 ; sc:citation , "pubmed:25957348" ; sc:description "INference of Synthesis, Processing and dEgradation rates in Course-Time experiments analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels." ; sc:featureList edam:operation_2478 ; sc:license "GPL-2.0" ; sc:name "INSPEcT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/INSPEcT.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3315 ; sc:citation , "pmcid:PMC7379887", "pubmed:32765590" ; sc:description """INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. de Pretis S., Furlan M. and Pelizzola M. Modeling RNA synthesis, processing and degradation with RNA-seq data. INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data. INSPEcT - INference of Synthesis, Processing and dEgradation rates from Transcriptomic data. GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse. 2 Run the application from an R session. 3 Presentation of the Graphical User Interface.""" ; sc:featureList edam:operation_2409, edam:operation_2426, edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "INSPEcT-GUI" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/INSPEcT/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654, edam:format_3834 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:16013882", "pubmed:16083278" ; sc:description "Inspect is a general purpose database search algorithm, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, Inspect implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode." ; sc:featureList edam:operation_2428, edam:operation_3643, edam:operation_3644, edam:operation_3645, edam:operation_3646 ; sc:name "InsPecT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/Software/Inspect/" ; biotools:primaryContact "Natalie Castellana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3127, edam:topic_3295 ; sc:citation ; sc:description "INSPIIRED is a software suite designed to study viral integration sites and the longitudinal outcomes of gene therapy patients." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "INSPIIRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BushmanLab/INSPIIRED" ; biotools:primaryContact "Frederic D. Bushman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520, edam:topic_3922 ; sc:citation , "pmcid:PMC9720494", "pubmed:36280141" ; sc:description "An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction." ; sc:featureList edam:operation_3643, edam:operation_3649, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "inSPIRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://figshare.com/articles/software/inSPIRE_Models/20368035" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3315, edam:topic_3384 ; sc:description "2D prototype to integrate InSPIRE into Radiation Oncology treatment planning." ; sc:isAccessibleForFree true ; sc:name "InSPIRE: ITK Matlab GUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/35098-inspire-itk-matlab-gui" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "My challenge paper listed on my profile relies on reducing a multi-modal to mono-modal def reg." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "InSPIRE utility to deform a 3D image" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36401-inspire-utility-to-deform-a-3d-image" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2572 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3320, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC10250204", "pubmed:37026474" ; sc:description "Effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads." ; sc:featureList edam:operation_0446, edam:operation_1812, edam:operation_2499 ; sc:isAccessibleForFree true ; sc:name "Insplico" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://gitlab.com/aghr/insplico" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2269, edam:topic_3125, edam:topic_3174 ; sc:citation ; sc:description """Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL. Large genome reassembly based on Hi-C data, continuation of GRAAL. Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries. This work is under continuous development/improvement - see GRAAL for information about the basic principles. sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal. Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)""" ; sc:featureList edam:operation_0282, edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "instaGRAAL" ; sc:url "https://github.com/koszullab/instaGRAAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:33105480" ; sc:description """A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Get in touch with Team InstaDock.""" ; sc:featureList edam:operation_0337, edam:operation_3899, edam:operation_3938 ; sc:name "InstaDock" ; sc:url "https://hassanlab.org/instadock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """An easy-to-use deep learning pipeline for image segmentation and classification. InstandDL: An easy and convenient deep learning pipeline for image segmentation and classification. InstantDL enables experts and non-experts to use state-of-the art deep learning methods on biomedical image data. InstantDL offers the four most common tasks in medical image processing: Semantic segmentation, instance segmentation, pixel-wise regression and classification. For more in depth discussion on the methods, as well as comparing the results and bechmarks using this package, please refer to our preprint on bioRxiv here.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3659 ; sc:license "MIT" ; sc:name "InstantDL" ; sc:url "https://github.com/marrlab/InstantDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_0820, edam:topic_0821 ; sc:citation "pubmed:11590105", "pubmed:12456873", "pubmed:12724305", "pubmed:12824327", "pubmed:15048825", "pubmed:15180935", "pubmed:15539454", "pubmed:15608195", "pubmed:15653630", "pubmed:15769473", "pubmed:15955779", "pubmed:9325115", "pubmed:9769220" ; sc:description "A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0270, edam:operation_0303, edam:operation_0474 ; sc:name "Institute of Enzymology Servers" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ttk.mta.hu/en/szolgaltatas/adatbazisok/" ; biotools:primaryContact "Istva´n Simon*" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174 ; sc:description "InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification" ; sc:featureList edam:operation_0484, edam:operation_3209 ; sc:name "InStrain" ; sc:url "https://instrain.readthedocs.io/en/latest/#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0611, edam:topic_2828, edam:topic_3448, edam:topic_3452 ; sc:citation , "pubmed:34866631" ; sc:description "Integrating High-End Services for Translational Research in Structural Biology." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3457 ; sc:isAccessibleForFree true ; sc:name "Instruct-ERIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://instruct-eric.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3071, edam:topic_3301 ; sc:citation "pubmed:26607491" ; sc:description "Browser that helps navigate among abundant homologies, syntenies and genes annotations." ; sc:featureList edam:operation_2409 ; sc:name "Insyght" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.jouy.inra.fr/Insyght" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0634, edam:topic_3053, edam:topic_3063 ; sc:citation "pubmed:14685227", "pubmed:15153999", "pubmed:16251469", "pubmed:17943122", "pubmed:17943131" ; sc:description "Tool that will allow researchers to find genes and genetic variations that affect health and disease." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_0488, edam:operation_3196, edam:operation_3197 ; sc:name "International HapMap Project" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.gov/10001688" ; biotools:primaryContact "Lisa D. Brooks" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331, edam:format_3752 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130 ; sc:author , , ; sc:citation , ; sc:contributor ; sc:description "Calculates the residue Interaction Energy Matrix for any protein structure and offers comprehensive analysis of the interfaces in protein–DNA complexes." ; sc:featureList edam:operation_0250, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:name "Amino Acids Interactions Web Server" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://bioinfo.uochb.cas.cz/INTAA/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation ; sc:description "Protein interaction database and analysis system." ; sc:featureList edam:operation_0224 ; sc:name "IntAct" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI Databases" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/intact/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0621, edam:topic_3047, edam:topic_3168 ; sc:citation , "pubmed:33961020" ; sc:description "IntAct App is a Cytoscape application for molecular interaction network visualisation and analysis." ; sc:featureList edam:operation_0224, edam:operation_2949, edam:operation_3925 ; sc:name "IntAct App" ; sc:softwareHelp ; sc:url "https://apps.cytoscape.org/apps/intactapp" ; biotools:primaryContact "Henning Hermjakob", "Pablo Porras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3295 ; sc:description "The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step." ; sc:featureList edam:operation_0337, edam:operation_2423 ; sc:license "GPL-2.0" ; sc:name "InTAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/InTAD.html" ; biotools:primaryContact "Konstantin Okonechnikov" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID (NCBI)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Genome map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc:description "This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package." ; sc:featureList edam:operation_0361, edam:operation_2518 ; sc:license "Artistic-2.0" ; sc:name "intansv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/intansv.html" ; biotools:primaryContact "Wen Yao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33016988" ; sc:description """Integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles. IntAPT is a C++ package to identify alternatively spliced isoforms using multiple RNA-seq data. The user manual of IntAPT is available here. We have provided both precompiled binaries (require gcc 5.4.0 or newer) and source code.""" ; sc:featureList edam:operation_0264, edam:operation_0310, edam:operation_2238 ; sc:name "IntAPT" ; sc:url "http://github.com/henryxushi/IntAPT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3466, edam:format_3508, edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2331, edam:format_3508 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2330 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2330 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3466, edam:format_3508, edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Patrick Wright" ; sc:citation , "pmcid:PMC4086077", "pubmed:24838564" ; sc:description "sRNA target prediction." ; sc:featureList edam:operation_0278 ; sc:isAccessibleForFree true ; sc:name "IntaRNA - RNA-RNA interaction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "1.2.5" ; sc:url "http://rna.informatik.uni-freiburg.de/IntaRNA/" ; biotools:primaryContact , "Patrick Wright" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3517 ; sc:citation , "pmcid:PMC7100855", "pubmed:32265990" ; sc:description """An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix. IntAssoPlot: Visualize Genome-Wide Association Study with Gene Annotation and Linkage Disequiblism. 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Unlike static databases, Interactome3D also allows biologists to upload newly discovered interactions and pathways in any species, select the best combination of structural templates and build three-dimensional models in a fully automated manner." ; sc:name "Interactome3D" ; sc:url "http://interactome3d.irbbarcelona.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:encodingFormat edam:format_2330 ; sc:name "Database ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0128, edam:topic_0199, edam:topic_3077 ; sc:citation ; sc:description "A tool to link genomic variant information with structural protein–protein interactomes." ; sc:featureList edam:operation_0276, edam:operation_2422, edam:operation_3197, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Interactome INSIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://interactomeinsider.yulab.org/" ; biotools:primaryContact "Juan Felipe Beltrán" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2830, edam:topic_3168, edam:topic_3957 ; sc:citation , "pmcid:PMC7319578", "pubmed:32402076" ; sc:description """A web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data. InteractomeSeq: a web server for the identification and profiling of domains and epitopes from Phage Display and Next Generation Sequencing data. InteractomeSeq is a webtool allowing either genomic or single gene domainome analysis of phage libraries generated and selected by following the interactome-sequencing approach. Home. Interactome Sequencing Platform. InteractomeSeq is a web server allowing domainome data analysis from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an interactome-sequencing approach. InteractomeSeq allows users to upload raw-sequencing data and to easily obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis procedure.""" ; sc:featureList edam:operation_0416, edam:operation_2495, edam:operation_3192 ; sc:name "InteractomeSeq" ; sc:url "https://InteractomeSeq.ba.itb.cnr.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_0769, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description "InterARTIC is an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses." ; sc:featureList edam:operation_3185, edam:operation_3200, edam:operation_3933 ; sc:license "MIT" ; sc:name "InterARTIC" ; sc:url "https://github.com/Psy-Fer/interARTIC/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3047 ; sc:citation , "pubmed:34499117" ; sc:description "The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure." ; sc:featureList edam:operation_0387, edam:operation_1836, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "INTERCAAT" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://gitlab.com/fiserlab.org/intercaat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3300, edam:topic_3308 ; sc:citation , "pmcid:PMC8752611", "pubmed:35017628" ; sc:description "InterCellar enables interactive analysis and exploration of cell-cell communication in single-cell transcriptomic data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "InterCellar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/martaint/InterCellar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0634, edam:topic_3170 ; sc:citation , "pubmed:35980155" ; sc:description "Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors." ; sc:featureList edam:operation_3629, edam:operation_3659 ; sc:license "Artistic-2.0" ; sc:name "InteRD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/InteRD/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , ; sc:description "Creates a new Gff output, which corresponds to the region of two successive Elements." ; sc:featureList edam:operation_0335 ; sc:name "interelementgff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3958 ; sc:citation , "pmcid:PMC8950762", "pubmed:35328097" ; sc:description "An R Package for High-Dimensional Interaction Analysis of the Repeated Measurement Data" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "interep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/package=interep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files)." ; sc:featureList edam:operation_2499, edam:operation_2928, edam:operation_3435, edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "IntEREst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IntEREst.html" ; biotools:primaryContact "Ali Oghabian", "Mikko Frilander" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_2275 ; sc:citation "pubmed:23652426", "pubmed:27131368", "pubmed:29741647" ; sc:description "Ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking." ; sc:featureList edam:operation_0477, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "InterEvDock" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2" ; biotools:primaryContact , "Jessica Andreani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0130, edam:topic_0166 ; sc:citation "pubmed:22053089" ; sc:description "Database designed to explore 3D structures of homologous interfaces of protein complexes. Provides tools to retrieve and visualize these structures, including downloadable pre-computed multiple sequence alignments." ; sc:featureList edam:operation_0360, edam:operation_0492, edam:operation_2422 ; sc:name "InterEvol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodev.cea.fr/interevol/" ; biotools:primaryContact "Interevol coordinator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3295, edam:topic_3379 ; sc:citation , "pmcid:PMC6685260", "pubmed:31387579" ; sc:description "Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data | CancerDAP is a database molecularly characterizing subpathways involved in cellular response to 191 anticancer drugs | 1 Prospect the detailed information of each subpathway related to corresponding anticancer drug; 2 | CancerDAP has been formally launched and is freely available at:" ; sc:featureList edam:operation_2436, edam:operation_3557 ; sc:name "interface-CancerDAP" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/CancerDAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31792500" ; sc:description """Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. In recent years, increasing evidence has suggested that aberrant long non-coding RNA (lncRNA) copy number variation may contribute to the onset of human cancers. LncRNAs function in variety of biological pathways and processes. Investigating the functions of lncRNAs are important in uncovering the mechanisms of tumorigenesis and progression of cancers. Here we identified lncRNAs related subpathways (sub-regions of pathways) throughout 14 cancer types for characterizing functions of 4115 lncRNAs.""" ; sc:featureList edam:operation_2421 ; sc:name "interface-LncCASE" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/LncCASE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3047 ; sc:citation , "pubmed:32768452" ; sc:description """A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis. Download the spreadsheet dataset template. Fill in as indicated (see the included notations for reference). interferENZY Copyright ©2019-2020 Maria Filipa Pinto, Pedro M. Martins. When using interferENZY, the user-provided dataset is only kept as long as interferENZY analysis by GNU Octave takes place; once the output page is presented the submitted dataset has been eliminated to ensure user data confidentiality.""" ; sc:featureList edam:operation_0337, edam:operation_2428 ; sc:name "interferENZY" ; sc:url "https://interferenzy.i3s.up.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation "pubmed:18996892" ; sc:description "Open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_1781, edam:operation_2495, edam:operation_3223 ; sc:name "INTERFEROME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.interferome.org/" ; biotools:primaryContact "Paul J. Hertzog" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:15608201" ; sc:description "Browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrates data from a variety of sources, including InterPro, CluSTr and GO." ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3431 ; sc:name "Intergr8" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ebi.ac.uk/integr8/" ; biotools:primaryContact "Paul Kersey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A program to interleave and deinterleave FASTQ files" ; sc:name "interleafq" ; sc:url "https://github.com/quadram-institute-bioscience/interleafq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC7214017", "pubmed:32049311" ; sc:description "improved ligand-based virtual screening using topologically independent structural alignments." ; sc:featureList edam:operation_0295, edam:operation_3216, edam:operation_3938 ; sc:name "InterLig" ; sc:url "http://wallnerlab.org/InterLig" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2305 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2333 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3534 ; sc:citation , "pubmed:19528088" ; sc:description "Prediction of interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences." ; sc:featureList edam:operation_0272 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "InterMap3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://cbs.dtu.dk/services/InterMap3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0196, edam:topic_0749, edam:topic_3534 ; sc:citation , "pmcid:PMC8023803", "pubmed:33502860" ; sc:description "A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3898 ; sc:isAccessibleForFree true ; sc:name "InterMetalDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://intermetaldb.biotech.uni.wroc.pl/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3366 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984", "pubmed:24753429" ; sc:contributor "BBSRC", "NIH", "Wellcome Trust" ; sc:description "Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data." ; sc:featureList edam:operation_2421 ; sc:funder "BBSRC", "NIH", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "InterMine" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Cambridge", "gen.cam.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "5.0.0" ; sc:url "http://www.intermine.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0121, edam:topic_0203, edam:topic_0204, edam:topic_0797, edam:topic_1775, edam:topic_2259, edam:topic_2885, edam:topic_3320, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC3516146", "pubmed:23023984" ; sc:description "Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_2424, edam:operation_2436, edam:operation_3223 ; sc:license "LGPL-2.0" ; sc:name "InterMineR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/InterMineR.html" ; biotools:primaryContact "InterMine Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_3957 ; sc:citation "pubmed:15173116" ; sc:description "Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_2949, edam:operation_3439 ; sc:name "Interolog Regulog Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://interolog.gersteinlab.org/" ; biotools:primaryContact "Haiyuan Yu", "Xiaowei Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_3557 ; sc:citation "pubmed:15173116" ; sc:description "Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_2492, edam:operation_2949, edam:operation_3439 ; sc:name "Interolog Regulog Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://interolog.gersteinlab.org/" ; biotools:primaryContact "Haiyuan Yu", "Xiaowei Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_3557 ; sc:citation "pubmed:18508856" ; sc:description "Automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and clusters of orthologous proteins. The tool can be downloaded or used through the web application." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_2464, edam:operation_3083, edam:operation_3439 ; sc:name "InteroPORC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodev.extra.cea.fr/interoporc/" ; biotools:primaryContact "InteroPORC coordinator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3315, edam:topic_3452 ; sc:citation , "pmcid:PMC10565776", "pubmed:37829204" ; sc:description "Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3436, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "InterOpt" ; sc:url "https://github.com/asalimih/InterOpt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description """Assessment of Docked Peptide Conformations by a Deep Graph Network. Abstract Motivation Peptide-protein interactions between a smaller or disordered peptide stretch and a folded receptor make up a large part of all protein-protein interactions. A common approach for modelling such interactions is to exhaustively sample the conformational space by fast-fourier-transform docking, and then refine a top percentage of decoys. Commonly, methods capable of ranking the decoys for selection in short enough time for larger scale studies rely on first-principle energy terms such as electrostatics, Van der Waals forces, or on pre-calculated statistical pairwise potentials. Results We present InterPepRank for peptide-protein complex scoring and ranking""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3435 ; sc:name "InterPepRank" ; sc:url "http://wallnerlab.org/InterPepRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "This software encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms." ; sc:featureList edam:operation_2403, edam:operation_3435 ; sc:name "Interpol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.1" ; sc:url "https://www.uni-due.de/~hy0546/Interpol/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3053, edam:topic_3056, edam:topic_3574 ; sc:citation "pubmed:21210977" ; sc:description "Python API to access the HapMap dataset. It provides integration facilities with both the Python ecology of software (e.g. Biopython and matplotlib) and other relavant human population datasets (e.g. Ensembl and UCSC Known Genes)" ; sc:featureList edam:operation_2409 ; sc:name "interPopula" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://popgen.net/soft/interPop/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_3557 ; sc:citation , "pubmed:28263438" ; sc:description "A pipeline to identify and model protein–protein interactions." ; sc:featureList edam:operation_2464 ; sc:name "InterPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ifm.liu.se/inter/interpred/" ; biotools:primaryContact "Björn Wallner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:35348618" ; sc:description "A freely available server for ADMET properties evaluation, model interpretation and chemical optimization." ; sc:featureList edam:operation_2429, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "interpretable-ADMET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cadd.pharmacy.nankai.edu.cn/interpretableadmet/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1133 ; sc:name "InterPro accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1355 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein signature" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_0623 ; sc:citation , , , , , , , , , , , , "pmcid:PMC165493", "pmcid:PMC1899100", "pmcid:PMC2686546", "pmcid:PMC3245097", "pmcid:PMC4383996", "pmcid:PMC5210578", "pmcid:PMC540060", "pmcid:PMC7778928", "pubmed:11125043", "pubmed:12230031", "pubmed:12520011", "pubmed:15608177", "pubmed:17202162", "pubmed:18940856", "pubmed:21082426", "pubmed:22096229", "pubmed:25428371", "pubmed:27899635", "pubmed:30398656", "pubmed:33156333" ; sc:description "Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences." ; sc:featureList edam:operation_0224 ; sc:name "InterPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI Databases" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/interpro/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623 ; sc:author "InterPro team" ; sc:citation , ; sc:description "Scan sequences against the InterPro protein signature databases." ; sc:featureList edam:operation_0239, edam:operation_3092 ; sc:name "InterProScan (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/pfa/iprscan/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623 ; sc:author "InterPro team" ; sc:citation , , "pmcid:PMC3998142", "pmcid:PMC9252731", "pubmed:24451626", "pubmed:35412617" ; sc:description "Scan sequences against the InterPro protein signature databases." ; sc:featureList edam:operation_0239, edam:operation_3092 ; sc:name "InterProScan (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/interpro/search/sequence/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Tool that combines different protein signature recognition methods into one resource. It is a reimplementation of the traditional InterProScan 4.x series and adds features such as pathway annotations and signal peptide and transmembrane prediction using Phobius." ; sc:featureList edam:operation_2479 ; sc:name "InterProScan WS (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan5_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3344 ; sc:description "Intersection of two sets of positive integers (works much faster than built-in intersect)" ; sc:isAccessibleForFree true ; sc:name "intersect sets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/23171-intersect-sets" ; biotools:primaryContact "Nick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC4833453", "pubmed:27040832" ; sc:description "InterSIM is a software application tool for simulating multiple interrelated data types with realistic intra- and inter-relationships based on the DNA methylation, mRNA gene expression, and protein expression from the TCGA ovarian cancer study." ; sc:featureList edam:operation_3211 ; sc:license "GPL-3.0" ; sc:name "InterSIM" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.0" ; sc:url "https://cran.r-project.org/web/packages/InterSIM/index.html" ; biotools:primaryContact "Prabhakar Chalise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3557 ; sc:citation ; sc:description "INTER-Species Protein Interaction Analysis. Given a set of proteins of user's interest, it first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3501 ; sc:name "INTERSPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.konkuk.ac.kr/INTERSPIA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0622, edam:topic_3295, edam:topic_3318 ; sc:citation ; sc:description """Integration of Multi-Omics Data on Topological Associated Domains. InterTADs is an open-source tool written in R, for integrating multi-omics data (e.g. DNA methylation, expression, mutation) from the same physical source (e.g. patient) taking into account the chromatin configuration of the genome, i.e. the topologically associating domains (TADs).""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3431, edam:operation_3435 ; sc:license "MIT" ; sc:name "InterTADs" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/InterTADs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3325, edam:topic_3574 ; sc:citation , "pmcid:PMC5294755", "pubmed:28132688" ; sc:description "Helps human reviewers interpret the clinical significance of variants. InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 18 criteria." ; sc:featureList edam:operation_0338, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "InterVar" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/WGLab/InterVar" ; biotools:primaryContact "Kai Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2330, edam:format_3508, edam:format_3604 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps." ; sc:featureList edam:operation_0564, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Intervene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.8", "0.6.4" ; sc:url "https://bitbucket.org/CBGR/intervene" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:36943334" ; sc:description "A Shiny-based application to map the rolled intestinal tissue onto a line." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "IntestLine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://beta.fastgenomics.org/a/intestline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:21459847" ; sc:description "Integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction." ; sc:featureList edam:operation_0303, edam:operation_2415, edam:operation_2575 ; sc:name "IntFOLD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.reading.ac.uk/bioinf/IntFOLD/" ; biotools:primaryContact "Dr Liam J. McGuffin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3047, edam:topic_3172, edam:topic_3512 ; sc:citation , "pmcid:PMC10294874", "pubmed:37372118" ; sc:description "A manually curated database of inter-tissue communication molecules and their communication routes." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "IntiCom-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rnanut.net/inticomdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0769, edam:topic_3172 ; sc:citation , "pmcid:PMC10010601", "pubmed:36922980" ; sc:description "Identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3465 ; sc:isAccessibleForFree true ; sc:name "IntLIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://intlim.ncats.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Workflow" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , , ; sc:description "IntOGen is a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. The framework identifies cancer genes and pinpoints their putative mechanism of action across tumor types." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:funder "AECC", "AGAUR", "European Research Council", "La Marato TV3", "Spanish Ministry of Economy and Competitiveness" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Intogen" ; sc:operatingSystem "Linux" ; sc:provider "UPF" ; sc:softwareHelp , , ; sc:url "http://www.intogen.org/" ; biotools:primaryContact "La Marato TV3" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:description "Tool for integrating secretomics and transcriptomics data in order to uncover paracrine cell crosstalk mechanisms." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IntOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2" ; sc:url "https://github.com/herrsalmi/IntOmics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2885, edam:topic_3295, edam:topic_3958 ; sc:citation , "pmcid:PMC9396869", "pubmed:35996085" ; sc:description "IntOMICS: an efficient integrative framework based on Bayesian networks systematically analyses gene expression, copy number variation, DNA methylation, and biological prior knowledge to infer regulatory networks." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3928 ; sc:license "Not licensed" ; sc:name "IntOMICS" ; sc:url "https://gitlab.ics.muni.cz/bias/intomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0166 ; sc:citation ; sc:description "Structure-based predictor of protein–protein interaction sites." ; sc:featureList edam:operation_2464 ; sc:name "IntPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinf.org.uk/intpred/" ; biotools:primaryContact "Andrew Martin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:description "Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila." ; sc:featureList edam:operation_2454 ; sc:license "GPL-2.0" ; sc:name "IntramiRExploreR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IntramiRExploreR.html" ; biotools:primaryContact "Surajit Bhattacharya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3810 ; sc:citation ; sc:description """An Integrative Transcript Library to Enable Genome-Free Systematic Exploration of Bougainvillea. For better access experience, the webserver may take several minutes to initiate the working evironment at your first visit. Please be patient. The Bougainvillea is a genus of thorny ornamental vines, bushes, or trees.""" ; sc:featureList edam:operation_2421 ; sc:name "InTransBo" ; sc:url "http://www.bio-add.org/InTransBo/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3407 ; sc:citation ; sc:description "INTeractive dna REPair prEDiction is a collection of services for predicting properties relating to DNA repair. DNA repair is thought to exist in all organisms that have an active metabolism, and repair systems are crucial for repairing many types of DNA damage. External damage includes (but is not limited to) ionizing (UV) radiation, tobacco smoke, and chemical alteration. Examples of internal damage are DNA copying errors, oxygen byproducts resulting from metabolism, and hydrolysis." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "INTREPED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~jbbrown/dnaRepairPrediction/v2/index.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_1775, edam:topic_3510 ; sc:citation "pubmed:19443452" ; sc:description "The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available." ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_1777 ; sc:name "INTREPID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/berkeleyphylogenomics/intrepid" ; biotools:primaryContact "Kimmen Sjölander" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_3053 ; sc:citation , ; sc:description "Software package for mapping components of isolation in hybrids. It is an R-package that implements various methods for the analysis of gene introgression in hybrid zones." ; sc:featureList edam:operation_2429 ; sc:name "introgress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.23" ; sc:url "http://www.uwyo.edu/buerkle/software/introgress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0659, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC10190034", "pubmed:37198692" ; sc:description "Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_0446, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Introme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CCICB/introme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "A motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification" ; sc:featureList edam:operation_2929, edam:operation_3644, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "IntroSpect" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/BGI2016/IntroSpect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3325, edam:topic_3512 ; sc:citation , "pmcid:PMC9825543", "pubmed:36399497" ; sc:description "A comprehensive database of introns across human tissues." ; sc:featureList edam:operation_0232 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "IntroVerse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rytenlab.com/browser/app/introverse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0602, edam:topic_2229, edam:topic_3557 ; sc:citation "pubmed:22649056" ; sc:description "Web tool for confidence scoring of biological interactions. Individual interactions are weighted according to the likelihood that they actually take place in the cell, and can be used to filter out false positives." ; sc:featureList edam:operation_2429, edam:operation_2464, edam:operation_3436, edam:operation_3439, edam:operation_3695 ; sc:name "IntScore" ; sc:url "http://intscore.molgen.mpg.de" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1696 ; sc:name "Drug report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1365 ; sc:name "Fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3314 ; sc:citation , "pubmed:25380960" ; sc:description "Drug side effects are one of the main health threats worldwide, and an important obstacle in drug development. Understanding how adverse reactions occur requires knowledge on drug mechanisms at the molecular level. Despite recent advances, the need for tools and methods that facilitate side effect anticipation still remains. IntSide is a web server to elucidate the molecular processes involved in drug side effects through the integration of chemistry and biology. IntSide currently catalogues 1,175 side effects caused by 996 drugs, associated with drug features divided into eight categories, belonging to either biology or chemistry. On the biological side, IntSide reports drug targets and off-targets, pathways, molecular functions and biological processes. From a chemical viewpoint, it includes molecular fingerprints, scaffolds and chemical entities." ; sc:featureList edam:operation_3216 ; sc:name "IntSIde" ; sc:url "https://intside.irbbarcelona.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_2533, edam:topic_3168 ; sc:citation "pubmed:27164567" ; sc:description "This software package has been developed to simulate various genome mutations including germline and somatic variations from next generation sequencing data, and also to generate read data from mixed genomes by considering moderate levels of tumor purity." ; sc:featureList edam:operation_2426 ; sc:name "IntSIM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/intsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3320, edam:topic_3574 ; sc:citation "pubmed:27009626" ; sc:description "Tool to predict a splicing consequence of an SNV at intron positions -50 to -3 close the 3’ end of an intron of the human genome." ; sc:featureList edam:operation_2499 ; sc:name "IntSplice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3125, edam:topic_3176 ; sc:citation "pubmed:24504871" ; sc:description "This web-server was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster." ; sc:featureList edam:operation_0432 ; sc:name "iNuc-PseKNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/iNuc-PseKNC" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_3176 ; sc:citation , "pmcid:PMC8652021", "pubmed:34623394" ; sc:description "Given nucleosome genomic coordinates, ligation junctions (in pairs format) produced by the Pairtools program, the inucs command line tool identifies interactions falling into different nucleosomes and counts them." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iNucs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Karimi-Lab/inucs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3810 ; sc:citation ; sc:description """Analysing global economic costs of invasive alien species with the invacost R package. 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However, it does not account for the temporal dynamics of costs, and may thus underestimate the costs of invasions, especially for recent years for which we likely have incomplete data.""" ; sc:featureList edam:operation_0224, edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:name "invacost" ; sc:url "https://github.com/Farewe/invacost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168, edam:topic_3175, edam:topic_3473 ; sc:citation , "pmcid:PMC7057458", "pubmed:32138660" ; sc:description """Finding genomic inversions from high-throughput sequence data based on feature mining. We released three programs, InvBFM, fixRealData, and fixSimuData. Both fixRealData and fixSimuData are written in Shell for data preprocessing. InvBFM is written in Python which proposed in our paper.All three programs are packaged as executables, downloading from their source code and changed their permissions to executable for using as a tool.""" ; sc:featureList edam:operation_0310, edam:operation_3891, edam:operation_3937 ; sc:name "InvBFM" ; sc:url "https://github.com/wzj1234/InvBFM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3175 ; sc:description "invClust is a method to detect inversion-related haplotypes in SNP data" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "invClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/isglobal-brge/invClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "The inverse function of gradient()." ; sc:isAccessibleForFree true ; sc:name "Inverse Gradient" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/7906-inverse-gradient" ; biotools:primaryContact "Patrick Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_3168 ; sc:citation ; sc:description "Package to find genetic inversions in genotype (SNP array) data." ; sc:featureList edam:operation_0253 ; sc:license "GPL-2.0" ; sc:name "inveRsion" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/inveRsion.html" ; biotools:primaryContact "Alejandro Caceres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_0780, edam:topic_3068, edam:topic_3407 ; sc:citation , "pmcid:PMC9216569", "pubmed:35363307" ; sc:description "An expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "invertebratefungi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://invertebratefungi.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3175, edam:topic_3518 ; sc:citation , "pmcid:PMC8325862", "pubmed:34332539" ; sc:description "Bayesian inversion genotyping with Strand-seq data." ; sc:featureList edam:operation_3196, edam:operation_3208, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "InvertypeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/vincent-hanlon/InvertypeR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc:citation , , "pmcid:PMC6310983", "pmcid:PMC7072748", "pubmed:30594132", "pubmed:32085510" ; sc:contributor , ; sc:description "These scripts provide functions to analyse splice sites based on a genome sequence (FASTA) and a corresponding annotation (GFF3) provided by the NCBI. Next, RNA-Seq reads can be mapped via STAR and the resulting BAM files can be converted into customized coverage files (COV) which are required for the validation of splice sites. The usage of individual splice sites can be quantified based on the number of mapped and propperly splitted RNA-Seq reads. These scripts generate report files and figures for the documentation of the analysis process." ; sc:isAccessibleForFree true ; sc:name "investigation of (non canonical) splice sites" ; sc:softwareHelp ; sc:url "https://github.com/bpucker/ncss2018" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2815, edam:topic_3175, edam:topic_3325 ; sc:citation , "pmcid:PMC3965118", "pubmed:24253300" ; sc:description "Database that stores inversion predictions from healthy individuals and enables to search inversions by gene symbol, genomic position and inversion name." ; sc:featureList edam:operation_3197, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "InvFEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://invfestdb.uab.cat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3384, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC8204560", "pubmed:34130622" ; sc:description "An interactive tool for statistical analysis of omics data and clinical data." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "IOAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/WlSunshine/IOAT-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation , "pmcid:PMC4282680", "pubmed:25423016" ; sc:description """Real-time Genomic Analysis iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive""" ; sc:featureList edam:operation_0337 ; sc:name "Iobio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iobio.io/" ; biotools:primaryContact "iobio Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3070, edam:topic_3372 ; sc:citation "pubmed:21323670" ; sc:description "This project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software." ; sc:featureList edam:operation_3760 ; sc:name "IOCBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pearu/iocbio" ; biotools:primaryContact "Marko Vendelin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3169, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33096244" ; sc:description """An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. iODA, short for integrative Omics Data Analysis, is an evidence-based bioinformatics model and software tool for omics data analysis. iODA is a graphical user interface (GUI) local tool with the aim of integrating and analyzing data sets including mRNA, microRNA (miRNA), and protein–DNA interaction (chromatin immunoprecipitation followed by high-throughput sequencing, ChIP-Seq) for pathway consistency (Figure 1).""" ; sc:featureList edam:operation_0389, edam:operation_3792, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "iODA" ; sc:url "http://www.sysbio.org.cn/iODA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2258, edam:topic_3314 ; sc:citation , "pubmed:33368350" ; sc:description """A python library for reading, writing, and converting computational chemistry file formats and generating input files. IOData is a HORTON 3 module for input/output of quantum chemistry file formats. Documentation is here: https://iodata.readthedocs.io/en/latest/index.html.""" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_2476 ; sc:license "LGPL-3.0" ; sc:name "IOData" ; sc:url "https://github.com/theochem/iodata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3390, edam:topic_3407, edam:topic_3520, edam:topic_3810 ; sc:citation , "pmcid:PMC8181883" ; sc:description "USDA, NIH and FDA Iodine Database of U.S. Foods for Estimating Iodine Intakes." ; sc:featureList edam:operation_2428 ; sc:name "iodine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/methods-and-application-of-food-composition-laboratory/mafcl-site-pages/iodine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2640 ; sc:citation , "pubmed:36201885" ; sc:description "An interactive online feature selection tool for survival analysis." ; sc:featureList edam:operation_0224, edam:operation_3359, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IOFS-SA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfor.nefu.edu.cn/IOFS-SA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3520 ; sc:author "Jan Fesl" ; sc:contributor "Marie Doležalová" ; sc:description "Dedicated for MS data measured in high resolution mode and their interpretation. Primarily oriented on devices developed by the Thermo-Fisher Scientific company." ; sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:name "IoM - Interpreter of Mass" ; sc:operatingSystem "Windows" ; sc:provider "ELIXIR-CZ", "University of South Bohemia, Czech Republic" ; sc:softwareHelp ; sc:softwareVersion "1.0.0.0" ; sc:url "http://www.prf.jcu.cz/iom/" ; biotools:primaryContact "Jan Fesl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_3169, edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3676 ; sc:description "Cloud based workflow analysis framework for managing, analyzing and visualizing NGS data." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3227, edam:operation_3662 ; sc:name "IOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://interpretomics.co/iomics" ; biotools:primaryContact "Contact Form", "InterpretOmics Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3370, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC10413325", "pubmed:37505508" ; sc:description "Mass Spectrometry Imaging Data Analysis Platform for Continuous Ionization Techniques." ; sc:featureList edam:operation_2409, edam:operation_3215, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "i2i" ; sc:url "https://github.com/LanekoffLab/i2i" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3168, edam:topic_3810 ; sc:citation , "pmcid:PMC7372021", "pubmed:32714063" ; sc:description """bioinformatics plugins toward genomics-assisted breeding. Genotyping and genomic selection plugins for Ion Torrent NGS platform. version: 1.01 (March 12 2020 update). IonBreeders: automated bioinformatics plugins toward genomics-assisted breeding. The National Agriculture and Food Research Organization (hereinafter referred to as NARO) does not guarantee that defects, errors or malfunction will not occur with respect to IonBreeders.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3227, edam:operation_3557 ; sc:name "IonBreeders" ; sc:url "https://github.com/DEMETER298/IonBreeders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7487613", "pubmed:32907531" ; sc:description """A reference-based compression tool for ion torrent sequence files. IonCram is the first compression tool that efficiently compresses the Ion Torrent BAM files. IonCram extends the popular CRAM program by improving the compression of the flow signals. IonCram could improve the compression of CRAM by 13% achieving an overall space saving of about 45%.""" ; sc:featureList edam:operation_3198, edam:operation_3454 ; sc:name "IonCRAM" ; sc:url "https://github.com/ionCRAM/ionCRAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_2229, edam:topic_3173, edam:topic_3520 ; sc:citation , "pmcid:PMC8464566", "pubmed:34562172" ; sc:description "Galaxy tool for processing and analysis of ionomics data , based on the modification of R package IonFlow." ; sc:featureList edam:operation_2436, edam:operation_2939, edam:operation_3891, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IonFlow" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/wanchanglin/ionflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3301 ; sc:citation "pubmed:25953799" ; sc:description "Publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. 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It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. 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It consists of four databases: KIR, MHC, human platelet antigens and ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines." ; sc:featureList edam:operation_0346, edam:operation_3196, edam:operation_3202, edam:operation_3227, edam:operation_3435 ; sc:name "IPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/ipd/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_2830 ; sc:citation "pubmed:21071412" ; sc:description "Database that provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data." ; sc:featureList edam:operation_0224, edam:operation_2428, edam:operation_3218, edam:operation_3227, edam:operation_3431 ; sc:name "IMGT HLA database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/imgt/hla/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0089, edam:topic_0199, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC8118100", "pubmed:33985433" ; sc:description "Infectious Pathogen Detector (IPD) is an automated pathogen analysis pipeline for seamless analysis of single and paired-end data from heterogenous NGS platforms." ; sc:featureList edam:operation_0324, edam:operation_3227, edam:operation_3431, edam:operation_3799 ; sc:name "IPD" ; sc:softwareHelp ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0634, edam:topic_0781, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC7929363", "pubmed:33479725" ; sc:description """An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Infectious Pathogen Detector (IPD). IPD is an automated pathogen analysis pipeline for seamless analysis of single and paired-end data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS-CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation. IPD is an in-silico GUI-based automated pathogen analysis pipeline for seamless analysis of data from heterogenous NGS platforms. IPD performs integrated variants analysis, along with systematic quantification of pathogen genomes. IPD additionally has an in-built SARS- CoV-2 analysis module, for assignment of viral clades of the samples analyzed and an automated report generation.""" ; sc:featureList edam:operation_3192, edam:operation_3227, edam:operation_3461, edam:operation_3799 ; sc:name "IPD-pipeline" ; sc:url "http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_3420, edam:topic_3510, edam:topic_3538 ; sc:citation "pubmed:16796745", "pubmed:17553839" ; sc:description "iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence." ; sc:featureList edam:operation_0224, edam:operation_0267, edam:operation_0470, edam:operation_3092 ; sc:name "iPDA" ; sc:operatingSystem "Linux" ; sc:url "http://biominer.bime.ntu.edu.tw/ipda/" ; biotools:primaryContact "Chien-Yu Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3500 ; sc:citation , "pmcid:PMC8549166", "pubmed:34702185" ; sc:description "A PIWI-bound piRNAs database to mining NGS sncRNA data and beyond." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IPdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ipdb2.shinyapps.io/ipdb2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3365 ; sc:citation ; sc:description """Reconstruct Individual Patient Data from Published Kaplan-Meier Survival Curves. Map Digitized Survival Curves Back to Individual Patient Data. Trial Design – Innovative Methodologies. An implementation to reconstruct individual patient data from Kaplan-Meier (K-M) survival curves, visualize and assess the accuracy of the reconstruction, then perform secondary analysis on the reconstructed data.""" ; sc:featureList edam:operation_3435, edam:operation_3503 ; sc:license "GPL-2.0" ; sc:name "IPDfromKM" ; sc:url "http://trialdesign.org/one-page-shell.html#IPDfromKM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pubmed:32808437" ; sc:description "An R Shiny tool for analyzing and visualizing individual patient data meta-analyses of diagnostic test accuracy." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "IPDmada" ; sc:url "https://jwang7.shinyapps.io/ipdmada/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:32805005" ; sc:description """Identification of differentially methylated regions with interval p-values. Quality control and analysis tools for Illumina DNA methylation BeadChip. Tool kits for quanlity control, analysis and visulization of Illumina DNA methylation arrays.""" ; sc:featureList edam:operation_2428, edam:operation_3207, edam:operation_3659, edam:operation_3809 ; sc:license "Artistic-2.0" ; sc:name "ipDMR" ; sc:url "https://bioconductor.org/packages/release/bioc/html/ENmix.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:22564732" ; sc:description "Integrated pipeline for rational quality control and association analysis of genome-wide genetic studies." ; sc:featureList edam:operation_2403 ; sc:name "IPGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ipgwas/" ; biotools:primaryContact "Yan-HuiFan", "You-QiangSong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3304, edam:topic_3382 ; sc:citation , "pubmed:31947335" ; sc:description """An Open Non-Contact Imaging-Based Physiological Measurement Toolbox. In the past few years a lot of attention has been given to methods for remotely measuring physiological signals using low-cost cameras. Imaging PPG (iPPG) focuses on the measurement of volumetric changes in blood flow at distance from the body using imaging devices to capture changes in transmitted or reflected light. Imaging ballistocardiography (iBCG) typically leverages optical flow estimation to track the vertical motion of the head or body from a video sequence. Both iPPG and iBCG methods can be used to recover human vital signals.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "iPhys" ; sc:url "https://github.com/danmcduff/iphys-toolbox" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2384 ; sc:name "IPI protein ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0085, edam:topic_3366, edam:topic_3571 ; sc:citation ; sc:description "Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. It effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences." ; sc:featureList edam:operation_0338, edam:operation_2409, edam:operation_3672 ; sc:name "International protein index (IPI)" ; sc:url "http://www.ebi.ac.uk/IPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749, edam:topic_0769 ; sc:citation , "pubmed:34004411" ; sc:description "The iPick program is available as a module for the POKY and NMRFAM-SPARKY. It is highly recommended that you use the module instead of the command line tool. The main reasons are the ease of work and the extended capabilities provided in the module." ; sc:featureList edam:operation_2428, edam:operation_3215 ; sc:license "BSD-2-Clause" ; sc:name "iPick" ; sc:url "https://github.com/pokynmr/ipick" ; biotools:primaryContact , , "John L. Markley", "Woonghee Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_0659, edam:topic_3335, edam:topic_3474 ; sc:citation , "pmcid:PMC9662734", "pubmed:36301998" ; sc:description "Identification of piRNA-disease associations based on Graph Convolutional Network." ; sc:featureList edam:operation_2492, edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iPiDA-GCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/iPiDA-GCN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_0659, edam:topic_3335, edam:topic_3360 ; sc:citation , "pmcid:PMC9410559", "pubmed:35969645" ; sc:description "Identifying piwi-interacting RNA-disease associations based on Learning to Rank." ; sc:featureList edam:operation_0224, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "iPiDA-LTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bliulab.net/iPiDA-LTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_3520 ; sc:citation ; sc:description "Targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser" ; sc:featureList edam:operation_0337, edam:operation_3208 ; sc:name "iPiG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "r5" ; sc:url "http://sourceforge.net/projects/ipig/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2269, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC8756181", "pubmed:34718410" ; sc:description "Importance-Penalized Joint Graphical Lasso (IPJGL)." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3625, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "IPJGL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Wu-Lab/IPJGL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0780, edam:topic_2885 ; sc:citation , , , , , ; sc:description "A combination of several software tools for sequence analysis developed at the IPK Gatersleben. The BLAST server utilizes a homology search against the cereal genome resources (barley, rye and bread wheat). Kmasker plants is able to mask sequences originating from ten agronomically important plants based on mathematical defined repeats, furthermore, selection of sequences applicable for guideRNA construction for genome editing (CRISPR) or for fluorescence in situ hybridization is also possible. MISA web searches a sequence for microsatellites and is able generate molecular markers or primer. Using BRIDGE the complete barley collection of the IPK genebank can be visually explored in an interactive manner through diversity, certain phenotyped traits, and based on sequence polymorphisms. The barley genome explorer (BARLEX) is a system to visually inspect the reference genome sequence of barley, enriched with expression data, repeat and gene annotation and molecular marker data." ; sc:isAccessibleForFree true ; sc:name "Crop Analysis Tool Suite (CATS)" ; sc:url "https://cats.ipk-gatersleben.de/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "A homology search against the current barley sequences resources is provided. The complete sequences data set comprises the whole genome shotgun assemblies of the cultivars Morex, Barke and Bowman as well as the high and low confidence gene sets. The newest POPSEQ anchoring data is integrated. Furthermore, the barley exome capture targets are provided. Additionally, resources like bacterial artificial chromosome assemblies, BAC end sequences and full length cDNAs are included." ; sc:featureList edam:operation_0346 ; sc:name "IPK BLAST Server" ; sc:operatingSystem "Linux" ; sc:provider "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", "ipk" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://webblast.ipk-gatersleben.de" ; biotools:primaryContact "Dr. Uwe Scholz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0099 ; sc:citation , ; sc:description "IPknot provides services for predicting RNA secondary structures including a wide class of pseudoknots. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut." ; sc:featureList edam:operation_0271, edam:operation_0278, edam:operation_0492, edam:operation_2423 ; sc:name "IPknot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.3.1" ; sc:url "http://rtips.dna.bio.keio.ac.jp/ipknot/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0128, edam:topic_0166, edam:topic_0203 ; sc:citation ; sc:description """A knowledge-based approach for identifying protein-nucleic acid interaction hot spots. A webserver for identifying protein-nucleic acid interfaces hotspot residues. iPNHOT was developed by using support vector machine based on three different kinds of features including atom number of the residue, depth and protrusion index, solvent accessible surface area, electrostatic potential and secondary structure. It needs one input file: pdbfile which contains the coordinates of a protein-nucleic acid complex. More details can be found in the tutorial.""" ; sc:featureList edam:operation_0321, edam:operation_0389, edam:operation_0478, edam:operation_3092 ; sc:name "iPNHOT" ; sc:url "http://zhulab.ahu.edu.cn/iPNHOT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC4404568", "pubmed:25888443" ; sc:description "The outcome of XCMS data processing strongly depends on the parameter settings. Isotopologue Parameter Optimization is a parameter optimization tool that is applicable for samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. It uses natural, stable 13C isotopes to calculate peak picking score. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models." ; sc:featureList edam:operation_2425 ; sc:license "GPL-2.0" ; sc:name "IPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IPO.html" ; biotools:primaryContact "Thomas Riebenbauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293 ; sc:citation "pubmed:18989047" ; sc:description "Efficient enumerative algorithm for incomplete Perfect Phylogeny Haplotyping." ; sc:featureList edam:operation_0487 ; sc:name "IPP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://vlsi.cs.ucf.edu/nsf/software/ipph/" ; biotools:primaryContact "Dr. Amar Mukherjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_1317, edam:topic_3534 ; sc:citation "pubmed:26797600" ; sc:description "This web-server used to predict the Protein-Protein Binding Sites(PPBS)." ; sc:featureList edam:operation_2464 ; sc:name "iPPBS-Opt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iPPBS-Opt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_1317, edam:topic_3534 ; sc:citation "pubmed:26375780" ; sc:description "This web-server is used to predict the Protein-Protein Binding Sites(PPBS)." ; sc:featureList edam:operation_2464 ; sc:name "iPPBS-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iPPBS-PseAAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs." ; sc:featureList edam:operation_3222 ; sc:license "GPL-2.0" ; sc:name "IPPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IPPD.html" ; biotools:primaryContact "Martin Slawski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_1775, edam:topic_3474 ; sc:citation , "pubmed:36403184" ; sc:description "An integrated peptide and protein function prediction framework based on fused features and ensemble models." ; sc:featureList edam:operation_1777, edam:operation_3092 ; sc:license "Not licensed" ; sc:name "IPPF-FE" ; sc:url "https://github.com/Luo-SynBioLab/IPPF-FE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621 ; sc:citation ; sc:description "IPPI is a web server of inferring protein-protein interactions" ; sc:featureList edam:operation_2479 ; sc:name "IPPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/ppi-form.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3343 ; sc:citation ; sc:description "IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large variety of data is stored within IPPI-DB: structural, pharmacological, binding and activity profile, pharmacokinetic and cytotoxicity when available, as well as some data about the PPI targets themselves." ; sc:featureList edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iPPI-DB" ; sc:url "https://ippidb.pasteur.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0128 ; sc:citation "pubmed:25908206" ; sc:description "Ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC." ; sc:featureList edam:operation_2464 ; sc:name "iPPI-Esml" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iPPI-Esml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_3172, edam:topic_3520, edam:topic_3810 ; sc:citation , "pmcid:PMC9946207", "pubmed:36758069" ; sc:description """iPRESTO (integrated Prediction and Rigorous Exploration of biosynthetic Sub-clusters Tool) is a command line tool for the detection of gene sub-clusters in a set of Biosynthetic Gene Clusters (BGCs) in GenBank format.""" ; sc:featureList edam:operation_3216, edam:operation_3432, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "iPRESTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://git.wageningenur.nl/bioinformatics/iPRESTO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749 ; sc:citation , "pubmed:35038653" ; sc:description "A novel model based on generative adversarial learning for identifying promoters and their strength" ; sc:license "Not licensed" ; sc:name "iPro-GAN" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/Bovbene/iPro-GAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3173, edam:topic_3474 ; sc:citation , "pubmed:36161334" ; sc:description "A framework for identifying promoters in multiple species." ; sc:featureList edam:operation_0440, edam:operation_3359, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iPro-WAEL" ; sc:url "https://github.com/HaoWuLab-Bioinformatics/iPro-WAEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC4245931", "pubmed:25361964" ; 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Discovered a protein or a gene likely to be involved in a disease, and you want to find out what is known about its interactions with other proteins. 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IReNA performs modular regulatory network to reveal key transcription factors and significant regulatory relationships among modules, providing biological insights on regulatory mechanisms." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IReNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jiang-junyao/IReNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0621, edam:topic_0659, edam:topic_2229, edam:topic_3512 ; sc:citation ; sc:description """A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. IRESbase-A Comprehensive Database of Experimentally Verified Internal Ribosome Entry Site (IRES). 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Iranian traditional medicine (also called Persian Medicine), is an elaborate holistic system of healing grounded in a philosophical basis." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3559 ; sc:name "IrGO" ; sc:softwareHelp ; sc:url "http://ir-go.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3068, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC8372526", "pubmed:34422018" ; sc:description "A Robust in silico Method for Optimal Reference Gene Validation." ; sc:featureList edam:operation_0315, edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "iRGvalid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wlake.shinyapps.io/iRGvalid/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0780 ; sc:citation , "pubmed:34864888" ; sc:description "An integrated XGBoost model for detecting multitype post-translational modification sites in rice." ; sc:featureList edam:operation_0417, edam:operation_3647, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "iRice-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lin-group.cn/server/iRice-MS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3068, edam:topic_3382 ; sc:citation , "pmcid:PMC9138121", "pubmed:35634096" ; sc:description "Open source software for processing images from infrared thermal cameras." ; sc:featureList edam:operation_0460, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "IRimage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gpereyrairujo/IRimage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3301, edam:topic_3382 ; sc:citation ; sc:description "Image processing software that automatically quantifies several features of microbial colonies in high throughput." ; sc:featureList edam:operation_2495, edam:operation_3443 ; sc:name "Iris" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://critichu.github.io/Iris/" ; biotools:primaryContact "George Kritikos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """An integrative single-cell RNA-Seq interpretation system for functional gene module analysis. ---Integrative scRNA-Seq Interpretation System for Functional Gene Module analysis. Single-cell RNA-Seq data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases.""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3463 ; sc:name "IRIS-FGM" ; sc:url "https://github.com/OSU-BMBL/IRIS-FGM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3382 ; sc:citation ; sc:description """An accurate and efficient barcode calling tool for in situ sequencing. Information Refining for In situ Sequencing. See 'README.1.pyIRIS.md' for detail.""" ; sc:featureList edam:operation_0337, edam:operation_3185, edam:operation_3200 ; sc:license "BSD-3-Clause" ; sc:name "IRIS-py" ; sc:url "https://github.com/th00516/ISS_pyIRIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC7319566", "pubmed:32421805" ; sc:description """Integrated cell-type-specific regulon inference server from single-cell RNA-Seq. The underlying regulatory mechanisms that induce the identity of cell types or physiological states are normally uncovered in the single-cell RNA-Sequencing (scRNA-Seq) analyses. Here we propose IRIS3 (Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq) as the first-of-its-kind web server for CTS-R inference in human and mouse. integrated cell type specific Regulon inference from single-cell rna seq.""" ; sc:featureList edam:operation_0337, edam:operation_1781, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "IRIS3" ; sc:url "https://bmbl.bmi.osumc.edu/iris3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "IrisSpatialFeatures reads the output of the PerkinElmer inForm software and calculates a variety of spatial statistics. In addition to simple counts, it can derive average nearest neighbors for each cell-type and interaction summary profiles for each celltype. These statistics are derived across images, both overall and regions of interest as defined by user defined masks." ; sc:featureList edam:operation_3443 ; sc:license "MIT" ; sc:name "IrisSpatialFeatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IrisSpatialFeatures.html" ; biotools:primaryContact "Daniel Gusenleitner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:citation ; sc:description "IRMa ( Interprétation des Résultats Mascot)  toolbox provides an interactive application to assist in the validation of Mascot® search results. IRMa reads MASCOT® result (using Matrix Science® Parser distributed free of charge) and automatically filters identified peptides. All relevant information is displayed in a structured manner, showing “proteins hits” details. User can then manually or automatically confirm or reject individual peptide spectrum matches." ; sc:featureList edam:operation_2421, edam:operation_2428 ; sc:name "IRMa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.31.1" ; sc:url "http://biodev.extra.cea.fr/docs/irma/doku.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:36470433" ; sc:description "A novel computational method for effectively detecting N4-acetylcytidine sites in human mRNA." ; sc:featureList edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "iRNA-ac4C" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lin-group.cn/server/iRNA-ac4C/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web service" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0621, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7229270", "pubmed:32435427" ; sc:description """Computational identification of N6-methyladenosine sites in multiple tissues of mammals. Home About us Web-Server Contact us Download Citation. N6-methyladenosine (m6A) is the methylation of the adenosine at the nitrogen-6 position, which is the most abundant RNA methylation modification and involves a series of important biological processes. Type or copy paste the query RNA sequences into the input box at the center,or upload a FASTA file. Choose Species: Human Mouse Rat and Tissues: Brain Liver Kidney.""" ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_3937 ; sc:name "iRNA-m6A" ; sc:url "http://lin-group.cn/server/iRNA-m6A" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3295 ; sc:citation "pubmed:26314792" ; sc:description "This web-server was developed to identify the N6-methyladenosine (m6A). It was observed by the rigorous cross-validation test on the benchmark dataset that the accuracy achieved by the predictor in identifying m6A was 65.59%." ; sc:featureList edam:operation_3204 ; sc:name "iRNA-Methyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/iRNA-Methyl" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7137033", "pubmed:32296686" ; sc:description """The First Predictor to Identify RNA 5-Hydroxymethylcytosine Modifications Using Machine Learning. A generic webserver for predicting RNA 5hmC sites.""" ; sc:name "iRNA5hmC" ; sc:url "http://server.malab.cn/iRNA5hmC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7701324", "pubmed:33304452" ; sc:description """Accurate prediction of RNA 5-hydroxymethylcytosine modification by utilizing novel position-specific gapped k-mer descriptors. iRNA5hmC-PS: Accurate prediction of RNA 5-Hydroxymethylcytosine Modification by Utilizing Position-Specific k-mer and Position-Specific Gapped k-mer. Authors: Sajid Ahmed†, Zahid Hossain†, Mahtab Uddin, Ghazaleh Taherzadeh, Alok Sharma Swakkhar Shatabda*, Abdollah Dehzangi*.""" ; sc:featureList edam:operation_3659, edam:operation_3937 ; sc:name "iRNA5hmC-PS" ; sc:url "https://github.com/zahid6454/iRNA5hmC-PS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3127, edam:topic_3511 ; sc:citation ; sc:description "Identify DNA replication origins by three-window-based PseKNC." ; sc:featureList edam:operation_0253 ; sc:name "iRO-3wPseKNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.hitsz.edu.cn/iRO-3wPseKNC/" ; biotools:primaryContact "Bin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "iROAR (Immune Repertoire Over Amplification) is a tool for multiplex PCR-specific bias evaluation and correction to adjust clonal count of VDJtool output table." ; sc:featureList edam:operation_0308, edam:operation_3799, edam:operation_3965 ; sc:name "iROAR" ; sc:url "https://github.com/smiranast/iROAR" ; biotools:primaryContact "Alexander Komkov", "Ilgar Mamedov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3365, edam:topic_3382 ; sc:citation "pubmed:23422340" ; sc:description "Open-source project dedicated to providing a MATLAB framework for vibrational spectroscopy. The goal of the project is to provide a comprehensive and user-friendly environment for analysis, whilst facilitating development and validation of algorithms for computational biology using vibrational spectroscopy." ; sc:featureList edam:operation_3214 ; sc:name "irootlab" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://trevisanj.github.io/irootlab/" ; biotools:primaryContact "Júlio Trevisan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2229, edam:topic_3293, edam:topic_3945 ; sc:citation , "pmcid:PMC10581538", "pubmed:37793175" ; sc:description "Augmented tool to detect inverted repeats in plastid genomes." ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:name "IRplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://irscope.shinyapps.io/IRplus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0820, edam:topic_3400 ; sc:citation , "pmcid:PMC5907363", "pubmed:29669518" ; sc:description "High throughput immune receptor profiling." ; sc:featureList edam:operation_2996 ; sc:license "GPL-3.0" ; sc:name "IRProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://irprofiler.med.auth.gr:8080/" ; biotools:primaryContact "Christos Maramis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_0780 ; sc:citation ; sc:description "Visualize the junction sites of chloroplast genomes." ; sc:featureList edam:operation_3208 ; sc:name "IRscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://irscope.shinyapps.io/irapp/" ; biotools:primaryContact "Ali Amiryousefi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3127, edam:topic_3511 ; sc:citation , "pmcid:PMC3616736", "pubmed:23303794" ; sc:description "Identify recombination spots with pseudo dinucleotide composition." ; sc:featureList edam:operation_0451 ; sc:name "iRSpot-PseDNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin-group.cn/server/iRSpot-PseDNC" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3127, edam:topic_3511 ; sc:citation , "pmcid:PMC3958819", "pubmed:24469313" ; sc:description "Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components." ; sc:featureList edam:operation_0239 ; sc:name "iRSpot-TNCPseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC7052261", "pubmed:32158451" ; sc:description """A Web Server for Artificial Intelligence Based Prediction of Major Basmati Paddy Seed Varieties. “Basmati” derives its roots in two Sanskrit words “Vas”(vasay) meaning “aroma” and “Mati” (mayup) meaning ingrained from the origin, common usage could have resulted in change of vas to bas resulting in Basmati. According to a survey conducted by MoEF&CC, published in report ”Report on Identity Preservation of Basmati Rice at Various Stages in the Rice Supply Chain”, in Haryana, 80-85% farmers were able to identify the seed variety whereas, a large number of farmers (almost 20%) were still depending on the tag on seed bag they purchased whereas in Aligarh market area of Uttar Pradesh 100% farmers were depending on the tag on seed bag. Primary Basmati Quality Characteristics.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3443 ; sc:name "iRSVPred" ; sc:url "http://14.139.62.220/rice/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pmcid:PMC7495790", "pubmed:34565936" ; sc:description "An R Package for Estimating IRT Models With Guessing or Slipping Parameters." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "IRTBEMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/package=IRTBEMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3071 ; sc:citation "pubmed:12689096" ; sc:description "Tool designed to reduce the complexity of very large sets of data by decomposing it into so-called “modules”. In the context of gene expression data these modules consist of subsets of genes that exhibit a coherent expression profile only over a subset of microarray experiments." ; sc:featureList edam:operation_2409 ; sc:name "ISA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.unil.ch/cbg/index.php?title=ISA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3382, edam:topic_3489 ; sc:citation ; sc:description """A scalable Java library for creating ISA-Tab metadata. isa4j is a comprehensive and scalable Java Library for the programmatic generation of experimental metadata descriptions using the ISATab container format. We're assuming you're familiar with the ISA-Tab framework in the remainder of the manual; if you're not, please read up about it first. This is an XML namespace defined in the XML Linking Language (XLink) specification.""" ; sc:featureList edam:operation_0335 ; sc:license "MIT" ; sc:name "isa4j" ; sc:url "https://mvnrepository.com/artifact/de.ipk-gatersleben/isa4j" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382, edam:topic_3518 ; sc:citation ; sc:description """An open platform for interoperable life science experimental metadata. Built around the ‘Investigation’ (the project context), Study’ (a unit of research) and ‘Assay’ (analytical measurement) general-purpose Tabular format, the ISA tools helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable. The ISA API aims to provide you, the developer, with a set of tools to help you easily and quickly build your own ISA objects, validate, and convert between serializations of ISA-formatted datasets and other formats/schemas (e.g. SRA schemas). The ISA API is published on PyPI as the isatools package.""" ; sc:featureList edam:operation_1812, edam:operation_3096, edam:operation_3431 ; sc:name "ISA API" ; sc:url "http://github.com/ISA-tools/isa-api/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3071 ; sc:citation ; sc:description "Framework and tools that help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies." ; sc:featureList edam:operation_0224, edam:operation_2409 ; sc:name "ISA tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://isa-tools.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "ISAAC comprises of genome aligner and variant caller, by Illumina." ; sc:featureList edam:operation_3182, edam:operation_3227 ; sc:name "ISAAC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sequencing" ; biotools:primaryContact "ISAAC support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC9296836", "pubmed:35874605" ; sc:description "Accelerated 2D Classification With ISAC Using GPUs." ; sc:featureList edam:operation_3432, edam:operation_3458 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ISAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.gwdg.de/mpi-dortmund/sphire/cuISAC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0654, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:16845056", "pubmed:17468499" ; sc:description "Tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. It is included in the GEPAS package." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3463 ; sc:name "ISACGH" ; sc:url "http://bioinfo.cipf.es/isacghtrac" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3016 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3473, edam:topic_3796 ; sc:citation ; sc:description "A program for identifying a favored mutation in positive selective sweep. It enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals." ; sc:featureList edam:operation_2238, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "iSAFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/alek0991/iSAFE" ; biotools:primaryContact "Ali Akbari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2258, edam:topic_2814 ; sc:citation ; sc:description "Intelligent System for Analysis, Model Building And Rational Design." ; sc:featureList edam:operation_0477, edam:operation_2406 ; sc:name "ISAMBARD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://pypi.org/project/ISAMBARD/" ; biotools:primaryContact "C. Wood", "D.N. Woolfson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:19420060" ; sc:description "iSARST is a web server for protein structural similarity searches. 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sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_2269, edam:topic_3520 ; sc:citation , , "pubmed:21526793", "pubmed:23470796" ; sc:description "isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. 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Clusters were computed using the IsoRankN algorithm, which uses spectral methods, to combine sequence and PPI data to produce clusters of functionally related proteins. IsoBase may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword." ; sc:featureList edam:operation_0224, edam:operation_0277, edam:operation_3432, edam:operation_3459 ; sc:name "IsoBase" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://isobase.csail.mit.edu/" ; biotools:primaryContact "IsoBase Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196 ; sc:description "Use transcripts to assess a de novo assembly." ; sc:featureList edam:operation_0258, edam:operation_3180 ; sc:license "GPL-3.0" ; sc:name "Isoblat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/josephryan/isoblat" ; biotools:primaryContact "Joseph F. Ryan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3300 ; sc:citation , "pubmed:36002391" ; sc:description "An R package to streamline and standardize stable isotope calculations in ecological research." ; sc:featureList edam:operation_3638, edam:operation_3642, edam:operation_3705 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "isocalcR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/justinmathias/isocalcR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Plot isochores in DNA sequences." ; sc:featureList edam:operation_0430 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "isochore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/isochore.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3512 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Plot potential isochore features." ; sc:featureList edam:operation_0430 ; sc:name "isochore (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/seqstats/emboss_isochore" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510 ; sc:citation ; sc:description "Interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control." ; sc:featureList edam:operation_0320 ; sc:name "iSOCKET" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.3.1" ; sc:url "https://github.com/woolfson-group/isocket" ; biotools:primaryContact "Derek N Woolfson", "Jack W Heal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_2885, edam:topic_3676, edam:topic_3958 ; sc:citation , "pmcid:PMC8555218", "pubmed:34715772" ; sc:description "In silico optimization of copy number variant detection from targeted or exome sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "isoCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/sequentiateampublic/isocnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC9895077", "pubmed:36732615" ; sc:description """This repository contains an open source Python library that focuses on user defined (such as meteorological, spatial, etc.) and isotopic composition variables analysis and generating the regression – statistical estimation models. data_preparation.preprocess class. pip can be used for the installation:. Hassanzadeh, A., Valdivielso, S., Vázquez-Suñé, E., Criollo, R., Corbella, M., 2023.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Isocompy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/IDAEA-EVS/Isocompy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_3170, edam:topic_3320, edam:topic_3335 ; sc:author "Qiuyue Huang" ; sc:citation , "pubmed:33826865" ; sc:description "IsoDA is a tool for Isoform-Disease Association Prediction by Multiomics Data Fusion. A gene can be spliced into different isoforms by alternative splicing, which contributes to the functional diversity of protein species. Computational prediction of gene-disease associations (GDAs) has been studied for decades. However, the process of identifying the isoform-disease associations (IDAs) at a large scale is rarely explored, which can decipher the pathology at a more granular level. The main bottleneck is the lack of IDAs in current databases and the multilevel omics data fusion. To bridge this gap, we propose a computational approach called Isoform-Disease Association prediction by multiomics data fusion (IsoDA) to predict IDAs" ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_3436 ; sc:name "IsoDA" ; sc:url "http://www.sdu-idea.cn/codes_eng.php?name=IsoDA" ; biotools:primaryContact "Guoxian Yu", "Maozu Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation "pubmed:21504602" ; sc:description "Expectation maximization algorithm for estimating alternative splicing isoform frequencies" ; sc:featureList edam:operation_2238 ; sc:name "IsoEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dna.engr.uconn.edu/?page_id=105" ; biotools:primaryContact "Alex Zelikovsky", "Igor Mandric", "Ion Mandoiu", "Sahar Al Seesi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data." ; sc:featureList edam:operation_3223 ; sc:name "IsoEM2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mandricigor/isoem2" ; biotools:primaryContact "Igor Mandric", "Ion I. Măndoiu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_2815, edam:topic_3053 ; sc:citation , "pmcid:PMC4983006", "pubmed:27519173" ; sc:description "Web-based platform for isoform-level expression analysis in human cancer." ; sc:featureList edam:operation_2495 ; sc:name "ISOexpresso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wiki.tgilab.org/ISOexpresso/" ; biotools:primaryContact "In Seok Yang", "Sangwoo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0749, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:15215396" ; sc:description "IsoFinder is a tool for the prediction of isochores for a user-supplied sequence." ; sc:featureList edam:operation_0253, edam:operation_0369, edam:operation_0430 ; sc:name "IsoFinder" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://isofinder.sourceforge.net/" ; biotools:primaryContact "J. L. Oliver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A peptide-centric algorithm for protein inference." ; sc:featureList edam:operation_3767 ; sc:name "IsoformResolver" ; sc:url "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167374/" ; biotools:primaryContact "Natalie Ahn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3512 ; sc:citation , "pubmed:28584021" ; sc:description "Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well." ; sc:featureList edam:operation_2403, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "IsoformSwitchAnalyzeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/IsoformSwitchAnalyzeR/" ; biotools:primaryContact , "Kristoffer Vitting-Seerup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3308, edam:topic_3320 ; sc:citation , "pubmed:35997558" ; sc:description "IsofunGO, a tool, to differentiate massive functions of isoforms by GO embedding." ; sc:featureList edam:operation_0362, edam:operation_2454, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "IsofunGO" ; sc:url "http://www.sdu-idea.cn/codes.php?name=IsofunGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3321 ; sc:citation ; sc:description "This interface of the IsoGene package identifies genes with a monotonic trend in the expression levels with respect to the increasing doses through several test statistics." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "IsoGeneGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/IsoGeneGUI.html" ; biotools:primaryContact "Setia Pramana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_3168 ; sc:citation , "pubmed:32681163" ; sc:description """De novo prediction of isoform specific mucin-type O-glycosylation. Isoform Specific mucin-type o-glycosylation prediction. Isoform Specific O-Glycosylation Prediction (ISOGlyP).""" ; sc:featureList edam:operation_0303, edam:operation_0335, edam:operation_0417 ; sc:license "GPL-3.0" ; sc:name "ISOGlyP" ; sc:url "http://ISOGlyP.utep.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2640, edam:topic_3170, edam:topic_3320, edam:topic_3474 ; sc:citation , "pmcid:PMC6978412", "pubmed:31974522" ; sc:description """Functional annotation of protein-coding splice variants. The advent of RNA-seq technologies has switched the paradigm of genetic analysis from a genome to a transcriptome-based perspective. Alternative splicing generates functional diversity in genes, but the precise functions of many individual isoforms are yet to be elucidated. Gene Ontology was developed to annotate gene products according to their biological processes, molecular functions and cellular components. Despite a single gene may have several gene products, most annotations are not isoform-specific and do not distinguish the functions of the different proteins originated from a single gene. Several approaches have tried to automatically annotate ontologies at the isoform level, but this has shown to be a daunting task""" ; sc:featureList edam:operation_0303, edam:operation_2436, edam:operation_3557, edam:operation_3672 ; sc:name "ISOGO" ; sc:url "https://biotecnun.unav.es/app/isogo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:21951053" ; sc:description "Algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads." ; sc:featureList edam:operation_3258 ; sc:name "IsoLasso" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://alumni.cs.ucr.edu/~liw/isolasso.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "This package provides a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies." ; sc:featureList edam:operation_2998 ; sc:license "GPL-2.0" ; sc:name "ISoLDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ISoLDE.html" ; biotools:primaryContact "Christelle Reynès" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3295, edam:topic_3474, edam:topic_3518 ; sc:citation , "pubmed:32407457" ; sc:description """An integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps. To replicate the algorithm use the following steps:.""" ; sc:featureList edam:operation_0417, edam:operation_2409, edam:operation_3935 ; sc:name "iSOM-GSN" ; sc:url "https://github.com/NaziaFatima/iSOM_GSN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_2885, edam:topic_3170 ; sc:citation , "pmcid:PMC7852101", "pubmed:33522913" ; sc:description """A system for analyzing small-RNA-seq data in an integrative and user-friendly manner. The IsomiR Window project is a user-friendly tool that enables biologists to perform the analysis of small-RNA-seq data, uncovering the complexity of miRNA biogenesis.""" ; sc:featureList edam:operation_0463, edam:operation_3192, edam:operation_3792, edam:operation_3800 ; sc:name "IsomiR" ; sc:url "https://isomir.fc.ul.pt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:27036505" ; sc:description "The first tool implemented in order to perform reads alignment on miRNAs databases by considering the miRNA:mRNA interaction pairing aspects." ; sc:featureList edam:operation_3800 ; sc:name "isomiR-SEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://eda.polito.it/isomir-sea" ; biotools:primaryContact "Gianvito Urgese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3300, edam:topic_3512 ; sc:citation , "pubmed:36243964" ; sc:description """A miRNA expression database with isoform resolution. isomiRdb stores miRNA and isomiR expression values for 42499 miRNA-seq samples collected from miRMaster, The Cancer Genome Atlas and Sequence Read Archive and uniformly processed from raw reads using sRNAbench .""" ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "isomiRdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ccb.uni-saarland.de/isomirdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2885, edam:topic_3170, edam:topic_3473 ; sc:citation , "pubmed:33471076" ; sc:description """IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. IsoMiRmap is an open source python application for the fast, deterministic, and exhaustive mining of isomiRs. The tool produces output in HTML, miRGFF3, and in tab-delimited formats. isoMiRmap is a miRNA and isomiRs mining tool that let's you quickly, exhaustively and deterministically map your dataset.""" ; sc:featureList edam:operation_0306, edam:operation_0463, edam:operation_3192, edam:operation_3196, edam:operation_3792 ; sc:name "isoMiRmap" ; sc:url "https://cm.jefferson.edu/isoMiRmap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0659 ; sc:citation ; sc:description "Characterization of miRNAs and isomiRs, clustering and differential expression." ; sc:featureList edam:operation_3223, edam:operation_3432 ; sc:license "MIT" ; sc:name "isomiRs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/isomiRs.html" ; biotools:primaryContact "Lorena Pantano" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3668 ; sc:name "Disease name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC9583861", "pubmed:36275459" ; sc:description "A comprehensive portal of pan-cancer 5'-isomiR targeting." ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "isomiRTar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://isomirtar.hse.ru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0749, edam:topic_2229, edam:topic_3452 ; sc:citation ; sc:description "Isotropic Reconstruction of Electron Tomograms with Deep Learning." ; sc:featureList edam:operation_0337, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IsoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Heng-Z/IsoNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC10311309", "pubmed:37387174" ; sc:description "Reference-free transcriptome reconstruction from Oxford Nanopore data." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "isONform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aljpetri/isONform" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0114, edam:topic_0602, edam:topic_3320 ; sc:citation , "pubmed:32966552" ; sc:description """Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation. IsoResolve is a computational approach for isoform function prediction by leveraging the information of gene function prediction models with domain adaptation (DA). IsoResolve treats gene- level and isoform-level features as source and target domain, respectively. It employs DA to project the two domains to a latent variable (LV) space in such a way that the LVs projected from the gene and isoform domain features are of approximately the same distribution, enabling that the gene domain information can be leveraged for predicting isoform functions.""" ; sc:featureList edam:operation_0264, edam:operation_0303, edam:operation_0433 ; sc:name "IsoResolve" ; sc:url "https://github.com/genemine/IsoResolve" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2907 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation , "pubmed:25073878" ; sc:description "Proteomics software to quantify peptides based on the total ion intensity of the MS/MS spectra. The software provides also relative quantification of isobaric peptides co-fragmented in MS/MS spectra which share the same sequence but have distinct localizations of post-translational modifications (PTMs)." ; sc:featureList edam:operation_0346, edam:operation_3214 ; sc:isAccessibleForFree true ; sc:name "isoScale" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bmb.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/middle-down/Software" ; biotools:primaryContact "Simone Sidoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:25406361" ; sc:description "New method for transcript assembly  that incorporates change-point analysis to improve the 3′ UTR annotation process." ; sc:featureList edam:operation_3258 ; sc:name "IsoSCM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/shenkers/isoscm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_3512 ; sc:description "IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique." ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3237, edam:operation_3432, edam:operation_3933 ; sc:license "BSD-3-Clause-Clear" ; sc:name "IsoSeq3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/PacificBiosciences/IsoSeq" ; biotools:primaryContact "Pacific Biosciences" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation ; sc:description "IsoSolve an integrative framework to improve isotopic coverage and consolidate isotopic measurements by MS and/or NMR. IsoSolve is a Python module realizing an integrative framework for isotope labeling measurements. It can provide both symbolic and numeric solutions for integrating and consolidating heterogeneous measurements, e.g. NMR and MS measuring ¹³C labeling, to cite the most wide spread ones." ; sc:featureList edam:operation_3632, edam:operation_3638, edam:operation_3642 ; sc:license "GPL-2.0" ; sc:name "IsoSolve" ; sc:url "https://pypi.org/project/IsoSolve" ; biotools:primaryContact "Pierre Millard", "Sergueï Sokol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pubmed:34021065" ; sc:description "IsoSplitter is a de novo identification tool of alternative splicing sites using long-reads transcriptome without a reference genome." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_3359 ; sc:license "LGPL-3.0" ; sc:name "IsoSplitter" ; sc:url "https://github.com/Hengfu-Yin/IsoSplitter" ; biotools:primaryContact "Hengfu Yin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation ; sc:description "IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0314, edam:operation_0433, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "IsoTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MatthiasLienhard/isotools" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_2035 ; sc:name "Chemical formula" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "MATLAB and R code for calculating the isotopic distribution of a molecule (e.g. insulin)." ; sc:featureList edam:operation_3441, edam:operation_3632 ; sc:name "isotop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ms-utils.org/isotop.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_2035 ; sc:name "Chemical formula" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "MATLAB code for calculating isotopic fine structure." ; sc:featureList edam:operation_3441, edam:operation_3632 ; sc:name "isotop_fs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ms-utils.org/isotop_fs.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3930 ; sc:citation ; sc:description """ISOform-guided prediction of epiTOPEs in cancer. The following pipeline have been developed for the identification of cancer-specific splicing-derived epitopes from RNA-seq. The pipeline is divided in 4 parts, depending the event type the user wants to obtain:. For the obtention of exonizations, neoskipping and A5_A3 events, the first input are the read counts mapped to all posible junctions in the genome. This file (readCounts.tab) is created through Junckey (https://github.com/comprna/Junckey#1-format-star-output). From these junctions, ISOTOPE will obtain all splicing events expressed significantly.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3632, edam:operation_3638, edam:operation_3642 ; sc:license "GPL-3.0" ; sc:name "ISOTOPE" ; sc:url "https://github.com/comprna/ISOTOPE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_2035, edam:format_2330 ; sc:name "Chemical formula" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Console application for calculating isotope distributions based on Yergey's method." ; sc:featureList edam:operation_2238, edam:operation_3435, edam:operation_3632 ; sc:name "Isotope calculator" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.kombyonyx.com/isotopes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_0152, edam:topic_0154, edam:topic_0654 ; sc:citation "pubmed:15215474" ; sc:description "Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available." ; sc:featureList edam:operation_2929, edam:operation_3214, edam:operation_3631, edam:operation_3632, edam:operation_3694 ; sc:name "ISOTOPICA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://coco.protein.osaka-u.ac.jp/isotopica/" ; biotools:primaryContact "Fernandez-de-Cossio J." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3520 ; sc:description "Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input." ; sc:featureList edam:operation_0226 ; sc:name "IsotopIdent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://education.expasy.org/student_projects/isotopident/htdocs/" ; biotools:primaryContact "Erick Antezana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_0621, edam:topic_3361, edam:topic_3375 ; sc:citation , , "pubmed:32469660" ; sc:description "Isotope tracer addition experiments are used to answer a wide variety of biological, ecological and evolutionary questions. In these experiments, a labeled element is injected into a biological system and its fate is traced throughout the system to estimate the flux of matter across compartments. Tracer additions can be used across all levels of biological organization from cells and tissues, to organisms and ecosystems. The isotracer package provides tools to analyze data from such experiments." ; sc:featureList edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "isotracer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://matthieu-bruneaux.gitlab.io/isotracer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0108, edam:topic_0203, edam:topic_0769, edam:topic_3512 ; sc:citation , "pubmed:33585928" ; sc:description """Processing and visualizing functional features of translated transcript isoforms. IsoTV is Snakemake pipeline to analyze and visualize functional features of translated transcript isoforms. IsoTV incorporates various tools to predict protein domains, secondary structure, disordered regions, and post-translational modification sites. The visualization facilitates comparison of the set of transcript isoforms expressed across conditions and explored the functional consequences of isoform differences. IsoTV supports a range of transcriptome sequencing technologies, including short-reads, Oxford Nanopore (ONT) long-reads, Pacific Bio-sciences (PacBio) long-reads. It also supports other inputs, including single or multiple gene sequences.""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_0524, edam:operation_3185 ; sc:name "IsoTV" ; sc:softwareHelp ; sc:url "https://github.molgen.mpg.de/MayerGroup/IsoTV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885 ; sc:citation , "pmcid:PMC5490163", "pubmed:28659176" ; sc:description "Accurate somatic mutation identification in the absence of normal tissue controls." ; sc:featureList edam:operation_3197 ; sc:license "APSL-2.0" ; sc:name "ISOWN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ikalatskaya/ISOWN" ; biotools:primaryContact "Irina Kalatskaya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC8756298", "pubmed:35083040" ; sc:description "A approach to inferring gene-gene net-works using SPACE model with log penalty." ; sc:featureList edam:operation_2436, edam:operation_2437, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ispace-log" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wuqian77/SpaceLog" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_3047, edam:topic_3314 ; sc:citation , "pubmed:33556195" ; sc:description """A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software. We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule""" ; sc:featureList edam:operation_1812, edam:operation_2476, edam:operation_3214 ; sc:name "iSPECTRON" ; sc:url "https://github.com/ispectrongit/iSPECTRON/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3365, edam:topic_3366, edam:topic_3520 ; sc:citation "pubmed:18440977" ; sc:description "Provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2422 ; sc:name "ISPIDER Central" ; sc:url "http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0128, edam:topic_0749, edam:topic_2275, edam:topic_3534 ; sc:citation , "pmcid:PMC9316365", "pubmed:35879651" ; sc:description "Integrated structure-based protein interface prediction." ; sc:featureList edam:operation_0321, edam:operation_0474, edam:operation_2575, edam:operation_3659, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ISPIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eved1018/ISPIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:10764600", "pubmed:12824399" ; sc:description "iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains." ; sc:featureList edam:operation_0303, edam:operation_0465, edam:operation_0474, edam:operation_2575 ; sc:name "iSPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbm.bio.uniroma2.it/ispot/" ; biotools:primaryContact "Manuela Helmer Citterich" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1008 ; sc:encodingFormat edam:format_2330 ; sc:name "Polypeptide chain ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160 ; sc:author ; sc:citation , , "pubmed:28130235" ; sc:description "Prediction of interaction sites in proteins." ; sc:featureList edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "ISPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "4" ; sc:url "http://ispred4.biocomp.unibo.it/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331, edam:format_3475 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2814, edam:topic_3474 ; sc:citation , "pubmed:37356906" ; sc:description "Deep neural networks and embeddings for predicting interaction sites in protein sequences." ; sc:featureList edam:operation_2492, edam:operation_3092, edam:operation_3094, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "ISPRED-SEQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:url "https://ispredws.biocomp.unibo.it" ; biotools:primaryContact , "Castrense Savojardo", "Matteo Manfredi", "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3308, edam:topic_3360, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """A Machine Learning Model to Predict the Immune Subtype of Kidney Cancer Samples by Four Genes. The code and dataset used in the construction of ISPRF.""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3766 ; sc:name "ISPRF" ; sc:url "https://immunotype.shinyapps.io/ISPRF/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation "pubmed:19136549" ; sc:description "Short Sequence Assembly by K-mer search and 3' read Extension, Immunology version (iSSAKE)" ; sc:featureList edam:operation_0310 ; sc:license "GPL-2.0" ; sc:name "ISSAKE" ; sc:url "https://github.com/brwnj/repertoire/blob/master/assembly/iSSAKE" ; biotools:primaryContact "R.L. Warren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0593, edam:topic_0736, edam:topic_3542 ; sc:citation , "pmcid:PMC7643357", "pubmed:33153432" ; sc:description """Inferring contacts among protein secondary structure elements using deep object detection. ISSEC adopts deep learning to learn specific patterns within predicted inter-residue contacts and subsequently identifies the objects having these patterns as inter-SSE contacts.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0392, edam:operation_0474, edam:operation_2488 ; sc:name "ISSEC" ; sc:url "https://github.com/bigict/ISSEC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server is an attempt to help biologist identify Inteins hiding in their protein sequences." ; sc:featureList edam:operation_2945 ; sc:name "isspred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/isspred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_2814 ; sc:citation "pubmed:23369171" ; sc:description "An integrated predictor constructed by using sequence information and prediction results from different element predictors." ; sc:featureList edam:operation_3092 ; sc:name "iStable" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://predictor.nchu.edu.tw/istable/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3308, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description "ISTDECO (In Situ Transcriptomics Decoding by Deconvolution) is a simple tool for deconvolving combinatorial image data generated by FISH techniques into series of non-combinatorial images." ; sc:featureList edam:operation_0314, edam:operation_3443, edam:operation_3629 ; sc:license "MIT" ; sc:name "ISTDECO" ; sc:url "http://github.com/axanderssonuu/istdeco" ; biotools:primaryContact "Axel Andersson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_2269, edam:topic_2885 ; sc:citation "pubmed:15980517" ; sc:description "Tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required, some browser requirements and set-up necessary." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_0487, edam:operation_0488, edam:operation_2238 ; sc:name "ISTECH SNPAnalyzer" ; sc:url "http://snp.istech.info/istech/board/login_form.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3303, edam:topic_3379, edam:topic_3384 ; sc:citation , "pubmed:33405381" ; sc:description """Development and implementation of common data elements for venous thromboembolism research. Data Standards for Clinical Research. The International Society on Thrombosis and Haemostasis' Common Data Elements (CDE) provides pre-defined data standards for clinical research in venous thromboembolism (VTE). Researchers can review and download structured data elements that expedite the development of research datasets and case report forms (CRFs), and enable meta-analyses across studies using common definitions and coding. ISTH’s Common Data Elements (CDE) project provides investigators with pre-defined clinical data elements to reduce study design time and enable meta-analyses across studies.""" ; sc:featureList edam:operation_3435 ; sc:name "ISTH" ; sc:url "http://isth.breakthrough.healthcare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0601 ; sc:citation "pubmed:26084794" ; sc:description "This web-server is established for predicting the lysine succinylation sites in proteins." ; sc:featureList edam:operation_0417 ; sc:name "iSuc-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://app.aporc.org/iSuc-PseAAC" ; biotools:primaryContact "Yan Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0601 ; sc:citation "pubmed:26723495" ; sc:description "This web-server used to predict the lysine succinylation in protein." ; sc:featureList edam:operation_0417 ; sc:name "iSuc-PseOpt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/iSuc-PseOpt" ; biotools:primaryContact "Xiao Xuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0128, edam:topic_0166, edam:topic_3510 ; sc:citation , "pmcid:PMC4841585", "pubmed:27104833" ; sc:description "Prediction of S-sulfenylation Sites in Proteins with Physicochemical Properties of Amino Acids." ; sc:featureList edam:operation_3092 ; sc:name "iSulf-Cys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://app.aporc.org/iSulf-Cys/" ; biotools:primaryContact "Yan Xu Close" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0601, edam:topic_2229, edam:topic_3474 ; sc:citation , "pmcid:PMC8349168", "pubmed:34430072" ; sc:description "Prediction of lysine sumoylation sites using statistical moments and Chou's PseAAC." ; sc:featureList edam:operation_0417, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "iSUMOK-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/csbioinfopk/iSumoK-PseAAC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2229 ; sc:citation , "pubmed:21572175" ; sc:description "IsUnstruct is a new method based on the Ising model used for the prediction of disordered residues from protein sequence alone." ; sc:featureList edam:operation_0267, edam:operation_0477, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "IsUnstruct" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v2.02" ; sc:url "http://bioinfo.protres.ru/IsUnstruct/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC5490186", "pubmed:28659141" ; sc:description "Identification of sequence variant associated with splicing event using RNA-seq data." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "ISVASE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/isvase/" ; biotools:primaryContact "Hasan Awad Aljohi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2275, edam:topic_3047 ; sc:citation , "pmcid:PMC7758974", "pubmed:33376921" ; sc:description """Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. Swarm-CG is designed for automatically optimizing the bonded terms of a MARTINI-based coarse-grained (CG) molecular model, in explicit or implicit solvent, with respect to a reference all-atom (AA) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:. Evaluating the bonded parametrization of a CG model. Optimizing bonded terms of a CG model.""" ; sc:featureList edam:operation_0244, edam:operation_0394, edam:operation_3893 ; sc:license "MIT" ; sc:name "iSwarm-CG" ; sc:url "http://www.github.com/GMPavanLab/SwarmCG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_3361, edam:topic_3474 ; sc:citation , "pmcid:PMC7806399", "pubmed:33505516" ; sc:description "Identification of Bacterial Type III Secreted Effectors Using PSSM Profiles and XGBoost Feature Selection." ; sc:featureList edam:operation_0253, edam:operation_3092, edam:operation_3936 ; sc:name "iT3SE-PX" ; sc:url "https://github.com/taigangliu/iT3SE-PX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:25792550" ; sc:description "Tool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data." ; sc:featureList edam:operation_2403 ; sc:name "iTagPlot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/itagplot/" ; biotools:primaryContact "Jeong-Hyeon Choi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:citation ; sc:description "A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set." ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "ITALICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ITALICS.html" ; biotools:primaryContact "Guillem Rigaill" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC4983039", "pubmed:27519564" ; sc:description "A web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data." ; sc:featureList edam:operation_0438, edam:operation_2403 ; sc:name "iTAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://syslab3.nchu.edu.tw/iTAR/" ; biotools:primaryContact "Chao Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3293 ; sc:citation ; sc:description "iTaxoTools is a tool suite for integrative taxonomy. The suite contains tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests." ; sc:featureList edam:operation_0323, edam:operation_3200, edam:operation_3359 ; sc:license "GPL-3.0" ; sc:name "iTaxoTools" ; sc:softwareHelp ; sc:url "https://itaxotools.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3474, edam:topic_3930 ; sc:citation , "pmcid:PMC10203616", "pubmed:37229205" ; sc:description "Deep learning framework for identification of T cell epitopes by harnessing fusion features." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "iTCep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biostatistics.online/iTCep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0203, edam:topic_3303, edam:topic_3336, edam:topic_3375 ; sc:citation , "pubmed:36719094" ; sc:description "Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM." ; sc:featureList edam:operation_0306, edam:operation_0314, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "ITCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://itcm.biotcm.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_0632, edam:topic_3676 ; sc:citation , "pmcid:PMC9951415", "pubmed:36823555" ; sc:description "A method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application." ; sc:featureList edam:operation_0308, edam:operation_3227, edam:operation_3963 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ITDetect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cpmsnuh/itdetect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples." ; sc:featureList edam:operation_2990 ; sc:license "GPL-2.0" ; sc:name "iterativeBMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iterativeBMA.html" ; biotools:primaryContact "Ka Yee Yeung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3361, edam:topic_3518 ; sc:citation ; sc:description "Variable selection method for applying survival analysis to microarray data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "iterativeBMAsurv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iterativeBMAsurv.html" ; biotools:primaryContact "Ka Yee Yeung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pubmed:29579153" ; sc:description "A framework for performing clustering analysis iteratively." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "iterClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iterClust.html" ; biotools:primaryContact "Hongxu Ding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC7100596", "pubmed:32231869" ; sc:description """A barcode clustering algorithm for long fragment read analysis. The IterCluster is a barcode clustering algorithm fragment read analysis. There is pipeline for stLFR raw reads using the IterCluster.""" ; sc:featureList edam:operation_0524, edam:operation_3200, edam:operation_3216, edam:operation_3432, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "IterCluster" ; sc:url "https://github.com/JianCong-WENG/IterCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3295 ; sc:description "The package provides a flexible algorithm to screen features of two distinct groups in consideration of overfitting and overall performance. It was originally tailored for methylation locus screening of NGS data, and it can also be used as a generic method for feature selection. Each step of the algorithm provides a default method for simple implemention, and the method can be replaced by a user defined function." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "iteremoval" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/iteremoval.html" ; biotools:primaryContact "Jiacheng Chuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3292, edam:topic_3297, edam:topic_3474 ; sc:citation , "pmcid:PMC8902591", "pubmed:35273581" ; sc:description "iThermo: Thermophilic Protein Prediction uses the protein sequence information to predict the thermophilic proteins. 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Nell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_0769, edam:topic_3173, edam:topic_3382 ; sc:citation ; sc:description """Fast enumeration of single- and multi-copy CRISPR binding sites. JACKIE pipeline & database – Albert Cheng Lab. JACKIE (Jackie and Albert’s CRISPR K-mer Instances Enumerator) scans the genome and enumerate all potential SpCas9 binding sequences and output their copy number and locations. 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Janggu - Deep learning for Genomics. Janggu is a python package that facilitates deep learning in the context of genomics. 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JARVIS-Tools: an open-source software package for data-driven atomistic materials design. NIST-JARVIS (Joint Automated Repository for Various Integrated Simulations) is an integrated framework for computational science using density functional theory, classical force-field molecular dynamics and machine-learning. The NIST Materials Data Curation System (MDCS) provides a means for capturing, sharing, and transforming materials data into a structured format that is XML based amenable to transformation to other formats.""" ; sc:featureList edam:operation_2476, edam:operation_3443, edam:operation_3454 ; sc:name "JARVIS-STM" ; sc:url "https://jarvis.nist.gov/jarvisstm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_2885, edam:topic_3170, edam:topic_3175 ; sc:citation ; sc:description "JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges) is an automated pipeline for alignment and SV calling in long-read datasets. The tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:license "MIT" ; sc:name "Jasmine" ; sc:softwareHelp ; sc:url "https://github.com/mkirsche/Jasmine" ; biotools:primaryContact "Michael C. Schatz", "Sergey Aganezov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_2269, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc:description "JASP is an open-source statistics program that is free, friendly, and flexible. Armed with an easy-to-use GUI, JASP allows both classical and Bayesian analyses." ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3799 ; sc:license "AGPL-3.0" ; sc:name "JASP" ; sc:softwareHelp , ; sc:url "https://jasp-stats.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:name "Taxon" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:name "Text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2732 ; sc:name "Family name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1119 ; sc:name "JASPAR profile ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1077 ; sc:name "Transcription factor identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2755 ; sc:name "Transcription factor name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1119 ; sc:name "JASPAR profile ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1119 ; sc:encodingFormat edam:format_1367, edam:format_2330, edam:format_3464, edam:format_3475, edam:format_3750, edam:format_3752 ; sc:name "JASPAR profile ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0622, edam:topic_0749, edam:topic_0780, edam:topic_2815, edam:topic_3071 ; sc:citation , , , , , , , , , , "pmcid:PMC5753243", "pmcid:PMC7145627", "pmcid:PMC8728201", "pubmed:14681366", "pubmed:16381983", "pubmed:18006571", "pubmed:19906716", "pubmed:24194598", "pubmed:26531826", "pubmed:29140473", "pubmed:29253085", "pubmed:31701148", "pubmed:34850907" ; sc:contributor , , , , , , , , , , , , , , , "Alejandro Aguirre", "Paul Boddie", "Tiffany Y Leung" ; sc:description "JASPAR is a high-quality, open-access database that provides manually curated, non-redundant transcription factor (TF) binding profiles for six taxonomic groups (fungi, insecta, nematoda, plantae, urochordata, vertebrata). These profiles are stored as position frequency matrices (PFMs), which can be transformed into models to predict TF binding sites (TFBS) in DNA sequences. The database collects motifs both internally, analyzing sequences using a custom motif discovery pipeline, and externally from publications and other resources. All selected motifs are manually curated for quality and supporting evidence. JASPAR now offers a tool for TFBS enrichment analysis in user-provided genomic regions. Data is accessible through the JASPAR website, its RESTful API, Bioconductor, or the Python package pyJASPAR." ; sc:featureList edam:operation_0445, edam:operation_2421 ; sc:funder "The Research Council of Norway" ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "JASPAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , ; sc:url "http://jaspar.genereg.net/" ; biotools:primaryContact , , , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC5753243", "pubmed:29140473" ; sc:contributor "Jaime Abrahan Castro-Mondragon" ; sc:description "Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6)." ; sc:featureList edam:operation_3672 ; sc:license "GPL-2.0" ; sc:name "JASPAR2018" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.0" ; sc:url "http://bioconductor.org/packages/release/data/annotation/html/JASPAR2018.html" ; biotools:primaryContact "Ge Tan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0622, edam:topic_0749, edam:topic_0780, edam:topic_2815, edam:topic_3071 ; sc:citation , , , "pmcid:PMC5753243", "pmcid:PMC8728201", "pubmed:29140473", "pubmed:29253085", "pubmed:34850907" ; sc:description "JASPAR is a widely used open-access database containing curated, non-redundant transcription factor binding profiles. The JASPAR RESTful API enhances accessibility by enabling users to programmatically access the database by most programming languages.The API uses the Representational State Transfer (REST) architecture to provide data in multiple formats (JSON, JSONP, JASPAR, MEME, PFM, TRANSFAC, BED, and YAML). The JASPAR API is user-friendly, offering a browsable interface designed for bioinformatics tool developers." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "JASPAR RESTful API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://jaspar.genereg.net/api/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749 ; sc:description "Previously, a web service interface to the JASPAR database containing profiles of transcription factor binding sites. The SOAP API has been replaced with the JASPAR RESTful API." ; sc:featureList edam:operation_0438, edam:operation_2478 ; sc:name "Jaspar WS" ; sc:softwareVersion "1" ; sc:url "http://api.bioinfo.no/wsdl/Jaspar_webservice_0.2.wsdl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0749 ; sc:description "Previously, a web service interface to the JASPAR database containing profiles of transcription factor binding sites. The SOAP API has been replaced with the JASPAR RESTful API." ; sc:featureList edam:operation_0438 ; sc:name "JasparDB" ; sc:softwareVersion "1" ; sc:url "http://api.bioinfo.no/wsdl/JasparDB.wsdl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3382, edam:topic_3422, edam:topic_3500, edam:topic_3697 ; sc:citation ; sc:description "Jasper is a tool for visualizing profiles from 16S and whole-genome sequencing, and orders taxa along a space-filling Hilbert curve. The result is a Microbiome Map, where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order the taxa in two ways, and depending on the ordering, the maps can highlight \"hot spots\" of microbes that are either common to, or unique to, the biological conditions under study." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3200, edam:operation_3460 ; sc:name "Jasper" ; sc:operatingSystem "Mac" ; sc:url "http://biorg.cs.fiu.edu/jasper" ; biotools:primaryContact "Giri Narasimhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0780, edam:topic_3673 ; sc:citation , "pmcid:PMC10096238", "pubmed:37000853" ; sc:description "A fast genome polishing tool that improves accuracy of genome assemblies." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3227, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "JASPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alguoo314/JASPER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Extract data from JASPAR." ; sc:featureList edam:operation_1812 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "jaspextract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/jaspextract.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Scan DNA sequences for transcription factors." ; sc:featureList edam:operation_0445 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "jaspscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/jaspscan.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3590 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3590 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3590 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:author , , , , "Carla Lasry" ; sc:citation , ; sc:contributor "Bjarni Vilhjalmsson", "Chunzi Yao", "Vincent Laville" ; sc:description "software package that handles the computation of the joint statistics over sets of selected GWAS results, and the interactive exploration of the results through a web interface." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "JASS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.1, 2.0, 2.1, 2.2" ; sc:url "http://statistical-genetics.pages.pasteur.fr/jass/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0634, edam:topic_2229 ; sc:citation "pubmed:26142185" ; sc:description "Predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs." ; sc:featureList edam:operation_0417 ; sc:name "JASSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jassa.fr/" ; biotools:primaryContact "Guillaume Beauclair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:15180930" ; sc:description "Java TreeView is an enhanced, open source, cross-platform gene expression visualization tool. It interactivly display clustered gene expression data, similar to eisen’s TreeView." ; sc:featureList edam:operation_3432 ; sc:name "Java Treeview" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.6r4" ; sc:url "http://jtreeview.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2640, edam:topic_3474, edam:topic_3577 ; sc:citation ; sc:description """A Java-based Deep Learning Tool to Predict Drug Responses. Intelligent Molecular Discovery Laboratory. 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Useful for improving the expression of foreign genes in hosts with different codon usage." ; sc:featureList edam:operation_0284, edam:operation_0285, edam:operation_0286, edam:operation_2962, edam:operation_2964 ; sc:name "JCat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jcat.de/" ; biotools:primaryContact "Andreas Grote" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3303, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC9761970", "pubmed:36536280" ; sc:description "A joint continual learning neural network for biomedical information extraction." ; sc:featureList edam:operation_3096, edam:operation_3280, edam:operation_3625, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "JCBIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KaiHe-better/JCBIE.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308, edam:topic_3320, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:37833842" ; sc:description """circRNA full-length sequence assembly through integrated junction contigs. It enables efficient reconstruction of all types of circRNA full-length sequences and their alternative isoforms using splice graphs and fragment coverage.""" ; sc:featureList edam:operation_0232, edam:operation_0310, edam:operation_3180 ; sc:isAccessibleForFree true ; sc:name "JCcirc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cbbzhang/JCcirc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3395 ; sc:citation , "pmcid:PMC5975448", "pubmed:29843599" ; sc:description "Joint covariate detection tool for survival analysis on tumor expression profiles." ; sc:featureList edam:operation_0314 ; sc:license "GPL-2.0" ; sc:name "JCDSA" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bio-nefu.com/resource/jcdsa" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3314 ; sc:description "Integrates structure handling and visualizing capabilities within a Microsoft Office environment. 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This is a deep learning workflow for Progressive Multifocal Leukoencephalopathy (PML) lesion and brain segmentation from brain MRI using Python 3, Keras, and TensorFlow. The model generates segmentation masks of the brain parenchyma and lesions in PML patients. This work was conducted at the Neuroimmunology Clinic (NIC) and Translation Neuroradiology Section (TNS) of the National Institute of Neurological Disorders and Stroke (NINDS), in collaboration with colleagues at the National Institute of Mental Health, and the Henry Jackson Foundation at the National Institutes of Health.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "JCnet" ; sc:url "https://github.com/omarallouz/JCnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3418, edam:topic_3452, edam:topic_3474, edam:topic_3519 ; sc:citation , "pubmed:33600316" ; sc:description """An Explainable COVID-19 Diagnosis System by Joint Classification and Segmentation. Official repository of the paper: JCS: An explainable COVID-19 diagnosis system by joint classification and segmentation, IEEE Transactions on Image Processing (TIP) 2021.""" ; sc:featureList edam:operation_2423, edam:operation_2990 ; sc:name "JCS" ; sc:url "https://github.com/yuhuan-wu/JCS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1246 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence cluster (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1245 ; sc:encodingFormat edam:format_2546 ; sc:name "Sequence cluster (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0870 ; sc:encodingFormat edam:format_1423 ; sc:name "Sequence distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC4179140", "pubmed:25266120" ; sc:description "A Java package that utilises a series of D2 statistics to extract k-mers (subsequences at defined k length) from a set of biological sequences, and generate pairwise distances for each possible pair. 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However, gene expression data is prone to fluctuations, which may affect the accuracy of essential protein identification. Therefore, we propose an essential protein identification method to calculate the similarity of \"active\" and \"inactive\" state of gene expression in a cluster of the PPI network based on gene expression and the PPI network data. 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Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis." ; sc:featureList edam:operation_0224, edam:operation_0346, edam:operation_0492, edam:operation_2414, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Job Dispatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL - EBI" ; sc:softwareHelp , ; sc:url "http://www.ebi.ac.uk/jdispatcher/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0176, edam:topic_2258, edam:topic_3524 ; sc:citation ; sc:description "An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics." ; sc:featureList edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "Jdpd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zielesny/Jdpd" ; biotools:primaryContact "Achim Zielesny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0166, edam:topic_0601 ; sc:citation "pubmed:26245277" ; sc:description "Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs." ; sc:featureList edam:operation_0417 ; sc:name "jEcho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.healthinformaticslab.org/supp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description """Circular RNA Prediction based on Junction Encoders and Deep Interaction among Splice Sites. Abstract Circular RNA is a novel class of endogenous non-coding RNAs that have been largely discovered in eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backsplices to an upstream acceptor site. These circular form of RNAs are conserved across species, and often show tissue or cell-specific expression. Emerging evidences have suggested its vital roles in gene regulation, which are further associated with various types of diseases. As the fundamental effort to elucidate its function and mechanism, numerous efforts have been devoted to predicting circular RNA from its primary sequence""" ; sc:featureList edam:operation_0278, edam:operation_0433, edam:operation_2441 ; sc:name "JEDI" ; sc:url "https://github.com/hallogameboy/JEDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2269, edam:topic_3382 ; sc:citation , "pmcid:PMC8088583", "pubmed:33932974" ; sc:description "JEDi (Java Essential Dynamics Inspector) is a powerful tool for inspecting the dynamics of proteins from trajectories derived from MD or Geometric simulation." ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3891, edam:operation_3960 ; sc:license "GPL-3.0" ; sc:name "JEDi" ; sc:url "https://github.com/charlesdavid/JEDi" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3665 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation , "pmcid:PMC3051319", "pubmed:21217122" ; sc:description "A command-line algorithm for counting k-mers in DNA sequence." ; sc:featureList edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Jellyfish" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "2.3.0" ; sc:url "http://www.genome.umd.edu/jellyfish.html" ; biotools:primaryContact "Carl Kingsford", "Guillaume Marçais" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3512 ; sc:description "The GFP mRNA will express a green fluorescent protein, originally isolated from the jellyfish, Aequorea victoria. GFP could be used in a wide range of applications where they have functioned as a cell lineage tracer, reporter of gene expression, or as a measure of protein-protein interactions." ; sc:name "Jellyfish GFP mRNA" ; sc:url "https://integraterna.creative-biogene.com/jellyfish-gfp-mrna-item-pmrn-0001-470826.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622 ; sc:citation "pubmed:22945789" ; sc:description "Provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "JEnsemb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jensembl.sourceforge.net/" ; biotools:primaryContact "Roslin Bioinformatics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:26428293" ; sc:description "Novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype." ; sc:featureList edam:operation_2238 ; sc:name "JEPEG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dleelab.github.io/jepeg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Jerman Enhancement Filter is a MATLAB tool for enhancement of vessel/tube and blob/sphere like structures in 2D/3D images using hessian eigenvalues." ; sc:featureList edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Jerman Enhancement Filter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63171-jerman-enhancement-filter" ; biotools:primaryContact "Tim Jerman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0659 ; sc:citation "pubmed:10869029" ; sc:description "Software components to create and publish EST alignments and clusters." ; sc:featureList edam:operation_0292, edam:operation_0313 ; sc:name "JESAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.littlest.co.uk/software/bioinf/old_packages/jesam/jesam_paper.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0084, edam:topic_0166, edam:topic_0623, edam:topic_3293 ; sc:citation "pubmed:12537566", "pubmed:8609628" ; sc:description "Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins." ; sc:featureList edam:operation_0245, edam:operation_0321, edam:operation_0492, edam:operation_0499 ; sc:name "JEvTrace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.berkeley.edu/people/marcin/jevtrace/" ; biotools:primaryContact "JEvTrace team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3071, edam:topic_3372 ; sc:citation "pubmed:26454273" ; sc:description "JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and monitor workflows." ; sc:featureList edam:operation_3760 ; sc:name "Jflow" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jflow.toulouse.inra.fr/app/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2275, edam:topic_3047 ; sc:citation ; sc:description """A Multistaged Hyperparallel Optimization of the Fuzzy-Logic Mechanistic Model of Molecular Regulation. Elucidating mechanistic relationships among intracellular macromolecules is fundamental to understanding the molecular basis of normal and diseased processes. The classical fuzzy logic approach employs varying degrees of truth to describe relationships between interacting molecules. jFuzzyMachine implements the fuzzy logic approach to elucidate mechanistic relationships among biological molecules and makes more readily available the fuzzy logic inference approach in a freely available tool.""" ; sc:featureList edam:operation_1781, edam:operation_3435, edam:operation_3625 ; sc:name "JFuzzyMachine" ; sc:url "https://github.com/paiyetan/jfuzzymachine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC10484672", "pubmed:37526283" ; sc:description """Updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Custom scripts used in the analysis for JGI Plant Gene Atlas resource are available.""" ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0337, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "JGI Plant Gene Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plantgeneatlas.jgi.doe.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0780, edam:topic_3174 ; sc:citation "pubmed:22110030" ; sc:description "The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_0525, edam:operation_3216 ; sc:name "JGI Genome Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.jgi.doe.gov/" ; biotools:primaryContact "I.V. Grigoriev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3334, edam:topic_3337 ; sc:citation ; sc:description """A clinically and genomically annotated nerve sheath tumor biospecimen repository. Data and code required to analyze JHU Biobank Data. This repository contains the information about the RNA-seq processing and figure generation for the Scientific Data Biobank Manuscript. These instructions assume that you:.""" ; sc:featureList edam:operation_0362, edam:operation_3196, edam:operation_3227 ; sc:license "Apache-2.0" ; sc:name "jhubiobank" ; sc:url "https://github.com/Sage-Bionetworks/JHU-biobank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23685435" ; sc:description "Specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided." ; sc:featureList edam:operation_3562 ; sc:name "JiffyNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jiffynet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3292 ; sc:citation ; sc:description "Tool for managing large sets of biochemical model parametrizations." ; sc:featureList edam:operation_3660 ; sc:license "Artistic-2.0" ; sc:name "JigCell Run Manager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://copasi.org/Projects/JigCell_Run_Manager_2_0//" ; biotools:primaryContact "Alida Palmisano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models. The program provides an automated way to take advantage of the many succsessful methods for computational gene prediction and can provide substantial improvements in accuracy over an individual gene prediction program." ; sc:featureList edam:operation_2454 ; sc:license "Artistic-1.0" ; sc:name "JIGSAW" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/jigsaw/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """Joint Integration and Discrimination for Automated Single-Cell Annotation. JIND is a framework for automated cell-type identification based on neural networks. It directly learns a low-dimensional representation (latent code) inwhich cell-types can be reliably determined. To account for batch effects, JIND performs a novel asymmetric alignment in which the transcriptomic profileof unseen cells is mapped onto the previously learned latent space, hence avoiding the need of retraining the model whenever a new dataset becomes available. JIND also learns cell-type-specific confidence thresholds to identify and reject cells that cannot be reliably classified. We show on datasets with and without batch effects that JIND classifies cells more accurately than previously proposed methods while rejecting only a small proportion of cells. Moreover, JIND batch alignment is parallelizable, being more than five or six times faster than Seurat integration.""" ; sc:featureList edam:operation_2495, edam:operation_3937 ; sc:license "MIT" ; sc:name "JIND" ; sc:url "https://github.com/mohit1997/JIND" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0204, edam:topic_2269 ; sc:citation , "pubmed:36309196" ; sc:description "A unified multi-view-based joint representation learning for CircRNA binding sites prediction." ; sc:featureList edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "JLCRB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://82.157.188.204/JLCRB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_2572, edam:format_3016 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622 ; sc:citation , , ; sc:description "A toolkit to infer and analyse loss of heterozygosity (LOH) blocks starting from a reference genome (FASTA), mapped reads (BAM) and called variants (VCF)." ; sc:featureList edam:operation_0256, edam:operation_3197, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "JLOH" ; sc:operatingSystem "Linux" ; sc:softwareVersion "v1.0.1" ; sc:url "https://github.com/Gabaldonlab/jloh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168, edam:topic_3172, edam:topic_3173, edam:topic_3520 ; sc:citation , "pubmed:33179747" ; sc:description """Large enhancement of multi-omics data resources on the general Japanese population. jMorp: Japanese Multi Omics Reference Panel - Tohoku Medical Megabank Organization, Tohoku University.""" ; sc:featureList edam:operation_0524, edam:operation_3196, edam:operation_3644 ; sc:name "jMorp" ; sc:url "https://jmorp.megabank.tohoku.ac.jp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC5260066", "pubmed:28114896" ; sc:description "Software package for advanced time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data. Through a user-friendly graphical interface biomedical researchers and clinical radiologists can use state-of-the-art signal processing algorithms to analyse and quantify spectroscopic data: from a single spectrum to a full multidimensional MRSI dataset." ; sc:featureList edam:operation_3443 ; sc:name "jMRUI" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.jmrui.eu/" ; biotools:primaryContact "Michał Jabłoński" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2129 ; sc:encodingFormat edam:format_3244 ; sc:name "File format name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2129 ; sc:name "File format name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Interactively visualize the spectra and chromatograms in an mzML file." ; sc:featureList edam:operation_3203 ; sc:license "Apache-2.0" ; sc:name "jmzML" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://code.google.com/p/jmzml/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654, edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats." ; sc:featureList edam:operation_1812 ; sc:name "jmzReader" ; sc:softwareHelp ; sc:url "https://github.com/PRIDE-Utilities/jmzReader" ; biotools:primaryContact "PRIDE Helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172 ; sc:citation "pubmed:24659499" ; sc:description "Provides reading and writing capabilities, as well as supporting the validation of mzTab and the conversion of PRIDE XML and mzIdentML files to mzTab." ; sc:featureList edam:operation_2423 ; sc:name "jmzTab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/mztab/" ; biotools:primaryContact "Juan Antonio Vizcaíno" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3509 ; sc:encodingFormat edam:format_2332 ; sc:name "Ontology mapping" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3681 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0219, edam:topic_3172 ; sc:citation ; sc:description "Reference implementation for mzTab 2.0 for metabolomics" ; sc:featureList edam:operation_0335, edam:operation_0336, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "jmztab-m" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.6", "1.0.1", "1.0.2", "1.0.4", "1.0.5", "1.0.6" ; sc:url "https://github.com/lifs-tools/jmzTab-m" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0622, edam:topic_0654, edam:topic_3569 ; sc:citation "pubmed:22879375" ; sc:description "Package which implemented the joint matrix factorization technique to integrating multi-dimensional genomics data for the discovery of combinatorial patterns." ; sc:featureList edam:operation_3209 ; sc:name "jNMF" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://page.amss.ac.cn/shihua.zhang/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3391 ; sc:citation "pubmed:25411328" ; sc:description "Meta-analysis method for identification of DEGs based on joint non-negative matrix factorization." ; sc:featureList edam:operation_2945 ; sc:name "jNMFMA" ; sc:softwareHelp ; sc:url "http://micblab.iim.ac.cn/jnmfma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3068, edam:topic_3293 ; sc:citation ; sc:description "R package to visualize outputs from the Johnson-Neyman technique for categorical and continuous moderators, including options for phylogenetic regressions." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "JNplots" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/JNplots/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3321 ; sc:citation , "pmcid:PMC3236061", "pubmed:21693013" ; sc:description "This package implements three steps of an algorithm called JODA, which computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model)." ; sc:featureList edam:operation_1781 ; sc:license "GPL-2.0" ; sc:name "joda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/joda.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "This functions load, process and plot the data from the John Hopkins COVID-19 database." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "John Hopkins COVID-19 case data loader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.63" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74589-load-covid-19-case-data-from-john-hopkins-database" ; biotools:primaryContact "Axel Ahrens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0781, edam:topic_3324 ; sc:citation , "pubmed:32087114" ; sc:description "Online interactive dashboard for the Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)." ; sc:featureList edam:operation_0337 ; sc:name "Johns Hopkins Coronavirus Resource Center" ; sc:softwareHelp ; sc:url "https://coronavirus.jhu.edu/map.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474, edam:topic_3569 ; sc:citation , "pmcid:PMC6047371", "pubmed:9879902" ; sc:description "Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "joineRML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/joineRML/" ; biotools:primaryContact "Pete Philipson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_2269 ; sc:citation , "pubmed:34358294" ; sc:description "Multivariate elastic net regression through stacked generalisation" ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "joinet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rauschenberger/joinet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2229, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC9284445", "pubmed:35860412" ; sc:description """Joint-SNF method uses SNF to integrate the joint structure extracted by JIVE method to obtain the fusion matrix. The fused network enhances strong similarities and weakens spurious associations between samples while reducing the noise. The realization of Joint-SNF method relies on the following two important algorithms. 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Stöver", "Sarah Wiechers" ; sc:citation ; sc:contributor "Kai F. Müller" ; sc:description "An open source Java library for reading and writing various tree and alignment formats. Application developers are able to implement format-independent data processing by including event based readers via the abstract strategy pattern. All readers are designed to deal with large amounts of data (alignments with many and/or very long sequences, large trees) without using a great amount of resources (CPU or RAM)." ; sc:featureList edam:operation_1812, edam:operation_2409, edam:operation_3357 ; sc:funder "DFG (German Research Foundation)" ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "JPhyloIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "0.5.4" ; sc:url "http://bioinfweb.info/JPhyloIO/" ; biotools:primaryContact "Ben C. 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It can render complex trees, yet offers a simple method to do so. It leverages the recent XML schema definition specified for phylogenetic trees, phyloXML." ; sc:featureList edam:operation_0324 ; sc:name "jsPhyloSVG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.55" ; sc:url "https://github.com/guyleonard/jsPhyloSVG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3520, edam:topic_3678 ; sc:citation , "pubmed:32700239" ; sc:description """A new jsPsych plugin for psychophysics, providing accurate display duration and stimulus onset asynchrony. A jsPsych plugin for psychophysics. The jspsych-psychophysics plugin is developed for the purpose of conducting online/Web-based psychophysical experiments using jsPsych (de Leeuw, 2015). 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JUMPt uses a novel differential equation-based mathematical model to calculate the reliable and accurate protein turnover rates. The proposed method calculates the half-life of individual proteins by fitting the dynamic data of unlabeled free Lys and protein-bound Lys from individual proteins simultaneously." ; sc:featureList edam:operation_2476, edam:operation_3638, edam:operation_3715 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "JUMPt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JUMPSuite/JUMPt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , "pmcid:PMC5009739", "pubmed:27257077" ; sc:description "A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data." ; sc:featureList edam:operation_2454 ; sc:name "JunctionSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/JunctionSeq.html" ; biotools:primaryContact "Stephen Hartley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3318, edam:topic_3324 ; sc:citation ; sc:description """Open-source individual-based epidemiology simulation. This is the offical repository of JUNE, named after June Almeida, who was the female Scottish virologist that first identified the coronavirus group of viruses. checkout the release paper for a physical description of the model. A framework for high resolution Agent Based Modelling.""" ; sc:featureList edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "JUNE" ; sc:url "https://github.com/IDAS-Durham/JUNE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3068, edam:topic_3315, edam:topic_3372, edam:topic_3474 ; sc:citation ; sc:description "Jupyter Book is an open-source tool for building publication-quality books and documents from computational material." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Jupyter Book project" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://jupyterbook.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_2830, edam:topic_3966 ; sc:citation , "pubmed:36094101" ; sc:description "Computational extraction of structural properties of viral epitopes." ; sc:featureList edam:operation_0416, edam:operation_0480, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Jupytope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shamimarashid/Jupytope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0780, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC9583140", "pubmed:36275541" ; sc:description """Software tool with graphical and character user interfaces for deep learning-based object detection and segmentation in image analysis. Deep learning has been applied to solve various problems, especially in image recognition, across many fields including the life sciences and agriculture.""" ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "JustDeepIt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/biunit/JustDeepIt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3297 ; sc:citation , "pubmed:37523674" ; sc:description "Database of plant long noncoding RNA expression profiles and functional network." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "JustRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://JustRNA.itps.ncku.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0780, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:34021745" ; sc:description "Jutils is a visualization toolkit for differential alternative splicing events. 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Juxtapose, together with different similarity measures, can be utilized for comparative transcriptomics between a set of organisms." ; sc:featureList edam:operation_1781, edam:operation_3463, edam:operation_3766 ; sc:name "Juxtapose" ; sc:url "https://github.com/klovens/juxtapose" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2330 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Split bed file into several bed files where each region is separated of any other by N bases." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Jvarkit " ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/Biostar178713" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269 ; sc:citation "pubmed:25176396" ; sc:description "Plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams." ; sc:featureList edam:operation_0337 ; sc:name "jvenn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinfo.genotoul.fr/jvenn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:12824438" ; sc:description "Creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes." ; sc:featureList edam:operation_0387, edam:operation_0398, edam:operation_0403, edam:operation_2929 ; sc:name "JVirGel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jvirgel.de/" ; biotools:primaryContact "K. Hiller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC8409305", "pubmed:34370400" ; sc:description "A pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping." ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "JWES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/drzeeshanahmed/JWES-DB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3263 ; sc:citation , "pmcid:PMC8275349", "pubmed:34252969" ; sc:description "Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories." ; sc:featureList edam:operation_0224, edam:operation_3436 ; sc:license "MIT" ; sc:name "k-anonymity" ; sc:url "https://github.com/tzyRachel/K-anonymity-Expectation" ; biotools:primaryContact "Yun William Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3170 ; sc:citation ; sc:description "Model-based branching point detection in single-cell data by K-branches clustering." ; sc:featureList edam:operation_3459, edam:operation_3680 ; sc:name "K-Branches" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/theislab/kbranches" ; biotools:primaryContact "Fabian Theis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1008 ; sc:name "Polypeptide chain ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_2330 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130 ; sc:citation ; sc:description "Predictor of the Protein Folding Mechanism and Rate." ; sc:featureList edam:operation_2415 ; sc:name "K-Fold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://folding.biofold.org/k-fold/" ; biotools:primaryContact "Emidio Capriotti", "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3512 ; sc:citation ; sc:description "An EST clustering algorithm which mitigates the effect of chimeric sequences by using a variable linkage merging algorithm." ; sc:featureList edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "k-link" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.csiro.au/k-link/" ; biotools:primaryContact "Lauren Bragg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3336 ; sc:citation "pubmed:24812339" ; sc:description "Novel and user-friendly web-based program that systematically connects a set of query kinases to kinase inhibitors based on quantitative profiles of the kinase inhibitor activities. Users can find kinase inhibitors for a set of query kinases (obtained from high-throughput “omics” experiments) or to reveal new interactions between kinases and kinase inhibitors for rational drug combination studies." ; sc:featureList edam:operation_2492 ; sc:name "K-Map" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tanlab.ucdenver.edu/kMap/" ; biotools:primaryContact "Tan Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0152, edam:topic_0166, edam:topic_0749, edam:topic_2830 ; sc:citation ; sc:description """A unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains. Klebsiella species serotype predictor and surface antigens modeler. K-PAM (Klebsiella species serotype predictor and surface antigens modeler) is an in silico diagnostic tool that can predict the serotype of Klebsiella spp. (K- and O-types) using the gene protein sequences of proteins involved in biosynthesis and transportations of CPS and LPS. The following documentation is to help the user in usage of K-PAM web server.""" ; sc:featureList edam:operation_2421, edam:operation_2454, edam:operation_3431 ; sc:name "K-PAM" ; sc:softwareHelp ; sc:url "http://www.iith.ac.in/K-PAM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "K-Pax contains an implementation of a Bayesian model-based method for simultaneously classifying aligned proteins into functionally divergent subgroups and identifying their function specific residues" ; sc:featureList edam:operation_2479, edam:operation_2990 ; sc:name "K-Pax" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.helsinki.fi/bsg/software/K-PAX/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0625, edam:topic_0736, edam:topic_3120 ; sc:citation , "pubmed:37625584" ; sc:description "Database of kinetics data on proteins and mutants." ; sc:featureList edam:operation_0268, edam:operation_0337, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "K-Pro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://folding.biofold.org/k-pro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_0821, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:33772580" ; sc:description "k-seq (Kinetic sequencing) is an analytic toolbox for data from kinetic assay with DNA sequencing." ; sc:featureList edam:operation_3200, edam:operation_3219, edam:operation_3799 ; sc:name "k-Seq" ; sc:softwareHelp ; sc:url "https://github.com/ichen-lab-ucsb/k-seq" ; biotools:primaryContact "Irene A Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:34606462" ; sc:description "Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification." ; sc:featureList edam:operation_0362, edam:operation_2995, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "K2Mem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/davide92/K2Mem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3512 ; sc:citation "pubmed:18230758" ; sc:description "Web service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal." ; sc:featureList edam:operation_0278, edam:operation_0570, edam:operation_2441, edam:operation_3469 ; sc:name "K2N" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/k2nwww/" ; biotools:primaryContact "Rob Kight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0637, edam:topic_3172, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data. K2Taxonomer is an R package built around a "top-down" recursive partitioning framework to perform unsupervised learning of nested “taxonomy-like” subgroups from high-throughput -omics data. This framework was devised to be flexible to different data structures, enabling its applicability to analyze both bulk and single-cell data sets. In addition to implementing the algorithm, this package includes functionality to annotate estimated subgroups using gene- and pathway-level analyses.""" ; sc:featureList edam:operation_2495, edam:operation_3436, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "K2Taxonomer" ; sc:url "https://github.com/montilab/K2Taxonomer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:author ; sc:description "The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "kMetaShot" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/gdefazio/kMetaShot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3421, edam:topic_3444 ; sc:citation , "pubmed:31452014" ; sc:description "a novel software calculator program of the Objective Breast Cosmesis Scale (OBCS) | kOBCS© the digital calculator" ; sc:featureList edam:operation_3659 ; sc:name "kOBCS" ; sc:url "http://www.kobcs.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0769, edam:topic_3473 ; sc:citation , "pmcid:PMC10112952", "pubmed:37018156" ; sc:description "Knowledgeable biomedical relation extraction system." ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "K-RET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lasigeBioTM/K-RET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3473, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC10354155", "pubmed:37463925" ; sc:description "Known Antibody Search (KA-Search) is designed to facilitate the rapid and exhaustive search of antibody variable domains. It addresses a key challenge in immunology and biotechnology: the need to analyze and compare vast numbers of antibody sequences efficiently." ; sc:featureList edam:operation_0252, edam:operation_0480, edam:operation_0495, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "KA-Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/oxpig/kasearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_0602 ; sc:citation "pubmed:17526522" ; sc:description "Tool for ortholog assignment and pathway mapping. It provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways." ; sc:featureList edam:operation_0533, edam:operation_2429, edam:operation_3672 ; sc:name "KAAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.genome.jp/kegg/kaas/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0196 ; sc:citation "pubmed:25481007" ; sc:description "Helps you create interactive visualizations of BLAST results from your web browser. Find your most interesting alignments, list detailed parameters for each, and export a publication-ready vector image, all without installing any software." ; sc:featureList edam:operation_3184 ; sc:name "Kablammo" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://kablammo.wasmuthlab.org/" ; biotools:primaryContact "James Wasmuth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2640, edam:topic_3360, edam:topic_3520 ; sc:citation , "pmcid:PMC8268341", "pubmed:34238254" ; sc:description "Inference of kinase-signaling networks in human myeloid cell line models by Phosphoproteomics using kinase activity enrichment analysis (KAEA)." ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "KAEA" ; sc:softwareHelp ; sc:url "https://github.com/Mahmoudhallal/KAEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3516, edam:topic_3518 ; sc:citation , "pmcid:PMC9531401", "pubmed:36195962" ; sc:description "KAGE is a tool for efficiently genotyping short SNPs and indels from short genomic reads." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ivargr/kage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36017752" ; sc:description "KaIDA - Karlsruhe Image Data Annotation Tool. A modular tool for assisting image annotation in deep learning." ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:license "Not licensed" ; sc:name "KaIDA" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://git.scc.kit.edu/sc1357/kaida" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_3475 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:author "Anders Krogh", "Peter Menzel" ; sc:citation ; sc:contributor "Kim Lee Ng" ; sc:description "Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Kaiju" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Section for Bioinformatics, Department of Biology, University of Copenhagen", "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1.4.4" ; sc:url "http://kaiju.binf.ku.dk" ; biotools:primaryContact "Anders Krogh", "Peter Menzel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0196, edam:topic_0621, edam:topic_3053 ; sc:citation , "pmcid:PMC7918157", "pubmed:33645624" ; sc:description "KAIKObase is a silkworm genome database." ; sc:featureList edam:operation_0282, edam:operation_0362, edam:operation_0525, edam:operation_3196 ; sc:name "KAIKObase" ; sc:url "https://kaikobase.dna.affrc.go.jp" ; biotools:primaryContact "Akiya Jouraku" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3300, edam:topic_3382 ; sc:citation , "pmcid:PMC8586513", "pubmed:34777017" ; sc:description "Open-Source Software for the Analysis of Cardiac Optical Data Collected From Multiple Species." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KairoSight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kairosight/kairosight-2.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:20451164" ; sc:description "Adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into KaKs_Calculator." ; sc:featureList edam:operation_2478 ; sc:name "Kaks_Calculator" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/kakscalculator2/" ; biotools:primaryContact "Jun Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0769 ; sc:citation ; sc:description "A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures." ; sc:featureList edam:operation_0224, edam:operation_0313, edam:operation_3501 ; sc:name "Kaleidoscope" ; sc:url "https://kalganem.shinyapps.io/Kaleidoscope/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Erik Sonnhammer", "Timo Lassmann" ; sc:citation , ; sc:description "Fast and accurate multiple sequence alignment which handles large sequences." ; sc:featureList edam:operation_0492 ; sc:name "Kalign (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "Stockholm Bioinformatics Center" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/msa/kalign/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Fast and accurate multiple sequence alignment algorithm for DNA and protein sequences." ; sc:featureList edam:operation_0492 ; sc:name "Kaling API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/kalign_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622 ; sc:description "Kalign is a fast and accurate multiple sequence alignment algorithm." ; sc:featureList edam:operation_0492 ; sc:name "Kalign (SBC)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://msa.sbc.su.se" ; biotools:primaryContact "Oliver Frings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment." ; sc:featureList edam:operation_0314 ; sc:license "BSD-2-Clause" ; sc:name "kallisto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pachterlab.github.io/kallisto/about.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3474, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC7386246", "pubmed:32552725" ; sc:description """Improving genomic prediction accuracy of complex traits using machine learning determined parameters. 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Matton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:21097783" ; sc:description "It is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. 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It builds several models unsing kernel principal components regression and boosting and from them estimates the probability that each transcription factor regulates a gene." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3659, edam:operation_3891 ; sc:name "KBoost" ; sc:url "https://github.com/Luisiglm/KBoost" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "An EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services." ; sc:featureList edam:operation_2403 ; sc:name "KBWS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.g-language.org/wiki/kbws_readme" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929, edam:format_1982 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "A fast and accurate tool for performing codon-aware multiple sequence alignments" ; sc:featureList edam:operation_0492 ; sc:license "AFL-3.0" ; sc:name "kc-align" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/davebx/kc-align" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2840, edam:topic_3292, edam:topic_3343 ; sc:citation , "pubmed:35348625" ; sc:description "A tool to aid in the evaluation and classification of chemical carcinogens." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "kc-hits" ; sc:operatingSystem "Windows" ; sc:url "https://gitlab.com/i1650/kc-hits.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0152, edam:topic_0154 ; sc:citation "pubmed:15215393" ; sc:description "Takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm." ; sc:featureList edam:operation_0295, edam:operation_0509, edam:operation_0510, edam:operation_2422 ; sc:name "KCaM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.jp/tools/kcam/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0654 ; sc:citation "pubmed:27283950" ; sc:description "Very fast multi-threaded k-mer counting algorithm. It uses cache efficient burst tries to store k-mers" ; sc:featureList edam:operation_3472 ; sc:name "KCMBT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/abdullah009/kcmbt_mt" ; biotools:primaryContact "Abdullah-Al Mamun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_1317, edam:topic_3300, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC5679743", "pubmed:29021305" ; sc:description "Predicting the Functional Impact of KCNQ1 Variants with Artificial Neural Networks." ; sc:featureList edam:operation_0331, edam:operation_0480, edam:operation_3092, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "KCNQ1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.kcnq1predict.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3174 ; sc:citation , "pubmed:34849595" ; sc:description "An ultra-fast k-mer counter for assembled genome analysis." ; sc:featureList edam:operation_0525, edam:operation_3211, edam:operation_3472, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KCOSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kcoss-2021/KCOSS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3033 ; sc:name "Processed microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3365, edam:topic_3518 ; sc:citation ; sc:description "Multi sample aCGH analysis package using kernel convolution." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "KCsmart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/KCsmart.html" ; biotools:primaryContact "Jorma de Ronde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3047 ; sc:citation , "pubmed:33080214" ; sc:description """Identification of lncRNAs subcellular localization with multiple features and nonnegative matrix factorization. Long non-coding RNAs (lncRNAs) refer to functional RNA molecules with a length more than 200 nucleotides and have minimal or no function to encode proteins. In recent years, more studies show that lncRNAs subcellular localization has valuable clues for their biological functions. So it is count for much to identify lncRNAs subcellular localization. In this paper, a novel statistical model named KD-KLNMF is constructed to predict lncRNAs subcellular localization. Firstly, k-mer and dinucleotide-based spatial autocorrelation are incorporated as the feature vector. Then, Synthetic Minority Over-sampling Technique is used to deal with the imbalance dataset. Next, Kullback-Leibler divergence-based nonnegative matrix factorization is applied to select optimal features. And then we utilize support vector machine as the classifier after comparing with other classifiers""" ; sc:featureList edam:operation_2489, edam:operation_3472 ; sc:name "KD-KLNMF" ; sc:url "https://github.com/HuijuanQiao/KD-KLNMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_3473 ; sc:citation "pubmed:22641855" ; sc:description "The Comprehensive Knowledge Discovery System for Missense Variant (KD4v) webserver allows users to characterize and predict the phenotypic effects of missense variants." ; sc:featureList edam:operation_0331, edam:operation_2423, edam:operation_3225, edam:operation_3227 ; sc:name "KD4v" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://decrypthon.igbmc.fr/kd4v" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3366, edam:topic_3518 ; sc:citation "pubmed:25273109" ; sc:description "Cytoscape app to learn biological network topology and its changes using profiling data and domain knowledge. It takes input data and runs KDDN algorithm to construct the dependency network." ; sc:featureList edam:operation_2497 ; sc:name "KDDN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apps.cytoscape.org/apps/kddn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:24764459" ; sc:description "Non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample." ; sc:featureList edam:operation_0324 ; sc:name "kdetrees" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/grady/kdetrees" ; biotools:primaryContact "Grady Weyenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0821 ; sc:citation "pubmed:19176546" ; sc:description "Web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them." ; sc:featureList edam:operation_2949, edam:operation_3501 ; sc:name "KEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://amp.pharm.mssm.edu/lib/kea.jsp" ; biotools:primaryContact "Avi Ma’ayan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3174 ; sc:citation "pmcid:PMC6936898" ; sc:description """A Novel Visualization Tool to Explore Biodiversity in Metagenomes. A tool for viewing the contents of metagenomic samples. format_input.py: takes a file that contains a single BLAST query and taxon ID per line and formats it correctly as input for Keanu. The following command is used to create the taxonomy.dat and merged_deleted.dat databases necessary for running Keanu. There are no optional parameters. The input files - names.dmb, nodes.dmp, delnodes.dmp, and merged.dmp - come from the taxdmp file located at the NCBI Taxonomy FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/.""" ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Keanu" ; sc:url "https://github.com/IGBB/keanu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0654 ; sc:citation , "pubmed:25812745" ; sc:description "This package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences." ; sc:featureList edam:operation_2451 ; sc:license "GPL-2.0" ; sc:name "KeBABS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://www.bioinf.jku.at/software/kebabs/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0196, edam:topic_0621, edam:topic_0632 ; sc:citation , "pubmed:33755102" ; sc:description "KEC (short for K-mer exclusion by cross reference) is a searching tool for unique DNA RNA amino acid sequences in large datasets." ; sc:featureList edam:operation_0308, edam:operation_0363, edam:operation_2421, edam:operation_3192, edam:operation_3472 ; sc:name "KEC" ; sc:softwareHelp , ; sc:url "https://github.com/berybox/KEC" ; biotools:primaryContact "Pavel Beran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:24867942" ; sc:description "Command line tool for generating, for a given reference genome, a set of k-mers absent in that genome." ; sc:featureList edam:operation_2478 ; sc:name "KeeSeeK" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "0.4.0" ; sc:url "http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek" ; biotools:primaryContact "Stefano Toppo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622 ; sc:citation "pubmed:22130871" ; sc:description "Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps." ; sc:featureList edam:operation_0314 ; sc:name "KegArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.jp/kegg/expression/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases." ; sc:featureList edam:operation_2421 ; sc:name "KegDraw 0.1.14 beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kegg.jp/kegg/download/kegtools.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_3407 ; sc:citation , , , "pmcid:PMC102409", "pmcid:PMC6798127", "pmcid:PMC7779016", "pubmed:10592173", "pubmed:12539951", "pubmed:18477636", "pubmed:31441146", "pubmed:33125081", "pubmed:9847135" ; sc:description "Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. This tool comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). Its Atlas is a new tool for the global analysis of metabolic pathways." ; sc:featureList edam:operation_0533, edam:operation_1781, edam:operation_2429, edam:operation_2497, edam:operation_3660 ; sc:name "Kyoto encyclopedia of genes and genomes (KEGG)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.ad.jp/kegg/" ; biotools:primaryContact "Feedback Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0602, edam:topic_0621, edam:topic_3697 ; sc:citation , "pmcid:PMC9956942", "pubmed:36833314" ; sc:description "An Effective Extraction Tool for KEGG Orthologs." ; sc:featureList edam:operation_0362, edam:operation_0533, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "KEGG_Extractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xielisos567/KEGG_extractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3372, edam:topic_3571 ; sc:citation , "pmcid:PMC9985241", "pubmed:36870946" ; sc:description "A Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "kegg_pull" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.0" ; sc:url "https://pypi.org/project/kegg-pull/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3167, edam:format_3326, edam:format_3780 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0092, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Web-based tool for visualizing experimental data in the context of biological pathways. It produces animations or static images of KEGG pathways by overlaying public or user uploaded high-thourghput data over handdrawn KEGG pathway maps." ; sc:featureList edam:operation_3083, edam:operation_3695, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "KEGGanim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-EE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://biit.cs.ut.ee/kegganim" ; biotools:primaryContact "Priit Adler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_3620 ; sc:name "Protein family report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:encodingFormat edam:format_3603 ; sc:name "Pathway or network report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085 ; sc:author ; sc:citation ; sc:description "A tool for representing genomic potential and transcriptomic expression into KEGG pathways." ; sc:featureList edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "KEGGCharter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.3.4" ; sc:url "https://github.com/iquasere/KEGGCharter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation , "pmcid:PMC2682514", "pubmed:19307239" ; sc:description "Interface between a KEGG pathway and a graph object, as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers other functionalities including parsing, graph operation, visualization, etc." ; sc:featureList edam:operation_0337, edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "KEGGgraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/KEGGgraph.html" ; biotools:primaryContact "Jitao David Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602 ; sc:citation ; sc:description "See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "KEGGlincs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/KEGGlincs.html" ; biotools:primaryContact "Shana White" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3299 ; sc:citation ; sc:description "Graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs." ; sc:featureList edam:operation_0337 ; sc:license "Artistic-2.0" ; sc:name "keggorthology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/keggorthology.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3071 ; sc:citation "pubmed:23292739" ; sc:description "MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3096 ; sc:name "KEGGParser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mathworks.com/matlabcentral/fileexchange/37561" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. It facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples." ; sc:featureList edam:operation_0226, edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "KEGGprofile" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/KEGGprofile.html" ; biotools:primaryContact "Shilin Zhao" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie." ; sc:featureList edam:operation_2421, edam:operation_3282 ; sc:license "Artistic-2.0" ; sc:name "KEGGREST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/KEGGREST.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3071 ; sc:citation "pubmed:21700675" ; sc:description "Easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats." ; sc:featureList edam:operation_0335 ; sc:name "KEGGtranslator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ra.cs.uni-tuebingen.de/software/KEGGtranslator/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:19477978" ; sc:description "Kernel-reweighted logistic regression method for reverse engineering the dynamic interactions between genes based on their time series of expression values." ; sc:featureList edam:operation_3439 ; sc:name "KELLER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=430" ; biotools:primaryContact "Eric P. 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KiMONo is a network inference tool for multi-omics datasets. The multi-omics network is calculated by sparse-group-LASSO regression and can incorporate prior biological information using protein-protein Interactions.""" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3799, edam:operation_3927 ; sc:name "KiMONo" ; sc:url "https://github.com/cellmapslab/kimono" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3068 ; sc:citation , "pmcid:PMC9251768", "pubmed:35700393" ; sc:description "A python Package for Kinetic Modeling of the Chemical Mechanism." ; sc:featureList edam:operation_0337, edam:operation_3219, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KiMoPack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pypi.org/project/KiMoPack/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3375, edam:topic_3376 ; sc:citation , "pmcid:PMC4236735", "pubmed:25115331" ; sc:description "Web-based repository of experimental data for KInetic MOdels of biological SYStems." ; sc:featureList edam:operation_2421 ; sc:license "GPL-2.0" ; sc:name "KiMoSys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://kimosys.org/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0602 ; sc:citation ; sc:description "Novel computational method for predicting activating mutations in kinases. It is a machine learning approach that relies on structural and sequence data of proteins, such as environment residue, stability changes predictions, atomic interactions, graph-based signatures and residue conservation." ; sc:featureList edam:operation_0331, edam:operation_0417 ; sc:name "Kinact" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/kinact/" ; biotools:primaryContact "Carlos H. M. Rodrigues", "Dr. David B. Ascher", "Dr. Douglas E. V. Pires" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3332, edam:topic_3369 ; sc:citation ; sc:description "KinaFrag is an integrated database to explore the kinase-ligand fragment interaction space. KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery." ; sc:featureList edam:operation_2422, edam:operation_2492, edam:operation_4009 ; sc:name "KinaFrag" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/" ; biotools:primaryContact "Ge-Fei Hao", "Guang-Fu Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_0130, edam:topic_0602, edam:topic_2275 ; sc:citation "pubmed:21693559" ; sc:description "KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions." ; sc:featureList edam:operation_0322, edam:operation_2949, edam:operation_3456 ; sc:name "KINARI-Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kinari.cs.umass.edu/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "BLAST search against Kinase domains stored in Kinase SARfari." ; sc:featureList edam:operation_0346 ; sc:name "Kinase SARfari BLAST Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/protein" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "Search against small molecules stored in Kinase SARfari database." ; sc:featureList edam:operation_0339 ; sc:name "Kinase SARfari Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/compound" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0202, edam:topic_0602, edam:topic_2640 ; sc:citation , "pubmed:33137204" ; sc:description """Kinase mutations and drug response database. Mutations in kinases are abundant and critical to study signaling pathways and regulatory roles in human disease, especially in cancer. Somatic mutations in kinase genes can affect drug treatment, both sensitivity and resistance, to clinically used kinase inhibitors.""" ; sc:featureList edam:operation_2421, edam:operation_3227 ; sc:name "KinaseMD" ; sc:url "https://bioinfo.uth.edu/kmd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0160, edam:topic_0749, edam:topic_3510 ; sc:citation "pubmed:15980458" ; sc:description "Identify kinase-specific phosphorylation sites in protein sequences." ; sc:featureList edam:operation_0303, edam:operation_0417, edam:operation_2575, edam:operation_3092 ; sc:name "KinasePhos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kinasephos.mbc.nctu.edu.tw/" ; biotools:primaryContact "KinasePhos Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description """A Predictive Model for Estimating Ligand-Kinase Inhibitor Constant (pKi). Model to predict kinase-ligand pKi values. Kinases to predict Inhibitor constant in terms of pKI (where pKi is decadic logarithm of Ki). We used the data points that were specifically represent Ki values to train and test the models. Download the docker image docker pull sirimullalab/kinasepkipred:py2. Run the container docker run --rm sirimullalab/kinasepkipred:py2 . To run with a built-in sample, do docker run --rm sirimullalab/kinasepkipred:py2. Set up the conda environment and activate it.""" ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "kinasepkipred" ; sc:url "https://github.com/sirimullalab/KinasepKipred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3071, edam:topic_3293 ; sc:citation , "pmcid:PMC10208500", "pubmed:37224178" ; sc:description "A global database of kinship terminology." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:name "Kinbank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.kinbank.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:11252606" ; sc:description "MATLAB software package for likelihood-based analysis of kin-cohort data." ; sc:featureList edam:operation_2238 ; sc:name "KinCohort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dceg.cancer.gov/tools/analysis/kincohort" ; biotools:primaryContact "Nilanjan Chatterjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_0736, edam:topic_0749, edam:topic_3293 ; sc:citation ; sc:description """A web resource for structural classification of protein kinases and their inhibitors. Use the following command to create a virtual enviroment and install the necessary packages.""" ; sc:featureList edam:operation_0480, edam:operation_1839, edam:operation_2476, edam:operation_2950, edam:operation_2996 ; sc:name "Kincore" ; sc:url "http://dunbrack.fccc.edu/kincore" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:encodingFormat edam:format_1196 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0625, edam:topic_3047, edam:topic_3336, edam:topic_3375 ; sc:citation ; sc:description "Using graph-based signatures to predict small molecule CDK2 kinase inhibitors." ; sc:featureList edam:operation_2492, edam:operation_3196, edam:operation_3938, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "kinCSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biosig.unimelb.edu.au/kin_csm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0749, edam:topic_2229 ; sc:citation , "pmcid:PMC8756297", "pubmed:35083039" ; sc:description "A simple web tool for ranking pairwise associations in biomedical applications." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KinderMiner web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.kinderminer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0625, edam:topic_2885, edam:topic_3500 ; sc:citation ; sc:description "Functions, classes & app for simulating and estimating close-kin dispersal kernels" ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "kindisperse" ; sc:url "https://github.com/moshejasper/kindisperse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0157, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:16845019" ; sc:description "KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB)." ; sc:featureList edam:operation_0320, edam:operation_0474, edam:operation_2406, edam:operation_2416 ; sc:name "KinDOCK" ; sc:url "http://abcis.cbs.cnrs.fr/kindock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0099, edam:topic_0736, edam:topic_3500 ; sc:citation "pubmed:15980546" ; sc:description "Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots." ; sc:featureList edam:operation_0279, edam:operation_0483 ; sc:name "Kinefold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kinefold.curie.fr/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3314, edam:topic_3332 ; sc:citation "pubmed:19669750" ; sc:description "Generates a generalized mass action model from the chemical equations of reactions and an estimation of the structural parameters of these reactions" ; sc:featureList edam:operation_3664 ; sc:name "KInfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cosbi.eu/research/prototypes/kinfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3375, edam:topic_3384, edam:topic_3452 ; sc:citation ; sc:description "Reproducible PET Pharmacokinetic Modelling in R | ABSTRACT Quantification of Positron Emission Tomography (PET) data is performed using pharmacokinetic models. There exist many models for describing this data, each of which may describe the data better or worse depending on the specific application, and there are both theoretical, practical and empirical reasons to select any one model over another. As such, effective PET modelling requires a high degree of flexibility, while effective communication of all steps taken through scientific publications is not always feasible. Reproducible research practices address these concerns, in that researchers share analysis code, and data if possible, such that all steps are recorded, allowing an independent researcher to reproduce the results and assess their veracity. In this article, I present kinfitr : a software package for performing kinetic modelling using the open-source R language, in a reproducible manner" ; sc:featureList edam:operation_0337, edam:operation_3891 ; sc:name "kinfitr" ; sc:url "https://github.com/mathesong/kinfitr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0209, edam:topic_2828, edam:topic_3343 ; sc:citation ; sc:description """Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. KinFragLib: Kinase-focused fragment library. We present here KinFragLib, a data-driven kinase-focused fragment library based on the structural kinome data retrieved from the KLIFS database.""" ; sc:featureList edam:operation_2422, edam:operation_2929, edam:operation_3216, edam:operation_3359, edam:operation_3938 ; sc:license "MIT" ; sc:name "KinFragLib" ; sc:url "https://github.com/volkamerlab/KinFragLib" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_3698 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077 ; sc:description "Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP." ; sc:featureList edam:operation_0349, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Kingfisher" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/wwood/kingfisher-download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275 ; sc:description "KinImmerse translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE." ; sc:featureList edam:operation_3096, edam:operation_3429 ; sc:name "KinImmerse" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "0.5" ; sc:url "http://kinemage.biochem.duke.edu/software/kinimmerse.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation , "pubmed:16388833" ; sc:description "Fortran program that calculates the informativeness of markers in inferring pairwise relatedness or relationships." ; sc:featureList edam:operation_3625 ; sc:name "KinInfor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zsl.org/science/software/kininfor" ; biotools:primaryContact "JinliangWang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0623, edam:topic_0821, edam:topic_2815, edam:topic_3077 ; sc:citation , "pmcid:PMC5217312", "pubmed:28056780" ; sc:description "Web-based tool for interactive navigation through human kinome data." ; sc:featureList edam:operation_2942 ; sc:name "KinMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kinhub.org/kinmap/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0821, edam:topic_2815, edam:topic_3474 ; sc:citation , "pmcid:PMC4928150", "pubmed:27357839" ; sc:description "A random forest classifier of sequence variants in the human protein kinase superfamily." ; sc:featureList edam:operation_3225 ; sc:license "GPL-3.0" ; sc:name "KinMutRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kinmut2.bioinfo.cnio.es/KinMut2" ; biotools:primaryContact "Miguel vazquez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0623, edam:topic_3293, edam:topic_3407, edam:topic_3944 ; sc:citation ; sc:description "KinOrtho is method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. It is a combination of full-length and domain-based orthology inference methods." ; sc:featureList edam:operation_0224, edam:operation_0553, edam:operation_3663 ; sc:license "MIT" ; sc:name "KinOrtho" ; sc:url "https://github.com/esbgkannan/KinOrtho" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0121, edam:topic_0128, edam:topic_0601 ; sc:citation ; sc:description """A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. Welcome to the Github repository for the KinPred v1.0 project, which seeks to create sustainable and usable formats of whole human proteome predictions of kinases with site-specific substrates. Details of code are available within the Code and Data directory readme files. For orientation, the likely workflows you may be interested in, include:. Users of KinPred-formatted Prediction Algorithm Resources.""" ; sc:featureList edam:operation_0303, edam:operation_0417, edam:operation_3695, edam:operation_3802, edam:operation_3927 ; sc:license "MIT" ; sc:name "KinPred" ; sc:url "https://figshare.com/projects/KinPred_v1_0/86885" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:18440024" ; sc:description "Algorithm that performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure." ; sc:featureList edam:operation_2441 ; sc:name "Kinwalker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.bioinf.uni-leipzig.de/Software/Kinwalker/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9939366", "pubmed:36815050" ; sc:description "Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach." ; sc:featureList edam:operation_3436, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "KIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cadd.zju.edu.cn/kip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "KiPar is a standalone Java application for the retrieval of textual documents likely to contain information relevant for kinetic modelling of a given metabolic pathway." ; sc:featureList edam:operation_0224, edam:operation_2422 ; sc:name "KiPar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mcisb.org/resources/kipar/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3293 ; sc:author "Boas Pucker" ; sc:citation ; sc:description "Knowledge-based Identification of Pathway Enzymes (KIPEs) allows the identification of players in a pathway or gene families. The identification relies of sequence similarity and phylogenetic relationships. Additionally, it is possible to consider functionally relevant amino acids." ; sc:isAccessibleForFree true ; sc:name "Knowledge-based Identification of Pathway Enzymes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/bpucker/KIPEs" ; biotools:primaryContact "Boas Pucker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation "pubmed:26656932" ; sc:description "The basic command-line file versioning solution is a key-value data store that keeps track of when particular items are inserted or deleted (updates are deletes followed by inserts).It can recall versions by date or version id. It can keep versions in one or more volume files." ; sc:featureList edam:operation_0335 ; sc:name "Kipper" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Public-Health-Bioinformatics/kipper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation "pubmed:18786255" ; sc:description "Web-based tool for bisulfite sequencing analysis" ; sc:featureList edam:operation_3186 ; sc:name "Kismeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://katahdin.mssm.edu/kismeth" ; biotools:primaryContact "Kismeth Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3175, edam:topic_3308, edam:topic_3320 ; sc:description "Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data." ; sc:featureList edam:operation_2499 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "kissDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/kissDE.html" ; biotools:primaryContact "Aurélie Siberchicot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0154, edam:topic_0160 ; sc:citation , "pubmed:35536589" ; sc:description "Predicting Off-Targets from Structural Similarities in the Kinome." ; sc:featureList edam:operation_0337, edam:operation_0475, edam:operation_2929 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KiSSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/volkamerlab/kissim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3383 ; sc:citation , , "pmcid:PMC4908324", "pmcid:PMC9191203", "pubmed:27153705", "pubmed:35579370" ; sc:description "Kinetochore Tracking (KiT) is an open-source software package for tracking kinetochores from live-cell fluorescent movies." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "KiT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cmcb-warwick/KiT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_3293, edam:topic_3673 ; sc:citation , "pmcid:PMC7538862", "pubmed:33072720" ; sc:description """A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. KITSUNE: K-mer-length Iterative Selection for UNbiased Ecophylogenomics. KITSUNE is a toolkit for evaluation of the length of k-mer in a given genome dataset for alignment-free phylogenimic analysis.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3185, edam:operation_3192, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "KITSUNE" ; sc:url "https://github.com/natapol/kitsune" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382 ; sc:citation , "pubmed:34813472" ; sc:description "Overcomplete Convolutional Architectures for Biomedical Image and Volumetric Segmentation." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "KiU-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jeya-maria-jose/KiU-Net-pytorch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3053 ; sc:citation , "pmcid:PMC4269931", "pubmed:25496126" ; sc:description "Integration and visualization of network topology and gene-set analysis." ; sc:featureList edam:operation_0571, edam:operation_3083 ; sc:name "Kiwi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pythonhosted.org/KiwiDist/index.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0780, edam:topic_3170, edam:topic_3810 ; sc:citation , "pubmed:34333537" ; sc:description "A comprehensive resource for kiwifruit genomics." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3223, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "Kiwifruit Genome Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://kiwifruitgenome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3519 ; sc:citation "pubmed:18570886" ; sc:description "Tool that implements two algorithms to quantify the starting template in a PCR reaction. The first is a modified Ct strategy that assumes an ideal efficiency and is calculated for reference. The second employs a parametric fitting approach to construct a non-linear approximation to the reaction efficiency that is regressed backwards to establish a peak efficiency." ; sc:featureList edam:operation_3799 ; sc:name "KLab-PCR" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://compbio.med.wayne.edu/software/index.html" ; biotools:primaryContact "Stephen A.Krawetz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc:description "This application will give you explanations for clusters or groupings of entities described by ontology classes. For example, groups of patient profiles described by HPO classes." ; sc:featureList edam:operation_3432, edam:operation_3501, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Klarigi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/reality/klarigi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3174, edam:topic_3299, edam:topic_3697 ; sc:citation ; sc:description """Inferring Multiple Metagenomic Association Networks based on Variation of Environmental Factors. kLDM is designed to infer multiple association networks based on variation of environmental factors.""" ; sc:featureList edam:operation_2409, edam:operation_2495, edam:operation_3432 ; sc:license "Apache-2.0" ; sc:name "kLDM" ; sc:url "https://github.com/tinglab/kLDM.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3305, edam:topic_3673, edam:topic_3796 ; sc:citation ; sc:description """Genomic surveillance framework and global population structure for Klebsiella pneumoniae. Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:. A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).""" ; sc:featureList edam:operation_0525, edam:operation_3461, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "Kleborate" ; sc:url "https://github.com/katholt/Kleborate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3360, edam:topic_3500, edam:topic_3520 ; sc:citation ; sc:description "A web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry." ; sc:featureList edam:operation_3215, edam:operation_3767, edam:operation_3840 ; sc:name "Klebsiella MALDI TypeR" ; sc:url "https://maldityper.pasteur.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3172, edam:topic_3173, edam:topic_3179, edam:topic_3474 ; sc:citation , "pmcid:PMC7750932", "pubmed:32592464" ; sc:description """Multiple kernel learning for integrative consensus clustering of omic datasets. The code contained in this folder can be used to reproduce the pancancer analysis presented in Cabassi and Kirk (2020). The data used for the analysis are those of Hoadley et al. (2014), which can be downloaded from Synapse. The links to each dataset can be found at the beginning of the R scripts where needed.""" ; sc:featureList edam:operation_3432, edam:operation_3891 ; sc:license "MIT" ; sc:name "KLIC" ; sc:url "https://github.com/acabassi/klic-pancancer-analysis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2554 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1498 ; sc:name "Tanimoto similarity score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:name "Structural profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1712 ; sc:name "Chemical structure image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1481 ; sc:name "Structure alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:name "Protein-ligand complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:name "Molecular property (general)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0893 ; sc:name "Sequence-structure alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0890 ; sc:name "Structural (3D) profile alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0982 ; sc:name "Molecule identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:name "Protein structure image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0984 ; sc:name "Molecule name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0888 ; sc:name "Structure similarity score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_1317, edam:topic_2258, edam:topic_2814, edam:topic_3303, edam:topic_3332, edam:topic_3336, edam:topic_3369, edam:topic_3510, edam:topic_3534 ; sc:author ; sc:citation , , , ; sc:description "KLIFS — Kinase–Ligand Interaction Fingerprints and Structures — is a structural kinase database focusing on how kinase inhibitors interact with their targets. The aim of KLIFS is to support (structure-based) kinase research through the systematic collection, annotation, and processing of kinase structures." ; sc:featureList edam:operation_0244, edam:operation_0248, edam:operation_0250, edam:operation_0292, edam:operation_0295, edam:operation_0297, edam:operation_0339, edam:operation_0360, edam:operation_0482, edam:operation_0564, edam:operation_0570, edam:operation_2409, edam:operation_2422, edam:operation_2480, edam:operation_2487, edam:operation_2492, edam:operation_2996, edam:operation_3282 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "KLIFS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.2" ; sc:url "https://klifs.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC9461149", "pubmed:36076174" ; sc:description "KluDo (Diffusion Kernel-based Graph Node Clustering for Protein Domain Assignment), is an automatic framework that incorporates diffusion kernels on protein graphs as affinity measures between residues to decompose protein structures into structural domains." ; sc:featureList edam:operation_0303, edam:operation_0320, edam:operation_0321, edam:operation_0390, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "kludo" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/taherimo/kludo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation , "pmcid:PMC5389000", "pubmed:28403906" ; sc:description "Optimization process of WGCNA hierarchical clustering with k-means." ; sc:featureList edam:operation_0313 ; sc:name "km2gcn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/juanbot/km2gcn" ; biotools:primaryContact "Juan A. Botía" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_1915 ; sc:name "Count matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:encodingFormat edam:format_1915 ; sc:name "Map data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:encodingFormat edam:format_1915 ; sc:name "Sequence signature matches" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1984 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC6116485", "pubmed:30157759" ; sc:description "KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend." ; sc:featureList edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "KMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "https://bitbucket.org/genomicepidemiology/kma/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2533 ; sc:citation "pubmed:24828656" ; sc:description "New approach to alignment-free sequence comparison. While most alignment-free methods rely on exact word matches, it uses a distance measure based on inexact substing matches." ; sc:featureList edam:operation_3202 ; sc:name "kmacs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://kmacs.gobics.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description """KAUST Metagenomic Analysis Platform (KMAP), Enabling Access to Massive Analytics of Re-Annotated Metagenomic Data. Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com). Supplementary Table 1, Gene Catalogs, ENA Project Ids, Links to GITs and KMAP Annotations. KAUST Metagenomic Analysis Platform.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "KMAP" ; sc:softwareHelp , ; sc:url "http://www.cbrc.kaust.edu.sa/kmapBLAST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation "pubmed:25609798" ; sc:description "KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects." ; sc:featureList edam:operation_3472 ; sc:name "KMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pubmed:31038666" ; sc:description "Memory-frugal and retrieval-efficient encoding of counted k-mers." ; sc:featureList edam:operation_0524, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "kmcEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/lzhLab/kmcEx" ; biotools:primaryContact "Liang Zhao", "Limsoon Wong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_2640, edam:topic_3379 ; sc:citation , "pmcid:PMC8234134", "pubmed:34169314" ; sc:description "A curated database of reconstructed individual patient-level data from 153 oncology clinical trials." ; sc:featureList edam:operation_2421, edam:operation_3454, edam:operation_3503 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "KMDATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/raredd/kmdata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3518 ; sc:citation , "pubmed:36315078" ; sc:description "kmdiff provides differential k-mers analysis between two populations (control and case). Each population is represented by a set of short-read sequencing. Outputs are differentially represented k-mers between controls and cases." ; sc:featureList edam:operation_3196, edam:operation_3472, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "kmdiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tlemane/kmdiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3407 ; sc:citation "pubmed:15509612" ; sc:description "Comprehensive collection of single and multiple substrate enzyme reactions and regulatory mechanisms that extends Cellerator function for the mathematical modeling of enzyme reactions." ; sc:featureList edam:operation_2426 ; sc:name "kMech" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.igb.uci.edu/tools/sb/metabolic-modeling/35-kmech.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_3168 ; sc:citation ; sc:description "Fast, Accurate, and Complete SSR Detection in Genomic Sequences." ; sc:featureList edam:operation_0379 ; sc:name "Kmer-SSR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ridgelab/Kmer-SSR" ; biotools:primaryContact "Perry Ridge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3656 ; sc:citation "pubmed:23771147" ; sc:description "Web server uses a support vector machine with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of genomic assays." ; sc:featureList edam:operation_0253, edam:operation_0438, edam:operation_0445, edam:operation_2575 ; sc:name "kmer-SVM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://kmersvm.beerlab.org" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description """Reference-free SNP calling from raw reads based on matching. Kmer2SNP is a fast and accurate variants calling tool for next-generation sequencing data. It's a reference-free and alignment free method.""" ; sc:featureList edam:operation_0484, edam:operation_0524, edam:operation_3472, edam:operation_3661 ; sc:name "Kmer2SNP" ; sc:url "https://github.com/yanboANU/Kmer2SNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "Interactive visualization tool for nucleobase and k-mer frequencies." ; sc:featureList edam:operation_2939, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "kmerPyramid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jkruppa/kmerPyramid" ; biotools:primaryContact "Klaus Jung" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1667 ; sc:name "E-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3293, edam:topic_3474 ; sc:citation , "pmcid:PMC8194296", "pubmed:34122498" ; sc:description "An alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently." ; sc:featureList edam:operation_2422, edam:operation_3472, edam:operation_3478, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "kmerAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/kmerAnalyzer" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation ; sc:description "Kmerator is a prototype tool designed for the prediction of specific k-mers (also called tags) from input sequences, considering a reference genome and an ENSEMBL-like transcriptome. From these specific k-mers, it also outputs their corresponding specific contigs which are sequences of consecutive k-mers (overlapping length between k-mers must be k-1, otherwise, it's a new contig). Kmerator first uses Jellyfish to create 2 requestable indexes from the reference genome and transcriptome, and second, decomposes your input transcript or gene sequences to count the occurences of each k-mer in the genome and transcriptome." ; sc:featureList edam:operation_0314, edam:operation_0450, edam:operation_3472, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Kmerator" ; sc:softwareVersion "0.5.2" ; sc:url "https://github.com/Transipedia/kmerator" ; biotools:primaryContact "Thérèse Commes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3305 ; sc:citation , "pmcid:PMC3911411", "pubmed:24172157", "pubmed:24574292" ; sc:contributor ; sc:description "Prediction of bacterial species using a fast K-mer algorithm." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "KmerFinder" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://cge.cbs.dtu.dk/services/KmerFinder-1.2/" ; biotools:primaryContact "Ole Lund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths." ; sc:featureList edam:operation_0310 ; sc:name "KmerGenie" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://kmergenie.bx.psu.edu/" ; biotools:primaryContact "KmerGenie Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3174, edam:topic_3360 ; sc:citation , "pmcid:PMC7477287", "pubmed:32983048" ; sc:description """A Tool to Identify Group-Specific Sequences With k-mers. KmerGO is a user-friendly tool to identify the group-specific sequences on two groups of high throughput sequencing datasets. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered “group-specific” here. Furthermore, KmerGO can also be applied to capture trait-associated sequences for continuous-trait dataset.""" ; sc:featureList edam:operation_0310, edam:operation_3209, edam:operation_3472 ; sc:name "KmerGO" ; sc:url "https://github.com/ChnMasterOG/KmerGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885, edam:topic_3512, edam:topic_3673 ; sc:citation ; sc:description "KmerKeys is a web resource for searching indexed genome assemblies and variants. It provides performant, rapid query speeds for cloud computation on genome assemblies. It enable fuzzy as well as exact k-mer-based searches of assemblies. To enable robust and speedy performance, the website implements cache-friendly hash tables, memory mapping and massive parallel processing. Our method employs a scalable and efficient data structure that can be used to jointly index and search a large collection of human genome assembly information. One can include variant databases and their associated metadata such as the gnomAD population variant catalog. 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It can then perform various analyses on the generated indices. The counting is resource intensive, but this tool can divide the computation up, so that it can be run as sequential parts (to fit in memory), in parallel (to exploit multiple CPUs), or distributed (to use a cluster of computers)." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "kmx" ; sc:operatingSystem "Linux" ; sc:provider "imr.no" ; sc:softwareHelp ; sc:softwareVersion "0.4" ; sc:url "http://github.com/ketil-malde/kmx" ; biotools:primaryContact "Ketil Malde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:19835949" ; sc:description "Finds pairs of genes with similar behavior across a gene expression dataset. It is intended to be used as a comparative tool to compare the network size (number of output rows) between N datasets with the same numbers of biological samples (input columns) and measured genes (input rows)." ; sc:featureList edam:operation_3439 ; sc:name "Knet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.med.wayne.edu/software/KNet/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0099 ; sc:citation ; sc:description "New software for predicting the consensus secondary structure for a given alignment of RNA sequences. It uses an innovative classifier system (a hierarchical network of k-nearest neighbor classifiers) to compute for each pair of alignment positions a “base pair” or “no base pair” prediction." ; sc:featureList edam:operation_0258, edam:operation_2441 ; sc:name "KNetFold" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.4.4b" ; sc:url "https://binkley2.ncifcrf.gov/users/bshapiro/knetfold/kNetFold.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3068, edam:topic_3473, edam:topic_3810 ; sc:citation ; sc:description """A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.""" ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_2422, edam:operation_3925 ; sc:license "MIT" ; sc:name "KnetMiner" ; sc:softwareHelp ; sc:url "http://knetminer.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2350 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_2258, edam:topic_2259, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description "Open source graphical workbench for building workflows. Among others it provides various extensions for data analysis and life sciences." ; sc:featureList edam:operation_0531, edam:operation_2990, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Konstanz Information Miner (KNIME)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "3.5", "3.6", "3.7" ; sc:url "http://www.knime.org" ; biotools:primaryContact "Alexander Fillbrunn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pubmed:28757289" ; sc:description "This KNIME framework is a data mining platform including manifold libraries for image processing (based on Fiji/ImageJ) and data exploration. The platform provides access to workflows and pipelines for (large-scale) automated phenotype analysis." ; sc:featureList edam:operation_3443 ; sc:name "KNIME - phenotyping of image data" ; sc:url "https://hub.knime.com/manuel/spaces/Public/latest/NucleiClassificationTraining_OMICS2020" ; biotools:primaryContact "Manuel Gunkel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0622, edam:topic_0749 ; sc:citation "pubmed:21984761" ; sc:description "custom nodes for the interpretation of Next Generation Sequencing data with KNIME." ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "Knime4Bio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://code.google.com/p/knime4bio/" ; biotools:primaryContact "Pierre LINDENBAUM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Comprehensive toolbox for next generation sequencing analysis." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "KNIME4NGS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://ibisngs.github.io/knime4ngs/" ; biotools:primaryContact "Robert Kueffner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3068, edam:topic_3071, edam:topic_3474 ; sc:citation , "pubmed:33147622" ; sc:description """A comprehensive database of physicochemical properties for k-tuple nucleotides. A comprehensive database of k-nucleotide physicochemical property values. After your Node.js environment and MySQL are ready, find out the location of the source code of KNIndex that you unpack and enter this directory in command line program. Then execute the command npm install to install all the dependencies of the project.""" ; sc:featureList edam:operation_0349, edam:operation_2930, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "KNIndex" ; sc:url "https://knindex.pufengdu.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3512 ; sc:citation , "pubmed:33416865" ; sc:description """Interactive gene networks with KNIT. Knock-in/knock-out Interaction Tools. 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Altman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3517 ; sc:citation , "pubmed:36150388" ; sc:description "KnockoffTrio, a statistical method to identify putative causal genetic variants for father-mother-child trio design built upon a recently developed knockoff framework in statistics." ; sc:featureList edam:operation_3226, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "KnockoffTrio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/KnockoffTrio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description "KnotAli is an algorithm for predicting the pseudoknotted secondary structures of RNA using relaxed Hierarchical Folding." ; sc:featureList edam:operation_0278, edam:operation_0292, edam:operation_0502, edam:operation_0570, edam:operation_3469 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "KnotAli" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/mateog4712/KnotAli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:23369147" ; sc:description "Applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots." ; sc:featureList edam:operation_0475 ; sc:name "KnotShape" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cse.msu.edu/~achawana/KnotShape/" ; biotools:primaryContact "Rujira Achawanantakun", "Yanni Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3678 ; sc:citation , "pmcid:PMC8198535", "pubmed:34070606" ; sc:description "A Toolkit for Designing Personalised Dementia Care." ; sc:isAccessibleForFree true ; sc:name "Know-me" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://designfordementia.squarespace.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0218, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC9558693", "pubmed:36268112" ; sc:description "A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments' toxicities." ; sc:featureList edam:operation_2429, edam:operation_3096, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Knowledge4COVID-19" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SDM-TIB/Knowledge4COVID-19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:33872966" ; sc:description "KnowSeq is an R package for the automatic smart gene expression tool for retrieving relevant biological knowledge. 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KORP-PL is a novel sidechain-free coarse-grained knowledge-based scoring function for protein-ligand interactions developed together with Pablo Chacón from IQFR Madrid. Our Knowledge-base ORientational Potential (KORP-PL), developed in a joint-venture with Sergei Grudinin lab outperforms state-of-the-art statistical potentials using a 3D joint probability and a minimalist protein representation. Our side-chain independent potential is a fast and highly discriminative energy function for protein ligand docking, please have a try. 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biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:32746932" ; sc:description "Knowledge-primed neural networks developed in the Bock lab at CeMM. 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Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. 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It sketches sequences by k-mer substring space sampling/shuffling, please see Methods part of our preprint (https://www.biorxiv.org/content/10.1101/729665v1) for how it works. It handles DNA sequences of both fasta or fastq format, whether gzipped or not. 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Cobos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3304, edam:topic_3384, edam:topic_3421, edam:topic_3444 ; sc:citation , , "pubmed:33454411" ; sc:description """Enabling whole brain parcellation in the presence of large lesions. A workflow to allow Freesurfer recon-all to run on brain images with large lesions. VBG is a bash script tested in Mac OSX, Ubuntu 18.0 and CentOS.""" ; sc:featureList edam:operation_2409, edam:operation_3443, edam:operation_3659 ; sc:license "MPL-2.0" ; sc:name "KUL-VBG" ; sc:url "https://github.com/KUL-Radneuron/KUL_VBG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0128, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:20952400" ; sc:description "Provides protein-protein interaction (PPI) data. It allows users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, from five primary databases." ; sc:featureList edam:operation_2492, edam:operation_2949, edam:operation_3092, edam:operation_3695 ; sc:name "KUPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ittc.ku.edu/chenlab" ; biotools:primaryContact "Xue-wen Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description """A novel approach for validation and completeness of protein orthologous groups. A novel approach for validation and enrichment of protein orthologous groups. 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Through an easy-to-use web interface, L2L will mine a list of up- or down-regulated genes for Gene Ontology terms that are significantly enriched. L2L can also compare the list of genes to a database of hundreds of published microarray experiments, in order to identify common patterns of gene regulation. A downloadable command-line version can run customized and batch analyses." ; sc:featureList edam:operation_2495 ; sc:name "L2L" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2" ; sc:url "http://depts.washington.edu/l2l/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33360991" ; sc:description """Harnessing Multi-View Perspective of Light Fields for Low-Light Imaging. 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sc:additionalType edam:data_0943 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_3292 ; sc:citation ; sc:description "Open source application to generate 2D/3D bioimages of the elemental distribution of the elements present in a set from ICP-MS spectra." ; sc:featureList edam:operation_3694 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LA-iMageS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bioscope Group, University Nova of Lisbon", "GEPAM Group, University of Campinas", "SING Group, University of Vigo" ; sc:softwareHelp ; sc:softwareVersion "1.1.3" ; sc:url "http://www.la-images.net" ; biotools:primaryContact "LA-iMages support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0607, edam:topic_0622, edam:topic_0769 ; sc:description "Data workflow management platform to streamline NGS analyses." ; sc:featureList edam:operation_3760 ; sc:name "Lab7" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.lab7.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_3474 ; sc:citation "pubmed:23180633" ; sc:description "New computational approach for accurate prediction of the calpain substrate cleavage sites from amino acid sequences." ; sc:featureList edam:operation_0415 ; sc:name "LabCaS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/LabCaS/" ; biotools:primaryContact "Hong-Bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LABRAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TaliaferroLab/LABRAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0607, edam:topic_0621, edam:topic_0769, edam:topic_3489 ; sc:citation , "pmcid:PMC7575048", "pubmed:32502232" ; sc:description """Versatile databases for genomic sequencing and lab management. LabxDB comes with ready-to-use databases. Data is stored in PostgreSQL. LabxDB provides web-browser GUI and a programmatic API for intregration into pipelines. LabxDB for high-throughput sequencing (HTS) annotation. LabxDB seq organizes sample annotations using a structure of nested levels: from the top-level projects to the bottom level sequencing runs. LabxDB provides forms to easily create sample structure, to annotate and view (as captured by the image on the left) all levels at the same time. LabxDB seq comes with scripts to import HTS data from local sequencing facilities or public resources.""" ; sc:featureList edam:operation_0224 ; sc:license "MPL-2.0" ; sc:name "LabxDB" ; sc:url "https://labxdb.vejnar.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2269 ; sc:citation ; sc:description "LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly." ; sc:featureList edam:operation_0310, edam:operation_0525 ; sc:name "LACHESIS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://shendurelab.github.io/LACHESIS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0204, edam:topic_0602, edam:topic_0625, edam:topic_3407 ; sc:citation , "pubmed:35723033" ; sc:description "A free web-based lac operon simulation that enhances student learning of gene regulation concepts." ; sc:featureList edam:operation_0435, edam:operation_3196, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "LacOp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://flask-env.rnwhymamqf.us-west-2.elasticbeanstalk.com/lacop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_3053 ; sc:description "Designed to solve a problem in DNA genotyping. It helps in the construction of allelic ladders that drive the sizing and binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet containing a database of individual profiles and finds a minimum set of individuals, that covers the maximum number of alleles represented in the database, with all alleles represented only once." ; sc:featureList edam:operation_3196, edam:operation_3429 ; sc:name "LadderFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "http://services.appliedgenomics.org/software/ladderfinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622, edam:topic_0797 ; sc:citation "pubmed:12654723" ; sc:description "Tools for genomic alignment. These include the MLAGAN multiple alignment tool, and Shuffle-LAGAN for alignment with rearrangements.. 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LAMPA, LArge Multidomain Protein Annotator. This repository contains R package LAMPA presented in LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins by Gulyaeva AA, Sigorskih AI, Ocheredko ES, Samborskiy DV, Gorbalenya AE. Sorry, something went wrong. Reload?. Sorry, we cannot display this file. Collection of Jupyter notebooks that were used for LAMPA paper. Sorry, this file is invalid so it cannot be displayed.""" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_2421 ; sc:name "LAMPA" ; sc:softwareHelp ; sc:url "https://github.com/Gorbalenya-Lab/LAMPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:27412093" ; sc:description "Detect statistically significant epistatic interactions of two or more SNPs from GWAS data. 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Revision 1. LayNii_extras (work in progress...). Here are some extra scripts that we use in combination with LayNii.""" ; sc:featureList edam:operation_3435 ; sc:license "BSD-3-Clause" ; sc:name "LayNii" ; sc:url "https://github.com/ofgulban/LayNii_extras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0196, edam:topic_0621, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC8168326", "pubmed:34074310" ; sc:description "Economic Genome Assembly from Low Coverage Illumina and Nanopore Data" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LazyB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TGatter/LazyB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3300, edam:topic_3360, edam:topic_3422, edam:topic_3577 ; sc:citation , "pmcid:PMC9254641", "pubmed:35788654" ; sc:description "LBD (Lymphoma Biomarker Database) is a manually curated database of literature-supported biomarkers for lymphoma. It contains 793 biomarkers (715 single biomarkers and 78 combined biomarkers) for different subtypes of lymphoma which have been verified by experiments. The biomarkers are collected from 978 literatures from PubMed and are categorized into molecular (DNA, RNA, protein, chemical), cellular (cells or cell counts), image (imaging technologies or parameters), histopathological (characteristics of individuals' histopathological functioning), physiological (characteristics of individuals' normal functioning) biomarkers. By browsing and searching LBD, users can get access to comprehensive information about lymphoma biomarkers conveniently." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "LBD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bis.zju.edu.cn/LBD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation , "pmcid:PMC7869625", "pubmed:33571675" ; sc:description "Drug repurposing for COVID-19 via knowledge graph completion and literature-based discovery." ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_0478 ; sc:name "LBD-COVID19" ; sc:url "https://github.com/kilicogluh/lbd-covid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "Efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "LBE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/LBE.html" ; biotools:primaryContact "Cyril Dalmasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3646881", "pubmed:23667458" ; sc:description "We developed a method LBtope for predicting linear B-cell epitopes. We developed several models using various techniques (e.g., SVM, IBk)on a large dataset of B-cell epitopes and non-epitopes (12063 epitopes and 20589 non epitopes obtained from IEDB database)." ; sc:featureList edam:operation_2945 ; sc:name "lbtope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/lbtope/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "LC-IMS-MS Feature Finder is a command line software application that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time, and ion mobility drift time values." ; sc:featureList edam:operation_3432 ; sc:name "LC-IMS-MS Feature Finder" ; sc:operatingSystem "Windows" ; sc:url "http://omics.pnl.gov/software/lc-ims-ms-feature-finder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3390, edam:topic_3500, edam:topic_3518 ; sc:citation , "pmcid:PMC7672905", "pubmed:33203358" ; sc:description """A local consistency approach for nutrigenomics data analysis. Nutrigenomics aims at understanding the interaction between nutrition and gene information. Due to the complex interactions of nutrients and genes, their relationship exhibits non-linearity. One of the most effective and efficient methods to explore their relationship is the nutritional geometry framework which fits a response surface for the gene expression over two prespecified nutrition variables. However, when the number of nutrients involved is large, it is challenging to find combinations of informative nutrients with respect to a certain gene and to test whether the relationship is stronger than chance. Methods for identifying informative combinations are essential to understanding the relationship between nutrients and genes.

Results< h4>We introduce Local Consistency Nutrition to Graphics (LC-N2G), a novel approach for ranking and identifying combinations of nutrients with gene expression""" ; sc:featureList edam:operation_3463, edam:operation_3659, edam:operation_3766, edam:operation_3891 ; sc:name "LC-N2G" ; sc:url "http://shiny.maths.usyd.edu.au/LC-N2G/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "This function takes in images of cells infected with bacteria and quantifies intracellular signals from regions surrounding the pathogen." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "LC3B ROI Quantification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74203-lc3b-roi-quantification" ; biotools:primaryContact "Joaquin Quintana" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084 ; sc:citation , ; sc:description "Find the lowest common ancestor from a BLAST tabular file." ; sc:featureList edam:operation_0324 ; sc:name "lca" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1 beta" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/LCA/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697 ; sc:description "\"This tool identifies the lowest taxonomic rank for which a metagenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input.\" - Galaxy tool wrapper" ; sc:featureList edam:operation_3460 ; sc:name "Find lowest diagnostic rank" ; sc:url "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2269, edam:topic_3810 ; sc:citation , "pmcid:PMC7502249", "pubmed:32995081" ; sc:description """An R package to estimate the concordance correlation, Pearson correlation and accuracy over time. lcc is a package under development based on estimation procedures for longitudinal concordance correlation (lcc), longitudinal Pearson correlation (lpc), and longitudinal accuracy (la) through fixed effects and variance components of polynomial mixed-effect regression model. Longitudinal Concordance Correlation. 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Kechris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "A generic and automatic pre-processing tool for high resolution (HR) LC-MS and GC-MS data." ; sc:featureList edam:operation_3214 ; sc:name "LCMS TNO DECO" ; sc:provider "ELIXIR-NL" ; sc:softwareVersion "1" ; sc:url "http://metabocloud.com/?Processing_software___Pre-Processing___LCMS_TNO-DECO" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3712 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:33710902" ; sc:description "High-Performance 3D Visualization Software for Mass Spectrometry." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3704 ; sc:license "Other" ; sc:name "lcmsWorld" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PGB-LIV/lcmsWorld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3168 ; sc:citation , "pmcid:PMC7079445", "pubmed:32183707" ; sc:description """An efficient lossless compression tool of quality scores with random access functionality. This software implements the LCQS algorithm described in: Fu J , Ke B , Dong S . “LCQS: an efficient lossless compression tool of quality scores with random access functionality” [J]. BMC Bioinformatics, 2020, 21(1).""" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3435 ; sc:name "LCQS" ; sc:url "https://github.com/SCUT-CCNL/LCQS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation ; sc:description "An R package and tutorial on latent change score modelling." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "lcsm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://milanwiedemann.shinyapps.io/shinychange/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_0736 ; sc:citation , "pubmed:33378336" ; sc:description """Assessing the low complexity of protein sequences via the low complexity triangle. 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LCT follows the following steps:.""" ; sc:featureList edam:operation_0234, edam:operation_3359, edam:operation_3904 ; sc:name "LCT" ; sc:url "http://cbdm-01.zdv.uni-mainz.de/~munoz/lct/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0176, edam:topic_3382 ; sc:citation ; sc:description "Linear Combinations of Template Conformations (LCTC) is an efficient method to quantify structural distributions in heterogeneous cryo-EM datasets." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3458 ; sc:name "LCTC" ; sc:url "https://github.com/ghl1995/LCTC" ; biotools:primaryContact "Xuhui Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:14681826" ; sc:description "Analysis the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2." ; sc:featureList edam:operation_0488 ; sc:name "LD Select" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://droog.gs.washington.edu/ldSelect.html" ; biotools:primaryContact "Debbie Nickerson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3617 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172 ; sc:citation ; sc:description "The tool enables lipid annotation in high-throughput data derived from chromatography-coupled tandem mass spectrometry." ; sc:featureList edam:operation_0226, edam:operation_2480, edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Lipid Data Analyzer (LDA)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.tugraz.at/lda2" ; biotools:primaryContact "Gerhard Thallinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3474, edam:topic_3577, edam:topic_3934 ; sc:citation , "pmcid:PMC9948385", "pubmed:36823548" ; sc:description "Discovering patients phenotypes and cell populations within a single Bayesian framework." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LDA-DC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ElieElHachem/LDADC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3050 ; sc:citation , "pmcid:PMC8216892", "pubmed:34188865" ; sc:description "ldacov is an R package to estimate an LDA model with covariates using MCMC algorithms." ; sc:featureList edam:operation_2939, edam:operation_3659, edam:operation_3891, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LDAcov" ; sc:url "https://github.com/gilsonshimizu/ldacov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3382 ; sc:citation , "pubmed:33039785" ; sc:description """Latent Dirichlet allocation based generative adversarial networks. 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LDBlockShow is a fast and effective tool to generate linkage disequilibrium (LD) heatmap from VCF files. It is more time and memory saving than other current tools. LDBlockShow can generate the plots of LD heatmap and interested statistics or annotation results simultaneously. In addition, it also supports subgroup analysis.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_0487, edam:operation_3196 ; sc:license "MIT" ; sc:name "LDBlockShow" ; sc:url "https://github.com/BGI-shenzhen/LDBlockShow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3574 ; sc:citation "pubmed:26395773" ; sc:description "Method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome." ; sc:featureList edam:operation_0488 ; sc:name "LDetect" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/nygcresearch/ldetect" ; biotools:primaryContact "Tomas Berisa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2640, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC8686638", "pubmed:34930111" ; sc:description "An online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data." ; sc:featureList edam:operation_0282, edam:operation_0488, edam:operation_3196, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:name "LDexpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ldlink.nci.nih.gov/?tab=ldexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data." ; sc:featureList edam:operation_0451, edam:operation_2403 ; sc:name "LDhat" ; sc:softwareVersion "2.2a" ; sc:url "https://github.com/auton1/LDhat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3127 ; sc:citation "pubmed:23284288" ; sc:description "Software program for statistical inference of fine-scale crossover recombination rates from population genetic data." ; sc:featureList edam:operation_0451 ; sc:name "LDhelmet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ldhelmet/" ; biotools:primaryContact "Yun S. Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056 ; sc:citation , "pmcid:PMC7565767", "pubmed:33066733" ; sc:description """A parallel computing toolkit for linkage disequilibrium analysis. GUI package is under the GUI folder, please double-click the LDkit_GUI.jar to start. Run using Graphic User Interface (GUI).""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3695 ; sc:name "LDkit" ; sc:url "https://github.com/tangyou79/LDkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3673 ; sc:citation "pubmed:26139635" ; sc:description "Suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups." ; sc:featureList edam:operation_0488 ; sc:name "LDlink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://analysistools.nci.nih.gov/LDlink/" ; biotools:primaryContact "LDlink Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0625, edam:topic_3056 ; sc:citation , "pmcid:PMC7059597", "pubmed:32180801" ; sc:description """An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations. 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Linear Decomposition Model.""" ; sc:featureList edam:operation_3435, edam:operation_3797, edam:operation_3799 ; sc:name "LDM" ; sc:url "https://github.com/yijuanhu/LDM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3517 ; sc:citation , "pubmed:36794924" ; sc:description "Efficiently queryable compression of linkage disequilibrium matrices." ; sc:featureList edam:operation_0224, edam:operation_0488, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LDmat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/G2Lab/ldmat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:11754474" ; sc:description "Program to mapping the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies." ; sc:featureList edam:operation_0282 ; sc:name "LDMgen" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Genetic_Linkage_Analysis" ; biotools:primaryContact "Hongyu Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:11055377" ; sc:description "Program of mapping disease genes (including location and confidence interval) by using haplotypes with disease mutation and the haplotypes without disease mutation (or allele frequencies in normal population)." ; sc:featureList edam:operation_0282 ; sc:name "LDMhap" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Genetic_Linkage_Analysis" ; biotools:primaryContact "Hongyu Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pmcid:PMC7469344", "pubmed:32883200" ; sc:description """Prediction of long non-coding rna and disease association using network feature similarity and gradient boosting. LDNFSGB:Predicting lncRNA-disease associations using network feature similarity and gradient boosting.""" ; sc:featureList edam:operation_3927, edam:operation_3937 ; sc:name "LDNFSGB" ; sc:url "https://github.com/MLMIP/LDNFSGB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation "pubmed:21181893" ; sc:description "Method for detecting spurious associations using p-values. The strength of the method is its simplicity; it requires no other information but p-values." ; sc:featureList edam:operation_0415 ; sc:name "LDPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ldpac.cs.ucla.edu/" ; biotools:primaryContact "Buhm Han" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3337, edam:topic_3452, edam:topic_3517 ; sc:citation ; sc:description """Computing polygenic scores using LDpred2. prepare-corr: LD matrices for LDpred2 based on the 10K individuals in the validation set. prepare-genotypes: UKBB Europeans with imputed dosages for HapMap3 variants. This tutorial only uses fake data for educational purposes. You should also probably look at the code of the paper, particularly at the code to prepare summary statistics (including performing the quality control presented in the Methods section “Quality control of summary statistics” of the paper), at the code to read BGEN files into the data format used by bigsnpr, at the code to prepare LD matrices and at the code to run LDpred2 (genome-wide).""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3196, edam:operation_3557 ; sc:name "LDpred2" ; sc:url "https://privefl.github.io/bigsnpr/articles/LDpred2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_0780, edam:topic_3390, edam:topic_3810 ; sc:citation , "pmcid:PMC10151526", "pubmed:37143876" ; sc:description "Legumes disease resistance genes database." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "LDRGDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ldrgdb.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "LDSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bulik/ldsc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3517, edam:topic_3810 ; sc:citation ; sc:description """Pairwise Linkage Disequilibrium Estimation for Polyploids. Linkage Disequilibrium Shrinkage Estimation for Polyploids. Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2020) .""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "ldsep" ; sc:url "https://cran.r-project.org/package=ldsep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:22963363" ; sc:description "Completely self-contained program written in Fortran90. 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Although several tools facilitating in silico drug design are available, their results are usually difficult to integrate with publicly available information or require further processing to be fully exploited. The rational design of multi-target ligands (polypharmacology) and the repositioning of known drugs towards unmet therapeutic needs (drug repurposing) have raised increasing attention in drug discovery, although they usually require careful planning of tailored drug design strategies. Computational tools and data-driven approaches can help to reveal novel valuable opportunities in these contexts, as they enable to efficiently mine publicly available chemical, biological, clinical, and disease-related data" ; sc:featureList edam:operation_0482, edam:operation_2421, edam:operation_4009 ; sc:name "LigAdvisor" ; sc:softwareHelp ; sc:url "https://ligadvisor.unimore.it/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0097, edam:topic_0166, edam:topic_0176, edam:topic_2814 ; sc:citation "pubmed:20713281" ; sc:description "LigAlign: an automated system and structure visualization tool for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment." ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_0295, edam:operation_0448 ; sc:name "LigAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.toronto.edu/ligalign/" ; biotools:primaryContact "LigAlign support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:25726469" ; sc:description "A novel computational tool for scoring and ranking three-dimensional poses of small molecule ligands bound to RNA 3D structures." ; sc:featureList edam:operation_2239 ; sc:name "LigandRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ligandrna.genesilico.pl/" ; biotools:primaryContact "Anna Philips - Program developer", "Janusz Bujnicki - Project coordinator", "Kaja Milanowska - Server developer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0804, edam:topic_2259, edam:topic_3308 ; sc:citation "pubmed:23110343" ; sc:description "Allows integrative analysis and visualization of multiple lineages over whole time-course profiles." ; sc:featureList edam:operation_0443 ; sc:name "LIGAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.ics.aalto.fi/csb/software/ligap/" ; biotools:primaryContact "Tarmo Äijö" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2830, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:37054909" ; sc:description "LigBind is a relation-aware framework with graph-level pre-training to enhance the ligand-specific binding residue predictions for 1159 ligands, which can effectively cover the ligands with a few known binding proteins." ; sc:featureList edam:operation_2950, edam:operation_3897, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "LigBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/LigBind/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_0593, edam:topic_3375 ; sc:citation , "pmcid:PMC7059350", "pubmed:32181242" ; sc:description """A Multi-Target de novo Drug Design Approach. With the rapid development of systems-based pharmacology and poly-pharmacology, method development for rational design of multi-target drugs has becoming urgent. In this paper, we present the first de novo multi-target drug design program LigBuilder V3, which can be used to design ligands to target multiple receptors, multiple binding sites of one receptor, or various conformations of one receptor.""" ; sc:featureList edam:operation_2476, edam:operation_3897, edam:operation_3938 ; sc:name "LigBuilder V3" ; sc:url "http://www.pkumdl.cn/ligbuilder3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description """Spatial graph embedding and molecular descriptors assisted bioactivity prediction of ligand molecules for epidermal growth factor receptor on a cell line-based dataset. Predicting pIC50 and distinguishing hit compounds for ligands against human EGFR based on deep learning.""" ; sc:featureList edam:operation_0303, edam:operation_0478, edam:operation_3659 ; sc:name "LigEGFR" ; sc:url "https://ligegfr.vistec.ist" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:33046898" ; sc:description """Jointly defining cell types from multiple single-cell datasets using LIGER. LIGER (Linked Inference of Genomic Experimental Relationships). LIGER (liger) is a package for integrating and analyzing multiple single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.""" ; sc:featureList edam:operation_0313, edam:operation_3435, edam:operation_3625 ; sc:license "GPL-3.0" ; sc:name "LIGER" ; sc:url "https://github.com/MacoskoLab/liger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pmcid:PMC7656723", "pubmed:33292486" ; sc:description """A tool for filtering docked poses to improve virtual-screening hit rates. LigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON). It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters. Jacob Durrant software July 7, 2020July 10, 2020.""" ; sc:featureList edam:operation_3695, edam:operation_3899, edam:operation_3938 ; sc:name "LigGrep" ; sc:url "http://durrantlab.com/liggrep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308, edam:topic_3382, edam:topic_3512 ; sc:citation , , "pmcid:PMC9636025", "pubmed:36216958", "pubmed:36253646" ; sc:description "Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing." ; sc:featureList edam:operation_0314, edam:operation_1812, edam:operation_3200, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Light-Seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lightseq.io" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_1208 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_2229 ; sc:citation ; sc:description "Deep learning architecture and web server which predicts protein subcellular localization. It is based on protein language models and pre-trained Transformers." ; sc:featureList edam:operation_0418, edam:operation_0477, edam:operation_2489 ; sc:name "Light Attention" ; sc:url "https://github.com/HannesStark/protein-localization" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:27412092" ; sc:description "Lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other holding k-mers classified as likely correct, using a simple statistical test." ; sc:featureList edam:operation_0310 ; sc:name "LightAssembler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/SaraEl-Metwally/LightAssembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:33112379" ; sc:description """Computational prediction model of blood-brain-barrier penetration based on LightGBM. Identification of blood-brain barrier (BBB) permeability of a compound is a major challenge in neurotherapeutic drug discovery. Conventional approaches for BBB permeability measurement are expensive, time-consuming, and labor-intensive. BBB permeability is associated with diverse chemical properties of compounds. However, BBB permeability prediction models have been developed using small datasets and limited features, which are usually not practical due to their low coverage of chemical diversity of compounds.""" ; sc:featureList edam:operation_3938 ; sc:name "LightBBB" ; sc:url "http://ssbio.cau.ac.kr/software/bbb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3360, edam:topic_3474, edam:topic_3673, edam:topic_3697 ; sc:citation , "pmcid:PMC7816363", "pubmed:33468221" ; sc:description """A program for diagnosing IBD based on human gut microbiome data. The diagnosis of inflammatory bowel disease (IBD) and discrimination between the types of IBD are clinically important.""" ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3435 ; sc:name "LightCUD" ; sc:url "http://cqb.pku.edu.cn/ZhuLab/LightCUD/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:name "Protein complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation "pubmed:28968719" ; sc:description """It is a protein-protein docking framework based on the Glowworm Swarm Optimization algorithm. The framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, and it has support for the use of pre-calculated conformers for both receptor and ligand.""" ; sc:featureList edam:operation_2464 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "LightDock" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:softwareVersion "0.4.0" ; sc:url "https://life.bsc.es/pid/lightdock/" ; biotools:primaryContact "Brian Jimenez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_2275, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC10320125", "pubmed:37140054" ; sc:description "Artificial Intelligence-powered modeling of macromolecular interactions." ; sc:featureList edam:operation_0310, edam:operation_0482, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LightDock Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://server.lightdock.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929, edam:format_2182 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:25398208" ; sc:description "Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors." ; sc:featureList edam:operation_3195, edam:operation_3218, edam:operation_3472, edam:operation_3921 ; sc:name "Lighter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mourisl/Lighter" ; biotools:primaryContact "Li Song" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3305 ; sc:citation , "pubmed:36787138" ; sc:description "Introducing the Library of Guidance for Health Scientists (LIGHTS)." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "LIGHTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lights.science" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "LightStringGraphs (LSG) is an external memory string graph construction tool." ; sc:featureList edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LightStringGraph" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-BICOCCA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://lsg.algolab.eu/" ; biotools:primaryContact "Marco Previtali", "Paola Bonizzoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3343, edam:topic_3520 ; sc:citation , "pubmed:33190499" ; sc:description """A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. Ligand-similarity-based virtual screening is one of the most applicable computer-aided drug design techniques.""" ; sc:featureList edam:operation_3938 ; sc:name "LigMate" ; sc:url "http://cao.labshare.cn/ligmate/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2275, edam:topic_3336 ; sc:citation "pubmed:22594624" ; sc:description "Novel drug-design algorithm which combines structures of known binders to generate similar but structurally distinct compounds that can be tested for binding." ; sc:featureList edam:operation_2430 ; sc:name "LigMerge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nbcr.ucsd.edu/data/sw/hosted/ligmerge/" ; biotools:primaryContact "Steffen Lindert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3068, edam:topic_3315 ; sc:citation , "pmcid:PMC9261032", "pubmed:35794646" ; sc:description "LigninGraphs is an open-source software package in Python to generate feasible lignin structures." ; sc:featureList edam:operation_0320, edam:operation_0337, edam:operation_0479 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LigninGraphs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/VlachosGroup/ligningraphs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_2814 ; sc:citation , , "pubmed:21919503", "pubmed:7630882" ; sc:description "Program which plots schematic diagrams of protein-ligand interactions." ; sc:featureList edam:operation_0482 ; sc:name "LIGPLOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1566 ; sc:name "Protein-ligand interaction report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2814 ; sc:author "Roman Laskowski", "Thornton Group", "Tjaart de Beer" ; sc:citation ; sc:description "Identifies small molecules likely to bind to given protein." ; sc:featureList edam:operation_2575 ; sc:name "LigSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/LigSearch" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0209 ; sc:citation "pubmed:25336501" ; sc:description "New computational method for the structural alignment of small molecules." ; sc:featureList edam:operation_2928 ; sc:name "LIGSIFT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cssb.biology.gatech.edu/LIGSIFT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:31863748" ; sc:description "A automated server for template-based small-molecule docking." ; sc:featureList edam:operation_2421, edam:operation_2492, edam:operation_3899 ; sc:name "LigTBM" ; sc:url "https://ligtbm.cluspro.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3047 ; sc:citation , "pmcid:PMC8194164", "pubmed:34112240" ; sc:description "Ligand and structure-based target identification and activity prediction for small molecular compounds." ; sc:featureList edam:operation_0478, edam:operation_2489, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "LigTMap" ; sc:operatingSystem "Mac" ; sc:url "https://cbbio.online/LigTMap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_3344 ; sc:citation ; sc:description "Sample data and code for the LRT for changes in HEB" ; sc:isAccessibleForFree true ; sc:name "Likelihood ratio test for changes in homeolog expression bias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/62502-likelihood-ratio-test-for-changes-in-homeolog-expression-bias-sample" ; biotools:primaryContact "Ronald D Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2640, edam:topic_3372 ; sc:citation , "pubmed:33347435" ; sc:description """Algorithm and software package for practical identifiability analysis in systems biology. LikelihoodProfiler is a Julia language package for identifiability analysis and confidence intervals evaluation. LikelihoodProfiler is a package for identifiability analysis and confidence intervals evaluation which was originally written in Julia language. See https://github.com/insysbio/LikelihoodProfiler.jl This is the translation of the original Julia code to Python.""" ; sc:featureList edam:operation_0337, edam:operation_3928 ; sc:license "MIT" ; sc:name "LikelihoodProfiler" ; sc:url "https://github.com/insysbio/LikelihoodProfiler.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3305, edam:topic_3418 ; sc:citation , "pmcid:PMC7059906", "pubmed:32142521" ; sc:description "An R package for the estimation of excess Life Years Lost among patients with a given disease or condition." ; sc:featureList edam:operation_3503 ; sc:license "MIT" ; sc:name "lillies" ; sc:url "http://CRAN.R-project.org/package=lillies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "Online framework for the analysis of vascular networks in leaves." ; sc:featureList edam:operation_2423 ; sc:name "LIMANI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://limani.psb.ugent.be" ; biotools:primaryContact "Stijn Dhondt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3174, edam:topic_3697, edam:topic_3810 ; sc:citation , "pmcid:PMC7493373", "pubmed:32938362" ; sc:description """Metagenomic analysis through the extended Burrows-Wheeler transform. LiME is a novel lightweight alignment-free and assembly-free framework for metagenomic classification that is combinatorial by nature and allows us to use little internal memory. In [1], a preliminary version of LiME has been introduced together with a new sequence similarity measure based on the properties of the extended Burrows–Wheeler transform. In [2], we now implement two variants of the above similarity measure and improve the overall classification. In addition, the new version of our tool allows to use multiple processors/cores.""" ; sc:featureList edam:operation_0310, edam:operation_3211, edam:operation_3460, edam:operation_3472 ; sc:name "LiME" ; sc:url "https://github.com/veronicaguerrini/LiME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3305, edam:topic_3318 ; sc:citation ; sc:description """Trimmed Constrained Mixed Effects Models. Linear Mixed Effects Model with Trimming.""" ; sc:featureList edam:operation_3192, edam:operation_3435, edam:operation_3659 ; sc:license "BSD-2-Clause" ; sc:name "LimeTr" ; sc:url "https://github.com/zhengp0/limetr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Flexible and efficient linear mixed model library with interfaces to Python." ; sc:featureList edam:operation_3664 ; sc:name "Limix" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/PMBio/limix" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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Output is currently a portable document file." ; sc:featureList edam:operation_0282 ; sc:license "GPL-3.0" ; sc:name "LinkageMapView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.2" ; sc:url "https://cran.r-project.org/web/packages/LinkageMapView/" ; biotools:primaryContact "Lisa A Ouellette" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:21596792" ; sc:description "An R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type." ; sc:featureList edam:operation_2497 ; sc:name "linkcomm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/linkcomm/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3325, edam:topic_3518 ; sc:author "Melanie Bahlo" ; sc:citation , "pubmed:19435744" ; sc:description "Generation of linkage mapping input files for five different linkage mapping tools using as input genotype calls from Affymetrix and Illumina SNP chips or SNP genotypes inferred from sequencing data." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_0484, edam:operation_2429, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "LINKDATAGEN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinf.wehi.edu.au/software/linkdatagen/" ; biotools:primaryContact "Melanie Bahlo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0804, edam:topic_3400, edam:topic_3966 ; sc:citation , "pmcid:PMC8385794", "pubmed:34433410" ; sc:description "A linked data graph database for integrating immunological data." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LinkedImm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://linkedimm.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_2376, edam:format_3464, edam:format_3751 ; sc:name "Data reference" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_2376, edam:format_3464, edam:format_3750 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0605, edam:topic_0769, edam:topic_3316, edam:topic_3345, edam:topic_3366 ; sc:author ; sc:citation , , ; sc:description "Extract Transform Load for Linked Data" ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_2409, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LinkedPipes ETL" ; sc:softwareHelp ; sc:url "https://etl.linkedpipes.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:description """LinkEHR is a set of tools that enables the semantic interoperability of your data by: Creating clinical information models (archetypes) Transforming clinical data into standards such as openEHR, HL7 CDA, or ISO 13606""" ; sc:featureList edam:operation_2429, edam:operation_2430 ; sc:isAccessibleForFree true ; sc:name "LinkEHR" ; sc:url "https://linkehr.veratech.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pubmed:35139158" ; sc:description "Predicting, explaining and exploring links in large biomedical knowledge graphs." ; sc:featureList edam:operation_2422, edam:operation_3359, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LinkExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OpenBioLink/Explorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3053 ; sc:description "A set of programs will allow you to analyze the segregation results from pairwise sets of loci in outbred families for possible linkage relationships. The same input data file may be used to analyze linkage relationships among loci using either parent as the mapping parent." ; sc:featureList edam:operation_0283 ; sc:name "LINKMFEX" ; sc:operatingSystem "Windows" ; sc:softwareVersion "2.4" ; sc:url "http://www.uoguelph.ca/~rdanzman/software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625 ; sc:citation ; sc:description "Linkprep create LINKAGE style .pre and .dat files from AGRF style data. This creates standard format input files for linkage analysis software from human genotyping data." ; sc:featureList edam:operation_0283, edam:operation_0335, edam:operation_3196 ; sc:name "Linkprep" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2.9" ; sc:url "http://bioinf.wehi.edu.au/software/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description "LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3198, edam:operation_3216, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LINKS" ; sc:url "https://github.com/bcgsc/LINKS" ; biotools:primaryContact "Rene L. Warren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:23728796" ; sc:description "SNP detection tool with haplotype information from an individual sample." ; sc:featureList edam:operation_0484, edam:operation_0487 ; sc:name "linkSNPs 1.0 beta" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html" ; biotools:primaryContact "Eriko Sasaki", "Hideki Innan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large-scale count data. It transforms such datasets for parametric tests. Also the following pipelines are implemented: 1. Cell subpopluation analysis and visualization using PCA clustering, 2. Differential expression analysis or differential peak detection using limma, 3. Highly variable gene discovery and visualization, 4. Gene correlation network analysis and visualization. 5. Hierarchical clustering and plotting." ; sc:featureList edam:operation_2478 ; sc:license "MIT" ; sc:name "Linnorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Linnorm.html" ; biotools:primaryContact "Ken Shun Hang Yip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3071 ; sc:citation , "pmcid:PMC8378515", "pubmed:34415996" ; sc:description "A database for cancer-cell-specific perturbations of biological networks." ; sc:featureList edam:operation_0224, edam:operation_3223, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LINPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bcmslab.shinyapps.io/LINPSAPP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_3172, edam:topic_3308, edam:topic_3407 ; sc:citation , "pubmed:34928054" ; sc:description "A lipidomic data processing website aims to provide users a friendly pipeline for statistical analyses and lipidomic data mining." ; sc:featureList edam:operation_3928, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "LINT-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lintwebomics.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3070, edam:topic_3382 ; sc:citation ; sc:description "Conveniently explore, share and present large-scale biological trajectory data from a web browser." ; sc:featureList edam:operation_0244, edam:operation_0335, edam:operation_3890 ; sc:name "Linus" ; sc:url "https://imb-dev.gitlab.io/linus-manuscript/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0659, edam:topic_3542 ; sc:citation , "pubmed:36155620" ; sc:description "An integrated R package for effective prediction of ncRNA-protein interaction." ; sc:featureList edam:operation_0253, edam:operation_0267, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LION" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HAN-Siyu/LION/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2640, edam:topic_2830, edam:topic_3577 ; sc:citation , "pmcid:PMC6815019", "pubmed:31653243" ; sc:description """Single sample network inference in R. 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LipidCreator_HumanPlatelet_application.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3799 ; sc:name "LipidCreator_skyline" ; sc:url "https://panoramaweb.org/lipidcreator.url" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_0736, edam:topic_0820, edam:topic_2640 ; sc:citation , "pmcid:PMC9283888", "pubmed:35860415" ; sc:description "Unraveling membrane properties at the organelle-level with LipidDyn." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidDyn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ELELAB/LipidDyn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:29705063" ; sc:description "A tool for high-confidence LC-MS/MS (Liquid Chromatography-Mass Spectrometry) lipid identification." ; sc:featureList edam:operation_3214, edam:operation_3215, edam:operation_3803 ; sc:license "MIT" ; sc:name "LipiDex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/coongroup/LipiDex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description """Advanced informatics pipeline for lipidomics discovery applications. LipidFinder is an open-source Python workflow designed to facilitate further targeted lipidomics analysis. LipidFinder: A computational workflow for discovery of lipids. LipidFinder is an open-source Python workflow which searches a number of different databases to obtain putative identification of lipids, and assigns them to a class based on the LIPID MAPS® classification system.""" ; sc:featureList edam:operation_2940, edam:operation_3629, edam:operation_3649 ; sc:license "MIT" ; sc:name "LipidFinder" ; sc:softwareVersion "2.0" ; sc:url "http://lipidmaps.org/resources/tools/lipidfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0218, edam:topic_0634, edam:topic_2640, edam:topic_3407 ; sc:citation , "pubmed:34358314" ; sc:description "The LipiDisease tool performs disease enrichment analysis on lipids using biomedical literature data." ; sc:featureList edam:operation_0306, edam:operation_0310, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LipiDisease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbdm-01.zdv.uni-mainz.de:3838/piyusmor/LipiDisease/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0153, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc:description """A data transfer hub to support integration of large scale lipidomics datasets. The LipidLynxX project is aimed to provide a unified identifier for major lipids, especially oxidized lipids in the epilipidome. LipidLynxX on LIPID MAPS® Lipidomics Gateway. A robust and accurate converter can only be achieved by community-wide collaborations, thus any issue reports from general users and developers are welcome and will improve LipidLynxX project.""" ; sc:featureList edam:operation_0335, edam:operation_3282, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "LipidLynxX" ; sc:url "https://github.com/SysMedOs/LipidLynxX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_2269, edam:topic_3172, edam:topic_3303 ; sc:citation ; sc:description """Understanding the Lipidome at the Systems Level with lipidomeR. Integrative Visualizations of the Lipidome.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "lipidomeR" ; sc:url "https://lipidomer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3360, edam:topic_3407, edam:topic_3520, edam:topic_3577 ; sc:citation , "pubmed:31646749" ; sc:description """Current state of the art in a fast moving field. Lipidomics-Standards-Initiative (LSI). Regensburg, Lipidomics, LipidomicsRegensburg, LSI, Lipidomics-Standard-Initiative Lipidomics-Regensburg, Gerhard Liebisch, Silke Matysik, Lipid, Lipids, LCMS, GCMS, Mass Spectrometry, Gaschromatography, Analytical Chemistry, High-Resolution-MS. Welcome to the Lipidomics Standard Initiative (LSI)""" ; sc:featureList edam:operation_3431, edam:operation_3629, edam:operation_3891 ; sc:name "lipidomics" ; sc:url "https://lipidomics-standards-initiative.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0196, edam:topic_0203, edam:topic_0821, edam:topic_3047 ; sc:citation , "pubmed:34971364" ; sc:description "LipidOne is a freely available and easy-to-use software to discover the deeper features of building blocks in a lipidomic dataset." ; sc:featureList edam:operation_0310, edam:operation_3463, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LipidOne" ; sc:operatingSystem "Windows" ; sc:url "http://www.dcbb.unipg.it/LipidOne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3172, edam:topic_3473, edam:topic_3520 ; sc:citation , "pubmed:32168452" ; sc:description """A Software Tool for Data Mining and Analysis of Lipidomics Datasets. Data Mining and Analysis of Lipidomics Datasets. lipidr: Data Mining and Analysis of Lipidomics Datasets in R.""" ; sc:featureList edam:operation_1812, edam:operation_2939, edam:operation_2943, edam:operation_3891 ; sc:name "lipidr" ; sc:url "https://www.lipidr.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0625, edam:topic_0769, edam:topic_3172, edam:topic_3474 ; sc:citation , "pubmed:34048582" ; sc:description "LipidSig is a web-based tool for lipidomic data analysis. LipidSig is the first web-based platform which integrates a comprehensive analysis for streamlined data mining of lipidomic datasets. The user-friendly interface provides five main functions, namely Profiling, Differential expression, Machine learning, Correlation and Network, for assessment of lipid effects on biological mechanisms. The five functions provide unique aspects to analyze the lipidome profiling data based on different characteristics including lipid class, chain length, unsaturation, hydroxyl group, and fatty acid composition.', In summary, LipidSig enables users to perform intensive lipid analysis and create interactive plots with downloadable images and corresponding tables." ; sc:featureList edam:operation_3223, edam:operation_3501 ; sc:name "LipidSig" ; sc:url "http://chenglab.cmu.edu.tw/lipidsig" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pubmed:33950258" ; sc:description "LipidSuite is an interactive web server for lipidomics differential and enrichment analysis." ; sc:featureList edam:operation_1812, edam:operation_3501, edam:operation_3659, edam:operation_3891 ; sc:name "LipidSuite" ; sc:url "http://suite.lipidr.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0820, edam:topic_2229, edam:topic_3307 ; sc:citation , "pmcid:PMC4102414", "pubmed:25032790" ; sc:description "An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry." ; sc:featureList edam:operation_0270, edam:operation_0477 ; sc:name "LipidWrapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rocce-vm0.ucsd.edu/data/sw/hosted/lipidwrapper/" ; biotools:primaryContact "Rommie E. 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Its approach is kmer-based." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "Livermore Metagenomics Analysis Toolkit" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ebi.ac.uk" ; sc:softwareHelp ; sc:softwareVersion "Version 1-2-6" ; sc:url "http://computation.llnl.gov/projects/livermore-metagenomics-analysis-toolkit" ; biotools:primaryContact "Maya B Gokhale" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1075 ; sc:name "Protein family identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2343 ; sc:name "Pathway ID (KEGG)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1176 ; sc:name "GO concept ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3320, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC9575303", "pubmed:36253723" ; sc:description "A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals." ; sc:featureList edam:operation_0264, edam:operation_2436, edam:operation_3223, edam:operation_3431, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "LivestockExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo.njau.edu.cn/livestockExp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0202, edam:topic_3170, edam:topic_3303, edam:topic_3308 ; sc:citation , "pubmed:33982879" ; sc:description "LjaFGD is the Lonicera japonica functional genomics database.." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3672 ; sc:name "LjaFGD" ; sc:url "http://www.gzybioinformatics.cn/LjaFGD" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2830, edam:topic_3168, edam:topic_3379, edam:topic_3398 ; sc:citation , "pmcid:PMC8351782", "pubmed:34373858" ; sc:description "An open-source computational pipeline for robust nanobody humanization." ; sc:featureList edam:operation_0337, edam:operation_0480, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Llamanade" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sangzhe/Llamanade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9133536", "pubmed:35645753" ; sc:description "Local Label Point Correction for Edge Detection of Overlapping Cervical Cells." ; sc:featureList edam:operation_3096, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LLPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nachifur/LLPC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0601, edam:topic_0634, edam:topic_3300 ; sc:citation , "pmcid:PMC6943074", "pubmed:31906602" ; sc:description """A database of proteins undergoing liquid-liquid phase separation in vitro. 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Additionally, LMAP_S makes possible uncovering optimal estimations of both MSA and phylogenies. LMAP_S was designed for the workstation multi-core environment and integrates over 30 scientific software, for which provides easy installation. The LMAP_S package additionally includes our RYcode.pl application for purine/pyrimidine DNA/RNA (re-)coding.""" ; sc:featureList edam:operation_0492, edam:operation_0539, edam:operation_0551, edam:operation_2425 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LMAP_S" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://lmap-s.sourceforge.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3174, edam:topic_3673, edam:topic_3837 ; sc:citation , "pmcid:PMC9795473", "pubmed:36576131" ; sc:description "Evaluating metagenomic short de novo assembly methods through defined communities." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LMAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/B-UMMI/LMAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168, edam:topic_3301, edam:topic_3324 ; sc:citation "pubmed:26490433" ; sc:description "Bioinformatic pipeline that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis." ; sc:featureList edam:operation_2403 ; sc:name "LmCGST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/lmcgst/?source=navbar" ; biotools:primaryContact "Arthur W. 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Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "lmdme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/lmdme.html" ; biotools:primaryContact "Cristobal Fresno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517, edam:topic_3678 ; sc:description "Fit linear and generalized linear mixed-effects models. 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sc:softwareHelp ; sc:url "http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/lmm-lasso.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3172, edam:topic_3379 ; sc:citation , "pmcid:PMC6506811", "pubmed:31110642" ; sc:description "Linear mixed-effects modeling to improve clinical metabolomics information." ; sc:featureList edam:operation_3803, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "lmm2met" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kwanjeeraw/lmm2met" ; biotools:primaryContact "Sakda Khoomrung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0605, edam:topic_3070, edam:topic_3407 ; 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(VANTED). 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A modular approach to identify lncRNA related miRNA sponge modules in breast cancer. Until now, existing methods for identifying lncRNA related miRNA sponge modules mainly rely on lncRNA related miRNA sponge interaction networks, which may not provide a full picture of miRNA sponging activities in biological conditions. Hence there is a strong need of new computational methods to identify lncRNA related miRNA sponge modules. In this work, we propose a framework, LMSM, to identify LncRNA related MiRNA Sponge Modules from heterogeneous data. To understand the miRNA sponging activities in biological conditions, LMSM uses gene expression data to evaluate the influence of the shared miRNAs on the clustered sponge lncRNAs and mRNAs.""" ; sc:featureList edam:operation_0463, edam:operation_3432, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "LMSM" ; sc:url "https://github.com/zhangjunpeng411/LMSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3520 ; sc:citation , "pmcid:PMC8548730", "pubmed:34720899" ; sc:description "Novel Methodological Approach to Place Mouse Ultrasonic Vocalizations in Their Behavioral Contexts." ; sc:featureList edam:operation_2409, edam:operation_3196, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "LMT USV Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://usv.pasteur.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3324, edam:topic_3411, edam:topic_3673 ; sc:citation , "pmcid:PMC9084517", "pubmed:35533187" ; sc:description "A Listeria monocytogenes fast-tracing platform for global surveillance." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3840 ; sc:license "Other" ; sc:name "LmTraceMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lmtracemap.cgu.edu.tw/hua_map/test/upload.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0632, edam:topic_2885 ; sc:citation "pubmed:12824412" ; sc:description "Collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis, secondary structure prediction, and probe design for expression arrays, real time PCR, and SNP genotyping." ; sc:featureList edam:operation_0309, edam:operation_0475, edam:operation_2419, edam:operation_3095, edam:operation_3196 ; sc:name "LNAtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.exiqon.com/oligo-tools" ; biotools:primaryContact "Support in other countries", "Support in the US" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33219685" ; sc:description """An updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. lncRNA and cancer association database. Lnc2Cancer, is a manually curated database that provides comprehensive experimentally supported associations between lncRNA or circRNA and human cancer.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3680 ; sc:name "Lnc2Cancer" ; sc:softwareVersion "3.0" ; sc:url "http://www.bio-bigdata.net/lnc2cancer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC8728196", "pubmed:34850125" ; sc:description "An updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "LncACTdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.0" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/LncACTdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9941877", "pubmed:36824229" ; sc:description "An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information." ; sc:featureList edam:operation_0436 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LncCat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/a525076133/LncCat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9646749", "pubmed:36351980" ; sc:description "A machine learning-based tool for long non-coding RNA detection from RNA-Seq data." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0314, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LncDC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lim74/LncDC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0634, edam:topic_0659 ; sc:citation "pubmed:26887819" ; sc:description "Novel computational method and tool to predict the associations between lncRNAs and diseases." ; sc:featureList edam:operation_2423 ; sc:name "LncDisease" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.cuilab.cn/#tabs-4" ; biotools:primaryContact "Qinghua Cui(崔庆华)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3577 ; sc:citation , "pubmed:33219686" ; sc:description "A comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3659 ; sc:name "LnCeCell" ; sc:url "http://www.bio-bigdata.net/LnCeCell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3299, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7871587", "pubmed:33563213" ; sc:description "automated identification and conservation study of long noncoding RNAs." ; sc:featureList edam:operation_3258 ; sc:license "MIT" ; sc:name "lncEvo" ; sc:url "https://gitlab.com/spirit678/lncrna_conservation_nf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation , "pubmed:33045751" ; sc:description """An expression database of human long non-coding RNAs. Expression Database of Human Long non-coding RNAs. LncExpDB is a comprehensive database for lncRNA expression. It covers expression profiles of lncRNA genes across various biological contexts, predicts potential functional lncRNAs and their interacting partners, and thus provides essential guidance on experimental design.""" ; sc:featureList edam:operation_0337, edam:operation_2454, edam:operation_2495 ; sc:name "LncExpDB" ; sc:url "https://bigd.big.ac.cn/lncexpdb" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8407485", "pubmed:34464437" ; sc:description "A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data." ; sc:featureList edam:operation_0314, edam:operation_0362, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "lncExplore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lncexplore.bmi.nycu.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8314497", "pubmed:34315441" ; sc:description "A versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "lncGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ylab-hi/lncGSEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9985331", "pubmed:36869839" ; sc:description "Aggregated and inferred knowledge about human and mouse lncRNAs." ; sc:featureList edam:operation_2436, edam:operation_2489, edam:operation_3216, edam:operation_3436, edam:operation_3463 ; sc:name "lncHUB2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://maayanlab.cloud/lncHUB2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation , "pmcid:PMC5223071", "pubmed:28116287" ; sc:description "Lncident is a tool for rapid identification of long noncoding RNAs utilizing sequence intrinsic composition and open reading frame information." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "Lncident" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csbl.bmb.uga.edu/mirrors/JLU/Lncident/index.php" ; biotools:primaryContact "Ying Li" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_1929, edam:format_2305, edam:format_2306, edam:format_3003 ; sc:name "Gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1929, edam:format_2305, edam:format_2306, edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3473 ; sc:citation ; sc:description "A comprehensive compendium of human long non-coding RNA." ; sc:featureList edam:operation_0362 ; sc:name "LNCipedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:url "http://www.lncipedia.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:33635499" ; sc:description """A machine learning algorithm for long noncoding RNA annotation in plants. LncRNA prediction tool for plants. lncMachine requires python3 or newer.""" ; sc:featureList edam:operation_0436, edam:operation_3359, edam:operation_3937 ; sc:name "LncMachine" ; sc:url "https://github.com/hbusra/lncMachine.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7839966", "pubmed:33519912" ; sc:description """Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer. Increasing lncRNA-associated competing triplets were found to play important roles in cancers.""" ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_3463, edam:operation_3792 ; sc:license "MIT" ; sc:name "LncMiM" ; sc:url "https://github.com/xiaofengsong/LncMiM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0780, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC9590470", "pubmed:36304839" ; sc:description "A genome-wide lncRNAs regulated phenotypes database in plants." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "LncPheDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.lncphedb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3068, edam:topic_3360, edam:topic_3810 ; sc:citation , "pubmed:32766766" ; sc:description """A manually curated database for experimentally supported lncRNAs during various cancer metastatic events. A database for experimentally supported lncRNAs during various cancer metastatic events.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3799 ; sc:name "lncR2metasta" ; sc:url "http://lncR2metasta.wchoda.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_2885 ; sc:citation , "pubmed:33112702" ; sc:description "An updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2489 ; sc:name "LncRBase" ; sc:softwareVersion "2.0" ; sc:url "http://dibresources.jcbose.ac.in/zhumur/lncrbase2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation "pubmed:26315901" ; sc:description "New tool that calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames, translation scores based on ribosomal coverage, and conservation against characterized protein families." ; sc:featureList edam:operation_2495 ; sc:name "LncRNA-ID" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/zhangy72/LncRNA-ID" ; biotools:primaryContact "Yuan Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2269 ; sc:citation ; sc:description """An alignment-free predictor for long non-coding RNAs identification by multimodal deep learning. lncRNA_Mdeep is a computational tool for distinguishing lncRNAs from protein-coding transcripts. It efficiently incorporates the hand-crafted features and raw sequence information by a multimodal deep learning framework to predict the probability whether a transcript is lncRNA or not. LncRNA_Mdeep achieves a good performance on human dataset and multiple cross-species datasets.""" ; sc:name "lncRNA_Mdeep" ; sc:url "https://github.com/NWPU-903PR/lncRNA_Mdeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:21112873" ; sc:description "Database containing a comprehensive list of long noncoding RNAs (lncRNAs) that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_0438 ; sc:name "lncRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.lncrnadb.org/" ; biotools:primaryContact "Quek Xiu Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC10767967", "pubmed:37819033" ; sc:description "Database of long non-coding RNA-associated diseases." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "LncRNADisease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rnanut.net/lncrnadisease" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8728133", "pubmed:34791419" ; sc:description "A knowledgebase of lncRNA function in human cancer." ; sc:featureList edam:operation_0420, edam:operation_0463, edam:operation_3792, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "lncRNAfunc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ccsm.uth.edu/lncRNAfunc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC7536183", "pubmed:33020484" ; sc:description """Knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. Scripts for analyzing data displayed and deposited on the long non-coding RNA knowledgebase (lncRNAKB). LncRNAKB is an invaluable resource to understand the biological importance of long non-coding RNA (lncRNA) in tissue-specificity and disease association.""" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3431, edam:operation_3463, edam:operation_3766 ; sc:name "lncRNAKB" ; sc:url "http://www.lncrnakb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC9825536", "pubmed:36350671" ; sc:description "An database for functional variants in long non-coding RNAs." ; sc:featureList edam:operation_0331, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "lncRNASNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.0" ; sc:url "http://gong_lab.hzau.edu.cn/lncRNASNP3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0621, edam:topic_0659 ; sc:citation "pubmed:24813212" ; sc:description "This tool aims to be the lncRNA (long non-coding RNA) portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were collected from TCGA, GEO, ENCODE, and modENCODE (Organism: Human, Mouse, Fly, Worm, and Yeast)." ; sc:featureList edam:operation_2409, edam:operation_3431 ; sc:name "lncRNAtor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lncrnator.ewha.ac.kr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:37606159" ; sc:description "LncRTPred is a target prediction tool to predict the interaction between lncRNA and mRNA for both Human and Mouse species." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "LncRTPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bicresources.jcbose.ac.in/zhumur/lncrtpred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3169, edam:topic_3170 ; sc:citation , "pubmed:33045741" ; sc:description """A platform for long non-coding RNA related sets and enrichment analysis. Welcome to LncSEA a comprehensive human lncRNA sets resource and enrichment analysis platform.""" ; sc:featureList edam:operation_2421, edam:operation_2436, edam:operation_3222 ; sc:name "LncSEA" ; sc:url "http://bio.liclab.net/LncSEA/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:32193291" ; sc:description """LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms and tissue-specific therapeutic targets, especially the tissue elevated lncRNAs (TE lncRNAs), which expressed higher in a certain tissue or groups, and either not expressed or expressed at lower levels in other tissues.""" ; sc:featureList edam:operation_2421, edam:operation_3435, edam:operation_3799 ; sc:name "LncSpA" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/LncSpA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0659 ; sc:citation "pubmed:25524864" ; sc:description "Efficient tool for predicting RNA targets of lncRNAs (Long noncoding RNAs)" ; sc:featureList edam:operation_2423 ; sc:name "LncTar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cuilab.cn/lnctar" ; biotools:primaryContact "Dr. Qinghua Cui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3324, edam:topic_3396 ; sc:citation ; sc:description "LNetReduce is a tool for reducing linear dynamic networks with separated time scales. 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It takes as input a set of rooted phylogenetic trees given in Newick format (inputfile shows an example of input data)." ; sc:featureList edam:operation_0323 ; sc:name "LNETWORK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nclab.hit.edu.cn/~wangjuan/LNETWORK/" ; biotools:primaryContact "Juan Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293 ; sc:citation ; sc:description "Live-Neighbor-Joining, a heuristic for building a live phylogeny. We presented Live Neighbor-Joining, that extends the rationale of Neighbor-Joining by introducing the case where the creation of a live internal node results in a smaller sum of branch lengths. Thus, at each step of Live Neighbor-Joining, two options may apply: one as in Neighbor-Joining and another admitting a live internal node." ; sc:featureList edam:operation_3478 ; sc:name "LNJ" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://git.facom.ufms.br/bioinfo/LNJ" ; biotools:primaryContact "Nalvo F. Almeida" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "A new converter from Linkage-style to Morgan ver 3 style data files." ; sc:featureList edam:operation_0335 ; sc:name "lnkg2lmlnk" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20120312" ; sc:url "http://faculty.washington.edu/wijsman/software.shtml" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pubmed:10074416", "pubmed:15130847", "pubmed:15865995", "pubmed:17955155", "pubmed:9278277" ; sc:description "The LnLCorr package is designed to detect pairwise coevolutionary among residues in a set of proteins using likelihood ratio tests." ; sc:featureList edam:operation_2479 ; sc:name "LnLCorr" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.evolutionarygenomics.com/ProgramsData/lnlcorr/LnLCorr.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3421, edam:topic_3422, edam:topic_3474 ; sc:citation , , "pmcid:PMC9716136", "pmcid:PMC9767978", "pubmed:36465636", "pubmed:36568161" ; sc:description "Early distinction of lymph node metastasis in patients with soft tissue sarcoma and individualized survival prediction using the online available nomograms." ; sc:featureList edam:operation_2422, edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "LNM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tyxupup.shinyapps.io/OSofSTSpatientswithLNM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "The web server LnSignal (Labelling N-terminal Signal petide cleavage site) was developed by integrating position-specific amino acid propensities based on the highest average positions and conditional random fields." ; sc:featureList edam:operation_2479 ; sc:name "LnSignal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/LnSignal/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Load several FASTQ files from different conditions." ; sc:featureList edam:operation_1812 ; sc:name "load_multifastq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation , "pubmed:11983928" ; sc:description "Loop modelling server for protein structures." ; sc:featureList edam:operation_0481 ; sc:name "LOBO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://protein.bio.unipd.it/lobo/" ; biotools:primaryContact "Silvio Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc:citation , "pubmed:27322848" ; sc:description "Multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. It applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA." ; sc:featureList edam:operation_0226, edam:operation_3214 ; sc:license "GPL-3.0" ; sc:name "LOBSTAHS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/LOBSTAHS.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:22522390" ; sc:description "lobSTR is an alignment and genotyping tool for profiling short tandem repeats from next generation sequencing data" ; sc:featureList edam:operation_0380 ; sc:name "LobSTR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://lobstr.teamerlich.org/" ; biotools:primaryContact "Melissa Gymrek", "lobSTR user group mailing list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082, edam:topic_0166, edam:topic_0621 ; sc:citation "pubmed:12824321", "pubmed:14635133", "pubmed:15808855" ; sc:description "Database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_2489, edam:operation_3092 ; sc:name "Loc3D" ; sc:url "http://cubic.bioc.columbia.edu/db/LOC3d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Perform reciprocal blast against two databases to find RBH Orthologs" ; sc:featureList edam:operation_2421, edam:operation_3663, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Local Reciprocal Blast search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/45862-local-reciprocal-blast-search" ; biotools:primaryContact "Hengfu Yin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053 ; sc:citation "pubmed:11743722" ; sc:description "New algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data." ; sc:featureList edam:operation_0315, edam:operation_3432 ; sc:name "Local Clustering" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo.mbb.yale.edu/expression/cluster/" ; biotools:primaryContact "Mark Gerstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:25282642" ; sc:description "Fast and scalable local network alignment tool for the identification of functionally conserved modules in multiple networks." ; sc:featureList edam:operation_2928 ; sc:name "LocalAli" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/screamer/localali" ; biotools:primaryContact "Jialu Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0130, edam:topic_3510 ; sc:citation , "pmcid:PMC5232785", "pubmed:28076807" ; sc:description "Enables rapid and high-throughput analyses of a wide range of physico-chemical properties encoded by intrinsically disordered protein and region sequences." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "localCIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Pappulab/localCIDER" ; biotools:primaryContact , "Rohit V. Pappu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3377, edam:topic_3810 ; sc:citation , "pmcid:PMC8330612", "pubmed:34349611" ; sc:description "Nonparametric Methods for Generating High Quality Comparative Effectiveness Evidence" ; sc:featureList edam:operation_3503 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "LocalControl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://CRAN.R-project.org/package=LocalControl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3473 ; sc:description "This code is the detects abnormal region in retinal images using morphological operations" ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Localization of Hard Exudates in Retinal Fundus Images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/69542-localization-of-hard-exudates-in-retinal-fundus-images" ; biotools:primaryContact "Bagadam David" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0621, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:16845118" ; sc:description "Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information." ; sc:featureList edam:operation_0246, edam:operation_0269, edam:operation_0270, edam:operation_0303, edam:operation_3092 ; sc:name "Localizome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/katur/localizome" ; biotools:primaryContact "Jong Bhak", "Sangsoo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099, edam:topic_0176, edam:topic_2275 ; sc:citation "pubmed:18556754" ; sc:description "Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Through a sequence of local moves, e.g. local backbone modifications, it walks through the conformational space, looking for a configuration as close as possible to the input 3D model, while keeping his points on-lattice. 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sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3383 ; sc:citation ; sc:description "Local Z Projector is an ImageJ2 plugin to perform local-Z projection of a 3D stack, possibly over time, possibly very large." ; sc:license "BSD-3-Clause" ; sc:name "LocalZProjector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.pasteur.fr/iah-public/localzprojector" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3303, edam:topic_3382 ; sc:citation , "pubmed:35298593" ; sc:description "A python library for analyzing single-molecule localization microscopy data." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "LOCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/locan" . a sc:SoftwareApplication ; 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sc:operatingSystem "Linux", "Mac" ; sc:provider "University Freiburg" ; sc:softwareHelp ; sc:softwareVersion "1.8.9" ; sc:url "http://www.bioinf.uni-freiburg.de/Software/LocARNA/" ; biotools:primaryContact , "Sebastian Will" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929, edam:format_2200 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_1982, edam:format_3508 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_3466 ; sc:name "RNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097 ; sc:author , "Sebastian Will" ; sc:citation , "pmcid:PMC3334699", "pubmed:22450757" ; sc:description "Probabilistic structure-based multiple alignment of RNAs." ; sc:featureList edam:operation_0294 ; sc:isAccessibleForFree true ; sc:name "LocARNA-P" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "1.8.9" ; sc:url "http://www.bioinf.uni-freiburg.de/Software/LocARNA/" ; biotools:primaryContact , "Sebastian Will" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:21858125" ; sc:description "LOCAS low-coverage short-read assembler" ; sc:featureList edam:operation_0310 ; sc:name "LOCAS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www-ab.informatik.uni-tuebingen.de/software/locas" ; biotools:primaryContact "Juliane D. Klein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0621, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:16381849" ; sc:description "LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins." ; sc:featureList edam:operation_0270, edam:operation_0303, edam:operation_2489, edam:operation_3092 ; sc:name "LOCATE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://locate.imb.uq.edu.au/" ; biotools:primaryContact "Josefine Sprenger", "Rohan Teasdale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2269, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:32068122" ; sc:description """Subcellular localization of long non-coding RNAs using nucleotide compositions. Predict the SubCellular Location of lncRNAs by using Nucleotide Compositions. The system will take one RNA sequence at a time.""" ; sc:featureList edam:operation_2489, edam:operation_3936 ; sc:name "Locate-R" ; sc:url "http://locate-r.azurewebsites.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0219 ; sc:citation "pubmed:21071420" ; sc:description "Manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). 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Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB." ; sc:featureList edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "loci2path" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/loci2path.html" ; biotools:primaryContact "Tianlei Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:9322051" ; sc:description "Vector based protein structure superposition algorithm capable of recognizing distant structural similarities. Statistical significance values for alignments are provided." ; sc:featureList edam:operation_0295 ; sc:name "LOCK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://motif.stanford.edu/distributions/lock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2229 ; sc:citation "pubmed:25515756" ; sc:description "Support Vector Machine (SVM) predictor that locates classical nuclear export signals (NESs) in CRM1 cargoes. Export-Karyopherinβ CRM1 recognizes hundreds of broadly functioning proteins. Most CRM1 cargoes contain the classical NES (also known as leucine-rich NESs), a peptide with 8-15 amino acids, regularly spaced with conserved hydrophobic residues." ; sc:featureList edam:operation_2479 ; sc:name "LocNES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/LocNES/LocNES.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation , "pubmed:19261721" ; sc:description "Designed to LOCate putative Pilus operons in Gram-positive prokaryotes. This is done in two steps: First, pilus-related sequences are identified by hmmsearch with a carefully selected set of profile Hidden Markov Models. Second, chromosome regions with statistically significant clustering of hits are located using hypergeometrical distribution and Monte Carlo simulations." ; sc:featureList edam:operation_2479, edam:operation_3432 ; sc:name "LOCP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ekhidna.biocenter.helsinki.fi/locp/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation "pubmed:15724288" ; sc:description "Tool for local structure prediction from protein sequence using a structural alphabet approach." ; sc:featureList edam:operation_0474 ; sc:name "LOCPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dsimb.inserm.fr/~debrevern/TOOLS/LOCPRED/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3518 ; sc:citation "pubmed:23166601" ; sc:description "Produces piecewise polynomial models for one-dimensional signals of the type encountered in genomics." ; sc:featureList edam:operation_0415 ; sc:name "locsmoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/locsmoc/" ; biotools:primaryContact "Vincent Detours" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:15215440" ; sc:description "Tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks." ; sc:featureList edam:operation_0267, edam:operation_0418, edam:operation_2489, edam:operation_3439 ; sc:name "LOCtarget" ; sc:url "http://www.rostlab.org/services/LOCtarget/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123, edam:topic_2229 ; sc:author "Tatyana Goldberg", "Tobias Hamp" ; sc:citation ; sc:contributor "Burkhard Rost" ; sc:description "Framework to predict localization in life's three domains, including globular and membrane proteins (3 classes for archaea; 6 for bacteria and 18 for eukaryota). The resulting method, works well even for protein fragments. It uses a hierarchical system of support vector machines that imitates the cascading mechanism of cellular sorting.The method also accurately distinguishes membrane and non-membrane proteins." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:name "LocTree2" ; sc:operatingSystem "Linux" ; sc:provider "Technische Universität München", "tum.de" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://rostlab.org/owiki/index.php/Loctree2" ; biotools:primaryContact "General" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123, edam:topic_2229 ; sc:author "Guy Yachdav", "Maximilian Hecht", "Tatyana Goldberg", "Timothy Karl", "Tobias Hamp" ; sc:citation , ; sc:contributor "Alexander von Humboldt Foundation through German Federal Ministry for Education and Research", "Burkhard Rost", "Ernst Ludwig Ehrlich Studienwerk", "Henrik Nielsen" ; sc:description "Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea." ; sc:featureList edam:operation_2489 ; sc:funder "Alexander von Humboldt Foundation through German Federal Ministry for Education and Research", "Ernst Ludwig Ehrlich Studienwerk" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LocTree3" ; sc:operatingSystem "Linux" ; sc:provider "RostLab", "Technische Universität München" ; sc:softwareHelp ; sc:softwareVersion "1.0.8" ; sc:url "https://rostlab.org/services/loctree3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3320 ; sc:citation ; sc:description "LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a dynamic-programming algorithm for finding the optimal set of splice sites in a genomic region of interest with estimated prior length information." ; sc:featureList edam:operation_2454 ; sc:name "LOCUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://stormo.wustl.edu/resources.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0219, edam:topic_3053 ; sc:citation , "pubmed:26589274" ; sc:description "A data visualization and exploration tool for genetic association data." ; sc:featureList edam:operation_0571 ; sc:license "MIT" ; sc:name "LocusExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/oncogenetics/LocusExplorer" ; biotools:primaryContact "Tokhir Dadaev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """A web-based colocalization tool for the annotation and functional follow-up of GWAS. Explore GWAS Results with GTEx's eQTL Association Results. A Colocalization Tool to Prioritize Genes and Tissues from GWAS and eQTL Integration.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3799 ; sc:license "MIT" ; sc:name "LocusFocus" ; sc:softwareHelp , ; sc:url "https://locusfocus.research.sickkids.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:description "Computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci." ; sc:featureList edam:operation_0283, edam:operation_3429 ; sc:name "LOCUSMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://animalgene.umn.edu/locusmap/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0749, edam:topic_3168, edam:topic_3517 ; sc:citation ; sc:description """Interactive and embeddable visualization of genetic association study results. LocusZoom is a Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. To see functional examples of plots generated with LocusZoom.js see statgen.github.io/locuszoom and statgen.github.io/locuszoom/#examples. A Javascript/d3 embeddable plugin for interactively visualizing and navigating statistical genetic data from customizable sources. See github.com/statgen/locuszoom/wiki for full documentation and API reference. Shown here is a standard interactive LocusZoom plot, depicting GWAS association data with gene tracks loaded from a University of Michigan API. The LocusZoom.js library provides several pre-defined layouts for entire plots and subdivisions of plots such as panels, data layers, tool tips, etc.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3283 ; sc:license "MIT" ; sc:name "LocusZoom" ; sc:url "https://github.com/statgen/locuszoom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3360, edam:topic_3517 ; sc:citation "pubmed:26803157" ; sc:description "Software package for genome-wide association anal-ysis of biomarkers with a limit of detection." ; sc:featureList edam:operation_2945 ; sc:name "lodGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/lodGWAS/" ; biotools:primaryContact "Ilja M. Nolte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. 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A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing.""" ; sc:featureList edam:operation_3185, edam:operation_3198, edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "LongGF" ; sc:url "https://github.com/WGLab/LongGF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:22581622" ; sc:description "Mixed-model-based approach for performing association mapping which utilizes multiple phenotype measurements for each individual." ; sc:featureList edam:operation_2429 ; sc:name "longGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetics.cs.ucla.edu/longGWAS/" ; biotools:primaryContact "Nicholas Furlotte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3053 ; sc:citation , "pmcid:PMC5167071", "pubmed:27667791" ; sc:contributor ; sc:description "LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies." ; sc:featureList edam:operation_0310 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "LongISLND" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/bioinform/longislnd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3304 ; sc:citation , "pmcid:PMC6022641", "pubmed:29950021" ; sc:description "Gene Length-Dependent Expression Analysis Tool in Neuronal Cells." ; sc:featureList edam:operation_2495 ; sc:name "LONGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biohpc/longo" ; biotools:primaryContact "Tae-Hyuk Ahn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:description "Long Ranger is a set of five analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants." ; sc:featureList edam:operation_3182, edam:operation_3198, edam:operation_3227, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "Long Ranger" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , , , , , ; sc:url "https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Longshot" ; sc:softwareHelp ; sc:url "https://github.com/pjedge/longshot" ; biotools:primaryContact "Vikas Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769 ; sc:citation ; sc:description "A genome assembly correction and scaffolding pipeline using long reads." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LongStitch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/longstitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Automated Analysis of Long Read Spliced Alignment Accuracy." ; sc:featureList edam:operation_0292, edam:operation_3198, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "LongTron" ; sc:url "https://github.com/schatzlab/LongTron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:19679872" ; sc:description "AJAX-based browser for visualising deep sequencing data." ; sc:featureList edam:operation_0564, edam:operation_2421, edam:operation_3744, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LookSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/science/tools/lookseq" ; biotools:primaryContact "Dr Magnus Manske" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769 ; sc:citation ; sc:description """Comprehensive feedback loop detection in ordinary differential equation models. Comprehensive Feedback Loop Detection in ODE Models. Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. LoopDetect - comprehensive detection of feedback loops in ODE models.""" ; sc:featureList edam:operation_0337, edam:operation_0481 ; sc:license "BSD-3-Clause" ; sc:name "LoopDetect" ; sc:url "https://de.mathworks.com/matlabcentral/fileexchange/81928-loopdetect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_0821, edam:topic_3421, edam:topic_3542 ; sc:citation , "pubmed:35438789" ; sc:description "A web tool for transplanting dynamical loops for protein engineering." ; sc:featureList edam:operation_0244, edam:operation_0249, edam:operation_0479, edam:operation_0481, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:name "LoopGrafter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://loschmidt.chemi.muni.cz/loopgrafter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:26249814" ; sc:description "Method based on the Random Forest automatic learning technique, designed to select structural templates for protein loops among a dataset of candidates." ; sc:featureList edam:operation_2406 ; sc:name "LoopIng" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://circe.med.uniroma1.it/looping/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3168, edam:topic_3341 ; sc:citation ; sc:description """A uLoop Assembly Clone Verification Tool for Nanopore Sequencing Reads. Cloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life. Cloning can be difficult and time consuming as each plasmid is unique to a particular project and each sequence must be carefully selected, cloned and sequenced to determine correctness. Loop assembly (uLOOP) is a recursive, Golden Gate-like assembly method that allows rapid cloning of domesticated DNA fragments to robustly refactor novel pathways. With uLOOP methodologies, one can clone several sequences directionally to generate a library of transcriptional units (TUs) in plasmids within a single reaction but analysis of the plasmid population has been impeded by current sequencing and analysis methods""" ; sc:featureList edam:operation_0310, edam:operation_0363, edam:operation_3180, edam:operation_3184 ; sc:name "LoopViz" ; sc:url "https://gitlab.com/marielelensink325/loopseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3168 ; sc:citation "pubmed:22962451" ; sc:description "Assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool." ; sc:featureList edam:operation_2429 ; sc:name "LoQuM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.case.edu/loqum/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0153, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC10469370", "pubmed:37584663" ; sc:description "Lipid over-representation analysis based on structural information." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "LORA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lora.metabolomics.fgu.cas.cz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325 ; sc:citation "pmcid:PMC4765596", "pubmed:26958175" ; sc:description "LORD (linking opendata for rare diseases) - tool for browsing information about rare diseases. It aggregates the information from Orphanet, HPO and OMIM database." ; sc:featureList edam:operation_2421, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "LORD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://enlord.bndmr.fr/#homepage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3303 ; sc:citation ; sc:description "Sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data." ; sc:featureList edam:operation_3198, edam:operation_3211, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "lordFAST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/vpc-ccg/lordfast" ; biotools:primaryContact "Ehsan Haghshenas", "Faraz Hach" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_3071, edam:topic_3168 ; sc:citation "pubmed:25165095" ; sc:description "Program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads." ; sc:featureList edam:operation_3195 ; sc:name "LoRDEC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.atgc-montpellier.fr/lordec/" ; biotools:primaryContact "Eric Rivals", "Leena Salmela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC8111061", "pubmed:33996146" ; sc:description "LoReTTA (Long Read Template Targeted Assembler) is a reference assisted de novo assembler specifically designed to deal with PacBio reads generated from viral genomes. It is a user-friendly tool for assembling viral genomes from PacBio sequence data." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3196, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "LoReTTA" ; sc:url "https://github.com/salvocamiolo/LoReTTA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0625 ; sc:description "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)" ; sc:featureList edam:operation_2403, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "lorikeet" ; sc:softwareVersion "20" ; sc:url "https://github.com/AbeelLab/lorikeet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3053 ; sc:citation "pubmed:23419377" ; sc:description "LOw-Rank representation and Sparse regression for eQTL mapping. This algorithm accounts for confounding factors such as unobserved covariates, experimental artifacts, and unknown environmental perturbations." ; sc:featureList edam:operation_3659 ; sc:name "LORS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Genomic_Expression_Pathway_Analysis" ; biotools:primaryContact "Hongyu Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3277 ; sc:citation , "pubmed:34255820" ; sc:description "On the stability of log-rank test under labeling errors." ; sc:featureList edam:operation_2238, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LoRSI" ; sc:url "https://github.com/YakhiniGroup/LoRSI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "LOT (Linkage analysis of Ordinal Traits) is a software program that performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait." ; sc:featureList edam:operation_0283 ; sc:name "LOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2" ; sc:url "http://c2s2.yale.edu/software/LOT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_2258, edam:topic_2840, edam:topic_3047, edam:topic_3292 ; sc:author , , ; sc:citation , "pmcid:PMC9135406", "pubmed:35616633" ; sc:contributor , , ; sc:description "LOTUS is a comprehensive collection of documented structure-organism pairs. Within the frame of current computational approaches in Natural Products research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:license "MIT" ; sc:name "LOTUS" ; sc:softwareHelp , ; sc:url "https://lotus.naturalproducts.net" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:description "LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes." ; sc:featureList edam:operation_0253, edam:operation_3200 ; sc:name "lotus2" ; sc:softwareVersion "2.23" ; sc:url "https://lotus2.earlham.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634 ; sc:description "Detection and analysis of Lou Gehrig's disease by using Watershed Techniques as well as clustering." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "Lou Gehrig s disease detection by using Watershed Technique" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50106-lou-gehrig-s-disease-detection-by-using-watershed-technique" ; biotools:primaryContact "ALI AKBAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0199, edam:topic_3325, edam:topic_3574 ; sc:citation ; sc:description "The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes." ; sc:featureList edam:operation_2422, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LOVD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://www.lovd.nl/3.0/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:15215465" ; sc:description "Tool that searches for low complexity regions of DNA or protein sequences. Using it you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences." ; sc:featureList edam:operation_0234, edam:operation_0292, edam:operation_0447, edam:operation_2479 ; sc:name "LowComplexity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/" ; biotools:primaryContact "Yury Orlov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3500, edam:topic_3673 ; sc:citation ; sc:description "Moment Estimators of Relatedness From Low-Depth Whole-Genome Sequencing Data." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LowKi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/genostats/LowKi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1138 ; sc:encodingFormat edam:format_2330 ; sc:name "Pfam accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:encodingFormat edam:format_2330, edam:format_3547, edam:format_3603 ; sc:name "Sequence composition plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2330, edam:format_3547, edam:format_3603 ; sc:name "Sequence alignment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2330, edam:format_3547, edam:format_3603 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547, edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation , "pmcid:PMC4748640", "pubmed:26860319" ; sc:description "This package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or PFAM domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or PFAM domains of your interest." ; sc:featureList edam:operation_0296, edam:operation_0492, edam:operation_2479 ; sc:license "GPL-3.0" ; sc:name "LowMACA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/LowMACA.html" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168 ; sc:citation "pubmed:20538728" ; sc:description "Program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples." ; sc:featureList edam:operation_2495 ; sc:name "LOX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://medicine.yale.edu/lab/townsend/sand/index.aspx#page1" ; biotools:primaryContact "Townsend Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC7041288", "pubmed:32093606" ; sc:description """Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. The system LP-HCLUS and all the necessary files(lphclus.zip).""" ; sc:featureList edam:operation_3280, edam:operation_3432, edam:operation_3625 ; sc:name "LP-HCLUS" ; sc:url "http://www.di.uniba.it/~gianvitopio/systems/lphclus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623, edam:topic_2259 ; sc:citation "pubmed:19765306" ; sc:description "Allows the user to quickly find a high-quality community close to a queried protein in any network available from BioGRID or specified by the user." ; sc:featureList edam:operation_3767 ; sc:name "LPCF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gaussian.bu.edu/lpcf.html" ; biotools:primaryContact "Konstantin Voevodski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_0634, edam:topic_3418, edam:topic_3473 ; sc:citation , "pmcid:PMC8293037", "pubmed:34208910" ; sc:description "The Longitudinal Pediatric Data Resource (LPDR) is used for facilitating longitudinal collection of health information to inform clinical care and guide newborn screening efforts." ; sc:featureList edam:operation_0337, edam:operation_3196 ; sc:name "LPDR" ; sc:url "https://nbstrn.org/tools/lpdr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation ; sc:description "Used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. It is primarily used for analyzing data between two conditions. To use it for paired data, see library. For using it in multiple conditions, use HEM library." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "LPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/LPE.html" ; biotools:primaryContact "Nitin Jain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3569 ; sc:citation ; sc:description "Two options are added to the LPE algorithm, which original version sets all variances below the max variance in the ordered distribution of variances to the maximum variance. In the present version, this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. 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In the end, these encoded protein/RNA sequences are feed into a convolutional neural network to predict the lncRNA-protein interactions.""" ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3901 ; sc:name "LPI-CNNCP" ; sc:url "https://github.com/NWPU-903PR/LPI-CNNCP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:35785626" ; sc:description "A computational method LPI-CSFFR to predict lncRNA-protein interactions from sequences, secondary structure, and physicochemical property, which makes use of deep learning CNN and further improve its performance using feature reuse strategy." ; sc:featureList edam:operation_0267, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LPI-CSFFR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JianjunTan-Beijing/LPI-CSFFR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0203, edam:topic_0659 ; sc:citation , "pmcid:PMC7758075", "pubmed:33362868" ; sc:description """Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions. This model is proposed to predict lncRNA-protein interactions, which can be summarized in four steps:.""" ; sc:featureList edam:operation_0491, edam:operation_2492, edam:operation_3901 ; sc:name "LPI-SKF" ; sc:url "https://github.com/zyk2118216069/LPI-SKF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2814 ; sc:citation "pubmed:27016210" ; sc:description "Web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank." ; sc:featureList edam:operation_2949 ; sc:name "LPIcom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/lpicom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_0659, edam:topic_3300, edam:topic_3474 ; sc:citation , "pmcid:PMC9013167", "pubmed:35428172" ; sc:description "A webserver for lncRNA-protein interaction extraction from the literature." ; sc:featureList edam:operation_3280, edam:operation_3625, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "LPInsider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.csbg-jlu.info/LPInsider/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3382 ; sc:citation ; sc:description "LPMX, i.e, Local Package Manager X, is a pure rootless composable container system. 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For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used." ; sc:featureList edam:operation_3439 ; sc:license "Artistic-2.0" ; sc:name "lpNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/lpNet.html" ; biotools:primaryContact "Lars Kaderali" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:16597255" ; sc:description "Linear-time program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model.In more population genetic terms, LPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data." ; sc:featureList edam:operation_0487 ; sc:name "LPPH" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://csiflabs.cs.ucdavis.edu/~gusfield/lpph.html" ; biotools:primaryContact "Dan Gusfield" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." ; sc:featureList edam:operation_3214 ; sc:name "LPPtiger" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/SysMedOs/lpptiger" ; biotools:primaryContact "Issue tracker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0637, edam:topic_3303 ; sc:citation , "pubmed:36260450" ; sc:description "The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes and much more." ; sc:featureList edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "LPSN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lpsn.dsmz.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605 ; sc:citation ; sc:description "This package was derived from Rsymphony_0.1-17 from CRAN. 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Lag Penalized Weighted Correlation (LPWC) is a method for clustering short time series data. It is designed to identify groups of biological entities (for example, genes or phosphosites) that exhibit the same pattern of activity changes over time. LPWC allows lags to incorporate delayed responses in the biological data. For example, two genes may have similar expression changes over time, but one initiates those changes 5 minutes after the other. LPWC also supports irregular time intervals between time points collected in biological data. The LPWC website is available here.""" ; sc:featureList edam:operation_3432, edam:operation_3463, edam:operation_3501 ; sc:license "MIT" ; sc:name "LPWC" ; sc:url "https://github.com/gitter-lab/LPWC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3393, edam:topic_3575 ; sc:citation ; sc:description """Adapting Lot Quality Assurance Sampling to accommodate imperfect tests. This repository provides code that accompanies the Adapting Lot Quality Assurance Sampling (LQAS) to accommodate imperfect tests: application to COVID-19 serosurveillance in Haiti paper. The goal is to classify an area as “high” or “low” on some trait of interest. In our paper, we were interested in classifying hospitals as having high or low COVID-19 antibody prevalence among healthcare workers in Haiti. In the traditional form of LQAS, the sample size, n, and decision rule, d, are determined by the population size, N, and four parameters defined by users based on the specific context and goals.""" ; sc:license "MIT" ; sc:name "LQAS-IMP" ; sc:url "https://github.com/isabelfulcher/lqas_imp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0091, edam:topic_0196, edam:topic_3673 ; sc:citation ; sc:description """the Long Read Aligner for Sequences and Contigs. LRA, the long read aligner for sequences and assembly contigs LRA is a sequence alignment program that aligns long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. LRA implements seed chaining sparse dynamic programming with a convex gap function to read and assembly alignment, which is also extended to allow for inversion cases. Through the Truvari analysis of LRA, Minimap2 and NGM-LR alignments. LRA achieves higher f1 score over HG002 HiFi, CLR and ONT datasets. Home: https://github.com/ChaissonLab/LRA. Long read aligner for sequences and contigs.""" ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:name "lra" ; sc:url "https://anaconda.org/bioconda/lra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3047, edam:topic_3391 ; sc:citation "pubmed:26626453" ; sc:description "New method to discover molecular subtypes by detecting the low-dimensional intrinsic space of high-dimensional cancer multi-omics data." ; sc:featureList edam:operation_2990 ; sc:name "LRAcluster" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.au.tsinghua.edu.cn/member/jgu/lracluster/" ; biotools:primaryContact "Dingming Wu", "Jin Gu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3277, edam:topic_3474, edam:topic_3837 ; sc:citation , "pmcid:PMC9277797", "pubmed:35821155" ; sc:description "Binning long reads in metagenomics datasets using composition and coverage information." ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "LRBinner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/anuradhawick/LRBinner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_2814, edam:topic_2830 ; sc:citation "pubmed:26455801" ; sc:description "A computational method based on a combination of physicochemical and structural properties to predict the B-cell epitopes." ; sc:featureList edam:operation_0477, edam:operation_2480 ; sc:name "LRC" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bs.ipm.ir/softwares/LRC/" ; biotools:primaryContact "School of Biological Sciences" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pubmed:34850358" ; sc:description "An R package and Shiny application for processing lexical data." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "lrd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/npm27/lrd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3344, edam:topic_3519 ; sc:citation ; sc:description "LRE analysis (Rutledge R.G. BMC Biotech 2008) on raw data from a real time PCR machine" ; sc:featureList edam:operation_0307, edam:operation_0308 ; sc:isAccessibleForFree true ; sc:name "LRE analysis of Real Time PCR data" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/35174-lre-analysis-of-real-time-pcr-data" ; biotools:primaryContact "Diane" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621 ; sc:citation ; sc:description "LRensemble (LR Ensemble Localization Predictor) predicts 4 major locations for Yeast Proteins: Cytosol, Mitochondrion, Nucleus, Secretory. The prediction method is to build an ensemble over different available localization predictors. In the current version, our predict collects prediction results from up to 6 predictors and Logistic Regression is used as the ensemble algorithm." ; sc:featureList edam:operation_2423, edam:operation_2479, edam:operation_3659 ; sc:name "LRensemble" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mleg.cse.sc.edu/LRensemble/cgi-bin/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps." ; sc:featureList edam:operation_3217 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LR_Gapcloser" ; sc:url "https://github.com/CAFS-bioinformatics/LR_Gapcloser" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3360, edam:topic_3373 ; sc:citation , "pmcid:PMC8508984", "pubmed:34638849" ; sc:description "Predicting Associations between ncRNA and Drug Resistance via Linear Residual Graph Convolution." ; sc:featureList edam:operation_0321, edam:operation_3436, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LRGCPND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TroyePlus/LRGCPND" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0781 ; sc:citation "pubmed:27288498" ; sc:description "Tool for the LRI prediction in full viral genomes based on a multiple genome alignment." ; sc:featureList edam:operation_0415, edam:operation_0492, edam:operation_3182 ; sc:name "LRIscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rna.uni-jena.de/en/software/" ; biotools:primaryContact "Marcus Fricke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:35788263" ; sc:description "LRLoop is a full-featured R package for analyzing LR-Loops from bulk & single-cell RNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_2437, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "LRLoop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Pinlyu3/LRLoop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "LRMotifs is a novel method of DNA sequence motif discovery based on logistic regression and rigorous hypothesis testing." ; sc:featureList edam:operation_0238, edam:operation_3659 ; sc:name "LRMotifs" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://code.google.com/p/likelihood-ratio-motifs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC7403501", "pubmed:32849762" ; sc:description """An Overlap Detection Algorithm for Long Reads Based on k-mer Distribution. LROD can detect overlap regions among long reads.""" ; sc:featureList edam:operation_0525, edam:operation_3198, edam:operation_3472 ; sc:name "LROD" ; sc:url "https://github.com/luojunwei/LROD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation "pubmed:26607492" ; sc:description "LRpath performs gene set enrichment testing using logistic regression, and allows the data to remain on a continuous scale." ; sc:featureList edam:operation_2497, edam:operation_3659 ; sc:name "LRpath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lrpath.ncibi.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275 ; sc:description "Method that determines binding sites of small compounds (ligands) on the surface of proteinsExtraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based." ; sc:featureList edam:operation_2421 ; sc:name "lrrr 1.4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "beta1" ; sc:url "http://sourceforge.net/projects/lrrr/" ; biotools:primaryContact "Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_3510 ; sc:citation , "pubmed:25150822" ; sc:description "An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors." ; sc:featureList edam:operation_0239, edam:operation_2421 ; sc:name "LRRsearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.lrrsearch.com/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10358952", "pubmed:37428794" ; sc:description """Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. scTCR-seq data compliments the scRNA-seq data in the sense that it provides the clonotype information for each cell, and it is generally assumed that cells sharing the same clonotype share the same progenitor. By integrating scTCR-seq data with scRNA-seq data, we could have a detailed insight of transcriptional changes that occur as clonal related cells differentiate. The LRT package utilizes the complementary nature of these two data type and investigate clonal differentiation heterogeneity by integrative analysis of scTCR-seq data and scRNA-seq data.""" ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "LRT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JuanXie19/LRT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Linked-Read ToolKit (LRTK), is a unified and versatile toolkit to process human and metagenomic linked-read sequencing data from different linked-read sequencing technologies, including 10x Genomics, single-tube long fragment read (stLFR) and transposase enzyme linked long-read sequencing (TELL-Seq). LRTK provides functions to simulate linked-read sequencing data, perform barcode correction, barcode-aware alignment and metagenome assembly, reconstruction of virtual DNA fragments, and barcode-assisted genomic variant detection and phasing. LRTK also has the ability to perform automatic analysis from raw sequencing data to downstream analysis and support the analysis of multiple samples in parallel. In addition, LRTK could produce publication-ready visualizations and generate reproducible reports, summarizing the key parameters at multiple checkpoints such as library preparation." ; sc:name "LRTK" ; sc:softwareVersion "2.1" ; sc:url "https://github.com/ericcombiolab/LRTK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC8729064", "pubmed:34983367" ; sc:description "Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks." ; sc:featureList edam:operation_0463, edam:operation_3435, edam:operation_3927 ; sc:license "Not licensed" ; sc:name "LRWRHLDA" ; sc:url "https://github.com/wang-124/LRWRHLDA.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:19369493" ; sc:description "Web tool for genome-wide annotation of human SNPs. The current version provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features, inferred from three-dimensional experimental structures." ; sc:featureList edam:operation_0362, edam:operation_3661 ; sc:name "LS-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ls-snp.icm.jhu.edu/ls-snp-pdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:32086197" ; sc:description """Accurately Resolving People in Dense Crowds via Detection. This repository is the pytorch implementation for the crowd counting model, LSC-CNN, proposed in the paper - Locate, Size and Count: Accurately Resolving People in Dense Crowds via Detection.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "MIT" ; sc:name "LSC-CNN" ; sc:url "https://github.com/val-iisc/lsc-cnn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:21097471" ; sc:description "This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to their functions in leaf senescence or morphological phenotypes. Users can browse or search the database to obtain information including literatures, mutants, phenotypes, expression profiles, miRNA interactions, orthologs in other plants and cross links to other databases." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2421, edam:operation_2422 ; sc:name "LSD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://psd.cbi.pku.edu.cn/" ; biotools:primaryContact "Jingchu Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Fast dating using least-squares criteria and algorithms" ; sc:name "LSD" ; sc:operatingSystem "Linux" ; sc:url "http://www.atgc-montpellier.fr/LSD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press" ; sc:featureList edam:operation_2409 ; sc:name "LSGSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mlab.cb.k.u-tokyo.ac.jp/~moris/LSGSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:12214313" ; sc:description "This tool superposes macromolecular electron densities and computes a structural similarity score. Its computations scale linearly with the size of the molecules being compared." ; sc:featureList edam:operation_2406 ; sc:name "LSim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.molspaces.com/d_lsim-overview.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769 ; sc:citation ; sc:description "Comprehensive drug discovery and genomic research workbench, knowledgebase and data management system." ; sc:featureList edam:operation_0484, edam:operation_2403, edam:operation_2497 ; sc:name "Life Science Knowledge Bank (LSKB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.lskb.w-fusionus.com" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:description "Read image data from Zeiss Laser Scanning Confocal Microscope LSM files." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Zeiss Laser Scanning Confocal Microscope LSM file reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46892-zeiss-laser-scanning-confocal-microscope-lsm-file-reader" ; biotools:primaryContact "CY Y" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "MATLAB functions for reading info databases of Zeiss LSM confocal microscope files." ; sc:isAccessibleForFree true ; sc:name "LSM File Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/8412-lsm-file-toolbox" ; biotools:primaryContact "Peter Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_3570 ; sc:citation , "pmcid:PMC10336029", "pubmed:37421399" ; sc:description "Scaling multimodal data integration for single-cell genomics data analysis." ; sc:featureList edam:operation_0335, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "LSMMD-MA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/google-research/large_scale_mmdma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "LSNMF (Least Squared Non-negative Matrix Factorization) is a modified version of NMF (non-negative matrix factorization), it focus on gene expression patterns analysis on microarray datasets. 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Large-Scale Transcriptome Analysis Pipeline on Cloud. If you use LSTrAP-Cloud in your research, please cite:. This repository is built upon wirriamm/CoNeGC. LSTrAP-Cloud is a pipeline designed for building co-expression networks from RNA-seq data (fastq files from ENA) on Goolge Colaboratory (Colab). Leveraging on the user-friendliness of the Colab interface, LSTrAP-Cloud allows users to analyse large scale transcriptome data without having to access the linux terminal, making it accessible to both bioinformaticians and biologist. To get started, we have provided a tutorial based on example data found here. While the pipeline was designed for plants, we have also made the script compatible with non-plant organisms.""" ; sc:featureList edam:operation_1781, edam:operation_2454, edam:operation_3463 ; sc:name "LSTrAP-Cloud" ; sc:url "https://github.com/tqiaowen/LSTrAP-Cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3299 ; sc:citation ; sc:description """An automated pipeline to generate annotated gene expression atlases for kingdoms of life. By NTU Plants Systems Biology and Evolution Laboratory.""" ; sc:featureList edam:operation_2428 ; sc:name "LSTrAP-Kingdom" ; sc:url "https://github.com/wirriamm/plants-pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC9750125", "pubmed:36321857" ; sc:description "LTM is an in silico screen to infer genetic influences on circadian clock function. LTM uses natural variation in gene expression data and directly links gene expression variation to clock strength independent of longitudinal data." ; sc:featureList edam:operation_3454, edam:operation_3463, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gangwug/LTMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0218, edam:topic_0625, edam:topic_3303, edam:topic_3336 ; sc:citation , "pubmed:35306140" ; sc:description "A comprehensive database for the linking of Traditional Chinese Medicine with modern medicine at molecular and phenotypic levels." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LTM-TCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cloud.tasly.com/#/tcm/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC9396797", "pubmed:35999499" ; sc:description "A transfer learning based end-to-end method for RNA secondary structure prediction." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "LTPConstraint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jluF/LTPConstraint.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0749, edam:topic_0780 ; sc:citation ; sc:description "Parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons | A parallel wrapper for LTR_FINDER | ~ ~ ~ Run LTR_FINDER in parallel ~ ~ ~ | This is a Perl wrapper for LTR_FINEDR. All rights reserved to the original author. It's free for non-commercial use. For commercial use, a software agreement is required for LTR_FINDER. LTR_FINDER_parallel is released under open source license CC BY 4.0" ; sc:name "LTR-FINDER-P" ; sc:url "https://github.com/oushujun/LTR_FINDER_parallel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_0749, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:17485477" ; sc:description "LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences." ; sc:featureList edam:operation_0237, edam:operation_0379 ; sc:name "LTR_Finder" ; sc:url "http://tlife.fudan.edu.cn/ltr_finder/" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "LTR_retriever" ; sc:url "https://github.com/oushujun/LTR_retriever" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3473, edam:topic_3511 ; sc:citation "pubmed:12584121" ; sc:description "New data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format." ; sc:featureList edam:operation_0239 ; sc:name "LTR_STRUC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.mcdonaldlab.biology.gatech.edu/ltr_struc.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0622 ; sc:citation , "pmcid:PMC5379124", "pubmed:28421083" ; sc:description "Efficient tool to characterize structurally complex LTR retrotransposons and nested insertions on genomes." ; sc:featureList edam:operation_0253 ; sc:name "LTRtype" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.plantkingdomgdb.com/LTRtype/index.html" ; biotools:primaryContact "Li-Zhi Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3063 ; sc:citation "pubmed:22556366" ; sc:description "Software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power." ; sc:featureList edam:operation_3659 ; sc:name "LTSOFT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.hsph.harvard.edu/alkes-price/software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3295 ; sc:citation "pubmed:17474879" ; sc:description "R package implementing the methods for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions." ; sc:featureList edam:operation_3658 ; sc:name "LUCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stat.sfu.ca/statgen/research/luca.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_3489 ; sc:description "LuceGene is an open-source document/object search and retrieval system specially tuned for bioinformatics text databases and documents. LuceGene is similar in concept to the widely used, commercially successful, bioinformatics program SRS (Sequence Retrieval System)." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "LuceGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://www.gmod.org/wiki/LuceGene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation "pubmed:25429062" ; sc:description "Site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data." ; sc:featureList edam:operation_3755 ; sc:name "Luciphor2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://luciphor2.sourceforge.net/" ; biotools:primaryContact "Alexey I. Nesvizhskii" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:name "DNA sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation ; sc:description "A program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly." ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3219 ; sc:license "GPL-2.0" ; sc:name "Lucy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "https://sourceforge.net/projects/lucy/" ; biotools:primaryContact "Hui-Hsien Chou", "Michael Holmes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:32049324" ; sc:description """Metagenome SNP Calling via Read Colored de Bruijn Graphs. LueVari is a reference free metagenome SNP caller, based on the read-colored de Bruijn graph. LuVari is an extension of VARI (https://github.com/cosmo-team/cosmo/tree/VARI), in which the reads are stored as colors to allow the read-coherent traversal of de Bruijn graph.""" ; sc:featureList edam:operation_0484, edam:operation_0524, edam:operation_3472 ; sc:name "LueVari" ; sc:url "https://github.com/baharpan/cosmo/tree/LueVari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3518 ; sc:citation , "pmcid:PMC1891274", "pubmed:17540033" ; sc:description "This package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. 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LUMINATE (longitudinal microbiome inference and zero detection) includes four programs for inference in longitudinal microbiome datasets:. Note: Estimates of cLV parameters with LUMINATE is considered experimental. To train model parameters using pseudo-counts instead of denoised estimates, pass the --use-pseudo-counts flag instead.""" ; sc:featureList edam:operation_3454, edam:operation_3565, edam:operation_3799 ; sc:name "LUMINATE" ; sc:url "https://github.com/tyjo/luminate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC7585198", "pubmed:33097024" ; sc:description """lumbar multifidus muscle segmentation from ultrasound images. 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Alex Taylor", "Rich Johnson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2905 ; sc:encodingFormat edam:format_3752 ; sc:name "Lipid accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153 ; sc:citation ; sc:description "The first method offering a metric to compare pairwise distances between complete lipidomics. 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Phung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3518 ; sc:citation ; sc:description "Normalization of Agilent miRNA arrays." ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "LVSmiRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/LVSmiRNA.html" ; biotools:primaryContact "Stefano Calza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:17877794" ; sc:description "Uses a simple language for describing features on a genome or biological sequence and provides a browsable image of these features." ; sc:featureList edam:operation_0337 ; sc:name "lwgv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lwgv.sourceforge.net/" ; biotools:primaryContact "Jeremiah Faith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3372 ; sc:citation "pubmed:22813356" ; sc:description "Customized Linux distribution for bioinformatics research. 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M²aia extends the open source Medical Imaging and Interaction Toolkit (MITK; https://www.mitk.org) and provides powerful methods that the MSI community can adopt, exploit and improve further. In it’s current state, it is designed to enable multi-modal 2D registration and 3D MSI reconstruction." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "M2aia" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , , , , ; sc:url "https://m2aia.github.io/m2aia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3335 ; sc:citation , "pmcid:PMC7579830", "pubmed:33087064" ; sc:description """Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model. Predicting MiRNA-disease Associations by Multiple Meta-paths Fusion Graph Embedding Model(M2GMDA). (1)M2GMDA.py:gereating meta-paths from the dataset of miRNA-disease associations,disease semantic similarity, miRNA functional similarity. all the result is saved in the folds named "5.mid result" and "6.meta path", which need to be created by yourselves.""" ; sc:featureList edam:operation_0463, edam:operation_3436, edam:operation_3927 ; sc:name "M2GMDA" ; sc:url "https://github.com/dangdangzhang/M2GMDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3697 ; sc:citation , "pubmed:32176258" ; sc:description """A web server for microbiome and metabolome integrative analysis. M2IA is a web-based server for the Microbiome and Metabolome data integration analysis. M2IA integrates a variety of statistical analysis methods, including univariate analysis, multivariate modeling, and functional network analysis. Users can upload data, customize parameters, and submit a job by one click. An html-based summarized report will be generated automatically for overview, accompanied by supporting tables and high-resolution figures available for downloading.""" ; sc:featureList edam:operation_3463, edam:operation_3659, edam:operation_3891, edam:operation_3927 ; sc:name "M2IA" ; sc:url "http://m2ia.met-bioinformatics.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071 ; sc:citation "pubmed:25346941" ; sc:description "Lightweight, easily pluggable, and extremely fast conversion software tool. 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It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles." ; sc:featureList edam:operation_0430 ; sc:license "Artistic-2.0" ; sc:name "M3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/M3D.html" ; biotools:primaryContact "Tom Mayo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3374, edam:topic_3474 ; sc:citation , "pubmed:32961295" ; sc:description """A novel machine learning approach for predicting the 3D printability of medicines. Select a tested drug product Example 1 Example 2 Example 3 Example 4 Load materials.""" ; sc:featureList edam:operation_3431 ; sc:name "M3DISEEN" ; sc:url "http://m3diseen.com/predictions/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells." ; sc:featureList edam:operation_2426, edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "M3Drop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/M3Drop.html" ; biotools:primaryContact "Tallulah Andrews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0102, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:17517764" ; sc:description "Comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments." ; sc:featureList edam:operation_0477, edam:operation_0492, edam:operation_0504, edam:operation_2429 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "M4T" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://manaslu.fiserlab.org/M4T/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3320, edam:topic_3512, edam:topic_3674 ; sc:citation , "pmcid:PMC8728298", "pubmed:34986603" ; sc:description "A database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome." ; sc:featureList edam:operation_0278, edam:operation_0314, edam:operation_0463, edam:operation_0502 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "m5C-Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.xjtlu.edu.cn/biologicalsciences/m5c-atlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0780, edam:topic_3170, edam:topic_3474, edam:topic_3500 ; sc:citation , , "pmcid:PMC7602301", "pubmed:33126851" ; sc:description """A novel method for predicting m5C sites of RNA. m5CPred-SVM: A webserver for predicting m5C sites of RNA based on SVM. A webserver for m5C Sites Identification of RNA. m5CPred-SVM was developed by using support vector machine based on six different kinds of features extracted from RNA sequences. Now it is for three different species including H. sapiens, M. musculus and A. thaliana. The benchmark datasets can be download here. The input for the server is the RNA sequence. More details can be found in the tutorial.""" ; sc:featureList edam:operation_0417, edam:operation_0433, edam:operation_0443 ; sc:name "m5CPred-SVM" ; sc:url "http://zhulab.ahu.edu.cn/m5CPred-SVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3295, edam:topic_3320, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC7595847", "pubmed:33230471" ; sc:description """A Web Server for the Prediction of RNA 5-Methyluridine Sites from Sequences. As one of the widely occurring RNA modifications, 5-methyluridine (m5U) has recently been shown to play critical roles in various biological functions and disease pathogenesis, such as, under stress response and during breast cancer development.""" ; sc:featureList edam:operation_0417, edam:operation_0443, edam:operation_2422 ; sc:name "m5UPred" ; sc:url "https://www.xjtlu.edu.cn/biologicalsciences/m5u" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC6498663", "pubmed:31046660" ; sc:description "Large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network." ; sc:featureList edam:operation_0417, edam:operation_3207, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:name "m6Acomet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://xjtlu.edu.cn/biologicalsciences/m6acomet" ; biotools:primaryContact "Jia Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:35314342" ; sc:description "Prediction of m6A regulated expression genes by integrating m6A sites and reader binding information in specific- context" ; sc:featureList edam:operation_2495, edam:operation_2575, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "m6 Aexpress-Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NWPU-903PR/m6AexpressReader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_2885, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC10768109", "pubmed:37587690" ; sc:description """Updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species. N6-methyladenosine (m6A) is the most abundant internal chemical modification on mRNAs and lncRNAs and has a broad function in biological metabolism. m6A-Atlas v2.0 was expanded to include 797,091 reliable m6A sites among 7 species , with 13 high-resolution technologies and 109 conditions.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3222, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "m6A-Atlas v2.0" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rnamd.org/m6a" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3295, edam:topic_3304, edam:topic_3512 ; sc:citation , "pmcid:PMC8599805", "pubmed:34417605" ; sc:description "Uncovering complex and condition-specific m6A regulation of gene expression." ; sc:featureList edam:operation_0417, edam:operation_3222, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "m6A-express" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Yufei-Huang-Lab/m6Aexpress" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3264 ; sc:name "COSMIC ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0659, edam:topic_2640, edam:topic_3295, edam:topic_3512 ; sc:citation ; sc:description "Unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues." ; sc:featureList edam:operation_0314, edam:operation_0331, edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "m6A-TSHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/m6ats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3320, edam:topic_3407, edam:topic_3512 ; sc:citation , "pubmed:32392583" ; sc:description """A comprehensive database for targets of m6A writers, erasers and readers. N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs""" ; sc:featureList edam:operation_2495 ; sc:name "m6A2Target" ; sc:url "http://m6a2target.canceromics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_0749, edam:topic_2640, edam:topic_3407 ; sc:citation , "pubmed:33906563" ; sc:description "m6ADD is a database containing manually collected experimentally confirmed m6A (N6-methyladenosine)-disease data and data obtained from high-throughput disease m6A modification profiles, aimed at exploring the association between m6A modified gene disorders and diseases" ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3223 ; sc:name "M6ADD" ; sc:url "http://m6add.edbc.org/" ; biotools:primaryContact "Yan Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_3295 ; sc:citation , "pubmed:35091075" ; sc:description "Analysis of m6A profile matrix based on graph regularized non-negative matrix factorization." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:name "m6Adecom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rnanut.net/m6adecom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8191635", "pubmed:34122525" ; sc:description "A Predictor for N6-Methyladenosine Sites Identification Utilizing Sequence Characteristics and Graph Embedding-Based Geometrical Information." ; sc:featureList edam:operation_0253, edam:operation_0337, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "m6AGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bokunoBike/m6AGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3047, edam:topic_3512 ; sc:citation , "pubmed:33540081" ; sc:description "Identifying RNA N6, 2'-O-dimethyladenosine (m6Am) sites based on sequence-derived information." ; sc:featureList edam:operation_0443 ; sc:name "m6AmPred" ; sc:url "https://www.xjtlu.edu.cn/biologicalsciences/m6am" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description "Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework." ; sc:featureList edam:operation_0314, edam:operation_3557, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "m6Anet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GoekeLab/m6anet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3474, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC7431669", "pubmed:32850851" ; sc:description """Epitranscriptome Target Prediction and Functional Characterization of a sequence-based N6-methyladenosine (m6A) modification site predictor. Among the various types of RNA modification, the methylation of adenosine at the N6 position (m6A) is characterized as the most abundant post-transcriptional modification in mRNA.""" ; sc:featureList edam:operation_0417, edam:operation_2422, edam:operation_2575 ; sc:name "m6Areader" ; sc:url "http://m6areader.rnamd.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0634, edam:topic_3373, edam:topic_3407 ; sc:citation , "pubmed:36134713" ; sc:description "A database for m6A-centered regulation of disease development and drug response." ; sc:featureList edam:operation_2421, edam:operation_2437, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "M6AREG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/m6areg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31504776" ; sc:description "Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing | Code and data associated with m7G-MaP-Seq paper" ; sc:featureList edam:operation_0417, edam:operation_0463, edam:operation_2495 ; sc:name "m7G-MaP-seq" ; sc:url "https://github.com/jeppevinther/m7g_map_seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885, edam:topic_3295, edam:topic_3512 ; sc:citation , "pubmed:32163126" ; sc:description """Deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Search by RsID, Gene, Region or Disease:. Links MeT-DB Whistle DRUM DRRMSDB. A database for the disease-associated genetic variants that may affect m7G sites.""" ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3222 ; sc:name "m7GHub" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/m7ghub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_3474 ; sc:citation , "pmcid:PMC6602427", "pubmed:31114883" ; sc:description "Machine learning computational tool designed to more accurately predict the effects of missense mutations on protein–protein interaction binding affinity." ; sc:featureList edam:operation_0331, edam:operation_2492, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "mCSM-PPI2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/mcsm_ppi2/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3398 ; sc:citation , "pubmed:31504182" ; sc:description "Gene relevance based on multiple evidences in complex networks | Noemi Di Nanni (1, 2), Matteo Gnocchi (1), Marco Moscatelli (1), Luciano Milanesi (1) and Ettore Mosca (1, *)" ; sc:featureList edam:operation_3223, edam:operation_3439, edam:operation_3501 ; sc:name "mND" ; sc:softwareVersion "0.1.7" ; sc:url "https://www.itb.cnr.it/mnd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3174, edam:topic_3697, edam:topic_3855 ; sc:citation , "pmcid:PMC6854712", "pubmed:31727118" ; sc:description """A novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. mPies: metaProteomics in environmental sciences. Werner, J., Géron, A., Kerssemakers, J. et al. mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation. Biol Direct 14, 21 (2019) doi: 10.1186/s13062-019-0253-x""" ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "mPies" ; sc:url "https://github.com/johanneswerner/mPies/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3572 ; sc:author ; sc:citation , "pubmed:30401579" ; sc:description "Quality visualization tool specific for ribosome profiling data" ; sc:featureList edam:operation_0447, edam:operation_3218, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mQC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.10" ; sc:url "https://github.com/Biobix/mQC" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3071, edam:topic_3518 ; sc:citation "pubmed:18430991" ; sc:description "This environment offers an interactive multi-user interface which includes all steps of a microarray study: from MIAME-compliant storage of experiments and raw data processing to analysis of differentially regulated genes. In addition, it offers functional insight into gene expression data by using an original approach combining biological knowledge annotation with gene expression data through interactive graph." ; sc:featureList edam:operation_2409 ; sc:name "M IA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://maia.genouest.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Comprehensive online resource to visualise mouse development and investigate gene expression in the mouse embryo." ; sc:featureList edam:operation_2422, edam:operation_2495 ; sc:name "ma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.emouseatlas.org/emap/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3518 ; sc:citation ; sc:description "Model-based Analysis of 2-Color Arrays is a model-based algorithm for analyzing 2-color microarrays.A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches." ; sc:featureList edam:operation_2238, edam:operation_2428, edam:operation_2495 ; sc:name "MA2C" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.1" ; sc:url "http://liulab.dfci.harvard.edu/MA2C/MA2C.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3377 ; sc:citation , "pubmed:37419308" ; sc:description "A Multi-Arm Two-Stage (MATS) design for proof-of-concept and dose optimization in early-phase oncology trials." ; sc:featureList edam:operation_0479, edam:operation_3454, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MATS" ; sc:url "https://matsdesign.shinyapps.io/mats/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "maanova" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.44.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/maanova.html" ; biotools:primaryContact "Keith Sheppard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC8356463", "pubmed:34376236" ; sc:description "MAAPER is a computational method for model-based analysis of alternative polyadenylation using 3’ end-linked reads. It uses a probabilistic model to predict polydenylation sites (PASs) for nearSite reads with high accuracy and sensitivity, and examines different types of alternative polyadenylation (APA) events, including those in 3’UTRs and introns, using carefully designed statistics." ; sc:featureList edam:operation_3192, edam:operation_3223, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MAAPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Vivianstats/MAAPER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3174 ; sc:description "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3435, edam:operation_3695 ; sc:license "Other" ; sc:name "MaAsLin2" ; sc:url "https://huttenhower.sph.harvard.edu/maaslin/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC10416524", "pubmed:37563669" ; sc:description "Genotyping thousands of microbial strains. Type SNPs from a set of whole genome assemblies and sequencing reads from beginning to end in one single command line." ; sc:featureList edam:operation_0484, edam:operation_0525, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Maast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zjshi/Maast" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , ; sc:description """An Integrated and Visual Tool for Microbiome Data Analyses. A Multifunctional and Visual Tool for Microbiomic Data Analyses.""" ; sc:featureList edam:operation_0337, edam:operation_0524, edam:operation_3192, edam:operation_3460 ; sc:name "MAAWf" ; sc:url "http://www.maawf.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269 ; sc:citation , , "pmcid:PMC3517402", "pubmed:22932419", "pubmed:28881959" ; sc:description "Simulating continuous/discrete time Markov processes, applied on a Boolean network." ; sc:featureList edam:operation_3562 ; sc:name "MaBoSS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://maboss.curie.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:34935911" ; sc:description "Marker-based automatic cell-type annotation for single cell expression data" ; sc:featureList edam:operation_0313, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MACA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ImXman/MACA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0632, edam:topic_2885, edam:topic_3170 ; sc:citation , "pmcid:PMC9646992", "pubmed:36388568" ; sc:description "A comprehensive platform for germplasm innovation and functional genomics in Macadamia." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_3182, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MacadamiaGGD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://MacadamiaGGD.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3307, edam:topic_3344 ; sc:citation , "pmcid:PMC29726922", "pubmed:29726922" ; sc:description "MACARON (Multi-bAse Codon-Associated variant Re-annotatiON) is a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data. Starting from a standard VCF file, MACARON identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon." ; sc:featureList edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MACARON" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.6" ; sc:url "http://www.genmed.fr/index.php/fr/recherche/publications" ; biotools:primaryContact "Waqasuddin Khan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:34864867" ; sc:description "Macarons is an algorithm designed to recover single nucleotide polymorphisms (SNPs) that are related with a phenotype in genome wide association studies (GWAS) by taking into account of the dependencies between them." ; sc:featureList edam:operation_3196, edam:operation_3661, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Macarons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/serhan-yilmaz/macarons" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0203, edam:topic_3053 ; sc:citation , "pubmed:15572464" ; sc:description "This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It implements an statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia." ; sc:featureList edam:operation_0315, edam:operation_2478 ; sc:license "Artistic-2.0" ; sc:name "macat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/macat.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3172, edam:topic_3300 ; sc:citation , "pmcid:PMC10767829", "pubmed:37897362" ; sc:description "Visual interactive knowledgebase of metabolite-associated cell communications." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:name "MACC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://macc.badd-cao.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:2606395" ; sc:description "Computer program for phylogenetic analysis. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts." ; sc:featureList edam:operation_0324 ; sc:name "MacClade" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://macclade.org/index.html" ; biotools:primaryContact "David Maddison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3068, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC10320464", "pubmed:37027007" ; sc:description "A curated knowledgebase for metabolic associations across human cancers." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2422, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "MACdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://ngdc.cncb.ac.cn/macdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3071, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:35576088" ; sc:description "An Open Access Data Repository of Mass Spectra for Chemical Ecology." ; sc:featureList edam:operation_3431, edam:operation_3801, edam:operation_3803, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "MACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.oc.tu-bs.de/schulz/html/MACE.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3572 ; sc:citation , "pmcid:PMC8443542", "pubmed:34594153" ; sc:description "Molecular Acquisition, Cleaning, and Evaluation in R (MACER) is an R package to assist biological researchers in assembling taxonomically and marker focused molecular sequence data set." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MACER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/rgyoung6/MACER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3055, edam:topic_3516 ; sc:citation , "pmcid:PMC3175618", "pubmed:21058334" ; sc:description "Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals." ; sc:featureList edam:operation_0487, edam:operation_3557 ; sc:license "Not licensed" ; sc:name "MACH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://csg.sph.umich.edu/abecasis/mach/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC3524415", "pubmed:23074066" ; sc:description "Genotype imputation software that extends the capabilities of MaCH 1.0. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual. This reference selection method generates better imputation quality in shorter running time. It also separates model parameter estimation from imputation. 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MACPET reads ChIA-PET data in BAM or SAM format and separates the data into Self-ligated, Intra- and Inter-chromosomal PETs. Furthermore, MACPET breaks the genome into regions and applies 2D mixture models for identifying candidate peaks/binding sites using skewed generalized students-t distributions (SGT). 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In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). 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A Tool for Multiple Accessions' Distinguishing through Hierarchical Decision Tree.""" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_0487, edam:operation_2422, edam:operation_3196 ; sc:name "MAD-HiDTree" ; sc:url "https://bioinfo.noble.org/MAD-HiDTree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3452, edam:topic_3474, edam:topic_3954 ; sc:citation , "pubmed:33222222" ; sc:description """A deep U-shaped network combined with an attention mechanism for pancreas segmentation in CT images. Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras.""" ; sc:featureList edam:operation_3435, edam:operation_3937 ; sc:license "MIT" ; sc:name "MAD-UNet" ; sc:url "https://github.com/Mrqins/pancreas-segmentation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3047, edam:topic_3071 ; sc:citation , "pubmed:36656159" ; sc:description "The Martini Database (MAD) is a web server dedicated to (a) sharing structures and topologies of molecules parameterized with the Martini coarse-grained (CG) force field; (b) converting atomistic structures into CG structures; (c) preparing complex systems (including proteins, nucleic acids, lipids etc.) for molecular dynamics (MD) simulations at the CG level." ; sc:featureList edam:operation_0477, edam:operation_2476, edam:operation_3893 ; sc:isAccessibleForFree true ; sc:name "MAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mad.ibcp.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9371110", "pubmed:35957406" ; sc:description "An Open-Source Python Package for Annotation and Analysis of Time-Series Data." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3565 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MaD GUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sonarcloud.io/component_measures?id=MalteOlle_mad-gui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_0769, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC7672854", "pubmed:33203349" ; sc:description """A web service for analysing DNA methylation array data. MADA is developed for the whole process of methylation array data analysis""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3204, edam:operation_3435 ; sc:name "MADA" ; sc:url "http://bioinformatics.csu.edu.cn/MADA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3168, edam:topic_3179, edam:topic_3512 ; sc:citation "pubmed:14681364", "pubmed:17526516" ; sc:description "MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. 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The Maryland Analysis of Developmental EEG (MADE) Pipeline. Version 1.0. Developed at the Child Development Lab, University of Maryland, College Park.""" ; sc:featureList edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "MADE" ; sc:url "https://github.com/ChildDevLab/MADE-EEG-preprocessing-pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3518 ; sc:citation , "pubmed:15797915" ; sc:description "Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4." ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:license "Artistic-2.0" ; sc:name "made4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/made4.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_2640, edam:topic_3053 ; sc:citation "pubmed:25573922" ; sc:description "This R package fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver." ; sc:featureList edam:operation_3658 ; sc:name "MADGiC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.biostat.wisc.edu/~kendzior/MADGiC/" ; biotools:primaryContact "Keegan Korthauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3473, edam:topic_3518, edam:topic_3557 ; sc:citation "pubmed:18480121" ; sc:description "Data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. 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MAELASviewer: Online visualization of magnetostriction. MAELASviewer is an online tool to visualize magnetostriction. This interactive applet shows the magnetostriction for some crystal systems. You can simulate the Joule and Wiedemann effects. 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Motifs from Annotated Groups in Alignments. MAGA is a new simpler way to infer information from alignments. Based on a regular procedure usually done visually by experts, it looks for group-conserved residues in an alignment. 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Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis." ; sc:featureList edam:operation_0337, edam:operation_2424, edam:operation_2428, edam:operation_2436, edam:operation_2497, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "MAGeCKFlute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html" ; biotools:primaryContact "Wubing Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3365, edam:topic_3473 ; sc:citation ; sc:description "An online tool that facilitates curation of MAGE-TAB. It combines text-mining and the Experimental Factor Ontology (EFO) to create a semi-automatic environment for faster annotation, guided data-manipulation and content summary." ; sc:featureList edam:operation_0226 ; sc:name "MageComet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/fgpt/sw/magecomet" ; biotools:primaryContact "Helen Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3056 ; sc:citation , "pmcid:PMC5018160", "pubmed:27613390" ; sc:description "MaGelLAn is a software that facilitates quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information" ; sc:featureList edam:operation_2403 ; sc:license "Other" ; sc:name "MaGelLAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://lissp.irb.hr/software/magellan-1-0/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:36086594" ; sc:description "A multi-agent architecture for feature selection, called MAgentOmics, to consider all omics data together. MAgentOmics extends the ant colony optimization algorithm to multi-omics data, which iteratively builds candidate solutions and evaluates them. Moreover, a new fitness function is introduced to assess the candidate feature subsets without using prediction target such as survival time of patients." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MAgentOmics" ; sc:url "https://github.com/SinaTabakhi/MAgentOmics" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_2330 ; sc:name "Resource metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_1930 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2573, edam:format_3016 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0634 ; sc:citation ; sc:description "A software for analyzing UMI-tagged data for detecting ultra-rare variants." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MAGERI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mikessh/mageri" ; biotools:primaryContact "Dmitriy M. Chudakov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0749, edam:topic_3169, edam:topic_3173 ; sc:citation ; sc:description """Leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. MAGGIE provides a framework for identifying DNA sequence motifs mediating transcription factor binding and function. By leveraging measurements and genetic variation information from different genotypes (human individuals, animal strains, or alleles), MAGGIE associates the mutation of DNA sequence motif with various types of epigenomic features, including but not limited to transcription factor binding, open chromatin, histone modification, and stimulus response of regulatory elements.""" ; sc:featureList edam:operation_0445, edam:operation_3196, edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "MAGGIE" ; sc:url "https://github.com/zeyang-shen/maggie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3345, edam:topic_3366 ; sc:author , ; sc:description "Sharing descriptive metadata is the first essential step towards the “Open Data” approach. With this in mind, the Maggot tool was specially designed to allow users to easily add descriptive metadata to datasets produced within a collective (research unit, platform, multi-partner project, etc.), thus promoting the sharing of metadata within this same collective and beyond." ; sc:featureList edam:operation_2429, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Maggot" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://inrae.github.io/pgd-mmdt/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3070 ; sc:citation "pubmed:25881248" ; sc:description "Single-animal tracking system for Drosophila larval locomotion analysis." ; sc:featureList edam:operation_2945 ; sc:name "MaggotTracker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wormloco.org/mag/doc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3053 ; sc:citation "pubmed:26020500" ; sc:description "Publicly available web application to explore and annotate cancer genomics data." ; sc:featureList edam:operation_0226 ; sc:name "MAGI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://magi.brown.edu/" ; biotools:primaryContact "Raphael Lab, Princeton University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0622, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc:description "Merging affected genes into integrated networks - multiple seeds: Seed-centric module discovery using multiple seeds." ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MAGI-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jchow32/MAGI-MS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:20484379", "pubmed:22618880" ; sc:description "Web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene expression data." ; sc:featureList edam:operation_0314, edam:operation_0438, edam:operation_1781, edam:operation_2495, edam:operation_3439 ; sc:name "MAGIA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gencomp.bio.unipd.it/magia2/start/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:name "Gene transcript report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3308 ; sc:citation ; sc:description "Access portal to a cross-platform gene expression compendium for maize." ; sc:featureList edam:operation_2495 ; sc:name "Magic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/magic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "MAGIC (Multi-scAle heteroGeneity analysIs and Clustering) is a multi-scale semi-supervised clustering method that aims to derive robust clustering solutions across different scales for brain diseases." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:license "MIT" ; sc:name "MAGIC" ; sc:url "https://github.com/anbai106/MAGIC" ; biotools:primaryContact "Christos Davatzikos", "Junhao Wen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3179, edam:topic_3308 ; sc:citation , "pmcid:PMC7162552", "pubmed:32251445" ; sc:description """A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. The manuscript accompanying this script is: MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data. Roopra, A. 2020 PLoS Computational Biology.""" ; sc:featureList edam:operation_0372, edam:operation_2436, edam:operation_3802 ; sc:name "MAGIC_Encode" ; sc:url "https://go.wisc.edu/magic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_3520 ; sc:citation , "pubmed:25629585" ; sc:description "Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach." ; sc:featureList edam:operation_3631 ; sc:name "MAGIC" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ms.iis.sinica.edu.tw/COmics/Software_MAGIC.html" ; biotools:primaryContact "T.-Y. Sung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3047, edam:topic_3318, edam:topic_3382 ; sc:citation , "pubmed:34445865" ; sc:description "Navigation in the Ring Chemical Space Guided by the Bioactive Rings." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Magic Rings" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bit.ly/magicrings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "MAGIC Tool is an integrated microarray data analysis software." ; sc:featureList edam:operation_2495, edam:operation_3432 ; sc:name "MAGIC Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://www.bio.davidson.edu/projects/magic/magic.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3337, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC9674945", "pubmed:36198314" ; sc:description "Machine-learning-based genotype imputation quality calibration." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MagicalRsq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/quansun98/MagicalRsq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3676 ; sc:citation ; sc:description "Large-scale short reads and sequencing depth visualization." ; sc:featureList edam:operation_0337, edam:operation_0484 ; sc:name "MagicViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.zj.cn/magicviewer/index.php" ; biotools:primaryContact "Erle Zhu", "Huabin Hou", "Jinyu Wu", "Linglin Zhou", "Zhongsheng Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3473, edam:topic_3510 ; sc:citation "pubmed:16845025" ; sc:description "MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented." ; sc:featureList edam:operation_2479, edam:operation_3092 ; sc:name "MAGIIC-PRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biominer.bime.ntu.edu.tw/magiicpro/" ; biotools:primaryContact "Chien-Yu Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3170, edam:topic_3172, edam:topic_3308 ; sc:citation ; sc:description """A computational framework to explore cellular response mechanisms from multi-omics datasets. MAGINE : Mechanism of Action Generator involving Network Analysis. MAGINE is a framework for the analysis of quantitative multi-omics data. It was designed to handle multi-sample (time points) and multi-omics (rnaseq, label-free proteomics, etc). Users are provided access to tools driven around their experimental data. Provides access to enrichment analysis, biological network construction and various visualization methods.""" ; sc:featureList edam:operation_3501, edam:operation_3638, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "MAGINE" ; sc:softwareHelp ; sc:url "https://github.com/lolab-vu/magine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:17517778" ; sc:description "This tool can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3463 ; sc:name "MAGMA" ; sc:url "http://www.magma-fgcz.unizh.ch/pages/loginuser.jsf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0204, edam:topic_0602 ; sc:citation "pubmed:22300316" ; sc:description "Fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes" ; sc:featureList edam:operation_0238, edam:operation_0438 ; sc:name "Magma" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://stormo.wustl.edu/Magma/" ; biotools:primaryContact "Gary D. Stormo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3172, edam:topic_3375, edam:topic_3407 ; sc:citation , "pmcid:PMC9685347", "pubmed:36467581" ; sc:description "MagMD is a database mainly describing the interactions between human gut microbes, enzymes and active substances. Later, we may add some prediction results of the interaction of gut microbes, enzymes and active substances(mainly pharmaceutical)." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MagMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.unimd.org/magmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3444 ; sc:citation , "pubmed:37265034" ; sc:description "A fully automated web server for targeted nuclear magnetic resonance metabolomics of plasma and serum." ; sc:featureList edam:operation_3454, edam:operation_3799, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:name "MagMet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://magmet.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3299 ; sc:citation "pubmed:25792552" ; sc:description "Software tool for pairwise global network alignment. It is an extension of MAGNA. An example of an application domain where this tool is useful is computational biology – It can be used for biological network alignment." ; sc:featureList edam:operation_2425 ; sc:name "MAGNA++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www3.nd.edu/~cone/MAGNA++/" ; biotools:primaryContact "Tijana Milenkovic, Ph.D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_3444, edam:topic_3518 ; sc:citation "pubmed:22669910" ; sc:description "Microarray Gene Expression and Network Evaluation Toolkit (MAGNET) is a web tool with three components: generation of coexpression networks, weighted protein-protein interaction networks and bimodality of coexpression." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:name "MAGNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://magnet.case.edu" ; biotools:primaryContact "Gürkan Bebek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3444 ; sc:description "Efficient method to measure the magnetic susceptibility of the materials with arbitrary shape using B0 inhomogeneity map." ; sc:isAccessibleForFree true ; sc:name "Magnetic susceptibility measurement" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70296-the-codes-for-measuring-magnetic-susceptibility" ; biotools:primaryContact "Seon ha Hwang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3335 ; sc:citation , "pmcid:PMC9641957", "pubmed:36345035" ; sc:description "An interactive web application to explore transcriptome signatures of heart failure." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3695, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Magnetique" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny.dieterichlab.org/app/magnetique" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3050, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:35703559" ; sc:description "An automated workflow for genome-resolved metagenomics" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3192, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MAGNETO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3512 ; sc:citation "pubmed:18515348" ; sc:description "MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the data, and searches for a specific evolutionary pattern." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0504, edam:operation_2478 ; sc:name "MAGNOLIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.lifl.fr/magnolia" ; biotools:primaryContact "Magnolia team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3366 ; sc:citation ; sc:description "MAGPIE is a web server application that enables researchers from different domains to publish, exchange and execute models on-line, as well as publish and exchange data." ; sc:featureList edam:operation_0335, edam:operation_3436, edam:operation_3664, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MAGPIE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://magpie.imb.medizin.tu-dresden.de/" ; biotools:primaryContact "Christoph Baldow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:21254215" ; sc:description "Software which was developed for predicting highly polymorphic gene alleles using unphased SNP data." ; sc:featureList edam:operation_0253 ; sc:name "MAGprediction" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://qge.fhcrc.org/MAGprediction/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "MAGpy is a Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs)." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_0558 ; sc:name "MAGpy" ; sc:url "https://github.com/WatsonLab/MAGpy" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091 ; sc:citation , "pubmed:33252662" ; sc:description """Multiple Sequence Alignment using Graph Clustering. A few basic ways of running MAGUS are shown below. MAFFT (linux version is included).""" ; sc:featureList edam:operation_0291, edam:operation_0492, edam:operation_3454 ; sc:name "MAGUS" ; sc:url "https://github.com/vlasmirnov/MAGUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3512 ; sc:citation ; sc:description "This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "maigesPack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/maigesPack.html" ; biotools:primaryContact "Gustavo H. Esteves" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0611, edam:topic_2814 ; sc:citation , "pubmed:32621234" ; sc:description """Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin. MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map. MAINMAST is a fully automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. This new de novo modeling method has several advantages; (1) It does not require reference structures; (2) It does not requre manual interventions; (3) a pool of candidate models are generated.""" ; sc:featureList edam:operation_0302, edam:operation_0477, edam:operation_0495, edam:operation_2429 ; sc:name "MAINMAST" ; sc:url "http://kiharalab.org/mainmast/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0736, edam:topic_3382 ; sc:citation , "pubmed:32197044" ; sc:description """Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map. MAINMAST is a fully automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. This new de novo modeling method has several advantages; (1) It does not require reference structures; (2) It does not requre manual interventions; (3) a pool of candidate models are generated.""" ; sc:featureList edam:operation_0477, edam:operation_2429 ; sc:name "MAINMASTseg" ; sc:url "http://kiharalab.org/mainmast_seg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3063, edam:topic_3263 ; sc:citation , "pubmed:32871006" ; sc:description """Privacy-Preserving Record Linkage using Secure Multi-Party Computation. This repository is a fork of the official Mainzelliste project, embodying the features described in the paper “Mainzelliste SecureEpiLinker (MainSEL): Privacy-Preserving Record Linkage using Secure Multi-Party Computation”. It is intended that these new features will eventually be integrated back into the official Mainzelliste software.: https://bitbucket.org/medicalinformatics/mainzelliste/src.""" ; sc:featureList edam:operation_0283, edam:operation_2422 ; sc:license "AGPL-3.0" ; sc:name "MainSEL" ; sc:url "https://github.com/medicalinformatics/MainzellisteSEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3377 ; sc:citation , "pubmed:34042740" ; sc:description "MainzelHandler is library for a simple integration and usage of the Mainzelliste, a web-based first-level pseudonymization service." ; sc:license "MIT" ; sc:name "MainzelHandler" ; sc:url "https://github.com/DanielPreciado-Marquez/MainzelHandler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3047, edam:topic_3474 ; sc:citation ; sc:description """A web service for predicting blood-stage malaria inhibitors. Prediction platform to give access to a consensus approach of anti-malaria models.s. MAlaria Inhibitor Prediction platform. The malaria inhibitor prediction (MAIP) platform is the result of a public-private collaboration whose aim is to develop a consensus model for predicting blood stage malaria inhibition. Five Pharma and not-for-profit partners trained a model (using code developed by EMBL-EBI) on their private datasets. The resulting models were combined by EMBL-EBI and made available through this public prediction platform.""" ; sc:featureList edam:operation_3431, edam:operation_3935, edam:operation_3938 ; sc:name "MAIP" ; sc:url "https://www.ebi.ac.uk/chembl/maip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0219, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:33961227" ; sc:description "MAISEN is the first web tool to combine advantages of automatic and manual genome annotation. MAISEN lets you browse results of many functional annotation programs in one place." ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_2454, edam:operation_3192 ; sc:name "MAISEN" ; sc:url "http://maisen.ddlemb.com" ; biotools:primaryContact "Lukasz Dziewit" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "Fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms." ; sc:featureList edam:operation_0477 ; sc:name "Maistas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareVersion "1.0" ; sc:url "http://maistas.bioinformatica.crs4.it/" ; biotools:primaryContact "Domenico Raimondo", "Matteo Floris" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3650 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3361 ; sc:citation , "pmcid:PMC4071204", "pubmed:24642061" ; sc:description "This package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions." ; sc:featureList edam:operation_2238, edam:operation_3215 ; sc:license "GPL-2.0" ; sc:name "MAIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MAIT.html" ; biotools:primaryContact "Francesc Fernandez-Albert" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2798 ; sc:name "MaizeDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780 ; sc:citation ; sc:description "Biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information." ; sc:featureList edam:operation_0224 ; sc:name "Maize genetics and genomics database (MaizeGDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.maizegdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0798 ; sc:citation "pubmed:12824388" ; sc:description "This tool is designed to facilitate automated analysis of miniature inverted repeat transposable elements (MITEs)." ; sc:featureList edam:operation_2481 ; sc:name "MAK" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://perl.idmb.tamu.edu/mak.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web." ; sc:featureList edam:operation_3443, edam:operation_3630 ; sc:name "Make2D-DB II" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://world-2dpage.expasy.org/make2ddb/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2546 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2546 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:description "Generate random database through Markov process." ; sc:featureList edam:operation_0364 ; sc:license "GPL-3.0" ; sc:name "make_random" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.ms-utils.org/make_random.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3321 ; sc:citation ; sc:description "This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "makecdfenv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/makecdfenv.html" ; biotools:primaryContact "James W. MacDonald" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7056914", "pubmed:32001327" ; sc:description """Fully Automated Generation of UCSC Genome Browser Assembly Hubs. MakeHub is a command line tool for the fully automatic generation of of track data hubs1 for visualizing genomes with the UCSC genome browser2. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3208 ; sc:license "GPL-3.0" ; sc:name "MakeHub" ; sc:url "https://github.com/Gaius-Augustus/MakeHub" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Create random nucleotide sequences." ; sc:featureList edam:operation_0364 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "makenucseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/makenucseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Create random protein sequences." ; sc:featureList edam:operation_0364 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "makeprotseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/makeprotseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654 ; sc:citation , , "pmcid:PMC2134774", "pmcid:PMC3280279", "pubmed:18025269", "pubmed:22192575" ; sc:description "Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases." ; sc:featureList edam:operation_0362 ; sc:license "Artistic-2.0" ; sc:name "MAKER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.yandell-lab.org/software/maker.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3168 ; sc:description "Pipeline designed to annotate novel plant genomes and is build on the MAKER annotation tool. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes." ; sc:featureList edam:operation_0362 ; sc:license "Artistic-2.0" ; sc:name "MAKER-P" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.yandell-lab.org/software/maker-p.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation , ; sc:description "Create a .png file with distribution of peaks heights for ChIP and Control sample." ; sc:featureList edam:operation_0415 ; sc:name "makestatschipseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/makestatschipseq/makeStatsChIPSeq/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3508 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation , ; sc:description "Get peak distribution around TSS." ; sc:featureList edam:operation_3222 ; sc:name "maketssdist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/maketssdist/makeTSSdist/1.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3335, edam:topic_3403, edam:topic_3421, edam:topic_3422 ; sc:citation , "pmcid:PMC7857831", "pubmed:33564433" ; sc:description """Development and internal validation of a prediction model for hospital-acquired acute kidney injury. ACUTE KIDNEY INJURY RISK CALCULATOR. MAKIPS ACUTE KIDNEY INJURY RISK CALCULATOR.""" ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659 ; sc:name "MAKIPS" ; sc:url "http://www.bioestadistica.net/MAKIPS.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc:description "Mako is a bottom-up guided model-free CSV detection tool. It first builds a mutational signal graph and utilizes pattern growth to detect maximal subgraphs as CSVs." ; sc:featureList edam:operation_0452, edam:operation_3198, edam:operation_3963 ; sc:name "Mako" ; sc:softwareHelp , ; sc:url "https://github.com/xjtu-omics/Mako" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0601, edam:topic_3474 ; sc:citation , "pmcid:PMC7682087", "pubmed:33225896" ; sc:description """Computational prediction of protein Malonylation sites via machine learning based feature integration. Mal-Prec is a supervised machine learning classification to predict malonylated sites. In Mal-Prec, three encoding method including One-hot encoding, physiochemical properties (AAindex), and composition of k-spaced acid pairs (CKSAAP) were initially performed to extract sequence features. PCA was then applied to select optimal feature subsets while SVM was adopted to predict the malonylation sites. Five-fold cross-validation test and independent test results showed that Mal-Prec can achieve better prediction performance compared with other approaches.""" ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_3645, edam:operation_3891, edam:operation_3935 ; sc:name "Mal-Prec" ; sc:url "https://github.com/flyinsky6/Mal-Prec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Designed for the analysis of Microarray data. The rational data representing the gene expressions is discretized into a limited number of intervals for each cell of the array; the obtained discrete variables are then used to select a small subset of the genes that have strong discriminating power for the considered classes. The optimization algorithms for feature selection and logic formula extraction are then used to identify networks of genes that characterize the classes." ; sc:featureList edam:operation_2495 ; sc:name "MALA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dmb.iasi.cnr.it/mala.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2269, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC7394446", "pubmed:32692749" ; sc:description """Bayesian modelling of high-throughput sequencing assays with malacoda. The goal of malacoda is to enable Bayesian analysis of high-throughput genomic assays like massively parallel reporter assays (MPRA) and CRISPR screens.""" ; sc:featureList edam:operation_0362, edam:operation_3200, edam:operation_3227 ; sc:name "malacoda" ; sc:url "http://github.com/andrewGhazi/malacoda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510 ; sc:citation "pubmed:20556859" ; sc:description "A program for automatic detection of aligned blocks in multiple protein alignment." ; sc:featureList edam:operation_0492 ; sc:name "Malakite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mouse.belozersky.msu.ru/tools/malakite.html" ; biotools:primaryContact "Russian Foundation for Basic Research" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_2258 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "BLAST search against protein targets stored in Malaria Data database." ; sc:featureList edam:operation_0346 ; sc:name "Malaria Data BLAST Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/malaria/target" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2258 ; sc:author "ChEMBL Team" ; sc:citation ; sc:description "Search against small molecules stored in Malaria Data database." ; sc:featureList edam:operation_0339 ; sc:name "Malaria Data Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/chembl/malaria/compound" ; biotools:primaryContact "Mark Davies" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3173, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "Association testing of bisulfite sequencing methylation data via a Laplace approximation." ; sc:featureList edam:operation_3204 ; sc:name "MALAX" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/omerwe/MALAX" ; biotools:primaryContact "Eran Halperin", "Omer Weissbrod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:37551970" ; sc:description "Package for standardized implementation of batch correction methods for omics data." ; sc:featureList edam:operation_3359, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "malbacR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pmartR/malbacR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC8278594", "pubmed:34261498" ; sc:description "A web-based application for gene regulatory network analysis in Plasmodium falciparum." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2428, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MALBoost" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://malboost.bi.up.ac.za" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:author , ; sc:citation ; sc:description "MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions." ; sc:featureList edam:operation_0337, edam:operation_3215, edam:operation_3627, edam:operation_3799, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MALDIquant" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=MALDIquant" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3360, edam:topic_3520 ; sc:citation , "pubmed:37043374" ; sc:description "R package and Shiny app for more specific identification of MALDI imaging proteolytic peaks using LC-MS/MS-based proteomic biomarker discovery data." ; sc:featureList edam:operation_3643, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MALDImID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biosciences.shinyapps.io/Maldimid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation , "pmcid:PMC2042066", "pubmed:17601805" ; sc:description "A tool to quantify MALDI peptides (SILAC) from Phenyx output" ; sc:featureList edam:operation_3630 ; sc:name "MALDIPepQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/maldipepquant/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3056 ; sc:citation , "pmcid:PMC1182107", "pubmed:15386213" ; sc:description "Admixture mapping of complex trait loci, using case-control data." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "MALDsoft" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.stanford.edu/group/pritchardlab/software/maldsoft_download.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:citation "pubmed:26637292" ; sc:description "Tool for aligning molecular or insilico restriction maps to a reference map." ; sc:featureList edam:operation_0292 ; sc:name "Maligner" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/LeeMendelowitz/maligner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3511 ; sc:description "Program for screening 16S rRNA clone libraries, and similar multiple sequence alignments for chimeras and other anomalies.The program is based on the Pintail algorithm which works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene." ; sc:featureList edam:operation_0224 ; sc:name "Mallard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.02" ; sc:url "http://www.softsea.com/review/Mallard.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3277, edam:topic_3411 ; sc:citation , "pmcid:PMC9714854", "pubmed:36454982" ; sc:description "Automated landmarking through pointcloud alignment and correspondence analysis." ; sc:featureList edam:operation_2939, edam:operation_3891, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:name "MALPACA" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SlicerMorph/Tutorials/tree/main/ALPACA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "MaLTA is a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data." ; sc:featureList edam:operation_0310, edam:operation_3258 ; sc:name "MaLTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://alan.cs.gsu.edu/NGS/?q=malta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0769, edam:topic_3172, edam:topic_3372 ; sc:citation ; sc:description "Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. Its aim is to provide reusable, efficient datastructures, abstracting from the various low-level data-formats like netcdf, mzXML, mzData and mzML and providing consistent access to data features like mass spectra, chromatograms and metadata." ; sc:featureList edam:operation_2409 ; sc:name "Maltcms" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0" ; sc:url "http://maltcms.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2305 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3796 ; sc:citation , ; sc:description """MALVIRUS is a fast and accurate tool for genotyping haploid individuals that does not require to assemble the read nor mapping them to a reference genome. It is tailored to work with virological data and can genotype an individual directly from sequencing data in minutes. MALVIRUS is divided into two logically distinct steps: the creation of a variant catalog from a set of assemblies and the genotype calling. The first step is based on mafft and snp-sites, whereas the second step is based on KMC and MALVA. The variant catalog can be built once and reused for genotyping multiple individuals. Please see the website for additional details. MALVIRUS is distributed as a Docker image and is publicly available on GitHub and Docker Hub under the terms of the GNU General Public License version 3 or later. MALVIRUS was mainly developed and tested under Ubuntu GNU/Linux version 18.04 but works wherever Docker is available.""" ; sc:featureList edam:operation_0484 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MALVIRUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.1" ; sc:url "https://algolab.github.io/MALVIRUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0157, edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:15980474" ; sc:description "Takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0499, edam:operation_3182 ; sc:name "MaM" ; sc:url "http://compbio.cs.sfu.ca/MAM.htm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:encodingFormat edam:format_2330 ; sc:name "Locus ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Monoallelic DNA-methylation pipeline for enrichment-based sequencing technologies." ; sc:featureList edam:operation_3204 ; sc:name "MAM-pipeline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.biobix.be/mam/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description """Perception of Chemical Bonds via Machine Learning. A tool for the perception of chemical bonds via machine learning. A python tool for the perception of chemical bonds via machine learning. Internally uses RDKit, numpy, pandas and scikit-learn python packages.""" ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3893 ; sc:license "BSD-3-Clause" ; sc:name "mamba" ; sc:url "https://github.com/CHLoschen/mamba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:33980133" ; sc:description "MAmBA is an analysis pipeline to assess m5C in microRNAs following Bisulfite small RNA sequencing. Bisulphite miRNA-seq reveals widespread CpG and non-CpG 5-(hydroxy)methyl-Cytosine in human microRNAs." ; sc:featureList edam:operation_0463, edam:operation_3192, edam:operation_3792, edam:operation_3919 ; sc:license "MIT" ; sc:name "MAmBA" ; sc:url "https://github.com/flcvlr/MAmBA" ; biotools:primaryContact "Valerio Fulci" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_3706 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3617 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3174, edam:topic_3473, edam:topic_3697 ; sc:citation ; sc:description "MAMBO (Metabolomic Analysis of Metagenomes using fBa and Optimization) is an algorithm which assesses and optimizes correlations between genome-scale, constraint-based metabolic models and microbial abundance profiles obtained from shotgun sequence data." ; sc:featureList edam:operation_0226, edam:operation_3465, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MAMBO" ; sc:softwareHelp ; sc:url "https://github.com/danielriosgarza/MAMBO" ; biotools:primaryContact "Bas E. Dutilh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description """An automated machine learning pipeline with a microbiome repository for human disease classification. Flowchart of the mAML pipeline. Two files indicated at the beginning of the pipeline should be submitted to the mAML web server. Operation steps before training are indicated in the blue inverse-trapezoids. Automated machine learning model building pipeline for microbiome data.""" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "mAML" ; sc:url "https://github.com/yangfenglong/mAML1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2815, edam:topic_3168, edam:topic_3512 ; sc:citation , , "pmcid:PMC139241", "pubmed:10521335", "pubmed:12477932" ; sc:description "Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Mammalian Gene Collection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://mgc.nci.nih.gov/" ; biotools:primaryContact "National Institute of Health" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3382 ; sc:description "cancer cell localization using image processing matlab function" ; sc:featureList edam:operation_3443, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "mammogram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/40653-mammogram" ; biotools:primaryContact "deepukv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382 ; sc:description "Enhancement of mammogran images for clear view of pictorial muscles and cancer affected region" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Mammogram image enhancement" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50281-mammogram-image-enhancement" ; biotools:primaryContact "Darshan Yogendra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3175, edam:topic_3474 ; sc:citation , "pubmed:35580841" ; sc:description "Detecting and genotyping deletions and insertions based on long reads and a deep learning approach." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3228, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MAMnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/micahvista/MAMnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3372 ; sc:citation ; sc:description "It is a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization." ; sc:featureList edam:operation_2495 ; sc:name "MAmodel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20060511" ; sc:url "http://www.cs.tut.fi/sgn/csb/mamodel/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0749 ; sc:description "C++ program for HMM models" ; sc:featureList edam:operation_0226 ; sc:name "MAMOT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bcf.isb-sib.ch/mamot/" ; biotools:primaryContact "Mauro Delorenzi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes." ; sc:featureList edam:operation_3501 ; sc:name "MamPhEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://evol.nhri.org.tw/phenome/index.jsp?platform=mmus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3403 ; sc:citation ; sc:description "A Web Based Dynamic MANA Nomogram for Predicting the Malignant Cerebral Edema in patients with large hemispheric infarction." ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "MANA nomogram" ; sc:url "http://www.MANA-nom.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2259, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC8195153", "pubmed:33852839" ; sc:description "Merged Affinity Network Association Clustering (MANAclust) is a coding-free, automated pipeline enabling integration of categorical and numeric data spanning clinical and multi-omic profiles for unsupervised clustering to identify disease subsets. Using simulations and real-world data from The Cancer Genome Atlas, it is demonstrated that MANAclust's feature selection algorithms are accurate and outperform competitors." ; sc:featureList edam:operation_3432, edam:operation_3936 ; sc:name "MANAclust" ; sc:url "https://bitbucket.org/scottyler892/manaclust/src/master/" ; biotools:primaryContact "Supinda Bunyavanich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071 ; sc:description "A GUI designed to management of big amount of accession numbers." ; sc:isAccessibleForFree true ; sc:name "Management of Accession Numbers and sequences" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47871-management-of-accession-numbers-and-sequences" ; biotools:primaryContact "José Luis Ruiz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3305, edam:topic_3315, edam:topic_3796 ; sc:citation ; sc:description "Visualising microbial population structure by embedding millions of genomes into a low-dimensional representation." ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Mandrake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gtonkinhill.github.io/mandrake-web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_2269 ; sc:citation "pubmed:26034063" ; sc:description "Complete ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag sequencing) data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity." ; sc:featureList edam:operation_2238, edam:operation_2945 ; sc:name "Mango" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dphansti/mango" ; biotools:primaryContact "PHANSTIEL LAB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:31812694" ; sc:description """Exploratory Data Analysis for Large-Scale Sequencing Datasets. Mango User Guide — bdgenomics.mango 0.0.5 documentation. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_3208, edam:operation_3218 ; sc:name "Mango_EDA" ; sc:url "https://bdg-mango.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "MANGO: Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)" ; sc:featureList edam:operation_2945 ; sc:name "mango : Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/mango/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3390 ; sc:citation , "pmcid:PMC10058708", "pubmed:36986961" ; sc:description "A Genomics Portal and Gene Expression Atlas for Mangifera indica." ; sc:featureList edam:operation_3208, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "MangoBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mangobase.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2885, edam:topic_3517 ; sc:description "A function for plotting a Manhattan Plot in MATLAB directly from a text file of GWAS statistics from PLINK, BOLT-LMM or SAIGE." ; sc:featureList edam:operation_0337, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "Manhattan Plots for visualisation of GWAS results" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/69549-manhattan-plots-for-visualisation-of-gwas-results" ; biotools:primaryContact "Harry Green" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:33973997" ; sc:description "MANIEA is a microbial association network inference method based on improved Eclat association rule mining algorithm." ; sc:featureList edam:operation_2495, edam:operation_3625, edam:operation_3766 ; sc:license "Not licensed" ; sc:name "MANIEA" ; sc:url "https://github.com/MaidiL/MANIEA" ; biotools:primaryContact "Kewei Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0625, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6936142", "pubmed:31888454" ; sc:description """A novel manifold learning approach to reveal the functional links between gene networks. A novel manifold learning approach to reveal thefunctional links between gene networks.""" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3432 ; sc:name "ManiNetCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/daifengwanglab/ManiNetCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3321, edam:topic_3518 ; sc:citation ; sc:description "Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3218, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "MANOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MANOR.html" ; biotools:primaryContact "Pierre Neuvial" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0632, edam:topic_2828, edam:topic_3474 ; sc:citation , "pubmed:34614393" ; sc:description "A machine learning platform to guide protein-ligand design by anchors and influential distances." ; sc:featureList edam:operation_2429, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MANORAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://manoraa.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3169, edam:topic_3295, edam:topic_3517 ; sc:citation "pubmed:22424423" ; sc:description "Simple and effective method for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications." ; sc:featureList edam:operation_0389 ; sc:name "MAnorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3169, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description """MAnorm2 for quantitatively comparing groups of ChIP-seq samples. To pre-process a set of ChIP-seq samples. MAnorm2_utils is designed to coordinate with MAnorm2, an R package for differential analysis with ChIP-seq signals between two or more groups of replicate samples. MAnorm2_utils is primarily used for processing a set of ChIP-seq samples into a regular table recording the read abundances and enrichment states of a list of genomic bins in each of these samples.""" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3435, edam:operation_3658, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "MAnorm_2" ; sc:softwareVersion "2" ; sc:url "https://pypi.org/project/MAnorm2-utils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308 ; sc:citation ; sc:description "Tools for robust comparative metatranscriptomics." ; sc:featureList edam:operation_3258 ; sc:license "Artistic-2.0" ; sc:name "manta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/manta.html" ; biotools:primaryContact "Adrian Marchetti", "Chris Berthiaume" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3318, edam:topic_3489, edam:topic_3697 ; sc:citation , "pmcid:PMC7717536", "pubmed:33275647" ; sc:description """Integrative database and analysis platform that relates microbiome and phenotypic data. MANTA (Microbiota And pheNotype correlaTion Analysis platform) is an integrative database and analysis platform that relates microbiome and phenotypic data. MANTA is a web application that works on most of the modern web browsers. Microbiota And pheNotype correlaTion Analysis platform.""" ; sc:featureList edam:operation_2937, edam:operation_2940, edam:operation_3460 ; sc:license "MIT" ; sc:name "MANTA_DB" ; sc:url "https://mizuguchilab.org/manta/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3175 ; sc:citation "pubmed:26647377" ; sc:description "Calls structural variants (SVs) and indels from mapped paired-end sequencing reads." ; sc:featureList edam:operation_3227 ; sc:name "Manta" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/Illumina/manta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3071, edam:topic_3474 ; sc:citation , "pmcid:PMC10168000", "pubmed:37159241" ; sc:description "Machine learning-based tool to automate the identification of biological database IDs." ; sc:featureList edam:operation_2421, edam:operation_3282, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "MantaID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://molaison.shinyapps.io/MantaID/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269 ; sc:citation , "pmcid:PMC3001747", "pubmed:21092291" ; sc:description "Performs Mantel-Haenszel's test for k strata of 2x2 tables. Mantel and Haenszel proposed this asymptotic test based on the chi-2 distribution. Assuming no three-way interaction (k independent strata)." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "Mantel-Haenszel test" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29820-mantel-haenszel-s-test" ; biotools:primaryContact "Steinar Thorvaldsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data)." ; sc:featureList edam:operation_3465 ; sc:license "GPL-2.0" ; sc:name "MantelCorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.44.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MantelCorr.html" ; biotools:primaryContact "Brian Steinmeyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0749, edam:topic_3510 ; sc:citation , "pmcid:PMC8027985", "pubmed:33729755" ; sc:description "MANTI is an tool for automated annotation of protein N-termini for rapid interpretation of N-terminome data sets." ; sc:featureList edam:operation_3642, edam:operation_3646, edam:operation_3755 ; sc:license "Artistic-2.0" ; sc:name "MANTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://MANTI.sourceforge.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3299, edam:topic_3324, edam:topic_3524 ; sc:citation , "pmcid:PMC4445977", "pubmed:26017358" ; sc:description "An R package that simulates multilocus models of pathogen evolution." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "MANTIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.eeid.ox.ac.uk/mantis" ; biotools:primaryContact "Jose Lourenco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3322, edam:topic_3335, edam:topic_3422, edam:topic_3474 ; sc:citation , "pmcid:PMC7212270", "pubmed:32386536" ; sc:description "Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning." ; sc:featureList edam:operation_2454, edam:operation_3226, edam:operation_3891 ; sc:license "MPL-2.0" ; sc:name "mantis-ml" ; sc:url "https://dvitsios.github.io/mantis-ml-predictions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0218, edam:topic_0621, edam:topic_3174 ; sc:citation ; sc:description """Flexible and consensus-driven genome annotation. This tool can be used for protein function annotation, it is a standalone tool that uses HMMER to match sequences against multiple reference datasets, producing a consensus annotation using text mining. It accepts as input one or multiple aminoacids sequence fasta.""" ; sc:featureList edam:operation_0306, edam:operation_0362, edam:operation_2421 ; sc:license "MIT" ; sc:name "Mantis_GA" ; sc:url "https://github.com/PedroMTQ/mantis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_3170, edam:topic_3315 ; sc:citation , "pubmed:35325039" ; sc:description "Mantis is a space-efficient data structure that can be used to index thousands of raw- read experiments and facilitate large-scale sequence searches on those experiments. Mantis uses counting quotient filters instead of Bloom filters, enabling rapid index builds and queries, small indexes, and exact results, i.e., no false positives or negatives." ; sc:featureList edam:operation_0524, edam:operation_2421, edam:operation_2422, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Mantis" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/splatlab/mantis/tree/mergeMSTs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1775 ; sc:citation ; sc:description "Mantis is a homology-based protein function annotation tool that integrates multiple reference data sources. It uses multiple high-quality data sources as a reference, however custom reference data sources can also be added. Mantis does not use a pre-built database, instead, it dynamically integrates the multiple sources into a consensus-driven output. Mantis is extensively customizable and is available on Linux." ; sc:featureList edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Mantis" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.01" ; sc:url "https://github.com/PedroMTQ/mantis" ; biotools:primaryContact "Pedro Queirós" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2259, edam:topic_2269, edam:topic_3336 ; sc:citation "pubmed:24558125" ; sc:description "Computational tool for the analysis of the Mode of Action (MoA) of novel drugs and the identification of known and approved candidates for “drug repositioning”. It is based on network theory and non-parametric statistics on gene expression data." ; sc:featureList edam:operation_2497 ; sc:name "MANTRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mantra.tigem.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736 ; sc:citation , "pmcid:PMC9825755", "pubmed:36495196" ; sc:description "An efficient and flexible library for training and validating protein folding models." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "ManyFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/instadeepai/manyfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_3047, edam:topic_3172 ; sc:citation ; sc:description """One Molecular Fingerprint to Rule them All. Extended-Benchmark: compounds and query lists used for the peptide benchmark. MAP4-Similarity-Search: source code for the similarity search app. Supplementary Material for the manuscript: "One Molecular Fingerprint to Rule them All: Drugs, Biomolecules, and the Metabolome". 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Users input a set of protein-protein complexes and MAPPIS returns a list of shared interaction properties of the interfaces." ; sc:featureList edam:operation_0303, edam:operation_0492, edam:operation_2464, edam:operation_2949 ; sc:name "MAPPIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/MAPPIS" ; biotools:primaryContact "Alexandra Shulman-Peleg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3277 ; sc:citation "pmcid:PMC1461083", "pubmed:10790413" ; sc:description "MapPop is a software for choosing good samples from mapping populations and for locating new markers on pre-existing maps." ; sc:featureList edam:operation_2429 ; sc:name "MapPop" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://labs.bio.unc.edu/Vision/mappop/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:16470651" ; sc:description "Image analysis\" of LC-MS features, deconvolution etc." ; sc:featureList edam:operation_3203, edam:operation_3215, edam:operation_3432, edam:operation_3629, edam:operation_3630, edam:operation_3634, edam:operation_3694, edam:operation_3695 ; sc:name "MapQuant" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://arep.med.harvard.edu/MapQuant/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3303 ; sc:citation ; sc:description "This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types." ; sc:featureList edam:operation_2990 ; sc:license "GPL-2.0" ; sc:name "maPredictDSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/maPredictDSC.html" ; biotools:primaryContact "Adi Laurentiu Tarca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8056608", "pubmed:33879063" ; sc:description "MAPS is a machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy." ; sc:featureList edam:operation_2429, edam:operation_3443, edam:operation_3891, edam:operation_3935 ; sc:license "MIT" ; sc:name "MAPS" ; sc:url "https://github.com/jessecanada/MAPS/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:name "Raw image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:name "Phylogenetic data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3546 ; sc:name "Image metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_2640 ; sc:citation ; sc:description "A E-scape tool for interactive visualization of spatial clonal evolution." ; sc:featureList edam:operation_2426, edam:operation_2497, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MapScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/release/bioc/html/mapscape.html" ; biotools:primaryContact "Maia Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "MAPSCI is an algorithm to compute a multiple structure alignment for a set of proteins and to generate a consensus structure." ; sc:featureList edam:operation_0295, edam:operation_0492, edam:operation_0504, edam:operation_2479 ; sc:name "MAPSCI" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.geom-comp.umn.edu/mapsci/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_2182 ; sc:name "Nucleic acid sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "A targeted assembly software." ; sc:featureList edam:operation_3183 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Mapsembler" ; sc:operatingSystem "Linux" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:softwareVersion "2.2.4" ; sc:url "https://colibread.inria.fr/mapsembler2/" ; biotools:primaryContact "Pierre Peterlongo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0659 ; sc:citation ; sc:description "Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis ." ; sc:featureList edam:operation_3472 ; sc:name "MAPseq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jfmrod/mapseq" ; biotools:primaryContact "Christian von Mering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:20802226" ; sc:description "Highly sensitive and specific tool in the detection of splices as well as CPU and memory efficiency. It can be applied to both short (<75 bp) and long reads (>=75 bp) and it is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. The tool leverages the quality and diversity of read alignments of a given splice to increase accuracy." ; sc:featureList edam:operation_2429 ; sc:name "MapSplice" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.netlab.uky.edu/p/bioinfo/MapSplice" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0203, edam:topic_3053, edam:topic_3307 ; sc:citation "pubmed:19369497" ; sc:description "An information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. It supports a compact alignment view for both single-end and pair-end short reads, multiple navigation and zoom modes, and multi-thread processing. It offers automated genetic variation detection." ; sc:featureList edam:operation_0492, edam:operation_2409, edam:operation_3197, edam:operation_3198 ; sc:name "MapView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://evolution.sysu.edu.cn/mapview/" ; biotools:primaryContact "Hua Bao", "Suhua Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , , "pmcid:PMC2577856", "pmcid:PMC3694458", "pubmed:18714091", "pubmed:23758764" ; sc:description "Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "MAQ" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://maq.sourceforge.net/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation "pubmed:19620971" ; sc:description "Complete pipeline for mutant discovery, with web front end." ; sc:featureList edam:operation_3197, edam:operation_3661 ; sc:name "MAQGene" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://maqweb.sourceforge.net/" ; biotools:primaryContact "Henry Bigelow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092 ; sc:description "Graphical read alignment viewer. It is specifically designed for the Maq alignment file and allows visualization of the mismatches, base qualities and mapping qualities. Maqview is nothing fancy as Consed or GAP, but just a simple viewer for visualizing what happens in a particular region." ; sc:featureList edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "Maqview" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://maq.sourceforge.net/maqview.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3170, edam:topic_3512, edam:topic_3810 ; sc:citation , "pmcid:PMC8973887", "pubmed:35361110" ; sc:description "ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3431, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MARACAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fran-romero-campero/MARACAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168, edam:topic_3673 ; sc:citation ; sc:description "MARBL is an open-source package for indexing the text components of GenBank records and the NLM article abstracts associated with them. A few demonstrations of the package are also available at this website." ; sc:featureList edam:operation_0306, edam:operation_2422 ; sc:name "MARBL" ; sc:operatingSystem "Linux" ; sc:url "http://www.cs.uni.edu/~okane/source/MARBL/proc1.html" ; biotools:primaryContact "Kevin C. O'Kane" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3387, edam:topic_3473 ; sc:author "The MMP team" ; sc:citation , "pmcid:PMC5753341", "pubmed:29106641" ; sc:description "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine microorganisms derived from metagenomics samples." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-3.0" ; sc:name "MarCat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mmp.sfb.uit.no/databases/" ; biotools:primaryContact "The MMP team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0081, edam:topic_0121, edam:topic_0736, edam:topic_3542 ; sc:citation , "pubmed:12016059" ; sc:description "predicting coiled-coils in protein sequences" ; sc:featureList edam:operation_2423 ; sc:name "MARCOIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcf.isb-sib.ch/webmarcoil/webmarcoilINFOC1.html" ; biotools:primaryContact "Mauro Delorenzi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:35420135" ; sc:description "A method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering." ; sc:featureList edam:operation_0313, edam:operation_2844, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MarcoPolo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/chanwkimlab/MarcoPolo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301, edam:topic_3387, edam:topic_3473 ; sc:author "MMP team" ; sc:citation , "pmcid:PMC5753341", "pubmed:29106641" ; sc:description "Includes all non-complete marine microbial genomes regardless of the level of completeness." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-3.0" ; sc:name "MarDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mmp.sfb.uit.no/databases/mardb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3070, edam:topic_3372 ; sc:citation , "pmcid:PMC7199472", "pubmed:32369166" ; sc:description """Processing Big Data with application containers on Apache Spark. Italian, pronounced: /ˈmare/. Noun: Sea. MaRe has been developed with scientific application in mind. High-throughput methods produced massive datasets in the past decades, and using frameworks like Spark and Hadoop is a natural choice to enable high-throughput analysis. In scientific applications, many tools are highly optimized to resemble, or detect some phenomena that occur in a certain system. Hence, sometimes the effort of reimplementing scientific tools in Spark or Hadoop can't be sustained by research groups. MaRe aims to provide the means to run existing serial tools in MapReduce fashion. Since many of the available scientific tools are trivially parallelizable, MapReduce is an excellent paradigm that can be used to parallelize the computation.""" ; sc:featureList edam:operation_3227, edam:operation_3359 ; sc:license "Apache-2.0" ; sc:name "MaRe" ; sc:url "https://github.com/mcapuccini/MaRe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3387 ; sc:citation ; sc:description "Tool to evaluate the effectiveness of no-take marine reserves." ; sc:featureList edam:operation_3439 ; sc:name "MAREA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/turfeffect/MAREA" ; biotools:primaryContact "Juan Carlos Villaseñor-Derbez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_0769, edam:topic_3050, edam:topic_3387 ; sc:citation , "pmcid:PMC7334202", "pubmed:32620910" ; sc:description """Replicable pipeline and curated reference database for marine eukaryote metabarcoding. Building custom reference databases for metabarcoding. This pipeline can be used to develop a de-contamination database (i.e used to create a database of potential contaminants), or as a database for general purpose metabarcoding. We have provided three databases - a very small database composed of common contaminants (i.e human, sheep, goat, flies etc), as well as two metabarcoding databases for marine eukaryotes. These scripts support the MARES (MARine Eukaryote Species) pipeline used to create the MARES database of COI sequences for metabarcoding studies (presented in Arranz, Pearman, Aguirre, Liggins, in prep.).""" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3192, edam:operation_3460 ; sc:name "MARES" ; sc:url "https://github.com/wpearman1996/MARES_database_pipeline" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8769703", "pubmed:34664074" ; sc:description "Predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network." ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MAResNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://csbio.njust.edu.cn/bioinf/maresnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:35639499" ; sc:description "MARGARET is a computational tool for Trajectory Inference i.e. for inferring trajectories underlying biological developmental processes like cell-differentiation." ; sc:featureList edam:operation_3799, edam:operation_3890, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MARGARET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Zafar-Lab/Margaret" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation ; sc:description "It is a robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. The framework has three main functions: MARGE-potential, MARGE-express, and MARGE-cistrome." ; sc:featureList edam:operation_3222 ; sc:license "Not licensed" ; sc:name "MARGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cistrome.org/MARGE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "Assess downstream causality between two variables." ; sc:featureList edam:operation_2426, edam:operation_3439 ; sc:name "MarginalCausality" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Monneret/MarginalCausality" ; biotools:primaryContact "Gilles Monneret" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2182 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2573 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:encodingFormat edam:format_2072 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2573 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0102 ; sc:author "Benedict Paten" ; sc:citation ; sc:description "The marginAlign package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads." ; sc:featureList edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "marginAlign" ; sc:url "https://github.com/benedictpaten/marginAlign" ; biotools:primaryContact "Benedict Paten", "Mark Akeson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625 ; sc:description "MarginPhase is a program for simultaneous haplotyping and genotyping." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "marginPhase" ; sc:url "https://github.com/benedictpaten/marginPhase" ; biotools:primaryContact "Benedict Paten" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0821, edam:topic_1775 ; sc:citation "pubmed:19696044" ; sc:description "Algorithm for metabolite and reaction inference based on enzyme specificities. It has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. It employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA." ; sc:featureList edam:operation_2426 ; sc:name "MaRIboES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://trac.nbic.nl/mariboes/" ; biotools:primaryContact "Thomas Abeel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3373 ; sc:citation , "pmcid:PMC10455768", "pubmed:37623730" ; sc:description "Database of biosynthetic gene clusters in marine species." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MariClus" ; sc:url "https://www.mariclus.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0605, edam:topic_3303, edam:topic_3344 ; sc:citation , "pmcid:PMC6226017", "pubmed:30416754" ; sc:description """Citizen Science for Mining the Biomedical Literature. Scientific communication is broken. Progress in biomedical science is all about incrementally building off of the work of others. Currently, it takes far too long for one scientist's work to reach all the other scientists that would benefit. Mark2Cure will make scientific communication more efficient for everyone, leading to faster discoveries and cures for disease.""" ; sc:featureList edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:name "Mark2Cure" ; sc:url "http://mark2cure.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Marks all duplicate reads in a provided SAM or BAM file and either removes them or flags them." ; sc:featureList edam:operation_0253 ; sc:name "MarkDuplicates (IP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/picard_pasteur_wrapper/rgPicardMarkDups/1.56.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3452 ; sc:citation , "pmcid:PMC6612841", "pubmed:31510669" ; sc:description "A joint method for marker-free alignment of tilt series in electron tomography | This is an alpha version of the joint method for marker-free alignment. Currently, it may be not so robust and include third-part modules. The third-part modules will be removed in beta version | The files is build in fedora 25." ; sc:featureList edam:operation_3798 ; sc:name "marker-free" ; sc:url "https://github.com/icthrm/joint-marker-free-alignment" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Explainable Single Cell Typing using Capsule Networks. MarkerCapsule is a genneral framework for identifying cell types from single cell scRA-seq data. MarkerCapsule is based on Capsule Networks, which reflect most recent and most advanced progress in deep learning, automatizes the annotation step, enables to coherently integrate heterogeneous data, and supports a human-mind-friendly interpretation of results, by relating marker genes with the fundamental units of capsule networks.""" ; sc:featureList edam:operation_3463 ; sc:name "MarkerCapsule" ; sc:url "https://github.com/sumantaray/MarkerCapsule" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2885, edam:topic_3360, edam:topic_3407 ; sc:citation , "pubmed:33245771" ; sc:description """An online database of molecular biomarkers. MarkerDB is a freely available electronic database that attempts to consolidate information on all known clinical and a selected set of pre-clinical biomarkers into a single resource.""" ; sc:featureList edam:operation_0306, edam:operation_0415, edam:operation_2421 ; sc:name "MarkerDB" ; sc:url "https://markerdb.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3407 ; sc:citation , "pmcid:PMC9710573", "pubmed:36699388" ; sc:description "NLP-enabled text-mining system for biomedical entity relation extraction." ; sc:featureList edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MarkerGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.genegeniedx.com/markergenie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3174, edam:topic_3293 ; sc:citation , "pubmed:35713513" ; sc:description "Linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads." ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3233 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MarkerMAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/songweizhi/MarkerMAG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3360, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:35662460" ; sc:description "Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:name "MarkerML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://microbiome.igib.res.in/markerml/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3676 ; sc:author ; sc:citation , "pubmed:33904573" ; sc:description "markerpen is an R library for the identification of cell-type-specific marker genes from co-expression patterns in tissue samples." ; sc:featureList edam:operation_3232, edam:operation_3463, edam:operation_3629 ; sc:license "GPL-2.0" ; sc:name "markerpen" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=markerpen" ; biotools:primaryContact , "Kathryn Roeder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0623, edam:topic_2269, edam:topic_3293 ; sc:citation "pubmed:26363176" ; sc:description "Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data." ; sc:featureList edam:operation_0324 ; sc:name "markophylo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/markophylo/" ; biotools:primaryContact "Utkarsh J. Dang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3315, edam:topic_3934 ; sc:citation ; sc:description """Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data. MarkovHC is an open-source R package designed for explore hierarchical structures of biological data, especially in cell type and critical point identification and cell transition tracking in development.""" ; sc:featureList edam:operation_0244, edam:operation_3432, edam:operation_3935 ; sc:name "MarkovHC" ; sc:url "https://github.com/ZhenyiWangTHU/MarkovHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0123, edam:topic_1775, edam:topic_2814 ; sc:citation "pubmed:21672961" ; sc:description "MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins." ; sc:featureList edam:operation_1778, edam:operation_2483, edam:operation_2487, edam:operation_2930 ; sc:name "MarkUs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3071 ; sc:citation "pubmed:25480679" ; sc:description "It is able to annotate biomedical texts using different annotation classes. You only need a server with php technology and one database to annotate documents with a browser. Users can enter biomedical documents to be annotated by other users and get annotations for relevant terms, such as diseases, symptoms and treatments." ; sc:featureList edam:operation_0226, edam:operation_0335 ; sc:name "Marky" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://sing.ei.uvigo.es/marky/" ; biotools:primaryContact "Martín Pérez Pérez" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2200 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2330 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "RNA Team Freiburg" ; sc:citation , "pubmed:15972285" ; sc:description "Sequence-structure alignment of RNAs." ; sc:featureList edam:operation_0294 ; sc:isAccessibleForFree true ; sc:name "MARNA web server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://rna.informatik.uni-freiburg.de/MARNA/" ; biotools:primaryContact , "RNA Team Freiburg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3511 ; sc:author ; sc:citation , "pmcid:PMC6698742", "pubmed:31265077" ; sc:description "MARome is a resource for annotation of Scaffold and Matrix Attachment Regions (S/MARs) in Human Genome such as associated genes, genomic region, associated S/MAR binding proteins, associated Retroviral Integration sites for HIV and HTLV (Source: RID) etc. MARome is interlinked to other genomic resources such as, UCSC Genome Browser (For visualization of S/MAR genomic location), ensemble, NCBI-Gene." ; sc:name "MARome" ; sc:softwareHelp ; sc:url "http://bioinfo.net.in/MARome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0634 ; sc:citation "pubmed:20513648" ; sc:description "Web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2495, edam:operation_3223 ; sc:name "MARQ" ; sc:url "http://marq.dacya.ucm.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3305, edam:topic_3518, edam:topic_3520 ; sc:citation , "pmcid:PMC8424977", "pubmed:34493210" ; sc:description "This app provides a user interface for the open-source R package marr, which implements the method Maximum Rank Reproducibility (MaRR), a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data." ; sc:featureList edam:operation_3557, edam:operation_3627, edam:operation_3803, edam:operation_3860, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MaRR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://maxmcgrath.shinyapps.io/marr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3518 ; sc:citation ; sc:description "Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking." ; sc:featureList edam:operation_2990 ; sc:license "GPL-3.0" ; sc:name "marray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/marray.html" ; biotools:primaryContact "Yee Hwa (Jean) Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3344, edam:topic_3518 ; sc:citation ; sc:description "MArray is a tool for analysing single, replicated or reversed microarray experiments." ; sc:featureList edam:operation_0363 ; sc:isAccessibleForFree true ; sc:name "MArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/14634-marray" ; biotools:primaryContact "junbai wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301, edam:topic_3387, edam:topic_3473 ; sc:citation , "pmcid:PMC5753341", "pubmed:29106641" ; sc:description "MarRef is a manually curated marine microbial genome database that contains complete genomes." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-3.0" ; sc:name "MarRef" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mmp.sfb.uit.no/databases/" ; biotools:primaryContact "The MMP team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3077, edam:topic_3325 ; sc:citation ; sc:description "Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome." ; sc:featureList edam:operation_2421 ; sc:name "MARRVEL" ; sc:softwareHelp ; sc:url "http://marrvel.org/" ; biotools:primaryContact "Zhandong Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:15452431" ; sc:description "Program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar couplings can be used to enhance assignment." ; sc:featureList edam:operation_0479 ; sc:name "MARS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm" ; biotools:primaryContact "Markus Zweckstetter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2640, edam:topic_3304, edam:topic_3474, edam:topic_3500 ; sc:citation , , "pmcid:PMC7413276", "pubmed:32706737" ; sc:description """A software pipeline for automated analysis of social behaviors in mice. Assessing Apps for Patients with Genitourinary Tumors Using the Mobile Application Rating Scale (MARS). The Mouse Action Recognition System (MARS) is a deep learning based system for automated pose estimation and social behavior classification in pairs of interacting mice. It combines a user-friendly graphical user interface with fast and powerful computer vision and machine learning algorithms. MARS's novel approach to extracting features from the animals' poses and trajectories allows for highly accurate classification of social behavior.""" ; sc:featureList edam:operation_0444, edam:operation_3799, edam:operation_3891 ; sc:name "MARS_ML" ; sc:url "https://neuroethology.github.io/MARS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3125, edam:topic_3175 ; sc:citation ; sc:description "A package for Multiple Samples Alignment-base SV Calling and Refinement." ; sc:featureList edam:operation_0310, edam:operation_0452, edam:operation_3196, edam:operation_3228, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MARS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maiziex/MARS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find matrix/scaffold recognition (MRS) signatures in DNA sequences." ; sc:featureList edam:operation_0444 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "marscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/marscan.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_3053 ; sc:citation ; sc:description "Metabolite Analogues for Strain Improvement." ; sc:featureList edam:operation_3095 ; sc:name "MARSI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/biosustain/marsi" ; biotools:primaryContact "Markus J Herrgård" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2229 ; sc:citation "pubmed:21400228" ; sc:description "Prediction method  for discrimination between Mitochondrial-AARSs and Cytosolic-AARSs." ; sc:featureList edam:operation_2489 ; sc:name "MARSpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/marspred/" ; biotools:primaryContact "Bharat Panwar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation ; sc:description "martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork." ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "martini" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/martini.html" ; biotools:primaryContact "Hector Climente-Gonzalez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0153, edam:topic_0176, edam:topic_3306, edam:topic_3382 ; sc:citation , , "pubmed:33782607", "pubmed:33782608" ; sc:description "Martini 3 is a general purpose force field for coarse-grained molecular dynamics with an eye for atomic detail. The Martini force field is a coarse-grain (CG) force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parametrized in a systematic way, combining top-down and bottum-up strategies: Non-bonded interactions are based on the reproduction of experimental partitioning free energies between polar and apolar phases of a large number of chemical compounds, whereas bonded interactions are derived from reference all-atom simulations." ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_2492, edam:operation_3891 ; sc:name "Martini 3" ; sc:url "http://cgmartini.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3366, edam:topic_3489, edam:topic_3512 ; sc:citation "pubmed:14707178" ; sc:description "Tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface it allows you to apply a series of filters to create custom datasets which can be converted to several useful output formats." ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_2422, edam:operation_3695 ; sc:name "MartView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biomart.org/biomart/martview/" ; biotools:primaryContact "Arek Kasprzyk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625 ; sc:citation , "pmcid:PMC5311849", "pubmed:28209135" ; sc:description "Multi-phenotype Analysis of Rare Variants." ; sc:featureList edam:operation_3197 ; sc:license "BSD-3-Clause" ; sc:name "MARV" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ImperialStatGen/MARV" ; biotools:primaryContact "Marika Kaakinen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10018366", "pubmed:36631981" ; sc:description "An integrated alternative splicing analysis platform for single-cell RNA sequencing data." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MARVEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wenweixiong.github.io/MARVEL_Plate.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:27153730" ; sc:description "Algorithm that models  linkage-disequilibrium (LD) using a simple multivariate Gaussian distribution." ; sc:featureList edam:operation_2425 ; sc:name "MarViN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/illumina/marvin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0621, edam:topic_0622, edam:topic_3316 ; sc:citation , "pmcid:PMC8501643", "pubmed:34627149" ; sc:description "Manual Annotation Studio (MAS) is a web server which assists users in the process of identifying coding regions and determining the function of genes." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_3431, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BDRD-Genomics/MAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23300135" ; sc:description "Perl implementation of our MaSC approach to estimating fragment length from short-read high-throughput sequencing data." ; sc:featureList edam:operation_2478 ; sc:name "MaSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.perkinslab.ca/Software.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3713 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3655 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Converts Mascot search results in .dat files to pepXML (.xml) format." ; sc:featureList edam:operation_0335 ; sc:name "Mascot2XML" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:Mascot2XML" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:17203510" ; sc:description "A library to fully parse and analyse MASCOT MS/MS search results." ; sc:featureList edam:operation_3438 ; sc:name "Mascotdatfile" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareVersion "3.4.42" ; sc:url "http://compomics.github.io/projects/mascotdatfile.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0780, edam:topic_3047 ; sc:citation "pubmed:24167507" ; sc:description "Proteomics aggregation utility  that queries and aggregates information from a variety of online Arabidopsis proteomic resources." ; sc:featureList edam:operation_3436 ; sc:name "MASCP Gator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gator.masc-proteomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:3154283" ; sc:description "Tool designed to simplify the manipulation of aligned sequence sets. It contains functionality for many of the common tasks related to this goal. In addition, mase was designed with a very modular approach, making additions or modifications to the code straightforward." ; sc:featureList edam:operation_0292 ; sc:name "MASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.girinst.org/downloads/software/mase/" ; biotools:primaryContact "Database Administor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2269, edam:topic_2533, edam:topic_3174 ; sc:citation , "pmcid:PMC4915045", "pubmed:27323842" ; sc:description "Fast genome and metagenome distance estimation using MinHash." ; sc:featureList edam:operation_0289 ; sc:license "CC-BY-4.0" ; sc:name "Mash" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/marbl/mash" ; biotools:primaryContact "Adam M. Phillippy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_2269, edam:topic_3520 ; sc:citation , "pmcid:PMC7728713", "pubmed:32786689" ; sc:description """A Universal Software Environment for Top-Down Proteomics. A Comprehensive User-friendly Software Environment for Top-Down Proteomics. MASH Explorer is a comprehensive and user-friendly software environment for top-down proteomics, which includes a downloadable software package, MASH Explorer App, as a versatile, comprehensive platform for top-down proteomics with the capability to process data from various vendor formats and incorporate multiple algorithms for deconvolution and database searching. It is developed by an interdisciplinary team consisting of experts in top-down mass spectrometry-based proteomics, computational data science, and bioinformatics/biostatistics.""" ; sc:featureList edam:operation_2421, edam:operation_3629, edam:operation_3755 ; sc:name "MASH Explorer" ; sc:url "http://ge.crb.wisc.edu/MASH_Explorer/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description "MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using k-mers" ; sc:featureList edam:operation_0292, edam:operation_0523, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MashMap" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/marbl/MashMap" ; biotools:primaryContact "Adam Phillippy", "Srinivas Aluru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2840, edam:topic_3375, edam:topic_3390, edam:topic_3697 ; sc:citation , "pubmed:33125077" ; sc:description """Microbiota-active substance interactions database. Active Substance Interaction database. Try Examples: Bifidobacterium adolescentis, Enterococcus faecalis, Acarbose, Caffeic acid, Oxaprozin, Obesity, Colorectal cancer. A centralized and standardized database to catalog Microbiota-Active Substance Interaction (MASI) will be very useful for related research fields, including microbiota-related precision medicine, pharmaceutical research, food and nutrition research, clinical pharmacy, health management studies. Accumulating evidence about the interaction between human microbiota and active substances, especially for those therapeutically-relevant substances such as clinical used drugs and traditional medicines/herbs, is deepenning our understanding in the role of "our second genome" in human health and diseases, and opens new avenue for managing/treating human healthy problems/diseases by manipulating microbiota-human interactions.""" ; sc:featureList edam:operation_0544 ; sc:name "MASI" ; sc:url "http://www.aiddlab.com/MASI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3321, edam:topic_3518 ; sc:citation ; sc:description "Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments." ; sc:featureList edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "maSigPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/maSigPro.html" ; biotools:primaryContact "Maria Jose Nueda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0654, edam:topic_0780 ; sc:citation ; sc:description "Mapping and Analysis of SIreVirus Elements is an expertly-built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis, and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences." ; sc:featureList edam:operation_2429, edam:operation_2945 ; sc:name "MASiVE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20130721" ; sc:url "http://bat.ina.certh.gr/tools/masive/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Mask all ambiguity characters in nucleotide sequences with N." ; sc:featureList edam:operation_0368 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "maskambignuc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/maskambignuc.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Mask all ambiguity characters in protein sequences with X." ; sc:featureList edam:operation_0368 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "maskambigprot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/maskambigprot.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "Package includes functions to analyze and mask microarray expression data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "maskBAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/maskBAD.html" ; biotools:primaryContact "Michael Dannemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC10311327", "pubmed:37387138" ; sc:description "Effects of spaced k-mers on alignment-free genotyping." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MaskedPanGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hhaentze/MaskedPangenie" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Write a sequence with masked features." ; sc:featureList edam:operation_0368 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "maskfeat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/maskfeat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32445109" ; sc:description """A deep learning framework for fully supervised, weakly supervised, and unsupervised mitosis detection in histopathology images. Codes for our Medical & Biological Engineering & Computing paper "MaskMitosis: a deep learning framework for fully supervised, weakly supervised, and unsupervised mitosis detection in histopathology images". Please see the paper for more details.""" ; sc:featureList edam:operation_0479, edam:operation_3553, edam:operation_3927 ; sc:name "MaskMitosis" ; sc:url "https://github.com/MeriemSebai/MaskMitosis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3127 ; sc:description "Masks recombinant regions in an alignment based on ClonalFrameML or Gubbins output" ; sc:featureList edam:operation_0337, edam:operation_0451 ; sc:license "GPL-3.0" ; sc:name "maskrc-svg" ; sc:url "https://github.com/kwongj/maskrc-svg" ; biotools:primaryContact , "Jason Kwong" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Write a sequence with masked regions." ; sc:featureList edam:operation_0368 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "maskseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/maskseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "A fast, feature-rich and hackable read simulator for the simulation of NGS and Sanger data." ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_2429 ; sc:license "GPL-3.0" ; sc:name "Mason" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.seqan.de/apps/mason/" ; biotools:primaryContact "Manuel Holtgrewe" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:name "Locus ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_2305 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10158992", "pubmed:36750372" ; sc:description "Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server." ; sc:featureList edam:operation_3095, edam:operation_3192, edam:operation_3223, edam:operation_3680, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MASON" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.helmholtz-hiri.de/en/datasets/mason" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3071, edam:topic_3520 ; sc:citation "pubmed:20455215" ; sc:description "Freely available platform for integrating MS protein identifications with information from the major bioinformatics databases (ontologies, domains, literature, etc.)" ; sc:featureList edam:operation_3767 ; sc:name "MASPECTRAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.tugraz.at/maspectras/maspectras_description.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3518, edam:topic_3572 ; sc:citation "pubmed:16899490" ; sc:description "Provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. 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MASS: Protein Single-Model Global Quality Assessment by Random Forest and Various Energies. Tong Liu and Zheng Wang. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. BMC Bioinformatics (2020) 21:246.""" ; sc:featureList edam:operation_0267, edam:operation_0477, edam:operation_3694 ; sc:name "MASS-p" ; sc:url "http://dna.cs.miami.edu/MASS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3654, edam:format_3752 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3752 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3752 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3360, edam:topic_3520 ; sc:author "SING Group" ; sc:citation ; sc:contributor "Bioscope Reseearch Group" ; sc:description "Open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data." ; sc:featureList edam:operation_0531, edam:operation_1812, edam:operation_2409, edam:operation_2990, edam:operation_3215, edam:operation_3432, edam:operation_3435, edam:operation_3648, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Mass-Up" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.13" ; sc:url "http://www.sing-group.org/mass-up" ; biotools:primaryContact "Hugo López-Fernández" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , , "pubmed:34647461" ; sc:description "A software platform for analysis and visualization of label-free and tandem mass tag (TMT) data-dependent acquisition (DDA) bottom-up proteomics data, including pathway and gene set enrichment analyses." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:name "Mass Dynamics" ; sc:softwareVersion "1.0", "2.0" ; sc:url "https://massdynamics.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3651 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3547 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Free (Windows/WINE) tool for analysis of MS/MS, bottom-up proteomics data, including non-standard PTMs and more." ; sc:featureList edam:operation_0531, edam:operation_3629, edam:operation_3631, edam:operation_3645, edam:operation_3646, edam:operation_3647, edam:operation_3694, edam:operation_3695, edam:operation_3767 ; sc:name "MassAI" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.massai.dk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295 ; sc:citation ; sc:description "This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2428, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "MassArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MassArray.html" ; biotools:primaryContact "Reid F. Thompson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3172 ; sc:author "The MassBank Project" ; sc:citation ; sc:description "MassBank is a public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains spectra from EI‐MS, fast atom bombardment MS, electrospray ionization (ESI)‐MSn data of thousands of authentic standards, EI‐MS and other‐MS data of thousands of volatile natural and synthetic compounds, and ESI‐MS2 data of synthetic drugs contributed by research groups worldwide. ESI‐MS2 data were analyzed under nonstandardized, independent experimental conditions. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS2 data. MassBank is useful for the identification of chemical compounds and the publication of experimental data." ; sc:isAccessibleForFree true ; sc:name "MassBank" ; sc:url "https://massbank.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC8215474", "pubmed:34177338" ; sc:description "A large-scaled depository of mass spectrometry datasets for metabolome analysis." ; sc:featureList edam:operation_2422, edam:operation_3203, edam:operation_3215, edam:operation_3431, edam:operation_3637 ; sc:isAccessibleForFree true ; sc:name "MassBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webs2.kazusa.or.jp/massbase/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3244, edam:format_3475, edam:format_3654, edam:format_3752 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3244, edam:format_3475, edam:format_3654 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:21751374" ; sc:description "XIC extraction and quantitation from LC-MS data." ; sc:featureList edam:operation_3203, edam:operation_3215, edam:operation_3628, edam:operation_3630, edam:operation_3634, edam:operation_3635, edam:operation_3636, edam:operation_3638, edam:operation_3704 ; sc:name "MassChroQ" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://pappso.inra.fr/bioinfo/masschroq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:35944213" ; sc:description "massdatabase is an R package that operates the online public databases and combines with other tools for streamlined compound annotation and pathway enrichment analysis. massDatabase is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the users to leverage all the online public databases for biological function mining." ; sc:featureList edam:operation_2409, edam:operation_3501, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "massDatabase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://massdatabase.tidymass.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3047, edam:topic_3520, edam:topic_3524 ; sc:citation ; sc:description """Robust linear deconvolution by optimal transport. This repository contains software tools which allow to compare spectra using the Wasserstein distance and estimate relative abundances of molecules from the spectrum by minimizing the Wasserstein distance. The tools are distributed as a Python3 package called masserstein. Basic functionality is also available as a set of commandline applications: WSDistance to compute the Wasserstein distance and WSDeconv to estimate proportions.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3659, edam:operation_3799, edam:operation_3860 ; sc:license "MIT" ; sc:name "Masserstein" ; sc:url "https://github.com/mciach/masserstein" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Access raw data from Agilent MassHunter GC/MS and GC/MS/MS, export to plain text." ; sc:featureList edam:operation_0335, edam:operation_3203, edam:operation_3694 ; sc:name "MassHunter File Reader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.quadtechassociates.com/freeware.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Kalman filter based on binless peak picking and quantitation in XCMS." ; sc:featureList edam:operation_3215 ; sc:name "massifquant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/xcms.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3547 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203 ; sc:citation , "pmcid:PMC4080740", "pubmed:24659105" ; sc:description "Predicts the sex of samples in gene expression microarray datasets." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "massiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/massiR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082 ; sc:description "Enhanced version of AlphaFold2 that allows an extended sampling. 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Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction." ; sc:featureList edam:operation_0272, edam:operation_2429, edam:operation_2464, edam:operation_2492, edam:operation_2949 ; sc:name "MassNet" ; sc:url "http://massnet.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC5608769", "pubmed:28989334" ; sc:description "Processes high resolution mass spectrometry imaging data, performs multivariate statistics (PCA, clustering) and lipid identification." ; sc:featureList edam:operation_3214, edam:operation_3443 ; sc:name "massPix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hallz/massPix" ; biotools:primaryContact "Julian L. Griffin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3315, edam:topic_3407 ; sc:citation ; sc:description """Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics. MASSpy is a package for kinetic modeling and simulation of biological networks. 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Registration at the site is free and is required to use it." ; sc:featureList edam:operation_0372, edam:operation_0438, edam:operation_0445, edam:operation_3209, edam:operation_3649 ; sc:name "Match" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.gene-regulation.com/pub/programs.html#match" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325 ; sc:author "MacArthur Lab" ; sc:citation , "pmcid:PMC6250066", "pubmed:30240502" ; sc:description "Open source software matching patients across genomic centers and finding the individual patients with the same candidate gene and overlapping phenotypic feature. Search for novel genetic causes of rare disease is based on the algorithm that determines the similarity between two distinct patients." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "matchbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://seqr.broadinstitute.org/matchmaker/matchbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3169, edam:topic_3176, edam:topic_3179, edam:topic_3474 ; sc:citation , "pmcid:PMC7299183", "pubmed:32550271" ; sc:description """Probing multi-way chromatin interaction with hypergraph representation learning. This is the implementation of the algorithm MATCHA for analyzing multi-way chromatin interaction data via hypergraph representation learning.""" ; sc:featureList edam:operation_0272, edam:operation_2939 ; sc:license "MIT" ; sc:name "MATCHA" ; sc:url "https://github.com/ma-compbio/MATCHA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3344 ; sc:citation ; sc:description """A guide to student-faculty connections in PhD programs. R Shiny app to match two sets of people based on mutual interests (e.g. students and faculty based on research interest). Created for the Matchathon event for the Program in Biomedical Sciences (PIBS) incoming first-year student Matchathon event. To help students find faculty members with mutual research interests, we use this algorithm to match first-year PhD students and faculty who are in search of trainees based on mutual research interests. Then these students and faculty meet during a two hour Matchathon event. At the event students meet individually with 12 different faculty members for 5 minutes each.""" ; sc:featureList edam:operation_2421 ; sc:license "MIT" ; sc:name "Matchathon" ; sc:url "https://UM-OGPS.shinyapps.io/matchathon/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_2269 ; sc:citation , "pubmed:15846361" ; sc:description "This package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance." ; sc:featureList edam:operation_2409, edam:operation_3223 ; sc:license "Artistic-2.0" ; sc:name "matchBox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/matchBox.html" ; biotools:primaryContact "Anuj Gupta", "Luigi Marchionni" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Waterman-Eggert local alignment of two sequences." ; sc:featureList edam:operation_0491 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "matcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/matcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Pairwise sequence alignment of DNA or protein sequences using Waterman-Eggert local alignment." ; sc:featureList edam:operation_0491 ; sc:name "matcher-api (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_matcher_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Waterman-Eggert local alignment of two sequences." ; sc:featureList edam:operation_0491, edam:operation_0495 ; sc:name "matcher (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/psa/emboss_matcher" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Finds the best local alignments between two sequences. It compares two sequences looking for local sequence similarities using a rigorous algorithm." ; sc:featureList edam:operation_2403 ; sc:name "matcher WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/matcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3374 ; sc:citation ; sc:description """A Deep Learning Framework for Drug Synergy Prediction. Drug combination therapies have been a viable strategy for the treatment of complex diseases such as cancer due to increased efficacy and reduced side effects.""" ; sc:featureList edam:operation_2495, edam:operation_3435 ; sc:license "MIT" ; sc:name "MatchMaker" ; sc:url "https://github.com/tastanlab/matchmaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3325, edam:topic_3473 ; sc:citation , "pmcid:PMC4610002", "pubmed:26295439" ; sc:description "A platform for rare disease gene discovery. It connects databases of genotypes and rare phenotypes via a common application programming interface (API)." ; sc:featureList edam:operation_2421, edam:operation_3197, edam:operation_3431, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Matchmaker exchange" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.matchmakerexchange.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3391, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:12702208" ; sc:description "MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references." ; sc:featureList edam:operation_2454, edam:operation_3223, edam:operation_3224, edam:operation_3282 ; sc:name "MatchMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://discover.nci.nih.gov/matchminer/" ; biotools:primaryContact "MatchMiner Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:31904810" ; sc:description """A cross-platform normalization method for gene expression data integration. MOTIVATION:Combining gene expression (GE) profiles generated from different platforms enables previously infeasible studies due to sample size limitations. Several cross-platform normalization methods have been developed to remove the systematic differences between platforms, but they may also remove meaningful biological differences among datasets. In this work, we propose a novel approach that removes the platform, not the biological differences. Dubbed as 'MatchMixeR', we model platform differences by a linear mixed effects regression (LMER) model, and estimate them from matched GE profiles of the same cell line or tissue measured on different platforms. The resulting model can then be used to remove platform differences in other datasets""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3659 ; sc:name "MatchMixeR" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=31904810" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3464, edam:format_3651 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2855 ; sc:encodingFormat edam:format_3464 ; sc:name "Distance matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0888 ; sc:encodingFormat edam:format_3464 ; sc:name "Structure similarity score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Tool to import, process, clean, and compare mass spectrometry data." ; sc:featureList edam:operation_0336, edam:operation_3695, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Matchms" ; sc:softwareVersion "0.20.0", "0.9.2" ; sc:url "https://github.com/matchms/matchms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0654, edam:topic_3168 ; sc:citation , "pmcid:PMC7605269", "pubmed:32963029" ; sc:description """Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. This repository provides the following 3 perl scripts for reconstructing the structure of double-stranded DNA fragments from deeply sequenced single-stranded DNA libraries:. Each script includes a help menu with further instructions and available options (accessible by executing the scripts without specifying an input file).""" ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3196 ; sc:license "MIT" ; sc:name "MatchSeq" ; sc:url "https://github.com/mpieva/matchseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "Measure fluorescence signal colocalisation in biological systems." ; sc:featureList edam:operation_3443 ; sc:name "MatCol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.cmri.org.au/bioinformatics.htm" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:32637981" ; sc:description """A MATLAB toolbox for feature ranking. The matFR toolbox has already integrated 42 methods. Among them, 12 methods are from FSLib [1], 9 methods from mutual information (MI) based feature selection repository [2], 7 methods are used in MATLAB (“rankfeatures”, “relieff” and “lasso”), and others are accessible online. FR methods can be grouped into supervised and unsupervised methods. In this toolbox, there are 29 supervised and 13 unsupervised methods. FR methods can also be categorized from theoretical perspective. The matFR contains 12 MI based methods, 8 statistical analysis based methods, 8 structure learning based methods and others.""" ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3802 ; sc:name "matFR" ; sc:url "http://github.com/NicoYuCN/matFR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_0602, edam:topic_3172 ; sc:citation "pubmed:17166258" ; sc:description "Facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots" ; sc:featureList edam:operation_3214 ; sc:name "MathDAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mathdamp.iab.keio.ac.jp/" ; biotools:primaryContact "Martin Robert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3315, edam:topic_3474 ; sc:citation ; sc:description """Feature Extraction Package for Biological Sequences Based on Mathematical Descriptors. Home • Documentation • List of files • Dependencies • Installing • Descriptors • How To Use • Citation. Feature Extraction Package for Biological Sequences. Machine learning algorithms have been very successfully applied to extract new and relevant knowledge from biological sequences.""" ; sc:featureList edam:operation_2429, edam:operation_3936, edam:operation_3937 ; sc:name "MathFeature" ; sc:url "https://bonidia.github.io/MathFeature/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2229, edam:topic_3474 ; sc:citation , "pmcid:PMC10164589", "pubmed:36912104" ; sc:description "Multi-task framework for learning from single-cell multimodal omics data." ; sc:featureList edam:operation_0335, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Matilda" ; sc:url "https://github.com/PYangLab/Matilda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3300, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC8114487", "pubmed:33975602" ; sc:description "MATISSE is a method for improved single cell segmentation in imaging mass cytometry. MATISSE method combines fluorescence microscopy and multiplex IMC to achieve improved segmentation." ; sc:featureList edam:operation_3552, edam:operation_3553, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "MATISSE" ; sc:url "https://github.com/VercoulenLab/MATISSE-Pipeline" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:description "MATLAB is a general use development environment and scientific computing language." ; sc:isAccessibleForFree false ; sc:name "MATLAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.mathworks.com/products/matlab.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344 ; sc:description "This repository aim to share some of my matlab functions for biomechanical data analyses" ; sc:isAccessibleForFree true ; sc:name "MATLAB biomech functions" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/72425-matlab_biomech_functions" ; biotools:primaryContact "cedric MORIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Panel Data Toolbox for MATLAB" ; sc:isAccessibleForFree true ; sc:name "Panel Data Toolbox for MATLAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51320-panel-data-toolbox-for-matlab" ; biotools:primaryContact "Javier Barbero Jiménez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32784135" ; sc:description """Motion-Attentive Transition Network for Zero-Shot Video Object Segmentation. Motion-Attentive Transition for Zero-Shot Video Object Segmentation. [2020/06/15] Update results for DAVIS-17 test-dev set!. This is a PyTorch implementation of our MATNet for unsupervised video object segmentation. [2020/03/04] Update results for DAVIS-17 validation set!.""" ; sc:featureList edam:operation_3799, edam:operation_3907 ; sc:name "MATNet" ; sc:url "https://github.com/tfzhou/MATNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0199 ; sc:citation , "pmcid:PMC9344837", "pubmed:35731204" ; sc:description "matOptimize is a program to rapidly and effectively optimize a mutation-annotated tree (MAT) for parsimony using subtree pruning and regrafting (SPR) moves within a user-defined radius." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0558, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "matOptimize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yceh/matOptimize-experiments" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:license "MIT" ; sc:name "Matplotlib" ; sc:softwareHelp ; sc:softwareVersion "3.6.0 Released" ; sc:url "https://matplotlib.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3321, edam:topic_3382 ; sc:citation ; sc:description "Automated classification and characterization of the mitotic spindle following knockdown of a mitosis-related protein." ; sc:featureList edam:operation_3432, edam:operation_3443 ; sc:name "MatQuantify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/matquantify/" ; biotools:primaryContact "Matloob Khushi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0166, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:10944398", "pubmed:12824329" ; sc:description "MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures." ; sc:featureList edam:operation_0320, edam:operation_0477, edam:operation_2487, edam:operation_2488 ; sc:name "MATRAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://strcomp.protein.osaka-u.ac.jp/matras/" ; biotools:primaryContact "MATRAS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0623, edam:topic_0736, edam:topic_2229 ; sc:citation , "pmcid:PMC7852309", "pubmed:33543012" ; sc:description """In-silico definition of the Drosophila melanogaster matrisome. The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster< i> has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans< i>""" ; sc:featureList edam:operation_0269, edam:operation_0310, edam:operation_3663 ; sc:name "matrisome" ; sc:url "http://matrisome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_1419, edam:format_3475 ; sc:name "Position frequency matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1246 ; sc:name "Sequence cluster (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_2330 ; sc:name "Position frequency matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3511 ; sc:author "Jaime Castro-Mondragon" ; sc:citation ; sc:contributor "Denis Thieffry", "Jacques van Helden", "Morgane Thomas-Chollier" ; sc:description "Taking as input one or several sets of position-specific scoring matrices, this program applies hierarchical clustering to identify clusters of similar motifs. It produces a set of trees (one per cluster) and builds branch motifs at each node of each tree by merging the matrices of all descendent nodes." ; sc:featureList edam:operation_0240, edam:operation_3459 ; sc:isAccessibleForFree true ; sc:name "matrix-clustering" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2017-01" ; sc:url "http://rsat.eu/" ; biotools:primaryContact "Jacques van Helden", "Jaime Castro-Mondragon", "Morgane Thomas-Chollier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053, edam:topic_3365, edam:topic_3382, edam:topic_3518 ; sc:citation "pubmed:12538257" ; sc:description "Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast,easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. A web interface is included." ; sc:featureList edam:operation_0335, edam:operation_2409, edam:operation_2422 ; sc:name "Matrix2png" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://chibi.ubc.ca/matrix2png" ; biotools:primaryContact "Paul Pavlidis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:22492648" ; sc:description "Model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors." ; sc:featureList edam:operation_2945 ; sc:name "Matrix eQTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/" ; biotools:primaryContact "Andrey A. Shabalin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "MatrixCGH is an extensible software framework for array CGH processing" ; sc:featureList edam:operation_2409 ; sc:name "MatrixCGH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.52" ; sc:url "http://www.informatik.uni-ulm.de/ni/staff/HKestler/mcgh2/doc.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2855 ; sc:name "Distance matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:18033794" ; sc:description "A Matlab toolbox for fuzzy clustering of a symmetric matrix, typically the weighted adjacency matrix of an undirected network." ; sc:featureList edam:operation_3432 ; sc:name "MatrixClust" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/MatrixClust" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0623 ; sc:citation , , "pmcid:PMC4383919", "pmcid:PMC6324007", "pubmed:20852260", "pubmed:25378329", "pubmed:30371822" ; sc:description "It is a database focused on interactions established by extracellular proteins and polysaccharides. 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In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space." ; sc:featureList edam:operation_2479 ; sc:name "Maxflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ekhidna.biocenter.helsinki.fi/gtg/start" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169, edam:topic_3517, edam:topic_3940 ; sc:citation ; sc:description """Robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments. MaxHiC is a background correcting model for General and Capture Hi-C experiments that assigns significance to the recorded interactions. 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For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios." ; sc:featureList edam:operation_2950, edam:operation_3214, edam:operation_3635, edam:operation_3694 ; sc:name "MaXIC-Q" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ms.iis.sinica.edu.tw/MaXIC-Q" ; biotools:primaryContact "Systems Proteomics Laboratory, Institute of Information Science, Academia Sinica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation ; sc:description "Automated tool for quantifying the total and air-free volume of the maxillary sinus based on computed tomography images. The quantification tool seeks to standardize maxillary sinus volume measurements, thus allowing better comparisons and determinations of factors that influence maxillary sinus size. The automated tool utilized image processing techniques (watershed, threshold, and morphological operators)." ; sc:featureList edam:operation_3443 ; sc:name "Maxillary-Sinus-Quantification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dianapina/Maxillary-Sinus-Quantification" ; biotools:primaryContact "Diana Rodrigues de Pina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "MIP-viewer, in which the color represents the depth of the voxel with the maximum intensity." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Maximum Intensity Projection with color coding for depth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48633-maximum-intensity-projection-with-color-coding-for-depth" ; biotools:primaryContact "Job" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "Hybrid reference and de novo assembly pipeline" ; sc:featureList edam:operation_0310 ; sc:name "MAXIMUS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://maximuspipeline.sourceforge.net/main/" ; biotools:primaryContact "Aldrin Yim", "Allen Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2640 ; sc:citation "pubmed:24849579" ; sc:description "Thus tool find and rank cancer gene candidates by their connectivity to known cancer genes. 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Cowell" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1470 ; sc:name "C-alpha trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:author "Liisa Holm" ; sc:citation , ; sc:description "Generate protein backbone and side chain co-ordinates from a C(alpha) trace." ; sc:featureList edam:operation_0477 ; sc:name "MaxSprout (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Helsinki" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/structure/maxsprout/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:20375461" ; sc:description "Extensible platform for visual data exploration and interactive analysis and provides many methods for dissecting complex transcriptome datasets." ; sc:featureList edam:operation_0571, edam:operation_2495 ; sc:name "MAYDAY" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www-ps.informatik.uni-tuebingen.de/mayday/wp/?p=134" ; biotools:primaryContact "Kay Nieselt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655, edam:format_3752 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655, edam:format_3752 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Estimates protein identification false discovery rates." ; sc:featureList edam:operation_2238, edam:operation_3441, edam:operation_3648 ; sc:name "Mayu" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://proteomics.ethz.ch/muellelu/web/LukasReiter/Mayu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "To address the challenge of simulating realistic microbiome data, we designed a novel simulation framework termed MB-GAN, by using a generative adversarial network (GAN) and utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from a given microbial abundances and compute simulated abundances that are indistinguishable from it. In practice, MB-GAN showed the following advantages. First, MB-GAN avoids explicit statistical modeling assumptions, and it only requires real datasets as inputs. Second, unlike the traditional GANs, MB-GAN is easily applicable and can converge efficiently. MB-GAN is freely available at: https://github.com/zhanxw/MB-GAN" ; sc:name "MB-GAN" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/zhanxw/MB-GAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_2814 ; sc:citation "pubmed:16646822" ; sc:description "Java program for automated assignment and assessment of uncertainty of protein backbone NMR. It is based on a statistical model for NMR spectra, and employs a tree-based algorithm of stochastic optimization." ; sc:featureList edam:operation_0474 ; sc:name "MBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.stat.purdue.edu/~ovitek/mba/mba.html" ; biotools:primaryContact "Olga Vitek Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3295, edam:topic_3511 ; sc:citation ; sc:description "This package provides a function for reconstructing DNA methylation values from raw measurements. 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Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress input sequences, pick syncmers from hpc-compressed sequences, connect syncmers with an edge if they are adjacent in a read, unitigify. Suggested input is PacBio HiFi/CCS reads. May or may not work with Illumina reads. Algorithmic details: https://www.biorxiv.org/content/10.1101/2020.09.18.303156v1.""" ; sc:featureList edam:operation_0524, edam:operation_3216, edam:operation_3472 ; sc:license "MIT" ; sc:name "MBG" ; sc:url "https://anaconda.org/bioconda/mbg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3344 ; sc:citation , "pmcid:PMC8719748", "pubmed:34972193" ; sc:description "A Shiny application for teaching model-based geostatistics to population health scientists." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MBGapp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://olatunjijohnson.shinyapps.io/mbgapp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622 ; sc:citation ; sc:description """Multiple Bacteria Genome Compressor. Multiple Bacteria Genome Compressor (MBGC) is a tool for compressing genomes in FASTA (or gzipped FASTA) input format. It is tailored for fast and efficient compression of bacteria species collections.""" ; sc:name "MBGC" ; sc:url "http://github.com/kowallus/mbgc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0625 ; sc:citation "pubmed:19906735" ; sc:description "The microbial genome database for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature is that it allows users to create ortholog groups using a specified subgroup of organisms." ; sc:featureList edam:operation_0362, edam:operation_3194, edam:operation_3672 ; sc:name "Microbial Genome Database (MBGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mbgd.genome.ad.jp/" ; biotools:primaryContact "Ikuo Uchiyama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3071 ; sc:citation ; sc:description "Search MBInfo database for interactions using a protein id." ; sc:featureList edam:operation_2422 ; sc:name "MBInfo" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/MICommunity/psicquic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Fast clustering for single cell data using mini-batch k-means. 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Rancoita" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820, edam:topic_3534 ; sc:citation "pubmed:27048983" ; sc:description "Profile Hidden Markov Model based method capable of predicting membrane binding proteins (MBPs)." ; sc:featureList edam:operation_2575 ; sc:name "MBPpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://aias.biol.uoa.gr/MBPpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3518 ; sc:citation ; sc:description "Microarray Blob Remover is a microarray tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step. 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GerberEmail author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0769, edam:topic_2275, edam:topic_3277, edam:topic_3474 ; sc:citation , "pmcid:PMC10348832", "pubmed:37417958" ; sc:description "A posteriori sampling of important protein conformations from biomolecular simulations." ; sc:featureList edam:operation_0244, edam:operation_0335, edam:operation_0478, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MDSubSampler" ; sc:url "https://github.com/alepandini/MDSubSampler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3314, edam:topic_3318, edam:topic_3372 ; sc:citation , "pmcid:PMC9921696", "pubmed:36774469" ; sc:description "MDSuite is a software designed specifically for the molecular dynamics community to enable fast, reliable, and easy-to-run calculations from simulation data." ; sc:featureList edam:operation_0244, edam:operation_2422, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MDSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zincware/MDSuite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:description "It prepares a raw frequency table, given information from MODELLER alignments and/or PDB files. The sample for generating the frequencies N is obtained depending on the type of features a, b, c, …, d. The sample can contain individual proteins, pairs of proteins, pairs of residues in proteins, pairs of aligned residues, pairs of aligned pairs of residues, chemical bonds, angles, dihedral angles, and pairs of tuples of atoms." ; sc:featureList edam:operation_2479 ; sc:name "MDT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "5.3" ; sc:url "http://salilab.org/mdt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3335, edam:topic_3382, edam:topic_3390 ; sc:citation , "pmcid:PMC9931248", "pubmed:36812612" ; sc:description "A deep learning approach replicating ophthalmologist's diagnostic process of arteriolosclerosis." ; sc:featureList edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MDTNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/conscienceli/MDTNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168 ; sc:citation ; sc:description "A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value." ; sc:featureList edam:operation_3644 ; sc:license "Artistic-2.0" ; sc:name "MDTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MDTS.html" ; biotools:primaryContact "Jack M.. Fu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1964 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0176, edam:topic_2275, edam:topic_3306 ; sc:citation ; sc:description "Web-based platform to help access to molecular dynamics (MD). The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories are also incorporated." ; sc:featureList edam:operation_0570, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:name "MDWeb" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://mmb.irbbarcelona.org/MDWeb2" ; biotools:primaryContact "Institute for Research in Biomedicine Barcelona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0749, edam:topic_0798, edam:topic_3168 ; sc:citation , "pmcid:PMC7035633", "pubmed:32110248" ; sc:description """Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. ME-Scan analysis codes for the Alu, LINE, and SVA libraries. MEScanner is an intergrated tool for identifying polymorphic mobile element insertions (MEIs) using targeted high throughput sequencing.""" ; sc:featureList edam:operation_0427, edam:operation_3194, edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "ME-Scan" ; sc:url "https://github.com/JXing-Lab/ME-SCAN_2018" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3063, edam:topic_3305, edam:topic_3418 ; sc:citation , "pmcid:PMC8633963", "pubmed:34877511" ; sc:description "A site to help depressed patients select an antidepressant tahat is most likely to help them" ; sc:isAccessibleForFree true ; sc:name "Me Again Meds" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hi.gmu.edu/ad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3173, edam:topic_3674 ; sc:citation ; sc:description "A Methylomic and Epigenomic Allele-specific analysis pipeline" ; sc:featureList edam:operation_0487, edam:operation_3207, edam:operation_3227, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MEA" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/julienrichardalbert/MEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:16624918" ; sc:description "Fortran program to estimate the admixture proportions and genetic drift using DNA sequence data, based on a coalescent estimator." ; sc:featureList edam:operation_2478 ; sc:name "MEAdmix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zsl.org/science/software/meadmix" ; biotools:primaryContact "Prof. Ken Norris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:25480373" ; sc:description "Performs functional/pathway enrichment test while integrating network information from biological interactome (e.g. protein-protein interaction network) using graphical algorithm techniques." ; sc:featureList edam:operation_2436 ; sc:name "MEAGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/MEAGA" ; biotools:primaryContact "Alex Lam C Tsoi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3033 ; sc:name "Processed microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_2885, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description "Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated." ; sc:featureList edam:operation_3204 ; sc:license "Artistic-2.0" ; sc:name "MEAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MEAL.html" ; biotools:primaryContact "Carlos Ruiz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3374 ; sc:description "The process of mean-centering is to calculate the average spectrum of the data set and subtract that" ; sc:featureList edam:operation_0337, edam:operation_3755, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "Mean centering spectrum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42556-mean-centering-spectrum" ; biotools:primaryContact "reza ha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation "pubmed:23605045" ; sc:description "A tool for comparative genomics aiming to aid researchers in identifying and visualizing Structural Variations with the use of Hilbert curves" ; sc:name "Meander" ; sc:url "https://sites.google.com/site/meanderviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0610, edam:topic_3293, edam:topic_3500, edam:topic_3673 ; sc:citation , "pubmed:34941991" ; sc:description "An efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MEANGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YanCCscu/meangs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3569 ; sc:citation , "pmcid:PMC5018365", "pubmed:27153663" ; sc:description "Moment Expansion Approximation, iNference and Simulation (MEANS) is a tool implementing an efficient moment expansion approximation with parametric closures that integrates well with the IPython interactive environment" ; sc:featureList edam:operation_3562 ; sc:license "MIT" ; sc:name "MEANS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/theosysbio/means" ; biotools:primaryContact "Michael P. H. Stumpf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "MEAP is an R package for large-scale exon array data analysis.It includes a novel algorithm (PM-BayesBG) to estimate sequence-based backgrounds that allows more reliable expression estimation than the existing background correction methods. MEAP also contains algorithms for generating robust expression estimates at exon, alternatively spliced variant and gene levels that facilitates the quantitative analysis of alternative spliced variants in the whole transcriptome." ; sc:featureList edam:operation_2495 ; sc:name "MEAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.2" ; sc:url "http://csbi.ltdk.helsinki.fi/meap/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3306 ; sc:citation , "pubmed:32648042" ; sc:description """A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity. 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It can automatically recognize the active site of the given metalloenzyme, extract active site features, and superimpose metalloenzymes. This tool can be used to find important information to develop new specific metalloenzyme inhibitors, and it will be also useful for protein function prediction, drug repurposing, inhibitor selectivity investigation, and so on." ; sc:featureList edam:operation_1831, edam:operation_1834, edam:operation_3898 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MeCOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mecom.ddtmlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC9235486", "pubmed:35758820" ; sc:description "A new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites." ; sc:featureList edam:operation_3186, edam:operation_3207, edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MeConcord" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WangLabTHU/MeConcord" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2815 ; sc:citation , "pubmed:34311414" ; sc:description "An R package for measurement error correction in linear regression models with a continuous outcome." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "mecor" ; sc:url "https://github.com/LindaNab/mecor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654 ; sc:citation ; sc:description "MED is a non-supervised prokaryotic gene prediction method which integrates MED2.0 and TriTISA, an iterative self-learning translation initiation site (TIS) prediction algorithm. As the update of MED2.0, MED 2.1 modifies the TIS model by replacing the previous one to TriTISA, which imoroves the prediction accuracies for both 3′ and 5′ ends." ; sc:featureList edam:operation_2423, edam:operation_2454 ; sc:name "MED" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "2.1" ; sc:url "http://cqb.pku.edu.cn/ZhuLab/med2_1/MED2.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:32622194" ; sc:description """A clinical decision support tool for differential diagnosis of TMA with enhanced accuracy using an ensemble method. Failed to generate visualization... MED-TMA: Machine learning-based Ensemble model for Diagnosis of TMA.""" ; sc:featureList edam:operation_0337, edam:operation_3936 ; sc:name "MED-TMA" ; sc:url "http://hematology.snu.ac.kr/medtma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0218, edam:topic_3384 ; sc:citation ; sc:description "A medication extraction algorithm for electronic health records using the R programming language | Objective: We developed medExtractR, a natural language processing system to extract medication dose and timing information from clinical notes. Our system facilitates creation of medication-specific research datasets from electronic health records. Materials and Methods: Written using the R programming language, medExtractR combines lexicon dictionaries and regular expression patterns to identify relevant medication information ('drug entities'). 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An rooted directed minimal spanning tree (RDMST) to represent aneuploidy evolution of tumor cells. The focal and broad copy number alterations associated with lineage expansion.""" ; sc:featureList edam:operation_0546, edam:operation_2436, edam:operation_3478 ; sc:license "MIT" ; sc:name "MEDALT" ; sc:url "https://github.com/KChen-lab/MEDALT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33084905" ; sc:description """A Metazoan Developmental Alternative Splicing database. 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Free trial available.""" ; sc:featureList edam:operation_3096, edam:operation_3454, edam:operation_3659, edam:operation_3891 ; sc:name "MedCalc" ; sc:url "http://www.medcalc.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3168, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC7263192", "pubmed:32424069" ; sc:description """Analysis of transcription factor binding motifs in accessible chromatin. 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It applies matrix factorization with biologically motivated constratints and regularization to discover and quantify latent components in methylomes of multi-cellual samples." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:name "MeDeCom" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Hein Lab", "Walter lab", "hdhub" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "http://public.genetik.uni-sb.de/medecom/" ; biotools:primaryContact "Pavlo Lutsik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820, edam:topic_2275 ; sc:citation "pubmed:20926421" ; sc:description "A MP(Membrane proteins)-specific homology-based coordinate generation method,  which is optimized to build highly reliable core models." ; sc:featureList edam:operation_0477 ; sc:name "MEDELLER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opig.stats.ox.ac.uk/webapps/medeller/home.pl?app=MEDELLER" ; biotools:primaryContact "Charlotte Deane" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3063, edam:topic_3303 ; sc:citation , "pmcid:PMC8460636", "pubmed:34556781" ; sc:description "MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "MEDI-2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.vumc.org/wei-lab/medi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071, edam:topic_3314, edam:topic_3407, edam:topic_3500 ; sc:citation , "pubmed:36134710" ; sc:description "A Database of Chemically-Defined Growth Conditions. 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The depository support training and testing BERT-CNN model on three medical relation extraction corpora: BioCreative V CDR task corpus, traditional Chinese medicine literature corpus, and i2b2 temporal relation corpus. This is an implementation of BERT-CNN model used in our paper "A General Approach for Improving Deep Learning-based Medical Relation Extraction using a Pre-trained Model and Fine-tuning".""" ; sc:featureList edam:operation_3625, edam:operation_3778, edam:operation_3907 ; sc:license "MIT" ; sc:name "medical relation extraction" ; sc:url "https://github.com/chentao1999/MedicalRelationExtraction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC7319183", "pubmed:32237745" ; sc:description """A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. MEDICASCY is a multi-label based boosted random forest machine learning method that predicts small molecule’s side effects, indications, efficacy and mode of action proteins. MEDICASCY server takes a small molecule’s SMILES string (example: CC(C)(c1ccc(O)cc1)c2ccc(Cl)cc2 ) as input and predicts the molecule’s side effects and indications and sends output via user provided email to the user.""" ; sc:featureList edam:operation_2489, edam:operation_3092, edam:operation_3938 ; sc:name "MEDICASCY" ; sc:url "http://pwp.gatech.edu/cssb/MEDICASCY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_3943 ; sc:citation ; sc:description "Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2. Chromosomal instability (CIN) and somatic copy number alterations (SCNA) play a key role in the evolutionary process that shapes cancer genomes. SCNAs comprise many classes of clinically relevant events, such as localised amplifications, gains, losses, loss-of-heterozygosity (LOH) events, and recently discovered parallel evolutionary events revealed by multi-sample phasing. These events frequently appear jointly with whole genome doubling (WGD), a transformative event in tumour evolution, which generates tetraploid or near-tetraploid cells. WGD events are often clonal, occuring before the emergence of the most recent common ancestor, and have been associated with increased CIN, poor patient outcome and are currently being investigated as potential therapeutic targets" ; sc:featureList edam:operation_0323, edam:operation_0487, edam:operation_3454, edam:operation_3745 ; sc:license "GPL-3.0" ; sc:name "MEDICC2" ; sc:url "https://bitbucket.org/schwarzlab/medicc2" ; biotools:primaryContact "Roland F Schwarz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:36178571" ; sc:description "MedicDeepLabv3plus is a convolutional neural network based on DeepLabv3+ implemented in Python and Pytorch to extract the brain mask and the contralateral hemisphere of rodent MRI brain scans with lesions." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MedicDeepLabv3+" ; sc:url "https://github.com/jmlipman/MedicDeepLabv3Plus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3295, edam:topic_3316, edam:topic_3674 ; sc:citation , "pmcid:PMC10348834", "pubmed:37402621" ; sc:description "Automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis." ; sc:featureList edam:operation_3218, edam:operation_3436, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MEDIPIPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yzeng-lol/MEDIPIPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC3892689", "pubmed:24227674" ; sc:description "This tool was developed for analyzing data derived from Methylated DNA ImmunoPrecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, it provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis." ; sc:featureList edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "MEDIPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MEDIPS.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1088 ; sc:name "Article ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0972 ; sc:name "Text mining report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0218 ; sc:citation , "pmcid:PMC2703945", "pubmed:19429696" ; sc:description "This web server offers a flexible and fast statistical ranking of PubMed abstracts for topics of interest without expert knowledge." ; sc:featureList edam:operation_0305, edam:operation_0306 ; sc:name "Medline Ranker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbdm.uni-mainz.de/medlineranker" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218 ; sc:citation "pubmed:19429696" ; sc:description "The MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge." ; sc:featureList edam:operation_0306 ; sc:name "MedlineRanker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbdm-01.zdv.uni-mainz.de/~jfontain/cms/?page_id=4" ; biotools:primaryContact "Jean Fred Fontaine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3656, edam:topic_3674 ; sc:citation ; sc:description "A tool allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments." ; sc:featureList edam:operation_3809 ; sc:license "GPL-2.0" ; sc:name "MEDME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MEDME.html" ; biotools:primaryContact "Mattia Pelizzola" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3179, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:10631500" ; sc:description "MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters. The PubMed search can also be done independently of a microarray gene set. Results are grouped based on a set of relational keywords." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "MedMiner" ; sc:url "http://discover.nci.nih.gov/host/1999_medminer_abstract.jsp" ; biotools:primaryContact "MedMiner Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_3071 ; sc:citation , "pubmed:35960154" ; sc:description "An open-source data management system for tracking environmental DNA samples and metadata." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "medna-metadata" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://demo.metadata.maine-edna.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2275, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15991337" ; sc:description "MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site." ; sc:featureList edam:operation_0445, edam:operation_0478, edam:operation_0482, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MEDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://medock.ee.ncku.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0601, edam:topic_0621, edam:topic_0780, edam:topic_2640 ; sc:citation , "pmcid:PMC8342855", "pubmed:34527190" ; sc:description "MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex and rarely explored domain of Mediator proteins and its implications in all eukaryotic kingdoms." ; sc:featureList edam:operation_0253, edam:operation_0417, edam:operation_0495, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "MedProDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nipgr.ac.in/MedProDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053 ; sc:description "MedSavant is a tool that helps find the genetic causes of disease." ; sc:featureList edam:operation_2421 ; sc:name "MedSavant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.6" ; sc:url "http://www.genomesavant.com/p/medsavant/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC8684237", "pubmed:34922517" ; sc:description "A portable and customizable annotation tool for biomedical documents." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3283, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MedTAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MedTAG/medtag-core" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0218, edam:topic_3303, edam:topic_3500 ; sc:citation , "pubmed:34983060" ; sc:description "MedTator is a serverless text annotation tool for corpus development. It is built on HTML5 techniques and many open-source packages, and was designed to be easy-to-use for your annotation task." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MedTator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ohnlp.github.io/MedTator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0797 ; sc:author "Emanuele Bosi" ; sc:citation ; sc:description "Algorithm for genome scaffoldin which exploits information obtained from a set of genomes from related organisms to determine the correct order and orientation of the contigs. It formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. It does not require either prior knowledge on the microrganisms dataset under analysis or the availability of paired end read libraries." ; sc:featureList edam:operation_0525 ; sc:name "MeDuSa" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-FIRENZE", "University of Florence" ; sc:softwareHelp ; sc:softwareVersion "1.6" ; sc:url "http://combo.dbe.unifi.it/medusa" ; biotools:primaryContact "Emanuele Bosi", "Marco Fondi", "Marco Galardini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0176, edam:topic_0736, edam:topic_2828 ; sc:citation , "pubmed:33972018" ; sc:description "MEDUSA (Multiclass flexibility prediction from sequences of amino acids) is a deep learning approach for prediction of protein flexibility from sequence. MEDUSA takes as input an amino acid sequence and returns a flexibility class of each residue in terms of the expected normalized B-factor value range. Prediction is simultaneously performed in two-, three- and five classes using a convolutional neural network trained on a dataset of non-redundant X-ray structures." ; sc:featureList edam:operation_0244, edam:operation_0474, edam:operation_2476 ; sc:name "MEDUSA" ; sc:url "https://www.dsimb.inserm.fr/MEDUSA" ; biotools:primaryContact "Jean-Christophe Gelly", "Tatiana Galochkina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation "pubmed:16188923", "pubmed:21978489" ; sc:description "Visualization of networks with multi-edge connections" ; sc:name "Medusa3" ; sc:url "https://sites.google.com/site/medusa3visualization/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3053, edam:topic_3125 ; sc:citation "pubmed:17934055" ; sc:description "Integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting, to enable feature selection from the high-dimensional search space of candidate binding sequences while avoiding overfitting." ; sc:featureList edam:operation_0445 ; sc:name "MEDUSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbio.mskcc.org/leslielab/software/medusa" ; biotools:primaryContact "Christina Leslie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3519 ; sc:citation "pubmed:11448885" ; sc:description "Tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects." ; sc:featureList edam:operation_0308 ; sc:name "medusa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sonnhammer.sbc.su.se/download/software/medusa/" ; biotools:primaryContact "Erik Shonhammer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC7213742", "pubmed:32348298" ; sc:description """Software to build and analyze ensembles of genome-scale metabolic network reconstructions. Medusa - Analysis of ensembles of metabolic network reconstructions. Medusa is a tool for constraint-based reconstruction and analysis (COBRA) of ensembles. It builds on the COBRApy package (https://github.com/opencobra/cobrapy) by extending most single-model functionality to efficient ensemble-scale analysis. Additionally, Medusa provides novel functions for the analysis of ensembles. Welcome to medusa’s documentation! — medusa 0.2.0 documentation. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3660 ; sc:license "MIT" ; sc:name "Medusapy" ; sc:softwareHelp , ; sc:url "https://github.com/opencobra/Medusa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation , "pubmed:36121943" ; sc:description "Medical Vision Language Learner (MedViLL), which adopts a BERT-based architecture combined with a novel multi-modal attention masking scheme to maximize generalization performance for both vision-language understanding tasks (diagnosis classification, medical image-report retrieval, medical visual question answering) and vision-language generation task (radiology report generation)." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MedViLL" ; sc:url "https://github.com/SuperSupermoon/MedViLL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_2229 ; sc:citation , "pmcid:PMC4847874", "pubmed:27120189" ; sc:description "Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks." ; sc:featureList edam:operation_2476 ; sc:name "MEDYAN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.medyan.org/" ; biotools:primaryContact "James Komianos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2640, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc:description "Meerkat is designed to identify structure variations (SVs) in human cancer genomes from paired end high throughput sequencing data." ; sc:featureList edam:operation_2403, edam:operation_3202, edam:operation_3228 ; sc:name "Meerkat" ; sc:url "http://compbio.med.harvard.edu/Meerkat/" ; biotools:primaryContact "Lixing Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3360, edam:topic_3379, edam:topic_3384 ; sc:citation , "pmcid:PMC8883304", "pubmed:35237353" ; sc:description "Application of the Meet-URO score to metastatic renal cell carcinoma patients treated with second- and third-line cabozantinib." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Meet-URO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://proviso.shinyapps.io/Meet-URO15_score/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3308, edam:topic_3697 ; sc:citation ; sc:description """Identifying temporal and spatial patterns of variation from multi-modal data using MEFISTO. This repository contains application of MEFISTO to simulated and multi-modal omics data:. MEFISTO provides an unsupervised approach to integrate multi-modal data with continuous structures among the samples, e.g. given by spatial or temporal relationships. The aim of MEFISTO is to exploit such relationships between samples in the dimensionality reduction and disentangle smooth sources of variation given by factors that change gradually along the covariate and other source of variation that are independent of the covariate. Furthermore, it enables to interpolate/extrapolate to unseen timepoints or locations.""" ; sc:featureList edam:operation_0244, edam:operation_2495, edam:operation_3935 ; sc:name "MEFISTO" ; sc:url "https://biofam.github.io/MOFA2/MEFISTO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC5134250", "pubmed:27905885" ; sc:description "This pipeline will merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality." ; sc:featureList edam:operation_0232, edam:operation_3695 ; sc:license "Apache-1.0" ; sc:name "MeFiT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/nisheth/MeFiT" ; biotools:primaryContact "Hardik I. Parikh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3068, edam:topic_3172, edam:topic_3303 ; sc:citation ; sc:description """A curated natural product database specific to secondary metabolites of medicinal fungi. Medicinal Fungi Secondary metabolites And Therapeutics. MeFSAT (Medicnal Fungi Secondary metabolites and Therapeutics). Medicinal Fungi Secondary Metabolite And Therapeutics (MeFSAT) is a curated database which has been constructed via literature mining followed by manual curation of information gathered from more than 900 published research articles, 6 specialized books on medicinal fungi and other existing resources.""" ; sc:featureList edam:operation_0267, edam:operation_0306, edam:operation_2488 ; sc:name "MeFSAT" ; sc:url "https://cb.imsc.res.in/mefsat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3053, edam:topic_3056, edam:topic_3293 ; sc:citation , , , , , , , , , , , , "pmcid:PMC2562624", "pmcid:PMC3203626", "pmcid:PMC3467750", "pmcid:PMC3840312", "pmcid:PMC5967553", "pmcid:PMC7086165", "pmcid:PMC8210823", "pmcid:PMC8233496", "pubmed:11751241", "pubmed:15260895", "pubmed:17488738", "pubmed:18417537", "pubmed:21546353", "pubmed:22923298", "pubmed:24132122", "pubmed:27004904", "pubmed:29722887", "pubmed:31904846", "pubmed:33892491", "pubmed:8019868" ; sc:description "Software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments." ; sc:featureList edam:operation_0540, edam:operation_0545, edam:operation_0547, edam:operation_0550, edam:operation_3197 ; sc:license "Proprietary" ; sc:name "MEGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.megasoftware.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:36529897" ; sc:description "Mega-scale Bayesian Regression methods for genome-wide prediction and association studies with thousands of traits." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MegaBayesC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Jiayi-Qu/Mega-BayesC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3174, edam:topic_3474, edam:topic_3577, edam:topic_3697 ; sc:citation , "pmcid:PMC9143510", "pubmed:35629336" ; sc:description "Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples." ; sc:featureList edam:operation_3435, edam:operation_3460, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MegaD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioHPC/MegaD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """Megadepth is also available under R/Bioconductor. megadepth: BigWig and BAM related utilities. This package provides an R interface to Megadepth by Christopher Wilks available at (). It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by .""" ; sc:featureList edam:operation_2422, edam:operation_3799, edam:operation_3802 ; sc:license "Artistic-2.0" ; sc:name "Megadepth" ; sc:url "https://github.com/ChristopherWilks/megadepth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275 ; sc:citation "pubmed:25100686" ; sc:description "Fft-based protein-protein docking system for all-to-all protein-protein interaction predictions." ; sc:featureList edam:operation_0478, edam:operation_2464 ; sc:name "MEGADOCK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.bi.cs.titech.ac.jp/megadock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "It is an integrated database of high-throughput structure-based PPI predictions." ; sc:featureList edam:operation_2464 ; sc:isAccessibleForFree true ; sc:name "MEGADOCK-Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bi.cs.titech.ac.jp/megadock-web/" ; biotools:primaryContact "Masahito Ohue", "Yutaka Akiyama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , , "pubmed:33661648" ; sc:description """A fast yet powerful approach to assess functional similarity across meta-omics data sets. Calculate semantic distance for sets of Gene Ontology terms.""" ; sc:featureList edam:operation_3672 ; sc:license "MIT" ; sc:name "MegaGO" ; sc:softwareHelp , ; sc:url "https://megago.ugent.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0610, edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:25609793" ; sc:description "Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible." ; sc:featureList edam:operation_0525 ; sc:name "MEGAHIT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/voutcn/megahit" ; biotools:primaryContact "L3 Bioinformatics Limited" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description """Mega-scale linear mixed models for genomic predictions with thousands of traits. Scripts to run all analyses and make all figures in the paper: MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits, by Daniel Runcie, Jiayi Qu, Hao Cheng and Lorin Crawford.""" ; sc:featureList edam:operation_3435, edam:operation_3791 ; sc:license "GPL-3.0" ; sc:name "MegaLMM" ; sc:url "https://github.com/deruncie/MegaLMM_analyses" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC10552921", "pubmed:37810401" ; sc:description "Web server and standalone pipeline for detecting and annotating LTR-retrotransposons in plant genomes." ; sc:featureList edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MegaLTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinformatics.um6p.ma/MegaLTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:23052906" ; sc:description "Computational pipeline for positional cloning of mutations by whole genome sequencing." ; sc:featureList edam:operation_3202 ; sc:name "MegaMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://wiki.med.harvard.edu/SysBio/Megason/MegaMapper" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Merge two large overlapping DNA sequences." ; sc:featureList edam:operation_0232, edam:operation_0288 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "megamerger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/megamerger.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Merge two large overlapping nucleic acid sequences." ; sc:featureList edam:operation_2478 ; sc:name "megamerger WS (husar)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/megamerger.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:17255551" ; sc:description "Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results." ; sc:featureList edam:operation_2403, edam:operation_3460 ; sc:name "MEGAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/" ; biotools:primaryContact "Huson DH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Comprehensive toolbox for interactively analyzing microbiome data. It can perform taxonomic analysis using the NCBI taxonomy. Perform functional analysis using InterPro2GO, SEED, eggNOG or KEGG. Make bar chartsm word clouds, Coronoi tree maps and other charts. Perform PCoA, clustering and networks." ; sc:featureList edam:operation_0323, edam:operation_0567, edam:operation_3460 ; sc:license "Proprietary" ; sc:name "MEGAN6" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ab.inf.uni-tuebingen.de/software/megan6/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC9991050", "pubmed:36825821" ; sc:description "Facilitating interactive access to metagenomic data on a server." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Megan Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://software-ab.cs.uni-tuebingen.de/download/megan6" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC3894707", "pubmed:24253915" ; sc:description "Perform genomic sequence annotations by uploading a sequence and selecting the species to query. Automatically runs several analysis and integrates the results to select the appropriate consensus exon-intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with GBrowse and the results can be downloaded in Microsoft Excel format." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_0436 ; sc:name "MEGANTE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://megante.dna.affrc.go.jp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3174, edam:topic_3324 ; sc:citation , "pmcid:PMC7751095", "pubmed:33349238" ; sc:description """Sensitive and rapid pathogen detection using metagenomic NGS data. Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference sequence of a close relative, or with a high load of mutations compared to its predecessors, read mapping fails due to a low similarity between the pathogen and reference sequence, which in turn leads to insensitive and inaccurate pathogen""" ; sc:featureList edam:operation_0310, edam:operation_0495, edam:operation_3198, edam:operation_3227 ; sc:name "MegaPath" ; sc:url "https://sourceforge.net/projects/megapath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0625, edam:topic_3174, edam:topic_3474, edam:topic_3577, edam:topic_3697 ; sc:citation , "pmcid:PMC7814621", "pubmed:33461494" ; sc:description """An interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning. MegaR: A user-friendly interactive machine learning interface for metagenomic analysis to identify and predict disease sample accurately. Machine learning has been utilized in many applications from biomedical imaging to business analytics. Machine learning is stipulated to be a strong method for diagnostics and even for determining therapeutics in future as we move to personalized medicine. MegaR provides an unprecedented opportunity to develop machine learning models from metagenomic data available publicly as well as to perform classification of data samples based on the optimal model we developed.""" ; sc:featureList edam:operation_3192, edam:operation_3359, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "MegaR" ; sc:url "https://github.com/BioHPC/MegaR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_2815 ; sc:citation , "pmcid:PMC9315191", "pubmed:35668699" ; sc:description "A parametric class of general hazard models for clustered survival data." ; sc:featureList edam:operation_3432, edam:operation_3659, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MEGH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FJRubio67/MEGH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "ur company provides aeps cash withdrawal service to the best of our abilities. It is easy to start serving customers once you download the mego app, register & begin using it." ; sc:name "Mego Pay" ; sc:url "https://mymego.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation "pubmed:22824070" ; sc:description "Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "Megraft" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://microbiology.se/software/megraft" ; biotools:primaryContact "Johan Bengtsson-Palme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3308, edam:topic_3391 ; sc:citation "pubmed:17518769" ; sc:description "MEGU is a web application that visualizes complex omics data of multiple layers simultaneously, including transcriptome, pro-teome, and metabolome, onto an integrated pathway diagram de-rived by connecting the individual KEGG pathway maps; the mapped images are generated in Scalable Vector Graphics for easy editing by hand or with computer programs or drawing software." ; sc:featureList edam:operation_3096 ; sc:name "MEGU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://megu.iab.keio.ac.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2258, edam:topic_2259 ; sc:citation , "pmcid:PMC4025564", "pubmed:24885957" ; sc:description "Open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics." ; sc:featureList edam:operation_2425 ; sc:name "MEIGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nautilus.iim.csic.es/~gingproc/meigo.html" ; biotools:primaryContact "Julio R. Banga", "Julio Saez-Rodríguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3572 ; sc:citation ; sc:description "A software suite based on metaheuristics for global optimization in systems biology and bioinformatics." ; sc:featureList edam:operation_2425 ; sc:license "GPL-3.0" ; sc:name "MEIGOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MEIGOR.html" ; biotools:primaryContact "Jose Egea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0219, edam:topic_0621, edam:topic_3068 ; sc:citation , "pmcid:PMC8415030", "pubmed:34485275" ; sc:description "A Manually Curated Database for Tracking and Predicting Genes Associated With Meiosis." ; sc:featureList edam:operation_2421, edam:operation_2454, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "MeiosisOnline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mcg.ustc.edu.cn/bsc/meiosis/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3510, edam:topic_3512 ; sc:citation , "pmcid:PMC7493370", "pubmed:32938397" ; sc:description """Improving score-based motif enrichment by incorporating sequence bias covariates. Motif Enrichment In Ranked Lists Of Peaks. This project analyzes the relative enrichment of transcription factor binding motifs found in peaks at the top or bottom of a given ranking/score. It does this by calculating motif enrichment using a logistic regression model that describes the likelihood of a motif being present in sequences with higher/lower scores, while accounting for the effect of multiple covariates. The design is based on MOODS and statsmodels. To get started using MEIRLOP, see our documentation, which gives you a quick idea of what goes into and out of MEIRLOP so you can use it for your own experiments. For a full usage example that downloads and generates all the data it needs on the fly, see our walkthrough, which recreates commands and output for the section "MEIRLOP identifies enriched TF binding motifs in DNase I Hypersensitive Sites" from the MEIRLOP manuscript.""" ; sc:featureList edam:operation_0239, edam:operation_2436, edam:operation_3222, edam:operation_3659, edam:operation_3891 ; sc:license "MIT" ; sc:name "MEIRLOP" ; sc:url "https://github.com/npdeloss/meirlop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0634, edam:topic_3293, edam:topic_3474 ; sc:citation , "pmcid:PMC8019903", "pubmed:33828582" ; sc:description "MEL-MP is a tool for De novo prediction of moonlighting proteins using multimodal deep ensemble learning." ; sc:featureList edam:operation_2488, edam:operation_3501, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "MEL-MP" ; sc:url "http://ml.csbg-jlu.site/mel-mp/" ; biotools:primaryContact "Wei Du" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0942 ; sc:name "2D PAGE image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation ; sc:description "Offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels." ; sc:featureList edam:operation_3443 ; sc:name "Melanie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:softwareVersion "8" ; sc:url "http://world-2dpage.expasy.org/melanie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218 ; sc:author "Andrés Cañada", "Martin Krallinger" ; sc:description "Text mining for melanoma." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3625 ; sc:name "MelanomaMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Spanish Cancer Research Center", "Spanish National Bioinformatics Institute", "cnio.es" ; sc:softwareVersion "0.1" ; sc:url "http://melanomamine.bioinfo.cnio.es/" ; biotools:primaryContact "Andrés Cañada", "Martin Krallinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3304, edam:topic_3334, edam:topic_3384, edam:topic_3421 ; sc:citation ; sc:description """Predictors of lesion location and postsurgical seizure freedom in focal cortical dysplasia. Website for Multi-centre Epilepsy Lesion Detection (MELD) Project. Updates from the Multi-centre Epilepsy Lesion Detection (MELD) Project. The Multi-centre Epilepsy Lesion Detection (MELD) project is an international collaboration dedicated to improving the detection of lesions in patients with drug-resistant epilepsy.""" ; sc:featureList edam:operation_3435 ; sc:name "MELD" ; sc:url "https://meldproject.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:17537821" ; sc:description "Run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MelinaII" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://melina2.hgc.jp/public/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Open source framework providing analysis methods for raw GC- and LC-MS metabolome datasets and offers methods to combine the respective results. Flexible tool pipelines allow both the import of pre-processed data as well as the integration of existing open source analysis packages such as XCMS, MassSpecWavelet or metaB. For the identification of metabolites based on mass spectra either the GMD database or user defined libraries in NIST are queried." ; sc:featureList edam:operation_2238, edam:operation_3203, edam:operation_3214, edam:operation_3215 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MeltDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bielefeld University", "CeBiTec", "bigi" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://meltdb.cebitec.uni-bielefeld.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097, edam:topic_0099, edam:topic_0654 ; sc:citation "pubmed:22591039" ; sc:description "Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA." ; sc:featureList edam:operation_2481 ; sc:name "Melting" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/compneur-srv/melting/" ; biotools:primaryContact "Nicolas Le Novère" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3068, edam:topic_3305 ; sc:citation ; sc:description """A user-friendly online tool for epidemiological investigation using High Resolution Melting data. R script for strains clustering/typing and epidemiological investigation using High Resolution Melting (HRM) temperatures. 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MEM uses rank aggregation to merge information from different datasets into a single global ordering with simultaneous statistical significance estimation. 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sc:name "Sequence motif" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:name "Statistical estimate score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:name "Statistical estimate score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1353 ; sc:encodingFormat edam:format_1360 ; sc:name "Sequence motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0736, edam:topic_0749, edam:topic_3125 ; sc:citation , "pubmed:16845028", "pubmed:19458158", "pubmed:7584402", "pubmed:7584439", "pubmed:8877500", "pubmed:8902357", "pubmed:9283754", "pubmed:9366496" ; sc:description "Unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains." ; sc:featureList edam:operation_0226, edam:operation_0230, edam:operation_0233, edam:operation_0236, edam:operation_0238, edam:operation_0239, edam:operation_0291, edam:operation_0300, edam:operation_0324, edam:operation_0327, edam:operation_0335, edam:operation_0337, edam:operation_0338, edam:operation_0361, edam:operation_0369, edam:operation_0415, edam:operation_0445, edam:operation_1812, edam:operation_2238, edam:operation_2421, edam:operation_2424, edam:operation_2426, edam:operation_2575, edam:operation_2995, edam:operation_3081, edam:operation_3096, edam:operation_3429, edam:operation_3434, edam:operation_3438, edam:operation_3480, edam:operation_3501 ; sc:name "MEME Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://meme-suite.org/" ; biotools:primaryContact "MEME Suite Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0166, edam:topic_0769, edam:topic_3169 ; sc:author ; sc:citation ; sc:description """memes is an R interface to the MEME Suite family of tools, which provides several utilities for performing motif analysis on DNA, RNA, and protein sequences. memes works by detecting a local install of the MEME suite, running the commands, then importing the results directly into R. A docker container for motif analysis in R using the memes packge. Currently, this container is build from the development branch of bioconductor_docker_meme, which builds a bioconductor docker image + the most current MEME Suite version. This container additionally contains an install of the most recent {memes} package along with all dependencies. It can be used to test out {memes} or to perform containerized data analysis. This repository contains all analysis code associated with the paper 'Memes: an R interface to the MEME Suite'. motif matching, comparison, and de novo discovery using the MEME Suite.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240, edam:operation_3222 ; sc:license "MIT" ; sc:name "memes" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/memes" ; biotools:primaryContact "Daniel J. McKay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0820, edam:topic_3524 ; sc:citation "pubmed:25957354" ; sc:description "Creates multi-component lipid bilayer membranes for molecular dynamics simulations." ; sc:featureList edam:operation_2476 ; sc:name "MemGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://memgen.uni-goettingen.de/" ; biotools:primaryContact "Dr. Jochen Hub" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3475 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3520 ; sc:author "Véronique Hourdel" ; sc:citation ; sc:description "This tool allows users to perform an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2997 ; sc:isAccessibleForFree true ; sc:name "MEMHDX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bioinformatics and Biostatistics Hub", "Institut Pasteur", "Structural Mass Spectrometry and Proteomics" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://memhdx.c3bi.pasteur.fr/" ; biotools:primaryContact "Marie-Agnès Dillies", "Stevenn Volant", "Sébastien Brier", "Véronique Hourdel" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0621, edam:topic_0820 ; sc:citation ; sc:description "Predictor for the subcellular localization of proteins associated or inserted in eukaryotes membranes." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:name "MemLoci" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mu2py.biocomp.unibo.it/memloci" ; biotools:primaryContact , "Andrea Pierleoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0153, edam:topic_0154, edam:topic_0736, edam:topic_0820 ; sc:citation , "pubmed:33119751" ; sc:description """The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. MemMoRF database of membrane associated disordered protein regions. Membrane-binding Molecular Recognition Features.""" ; sc:featureList edam:operation_0250, edam:operation_2476, edam:operation_3092, edam:operation_3431 ; sc:name "MemMoRF" ; sc:url "https://memmorf.hegelab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3474, edam:topic_3518, edam:topic_3674 ; sc:citation "pubmed:16845004" ; sc:description "Server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM)." ; sc:featureList edam:operation_0417, edam:operation_2454, edam:operation_3204 ; sc:name "MEMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MEMO-toolbox/MEMO" ; biotools:primaryContact "Eva-Maria Geissen", "Nicole E. Radde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Ms2 basEd saMple vectOrization (MEMO) is a method allowing a Retention Time (RT) agnostic alignment of metabolomics samples using the fragmentation spectra (MS2) of their consituents. The occurence of MS2 peaks and neutral losses (to the precursor) in each sample is counted and used to generate an MS2 fingerprint of the sample. These fingerprints can in a second stage be aligned to compare different samples." ; sc:isAccessibleForFree true ; sc:name "MEMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1.4" ; sc:url "https://github.com/mandelbrot-project/memo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2640 ; sc:citation "pubmed:23504936" ; sc:description "Method for identifying mutually exclusive driver networks in cancer. The method identifies networks defined by three properties: first, member genes are recurrently altered via somatic mutation or copy number changes; second, member genes are likely to participate in the same biological pathway or process, as determined from prior pathway and network knowledge; and third, genomic events within the network exhibit a statistically significant level of mutual exclusivity." ; sc:featureList edam:operation_3439 ; sc:name "MEMo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbio.mskcc.org/tools/memo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_0820, edam:topic_2275 ; sc:citation "pubmed:23640332" ; sc:description "Memoir is a web server for template based structure prediction for membrane proteins. Input is a structural template and sequence to be modelled." ; sc:featureList edam:operation_0267, edam:operation_0322, edam:operation_0474, edam:operation_0477, edam:operation_0481 ; sc:name "Memoir" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opig.stats.ox.ac.uk/webapps/memoir" ; biotools:primaryContact "Oxford Protein Informatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3407 ; sc:citation "pubmed:24532766" ; sc:description "Web based bioinformatics platform for the management, storage, and development of metabolic models. It supports the development of new models by providing a built in version control system which offers access to the complete reconstruction history." ; sc:featureList edam:operation_3660 ; sc:name "MEMOSys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://icbi.at/software/memosys/memosys.shtml" ; biotools:primaryContact "Zlatko Trajanoski (Director)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:description "Testing of metabolic models" ; sc:featureList edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "memote" ; sc:softwareHelp ; sc:url "https://github.com/opencobra/memote" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:citation "pubmed:19910368" ; sc:description "Database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and functional features and editable." ; sc:featureList edam:operation_0245, edam:operation_0269, edam:operation_0270, edam:operation_3092 ; sc:name "MeMotif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://projects.biotec.tu-dresden.de/memotif" ; biotools:primaryContact "Annalisa Marsico" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3892 ; sc:citation ; sc:description "MemProtMD is a database of over 5000 intrinsic membrane protein structures identified in the Protein Data Bank, inserted into simulated lipid bilayers using Coarse-Grained Self Assembly Molecular Dynamics simulations." ; sc:name "MemProtMD" ; sc:url "http://memprotmd.bioch.ox.ac.uk/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0621, edam:topic_0820 ; sc:citation ; sc:description "Prediction of topology and subcellular localization of Eukaryotic membrane proteins." ; sc:featureList edam:operation_0418, edam:operation_0422, edam:operation_0468, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:name "MemPype" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mu2py.biocomp.unibo.it/mempype" ; biotools:primaryContact "Andrea Pierleoni", "Pier Luigi Martelli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation , "pubmed:33118018" ; sc:description """Allowing mutations in maximal matches boosts genome compression performance. Memrgc is a tool for compression genome sequence. The program is written in C++11 and tested on Red Hat Enterprise Linux 7.5 (64 bit).""" ; sc:featureList edam:operation_2421, edam:operation_3211, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "memRGC" ; sc:url "https://github.com/yuansliu/memRGC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814 ; sc:citation ; sc:description "MEMSATSVM is a SVM (support vector machines) based TM (Transmembrane Protein) protein topology predictor." ; sc:featureList edam:operation_0271, edam:operation_0474, edam:operation_2423, edam:operation_2479 ; sc:name "MEMSAT-SVM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://bioinfadmin.cs.ucl.ac.uk/downloads/memsat-svm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3304, edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC9682919", "pubmed:36437986" ; sc:description "Correctness and response time distributions in the MemTrax continuous recognition task." ; sc:featureList edam:operation_2422, edam:operation_3283, edam:operation_3357 ; sc:isAccessibleForFree true ; sc:name "MemTrax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://memtrax.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820, edam:topic_2814 ; sc:citation "pubmed:17586467" ; sc:description "2-layer predictor for predicting membrane protein types, the first layer will predict whether the query sequence belongs to membrane proteins or not; and the second layer aims to predict exactly the membrane protein types when the output of the first layer is “membrane proteins”." ; sc:featureList edam:operation_0474 ; sc:name "MemType-2L" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/MemType/" ; biotools:primaryContact "Hong Bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3056 ; sc:citation ; sc:description "This software program performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several novel, statistical genetic tests. Data sets can consist of qualitative or quantitative traits, pedigree or population samples, limited loci or dense SNPs." ; sc:featureList edam:operation_3197 ; sc:license "Other" ; sc:name "Mendel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://software.genetics.ucla.edu/mendel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3053, edam:topic_3168 ; sc:description "This tool uses OpenCL kernels to rapidly impute genotypes using linkage disequilibrium patterns in unrelated subjects. It is appropriate for resequencing data." ; sc:featureList edam:operation_3557 ; sc:name "mendel-gpu" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/p/mendel-gpu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "Mendelgen is a plasmid editing app that features cloning, sequencing alignment, vaccine design tools, and more." ; sc:featureList edam:operation_0361, edam:operation_0491, edam:operation_0492, edam:operation_0560, edam:operation_0575, edam:operation_0578, edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "Mendelgen" ; sc:softwareHelp ; sc:url "https://mendelgen.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325 ; sc:citation ; sc:description "R-package for heuristic variant filtering." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Mendelian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:url "https://github.com/BartBroeckx/Mendelian" ; biotools:primaryContact , "Filip Van Nieuwerburgh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3053 ; sc:citation , "pmcid:PMC5510723", "pubmed:28398548" ; sc:description "Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods." ; sc:featureList edam:operation_2238 ; sc:name "MendelianRandomization" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/MendelianRandomization/" ; biotools:primaryContact "Stephen Burgess" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_3752 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1775, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Online tool created to help doctors and scientists to identify disease causing variants in human exome/genome sequencing data from patients with Mendelian disorders." ; sc:featureList edam:operation_3197, edam:operation_3672, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Mendel,MD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mendelmd.org/" ; biotools:primaryContact "Sérgio D. J. Pena" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3517 ; sc:citation ; sc:description """Gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. Initial set-up for standalone MendelVar usage. A new tool that blends your everyday work apps into one. It's the all-in-one workspace for you and your team.""" ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_3501 ; sc:name "MendelVar" ; sc:url "https://mendelvar.mrcieu.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3301, edam:topic_3305, edam:topic_3379, edam:topic_3673 ; sc:citation , "pubmed:33055180" ; sc:description """A Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications. Public databases for molecular typing and microbial genome diversity. A collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.""" ; sc:featureList edam:operation_0252, edam:operation_0560, edam:operation_2421, edam:operation_3840 ; sc:name "MenDeVAR" ; sc:url "https://pubmlst.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC5302834", "pubmed:28129330" ; sc:description "Topological gap-filling of genome-scale draft metabolic networks." ; sc:featureList edam:operation_3660, edam:operation_3715, edam:operation_3803 ; sc:license "GPL-3.0" ; sc:name "meneco" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.5" ; sc:url "https://bioasp.github.io/meneco/" ; biotools:primaryContact "Anne Siegel", "Sylvain Prigent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3305, edam:topic_3325, edam:topic_3360, edam:topic_3384 ; sc:citation , "pmcid:PMC6992687", "pubmed:32025573" ; sc:description """Individual-patient prediction of meningioma malignancy and survival using the Surveillance, Epidemiology, and End Results database. Meningioma.app is the companion app to our paper, "Individual-patient prediction of meningioma malignancy and survival using the Surveillance, Epidemiology, and End Results database". Individual-patient prediction of meningioma malignancy and survival.""" ; sc:featureList edam:operation_3196, edam:operation_3503, edam:operation_3659 ; sc:name "meningioma" ; sc:url "http://www.meningioma.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3301 ; sc:description "In silico typing of Neisseria meningitidis contigs." ; sc:featureList edam:operation_3196, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "meningotype" ; sc:url "https://github.com/MDU-PHL/meningotype" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3292 ; sc:citation , "pmcid:PMC8711798", "pubmed:34634538" ; sc:description "Multi-start Evolutionary Nonlinear OpTimizeR (MENOTR)." ; sc:featureList edam:operation_0455, edam:operation_0475 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MENOTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZachIngram/2021-MENOTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0820, edam:topic_3382, edam:topic_3542 ; sc:citation , "pmcid:PMC8023553", "pubmed:33822911" ; sc:description "MENSAdb (Data-Driven Molecular Design) is a thorough structural analysis of membrane protein dimers." ; sc:featureList edam:operation_2422, edam:operation_3192, edam:operation_3891, edam:operation_3937 ; sc:name "MENSAdb" ; sc:url "http://www.moreiralab.com/resources/mensadb" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3210 ; sc:encodingFormat edam:format_3590 ; sc:name "Genome index" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3492 ; sc:encodingFormat edam:format_3475 ; sc:name "Nucleic acid signature" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "A MLST caller based on a k-mer counting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes." ; sc:featureList edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MentaLiST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.2.1" ; sc:url "https://github.com/WGS-TB/MentaLiST" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3325 ; sc:author "Alberto Calderone" ; sc:citation , "pubmed:23900247" ; sc:contributor "Gianni Cesareni" ; sc:description "Resource for protein-protein interactions (PPI). It integrates data curated by experts in compliance with IMEx curation policies, using the PSICQUIC protocol to implement an automatic procedure that automatically aligns the integrated database with data regularly annotated by the primary databases" ; sc:featureList edam:operation_2421, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "mentha" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA", "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mentha.uniroma2.it/" ; biotools:primaryContact "Alberto Calderone", "Luana Licata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071 ; sc:description "A simple menu builder." ; sc:featureList edam:operation_3429 ; sc:name "menu-builder" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BioJS" ; sc:softwareHelp ; sc:softwareVersion "0.0.6" ; sc:url "https://github.com/greenify/menu-builder" ; biotools:primaryContact "greenify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3303 ; sc:citation , "pmcid:PMC7216538", "pubmed:32393166" ; sc:description """An interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny. Medical and Pharmaceutical Statistics Based on Shiny. MEPHAS is a shiny-based statistical software that was developed to support statistical data analyses for medical and pharmaceutical students, researchers, and doctors.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3664 ; sc:name "MEPHAS" ; sc:softwareHelp ; sc:url "https://alain003.phs.osaka-u.ac.jp/mephas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC9575187", "pubmed:36267125" ; sc:description "Motif Enrichment Positional Profiling (MEPP) quantifies a positional profile of motif enrichment along the length of DNA sequences centered on e.g. transcription start sites or transcription factor binding motifs." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MEPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/npdeloss/mepp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3047 ; sc:citation "pubmed:26231428" ; sc:description "Cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective." ; sc:featureList edam:operation_2426 ; sc:name "MEPSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioweb.cbm.uam.es/software/MEPSA/" ; biotools:primaryContact "Inigo Marcos-Alcalde", "Paulino G´omez-Puertas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3572, edam:topic_3674 ; sc:citation ; sc:description "MeQA is a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:name "MeQA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://life.tongji.edu.cn/meqa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:21876754" ; sc:description "De novo genome assembler from short reads." ; sc:featureList edam:operation_0524 ; sc:name "Meraculous" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jgi.doe.gov/data-and-tools/meraculous/" ; biotools:primaryContact "Eugene Goltsman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3295, edam:topic_3511 ; sc:citation "pubmed:26543174" ; sc:description "Versatile high performance toolkit for complete analysis of methylated RNA data." ; sc:featureList edam:operation_3204 ; sc:name "meRanTK" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www.icbi.at/software/meRanTK/merantk.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2640, edam:topic_3518 ; sc:citation "pubmed:26626150" ; sc:description "Web-based tool that can query a database comprising ~4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors." ; sc:featureList edam:operation_2495 ; sc:name "MERAV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://merav.wi.mit.edu/" ; biotools:primaryContact "Yoav Shaul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:citation ; sc:description "It is an orthology mapping program suitable for multiple genomes.Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes." ; sc:featureList edam:operation_2429, edam:operation_3429 ; sc:name "Mercator" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2013.01.11" ; sc:url "http://www.biostat.wisc.edu/~cdewey/mercator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3168 ; sc:citation , "pubmed:24237261" ; sc:description "Web server for genome scale functional annotation of plant sequence data." ; sc:featureList edam:operation_0362 ; sc:name "Mercator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mapman.gabipd.org/web/guest/app/Mercator" ; biotools:primaryContact "MARC LOHSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303 ; sc:citation ; sc:description "An R Package for Visualization of Distance Matrices | Clustering and Visualizing Distance Matrices | Defines the classes used to explore, cluster and visualize distance matrices, especially those arising from binary data" ; sc:featureList edam:operation_2939, edam:operation_3432 ; sc:license "Apache-2.0" ; sc:name "MercatorR" ; sc:url "https://cran.r-project.org/web/packages/Mercator/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625 ; sc:citation ; sc:description "Evaluate variant calls and its combination with k-mer multiplicity" ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3227, edam:operation_3472, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Merfin" ; sc:url "https://github.com/arangrhie/merfin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:37218737" ; sc:description "Multifunctional R pipeline for small molecule LC-MS/MS data processing, searching, and organizing." ; sc:featureList edam:operation_2421, edam:operation_2480, edam:operation_3767, edam:operation_3801 ; sc:name "meRgeION" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/daniellyz/meRgeION2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3518 ; sc:citation ; sc:description "This R extension studies gene expression array data. Its main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculates the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "MergeMaid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MergeMaid.html" ; biotools:primaryContact "Xiaogang Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602, edam:topic_3391, edam:topic_3517, edam:topic_3678 ; sc:citation , "pmcid:PMC5016927", "pubmed:27612452" ; sc:description "Multidimensional Data Integration. This web aplication serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. 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The pipeline has several steps as shown in the DAG below.""" ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3227 ; sc:name "MEScan" ; sc:url "https://github.com/MarkeyBBSRF/MEScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0798, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC9171953", "pubmed:35668366" ; sc:description "High-quality clustering of DNA sequences using the mean shift algorithm and alignment-free identity scores." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MeShClust" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "3.0" ; sc:url "https://github.com/BioinformaticsToolsmith/MeShClust2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0967 ; sc:encodingFormat edam:format_2195 ; sc:name "Ontology concept data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3509 ; sc:encodingFormat edam:format_2195 ; sc:name "Ontology mapping" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2195 ; sc:name "Ontology" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3071 ; sc:citation , "pmcid:PMC4343279", "pubmed:25887539" ; sc:description "The package is a unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interfaced to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "MeSHDbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MeSHDbi.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3344 ; sc:citation ; sc:description "NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. This tool supports enrichment analysis of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups." ; sc:featureList edam:operation_0227 ; sc:license "Artistic-2.0" ; sc:name "meshes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/meshes.html" ; biotools:primaryContact "Guangchuang Yu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:encodingFormat edam:format_2195, edam:format_2330 ; sc:name "Gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2195, edam:format_2330 ; sc:name "Ontology" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3509 ; sc:encodingFormat edam:format_2330 ; sc:name "Ontology mapping" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3572 ; sc:citation , "pmcid:PMC5032990", "pubmed:26036323" ; sc:description "A set of annotation maps describing the entire MeSH assembled using data from MeSH." ; sc:featureList edam:operation_2436 ; sc:license "Artistic-2.0" ; sc:name "meshr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/meshr.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2020, edam:format_2195 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2020, edam:format_2195 ; sc:name "Ontology" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063 ; sc:citation ; sc:description "Provide for measuring semantic similarity over MeSH headings and MEDLINE documents." ; sc:featureList edam:operation_3278, edam:operation_3352 ; sc:license "GPL-2.0" ; sc:name "MeSHSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MeSHSim.html" ; biotools:primaryContact "Jing ZHou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0091 ; sc:contributor , , ; sc:description "A tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MesKit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Niinleslie/MesKit" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_1317 ; sc:citation "pubmed:25673340" ; sc:description "Scientific tool designed to identify characteristic structures or components in heterogenous solutions from bulk-average data. It does this by evolving a population of ensembles containing candidate components, selecting only ensembles that fit the available experimental data better than their peers." ; sc:featureList edam:operation_2480 ; sc:name "MESMER" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/mesmer/" ; biotools:primaryContact "Mark P. Foster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3064, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC6824906", "pubmed:31527839" ; sc:description "Open-source light-sheet microscopes for imaging cleared tissue | Hardware documentation for the mesoSPIM microscope project | Control software for mesoSPIM microscopes | MATLAB tools for handling mesoSPIM data | The mesoSPIM (mesoscale selective plane illumination microscopy) project creates open-hardware microscopy platforms for imaging cleared tissue | Members of the mesoSPIM initiative organize a variety of workshops for the community" ; sc:featureList edam:operation_3552 ; sc:name "mesoSPIM initiative" ; sc:url "http://www.mesospim.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3489, edam:topic_3573 ; sc:citation , "pubmed:35559777" ; sc:description "A mesocosm database management system for environmental nanosafety." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "mesocosm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://aliayadi.github.io/MESOCOSM-database/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3332 ; sc:citation ; sc:description "A tool for stochastic simulation of reactions and diffusion." ; sc:featureList edam:operation_2426 ; sc:name "MesoRD" ; sc:operatingSystem "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://mesord.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3292, edam:topic_3375, edam:topic_3520 ; sc:citation , "pmcid:PMC6964822", "pubmed:31945070" ; sc:description """Automated recommendation of metabolite substructures from tandem mass spectra. MESSAR 0.1 (MEtabolite SubStructure Auto-Recommender).""" ; sc:featureList edam:operation_3801, edam:operation_3803, edam:operation_3860 ; sc:name "MESSAR" ; sc:url "http://messar.biodatamining.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC10386444", "pubmed:37512549" ; sc:description "Software for transforming messy research datasets into clean submissions to metabolomics workbench for public sharing." ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MESSES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://moseleybioinformaticslab.github.io/MESSES/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3500 ; sc:citation ; sc:description """Identifying signaling genes in spatial single cell expression data. MESSI (Mixture of Experts for Spatial Signaling genes Identification) is a predictive framework to identify signaling genes active in cell-cell interaction. It jointly models gene interactions within and between cells, using the recently developed spatial single cell expression data. MESSI combines the ability to subdivide cell types with multi-task learning to accurately infer the expression of a set of response genes based on signaling genes and to provide useful biological insights about key signaling genes and cell subtypes.""" ; sc:featureList edam:operation_0313, edam:operation_2454, edam:operation_3799 ; sc:license "MIT" ; sc:name "MESSI" ; sc:url "https://github.com/doraadong/MESSI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3344, edam:topic_3360 ; sc:citation , "pmcid:PMC2671167", "pubmed:19399185" ; sc:description "Collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression." ; sc:featureList edam:operation_2990, edam:operation_3223, edam:operation_3503 ; sc:license "EPL-1.0" ; sc:name "messina" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/messina.html" ; biotools:primaryContact "Mark Pinese" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3168, edam:topic_3169 ; sc:citation ; sc:description "The Motif Enrichment Tool (MET) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif. The tool is available for a number of model organisms (human, mouse, zebrafinch, stickleback, fruitfly, etc). It incorporates transcription factor DNA-specificity motifs taken from literature curation, bacterial one-hybrid assays, high-throughput SELEX experiments, and protein binding microarrays." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2436, edam:operation_3224 ; sc:name "MET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://veda.cs.uiuc.edu/MET/" ; biotools:primaryContact "Charles Blatti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC10066191", "pubmed:37002244" ; sc:description "Mass spectrum-oriented computational method for ion mobility-resolved untargeted metabolomics." ; sc:featureList edam:operation_3215, edam:operation_3799, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "Met4DX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZhuMetLab/Met4DX" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585, edam:format_3822 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:author "Clément Frainay", "Ludovic Cottret" ; sc:description "Java library for metabolic networks. Singularity and docker containers allow to use met4j without installing Java or computational skills. Met4j apps allow to parse and edit SBML and to analyse the network with graph analysis." ; sc:featureList edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.1" ; sc:name "met4j" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://forgemia.inra.fr/metexplore/met4j" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Enrique Blanco" ; sc:citation , "pmcid:PMC1464811", "pubmed:16733547" ; sc:description "meta is a program to produce and to align the TF-maps of two gene promoter regions. meta is very useful to characterize promoter regions from orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "meta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://big.crg.cat/services/meta" ; biotools:primaryContact "Enrique Blanco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3168, edam:topic_3174, edam:topic_3512 ; sc:citation ; sc:description "A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads." ; sc:featureList edam:operation_0265, edam:operation_0491, edam:operation_3198 ; sc:name "Meta-Align" ; sc:url "https://github.com/shravan-repos/Metaalign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0199, edam:topic_0203, edam:topic_0219, edam:topic_0622, edam:topic_3173, edam:topic_3534, edam:topic_3958 ; sc:citation , "pubmed:32750853" ; sc:description "META-BASE is a big repository of genomic datasets homogenized with the Genomic Data Model format, including Encode, TCGA, Roadmap Epigenomics, 1000 Genomes and others." ; sc:name "META-BASE" ; sc:url "http://www.bioinformatics.deib.polimi.it/GMQLsystem/datasets/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation "pubmed:15215454" ; sc:description "A tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure." ; sc:featureList edam:operation_0267, edam:operation_2416, edam:operation_2487, edam:operation_2488 ; sc:name "Meta-BASIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://basic.bioinfo.pl/" ; biotools:primaryContact "Krzysztof Ginalski", "Leszek Rychlewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3474 ; sc:citation , "pubmed:36222566" ; sc:description "META-BOA (METAbolomics data Balancing with Over-sampling Algorithms) is a software solution for handling sample imbalance primarily for metabolomics and lipidomics datasets." ; sc:featureList edam:operation_2939, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "META-BOA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://complimet.ca/meta-boa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3400, edam:topic_3678 ; sc:citation , "pmcid:PMC9707040", "pubmed:36443653" ; sc:description "A web application for meta-analysis of diagnostic test accuracy data." ; sc:featureList edam:operation_3435, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Meta-DiSc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.metadisc.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0160, edam:topic_0621, edam:topic_0632, edam:topic_0769, edam:topic_3050 ; sc:citation , "pubmed:34269417" ; sc:description "A generalised, dynamic DNA reference library for metabarcoding of fishes" ; sc:featureList edam:operation_3200, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Meta-Fish-Lib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/genner-lab/meta-fish-lib" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:encodingFormat edam:format_2333 ; sc:name "Taxonomic classification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Set of post-processing tools aimed at improving the taxonomical classification and at providing additional information to enhance metagenomics analyses. The developed tools provide additional proofs in the presence of low-abundant species, information of the mapping quality in coding and noncoding regions, etc." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "META-GECKO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "uma.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bitlab-es.com/gecko/template.php#META-GECKO" ; biotools:primaryContact "Esteban Pérez-Wohlfeil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3295, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:32910169" ; sc:description """An interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. DNA N6-Methyladenine Site predictor.""" ; sc:featureList edam:operation_0415, edam:operation_3659, edam:operation_3937 ; sc:name "Meta-i6mA" ; sc:softwareHelp ; sc:url "http://kurata14.bio.kyutech.ac.jp/Meta-i6mA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:32557165" ; sc:description """A sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation. PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using Scoring Card Method. In this work, we developed a novel PVP predictor named PVPred-SCM which is an efficient and interpretable method for predicting and analyzing PVPs.""" ; sc:featureList edam:operation_0244, edam:operation_3092, edam:operation_3936 ; sc:name "Meta-iPVP" ; sc:url "http://camt.pythonanywhere.com/Meta-iPVP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623 ; sc:citation "pubmed:9283754" ; sc:description "Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif." ; sc:featureList edam:operation_0239, edam:operation_0253, edam:operation_0338, edam:operation_0346, edam:operation_2426 ; sc:name "Meta-MEME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metameme.sdsc.edu/" ; biotools:primaryContact "Grundy W. 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META-pipe offers insight into the phylogenetic diversity, metabolic capabilities, and functional potential of these environmental communities. 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Meta-Prism aims to conduct quick query in large-scale metagenomics database. The method is based on three computational techniques: dual-indexing approach for sample sub-grouping, refined scoring function that could scrutinize the minute differences among samples, and parallel computation based on GPU computing.""" ; sc:featureList edam:operation_2421, edam:operation_3659, edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "Meta-Prism" ; sc:url "https://github.com/HUST-NingKang-Lab/metaPrism" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2209 ; sc:encodingFormat edam:format_2330 ; sc:name "Mutation ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2331 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0634 ; sc:author ; sc:citation "pmcid:PMC3839641", "pubmed:23819846" ; sc:description "Meta-predictor of disease causing variants." ; sc:featureList edam:operation_3225 ; sc:isAccessibleForFree true ; sc:name "Meta-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://snps.biofold.org/meta-snp" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_3071, edam:topic_3174 ; sc:citation "pubmed:24363375" ; sc:description "Metagenomic database system toolkit to systematically and efficiently organize and search metagenomic data." ; sc:featureList edam:operation_2421 ; sc:name "Meta-Storms" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://computationalbioenergy.org/meta-storms.html" ; biotools:primaryContact "Su, Xiaoquan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1154 ; sc:encodingFormat edam:format_2330 ; sc:name "KEGG object identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:author "Massimo Porcheddu" ; sc:description "Meta4P (MetaProteins-Peptides-PSMs Parser) is an easy-to-use bioinformatic application designed to integrate label-free quantitative metaproteomic data with taxonomic and functional annotations. 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A rule-based model of insulin signalling pathway. Di Camillo B, Sambo F, Toffolo G, Cobelli C. ABACUS: an entropy based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. Bioinformatics 30(3):384-391. Patuzzi I., Baruzzo G., Losasso C., Ricci A., Di Camillo B. "metaSPARSim: a 16S rRNA gene sequencing count data simulator", Submitted to BMC Bioinformatics, October 2018""" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3562, edam:operation_3799 ; sc:name "metaSPARSim" ; sc:url "http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3377 ; sc:citation , "pubmed:33306787" ; sc:description """A comprehensive database on adverse drug events. MetaADEDB is an online database we developed to integrate comprehensive information of adverse drug events (ADEs). The new version consists of 744,709 drug-ADE associations between 8,498 compounds (including more than 3000 drugs) and 13,193 ADEs by integrating more and newer data from U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Data-base in addition to the Comparative Toxicogenomics Database (CTD), SIDER and OFFSIDES. Additionally, Compared to the previous version, MetaADEDB 2.0 has an over 40% increase in drug-ADE associations and almost 200% growth in the total number of compounds. Notably, we directly generated a unique identifier for each compound based on the chemical structure, and UMLS ID was used as unique identifier for ADE to ensure the quality of data.""" ; sc:featureList edam:operation_2421 ; sc:name "MetaADEDB" ; sc:url "http://lmmd.ecust.edu.cn/metaadedb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3174, edam:topic_3335, edam:topic_3360 ; sc:citation , "pmcid:PMC9795700", "pubmed:36577938" ; sc:description "A user-friendly tool for metagenomic biomarker detection and phenotype classification." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "MetaAnalyst" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mshawaqfeh/MetaAnalyst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3071, edam:topic_3518 ; sc:citation ; sc:description "Data transformation for meta-analysis of microarray data: Transformation of gene expression data to signed probability scale (MCMC/EM methods). Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "metaArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metaArray.html" ; biotools:primaryContact "Hyungwon Choi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3172 ; sc:citation , "pubmed:21697128" ; sc:description "R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, it considerably speeds up the data mining process in metabolomics and produces better quality results." ; sc:featureList edam:operation_0335, edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "Metab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Metab.html" ; biotools:primaryContact "Raphael Aggio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0632, edam:topic_0654, edam:topic_0769 ; sc:citation ; sc:description """An R package for the evaluation and improvement of DNA metabarcoding data quality. Evaluation and Improvement of DNA Metabarcoding Data Quality. metabaR is an R package enabling the import, handling and processing of DNA metabarcoding data that have been already processed through bioinformatic pipelines. It provides functions to reveal and filter common molecular artifacts produced during the experimental workflow. This package can be easily used in combination with others R packages commonly used in ecology (vegan, ade4, ape, picante, etc.), and provides flexible graphic systems based on ggplot2 to visualise the data under both ecological and experimental perspectives.""" ; sc:featureList edam:operation_0337, edam:operation_3797 ; sc:name "metabaR" ; sc:url "https://metabarfactory.github.io/metabaR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0621, edam:topic_2259, edam:topic_3070, edam:topic_3489 ; sc:citation "pubmed:22139927" ; sc:description "The database of biological databases. A community-curated database containing more than 2000 commonly used biological databases." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_3561 ; sc:name "MetaBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://metadatabase.org/wiki/Main_Page" ; biotools:primaryContact "Dan M. Bolser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC7355282", "pubmed:32657364" ; sc:description "Metagenomics binning by coverage and composition for long reads." ; sc:featureList edam:operation_0310, edam:operation_3472, edam:operation_3798, edam:operation_3935 ; sc:license "GPL-2.0" ; sc:name "MetaBCC-LR" ; sc:url "https://github.com/anuradhawick/MetaBCC-LR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:33724799" ; sc:description "metabCombiner is a R package for paired untargeted LC-HR-MS metabolomics feature matching and concatenation of disparately acquired datasets." ; sc:featureList edam:operation_0310, edam:operation_3628, edam:operation_3633 ; sc:name "metabCombiner" ; sc:url "https://github.com/hhabra/metabCombiner" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:22496776" ; sc:description "Program for accurate, fast and highly sensitive taxonomic assignments of metagenomic sequences" ; sc:featureList edam:operation_3460 ; sc:name "MetaBin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://metabin.riken.jp/application" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "A high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities." ; sc:featureList edam:operation_0310, edam:operation_3798, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaBinner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ziyewang/MetaBinner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0821, edam:topic_3174, edam:topic_3297 ; sc:citation "pubmed:19906710" ; sc:description "MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes." ; sc:featureList edam:operation_0314, edam:operation_0362, edam:operation_0477, edam:operation_2422 ; sc:name "MetaBioME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metasystems.riken.jp/metabiome/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; 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sc:license "GPL-3.0" ; sc:name "MetaboAnalyst" ; sc:softwareHelp , , ; sc:softwareVersion "4.0", "5.0" ; sc:url "http://www.metaboanalyst.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3172 ; sc:author , "Faustine Souc" ; sc:contributor , , ; sc:description "Web portal to gather tools to improve metabolomic annotations through API microservices based on a cloud infrastructure." ; sc:featureList edam:operation_0226, edam:operation_2421 ; sc:name "metabocloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider , , ; sc:url "https://metabocloud.mesocentre.uca.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3172 ; sc:citation ; sc:description "Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome." ; sc:featureList edam:operation_3083 ; sc:name "MetaboCraft" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/argymeg/MetaboCraft/" ; biotools:primaryContact "Karl Burgess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0797, edam:topic_3172 ; sc:citation ; sc:description "Differential metabolomic analysis." ; sc:featureList edam:operation_3209 ; sc:license "MIT" ; sc:name "MetaboDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/andreasmock/MetaboDiff/" ; biotools:primaryContact "Andreas Mock" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3752 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC9936664", "pubmed:36803638" ; sc:description "An analytical pipeline for the processing of FT-ICR MS-based metabolomic data. A comprehensive command-line based pipeline for the analysis of direct injection FT-ICR mass spectrometry data." ; sc:featureList edam:operation_0226, edam:operation_2939, edam:operation_3215, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaboDirect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Coayala/MetaboDirect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_3172, edam:topic_3343, edam:topic_3520 ; sc:citation , "pubmed:32519713" ; sc:description """A comprehensive data extraction tool for untargeted metabolomics. We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis""" ; sc:featureList edam:operation_3215, edam:operation_3799, edam:operation_3803 ; sc:name "MetaboKit" ; sc:url "https://github.com/MetaboKit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407, edam:topic_3697 ; sc:citation ; sc:description "A scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes | A scalable high-throughput metabolic and biogeochemical functional trait profiler | This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets. These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or pure culture sequenced genomes. It can also calculate the genome coverage. The information is parsed and diagrams for elemental/biogeochemical cycling pathways (currently Nitrogen, Carbon, Sulfur and \"other\") are produced" ; sc:featureList edam:operation_1812, edam:operation_3660, edam:operation_3715 ; sc:name "metabolic" ; sc:url "https://github.com/AnantharamanLab/METABOLIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3298 ; sc:citation ; sc:description "Linking metabolic network features to phenotypes using sparse group lasso." ; sc:featureList edam:operation_2497 ; sc:name "Metabolic Network SGL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/metabolic-network-sgl/git/ci/master/tree/" ; biotools:primaryContact "Holger Fröhlich", "Satya Swarup Sama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:31879763" ; sc:description """A deep learning architecture for metabolic pathway prediction. This code is an implementation of our graph-convolutional network (GCN) and random forest (RF) classifiers for predicting one or many metabolic pathway classes for a query compound (paper accepted at Bioinformatics, Oxford University Press). Baranwal, Mayank, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, and Alfred Hero. "A deep learning architecture for metabolic pathway prediction." Bioinformatics (2019).""" ; sc:featureList edam:operation_0533, edam:operation_3439, edam:operation_3660 ; sc:license "Apache-2.0" ; sc:name "metabolic pathway prediction" ; sc:url "https://github.com/baranwa2/MetabolicPathwayPrediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , , , , "pubmed:26209309", "pubmed:32209698", "pubmed:34282017", "pubmed:36169223" ; sc:description "Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications. Metabolic Atlas is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. In short, the vision is to create a one-stop-shop for everything metabolism related." ; sc:featureList edam:operation_0533, edam:operation_0573, edam:operation_3926 ; sc:license "GPL-3.0" ; sc:name "Metabolic Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0 - 1.7", "2.0 - 2.6", "3.0 - 3.3+" ; sc:url "https://metabolicatlas.org" ; biotools:primaryContact "Mihail Anton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Database for Metabolomics experiments and derived information." ; sc:featureList edam:operation_0224 ; sc:name "MetaboLights" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI Databases" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/metabolights/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0160, edam:topic_0194, edam:topic_0602, edam:topic_3407 ; sc:citation ; sc:description """Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways. Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs. metabolisHMM: a tool for exploration of microbial phylogenies and metabolic pathways. Constructing phylogenies and performing functional annotations with HMM markers. Welcome to the metabolisHMM wiki!. metabolisHMM is a pipeline for visualizing the distribution and evolutionary relationships using curated and custom Hidden Markov Model (HMM) profiles. metabolisHMM is a tool for visualizing the distributions and evolutionary histories of specific metabolic markers""" ; sc:featureList edam:operation_0323, edam:operation_0337, edam:operation_0362 ; sc:license "GPL-3.0" ; sc:name "metabolisHMM" ; sc:softwareHelp ; sc:url "https://github.com/elizabethmcd/metabolisHMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:33196775" ; sc:description """An integrated userfriendly workflow for metabolomics multi-study analysis. This is a Shiny-App with the aim of facilitating association and covariate selection for targeted metabolomics data from multiple studies with a wide range of factors (demographic, lifestyle, etc.). Features of the App are:.""" ; sc:featureList edam:operation_1812, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Metabolite-Investigator" ; sc:url "https://apps.health-atlas.de/metabolite-investigator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "An application to process and visualise metabolite data in the web-browser." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3219, edam:operation_3803 ; sc:name "Metabolite_AutoPlotter" ; sc:url "https://mpietzke.shinyapps.io/autoplotter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172 ; sc:citation "pubmed:19358599" ; sc:description "QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments." ; sc:featureList edam:operation_2423 ; sc:name "MetaboliteDetector" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://metabolitedetector.tu-bs.de/" ; biotools:primaryContact "K. Hiller - Software Developer", "Nils koschnitzki - Administrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC6397295", "pubmed:30854222" ; sc:description "Metabolizer is a web tool for analysis of modular architecture of metabolic pathways using transcriptomic data. Metabolizer calculates impact of modules on production of metabolites. These modules are conserved part of metabolism which starts with substrate(s) and ends with a product." ; sc:isAccessibleForFree true ; sc:name "Metabolizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.7.0" ; sc:url "http://metabolizer.babelomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2259 ; sc:citation ; sc:description "Metabolome Searcher, a web-based tool, facilitates putative compound identification of MS output based on genome-restricted metabolic capability." ; sc:featureList edam:operation_2429 ; sc:name "Metabolome Searcher" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://procyc.westcent.usu.edu/cgi-bin/MetaboSearcher.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "An international data aggregation and notification service for metabolomics." ; sc:featureList edam:operation_2422 ; sc:name "MetabolomeXchange" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareHelp ; sc:url "http://metabolomexchange.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9512519", "pubmed:36177485" ; sc:description "MetabolomicsR is a streamlined R package to preprocess, analyze, and visualize metabolomic data." ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-2.0" ; sc:name "metabolomicsR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XikunHan/metabolomicsR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC5550549", "pubmed:28890673" ; sc:description "Freely-available software tools for metabolomics analysis." ; sc:featureList edam:operation_2421 ; sc:name "MetabolomicsTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RASpicer/MetabolomicsTools" ; biotools:primaryContact "Christoph Steinbeck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC7383707", "pubmed:32765840" ; sc:description """Pathway sharing and multi-omics data visualization in metabolic context. MetaboMAPS is a web project for manipulating metabolic pathways in SVG format. MetaboMAPS consists of two main parts: the visualization tool, where users can plot their own data set, and the plot box editor, where users can add or change the areas for visualization (plot boxes) and assign identifiers to them.""" ; sc:featureList edam:operation_0533, edam:operation_2422, edam:operation_2943, edam:operation_3926, edam:operation_3929 ; sc:license "GPL-3.0" ; sc:name "MetaboMAPS" ; sc:url "https://metabomaps.brenda-enzymes.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3382 ; sc:citation "pubmed:19040747" ; sc:description "Tool which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. It is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data." ; sc:featureList edam:operation_3715 ; sc:name "MetaboMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/metabominer/" ; biotools:primaryContact "Jianguo Xia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "metabomxtr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metabomxtr.html" ; biotools:primaryContact "Michael Nodzenski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3407 ; sc:description "A toolbox to interactively create, customize and explore multi-systemic metabolic reaction networks" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "MetaboNetworks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42684-metabonetworks" ; biotools:primaryContact "Joram Posma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172 ; sc:citation ; sc:description "A pipeline of metabolomics data processing and quality control" ; sc:featureList edam:operation_3435, edam:operation_3695, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "metaboprep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MRCIEU/metaboprep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3489 ; sc:citation ; sc:description "Performs mass-based metabolite search simultaneously against the four major metabolite databases: Human Metabolome DataBase (HMDB), Madison Metabolomics Consortium Database (MMCD), Metlin, and LipidMaps." ; sc:featureList edam:operation_2421 ; sc:name "metabosearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://omics.georgetown.edu/metabosearch.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3172 ; sc:citation , "pmcid:PMC5408820", "pubmed:28011775" ; sc:description "R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling or enzymatic genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes." ; sc:featureList edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "MetaboSignal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MetaboSignal.html" ; biotools:primaryContact "Andrea Rodriguez-Martinez", "Rafael Ayala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3172, edam:topic_3360, edam:topic_3407 ; sc:citation , "pmcid:PMC9965648", "pubmed:36837783" ; sc:description "Exploring Individual Variation in Metabolite Levels." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaboVariation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shubbham28/MetaboVariation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation ; sc:description """Automated exploration and contextualization of metabolic data. Visualizing and Analyzing Metabolic Networks. Integrating multi- or single-omic metabolic data upon the metabolic network can be challenging for a variety of reasons. Metaboverse seeks to simplify this task for users by providing a simple, user-friendly interface for layering their data on a dynamic representation of the metabolic network and automatically searching the network for interesting regulatory or other patterns. Additionally, Metaboverse provides several tools to enable the contextualization of metabolic data:.""" ; sc:featureList edam:operation_1781, edam:operation_3660, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "Metaboverse" ; sc:softwareHelp ; sc:url "https://github.com/Metaboverse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0602 ; sc:citation ; sc:description "Enabling network-based integrative analysis via direct protein interactors of metabolites." ; sc:featureList edam:operation_2949 ; sc:license "GPL-3.0" ; sc:name "MetaBridge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.metabridge.org/" ; biotools:primaryContact "Robert E W Hancock" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation ; sc:description "Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid" ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "metabuli" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://metabuli.steineggerlab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3174, edam:topic_3500, edam:topic_3837 ; sc:citation , "pmcid:PMC7069206", "pubmed:32164527" ; sc:description "A big data approach to metagenomics for all-food-sequencing." ; sc:featureList edam:operation_3432, edam:operation_3472, edam:operation_3799 ; sc:name "MetaCacheSpark" ; sc:url "https://github.com/jmabuin/MetaCacheSpark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC4920109", "pubmed:27153689" ; sc:description "Performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness." ; sc:featureList edam:operation_3659 ; sc:license "MIT" ; sc:name "metaCCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metaCCA.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation ; sc:description """Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning. MetaChrom is a transfer learning framework that takes advantage of both an extensive compendium of publicly available chromatin profiles data, and epigenomic profiles of cell types related to specific phenotypes of interest. It's capable of predicting the genomic variant effect on epigenomic profiles with single-nucleotide resolution. Please see paper for details.""" ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3227, edam:operation_3359 ; sc:license "GPL-3.0" ; sc:name "MetaChrom" ; sc:url "https://metachrom.ttic.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33085002" ; sc:description """A machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data. Detection of Low-Quality Peaks in Untargeted Metabolomics Data.""" ; sc:featureList edam:operation_2428, edam:operation_3215, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "MetaClean" ; sc:url "https://CRAN.R-project.org/package=MetaClean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3174, edam:topic_3293, edam:topic_3301 ; sc:citation "pubmed:24564377" ; sc:description "Unsupervised binning method for metagenomic sequences. Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorganisms and phylogenetic markers." ; sc:featureList edam:operation_0361 ; sc:name "MetaCluster" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://i.cs.hku.hk/~alse/MetaCluster/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description """A consensus approach to infer accurate copy numbers from low coverage data. The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples.""" ; sc:featureList edam:operation_3435 ; sc:name "MetaCNV" ; sc:url "https://bitbucket.org/sonnhammergroup/metacnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "MetaCoAG is a metagenomic contig binning tool that makes use of the connectivity information found in assembly graphs, apart from the composition and coverage information. MetaCoAG makes use of single-copy marker genes along with a graph matching technique and a label propagation technique to bin contigs. MetaCoAG is tested on contigs obtained from next-generation sequencing (NGS) data. Currently MetaCoAG supports contigs assembled using metaSPAdes and MEGAHIT." ; sc:featureList edam:operation_0310, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaCoAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Vini2/MetaCoAG" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_3706 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2006, edam:format_3547 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0092, edam:topic_0637 ; sc:citation ; sc:description "Package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data." ; sc:featureList edam:operation_0323, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metacoder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/grunwaldlab/metacoder" ; biotools:primaryContact "GitHub Issues", "Niklaus J. Grünwald" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3174 ; sc:citation ; sc:description "Tool for meta-omics comparative analysis." ; sc:featureList edam:operation_2478, edam:operation_3744 ; sc:name "MetaComp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cqb.pku.edu.cn/ZhuLab/MetaComp/" ; biotools:primaryContact "Huaiqiu Zhu", "Longshu Yang", "Peng Zhai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:description "MetaCompass is a software package for comparative assembly of metagenomic reads. MetaCompass achieves comparable assembly performance to the state of the art de novo assemblers, but these two different approaches complement each other a lot. So combining contigs between MetaCompass and other independent de novo assemblers give us the best overall metagenomic assembly." ; sc:featureList edam:operation_0310 ; sc:name "MetaCompass" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://metacompass.cbcb.umd.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3174, edam:topic_3382, edam:topic_3837 ; sc:citation , "pmcid:PMC9889960", "pubmed:36722204" ; sc:description "Capturing variation in metagenomic assembly graphs with MetaCortex." ; sc:featureList edam:operation_0310, edam:operation_3472, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaCortex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SR-Martin/metacortex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2815, edam:topic_3678 ; sc:citation , "pubmed:36772980" ; sc:description "A web-application for living meta-analyses of COVID-19 trials." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "metaCOVID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://covid-nma.com/metacovid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:26895947" ; sc:description "Pipeline for taxonomy identification and lossless compression of FASTA-format metagenomic reads.  It integrates algorithms for taxonomy identification, read alignment, assembly, and finally, a reference-based compression method in a parallel manner." ; sc:featureList edam:operation_0310, edam:operation_3460 ; sc:name "MetaCRAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web.engr.illinois.edu/~mkim158/metacram.html" ; biotools:primaryContact "Minji Kim", "Xiejia Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_0821, edam:topic_3407 ; sc:citation , "pmcid:PMC3245004", "pubmed:22086948" ; sc:description "Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models." ; sc:featureList edam:operation_2429, edam:operation_3282, edam:operation_3561, edam:operation_3660, edam:operation_3715 ; sc:license "Unlicense" ; sc:name "MetaCrop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metacrop.ipk-gatersleben.de/" ; biotools:primaryContact "Falk Schreiber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3168, edam:topic_3174 ; sc:description "MetaCV is a composition and phylogeny based algorithm to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. MetaCV performs (for both sensitivity and specificity) as good as BlastX-based methods on simulated short reads, but runs 300 times faster thus provides effectively and efficiently analysis on huge amount of NGS data." ; sc:featureList edam:operation_3198, edam:operation_3460 ; sc:name "MetaCV" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/metacv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3068, edam:topic_3407 ; sc:citation "pubmed:19850718", "pubmed:22102576" ; sc:description "The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3439, edam:operation_3660 ; sc:name "MetaCyc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metacyc.org/" ; biotools:primaryContact "MetaCyc Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269 ; sc:citation , ; sc:description "This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "MetaCyto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/release/bioc/html/MetaCyto.html" ; biotools:primaryContact "Zicheng Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC7888140", "pubmed:33596922" ; sc:description """A method of using global evidence for local decision making. Metadataset (www.metadataset.com) is a collection of open data from scientific publications. These publications are about the management of agricultural and natural resources (e.g., crops, soil, water, and wildlife). The data are extracted from scientific publications, standardized, and summarized using dynamic meta-analysis. Metadataset is a collection of open data from scientific publications.""" ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:license "MIT" ; sc:name "Metadataset" ; sc:url "http://www.metadataset.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3125 ; sc:citation "pubmed:21689482" ; sc:description "Meta web server to predict DNA-binding residues for DNA-binding proteins. It integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, BindN-rf, DP-Bind and DBS-PRED and it solely uses sequence information of proteins." ; sc:featureList edam:operation_0415, edam:operation_2479 ; sc:name "metaDBSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://projects.biotec.tu-dresden.de/metadbsite/" ; biotools:primaryContact "Dr. Bingding Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0634, edam:topic_3295, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC8496798", "pubmed:34570756" ; sc:description "meta-analysis of differential expression analyses (metaDEA) is a simple package that provide easy functions to integrate the results of previously computed differential expression analyses to find out the genes that are more consistently differentially expressed across different comparisons and their statistics." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3463 ; sc:name "metaDEA" ; sc:url "https://github.com/Ilarius/metaDEA" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3308, edam:topic_3320, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC9653213", "pubmed:36388152" ; sc:description "A background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites." ; sc:featureList edam:operation_1812, edam:operation_3435, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Metadensity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YeoLab/Metadensity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation "pubmed:26134005" ; sc:description "Java/R-based software package that performs differential expression analysis on RNA-Seq based data." ; sc:featureList edam:operation_2495 ; sc:name "MetaDiff" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jiach/MetaDiff" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_1964 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "Prediction method that molds various sources of information predominantly obtained from orthogonal prediction methods which focus on different types of disordered regions." ; sc:featureList edam:operation_0267 ; sc:name "MetaDisorder" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "mytum.de" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/Rostlab/MetaDisorder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_2275, edam:topic_3336 ; sc:citation , "pmcid:PMC9933224", "pubmed:36816658" ; sc:description "A Combinatorial Molecular Docking Approach." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MetaDOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.hpppi.iicb.res.in/metadock/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3384, edam:topic_3954 ; sc:citation , "pubmed:37640914" ; sc:description "An R shiny application for meta-analysis of diagnostic test accuracy and sensitivity analysis of publication bias." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaDTA" ; sc:softwareHelp ; sc:url "https://crsu.shinyapps.io/MetaDTA/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:encodingFormat edam:format_2330 ; sc:name "Structural profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_2331 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3332 ; sc:author "Petr Hosek", "Vojtech Spiwok" ; sc:citation ; sc:contributor "Czech Science Foundation 15-17269S" ; sc:description "An interactive web viewer of metadynamics results." ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:funder "Czech Science Foundation 15-17269S" ; sc:isAccessibleForFree true ; sc:name "Metadyn View" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-CZ", "University of Chemistry and Technology Prague, Czech Republic" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://metadyn.vscht.cz" ; biotools:primaryContact "Vojtech Spiwok" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_2330 ; sc:name "Trajectory data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3892 ; sc:description "Molecular simulations are slow because the system usually gets stuck in local energy minima. To address this problem, metadynamics uses an artificial bias potential calculated adaptivly during the simulation. Metadynminer is R package for analysis and visualization of metadynamics results, primarily from popular Plumed package." ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "metadynminer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "v0.1.0", "v0.1.1", "v0.1.2", "v0.1.3", "v0.1.4" ; sc:url "http://www.metadynamics.cz/metadynminer/" ; biotools:primaryContact "Vojtech Spiwok" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0176 ; sc:description "Metadynreporter is a Galaxy portal that generates a PDF report based on data from metadynamics simulation done in Plumed (https://www.plumed.org/)." ; sc:isAccessibleForFree true ; sc:name "metadynreporter" ; sc:operatingSystem "Linux" ; sc:url "http://metadynreporter.cz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation ; sc:description """MetaFetcheR is an R package designed to link metabolites IDs from different Metabolome databases with eachother in a step to resolve ambiguity and standardize metabolites representation and annotation. Currently the package supports resolving IDs for the following databases: Human Metabolome Database (HMDB), Chemical Entities of Biological Interest (ChEBI) PubChem, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Lipidomics Gateway (LipidMaps).""" ; sc:featureList edam:operation_0224, edam:operation_2429, edam:operation_3929 ; sc:license "MIT" ; sc:name "MetaFetcheR" ; sc:url "https://github.com/komorowskilab/MetaFetcheR/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172 ; sc:citation "pubmed:18986526" ; sc:description "Java-based feature analysis tool that enables real-time, interactive correlation analysis of feature sets, discovery of addtional related features and analysis of related metabolites. It is designed specifically to aid feature analysis within NMR metabolomics data." ; sc:featureList edam:operation_3465 ; sc:name "MetaFIND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mlg.ucd.ie/metabol.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3678 ; sc:citation ; sc:description "MetaFun is a web tool for the integration and functional characterization by unveiling sex differences in multiple omics studies through comprehensive functional meta-analysis." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MetaFun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.cipf.es/metafun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation ; sc:description """Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes. Create the nrgo database for the metafunc workflow.""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3460, edam:operation_3463 ; sc:name "MetaFunc" ; sc:url "https://gitlab.com/schmeierlab/workflows/metafunc.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3168, edam:topic_3174, edam:topic_3519 ; sc:citation , "pmcid:PMC8547451", "pubmed:34546069" ; sc:description "An Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes." ; sc:featureList edam:operation_0308, edam:operation_3237, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaFunPrimer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jialiu232/MetaFunPrimer_paper_info.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0114, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description "A high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates." ; sc:featureList edam:operation_0335, edam:operation_3695 ; sc:name "MetaFusion" ; sc:softwareHelp ; sc:url "https://github.com/ccmbioinfo/MetaFusion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_0659, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description """MetaGenomic analysis of short and long reads. This directory contains the query files used to test MetaG. Due to file size limitations, the databases can be found here:.""" ; sc:featureList edam:operation_0224, edam:operation_3460, edam:operation_3461 ; sc:name "MetaG" ; sc:url "http://bioinformatics.uni-muenster.de/tools/metag/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation ; sc:description """Reconstruction of genome scale metabolic models directly from metagenomes. A Snakemake-based workflow to generate high quality metagenome assembled genomes from short read paired-end data, reconstruct genome scale metabolic models, and perform community metabolic interaction simulations on high performance computing clusters. metaGEM integrates an array of existing bioinformatics and metabolic modeling tools using Snakemake, for the purpose of interrogating social interactions in bacterial communities of the human gut microbiome. From WMGS datasets, metagenome assembled genomes (MAGs) are reconstructed, which are then converted into genome-scale metabolic models (GEMs) for in silico simulations of cross feeding interactions within sample based communities. Additional outputs include abundance estimates, taxonomic assignment, growth rate estimation, pangenome analysis, and eukaryotic MAG identification.""" ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_3660 ; sc:license "MIT" ; sc:name "metaGEM" ; sc:url "https://github.com/franciscozorrilla/metaGEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in", "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:28108451" ; sc:description "metagen performs meta-analysis using fixed- and random-effects logistic regression models, treating the multiple genotypes as independent variables" ; sc:featureList edam:operation_0224, edam:operation_2238 ; sc:name "METAGEN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.compgen.org/tools/metagen" ; biotools:primaryContact "Pantelis Bagos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474 ; sc:citation "pubmed:22645318" ; sc:description "User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing." ; sc:featureList edam:operation_0291, edam:operation_0337, edam:operation_2238 ; sc:name "METAGENassist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.metagenassist.ca" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_3003 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "This package produces metagenic plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "Artistic-2.0" ; sc:name "metagene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metagene.html" ; biotools:primaryContact "Charles Joly Beauparlant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0622 ; sc:citation "pubmed:18940874" ; sc:description "Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences." ; sc:featureList edam:operation_0361 ; sc:name "MetaGeneAnnotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metagene.cb.k.u-tokyo.ac.jp/" ; biotools:primaryContact "Hideki Noguchi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3174, edam:topic_3577, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC8485520", "pubmed:34592929" ; sc:description "A standardized database to study deep sequenced metagenomic data from human fecal specimen." ; sc:featureList edam:operation_0335, edam:operation_2421, edam:operation_3431, edam:operation_3695, edam:operation_3891 ; sc:name "MetaGeneBank" ; sc:url "http://tcm.zju.edu.cn/mgb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3174 ; sc:description "MetaGeneMark is a tool for gene prediction in metagenomes, utilizing metagenome parameters and gene prediction." ; sc:featureList edam:operation_2454 ; sc:name "MetaGeneMark" ; sc:url "http://exon.gatech.edu/GeneMark/meta_gmhmmp.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC5405795", "pubmed:28451381" ; sc:description "Managing and analytical bioinformatics framework that is engineered to run dedicated Galaxy workflows for the detection and eventually classification of pathogens." ; sc:featureList edam:operation_0310, edam:operation_2495, edam:operation_3460 ; sc:license "GPL-2.0" ; sc:name "MetaGeneSense" ; sc:url "https://github.com/pgp-pasteur-fr/MetaGenSense" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Metagenome@Kin is an automated high throughput sequencing data analysis tool for the 16S/28S/ITS rRNA genes. It measures the composition and diversity of microbial and fungal species in natural environments." ; sc:featureList edam:operation_2238, edam:operation_3221 ; sc:name "Metagenome-Kin" ; sc:operatingSystem "Windows" ; sc:url "http://www.w-fusionus.com/metagenome-kin" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3113 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Sample annotation" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3567 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Reference sample report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3567 ; sc:encodingFormat edam:format_2330 ; sc:name "Reference sample report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3113 ; sc:encodingFormat edam:format_2330 ; sc:name "Sample annotation" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174 ; sc:citation ; sc:description "Developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment." ; sc:featureList edam:operation_2409, edam:operation_3460 ; sc:license "Artistic-2.0" ; sc:name "metagenomeFeatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html" ; biotools:primaryContact "Nathan D. Olson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3746, edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_3746, edam:format_3752 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations." ; sc:featureList edam:operation_0564, edam:operation_2238 ; sc:license "Artistic-2.0" ; sc:name "metagenomeSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html" ; biotools:primaryContact "Joseph N. Paulson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC7319469", "pubmed:32338757" ; sc:description """Comprehensive inference and meta-insights for microbial correlation networks. Microbial association networks are frequently used for understanding and comparing community dynamics from microbiome datasets. Inferring microbial correlations for such networks and obtaining meaningful biological insights, however, requires a lengthy data management workflow, choice of appropriate methods, statistical computations, followed by a different pipeline for suitably visualizing, reporting and comparing the associations.""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3925 ; sc:name "MetagenoNets" ; sc:url "https://web.rniapps.net/metagenonets" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_3468, edam:format_3475, edam:format_3752 ; sc:name "Genotype/phenotype report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_2269, edam:topic_2885 ; sc:author "Jordi Martorell-Marugán" ; sc:citation ; sc:description "MetaGenyo is a simple, ready-to-use software which has been designed to perform meta-analysis of genetic association studies." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "MetaGenyo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://metagenyo.genyo.es" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:description "metaGOflow is a pipeline based on MGnify and its workflows, aiming to address the challenges of the analysis of the European Marine Omics Biodiversity Observation Network (EMO BON) data. EMO BON is a long-term omics observatory of marine biodiversity that generates hundreds of metagenomic samples periodically from a range of stations around Europe." ; sc:featureList edam:operation_0524, edam:operation_2454, edam:operation_3219, edam:operation_3460, edam:operation_3672 ; sc:license "Apache-2.0" ; sc:name "metaGOflow" ; sc:softwareHelp ; sc:url "https://github.com/emo-bon/MetaGOflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3170, edam:topic_3174, edam:topic_3673 ; sc:citation ; sc:description """Indexing and Analysing Nucleotide Archives at Petabase-scale. This repository contains resources related to the manuscript describing the MetaGraph framework, such as supplemental data tables containing sample metadata, example scripts and interactive notebooks. Please find below a more detailed description of each category under the respective section. The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest. Read more in the paper preprint.""" ; sc:featureList edam:operation_0524, edam:operation_2421, edam:operation_2422, edam:operation_3211, edam:operation_3472 ; sc:name "MetaGraph" ; sc:url "https://metagraph.ethz.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC9651917", "pubmed:36386613" ; sc:description "metaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by transcripts." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3218, edam:operation_3472, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaGT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ablab/metaGT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3174, edam:topic_3474 ; sc:citation "pubmed:23735199" ; sc:description "Novel gene prediction method for metagenomic fragments based on a machine learning approach of SVM." ; sc:featureList edam:operation_2423 ; sc:name "MetaGUN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cqb.pku.edu.cn/ZhuLab/MetaGUN/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_1915 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_1915 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest." ; sc:featureList edam:operation_0524, edam:operation_3460, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "metagWGS" ; sc:operatingSystem "Linux" ; sc:provider "GenoToul bioinformatics facility" ; sc:softwareHelp ; sc:softwareVersion "2.3" ; sc:url "https://forgemia.inra.fr/genotoul-bioinfo/metagwgs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3518 ; sc:description "A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium." ; sc:featureList edam:operation_2436 ; sc:license "Artistic-2.0" ; sc:name "MetaGxOvarian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.99.7" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MetaGxOvarian.html" ; biotools:primaryContact "Michael Zon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3365 ; sc:citation ; sc:description "Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "metahdep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metahdep.html" ; biotools:primaryContact "John R. Stevens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3344 ; sc:citation ; sc:description "A metaheuristic method based on the reactive model of neighborhood consensus for continuous optimization." ; sc:isAccessibleForFree true ; sc:name "Metaheuristic reactive model-based on neighborhood consensus for continuous optimization" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70482-a-metaheuristic-method-based-on-the-reactive-model" ; biotools:primaryContact "Erik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3500, edam:topic_3511 ; sc:citation , "pubmed:24850854" ; sc:description "An information repository of mammalian imprinted genes." ; sc:featureList edam:operation_0224 ; sc:name "MetaImprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://202.97.205.76:8080/MetaImprint/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:25252781" ; sc:description "Tool to perform meta-analysis of summary statistics obtained from a series of related studies. The special feature of it is the ability to meta-analyze the results of multiple linear and logistic regression models, broadly used in genome-wide association studies (GWAS)." ; sc:featureList edam:operation_3659 ; sc:name "METAINTER" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://metainter.meb.uni-bonn.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3170, edam:topic_3174 ; sc:citation ; sc:description "Pseudoalignment for metagenomic read assignment." ; sc:featureList edam:operation_0527 ; sc:name "Metakallisto" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/pachterlab/metakallisto" ; biotools:primaryContact "L. Pachter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "Program that facilitates the meta-analysis of genomewide association scans." ; sc:featureList edam:operation_0282 ; sc:license "BSD-3-Clause" ; sc:name "Metal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/METAL_Program" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC7579964", "pubmed:33087062" ; sc:description """A flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. MetaLAFFA is a flexible, end-to-end, and compute cluster-compatible metagenomic functional annotation pipeline. MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional orthology groups. This process consists of several steps to go from raw FASTQs (with sequencing adapters removed) to functional profiles:.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495, edam:operation_3192, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "MetaLAFFA" ; sc:url "https://github.com/borenstein-lab/MetaLAFFA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3125, edam:topic_3510, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:21576237" ; sc:description "MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted." ; sc:featureList edam:operation_0249, edam:operation_0445, edam:operation_2575, edam:operation_3092, edam:operation_3222 ; sc:name "MetalDetector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metaldetector.dsi.unifi.it/v2.0/" ; biotools:primaryContact "Metal Detector v2.0 Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3303, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description """Efficient alignment-based metagenomic profiling via containment min hash. 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It can take multiple sequences as input, automatically identify the homogeneity and heterogeneity among sequences and cluster them into different groups given any wanted resolution, finally output multiple aligned sequence logos in one figure. 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EWAS meta-analysis of age in human skeletal muscle.""" ; sc:featureList edam:operation_0417, edam:operation_3207, edam:operation_3919 ; sc:name "MetaMeth" ; sc:url "https://sarah-voisin.shinyapps.io/MetaMeth/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830 ; sc:citation "pubmed:20483919" ; sc:description "Integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted." ; sc:featureList edam:operation_0252, edam:operation_0420, edam:operation_0465, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MetaMHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://datamining-iip.fudan.edu.cn/MetaMHCpan/index.php/pages/view/info" ; biotools:primaryContact "Cheng Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description "metaMIC is a fully automated tool for identifying and correcting misassemblies of (meta)genomic assemblies with the following three steps. Firstly, metaMIC extracts various types of features from the alignment between paired-end sequencing reads and the assembled contigs. 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Thirdly, metaMIC will localize misassembly breakpoints for each misassembled contig and then correct misassemblies by splitting into parts at the breakpoints." ; sc:featureList edam:operation_0310, edam:operation_3180, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "metaMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZhaoXM-Lab/metaMIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3399, edam:topic_3410, edam:topic_3697 ; sc:citation , "pmcid:PMC6469060", "pubmed:30991942" ; sc:description "R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models." ; sc:featureList edam:operation_3797 ; sc:isAccessibleForFree true ; sc:name "metamicrobiomeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nhanhocu/metamicrobiomeR" ; biotools:primaryContact "Nhan Thi Ho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3174, edam:topic_3301, edam:topic_3524 ; sc:citation , "pmcid:PMC5124289", "pubmed:27887570" ; sc:description "Metagenomic microbial interaction simulator based on microbial community profiles." ; sc:featureList edam:operation_3562, edam:operation_3660 ; sc:name "MetaMIS" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/metamis/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3174, edam:topic_3796 ; sc:citation "pubmed:26002885" ; sc:description "Bayesian mixture model framework for resolving complex metagenomic mixtures." ; sc:featureList edam:operation_3200 ; sc:name "metaMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/metaMix/" ; biotools:primaryContact "Sofia Morfopoulou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC10206287", "pubmed:37234699" ; sc:description "A web service for mobile phase determination and fast chromatography peaks evaluation for metabolomics." ; sc:featureList edam:operation_3215, edam:operation_3454, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:name "MetaMOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://metamope.cmdm.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description """A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta analysis.""" ; sc:featureList edam:operation_0436, edam:operation_2421, edam:operation_3208 ; sc:name "MetamORF" ; sc:url "http://metamorf.hb.univ-amu.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation , ; sc:description "MetAMOS is an open source and modular metagenomic assembly and analysis pipeline. 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The package will help you to:.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3891 ; sc:name "Metan" ; sc:url "https://tiagoolivoto.github.io/metan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308 ; sc:citation ; sc:description "MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting." ; sc:featureList edam:operation_2424 ; sc:license "MIT" ; sc:name "MetaNeighbor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MetaNeighbor.html" ; biotools:primaryContact "Manthan Shah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3174 ; sc:citation "pubmed:26692900" ; sc:description "Software tool in MATLAB for network construction and biologically significant module detection." ; sc:featureList edam:operation_3660 ; sc:name "MetaNet" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://biostatistics.csmc.edu/MetaNet/" ; biotools:primaryContact "Zhenqiu Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32403837" ; sc:description """A new paradigm for data sharing in photonics research. Jonathan Fan, Stanford University. GLobal Optimization NETwork or GLOnet is a global optimizer, based on a generative neural network, which can output ensembles of highly efficient topology-optimized metasurfaces. This is a toolbox to convert .mat files on MetaNet into GDS files.""" ; sc:featureList edam:operation_2939, edam:operation_3453 ; sc:name "MetaNetC" ; sc:url "http://metanet.stanford.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_2259, edam:topic_3172, edam:topic_3292 ; sc:citation , , , ; sc:description "MetaNetX/MNXref allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models." ; sc:featureList edam:operation_0277, edam:operation_3282, edam:operation_3439, edam:operation_3561 ; sc:license "CC-BY-4.0" ; sc:name "MetaNetX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://metanetx.org/" ; biotools:primaryContact "MetaNetX Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "metano is an open-source software toolbox for analyzing the capabilities of metabolic networks and for assisting in metabolic reconstruction." ; sc:featureList edam:operation_3660 ; sc:license "GPL-1.0" ; sc:name "metano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://metano.tu-bs.de/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3174, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC10310047", "pubmed:37327214" ; sc:description "An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets." ; sc:featureList edam:operation_2495, edam:operation_3643, edam:operation_3644, edam:operation_3649, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "MetaNovo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/uct-cbio/proteomics-pipelines/blob/master/MetaNovo.md" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_1775, edam:topic_3071 ; sc:citation "pubmed:22589089" ; sc:description "Tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experiment data in mind." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:name "MetaOmGraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.metnetdb.org/MetNet_MetaOmGraph.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "The server automates data analysis for the processing of metabolomics experiments." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:name "metaP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://metap.helmholtz-muenchen.de/metap2/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3172, edam:topic_3336, edam:topic_3407 ; sc:citation , "pubmed:33191610" ; sc:description "A Web Application for Analyzing the Biological Activity Spectrum of Organic Compounds Taking into Account their Biotransformation." ; sc:featureList edam:operation_3436, edam:operation_3860 ; sc:name "MetaPASS" ; sc:url "http://www.way2drug.com/metapass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "MetaPath is a tool for meta analysis pathway enrichment." ; sc:featureList edam:operation_2436, edam:operation_3928 ; sc:license "Apache-2.0" ; sc:name "MetaPath" ; sc:url "https://github.com/metaOmics/MetaPath" ; biotools:primaryContact "George C. Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:15712108", "pubmed:16155745", "pubmed:16362923", "pubmed:16986316", "pubmed:16986317", "pubmed:17483511" ; sc:description "MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3439, edam:operation_3660 ; sc:name "MetaPath Online" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scopes.biologie.hu-berlin.de/" ; biotools:primaryContact "Thomas Handorf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0637, edam:topic_3174 ; sc:citation "pubmed:26076725" ; sc:description "Modular software pipeline for integrated analysis of environmental sequence information. The software performs a series of popular analyses for taxonomic profiling and functional potential with limited data handling, allowing researchers to spend their time analyzing their data instead of performing complicated data transformations." ; sc:featureList edam:operation_3460 ; sc:name "MetaPathways" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hallam.microbiology.ubc.ca/MetaPathways/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3520 ; sc:description "MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool." ; sc:featureList edam:operation_3644, edam:operation_3767 ; sc:name "MetaPepSeq 0.8 Beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sourceforge.net/projects/metapepseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3300, edam:topic_3837 ; sc:citation , "pmcid:PMC9599279", "pubmed:36069454" ; sc:description "An automated pipeline for analyzing, annotating, and classifying bacteriophages in metagenomics sequencing data." ; sc:featureList edam:operation_0362, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaPhage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MattiaPandolfoVR/MetaPhage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC7242752", "pubmed:32499813" ; sc:description """Detecting and Decomposing Multivariate Associations From Univariate Genome-Wide Association Statistics. MetaPhat is an open sourced program to detect best subset traits on lead multivariate SNP associations from related sets of GWAS summary results. Best traits are derived from systematic decomposing multivariate associations into central traits based on optimal BIC and P-value from multivariate CCA models. Variant trace results are plotted and clustered to dissect and improve the specificity of phenotype(s)-genotype associations.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3791 ; sc:license "MIT" ; sc:name "MetaPhat" ; sc:url "https://sourceforge.net/projects/meta-pheno-association-tracer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3174 ; sc:citation ; sc:description "Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data." ; sc:featureList edam:operation_0324, edam:operation_2478 ; sc:license "MIT" ; sc:name "MetaPhlAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huttenhower.sph.harvard.edu/metaphlan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3293, edam:topic_3299 ; sc:citation , , "pmcid:PMC3061081", "pmcid:PMC7319458", "pubmed:21149260", "pubmed:32343307" ; sc:description "MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. Currently, over 117,131,162 of unique homologs are deposited in MetaPhOrs database. These predictions were retrieved from 8,246,911 Maximum Likelihood trees for 4,094 species. For each prediction, MetaPhOrs provides a Consistency Score and Evidence Level describing its goodness, together with number of trees and links to their source databases." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MetaPhors" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.5" ; sc:url "http://orthology.phylomedb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation "pubmed:21989143" ; sc:description "Novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length." ; sc:featureList edam:operation_3460 ; sc:name "MetaPhyler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://metaphyler.cbcb.umd.edu/" ; biotools:primaryContact "Bo Liu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2305 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_1957 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0085, edam:topic_0637, edam:topic_3174, edam:topic_3387 ; sc:citation ; sc:description "Please see entry at https://bio.tools/meta-pipe/" ; sc:featureList edam:operation_0525, edam:operation_2478, edam:operation_3460, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "META-pipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mmp2.sfb.uit.no/metapipe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:25344496" ; sc:description "Virtual laboratory which aims at assisting modellers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes. Its framework is based on a core module which enables to design and manage biological models, and an extensible set of plugins by which MP models can be generated, optimized, simulated and analysed." ; sc:featureList edam:operation_2426 ; sc:name "MetaPlab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mplab.sci.univr.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3174 ; sc:description "metaplasmidSPAdes - tool for assembling plasmids from metagenomic data sets" ; sc:featureList edam:operation_0310 ; sc:name "metaplasmidSPAdes" ; sc:url "http://cab.spbu.ru/software/spades" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1931 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3475 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:34570223" ; sc:description "MetaPlatanus is a de novo assembler for metagenome (microbiome). The features of this tool are as follows: (1) It can utilize various types of long-range information such as Oxford-Nanopore/PacBio long reads, mate-pairs (jumping libraries), and 10x linked reads (experimental). (2) Coverage depths, k-mer frequencies and results of the binning tool are also employed to extend sequences and correct mis-assemblies, reducing inter-species misassemblies. (3) Contig-assembly, scaffolding, gap-closing and binning are automatically executed at once. (4) MetaPlatanus requires at least one short-read paired-end library." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaPlatanus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rkajitani/MetaPlatanus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC9272804", "pubmed:35639952" ; sc:description "A Bioconductor package for joint pathway testing for untargeted metabolomics data." ; sc:featureList edam:operation_3501, edam:operation_3659, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "metapone" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/devel/bioc/html/metapone.html. a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0769, edam:topic_2885, edam:topic_3174 ; sc:citation , "pmcid:PMC8922842", "pubmed:35287721" ; sc:description "A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_2962, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MetaPopR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://de.cyverse.org/apps/agave/MetaPop-1.0.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workbench" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3344, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC8046258", "pubmed:33859865" ; sc:description "MetaPred is a meta-learning framework for Clinical Risk Prediction using limited patient Electronic Health Records (EHRs)." ; sc:featureList edam:operation_0303, edam:operation_3659, edam:operation_3927 ; sc:name "MetaPred" ; sc:url "https://github.com/sheryl-ai/MetaPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_0622, edam:topic_3299 ; sc:citation "pubmed:27378293" ; sc:description "Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs)." ; sc:featureList edam:operation_2464 ; sc:name "MetaPred2CS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metapred2cs.ibers.aber.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "MetaPred : A webserver for the Prediction of Cytochrome P450 Isoform responsible for Metabolizing a Drug Molecule" ; sc:featureList edam:operation_2945 ; sc:name "metapred webserver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/metapred/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0736, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC8553642", "pubmed:34480923" ; sc:description "A machine learning-based tool for predicting protein disorder." ; sc:featureList edam:operation_0303, edam:operation_0470, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "metapredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://metapredict.readthedocs.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3360, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description """A Toolkit for Joint Taxa/Gene Analysis of Metagenomic Sequencing Data. MetaPrism: A Toolkit for Joint Analysis of Meta-genomic Sequencing Data. MetaPrism provides joint profile (infer both taxonomical and functional profile) for shotgun metagenomic sequencing data. It also offer tools to 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) build asso-ciation and prediction models for comparative analysis.""" ; sc:featureList edam:operation_0286, edam:operation_2495, edam:operation_3460 ; sc:name "MetaPrism" ; sc:url "https://github.com/jiwoongbio/MetaPrism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_0821, edam:topic_3170, edam:topic_3697, edam:topic_3941 ; sc:citation ; sc:description """A scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. MetaPro: Meta-analysis pipeline for Transcriptomics + Genomics. The MetaPro Meta Transcriptomics/Genomics Pipeline is a software tool that will perform Transcriptomics and Genomic analysis on Paired and Single Reads of FASTQ data.""" ; sc:featureList edam:operation_0232, edam:operation_3192, edam:operation_3359, edam:operation_3460, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "MetaPro" ; sc:url "https://github.com/ParkinsonLab/MetaPro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3474, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC9426440", "pubmed:35950762" ; sc:description "An MS1 Profiling Approach for Large-Scale Microbiome Screening." ; sc:featureList edam:operation_3432, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaProClust-MS1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/northomics/MetaProClust-MS1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_3170 ; sc:citation ; sc:description "MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant genetic variants" ; sc:featureList edam:operation_3675, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MetaProFi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kalininalab/metaprofi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0632, edam:topic_3407, edam:topic_3697 ; sc:citation , ; sc:description """Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics. This repository contains the source code of the MetaProfiler software package. It provides calculations for local false discovery rates of protein-based stable isotopic probing (SIP) results and performs taxonomic, functional, phylogenetic, and time series analysis of microbiome dynamics.""" ; sc:featureList edam:operation_3638, edam:operation_3642, edam:operation_3649, edam:operation_3715 ; sc:name "MetaProfiler" ; sc:url "https://github.com/psmyth94/MetaProfiler.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "`prokka` optimized for large datasets" ; sc:name "metaprokka" ; sc:url "https://github.com/telatin/metaprokka" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_3651 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:25660940" ; sc:description "Pipeline to analyze metaproteomics data, supporting MGF and X!Tandem, OMSSA and Mascot." ; sc:featureList edam:operation_3646 ; sc:name "MetaProteomeAnalyzer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/meta-proteome-analyzer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_1317, edam:topic_2814 ; sc:citation "pubmed:25431331" ; sc:description "Algorithm incorporating different approaches of contact predictions implemented with a neural network in order to improve the accuracies of the predicted contacts." ; sc:featureList edam:operation_2492 ; sc:name "MetaPSICOV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.cs.ucl.ac.uk/MetaPSICOV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3678 ; sc:citation ; sc:description "MetaQC: A diagnosis tool for assessing quality of genomic studies for meta-analysis and determining inclusion/exclusion criteria." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:name "MetaQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.13" ; sc:url "http://www.pitt.edu/~tsengweb/MetaOmicsHome.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "MetaQTL is a Java package designed to perform the integration of data from the field of gene mapping experiments (e.g molecular markers, QTL, candidate genes, etc…). This package consists in a modular library and several programs written in pure Java. These programs can perform various tasks, including formatting, analyzing and visualizing data or results produced by MetaQTL." ; sc:featureList edam:operation_0282, edam:operation_0335, edam:operation_2429, edam:operation_2945 ; sc:name "MetaQTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://www.bioinformatics.org/mqtl/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174 ; sc:citation ; sc:description "Evaluates and compares metagenome assemblies based on alignments to close references. It is based on QUAST genome quality assessment tool, but addresses features specific for metagenome datasets." ; sc:featureList edam:operation_0525 ; sc:license "GPL-2.0" ; sc:name "MetaQUAST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://quast.sourceforge.net/metaquast.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3301, edam:topic_3697 ; sc:citation "pubmed:26104745" ; sc:description "Web application for rapid and quantitative analysis of specific genes in the human gut microbiome." ; sc:featureList edam:operation_0361, edam:operation_3799 ; sc:name "MetaQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metaquery.docpollard.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:encodingFormat edam:format_2333 ; sc:name "Pathway or network report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0602, edam:topic_2259, edam:topic_3053, edam:topic_3678 ; sc:citation , "pmcid:PMC3692047", "pubmed:23703204" ; sc:description "Prioritization of the entire protein-coding part of the human genome based on heterogeneous user-specified data sets." ; sc:featureList edam:operation_2423, edam:operation_2495, edam:operation_3196, edam:operation_3197, edam:operation_3233, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MetaRanker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/MetaRanker/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3170, edam:topic_3300, edam:topic_3308 ; sc:citation ; sc:description """R package for motif discovery via meta-analysis of microarrays and RNA-Seq. metaRE R Package for Meta-analysis of Transcriptome Data to Identify the Cis-regulatory Code behind the Transcriptional Reprogramming.""" ; sc:featureList edam:operation_0238, edam:operation_0441, edam:operation_0445 ; sc:name "metaRE" ; sc:url "https://github.com/cheburechko/MetaRE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "JCVI Metagenomics Reports." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "METAREP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.4.0-beta" ; sc:url "https://github.com/jcvi/METAREP" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0102, edam:topic_2275 ; sc:description "metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence." ; sc:featureList edam:operation_2429 ; sc:name "metaRNAmodules" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "http://rth.dk/resources/mrm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2815, edam:topic_3325 ; sc:citation ; sc:description "MetaRNN and MetaRNN-indel are pathogenicity prediction scores for human nonsynonymous SNVs (nsSNVs) and non-frameshift (NF) indels. They integrated information from 28 high-level annotation scores (16 functional prediction scores) and produce an ensemble prediction model with a deep recurrent neural network (RNN). The final prediction is the likelihood of a nsSNV or NF indel being pathogenic." ; sc:featureList edam:operation_3226, edam:operation_3461 ; sc:name "MetaRNN" ; sc:url "http://www.liulab.science/MetaRNN" ; biotools:primaryContact "Xiaoming Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC7814594", "pubmed:33468056" ; sc:description """A pipeline for prediction of Metagenome and whole-genome opeRons. MetaRon (Metagenomic opeRon prediction pipeline) is a computational workflow for the prediction of operons from metagenomic data. The pipeline predicts metagenomic operons without any any functional or experimental data. It comes with options to process the metagenomic data starting from filtered raw reads, which includes: assembly into scaffolds via IDBA, data manipulation, gene prediction via prodigal and lastly operon prediction based on gene's co-directionality, intergenic distance (IGD) and promoters.""" ; sc:featureList edam:operation_0435, edam:operation_0440, edam:operation_0579, edam:operation_3216, edam:operation_3803 ; sc:name "MetaRon" ; sc:url "https://github.com/zaidissa/MetaRon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3340, edam:topic_3385 ; sc:citation , "pmcid:PMC4015449", "pubmed:24564477" ; sc:description "Metaphase selection tool using a Gaussian-based classification technique." ; sc:featureList edam:operation_3443 ; sc:name "MetaSel" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www4a.biotec.or.th/GI/tools/metasel" ; biotools:primaryContact "Sissades Tongsima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation ; sc:description "The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method." ; sc:featureList edam:operation_2238 ; sc:license "Artistic-2.0" ; sc:name "metaSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metaSeq.html" ; biotools:primaryContact "Koki Tsuyuzaki" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2572, edam:format_3751 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation "pubmed:25452340" ; sc:description "Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way." ; sc:featureList edam:operation_0314, edam:operation_3223, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "metaseqR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/metaseqR.html" ; biotools:primaryContact "Panagiotis Moulos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:author "Panagiotis Moulos" ; sc:citation , "pubmed:32778872" ; sc:description "metaseqR2 provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way. 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Pesole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Metashot/prok-quality is a comprehensive and easy-to-use pipeline for assessing the quality of prokaryotic genomes." ; sc:featureList edam:operation_0310, edam:operation_3218, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "metashot prok-quality" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/metashot/prok-quality" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174 ; sc:citation "pubmed:18841204" ; sc:description "The software can be used to generate collections of synthetic reads." ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_2429 ; sc:name "MetaSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-ab.informatik.uni-tuebingen.de/software/metasim" ; biotools:primaryContact "Richter DC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "R package for multiple marker meta-analysis. It can carry out meta-analysis of SKAT, SKAT-O and burden tests with individual level genotype data or gene level summary statistics." ; sc:featureList edam:operation_2429 ; sc:license "GPL-3.0" ; sc:name "MetaSKAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.hsph.harvard.edu/skat/metaskat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3837 ; sc:citation , "pmcid:PMC5533426", "pubmed:28753663" ; sc:contributor ; sc:description "Pipeline for calling metagenomic single nucleotide variants (SNVs). 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It clusters all experimentally observed MS/MS spectra based on their spectral similarity and create a representative consensus spectrum for each cluster by using the spectrum clustering algorithm implemented in the spectral library search engine, SpectraST." ; sc:featureList edam:operation_3637, edam:operation_3644, edam:operation_3646, edam:operation_3797, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "metaSpectraST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bravokid47/metaSpectraST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:26403281" ; sc:description "Software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents." ; sc:featureList edam:operation_0525 ; sc:name "Metassembler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://schatzlab.cshl.edu/research/metassembler/" ; biotools:primaryContact "Michael Schatz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3388 ; sc:citation "pubmed:20925910" ; sc:description "MATLAB-based package which simulates 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database." ; sc:featureList edam:operation_3214 ; sc:name "MetAssimulo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cisbic.bioinformatics.ic.ac.uk/metassimulo/" ; biotools:primaryContact "Tim Ebbels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3542 ; sc:citation "pubmed:26549467" ; sc:description "Well-balanced Secondary Structure predictor." ; sc:featureList edam:operation_0267 ; sc:name "MetaSSPred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cs.uno.edu/~tamjid/Software.html" ; biotools:primaryContact "Hoque Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0622, edam:topic_3335, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:36564505" ; sc:description "Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies." ; sc:featureList edam:operation_0361, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaSTAAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/xihaoli/MetaSTAAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3174, edam:topic_3474 ; sc:citation "pubmed:19360128" ; sc:description "Employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher’s exact test." ; sc:featureList edam:operation_2403 ; sc:name "Metastats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metastats.cbcb.umd.edu/detection.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:author "Tobias Hamp" ; sc:citation ; sc:description "Metastudent predicts Gene Ontology (GO) terms from the Molecular Function Ontology (MFO) and Biological Process Ontology (BPO) for input protein sequences by homology-based inference from already annotated proteins." ; sc:featureList edam:operation_2479 ; sc:isAccessibleForFree true ; sc:name "MetaStudent" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Rostlab", "tum.de" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/Rostlab/MetaStudent" ; biotools:primaryContact "Rostlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3168 ; sc:citation "pubmed:25861968" ; sc:description "Accurate method-aware merging algorithm for structural variations." ; sc:featureList edam:operation_3228 ; sc:name "MetaSV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinform.github.io/metasv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_2275, edam:topic_2814 ; sc:citation ; sc:description "MetaTASSER is a protein tertiary prediction method that employs the 3D-Jury approach to select threading templates from SPARKS, SP3 and PROSPECTOR_3, which provides aligned fragments and tertiary restraints as an input to TASSER (Threading/ASSEmbly/Refinement) procedure to generate full-length models." ; sc:featureList edam:operation_0271, edam:operation_0310, edam:operation_0474, edam:operation_2423 ; sc:name "MetaTASSER" ; sc:operatingSystem "Linux" ; sc:url "http://cssb.biology.gatech.edu/skolnick/webservice/MetaTASSER/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3299, edam:topic_3697 ; sc:citation ; sc:description "MetaTrass is abbreviation to Metagenomics Taxonomic Reads For Assembly Single Species. MetaTrass is based on high-quality referencess with taxonomic tree and long-range information encoded within co-barcoded short-read sequences. The comprehensive use of co-barcoding information and references in our approach can reduce the false negative effects of genome taxonomy to assembly high-quality metagenomes from the sequencing data." ; sc:featureList edam:operation_0310, edam:operation_3196, edam:operation_3460, edam:operation_3731, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetaTrass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BGI-Qingdao/MetaTrass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3301 ; sc:citation "pubmed:27336370" ; sc:description "Visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches." ; sc:featureList edam:operation_0567 ; sc:name "MetaTreeMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metasystems.riken.jp/visualization/treemap/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3305 ; sc:citation "pubmed:19345563" ; sc:description "STATA program for estimating trends in cumulative meta-analysis. The author propose a simple and formal regression-based approach for detecting trends in cumulative meta-analysis." ; sc:featureList edam:operation_3659 ; sc:name "metatrend" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.compgen.org/tools/metatrend" ; biotools:primaryContact "Pantelis G. Bagos, Ph.D." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0196, edam:topic_3174, edam:topic_3941 ; sc:citation ; sc:description """Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequences predicted from genomes and metagenomes. METATRYP allows users to investigate the occurrance of tryptic peptides within the protein coding sequences predicted from genomes. Testing for the Corona-2 (COVID-19) virus has utilized RNA and antibody analytical methodologies to date. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequences predicted from genomes and metagenomes.""" ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3631, edam:operation_3767 ; sc:name "METATRYP" ; sc:url "https://metatryp.whoi.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33135046" ; sc:description """Deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. The MetaTX is aimed for plotting the transcriptomic distribution of RNA-related genomic features.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3435, edam:operation_3891 ; sc:name "MetaTX" ; sc:url "https://github.com/yue-wang-biomath/MetaTX.1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2885, edam:topic_3174, edam:topic_3697, edam:topic_3796 ; sc:citation ; sc:description """Introducing metavariant species models for reference-free metagenomic-based population genomics. metaVaR: MetaVariant Species (MVS) for reference-free and metagenomic-based population genomic analysis. metaVaR is a R package developed for population genomic analyses based on variants generated directly from metagenomic data without reference genomes or transcriptomes.""" ; sc:featureList edam:operation_0310, edam:operation_0487, edam:operation_3196, edam:operation_3227, edam:operation_3432 ; sc:name "metaVaR" ; sc:url "https://github.com/madoui/MetaVaR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads" ; sc:featureList edam:operation_0310 ; sc:name "MetaVelvet" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.2.01" ; sc:url "http://metavelvet.dna.bio.keio.ac.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3474, edam:topic_3673, edam:topic_3697 ; sc:citation , "pmcid:PMC8171044", "pubmed:34078257" ; sc:description "A MetaVelvet deep learning extension for de novo metagenome assembly." ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3211, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MetaVelvet-DL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.dna.bio.keio.ac.jp/metavelvet-dl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174 ; sc:description "metaviralSPAdes - tool for assembling plasmids from metagenomic data sets" ; sc:featureList edam:operation_0310, edam:operation_3461 ; sc:name "metaviralSPAdes" ; sc:url "http://cab.spbu.ru/software/spades/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0781 ; sc:citation ; sc:description "Software package that allows biologists and clinicians without specialized bioinformatics expertise to detect and assemble viral genomes from deep sequence datasets." ; sc:featureList edam:operation_0292, edam:operation_0310 ; sc:name "Metavisitor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ARTbio/metavisitor" ; biotools:primaryContact "Christophe Antoniewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC5887897", "pubmed:29529268" ; sc:description "Interactive visualization and exploration of metagenomic sequencing data. Provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots. It supports a flexible plugin framework so users can add new d3 visualizations." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3460 ; sc:name "Metaviz" ; sc:softwareHelp , ; sc:softwareVersion "4" ; sc:url "http://metaviz.cbcb.umd.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC5887897", "pubmed:29529268" ; sc:description "Websocket communication to the metaviz web app for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported, while providing an easy mechanism to support other data structures." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "metavizr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/metavizr.html" ; biotools:primaryContact "Hector Corrada Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_0769, edam:topic_3050, edam:topic_3697 ; sc:citation ; sc:description """A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments. MetaWorks consists of a Conda environment and Snakemake pipeline that is meant to be run at the command line to bioinformatically processes Illumina paired-end metabarcodes from raw reads through to taxonomic assignments. MetaWorks currently supports a number of popular marker gene amplicons and metabarcodes: COI (eukaryotes), rbcL (eukaryotes, diatoms), ITS (fungi), 16S (prokaryotes), 18S (eukaryotes, diatoms), 12S (fish), and 28S (fungi). Taxonomic assignments are made using the RDP classifier that uses a naive Bayesian method to produce taxonomic assignments with a measure of statistical support at each rank.""" ; sc:featureList edam:operation_0335, edam:operation_3192, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "MetaWorks" ; sc:url "https://github.com/terrimporter/MetaWorks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3673, edam:topic_3837 ; sc:author "Gherman V. Uritskiy" ; sc:citation ; sc:description "MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3192, edam:operation_3798, edam:operation_3933 ; sc:license "MIT" ; sc:name "MetaWRAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/bxlab/metaWRAP" ; biotools:primaryContact , "James Taylor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC5361702", "pubmed:28327092" ; sc:description "An Automatic and Comprehensive Pipeline for Processing Untargeted Metabolomics Data." ; sc:featureList edam:operation_3214 ; sc:license "GPL-3.0" ; sc:name "metaX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metax.genomics.cn/" ; biotools:primaryContact "Bo Wen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation "pubmed:21674231" ; sc:description "Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets" ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "Metaxa" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://microbiology.se/software/metaxa/" ; biotools:primaryContact "Johan Bengtsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:citation "pubmed:25732605" ; sc:description "Software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets." ; sc:featureList edam:operation_2990, edam:operation_3460 ; sc:name "Metaxa2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://microbiology.se/software/metaxa2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3174 ; sc:description "metaXplor is an interactive viral and microbial metagenomic data manager. It aims at storing large volumes of user-defined sample, sequence and assignment information while providing a user-friendly fine-filtering web-interface. This online GUI also offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. metaXplor is available as a set of Docker containers that make it simple to deploy on various infrastructures." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "metaXplor" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0-beta" ; sc:url "https://github.com/SouthGreenPlatform/metaXplor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3500 ; sc:citation , "pmcid:PMC8728262", "pubmed:34718719" ; sc:description "A database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species." ; sc:featureList edam:operation_0224, edam:operation_0264, edam:operation_0314, edam:operation_3431, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MetazExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo.njau.edu.cn/metazExp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3125, edam:topic_3534 ; sc:citation , "pubmed:35695777" ; sc:description "A Software Tool for Detection of Interaction between Metal Ion-RNA Base Pairs." ; sc:featureList edam:operation_1834, edam:operation_3898, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MetBP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/computational-biology/metbp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics." ; sc:featureList edam:operation_3214 ; sc:name "MetCCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.metabolomics-shanghai.org/MetCCS/" ; biotools:primaryContact "Zheng-Jiang Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3360, edam:topic_3407 ; sc:citation ; sc:description """Screening for inborn errors of metabolism using untargeted metabolomics and out-of-batch controls. This repository contains code and datasets used for the article Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism published in MDPI Metabolites:.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "Metchalizer" ; sc:url "https://github.com/mbongaerts/Metchalizer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3360, edam:topic_3407 ; sc:citation , "pmcid:PMC10322652", "pubmed:37424942" ; sc:description "Pipeline to explore structural similarity across metabolite modules." ; sc:featureList edam:operation_2844, edam:operation_3463, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MetChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/MetChem/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3172 ; sc:citation ; sc:description "This tool comprises a workflow to interactively explore metabolomics data by creating MSP or calculating m/z values and the similarity between precursors." ; sc:featureList edam:operation_3715 ; sc:license "GPL-2.0" ; sc:name "MetCirc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MetCirc.html" ; biotools:primaryContact "Thomas Naake" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3308, edam:topic_3387 ; sc:description "METdb is a genomic reference database dedicated to micro-eukaryotic marine species transcriptomes. Most datasets were from Marine Microbial Eukaryote Transcriptome Sequencing Project and others from Roscoff marine station and Tara research projects. All datasets were assembled and analyzed using two workflows dedicated to de novo assembly and functional annotation both developed with the CWL workflow management system. The assembly compartment includes evaluation, filtering and trimming of raw data and the de novo assembly and evaluation of assembled transcripts. The annotation compartment defines the presence of coding regions and functional annotation is performed. The resource includes transcriptome assemblies and associated data (metrics and annotations) of 463 distinct marine micro-eukaryotic taxa." ; sc:featureList edam:operation_0524, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "METdb" ; sc:softwareHelp ; sc:url "http://metdb.sb-roscoff.fr/metdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_0634, edam:topic_3407 ; sc:citation "pubmed:24713438" ; sc:description "App for Cytoscape, the bioinformatics network visualization tool. The app is used to annotate a metabolic network with MeSH disease terms, explore related diseases within a network, and link to PubMed references corresponding to any network node and selection of MeSH terms." ; sc:featureList edam:operation_0226 ; sc:name "MetDisease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metdisease.ncibi.org/" ; biotools:primaryContact "Alla Karnovsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3407 ; sc:citation "pubmed:24413519" ; sc:description "Creates visualizations of genome-scale, metabolic models. These “reaction maps” can be used to visualize high-throughput expression data using the companion program MetColor." ; sc:featureList edam:operation_3083 ; sc:name "MetDraw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.metdraw.com/" ; biotools:primaryContact "Dr. Jason A. Papin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0625, edam:topic_0769, edam:topic_3172 ; sc:citation ; sc:description """An R package and web application for metabolomics enrichment and pathway analysis in Metabolomics Workbench. Metabolite enrichment analysis and their associated enriched pathways. MetENP is a R package that enables detection of significant metabolites from metabolite information (names or names and concentration along with metadata information) and provides.""" ; sc:featureList edam:operation_3435, edam:operation_3501, edam:operation_3928 ; sc:license "MIT" ; sc:name "MetENP" ; sc:url "https://github.com/metabolomicsworkbench/MetENP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3306, edam:topic_3382 ; sc:citation , "pubmed:32006775" ; sc:description """An operational online three-dimensional forecasting platform for lake hydrodynamics. The online platform for monitoring and forecasting the bio-physical state of Swiss lakes. This product is developed, managed and maintained by Theo Baracchini and part of his PhD thesis. The application shares with the public some results of 3D hydrodynamic-biological simulations performed daily with the Delft3D modelling framework on a compute server. Additionally, it displays measurements from a field station with data connexion and remote sensing images downloaded from satellites in real-time.""" ; sc:featureList edam:operation_2426 ; sc:name "Meteolakes" ; sc:url "http://meteolakes.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:34859662" ; sc:description "Metabolomics Explorer Application for Natural Product Discovery." ; sc:featureList edam:operation_0337, edam:operation_3803, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "MetEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mo.princeton.edu/MetEx/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585, edam:format_3579, edam:format_3603, edam:format_3604, edam:format_3620, edam:format_3822 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service", "Workbench" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , , , "pmcid:PMC5860210", "pubmed:28968733", "pubmed:29718355" ; sc:description "Metabolic network curation, visualisation and omics data analysis. It is possible to curate and annotate metabolic networks in a collaborative environment. Several tools are available for metabolomics data mapping in networks and visualisation." ; sc:featureList edam:operation_0277, edam:operation_2497, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:name "MetExplore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.26", "2.27", "2.28", "2.30", "2.31" ; sc:url "http://www.metexplore.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3603 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation , "pubmed:27452369" ; sc:description "Web application designed for the identification of regulated metabolite families. This is possible on the basis of metabolite profiles for a set of MS¹ features as well as one MS/MS spectrum for each MS¹ feature. Group-discriminating MS¹ features are identified using a PCA of metabolite profiles and metabolite families are identified using a HCA of MS/MS spectra. Regulated metabolite families are identified by considering group-discriminating MS¹ features from corporate metabolite families." ; sc:featureList edam:operation_0226, edam:operation_0337, edam:operation_2996, edam:operation_3432, edam:operation_3502, edam:operation_3694, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MetFamily" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://msbi.ipb-halle.de/MetFamily/" ; biotools:primaryContact "Treutler, Hendrik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3375, edam:topic_3379, edam:topic_3520 ; sc:citation , "pmcid:PMC9925373", "pubmed:36781298" ; sc:description "Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities." ; sc:featureList edam:operation_3755, edam:operation_3891, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "metformin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yslproteomics.shinyapps.io/Metformin/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "It combines compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. It supports candidate structure retrieval from the compound databases PubChem, ChemSpider and KEGG or user defined structure data file(SDF). After in silico fragmentation in a combinatorial manner, candidates get filtered and scored on criteria like: occurrence of certain elements/substructures, retention time information and reference information." ; sc:featureList edam:operation_2423 ; sc:name "MetFrag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2" ; sc:url "http://msbi.ipb-halle.de/MetFragBeta/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172 ; sc:citation ; sc:description "Approach to combine the knowledge from spectral databases like MassBank with the multitude of candidates generated by fragmenters such as MetFrag." ; sc:featureList edam:operation_3214 ; sc:name "MetFusion" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://msbi.ipb-halle.de/MetFusion/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC9825483", "pubmed:36318250" ; sc:description "An updated database of DNA methylation across a variety of species." ; sc:featureList edam:operation_2421, edam:operation_3186, edam:operation_3207, edam:operation_3695, edam:operation_3809 ; sc:isAccessibleForFree true ; sc:name "MethBank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.0" ; sc:url "https://ngdc.cncb.ac.cn/methbank/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7216580", "pubmed:32393170" ; sc:description """A DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder. methCancer-gen is a deep neural network-based tool for generating DNA methylome dataset based on a user-specified cancer-type.""" ; sc:featureList edam:operation_3096, edam:operation_3204, edam:operation_3927 ; sc:license "MIT" ; sc:name "methCancer-gen" ; sc:url "https://github.com/cbi-bioinfo/methCancer-gen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7671405", "pubmed:33575640" ; sc:description "Tracing and tracking epiallele families in complex DNA populations." ; sc:featureList edam:operation_3204, edam:operation_3454, edam:operation_3891 ; sc:name "MethCoresProfiler" ; sc:url "https://github.com/84AP/MethCoresProfiler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation "pubmed:11125109" ; sc:description "The database contains information about the occurrence of methylated cytosines in the DNA." ; sc:featureList edam:operation_0308, edam:operation_3204 ; sc:name "DNA Methylation Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.methdb.de/" ; biotools:primaryContact "christoph.grunau@methdb.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_2640, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC10062925", "pubmed:36940213" ; sc:description "Compute DNA methylation heterogeneity levels from Bismark-aligned bisulfite sequencing data." ; sc:featureList edam:operation_3186, edam:operation_3198, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Metheor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dohlee/metheor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3170, edam:topic_3173, edam:topic_3674 ; sc:citation , "pmcid:PMC7257144", "pubmed:32471342" ; sc:description """Beb-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. A web-based bioinformatics software for correlating DNA methylation and gene expression. The web user-interface can be accessed through https://paoyang.ipmb.sinica.edu.tw/Software.html . Correlation analyses of genome-wide DNA methylation and gene expression. Ordinal association analyses with genes ranked by gene expression level.""" ; sc:featureList edam:operation_3186, edam:operation_3207, edam:operation_3223, edam:operation_3463, edam:operation_3919 ; sc:name "MethGET" ; sc:url "https://paoyang.ipmb.sinica.edu.tw/Software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation "pubmed:26680022" ; sc:description "Simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)." ; sc:featureList edam:operation_3204 ; sc:name "MethGo" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://paoyangchen-laboratory.github.io/methgo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3295, edam:topic_3674, edam:topic_3810 ; sc:citation , "pmcid:PMC7552496", "pubmed:33045983" ; sc:description """Combining allele-specific DNA methylation and SNPs for haplotype region identification. DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms.""" ; sc:featureList edam:operation_0487, edam:operation_3186, edam:operation_3196, edam:operation_3207, edam:operation_3216 ; sc:name "MethHaplo" ; sc:url "https://github.com/ZhouQiangwei/MethHaplo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:33270889" ; sc:description """Information repository of DNA methylation and gene expression in human cancer. Demonstration of searching results in MethHC. More Clinical and Experimentally Validated Data.""" ; sc:featureList edam:operation_0308, edam:operation_0417, edam:operation_3206, edam:operation_3207, edam:operation_3792 ; sc:name "MethHC" ; sc:softwareVersion "2.0" ; sc:url "http://awi.cuhk.edu.cn/~MethHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295 ; sc:citation ; sc:description "This package implements functions for calling methylation for all cytosines in the genome." ; sc:featureList edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "methimpute" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methimpute.html" ; biotools:primaryContact "Aaron Taudt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:description "Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset." ; sc:featureList edam:operation_3206, edam:operation_3809 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "methInheritSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methInheritSim.html" ; biotools:primaryContact "Pascal Belleau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0204, edam:topic_0601 ; sc:citation "pubmed:24560580" ; sc:description "Web server for identifying methylated lysines on histones and non-histone proteins." ; sc:featureList edam:operation_0417 ; sc:name "MethK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/MethK/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation "pubmed:19804638" ; sc:description "Design of DNA methylation assays for COBRA, bisulfite SNuPE, bisulfite pyrosequencing, MethyLight and MSP. It also implements a systematic workflow for design, optimization and (computational) validation of DNA methylation biomarkers. This workflow starts from a preselected differentially methylated region (DMR) and results in an optimized DNA methylation assay that is ready to be tested in a large-scale clinical trial." ; sc:featureList edam:operation_3204 ; sc:name "MethMarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://methmarker.mpi-inf.mpg.de/" ; biotools:primaryContact "MethMarker Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:34654919" ; sc:description "A software tool to capture metadata and generate comprehensive microscopy methods text." ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MethodsJ2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ABIF-McGill/MethodsJ2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3295, edam:topic_3360 ; sc:citation ; sc:description """A parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection. MethPanel is a computational pipeline in Linux operating system with an interactive graphical interface for rapid analysis of multiplex bisulphite PCR sequencing data. The tool covers a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. Moreover MethPanel offers important and unique features, such as a epipolymorphism score and a bisulphite PCR bias correction. MethPanel can be run in parallel by samples on either a personal computer or a high performance computer. The outputs are automatically forwarded to a shinyApp for convenient display, visualisation and sharing of data with collaborators and clinicians.""" ; sc:featureList edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:name "MethPanel" ; sc:url "https://github.com/thinhong/MethPanel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3511 ; sc:citation "pubmed:26911705" ; sc:description "Summarises the resultant DNA methylation pattern data from the output of Bismark bismark_methylation_extractor." ; sc:featureList edam:operation_3204 ; sc:name "Methpat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bjpop.github.io/methpat/" ; biotools:primaryContact "Bernie Pope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3295 ; sc:citation ; sc:description "Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. We developed a diagnostic classifier based on DNA methylation profiles. This tool is a toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version can classify the following: DIPG, Ependymoma, ETMR, GBM, MB3 and 4, MB_WNT, MB_SHH, and PiloAstro." ; sc:featureList edam:operation_2990, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "MethPed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MethPed.html" ; biotools:primaryContact "Helena Carén" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:24324667" ; sc:description "The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR)." ; sc:featureList edam:operation_3186 ; sc:license "GPL-3.0" ; sc:name "Methpipe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/methpipe/" ; biotools:primaryContact "MethPipe Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0769, edam:topic_3295, edam:topic_3512 ; sc:citation , "pubmed:32053166" ; sc:description """Analysis of modified nucleotides from nanopore sequencing. Plotting tools for nanopore methylation data. This script generates a browser view on a window using data from. i) nanopolish, either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py). methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES""" ; sc:featureList edam:operation_0337, edam:operation_3185, edam:operation_3204, edam:operation_3454 ; sc:license "MIT" ; sc:name "methplotlib" ; sc:softwareHelp ; sc:softwareVersion "0.14.1" ; sc:url "https://github.com/wdecoster/methplotlib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3295, edam:topic_3512, edam:topic_3674 ; sc:citation ; sc:description """Estimating the regulatory potential of DNA methylation in gene transcription. Assessing the regulatory potential of DNA methylation regions or sites on gene transcription. Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions.""" ; sc:featureList edam:operation_0372, edam:operation_1781, edam:operation_3207, edam:operation_3659, edam:operation_3809 ; sc:license "GPL-3.0" ; sc:name "MethReg" ; sc:url "https://bioconductor.org/packages/MethReg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:33346800" ; sc:description """An R/bioconductor package for systematic aggregation and analysis of bisulfite sequencing data. Fast and efficient summarization of generic bedGraph files from Bisufite sequencing. Bedgraph files generated by BS pipelines often come in various flavors. Critical downstream step requires aggregation of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.""" ; sc:featureList edam:operation_3436, edam:operation_3695, edam:operation_3891, edam:operation_3919 ; sc:license "MIT" ; sc:name "methrix" ; sc:softwareHelp ; sc:url "https://github.com/CompEpigen/methrix" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295 ; sc:citation ; sc:description "Perform step by step methylation analysis of Next Generation Sequencing data." ; sc:featureList edam:operation_3204 ; sc:license "Artistic-2.0" ; sc:name "MethTargetedNGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MethTargetedNGS.html" ; biotools:primaryContact "Muhammad Ahmer Jamil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "This package allows the visualization of DNA methylation data after bisulfite sequencing." ; sc:featureList edam:operation_0564, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "methVisual" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methVisual.html" ; biotools:primaryContact "Arie Zackay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "This package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data." ; sc:featureList edam:operation_3204 ; sc:license "Artistic-2.0" ; sc:name "methyAnalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methyAnalysis.html" ; biotools:primaryContact "Pan Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2640, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:34117863" ; sc:description "Methylation-eQTL analysis in cancer research" ; sc:featureList edam:operation_3207, edam:operation_3463, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "methyl-eQTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rstudio-prd-c1.pmacs.upenn.edu/methyl-eQTL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC6883691", "pubmed:31783894" ; sc:description """Technology-independent estimation of cell type composition using differentially methylated regions. R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms. Estimate the cell composition of whole blood in DNA methylation samples. A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing). For help with the methylCC R-package, there is a vignette available in the /vignettes folder. Hicks SC, Irizarry RA. (2019). Genome Biology (accepted and in press). This is a package to estimate the cell composition of whole blood in DNA methylation measured on any platform technology (e.g. Illumina 450K microarray, whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)). DNAMethylation, MethylSeq, MethylationArray, Microarray, Sequencing, Software, WholeGenome""" ; sc:featureList edam:operation_3809 ; sc:license "CC-BY-4.0" ; sc:name "methylCC" ; sc:url "https://github.com/stephaniehicks/methylCC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:30346483" ; sc:description "Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing." ; sc:featureList edam:operation_3207, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "methylGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/methylGSA" ; biotools:primaryContact "Xu Ren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0654, edam:topic_3295 ; sc:citation "pubmed:26673711" ; sc:description "R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide." ; sc:featureList edam:operation_3206 ; sc:name "MethylAction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jeffbhasin.github.io/methylaction/" ; biotools:primaryContact "Jeffrey Bhasin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_3578 ; sc:name "Microarray hybridisation data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3295, edam:topic_3572 ; sc:citation , "pubmed:25147358" ; sc:description "A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "MethylAid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MethylAid.html" ; biotools:primaryContact "M. van Iterson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3295, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC7814737", "pubmed:33461601" ; sc:description """A deep-learning framework that reveals promoter activity landscapes from DNA methylomes in individual tumors. Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene level remain elusive. Here we present MethylationToActivity (M2A), a machine learning framework that uses convolutional neural networks to infer promoter activities based on H3K4me3 and H3K27ac enrichment, from DNA methylation patterns for individual genes. Using publicly available datasets in real-world test scenarios, we demonstrate that M2A is highly accurate and robust in revealing promoter activity landscapes in various pediatric and adult cancers, including both solid and hematologic malignant neoplasms""" ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_0440 ; sc:name "MethylationToActivity" ; sc:url "https://platform.stjude.cloud/workflows/methylation-to-activity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_0780, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC9823188", "pubmed:36607439" ; sc:description "Comprehensive downstream pipeline for the analysis of genome-wide DNA methylation." ; sc:featureList edam:operation_3186, edam:operation_3207, edam:operation_3809, edam:operation_3891, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MethylC-analyzer" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/RitataLU/MethylC-analyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_2269 ; sc:citation "pubmed:33225898" ; sc:description "Estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "methylclock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "V0.0.9" ; sc:url "https://github.com/isglobal-brge/methylclock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3173, edam:topic_3295 ; sc:citation "pubmed:21724594" ; sc:description "Pipeline for fast, simple processing of BiSulfite-treated reads into methylation data. Includes scripts for analysis and visualization. In addition to a binary output, the direct output of methylcoder is a text file that indicates per-nucleotide methylation context (CG/CHG/CHH) and methylation levels (both coverage and C-T conversions)" ; sc:featureList edam:operation_3186, edam:operation_3198 ; sc:license "BSD-3-Clause" ; sc:name "MethylCoder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/brentp/methylcode" ; biotools:primaryContact "Brent Pedersen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2854 ; sc:encodingFormat edam:format_3583 ; sc:name "Position-specific scoring matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3173 ; sc:description "A (mostly) universal methylation extractor for BS-seq experiments." ; sc:featureList edam:operation_0260, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MethylDackel" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.5.3" ; sc:url "https://github.com/dpryan79/MethylDackel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:24627790" ; sc:description "User friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation." ; sc:featureList edam:operation_3204 ; sc:name "MethylExtract" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinfo2.ugr.es/MethylExtract/" ; biotools:primaryContact "Guillermo Barturen", "José L. Oliver", "Michael Hackenberg", "Ricardo Lebrón" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:27246923" ; sc:description "Software of cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing." ; sc:featureList edam:operation_3204 ; sc:name "methylFlow" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/hcorrada/methylFlow" ; biotools:primaryContact "Hector Corrada Bravo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3295 ; sc:citation ; sc:description "These models estimate several properties, such as the level of processivity and preference for hemimethylated CpG dyads over unmethylated ones, of DNA methyltransferases from double-stranded binary methylation data. The inference is done by Markov chain Monte Carlo methods under a Bayesian framework." ; sc:featureList edam:operation_3664 ; sc:license "GPL-3.0" ; sc:name "MethylHMM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://stephenslab.uchicago.edu/software.html#eqtlbma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:description "Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed." ; sc:featureList edam:operation_3809 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "methylInheritance" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methylInheritance.html" ; biotools:primaryContact "Astrid Deschenes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC3491415", "pubmed:23034086" ; sc:description "R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only." ; sc:featureList edam:operation_3204 ; sc:license "Artistic-2.0" ; sc:name "methylKit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methylKit.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "Algorithm implemented to identify hyper/hypomethylated genes for a disease. Based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. It uses the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression." ; sc:featureList edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "MethylMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MethylMix.html" ; biotools:primaryContact "Olivier Gevaert" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_3003 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description "To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation." ; sc:featureList edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "methylMnM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methylMnM.html" ; biotools:primaryContact "Yan Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3173, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation "pubmed:22140101" ; sc:description "Database of DNA methylation profiles of human and mouse brains." ; sc:featureList edam:operation_0308, edam:operation_3204, edam:operation_3207 ; sc:name "MethylomeDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.neuroepigenomics.org/methylomedb/index.html" ; biotools:primaryContact "Fatemeh G. Haghighi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0749, edam:topic_3053 ; sc:citation , "pmcid:PMC4587815", "pubmed:26415965" ; sc:description "Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data." ; sc:featureList edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "methylPipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methylPipe.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3295 ; sc:citation ; sc:description "Modular and reproducible pipelines for multi-omics predictors of complex traits." ; sc:featureList edam:operation_0417, edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MethylPipeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/marioni-group/MethylPipeR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:name "GO-term enrichment data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3953 ; sc:name "Pathway overrepresentation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC10125902", "pubmed:37039839" ; sc:description "Graphical interface for comprehensive DNA methylation array data analysis." ; sc:featureList edam:operation_2436, edam:operation_2939, edam:operation_3204, edam:operation_3891, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "methylR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://methylr.research.liu.se" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3176, edam:topic_3295, edam:topic_3674, edam:topic_3940 ; sc:citation ; sc:description """An R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. methylscaper is a Shiny app for visualizing methylation data. Install the package with.""" ; sc:featureList edam:operation_0337, edam:operation_0372, edam:operation_3204 ; sc:name "methylscaper" ; sc:url "https://github.com/rhondabacher/acmethylscaper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0749, edam:topic_3295 ; sc:citation , "pmcid:PMC3763559", "pubmed:23828043" ; sc:description "This is a package for the discovery of regulatory regions from Bis-seq data." ; sc:featureList edam:operation_3186 ; sc:license "GPL-2.0" ; sc:name "MethylSeekR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MethylSeekR.html" ; biotools:primaryContact "Lukas Burger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:24836530" ; sc:description "R package for analyzing whole-genome bisulfite sequencing (bis-seq), reduced representation bisulfite sequencing (RRBS), or enhanced RRBS experiments." ; sc:featureList edam:operation_3204 ; sc:name "MethylSig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sartorlab.ccmb.med.umich.edu/node/17" ; biotools:primaryContact "Maureen A. Sartor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3518 ; sc:description "methylSpectrum is a software for deconvolution of DNA methylation array data into source contributions from distinct cell types. The major application of this software is to determine the composition of white blood cells (WBCs) from DNA methylation array data assayed in whole blood" ; sc:featureList edam:operation_3629 ; sc:name "methylSpectrum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v2" ; sc:url "http://people.oregonstate.edu/~housemae/software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7359584", "pubmed:32660416" ; sc:description """A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data. A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data. To process a large number of WGBS samples in a consistent, documented and reproducible manner it is advisable to use a pipeline system. MethylStar is a fast, stable and flexible pre-processing pipeline for bulk or single-cell (de-multiplexed) WGBS data.""" ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3919, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "MethylStar" ; sc:softwareHelp ; sc:url "https://github.com/jlab-code/MethylStar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation ; sc:description "This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control are also included." ; sc:featureList edam:operation_3204 ; sc:license "GPL-2.0" ; sc:name "methylumi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methylumi.html" ; biotools:primaryContact "Sean Davis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3168, edam:topic_3175, edam:topic_3295, edam:topic_3511 ; sc:citation "pubmed:20959287" ; sc:description "This tool was developed from CpGviewer such that the program can now analyse up to four different methylation sites such as CpG, GpC, CpNpG or any four user defined sites. If a non-native DNA methylase is used to modify chromatin-bound DNA, the methylation pattern can be used to identify the binding sites of DNA-binding proteins." ; sc:featureList edam:operation_3204 ; sc:name "MethylViewer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/methylviewer/" ; biotools:primaryContact "Ian Carr." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3674 ; sc:description "This package provides facilities for differential methylation analysis based on variable importance measures (VIMs), a class of statistical target parameters that arise in causal inference. The estimation and inference procedures provided are nonparametric, relying on ensemble machine learning to flexibly assess functional relationships among covariates and the outcome of interest." ; sc:featureList edam:operation_3432, edam:operation_3809 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "methyvim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/methyvim.html" ; biotools:primaryContact "Nima Hejazi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3071, edam:topic_3172 ; sc:author ; sc:citation ; sc:description "metID is a R packge which is used for metabolite identification based on in-house database and public database based on accurate mass (m/z), rentention time (RT) and/or MS2 spectra." ; sc:featureList edam:operation_3501, edam:operation_3803 ; sc:license "GPL-3.0" ; sc:name "metID" ; sc:url "https://jaspershen.github.io/metID/" ; biotools:primaryContact "Michael Snyder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3370, edam:topic_3375, edam:topic_3520 ; sc:citation ; sc:description """Open-Source R Package to Decipher Small-Molecule Drugs Metabolism Through High Resolution Mass Spectrometry. MetIDfyR is an open-source, cross-platform and versatile R script to predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest.""" ; sc:featureList edam:operation_3454, edam:operation_3803 ; sc:license "GPL-3.0" ; sc:name "MetIDfyR" ; sc:url "https://github.com/agnesblch/MetIDfyR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Repository, in a prototype stage, of mass spectra of small chemical compounds for life science (<2000 Da). The database will contain MSn data acquired on different platforms by different research groups. MSn data will be annotated with chemical information about the fragments." ; sc:featureList edam:operation_0570 ; sc:license "GPL-3.0" ; sc:name "MetiTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareHelp ; sc:url "http://www.metitree.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3174, edam:topic_3678 ; sc:citation , "pmcid:PMC4968819", "pubmed:27479078" ; sc:description "MetLab is aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes." ; sc:featureList edam:operation_0449 ; sc:license "GPL-3.0" ; sc:name "MetLab" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/norling/metlab" ; biotools:primaryContact "Julliette Hayer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3297, edam:topic_3407 ; sc:description "A MATLAB package for metabolical modeling, analysis and optimization." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:name "MetMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/3287-metmap" ; biotools:primaryContact "Julio Vera" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation , "pmcid:PMC5192445", "pubmed:27827849" ; sc:description "MetMatch is a software tool for the semi-automated comparison of different LC-HRMS chromatograms of untargeted metabolomics experiments. It provides methods to correct the raw-LC-HRMS data for m/z and retention time shifts relative to one or several preprocessed reference chromatograms." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "MetMatch" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://metabolomics-ifa.boku.ac.at/MetMatch/index.html#" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:17988949" ; sc:description "Generalized meta-analysis method for combining information across discovery-oriented datasets and for testing between-study heterogeneity for each biological variable of interest. The method is based on non-parametric Monte Carlo permutation testing." ; sc:featureList edam:operation_2495 ; sc:name "METRADISC" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://biomath.med.uth.gr/default.aspx?id=232164AC-9C6B-4A27-A595-2A22C35B6260" ; biotools:primaryContact "Elias Zintzaras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0199, edam:topic_0203, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC9118130", "pubmed:35334221" ; sc:description "METRO is a new computational method that leverages expression data collected from multiple genetic ancestries to enhance Transcriptome-wide association studies (TWAS)." ; sc:featureList edam:operation_0282, edam:operation_2495, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "METRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhengli09/METRO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0749, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC7379836", "pubmed:32709217" ; sc:description """An automated method for robust quantification of subcellular fluorescence events at low SNR. METROID (Morphological Extraction of Transmembrane potential from Regions Of Interest Device) is a computational tool to filter cellular transmembrane potential signals obtained from low signal-to-noise ratio (SNR) regions of interest (ROIs) in single cell fluorescence images. Metroid can be executed as a software with a graphical user interface (Windows only, click here to download the installer) or its code can be run in jupyter notebooks (check the Examples folder). A simplified flowchart is shown below:.""" ; sc:featureList edam:operation_2422, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "METROID" ; sc:url "https://doi.org/10.6084/m9.figshare.11344046.v1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3172 ; sc:citation ; sc:description "Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data." ; sc:featureList edam:operation_3660 ; sc:name "MetScape 3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metscape.med.umich.edu/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "A diverse collection of metabolomics related statistical tools." ; sc:featureList edam:operation_2238 ; sc:license "Apache-2.0" ; sc:name "MetStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://cran.r-project.org/web/packages/MetStaT/index.html" ; biotools:primaryContact "Gooitzen Zwanenburg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172 ; sc:citation "pubmed:26220962" ; sc:description "Software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis." ; sc:featureList edam:operation_3214 ; sc:name "MetTailor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mettailor/" ; biotools:primaryContact "Choi H" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3305, edam:topic_3324 ; sc:citation , "pubmed:32530587" ; sc:description """Projecting the Course of COVID-19 in Turkey. COVID 19 Case Projection Model for Turkey. COVID-19 Salgın Yönetimi ve Çalışma Rehberi. To fit data using all observations up to latest known day and project 20 days in the future:. To fit using observations up to a certain date (e.g. May 12th, 2020):. ERİŞKİN YOĞUN BAKIM DOLULUK ORANI.""" ; sc:featureList edam:operation_2426, edam:operation_3659 ; sc:name "Projecting Course COVID-19 Turkey" ; sc:url "https://github.com/kansil/covid-19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Visualisation of genomic data, Differential Gene Expression based on DEGseq, DESeq and edgeR" ; sc:featureList edam:operation_0291, edam:operation_0337 ; sc:license "Artistic-2.0" ; sc:name "MeV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mev.tm4.org/#/welcome" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3390, edam:topic_3518, edam:topic_3577 ; sc:citation , "pmcid:PMC10354005", "pubmed:37326976" ; sc:description "Hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MEvA-X" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PanKonstantinos/MEvA-X" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "TCGA data mining tool." ; sc:featureList edam:operation_2421 ; sc:name "MEXPRESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.mexpress.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_3382, edam:topic_3421, edam:topic_3474 ; sc:citation , "pmcid:PMC8489024", "pubmed:34518364" ; sc:description "MEYE is a free and open-source tool to perform pupillometry in real-time (or on videos) in different subjects (human and mice) and in different experimental conditions (head-fixation, virtual reality, 2-photon calcium imaging)" ; sc:featureList edam:operation_3096, edam:operation_3359 ; sc:license "GPL-3.0" ; sc:name "MEYE" ; sc:softwareHelp , ; sc:url "http://github.com/fabiocarrara/meye" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3517 ; sc:citation , "pubmed:33047835" ; sc:description """Testing an optimally weighted combination of common and rare variants with multiple traits using family data. R program to implement MF-TOWmuT, a new method developed for large-scale genome wide association study with multiple genetic variants and multiple phenotypes using family data.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3791 ; sc:name "MF-TOWmuT" ; sc:url "https://github.com/gaochengPRC/MF-TOWmuT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC10170507", "pubmed:37058588" ; sc:description "The tool can be used to download, filter, and assemble the MF-PCBA datasets in a format that is easily usable for machine learning." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_3695, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MF-PCBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/davidbuterez/mf-pcba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "mfa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mfa.html" ; biotools:primaryContact "Kieran Campbell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "An MATLAB implementation of the (Mutliple) FAst MEdoid Selection algorithm (MFAMES)." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "Fast Medoid Selection using MFAMES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/41757-fast-medoid-selection-using-mfames" ; biotools:primaryContact "Stephen Pratt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:25649619" ; sc:description "This tool could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction." ; sc:featureList edam:operation_2575 ; sc:name "mFASD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://staff.ustc.edu.cn/~liangzhi/mfasd/" ; biotools:primaryContact "Zhi Liang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:32866496" ; sc:description """Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures. Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.""" ; sc:featureList edam:operation_0337 ; sc:name "MFAssignR" ; sc:url "https://github.com/skschum/MFAssignR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC8325680", "pubmed:34333519" ; sc:description "An automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology." ; sc:featureList edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MFCIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mfcis.online/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC7243272", "pubmed:32499814" ; sc:description """A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data. A method for detecting CNV using neural networks. There are six directories. 1.program This directory contains three files that have been coded, including code for training the model, for detecting simulation data, for detecting real data, for extracting eigenvalue form simulation data, for extracting eigenvalue form real data and for transforming .txt to .mat. 2.test This directory contains two subdirectories including RealData_mat and SimulationData_mat, OriginalData_bam and Reference.""" ; sc:featureList edam:operation_3196, edam:operation_3798, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "MFCNV" ; sc:url "https://github.com/BDanalysis/mfcnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:20709734" ; sc:description "Designed to reliably detect recent positive selection in a varying size population, even if you only have polymorphism data from a single locus (i.e. a very short piece of DNA)." ; sc:featureList edam:operation_0554 ; sc:name "MFDM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.picb.ac.cn/evolgen/softwares/index.html" ; biotools:primaryContact "LI Haipeng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0634, edam:topic_2814 ; sc:citation "pubmed:24573480" ; sc:description "Combines per-residue disorder probabilities predicted by MFDp with per-sequence disorder content predicted by DisCon, and applies novel post-processing filters to provide disorder predictions with improved predictive quality." ; sc:featureList edam:operation_0474 ; sc:name "MFDp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biomine-ws.ece.ualberta.ca/MFDp2/index.php" ; biotools:primaryContact "Dr. Lukasz Kurgan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3295, edam:topic_3337, edam:topic_3420 ; sc:citation ; sc:description """The Male Fertility Gene Atlas – A web tool for collecting and integrating data about epi-/genetic causes of male infertility. The Male Fertility Gene Atlas (MFGA) is a public platform for providing a fast, simple and straightforward access to OMICS data in the context of male infertility and germ cells. It is developed in the context of the DFG Clinical Research Unit "Male Germ Cells: From Genes to Function" (CRU 326) under the supervision of an interdisciplinary team of physicians, biologists and computer scientists. The MFGA aims to.""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3436 ; sc:name "MFGA" ; sc:url "https://mfga.uni-muenster.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:35981061" ; sc:description "An Efficient Lightweight Multi-Scale Feature Learning CNN for COVID-19 Diagnosis from CT Images." ; sc:featureList edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MFL-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AmoghJ001/MFL_Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:7668300" ; sc:description "Simple program which automates setting up likelihood calculations for linkage analysis using a variety of different transmission models, and then collating the results in order to produce a (nearly) model free lod score." ; sc:featureList edam:operation_0283, edam:operation_2238 ; sc:name "MFLINK" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.davecurtis.net/dcurtis/software.html" ; biotools:primaryContact "David Curtis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3301, edam:topic_3474 ; sc:citation "pubmed:27092947" ; sc:description "Web-based platform that predicts the bacterial central metabolism via machine learning, leveraging data from approximately 100 13C-MFA papers on heterotrophic bacterial metabolisms." ; sc:featureList edam:operation_2423, edam:operation_3660 ; sc:name "MFlux" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mflux.org/" ; biotools:primaryContact "Dr. Bao", "Dr. Tang", "Dr. Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2815, edam:topic_3295 ; sc:citation , "pubmed:26173767" ; sc:description "Taking Advantage from Founder Mutations in Genetics Diagnosis, Genetic Diversity and Migration History of the Mediterranean Population." ; sc:featureList edam:operation_2421 ; sc:name "MFMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mfmd.pasteur.ma/" ; biotools:primaryContact "Abdelhamid Barakat", "Hicham Charoute" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3542 ; sc:citation "pubmed:12824337", "pubmed:7516239" ; sc:description "Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:name "Mfold" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://mfold.rna.albany.edu/?q=mfold/download-mfold" ; biotools:primaryContact "Michael J. Muskus" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3710 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3713 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_3468 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:17533220" ; sc:description "Mascot file parsing and quantitation using ICAT and SILAC." ; sc:featureList edam:operation_0335, edam:operation_3630, edam:operation_3634, edam:operation_3635, edam:operation_3637, edam:operation_3638, edam:operation_3648, edam:operation_3741 ; sc:name "MFPaQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mfpaq.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "FASTA/FASTQ extractor for multiple sets of read names" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mfqe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/wwood/mfqe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "RESTful web service for high-throughput prediction of elemental compositions from accurate mass values detected by high-resolution mass spectrometers." ; sc:featureList edam:operation_2422 ; sc:name "MFSearcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://webs2.kazusa.or.jp/mfsearcher/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2799 ; sc:name "Gene ID (MfunGD)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC1347437", "pubmed:16381934" ; sc:description "Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc." ; sc:featureList edam:operation_0224 ; sc:name "MIPS mouse functional genome database (MfunGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bio2rdf.org/describe/?uri=http://bio2rdf.org/lsr:mfungd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3678 ; sc:citation , "pmcid:PMC2139991", "pubmed:18084642" ; sc:description "Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "Mfuzz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Mfuzz.html" ; biotools:primaryContact "Matthias Futschik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0804, edam:topic_3360, edam:topic_3512 ; sc:citation , "pubmed:35809855" ; sc:description "Comprehensive analysis of ncRNA involvement in brain microglia immunology." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "MG-ncRexplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/MG-ncRexplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:36791547" ; sc:description "Multi-level global-aware network for thymoma segmentation." ; sc:featureList edam:operation_3436, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MG-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Leejyuan/MGNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:18803844" ; sc:description "MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison" ; sc:featureList edam:operation_0226 ; sc:name "MG-RAST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://metagenomics.anl.gov" ; biotools:primaryContact "F. Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "Multiple Genome Aligner computes multiple genome alignments of large, closely related DNA sequences. MGA  is a software tool for efficiently aligning two or more sufficiently similar genomic sized sequences [HKO02]. It belongs to the category of anchor-based multiple alignment methods. mga uses multiMEMs (or MEMs, MUMs as special cases) to anchor the alignment. In essence, they are (hopefully long) stretches or regions of identical bases occuring in all input sequences." ; sc:featureList edam:operation_0492 ; sc:name "MGA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20030318" ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/mga/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation , "pmcid:PMC1629028", "pubmed:17022809" ; sc:description "For rapidly visualizing and aligning the most highly conserved regions in multiple genomes. It is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased." ; sc:featureList edam:operation_2424, edam:operation_3182, edam:operation_3209 ; sc:name "M-GCAT 2.0 beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://alggen.lsi.upc.es/recerca/align/mgcat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23396516" ; sc:description "New algorithm designed to detect modules with a strongly interconnected neighborhood in large scale biological interaction networks." ; sc:featureList edam:operation_3439 ; sc:name "MGclus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sonnhammer.sbc.su.se/download/software/MGclus/Readme" ; biotools:primaryContact "Erik L. L. Sonnhammer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:37244571" ; sc:description "Gene prediction in phage genomes with multiple genetic codes." ; sc:featureList edam:operation_0284, edam:operation_0489, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MgCod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gatech-genemark/MgCod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8760670", "pubmed:35030988" ; sc:description "A total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts." ; sc:featureList edam:operation_0314, edam:operation_3436, edam:operation_3563, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MGcount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hitaandrea/MGcount" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0621, edam:topic_0625, edam:topic_0634 ; sc:citation "pubmed:12519980", "pubmed:19864252", "pubmed:21051359", "pubmed:22075990" ; sc:description "Community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. It includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information." ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_2422, edam:operation_3196 ; sc:name "Mouse Genome Database (MGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.informatics.jax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3305, edam:topic_3315, edam:topic_3324 ; sc:citation ; sc:description """A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics. MGDrivE2: Mosquito Gene Drive Explorer 2. MGDrivE 2 is a new simulation platform which extends capabilities from the MGDrivE simulation package in a new mathematical and computational framework. For more information about MGDrivE, see our publication. Some of the notable capabilities of MGDrivE 2 include incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations.""" ; sc:featureList edam:operation_3431, edam:operation_3927, edam:operation_3946 ; sc:name "MGDrivE 2" ; sc:url "https://github.com/MarshallLab/MGDrivE/tree/master/MGDrivE2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:12603042" ; sc:description "Designed to find the optimal trees for multiple genome rearrangement by signed reversals. The problem is modeled as: For a given collection of genomes represented by signed permutations on genes, find a tree to connect the given genomes by reversal paths such that the number of all signed reversals is minimized." ; sc:featureList edam:operation_2451 ; sc:name "Mgenome" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://xungulab.com/software/mgenome/mgenome.html" ; biotools:primaryContact "Shiquan Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:20435682" ; sc:description "mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools and can be used to develop genomic arrays." ; sc:featureList edam:operation_3194, edam:operation_3209 ; sc:name "mGenomeSubtractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo-mml.sjtu.edu.cn/mGS/" ; biotools:primaryContact "Hong-Yu Ou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3274 ; sc:encodingFormat edam:format_3475, edam:format_3752 ; sc:name "MGI accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2298 ; sc:encodingFormat edam:format_3475, edam:format_3752 ; sc:name "Gene ID (HGNC)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:encodingFormat edam:format_3475, edam:format_3752 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3697 ; sc:citation ; sc:description "A web application for microglia gene list enrichment analysis." ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MGEnrichment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ciernialab.shinyapps.io/MGEnrichmentApp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0621, edam:topic_0798 ; sc:citation "pubmed:19762481" ; sc:description "De novo computational method identifies new LTR (long terminal repeat) retrotransposons without relying on a library of known elements. Specifically, the method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis." ; sc:featureList edam:operation_0427 ; sc:name "MGEScan-LTR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0623, edam:topic_0820, edam:topic_3293 ; sc:citation ; sc:description """Classification of multigene families of African swine fever viruses. MGFC: a web server for classifying multigene family proteins in ASFV. MGF proteins are classified into 31 groups based on sequence homology. Three, nine, three, eleven and five protein groups were obtained in MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505 families, respectively. This server provides a user-friendly interface for classifying MGF proteins into groups based on MGF protein sequences.""" ; sc:featureList edam:operation_0269, edam:operation_0417, edam:operation_2489 ; sc:name "MGF" ; sc:url "http://www.computationalbiology.cn/MGF/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "The package is designed to detect marker genes from Microarray gene expression data sets." ; sc:featureList edam:operation_0282 ; sc:license "GPL-3.0" ; sc:name "MGFM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MGFM.html" ; biotools:primaryContact "Khadija El Amrani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "The package is designed to detect marker genes from RNA-seq data." ; sc:featureList edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "MGFR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MGFR.html" ; biotools:primaryContact "Khadija El Amrani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , ; sc:description "It has shown that infections, psychosocial, nutritional, hygiene, and socioeconomic factors may be related in such an intricate way, that could be hardly detected using traditional regression based epidemiological techniques." ; sc:featureList edam:operation_2990 ; sc:name "MGGP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ciml/ciml-lib" ; biotools:primaryContact "Rafael V. Veiga" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC4384027", "pubmed:25348401" ; sc:description "Integrated genetic, genomic, and biological data for mouse." ; sc:featureList edam:operation_0224 ; sc:name "Mouse Genome Informatics (MGI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.informatics.jax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3318, edam:topic_3421, edam:topic_3810 ; sc:citation , "pmcid:PMC9652799", "pubmed:36371210" ; sc:description "A powerful tool to analyze plant multivariate data." ; sc:featureList edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MGIDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bit.ly/site-mgidi-pm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0605, edam:topic_0654, edam:topic_3168, edam:topic_3305 ; sc:citation "pubmed:19468047" ; sc:description "Suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain." ; sc:featureList edam:operation_2403, edam:operation_3227 ; sc:name "MGIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mgip.biology.gatech.edu" ; biotools:primaryContact "Lee S. Katz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174 ; sc:citation ; sc:description "Reference based mapping and taxonomy annotation of metagenomics sequence reads." ; sc:featureList edam:operation_0292, edam:operation_2478 ; sc:name "MGmapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cge.cbs.dtu.dk/services/MGmapper/" ; biotools:primaryContact "Thomas Nordahl Petersen", "Thomas Sicheritz-Pontén" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC7466374", "pubmed:32384576" ; sc:description """Membrane glycolipid mass spectrum simulator for polymicrobial samples. 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Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_2640, edam:topic_2828, edam:topic_2830 ; sc:citation , "pmcid:PMC9825574", "pubmed:36318236" ; sc:description "A database of MHC binding specificities and ligands." ; sc:featureList edam:operation_0252, edam:operation_0337, edam:operation_0416, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "MHC Motif Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mhcmotifatlas.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC7355292", "pubmed:32657386" ; sc:description """Predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model. 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The software implements allele-specific neural networks that use a novel architecture and peptide encoding scheme." ; sc:featureList edam:operation_0252 ; sc:license "Apache-2.0" ; sc:name "MHCflurry" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/openvax/mhcflurry" ; biotools:primaryContact "Timothy J. O'Donnell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2830, edam:topic_3400, edam:topic_3474 ; sc:citation , "pubmed:33374958" ; sc:description """MHCII3D-Robust Structure Based Prediction of MHC II Binding Peptides. MHC II Automated Server Benchmarks. The knowledge of MHC II binding peptides is highly desired in immunological research, particularly in the context of cancer, autoimmune diseases, or allergies. MHCII3D is a prediction tool based on structural scaffolds of MHC II-peptide complexes and statistical scoring functions (SSFs). Its prediction performance is among machine learning tools.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0478, edam:operation_3216 ; sc:name "MHCII3D" ; sc:url "http://tools.iedb.org/auto_bench/mhcii/weekly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0804, edam:topic_2830 ; sc:citation "pubmed:16539539" ; sc:description "Uses the additive method to predict the binding affinity of major histocompatibility complex (MHC) class I and II molecules and also to the Transporter associated with Processing (TAP)." ; sc:featureList edam:operation_2479 ; sc:name "MHCPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ddg-pharmfac.net/mhcpred/MHCPred/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:35443027" ; sc:description "Pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences." ; sc:featureList edam:operation_0252, edam:operation_0416 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MHCRoBERTa" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/FuxuWang/MHCRoBERTa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3400 ; sc:citation , "pubmed:34196671" ; sc:description "The tool for global and local false discovery rate (FDR) estimation for MHC-peptide binding prediction" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2238, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MHCVision" ; sc:url "https://github.com/PGB-LIV/MHCVision" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_2830, edam:topic_3520 ; sc:citation ; sc:description """Detailed Experimental Protocols and Rapid, User-Friendly Visualization of MHC I and II Ligand Datasets with MhcVizPipe. A reporting pipeline for visualization of immunopeptidomics MS data. Welcome to the MhcVizPipe (MVP) wiki!. MhcVizPipe connects the bioinformatic tools NetMHCpan, NetMHCIIpan and GibbsCluster and generates organized and easy-to-understand reports in HTML format. The reports are fully portable and can be viewed on any computer with a modern web browser. Here are some of the features of MhcVizPipe:.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3631 ; sc:license "MIT" ; sc:name "MhcVizPipe" ; sc:softwareHelp ; sc:url "https://github.com/CaronLab/MhcVizPipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3315, edam:topic_3940 ; sc:citation , "pmcid:PMC7068949", "pubmed:32164554" ; sc:description """Integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data. This documentation has three sections:. This documentation has two sections:. In order to have an integrated tool, we developed a Graphical User Interface for MHiC. This graphical User Interface enables the user to set parameters and generate significant interactions and also visualize a Hi-C contact map. We developed this part as an HTML page.""" ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3435 ; sc:name "MHiC" ; sc:url "https://github.com/MHi-C" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pubmed:32086216" ; sc:description """Prediction of lncRNA-disease associations based on multiple heterogeneous networks. Package: MHRWR Type: Package Title: MHRWR Prediction of lncRNA-disease associations based on multiple heterogeneous networks.""" ; sc:featureList edam:operation_2428, edam:operation_3927 ; sc:name "MHRWR" ; sc:url "https://github.com/yangyq505/MHRWR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC7355295", "pubmed:32657378" ; sc:description """Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. Multiple instance learning based classification for MSI data.""" ; sc:featureList edam:operation_3553, edam:operation_3860 ; sc:name "mi-CNN" ; sc:url "https://github.com/Vitek-Lab/mi-CNN_MSI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_2885, edam:topic_3056 ; sc:citation , "pmcid:PMC7119171", "pubmed:32245404" ; sc:description "marker informativeness for multi-ancestry admixed populations." ; sc:featureList edam:operation_0415, edam:operation_0487, edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:name "MI-MAAP" ; sc:softwareHelp ; sc:url "https://research.cchmc.org/mershalab/MI-MAAP/login/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3524, edam:topic_3697 ; sc:citation ; sc:description "Mathematical analysis software specifically for use with mechanistically described microbial interactions described in terms of reactions, substrates/reactants and products. It provides a user-friendly environment in which microbiologists, microbial ecologists and biological mathematicians can rapidly and robustly characterize the dynamics of ecological motifs of up to three microbial species, without the requirement to develop their own code, programme models or rely on a detailed knowledge of the mathematics of dynamical systems analysis." ; sc:featureList edam:operation_2426, edam:operation_3562 ; sc:name "MI-Sim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://uk.mathworks.com/matlabcentral/fileexchange/55492-mi-sim-mi-sim-final" ; biotools:primaryContact "Matthew J. Wade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174 ; sc:citation , "pubmed:31504158" ; sc:description "Weighted quality evaluation of assembled microbial genomes | SUMMARY:Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons. AVAILABILITY AND IMPLEMENTATION:miComplete is written in Python 3 and released under GPLv3" ; sc:featureList edam:operation_3180, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "miComplete" ; sc:url "https://bitbucket.org/evolegiolab/micomplete" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_3360 ; sc:citation , "pmcid:PMC6826485", "pubmed:31601051" ; sc:description """A Literature-Curated Database of microRNA Expression Patterns, in Diabetic Microvascular Complications. miR2Diabetes aims to provide a comprehensive resource of miRNA dysregulation in diabetic microvascular complications (DMC). Each entry in the miR2Diabetes contains detailed information on a miRNA-DMC relationship, including miRNA symbol, DMC name, experiment subjects, miRNA dysregulation pattern in a specific experimental design, and literature reference. microRNAs (miRNAs) have been established as critical regulators of the pathogenesis of diabetes mellitus (DM), and diabetes microvascular complications (DMCs). The annotations in the database cover 14 DM and DMC phenotypes, involving 156 miRNAs, by browsing diverse sample origins (e.g., blood, kidney, liver, and other tissues).""" ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3431 ; sc:name "miR2Diabetes" ; sc:url "http://mir2diabetes.yoonlab.or.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3518 ; sc:citation , "pubmed:31504780" ; sc:description "An online database for prediction of functional microRNA targets | MicroRNA Target Prediction Database | An Online Database for MicroRNA Target Prediction and Functional Studies | miRDB is an online database for miRNA target prediction and functional annotations | Choose one of the following search options: | HumanMouseRatDogChicken GenBank Accession NCBI Gene ID Gene Symbol" ; sc:featureList edam:operation_0463, edam:operation_2489, edam:operation_3792 ; sc:name "miRDB" ; sc:url "http://mirdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659 ; sc:citation ; sc:description "miRDRN (miRNA Disease Regulatory Network) is a useful platform for discovering potential novel disease networks and comorbidity genes by disease-associated miRNAs targeting pathways." ; sc:featureList edam:operation_0277, edam:operation_0463, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "miRDRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mirdrn.ncu.edu.tw/mirdrn/" ; biotools:primaryContact "Hoong-Chien Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC6321451", "pubmed:30562930" ; sc:description "Tool for the Prediction of Pre-miRNA⁻Protein Interactions." ; sc:featureList edam:operation_0239, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "miRNAmotif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mirnamotif.ibch.poznan.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0659 ; sc:citation , "pubmed:31691816" ; sc:description """A novel release of the miRNA Pathway Dictionary Database. Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https: mpd.bioinf.uni-sb.de. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data.""" ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_3695 ; sc:name "miRPathDB" ; sc:url "https://mpd.bioinf.uni-sb.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6827457", "pubmed:31695969" ; sc:description """Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. the experimentally validated microRNA-target interactions database. As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.""" ; sc:featureList edam:operation_0463, edam:operation_2495, edam:operation_3439 ; sc:name "miRTarBas" ; sc:url "http://mirtarbase.mbc.nctu.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC6266954", "pubmed:30497361" ; sc:description "Web application for the analysis of miRNA-target interactions in human tissues." ; sc:featureList edam:operation_0463, edam:operation_2497, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "miRTissue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://150.145.111.118:3838/mirTissue/" ; biotools:primaryContact "Translational Bioinformatics Laboratory at CNR-ICAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170 ; sc:author ; sc:citation , ; sc:description """> Slight manual curation of an auto-generated entry. Authors please revise and amend. (Matus Kalas @matuskalas) > MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'mirtop', 'isomiR', 'mirtop API', 'mirGFF3 mirtop' | Unification of miRNA and isomiR research | GFF3 format with miRNA and isomiR information from sequencing data | A proxy for miRNA/isomiR data analysis where all tools meet with the idea to create an ecosystem of data analysis promoting community collaboration | As discussed here: https://github.com/miRTop/incubator/issues/10 we've defined a GFF3 format for output of small RNA pipelines focused on miRNA data currently. We is an open community project (read more) and joint us! | This output is based on the current GFF3 definition: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md""" ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "miRTop" ; sc:url "http://mirtop.github.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3302 ; sc:citation , "pmcid:PMC6280396", "pubmed:30514392" ; sc:description "Tool for quality control and tracing taxonomic origins of microRNA sequencing data." ; sc:featureList edam:operation_0463, edam:operation_3192, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRTrace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/friedlanderlab/mirtrace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6785219", "pubmed:31596843" ; sc:description """Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and disease. Despite much effort, microRNA annotations still contain errors and are incomplete due especially to challenges related to identifying valid miRs that have small numbers of reads, to properly locating hairpin precursors and to balancing precision and recall. Here, we present miRWoods, which solves these challenges using a duplex-focused precursor detection method and stacked random forests with specialized layers to detect mature and precursor microRNAs, and has been tuned to optimize the harmonic mean of precision and recall. We trained and tuned our discovery pipeline on data sets from the well-annotated human genome, and evaluated its performance on data from mouse.""" ; sc:featureList edam:operation_0362, edam:operation_0463, edam:operation_3192, edam:operation_3792 ; sc:name "miRWoods" ; sc:url "https://github.com/hendrixlab/miRWoods" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6892182", "pubmed:31827401" ; sc:description """Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma. transcriptome-wide microRNA target prediction including lncRNAs. miRcode 11 (June 2012) based on: UCSC GRCh37/hg19, GENCODE 11 transcripts, Multiz 46 species, TargetScan6 families. MiRcode provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation, including >10,000 long non-coding RNA genes.""" ; sc:featureList edam:operation_0463, edam:operation_3659, edam:operation_3792 ; sc:name "miRcode" ; sc:url "http://www.mircode.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Confident detection of microRNA editing | Confident detection of A-to-I miRNA editing events in small-RNA seq data | miRmedon it's a python3 code which takes fastq file of trimmed small-RNA reads, and reports on A-to-I editing events detected in the data. In addition, miRmedon reports on read counts and sequence of both edited and non-edited miRNAs. miRmedon require several extrenal softwares and python libraries, as descirbed below" ; sc:featureList edam:operation_0463, edam:operation_3096, edam:operation_3792 ; sc:license "MIT" ; sc:name "miRmedon" ; sc:url "https://github.com/Amitai88/miRmedon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3518 ; sc:citation , "pubmed:31077152" ; sc:description "R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules." ; sc:featureList edam:operation_0463, edam:operation_3501, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRspongeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.10.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRspongeR.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6933624", "pubmed:31881825" ; sc:description """Identifying miRNA synergism using multiple-intervention causal inference. Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. A novel method for identifying miRNA synergism using multiple-intervention causal inference.""" ; sc:featureList edam:operation_0277, edam:operation_0463, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "miRsyn" ; sc:url "https://github.com/zhangjunpeng411/miRsyn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Web-based tool for microRNA Truncation and Tailing Analysis." ; sc:featureList edam:operation_0463, edam:operation_3192, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "miTRATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wasabi.ddpsc.org/~apps/ta/" ; biotools:primaryContact "Blake C. Meyers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3337, edam:topic_3517 ; sc:citation , "pubmed:37308034" ; sc:description "A genotype imputation server for high-dimensional data." ; sc:featureList edam:operation_3196, edam:operation_3359, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "MI-System" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://misystem.cgm.ntu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "An Open Source Standalone Deep Learning Application for Microscopic Image Analysis." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MIAnalyzer/MIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0219, edam:topic_0621, edam:topic_3489, edam:topic_3518 ; sc:citation "pubmed:12519949" ; sc:description "Compliant microarray data submission tool." ; sc:featureList edam:operation_0224, edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3431 ; sc:name "MIAMExpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/microarray/MIAMExpress/miamexpress.html" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC9344855", "pubmed:35748713" ; sc:description "Mutual Information-based Analysis of Multiplex Imaging data." ; sc:featureList edam:operation_3443, edam:operation_3463, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MIAMI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sealx017/MIAMI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3172, edam:topic_3173, edam:topic_3697 ; sc:citation , "pmcid:PMC9136154", "pubmed:35664224" ; sc:description "Human microbiome affect the host epigenome." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "MIAOME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://miaome.idrblab.net/ttd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC4863143", "pubmed:27167008" ; sc:contributor ; sc:description "miARma-Seq is a suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism." ; sc:featureList edam:operation_2478 ; sc:license "CC-BY-2.0" ; sc:name "miARma-Seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.7.2" ; sc:url "http://miarmaseq.idoproteins.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3385, edam:topic_3452 ; sc:citation , "pmcid:PMC4699692", "pubmed:26727152" ; sc:description "Microscopy image browser (MIB) is a software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data." ; sc:featureList edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "MIB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mib.helsinki.fi/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc:description "Microscopy Image Browser 2 (MIB2) is an update package for segmentation of multi-dimensional (2D-4D) microscopy datasets" ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Microscopy Image Browser 2 (MIB2)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.70" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63402-microscopy-image-browser-2-mib2" ; biotools:primaryContact "Ilya Belevich" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814, edam:topic_3534 ; sc:citation , "pubmed:35904542" ; sc:description "Metal ion-binding site prediction and modeling server." ; sc:featureList edam:operation_0474, edam:operation_3898, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "MIB2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.cmu.edu.tw/MIB2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3360 ; sc:citation , "pmcid:PMC7789220", "pubmed:33407076" ; sc:description """An interactive web application for multi-omics data exploration and integration. 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It includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, it can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. 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Using simple point-and-click interfaces, data can be readily imported, integrated and visualized...no coding required!""" ; sc:featureList edam:operation_0289, edam:operation_0490, edam:operation_0491, edam:operation_0540, edam:operation_0558, edam:operation_0567, edam:operation_2940, edam:operation_3436, edam:operation_3459, edam:operation_3503, edam:operation_3553, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MicrobeTrace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.1" ; sc:url "https://microbetrace.cdc.gov" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation "pubmed:9283758" ; sc:description "Microbial genome and functional analysis of Bacillus subtilis." ; sc:featureList edam:operation_0224 ; sc:name "Microbial advanced database organisation (Micado)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi" ; biotools:primaryContact "Annie Gendrault-Jacquemard", "Hélène Chiapello" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0622, edam:topic_0654, edam:topic_3382 ; sc:citation "pubmed:14988111" ; sc:description "Tool for visualization of microbial genomes. Chromosome wheels and linear genome maps with user specified features/color coding can be generated interactively. Graphics are created in SVG format." ; sc:featureList edam:operation_0282, edam:operation_0362, edam:operation_0487, edam:operation_2429, edam:operation_2871 ; sc:name "Microbial Genome Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cmbi.ru.nl/MGV/" ; biotools:primaryContact "Robert Kerkhoven" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:author "Leo Lahti" ; sc:citation , ; sc:description "Tools for the analysis of microbial community profiling data. Extends the phyloseq class." ; sc:featureList edam:operation_3096 ; sc:license "BSD-2-Clause" ; sc:name "microbiome" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "http://microbiome.github.io/microbiome/" ; biotools:primaryContact "Leo Lahti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description """MicrobiomeDASim: Simulating longitudinal differential abundance for microbiome data. Tools to simulate longitudinal differential abundance for microbiome data. Microbiome Differential Abundance Simulation. A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance. Microbiome, Software, Visualization. After installing Jupyter and the appopriate kernel you can access an interactive simulation session of microbiomeDASim using mvrnorm_demo.ipynb.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "MIT" ; sc:name "microbiomeDASim" ; sc:url "http://bioconductor.org/packages/microbiomeDASim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC9825749", "pubmed:36469345" ; sc:description "Methodological approaches to derive and visualize microbiome trajectories." ; sc:featureList edam:operation_2939, edam:operation_3890, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Microbiome Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://microbiome-toolbox.azurewebsites.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3170, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , "pubmed:31942082" ; sc:description """Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Note - MicrobiomeAnalystR is still under development - we cannot guarantee full functionality.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3501 ; sc:name "MicrobiomeAnalyst" ; sc:softwareHelp ; sc:url "https://www.microbiomeanalyst.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:31848574" ; sc:description """Current challenges and best-practice protocols for microbiome analysis. Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing. This review paper (https://doi.org/10.1093/bib/bbz155) aims to provide a comprehensive workflow to perform amplicon and shotgun metagenomics analysis. There are two workflows provided. First workflow for amplicon, using the standard mothur and dada2, and along with it some standard visualization are provided for the processed data. Second workflow for metagenomics, using a variety of tools openly available which have been stitched together to form a usable pipeline. Both the workflows are controlled by bash scripts: amplicon_analysis.sh and metagenomics_analysis.sh.""" ; sc:featureList edam:operation_0310, edam:operation_3184, edam:operation_3460 ; sc:license "MIT" ; sc:name "MicrobiomeBPR" ; sc:url "https://github.com/grimmlab/MicrobiomeBestPracticeReview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_2885, edam:topic_3517, edam:topic_3697 ; sc:citation , "pmcid:PMC9317577", "pubmed:35886007" ; sc:description "MicrobiomeGWAS is a software package for identifying host genetic variants associated with micorbiome distance matrix or beta-diversity. For each SNP, microbiome GWAS tests the main effect or the SNP-environment interaction." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "microbiomeGWAS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/lsncibb/microbiomeGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3342, edam:topic_3360, edam:topic_3474, edam:topic_3577, edam:topic_3697 ; sc:citation , "pubmed:35771644" ; sc:description "An R/Bioconductor package for microbiome marker identification and visualization." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "microbiomeMarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioconductor.org/packages/microbiomeMarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC7359232", "pubmed:32660471" ; sc:description """Dirichlet-tree multinomial regression models with Bayesian variable selection. In this folder you'll find code for the R package MicroBVS found in:. “MicroBVS: Dirichlet-Tree Multinomial Regression Models with Bayesian Variable Selection - an R Package” (Accepted by BMC Bioinformatics 2020), by MD Koslovsky and M Vannucci.""" ; sc:featureList edam:operation_0324, edam:operation_3659, edam:operation_3936 ; sc:name "MicroBVS" ; sc:url "https://github.com/mkoslovsky/MicroBVS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0637, edam:topic_3168 ; sc:citation ; sc:description "Methods for Taxonomic Classification of Prokaryotes." ; sc:featureList edam:operation_3460 ; sc:license "GPL-2.0" ; sc:name "microclass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://cran.r-project.org/web/packages/microclass/" ; biotools:primaryContact "Lars Snipen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659 ; sc:citation "pubmed:22041293" ; sc:description "Online machine learning algorithm based on SVM (support vector machine) to predict Human miRNA-mediated gene silencing: mRNA degradation or translational repression, and it can also determine whether a mRNA is a target of a miRNA according to Pictar and PITA." ; sc:featureList edam:operation_2495 ; sc:name "microDoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://reprod.njmu.edu.cn/cgi-bin/microdor/index.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:22851645" ; sc:description "Program that estimates allelic dropout rates from nonreplicated microsatellite genotype data. MicroDrop uses the estimated dropout rates to provide imputed data sets that sample missing genotypes (and replace some homozygous genotypes) using an allele frequency model with or without Hardy-Weinberg equilibrium." ; sc:featureList edam:operation_2478 ; sc:name "MicroDrop" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.stanford.edu/group/rosenberglab/microdrop.html" ; biotools:primaryContact "Noah A Rosenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3516 ; sc:citation "pubmed:20964757" ; sc:description "Computer program  for analysing the genotyping errors of microsatellites in parentage exclusion analysis." ; sc:featureList edam:operation_2478, edam:operation_3196 ; sc:name "MicroErrorAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zsl.org/science/software/microerroranalyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3421, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC9580939", "pubmed:36303759" ; sc:description "Extending Association Rule Mining to Microbiome Pattern Analysis.'" ; sc:featureList edam:operation_2422, edam:operation_2940, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "microFIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/qLSLab/microFIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0204, edam:topic_0749, edam:topic_3293 ; sc:citation "pubmed:11997340", "pubmed:12015878", "pubmed:12824433", "pubmed:16845027" ; sc:description "Identify the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter." ; sc:featureList edam:operation_0238, edam:operation_0327, edam:operation_0438 ; sc:name "MicroFootPrinter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio.cs.washington.edu/MicroFootPrinter.html" ; biotools:primaryContact "Martin Tompa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0199, edam:topic_3305, edam:topic_3945 ; sc:citation , "pmcid:PMC7330013", "pubmed:32670259" ; sc:description """A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences. MicroGMT: Microbial Genomics Mutation Tracker. MicroGMT is a python based package, which takes either raw sequence reads or assembled genome sequence as input and compares against database sequences to identify and characterize small indels and point mutations in the microbial genoems. Although our default setting is optimized for SARS-CoV-2 virus, the package can be also applied to any other microbial genomes.""" ; sc:featureList edam:operation_0525, edam:operation_3227, edam:operation_3695 ; sc:license "MIT" ; sc:name "MicroGMT" ; sc:url "https://github.com/qunfengdong/MicroGMT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3572 ; sc:citation , "pubmed:32276087" ; sc:description """A python package for cryo-EM micrograph cleaning using deep learning. MicrographCleaner (micrograph_cleaner_em) is a python package designed to segment cryo-EM micrographs into:.""" ; sc:featureList edam:operation_3458 ; sc:license "Apache-2.0" ; sc:name "MicrographCleaner" ; sc:url "https://github.com/rsanchezgarc/micrograph_cleaner_em" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC4066781", "pubmed:24803669" ; sc:description "R package for topological pathway analysis integrating gene and miRNA expression profiles using validated and/or predicted miRNA-target interactions. It is based on updated versions of graphite and CliPPER Bioconductor packages dedicated to pathway analyses recently proposed by our group." ; sc:featureList edam:operation_2497 ; sc:license "AGPL-3.0" ; sc:name "micrographite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "4.0" ; sc:url "http://romualdi.bio.unipd.it/micrographite" ; biotools:primaryContact "Chiara Romualdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description """A portable and extensible database of all published microhaplotype marker and frequency data. MicroHapDB is a portable database intended for scientists and researchers interested in microhaplotypes for forensic analysis.""" ; sc:featureList edam:operation_3196, edam:operation_3436, edam:operation_3629 ; sc:name "MicroHapDB" ; sc:url "https://github.com/bioforensics/MicroHapDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15980566" ; sc:description "Tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites." ; sc:featureList edam:operation_0389, edam:operation_0445, edam:operation_0463, edam:operation_2575, edam:operation_3222 ; sc:name "MicroInspector" ; sc:url "http://bioinfo.uni-plovdiv.bg/microinspector/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621, edam:topic_3068, edam:topic_3500 ; sc:citation "pubmed:19783819" ; sc:description "Database of proteins that localize in midbody, centrosome and/or kinetochore. The database contains experimentally verified microkit proteins from the scientific literature that have unambiguous supportive evidence for subcellular localization under fluorescent microscope. Moreover, the orthologous information was provided for these microkit proteins, and could be a useful resource for further experimental identification." ; sc:featureList edam:operation_0224, edam:operation_0245, edam:operation_0477, edam:operation_3092, edam:operation_3767 ; sc:name "MiCroKit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://microkit.biocuckoo.org/" ; biotools:primaryContact "Jian Ren", "Yu Xue", "Zexian Liu," . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3383 ; sc:citation "pubmed:20890901" ; sc:description "ImageJ Plugin for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. It works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging." ; sc:featureList edam:operation_3552 ; sc:name "microManager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://valelab.ucsf.edu/~MM/MMwiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3301 ; sc:author , ; sc:citation ; sc:contributor "U.S. Department of Agriculture | Agricultural Research Service (ARS)" ; sc:description """MicroMPN estimates most probable number (MPN) from lab microplates (how many viable bacteria are in a sample). It has been develeped for high-throughput screening of microbe suppression (e.g. of a pathogen of interest) in mixed populations, where we need to accurately distinguish viable pathogen cells from non-viable and non-target microbes. In-vitro dilutions are made with replication, and the number of tubes or wells with bacterial growth is recorded. This presence/absence, and dilution information are used to estimate the number of bacteria in the starting sample. With liquid-handling robots and plate reader, it can be faster than conventional plate counting or spotting on agar. 2 inputs from a plate reader: A plate layout file in Wellmap TOML format, and a CSV plate reader file with columns for the plate, the well or row+column, and the optical value used for determining growth. MicroMPN's MPN estimation function is usable for MPN calculation for other applications in Python.""" ; sc:featureList edam:operation_2238, edam:operation_2945, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "MicroMPN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/USDA-ARS-GBRU/micrompn" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_2206 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_3009 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2305 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "Specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data." ; sc:featureList edam:operation_0463 ; sc:name "microMUMMIE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://ohlerlab.mdc-berlin.de/software/microMUMMIE_99/" ; biotools:primaryContact "Uwe Ohler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640 ; sc:description "A new feature selection method called Biological Pathway-based Feature Selection (BPFS) for microarray data. Unlike most of the existing methods, the method integrates signaling and gene regulatory pathways with gene expression data to minimize the chance of overfitting of the method and to improve the test accuracy." ; sc:featureList edam:operation_2495 ; sc:name "microp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.cise.ufl.edu/microp.html" ; biotools:primaryContact "Tamer Kahveci" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_2546 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3070, edam:topic_3301 ; sc:author "Kristian Hovde Liland", "Lars Snipen" ; sc:citation ; sc:description "R package for the study of prokaryotic pan-genomes. A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species." ; sc:featureList edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "micropan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Norwegian University of Life Sciences", "UiO" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://cran.r-project.org/web/packages/micropan/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3301, edam:topic_3697 ; sc:citation ; sc:description "Microbe set enrichment analysis and disease similarity calculation based on a list of microbes." ; sc:featureList edam:operation_3461 ; sc:license "CC-BY-4.0" ; sc:name "MicroPattern" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cuilab.cn/micropattern" ; biotools:primaryContact "Qinghua Cui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0654, edam:topic_3512, edam:topic_3676 ; sc:citation ; sc:description "Microphaser is a tool for phasing small tumor DNA sequences - e.g. coding for small peptides - in linear time. It can be used in tumor neoantigen prediction to generate the neo-peptidome." ; sc:featureList edam:operation_0252, edam:operation_0487, edam:operation_3227, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Microphaser" ; sc:url "https://github.com/koesterlab/microphaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3174 ; sc:citation ; sc:description "MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes." ; sc:featureList edam:operation_0310, edam:operation_2421 ; sc:name "MicroPhenoDB" ; sc:url "http://www.liwzlab.cn/microphenodb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3298, edam:topic_3697 ; sc:citation , "pmcid:PMC5153691", "pubmed:27955641" ; sc:description "Microbial Phenomics Information Extractor (MicroPIE) is a natural language processing application that uses a robust supervised classification algorithm (Support Vector Machine) to identify characters from sentences in prokaryotic taxonomic descriptions, followed by a combination of algorithms applying linguistic rules with groups of known terms to extract characters as well as character states." ; sc:featureList edam:operation_2422 ; sc:license "Other" ; sc:name "MicroPIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/biosemantics/micropie2/tree/0.1.0" ; biotools:primaryContact "Jin Mao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation ; sc:description "The Micropilot software from EMBL is a computer program that can rapidly learn what a scientist is looking for in an experiment and then take over the laborious and time-consuming task, automatically performing complex microscopy experiments when it detects cells with interesting features." ; sc:featureList edam:operation_3443 ; sc:name "Micropilot" ; sc:operatingSystem "Windows" ; sc:softwareVersion "v094" ; sc:url "http://www.embl.de/almf/almf_services/hc_screeing/micropilot/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description """An end-to-end solution for high-quality complete bacterial genome construction. microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing. microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing.""" ; sc:featureList edam:operation_0525, edam:operation_3185, edam:operation_3192, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "MicroPIPE" ; sc:url "https://github.com/BeatsonLab-MicrobialGenomics/micropipe" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080 ; sc:citation , , ; sc:description "Selects samples from abundance tables based on various selection schemes." ; sc:featureList edam:operation_3799 ; sc:name "micropita" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://huttenhower.sph.harvard.edu/micropita" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3697 ; sc:citation "pubmed:25819674" ; sc:description "Package designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances)." ; sc:featureList edam:operation_3221 ; sc:name "micropower" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/brendankelly/micropower" ; biotools:primaryContact "Frederic Bushman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "MicroRazerS is a tool optimized for mapping short RNAs onto a reference genome." ; sc:featureList edam:operation_3198 ; sc:name "MicroRazerS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/seqan/seqan/tree/master/apps/micro_razers" ; biotools:primaryContact "Anne-Katrin Emde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation ; sc:description "Different data resources for miRNAs and some functions for manipulating them." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "microRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/microRNA.html" ; biotools:primaryContact "\"James F. Reid\"" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "MicroRNA prediction model based only on plant small RNA sequencing data." ; sc:featureList edam:operation_0463 ; sc:name "microRPM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://microrpm.itps.ncku.edu.tw/" ; biotools:primaryContact "Na-Sheng Lin", "Wen-Chi Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC8544657", "pubmed:34698276" ; sc:description "A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3'UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome." ; sc:featureList edam:operation_0239, edam:operation_0335, edam:operation_0441, edam:operation_0463, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MicroSalmon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/AndreassenLab/MicroSalmon/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622 ; sc:citation , "pmcid:PMC5034416", "pubmed:27659774" ; sc:description "MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data and includes integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "MicroScope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://microscopebioinformatics.org/" ; biotools:primaryContact "Bohdan B. Khomtchouk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """Python-based bespoke microscopy for bio-medical science. Cockpit is a microscope graphical user interface. It is a flexible and easy to extend platform aimed at life scientists using bespoke microscopes. More detailed information is available:. Micron Advanced Imaging Consortium. Micron Advanced Imaging ConsortiumMicron Advanced Imaging ConsortiumMicron Advanced Imaging Consortium.""" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:license "GPL-3.0" ; sc:name "Microscope-Cockpit" ; sc:url "https://micronoxford.com/python-microscope-cockpit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Read Digital Micrograph files for electron microscopy" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "Read .dm3 and .dm4 image files" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43005-read-dm3-and-dm4-image-files" ; biotools:primaryContact "Fred Sigworth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_2885 ; sc:citation "pubmed:20809528" ; sc:description "Web-based application which predicts the impact of a SNP on putative microRNA targets." ; sc:featureList edam:operation_3202 ; sc:name "MicroSNiPer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://epicenter.ie-freiburg.mpg.de/services/microsniper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3300, edam:topic_3384 ; sc:citation ; sc:description "+microstate is a MATLAB toolbox for performing microstate analysis in sensor- or source-reconstructed EEG or MEG data. +microstate can be used for individual- or group-level analyses, and applied to both resting-state or task-evoked data. As well as microstate analysis, +microstate includes functions for calculating microstate statistics and microstate-segmented functional connectivity, visualisation, and simulation of data." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "microstate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/plus-microstate/toolbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation , "pubmed:35760231" ; sc:description "A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.)." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "MicroSugar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://suc.gene-db.com/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0637, edam:topic_3301 ; sc:citation "pubmed:25990029" ; sc:description "Uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes." ; sc:featureList edam:operation_3460 ; sc:name "Microtaxi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metagenomics.iiserb.ac.in/microtaxi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:25492647" ; sc:description "microTSS is a machine-learning algorithm that provides highly accurate, single-nucleotide resolution predictions for intergenic miRNA transcription start sites (TSSs). MicroTSS integrates high-resolution RNA-sequencing data with active transcription marks derived from chromatin immunoprecipitation and DNase-sequencing to enable the characterization of tissue-specific promoters" ; sc:featureList edam:operation_0226 ; sc:name "microTSS" ; sc:url "http://www.microrna.gr/microTSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC9041221", "pubmed:35495207" ; sc:description "A low-cost platform for indoor marine swarm robotics research." ; sc:featureList edam:operation_0310, edam:operation_2428, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "microUSV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CalvinGregory/microUSV/releases/tag/v1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Automatic segmentation and morphological analysis of microvessels in histological tumour sections" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "Microvessel Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/67937-microvessel-segmentation-analysis-in-immunohistochemistry-slices" ; biotools:primaryContact "Constantino Carlos Reyes-Aldasoro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3169 ; sc:citation "pubmed:20375099" ; sc:description "Combines positional information with information on motif occurrences to better predict binding sites of transcription factors (TFs)" ; sc:featureList edam:operation_0240 ; sc:name "MICSA" ; sc:softwareHelp , ; sc:url "http://bioinfo-out.curie.fr/projects/micsa/" ; biotools:primaryContact "Emmanuel Barillot", "Valentina Boeva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:description "MID (Micro-Inversion Detector) is a tool to detect microinversions (MIs) by mapping initially unmapped short reads back onto reference genome sequence (i.e. human genome assebly hg19)." ; sc:featureList edam:operation_2423, edam:operation_2429 ; sc:name "MID" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20150504" ; sc:url "http://cqb.pku.edu.cn/ZhuLab/MID/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3047, edam:topic_3292 ; sc:citation "pubmed:24254576" ; sc:description "Software designed to compute the theoretical isotopic distribution for molecules of known elemental composition. It computes for a molecule simultaneously two isotopic distributions: the coarse-grained isotopic distribution and the fine-grained isotopic distribution." ; sc:featureList edam:operation_2479 ; sc:name "MIDAs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html" ; biotools:primaryContact "Aleksey Ogurtsov", "Gelio Alves" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3174, edam:topic_3837, edam:topic_3958 ; sc:citation ; sc:description "Metagenomic Intra-species Diversity Analysis System." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIDAS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/czbiohub/MIDAS2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0625, edam:topic_2830, edam:topic_3299, edam:topic_3930 ; sc:citation , "pmcid:PMC8284797", "pubmed:34228721" ; sc:description "R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MiDAS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Genentech/MiDAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0625, edam:topic_2830, edam:topic_3930 ; sc:citation ; sc:description """Meaningful Immunogenetic Data at Scale. Human immunogenetic variation in the form of HLA and KIR types has been shown to be strongly associated with a multitude of immune-related phenotypes. We present MiDAS, an R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions. MiDAS closes the gap between inference of immunogenetic variation and its efficient utilization to make meaningful discoveries.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3557, edam:operation_3659 ; sc:license "MIT" ; sc:name "MiDASR" ; sc:softwareHelp ; sc:url "https://github.com/Genentech/MiDAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:15980553" ; sc:description "Data normalization and analysis tool for microarray data." ; sc:featureList edam:operation_0571, edam:operation_2495, edam:operation_2949, edam:operation_3445 ; sc:name "MIDAW" ; sc:url "http://midaw.cribi.unipd.it/dnachip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC6717393", "pubmed:31470809" ; sc:description "Identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns | Welcome to the minor intron database (MIDB)! | Minor introns, or U12-type introns, were initially identified based on their divergent terminal dinucleotide sequences (Jackson, 1991) | MIDB contains the most recent information on minor introns and the genes they are found in, also called MIGs (minor intron-containing genes) | Species: Mus musculus Homo sapiens All" ; sc:featureList edam:operation_0264, edam:operation_0446, edam:operation_3501 ; sc:name "MIDB" ; sc:url "https://midb.pnb.uconn.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3315, edam:topic_3382 ; sc:citation , "pmcid:PMC8553042", "pubmed:34662338" ; sc:description "Measures the concentration of specific infections (SIN) in a virus sample based on a TCID50 endpoint dilution assay." ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "midSIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://midsin.physics.ryerson.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0659 ; sc:citation , , "pmcid:PMC10320052", "pmcid:PMC4987907", "pubmed:27131362", "pubmed:37177999" ; sc:description "MicroRNA enrichment analysis and annotation." ; sc:featureList edam:operation_0361, edam:operation_3501 ; sc:name "miEAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccb-compute2.cs.uni-saarland.de/mieaa_tool/" ; biotools:primaryContact "Backes C" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128 ; sc:citation "pubmed:26568623" ; sc:description "Method aims to characterize the energetic patterns of proteins binding to their partners." ; sc:featureList edam:operation_2492 ; sc:name "MIEC-SVM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://wanglab.ucsd.edu/MIEC-SVM/" ; biotools:primaryContact "Wei Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:16000013" ; sc:description "Matlab toolbox that uses mutual information and related measures to infer and display secondary structures (including pseudoknots). Given a sequence alignment It computes and displays the mutual and sequence information of the alignment. MIfold also uses a dynamic programming algorithm to predict the secondary structure with maximal total mutual information." ; sc:featureList edam:operation_2441 ; sc:name "MIfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/mifold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0634, edam:topic_3170, edam:topic_3334 ; sc:citation , "pmcid:PMC4501052", "pubmed:26169944" ; sc:description "Analysis and visualization of miRNA sequencing data in neurological disorders." ; sc:featureList edam:operation_0564, edam:operation_3680 ; sc:name "miFRame" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccb-compute2.cs.uni-saarland.de/miframe/" ; biotools:primaryContact "Keller A" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:24529207" ; sc:description "Pattern discovery for microsatellite genome analysis. MiGA is a user friendly programme for the detection of all microsatellite loci in genomic data." ; sc:featureList edam:operation_2945 ; sc:name "MiGA" ; sc:operatingSystem "Mac" ; sc:softwareHelp , ; sc:url "http://mlkd.csd.auth.gr/bio/miga/" ; biotools:primaryContact "Ioannis Kavakiotis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0637, edam:topic_3301 ; sc:citation ; sc:description "Classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts." ; sc:featureList edam:operation_3192, edam:operation_3460 ; sc:license "Artistic-2.0" ; sc:name "MiGA" ; sc:softwareHelp , ; sc:url "http://microbial-genomes.org/" ; biotools:primaryContact "Luis M. Rodriguez-R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081, edam:topic_0082, edam:topic_3293 ; sc:citation "pubmed:16844980" ; sc:description "Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure meta-tools as a pipeline of individual tools and intermediate filters." ; sc:featureList edam:operation_0258, edam:operation_0346, edam:operation_0499, edam:operation_0550, edam:operation_2479 ; sc:name "MIGenAS Toolkit" ; sc:url "https://www.migenas.mpg.de/home/index.jsp" ; biotools:primaryContact "Hermann Lederer", "MIGenAS support", "Markus Rampp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:name "Phenotype name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3068 ; sc:citation ; sc:description "An Evidence-based Database of Genes and Phenotypes of Male Infertility." ; sc:featureList edam:operation_2421, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "MIgene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://midb.geneworks.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7904194", "pubmed:33571195" ; sc:description "MIGNON (Mechanistic InteGrative aNalysis Of rNa-seq data) is a versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways." ; sc:featureList edam:operation_0314, edam:operation_3227, edam:operation_3680 ; sc:license "MIT" ; sc:name "MIGNON" ; sc:url "https://github.com/babelomics/MIGNON" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:25016583" ; sc:description "Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version." ; sc:featureList edam:operation_2238 ; sc:name "Migraine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kimura.univ-montp2.fr/~rousset/Migraine.htm" ; biotools:primaryContact "François Rousset" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:description "Massive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis." ; sc:featureList edam:operation_0337, edam:operation_2436 ; sc:license "GPL-2.0" ; sc:name "MIGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MIGSA.html" ; biotools:primaryContact "Juan C. Rodriguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2640 ; sc:citation ; sc:description "Learn a large class of causal or non-causal graphical models from purely observational data, while including the effects of unobserved latent variables, commonly found in many datasets. Starting from a complete graph, the method iteratively removes dispensable edges, by uncovering significant information contributions from indirect paths, and assesses edge-specific confidences from randomization of available data." ; sc:featureList edam:operation_3439 ; sc:name "MIIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/miic/index.html" ; biotools:primaryContact "Nadir Sella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3305, edam:topic_3384, edam:topic_3421 ; sc:citation , "pmcid:PMC9365762", "pubmed:35948579" ; sc:description "Interactive exploration of a global clinical network from a large breast cancer cohort." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "MIIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://miic.curie.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC8291130", "pubmed:34295233" ; sc:description "MIIND is a simulator that allows the creation, simulation and analysis of large-scale neural networks. It does not model individual neurons, but models populations directly, similarly to a neural mass models, except that we use population density techniques." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIIND" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dekamps/miind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6105091", "pubmed:30052957" ; sc:description "A lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus." ; sc:featureList edam:operation_0264, edam:operation_2454, edam:operation_3680 ; sc:license "LGPL-3.0" ; sc:name "Mikado" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/lucventurini/mikado" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC7272249", "pubmed:32523402" ; sc:description "Integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding." ; sc:featureList edam:operation_0282, edam:operation_0362, edam:operation_0524, edam:operation_0525, edam:operation_3192 ; sc:name "Mikan_GB" ; sc:url "https://mikan.dna.affrc.go.jp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3053, edam:topic_3300, edam:topic_3335, edam:topic_3577 ; sc:citation , "pmcid:PMC8626632", "pubmed:34900127" ; sc:description "A manually curated and comprehensive knowledge base for myocardial infarction." ; sc:featureList edam:operation_3454, edam:operation_3501, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:name "MIKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sysbio.org.cn/mikb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3395 ; sc:citation , "pmcid:PMC7053140", "pubmed:32122302" ; sc:description """Visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. Millefy is a tool for visualizing read coverage of single-cell RNA sequensing (scRNA-seq) datasets in genomic contexts. By dynamically and automatically reorder single cells based on 'locus-specific' pseudotime, Millefy highlights cell-to-cell heterogeneity in read covreage of scRNA-seq data.""" ; sc:featureList edam:operation_0337, edam:operation_3198, edam:operation_3891 ; sc:name "Millefy" ; sc:url "https://github.com/yuifu/millefy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3298, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC10579705", "pubmed:37530223" ; sc:description "Multi-omics database to accelerate the research of functional genomics and molecular breeding of millets." ; sc:featureList edam:operation_0308, edam:operation_2436, edam:operation_3096, edam:operation_3431, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "Milletdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://milletdb.novogene.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_2815 ; sc:citation "pubmed:23424114" ; sc:description "Method that outperforms a leading recent method, centipede, marginally in human but dramatically in yeast (average auROC across 20 TFs increases from 74% to 94%). The sofware is based on logistic regression and thus benefits from supervision, but we show that partially and completely unsupervised variants perform nearly as well." ; sc:featureList edam:operation_3659 ; sc:name "MILLIPEDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.duke.edu/~amink/software/millipede/" ; biotools:primaryContact "Alexander J. Hartemink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3934 ; sc:citation ; sc:description """Differential abundance testing on single-cell data using k-NN graphs. Milo is a method for differential abundance analysis on KNN graph from single-cell datasets. For more details, read our preprint.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "Milo" ; sc:url "https://github.com/MarioniLab/miloR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """Mixed Logistic Regression in Genome-Wide Association Studies. milorGWAS: MIxed LOgistic Regression in GWAS. This package is for Genome Wide Association Studies using a logistic mixed model, using fast approximate methods as described in (Milet and Perdry, 2020). One of these methods extends the GMMAT method by Chen et al. (Chen et al., 2016). A similar method was described in (Zhou et al., 2020).""" ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3799 ; sc:name "milorGWAS" ; sc:url "https://github.com/genostats/milorGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:22017798" ; sc:description "Calculates a measure of sequence specificity called Motif Independent Metric." ; sc:featureList edam:operation_2404 ; sc:name "MIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcb.dfci.harvard.edu/~gcyuan/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:description "Easily visualize and inspect microarrays for spatial artifacts." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mimager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mimager.html" ; biotools:primaryContact "Aaron Wolen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:36106996" ; sc:description "The Multi-Omic Integration by Machine Learning (MIMaL) method can be found as scripts and a web page." ; sc:featureList edam:operation_2428, edam:operation_2454, edam:operation_3799, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIMaL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mimal.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_2533 ; sc:citation "pubmed:27402903" ; sc:description "Quantitative effects of each mutation at each position in the RNA can be recovered with statistical certainty using this herein developed user-friendly, cross-platform software." ; sc:featureList edam:operation_2439 ; sc:name "MIMEAnTo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/maureensmith/MIMEAnTo" ; biotools:primaryContact "Maureen Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC10576642", "pubmed:37840574" ; sc:description """Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces. A new version of ShinyProxy is available Switch to new version!.""" ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "MiMed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mimed.micloud.kr:3838/app/mimed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0821, edam:topic_3172, edam:topic_3697 ; sc:citation , "pubmed:36215042" ; sc:description "The Microbial Metabolites Database (MiMeDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human microbiome. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain and link metabolite data, microbe data, host data, health and bioactivity data, and exposure data. Many data fields in the database are hyperlinked to other databases (FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank). The Microbial Metabolites Database supports extensive text, sequence, spectral, chemical structure and relational query searches." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:name "MiMeDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mimedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3474, edam:topic_3697, edam:topic_3941 ; sc:citation ; sc:description """Exploring Microbiome-Metabolome Relationships using Neural Networks. MiMeNet predicts the metabolomic profile from microbiome data and learns undelrying relationships between the two. MiMeNet uses microbial features to predict metabolite output features. To do so, neural network hyper-parameters are first tuned. Then models are evaluated in a cross-validated fashion resulting in Spearman correlation coefficients (SCC) for each metabolite representing how well they could be predicted.""" ; sc:featureList edam:operation_3435, edam:operation_3766, edam:operation_3929 ; sc:license "MIT" ; sc:name "MiMeNet" ; sc:url "https://github.com/YDaiLab/MiMeNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0196, edam:topic_0623, edam:topic_3174, edam:topic_3301 ; sc:citation , "pmcid:PMC8313253", "pubmed:34081399" ; sc:description "Minimal Microbial Consortia creation tool is a bioinformatic approach for generation of synthetic communities from metagenomes" ; sc:featureList edam:operation_3200, edam:operation_3731, edam:operation_3918 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "MiMiC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ClavelLab/MiMiC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3384, edam:topic_3398, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC7286793", "pubmed:32012003" ; sc:description """MimickNet, Mimicking Clinical Image Post- Processing Under Black-Box Constraints. The above is a cineloop of cardiac data with conventional delay-and-sum beamforming and ReFoCUS beamforming. We apply clinical-grade post-processing, MimickNet post-processing, and show the unscaled difference between the two.""" ; sc:featureList edam:operation_3359, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "MimickNet" ; sc:url "https://github.com/ouwen/MimickNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2815, edam:topic_3332 ; sc:citation , "pubmed:36811959" ; sc:description "An Efficient Toolkit for MiMiC-Based QM/MM Simulations. MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection" ; sc:featureList edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MiMiCPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/MiMiC-projects/mimicpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3305, edam:topic_3337, edam:topic_3407 ; sc:citation , "pmcid:PMC9344846", "pubmed:35695757" ; sc:description "R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR Metabolomics data." ; sc:featureList edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MiMIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DanieleBizzarri/MiMIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:34882225" ; sc:description "Accelerating bioactive peptide discovery via mutual information-based meta-learning." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MIMML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TearsWaiting/MIMML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "MIMO addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information." ; sc:featureList edam:operation_0224 ; sc:name "MIMO" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.picb.ac.cn/ClinicalGenomicNTW/MIMO.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0108, edam:topic_0607, edam:topic_2269, edam:topic_3063 ; sc:citation , , "pubmed:36073449", "pubmed:36084537" ; sc:description "Medical informatics and digital health multilingual ontology (MIMO): A tool to improve international collaborations which is hosted by HeTOP (Health Terminology/Ontology Portal)" ; sc:featureList edam:operation_0361, edam:operation_0558, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MIMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.hetop.eu/hetop/rep/en/EFMIMIMO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_3512, edam:topic_3557 ; sc:citation "pubmed:22053087" ; sc:description "A mimotope database. The MimoDB database also provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly." ; sc:featureList edam:operation_0339, edam:operation_0360, edam:operation_2421, edam:operation_3646 ; sc:name "MimoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://immunet.cn/mimodb/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation , "pmcid:PMC3862207", "pubmed:23887981" ; sc:description "Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "Artistic-2.0" ; sc:name "MIMOSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MIMOSA.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3697 ; sc:citation , "pubmed:34999748" ; sc:description "MIMOSA2 is a tool for metabolic model-based evaluation of paired microbiome and metabolomics datasets. MIMOSA2 1) constructs community metabolic models, 2) assesses whether metabolite measurements are consistent with estimated community metabolic potential, and 3) identifies specific taxa and reactions that can explain metabolite variation." ; sc:featureList edam:operation_3625, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MIMOSA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://elbo-spice.cs.tau.ac.il/shiny/MIMOSA2shiny/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3360 ; sc:citation ; sc:description """A deep multiple instance learning framework improves microsatellite instability detection from tumor next-generation sequencing. A deep, multiple instance learning based classifier for identifying Microsatellite Instability in Next-Generation Sequencing Results.""" ; sc:featureList edam:operation_3227, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "MiMSI" ; sc:url "https://github.com/mskcc/mimsi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:17545201" ; sc:description "MinActionPath calculates the most-probable trajectory between two known structural states of a protein." ; sc:featureList edam:operation_0249, edam:operation_0250, edam:operation_0477, edam:operation_2574 ; sc:name "MinActionPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lorentz.immstr.pasteur.fr/joel/index.php" ; biotools:primaryContact "Marc Delarue Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:22096233" ; sc:description "A database of metal ions in DNA and RNA. Complies info on innersphere, outsphere, and larger coordination environment of >70,000 metal ions of 36 elements fround in >2000 structures of nucleic acids." ; sc:featureList edam:operation_0279, edam:operation_0475, edam:operation_2481, edam:operation_2518, edam:operation_2950 ; sc:name "MINAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.minas.uzh.ch/" ; biotools:primaryContact "Joachim Schnabl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_3174 ; sc:description "MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes." ; sc:featureList edam:operation_0237 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "minced" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ctSkennerton/minced" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3442 ; sc:encodingFormat edam:format_3547 ; sc:name "MRI image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3444 ; sc:citation ; sc:description "An open source brain morphometry platform for analyzing human brain image data." ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Mindboggle" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mindboggle.info/" ; biotools:primaryContact "Arno Klein" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:name "Nucleic acid sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168 ; sc:citation , "pmcid:PMC4832496", "pubmed:27079510" ; sc:description "Next-generation variant caller specifically designed for InDel marker discovery. By taking in raw sequence reads and assembling them into contigs de novo, identifies InDel polymorphisms using a sliding window alignment from assembled contigs, rendering a unique advantage when a reference genome is unavailable." ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3227 ; sc:name "mInDel" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "https://github.com/lyd0527/mInDel" ; biotools:primaryContact "Dr. Yuanda Lv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3315, edam:topic_3360, edam:topic_3373, edam:topic_3577 ; sc:citation , "pubmed:34170297" ; sc:description "MinDrug is a method for predicting anti-cancer drug response by finding an optimal subset of drugs that have the most similarity with other drugs. This method predicts IC50 for a new cell-line." ; sc:featureList edam:operation_3659, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MinDrug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yassaee/MinDrug" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_2182 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "MindTheGap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://gatb.inria.fr/software/mind-the-gap/" ; biotools:primaryContact "Claire Lemaitre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_2259 ; sc:citation "pubmed:21938624" ; sc:description "A new information theoretic method to identify multivariate statistical dependencies between a transcription factor and one or more of its targets, conditional on the presence (or absence) of a candidate modulator gene." ; sc:featureList edam:operation_0440 ; sc:name "MINDY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/MINDY2?" ; biotools:primaryContact "Andrea Califano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3292, edam:topic_3407, edam:topic_3473 ; sc:citation , "pmcid:PMC9237697", "pubmed:35595247" ; sc:description "Enhanced biochemical coverage for peak identification in untargeted metabolomics." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://minedatabase.ci.northwestern.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Script" ; sc:applicationSubCategory edam:topic_3292, edam:topic_3332, edam:topic_3370 ; sc:citation , "pubmed:30950277" ; sc:description """mineXpert is a graphical user interface software piece that allows the user to: - load mass spectrometry data files [ (x,y) text files or mzML standard format ] - visualize the TIC chromatogram and the intensity=(mz, dt) colormap in case of ion mobility mass spectrometry - integrate the mass data in many different ways and display them, effectively permitting the exploration of the mass data in their full depth - many other features""" ; sc:featureList edam:operation_3203, edam:operation_3632, edam:operation_3694 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mineXpert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://msxpertsuite.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "The goal of this tool is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph." ; sc:featureList edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "MineICA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MineICA.html" ; biotools:primaryContact "Anne Biton" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3166 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , , "pmcid:PMC5104320", "pubmed:27832067", "pubmed:28431175" ; sc:description """A pathway analysis tool. MinePath identifies of differentially expressed functional paths or sub-paths within a gene regulatory network (GRN) using gene expression data analysis. The analysis takes advantage of interactions among genes (e.g. activation/expression, inhibition) as nodes of a graph network, which are derived from expression data.""" ; sc:featureList edam:operation_2495, edam:operation_2497, edam:operation_3083, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:name "MinePath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.minepath.org/" ; biotools:primaryContact "Lefteris Koumakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2814 ; sc:citation , "pubmed:37562062" ; sc:description "AlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MineProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://mineprot-demo.bmeonline.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0160, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:15573397", "pubmed:15980467" ; sc:description "Tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family)." ; sc:featureList edam:operation_0292, edam:operation_0448, edam:operation_0492, edam:operation_0499 ; sc:name "MINER" ; sc:url "http://coit-apple01.uncc.edu/MINER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "This package implements various algorithms for inferring mutual information networks from data." ; sc:featureList edam:operation_3439 ; sc:name "minet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/minet.html" ; biotools:primaryContact "Patrick E. Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC5408810", "pubmed:28035024" ; sc:description "Tools to analyze & visualize Illumina Infinium methylation arrays." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "Artistic-2.0" ; sc:name "minfi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/minfi.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3384, edam:topic_3474, edam:topic_3954 ; sc:citation , "pubmed:33755565" ; sc:description "Mini-COVIDNet is a efficient lightweight deep neural network for ultrasound-based point-of-care detection of COVID-19." ; sc:featureList edam:operation_3927 ; sc:name "Mini-COVIDNet" ; sc:url "https://github.com/navchetan-awasthi/Mini-COVIDNet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36307979" ; sc:description "We developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type-specific networks in plants. 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Brown" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_3976 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_3976 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC6966772", "pubmed:31984131" ; sc:description "A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs." ; sc:featureList edam:operation_3183, edam:operation_3230 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "minipolish" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v0.1.0", "v0.1.1", "v0.1.2", "v0.1.3" ; sc:url "https://github.com/rrwick/Minipolish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:description "Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. 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The web interface allows the users to search, visualize and download interactions data" ; sc:featureList edam:operation_2422, edam:operation_2497, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "MINT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Dept. of Molecular Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome" ; sc:url "https://mint.bio.uniroma2.it/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC8483015", "pubmed:34692239" ; sc:description "A metagenomic INserT integrated assembly and annotation tool." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MINTIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bios4Biol/MINTIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3325, edam:topic_3512 ; sc:citation , "pmcid:PMC8532352", "pubmed:34686194" ; sc:description "MINTIE is a tool for identifying novel, rare cryptic variants in cancer RNA-seq data. Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease. 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MINTyper is a tools designed to quickly a distance matrix from a set of input sequencing reads. It can take both short read from Illumina's sequencing platforms and long reads from Oxford Nanopore's platform.""" ; sc:featureList edam:operation_0310, edam:operation_0484, edam:operation_3185, edam:operation_3192, edam:operation_3933 ; sc:name "MINTyper" ; sc:url "https://cge.cbs.dtu.dk/services/MINTyper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC9272810", "pubmed:35642895" ; sc:description "MicroRNA target analysis system for Immuno-Oncology." ; sc:featureList edam:operation_0252, edam:operation_0463, edam:operation_3659, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mio.icbi.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_0769, edam:topic_3063, edam:topic_3308 ; sc:citation , "pmcid:PMC6902525", "pubmed:31823712" ; sc:description """Vertical and horizontal integration of multi-omics data with miodin. R software package for integration of multi-omics data""" ; sc:featureList edam:operation_2238, edam:operation_2495, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "miodin" ; sc:url "https://gitlab.com/algoromics/miodin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2259, edam:topic_3172, edam:topic_3292, edam:topic_3345, edam:topic_3361 ; sc:citation ; sc:description "The MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Biology Laboratory, Greece, appropriately filtered GOLM database peak information and Human Metabolome database information." ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_3215 ; sc:name "MESBL GC-MS metabolite peak database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://miolite2.iceht.forth.gr" ; biotools:primaryContact "Maria Klapa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3308 ; sc:description "MIOM (Mixed Integer Optimization for Metabolism) is a python library for creating and solving complex optimization problems using genome-scale metabolic networks, in just a few lines. 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Using it’s standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders." ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:name "MIPAV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mipav.cit.nih.gov/" ; biotools:primaryContact "Bugs", "Developers", "Ideas for features" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation "pubmed:24867941" ; sc:description "Fast, simple way to generate designs for MIP (Molecular Inversion Probes) assays targeting hundreds or thousands of genomic loci in parallel." ; sc:featureList edam:operation_2430 ; sc:name "MIPgen" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://shendurelab.github.io/MIPGEN/" ; biotools:primaryContact "Evan Boyle", "Jay Shendure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0166, edam:topic_0623, edam:topic_3510 ; sc:citation "pubmed:22080560" ; sc:description "A database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. 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MicroRNAs (miRNAs) have been found in many organisms and play essential roles in gene expression regulation of many critical cellular processes, including human cancers.""" ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_3792 ; sc:name "miR-TV" ; sc:url "http://mirtv.ibms.sinica.edu.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2259 ; sc:citation "pubmed:22784580" ; sc:description "For gene pattern discovery by enrichment analysis of their microRNA regulators is a web-accessible program, which is used to mine potential patterns for one single gene, multiple genes, and KEGG pathway genes based on miRNA set enrichment analysis of the miRNAs regulating given genes." ; sc:featureList edam:operation_2436 ; sc:name "miR2Gene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cuilab.cn/mir2gene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0204, edam:topic_0659 ; sc:citation "pubmed:25762653" ; sc:description "Web based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO (Functional analysis of genetic and somatic mutations in microRNAs) and miRpair2GO (Comparative functional analysis for microRNA pairs)." ; sc:featureList edam:operation_2495 ; sc:name "miR2GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.uthsc.edu/miR2GO/home.php" ; biotools:primaryContact "Yan Cui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:31070735" ; sc:description "Identification of Condition-Specific Targets of MicroRNA in Time-series Transcript Data using Gaussian Process Model and Spherical Vector Clustering." ; sc:featureList edam:operation_0463, edam:operation_3501, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mirTime" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mirTime/mirtime" ; biotools:primaryContact "Sun Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640 ; sc:citation "pubmed:25505085" ; sc:description "Software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches." ; sc:featureList edam:operation_2495 ; sc:name "miR_Path" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://comp-sysbio.org/miR_Path/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170 ; sc:citation "pubmed:15140833" ; sc:description "MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler" ; sc:featureList edam:operation_0310, edam:operation_0495, edam:operation_3198, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "MIRA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/p/mira-assembler/wiki/Home/" ; biotools:primaryContact "Bastien Chevreux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:26542525" ; sc:description "New tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations." ; sc:featureList edam:operation_2423 ; sc:name "miRA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mhuttner/miRA" ; biotools:primaryContact "Michael Huttner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_2229, edam:topic_3173, edam:topic_3940 ; sc:citation , "pmcid:PMC9517733", "pubmed:36068320" ; sc:description "Multimodal models for Integrated Regulatory Analysis, or MIRA, is a python package for analyzing the dynamic processes of gene regulation using single-cell multiomics datasets." ; sc:featureList edam:operation_0314, edam:operation_2939, edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "MIRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cistrome/MIRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6997536", "pubmed:32047509" ; sc:description """Improving Bioinformatics Prediction of microRNA Targets by Ranks Aggregation. A simple and efficient miRNA target prediction tool.""" ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3436, edam:operation_3792 ; sc:name "miRabel" ; sc:url "http://bioinfo.univ-rouen.fr/mirabel/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:21208986" ; sc:description "A Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. It can currently check pathways models written either in CSML or SBML." ; sc:featureList edam:operation_3799 ; sc:name "MIRACH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mirach/" ; biotools:primaryContact "Masao Nagasaki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3518 ; sc:citation "pubmed:25161257" ; sc:description "Web-application for handling reverse phase protein array chips." ; sc:featureList edam:operation_2495 ; sc:name "MIRACLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nanocan.github.io/MIRACLE/" ; biotools:primaryContact "Markus List" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:34020537" ; sc:description "miRACLe is an individual-specific approach to improve microRNA-target prediction based on a random contact model. The strength of miRNA-mRNA interactions (MMIs) in a biological system depends on both the sequence characteristics and expression patterns of RNAs." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2436, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "miRACLe" ; sc:url "https://github.com/PANWANG2014/miRACLe" ; biotools:primaryContact "Jie He", "Ke Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0204, edam:topic_0659, edam:topic_3518 ; sc:citation "pubmed:21596785" ; sc:description "Tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3566 ; sc:name "mirAct" ; sc:url "http://sysbio.ustc.edu.cn/software/mirAct" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3316, edam:topic_3810 ; sc:citation , "pmcid:PMC10470110", "pubmed:37662837" ; sc:description """Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction. miraculix is a C/CUDA library for mathematical operations on compressed genotype data. It provides highly efficient routines that can be used in statistical analyses of genomic information, e.g. genome-wide association studies, genomic breeding value estimation and population summary statistics. As such, it offers interfaces to allow integration into existing C utilities as well as interoperability with higher-level programming languages such as R, Julia or Fortran.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "miraculix" ; sc:url "https://github.com/alexfreudenberg/miraculix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_2640, edam:topic_3168, edam:topic_3360 ; sc:citation , "pmcid:PMC10340358", "pubmed:37444566" ; sc:description "An adaptable pipeline for next-generation sequencing analysis, reporting, and visualization for clinical decision making." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3233 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MIRACUM-Pipe" ; sc:url "https://github.com/AG-Boerries/MIRACUM-Pipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC8987502", "pubmed:35401578" ; sc:description "A Knowledgebase of RAG Regulators." ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_3192, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "miRAGDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://52.4.112.252/shiny/miragdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204 ; sc:citation , "pmcid:PMC3257129", "pubmed:22272132" ; sc:description "The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile." ; sc:featureList edam:operation_1781 ; sc:license "GPL-3.0" ; sc:name "MiRaGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MiRaGE.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_3293, edam:topic_3407, edam:topic_3943 ; sc:citation ; sc:description """A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model. Mirage is ancestral genome estimation software with high accuracy based on a phylogenetic mixture model and a RER model.""" ; sc:featureList edam:operation_0540, edam:operation_0553, edam:operation_3233, edam:operation_3478, edam:operation_3745 ; sc:name "Mirage-evol" ; sc:url "https://github.com/fukunagatsu/Mirage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170, edam:topic_3474 ; sc:citation "pubmed:19433510" ; sc:description "Web-server for identifying and analyzing miRNA in NGS sequencing experiments." ; sc:featureList edam:operation_0338, edam:operation_0463, edam:operation_0496, edam:operation_3792 ; sc:name "MiRanalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_0659 ; sc:citation , "pubmed:34297061" ; sc:description "miRAnno-network-based functional microRNA annotation." ; sc:featureList edam:operation_0463, edam:operation_3501, edam:operation_3792, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "miRAnno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ophid.utoronto.ca/miRAnno/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0102, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:21037258" ; sc:description "Repository for all microRNA sequences and annotation. It has mapped reads from short RNA deep-sequencing experiments to microRNAs and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression." ; sc:featureList edam:operation_0463, edam:operation_2429, edam:operation_3198, edam:operation_3695 ; sc:name "miRBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mirbase.org/" ; biotools:primaryContact "Sam Griffiths-Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3518 ; sc:description "A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "miRBaseConverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRBaseConverter.html" ; biotools:primaryContact "Taosheng Xu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3474, edam:topic_3534, edam:topic_3794 ; sc:citation , "pmcid:PMC9777820", "pubmed:36553590" ; sc:description "A Deep Learning Method for miRNA Binding Classification." ; sc:featureList edam:operation_0278, edam:operation_0463, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "miRBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ml-bioinfo-ceitec.github.io/miRBind/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3518, edam:topic_3794 ; sc:citation , "pmcid:PMC8509996", "pubmed:34637468" ; sc:description "Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_3792, edam:operation_3799, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "miRbiom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://scbb.ihbt.res.in/miRbiom-webserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Predicts mature miRNAs and their precursors from an sRNA dataset and a genome." ; sc:featureList edam:operation_0463 ; sc:name "MiRCat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://srna-workbench.cmp.uea.ac.uk" ; biotools:primaryContact "Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3168, edam:topic_3500 ; sc:citation ; sc:description "Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Part of the UEA small RNA Workbench." ; sc:featureList edam:operation_0463 ; sc:name "miRCat2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://srna-workbench.cmp.uea.ac.uk/mircat-2/" ; biotools:primaryContact "S. Moxon", "V. Moulton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0602, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC4788200", "pubmed:26967326" ; sc:description "Analyse miRNA-mRNA Interactions. Examples across Five Digestive Cancers." ; sc:featureList edam:operation_2478, edam:operation_2497 ; sc:name "MiRComb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mircomb.sourceforge.net/" ; biotools:primaryContact "Juanjo Lozano", "Maria Vila Casadesús" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3033 ; sc:name "Processed microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3518, edam:topic_3519, edam:topic_3572 ; sc:citation , "pmcid:PMC4802579", "pubmed:27000067" ; sc:description "Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves." ; sc:featureList edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "miRcomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRcomp.html" ; biotools:primaryContact "Matthew N. McCall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3519 ; sc:citation ; sc:description "Interactive assessment of qPCR-based microRNA quantification and quality control algorithms. Read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves." ; sc:featureList edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "miRcomp-Shiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.10.0" ; sc:url "https://laurenkemperman.shinyapps.io/mircomp/" ; biotools:primaryContact "Matthew N. McCall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:27428722" ; sc:description "Innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs." ; sc:featureList edam:operation_2495 ; sc:name "MirCompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://160.80.35.140/MirCompare/" ; biotools:primaryContact "Antonella Minutolo", "Stefano Pirro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:21558324" ; sc:description "Web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. It combines sequence information with gene expression data analysis to create a disease specific, genome wide regulatory network. Only supports human and mouse." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2495, edam:operation_3439, edam:operation_3463 ; sc:name "mirConnX" ; sc:url "http://www.benoslab.pitt.edu/mirconnx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:33382660" ; sc:description """Identifying Cooperating miRNAs via Kernel Based Interaction Tests. Although miRNAs can cause widespread changes in expression programs, single miRNAs typically induce mild repression on their targets. Cooperativity among miRNAs is reported as one strategy to overcome this constraint. Expanding the catalog of synergistic miRNAs is critical for understanding gene regulation and for developing miRNA-based therapeutics. In this study, we develop miRCoop to identify synergistic miRNA pairs that have weak or no repression on the target mRNA individually, but when act together induce strong repression. miRCoop uses kernel-based statistical interaction tests, together with miRNA and mRNA target information. We apply our approach to patient data of two different cancer types. In kidney cancer, we identify 66 putative triplets""" ; sc:featureList edam:operation_0463 ; sc:name "miRCoop" ; sc:url "https://github.com/guldenolgun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8140596", "pubmed:34055490" ; sc:description "miRcorrNet is a machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking. This tool allows you to make an integrated mRNA - miRNA profiles analysis. Via using this document you can easily execute the steps and you can obtain the results. Using this document you can easily repeat the experiments. miRcorrNet uses 2 different data sheets with same control-case column. It means you should have same samples in one column which should be both in mRNA and miRNA data sheet. In this study we used KNIME analytics platform. Therefore, the data is stored in \".table\" extension files." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_3792 ; sc:license "MIT" ; sc:name "miRcorrNet" ; sc:url "https://github.com/malikyousef/miRcorrNet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33381847" ; sc:description """A tool for quality control, filter and curation of microRNAs of animals and plants. MirCure: A tool for quality control, filter, and curation of microRNAs of animals and plants. Given a list of miRNA candidates, MirCure evaluates a number of miRNA-specific features based on gene expression, biogenesis, and conservation data, and generates a score that can be used to discard poorly supported miRNA annotations. MirCure can also curate and adjust the annotation of the 5p and 3p arms based on user-provided small RNA-seq data. We evaluated MirCure on a set of manually curated animal and plant microRNAs and demonstrated great accuracy. Moreover, we show that MirCure can be used to revisit previous bona fide miRNAs annotations to improve microRNA databases.""" ; sc:featureList edam:operation_0463, edam:operation_2428, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "MirCure" ; sc:url "https://github.com/ConesaLab/MirCure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3168 ; sc:citation "pubmed:18392026" ; sc:description "Discovering known and novel miRNAs from deep sequencing data." ; sc:featureList edam:operation_0463 ; sc:name "MiRDeep" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.mdc-berlin.de/8551903/en/" ; biotools:primaryContact "Nikolaus Rajewsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3794 ; sc:author "Marc Friedländer", "Sebastian Mackowiak" ; sc:description "miRDeep2 discovers active known or novel miRNAs from deep sequencing data." ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRDeep2" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:url "https://github.com/rajewsky-lab/mirdeep2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3500, edam:topic_3511 ; sc:citation , "pmcid:PMC4176371", "pubmed:25053842" ; sc:description "High stringency miRNA predictor identifies several novel animal miRNAs." ; sc:featureList edam:operation_0463 ; sc:name "miRdentify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncrnalab.dk/#mirdentify/mirdentify.php" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3170 ; sc:citation , "pmcid:PMC9825511", "pubmed:36453996" ; sc:description "Tissue context annotation and novel microRNA curation." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2421, edam:operation_3436, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "mirDIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "5.2" ; sc:url "https://ophid.utoronto.ca/mirDIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:33979731" ; sc:description "MirDNN is a novel deep learning method specifically designed for pre-miRNA prediction in genome-wide data. The model is a convolutional deep residual neural network that can automatically learn suitable features from the raw data, without manual feature engineering. This model is capable of successfully learn the intrinsic structural characteristics of precursors of miRNAs, as well as their context in a sequence. The proposal has been tested with several genomes of animals and plants and compared with state-of-the-art algorithms." ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3927 ; sc:license "MIT" ; sc:name "mirDNN" ; sc:url "http://sinc.unl.edu.ar/web-demo/mirdnn/" ; biotools:primaryContact "G. Stegmayer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0654, edam:topic_0659, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34875006" ; sc:description "A full end-to-end deep model based on Transformers for prediction of pre-miRNAs." ; sc:featureList edam:operation_0278, edam:operation_0463, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRe2e" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sinc.unl.edu.ar/web-demo/miRe2e/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0219, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description """A manually curated database of validated and putative editing events in microRNAs. MiREDiBase (miRNA Editing Database) is a catalog of validated and putative miRNA editing sites (Adenosine-to-Inosine and Cytosine-to-Uracil) and an online resource for functional prediction of miRNA editing.""" ; sc:featureList edam:operation_0463, edam:operation_3096, edam:operation_3792 ; sc:license "MIT" ; sc:name "MiREDiBase" ; sc:url "https://ncrnaome.osumc.edu/miredibase" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659 ; sc:description "This tool correlates the logarithm of expression fold changes of a set of genes with the motif content of the regulatory sequences of these genes. In particular, it correlates the genome wide mRNA log fold changes in experiments involving the knockout/knockdown/overexpression of one or more miRNAs with the motif content of the 3'UTRs. The model is based on linear regression, and is intended for genome-wide studies." ; sc:featureList edam:operation_0314 ; sc:name "miReduce" ; sc:operatingSystem "Linux" ; sc:url "https://www.mdc-berlin.de/10615841/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/mireduce" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_0659, edam:topic_3063, edam:topic_3518 ; sc:citation , "pmcid:PMC8696973", "pubmed:34988440" ; sc:description "R package and web application for miRNA text mining." ; sc:featureList edam:operation_0306, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRetrieve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://miretrieve.shinyapps.io/miRetrieve/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3519 ; sc:citation , "pubmed:34052284" ; sc:description "miREV is an online database and tool to uncover potential reference RNAs and biomarkers in small-RNA sequencing data sets from Extracellular Vesicles enriched samples. miREV was developed as an easy to use online tool with a graphical user interface. Main goal is to uncover potential reference RNAs from EV studies in relation to different experimental conditions. Because suitable reference RNAs, for instance to validate findings from NGS experiments or to perform meaningful expression analyses by RT-qPCR, can vary from study to study because the RNA fingerprint strongly depends on the kind of experimental methods used. miREV also serves as a database. Interested parties can download the raw read counts and the associated metadata for further analyzes." ; sc:featureList edam:operation_2428 ; sc:name "miREV" ; sc:url "https://www.physio.wzw.tum.de/mirev/" ; biotools:primaryContact "Alex Hildebrandt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3295, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc:description "MIREyA (MIRnas functioning through Enhancer Activation) is a computational approach to detect miRNA-directed gene activation. It is a pipeline for detection of miRNAs and their gene targets up-regulated through triggering their enhancer in the provided expression" ; sc:featureList edam:operation_0440, edam:operation_0463, edam:operation_3792 ; sc:name "MIREyA" ; sc:url "https://github.com/veania/MIREyA" ; biotools:primaryContact , "Yulia A. Medvedeva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3300 ; sc:citation ; sc:description """An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops. Defence Institute of Physiology and Allied Science. miRNA and Transcription Factors (TFs) are fundamental transcriptional and post-transcriptional regulators of the gene expression respectively, controlling important biological processes.""" ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_2437, edam:operation_3792 ; sc:name "miRFFLDB" ; sc:url "http://www.mirffldb.in" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2330 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2330 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "MIRfix automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. 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It was optimized on plant miRNAs." ; sc:featureList edam:operation_0438 ; sc:name "MiRfold" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://wwwabi.snv.jussieu.fr/research/publi/small_ncRNA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3168, edam:topic_3360 ; sc:citation , "pmcid:PMC8616193", "pubmed:34830818" ; sc:description "Galaxy-Based Framework for Interactive Analysis of microRNA and isomiR Sequencing Data." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "miRGalaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Glogobyte/miRGalaxy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """A comprehensive microRNA and tRF sequencing analysis pipeline. An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. Enables building small-RNA libraries for the organism of choice to use in the miRge pipeline.""" ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_3792 ; sc:license "MIT" ; sc:name "miRge3" ; sc:url "https://anaconda.org/bioconda/mirge3" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1869 ; sc:name "Organism identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:name "Sequence accession (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1097 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence accession (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:encodingFormat edam:format_2331 ; sc:name "RNA secondary structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2305, edam:format_3003 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_2330 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_2815, edam:topic_3299, edam:topic_3500 ; sc:author , "Kevin J. Peterson" ; sc:citation , , , "pmcid:PMC4743252", "pmcid:PMC6943042", "pmcid:PMC8728216", "pubmed:26473382", "pubmed:31598695", "pubmed:34850127" ; sc:description "MirGeneDB is a miRBase-derived database for microRNA genes that have been manually validated and annotated. Currently, microRNA genes are available for 75 metazoan species and can be browsed, blasted and downloaded." ; sc:featureList edam:operation_0224, edam:operation_0564, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "MirGeneDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Oslo" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://mirgenedb.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3474, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6992741", "pubmed:32001758" ; sc:description """integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator. microRNA-target binding site prediction tool.""" ; sc:featureList edam:operation_0463, edam:operation_2575, edam:operation_3792 ; sc:name "miRgo" ; sc:url "http://predictor.nchu.edu.tw/miRgo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC8046230", "pubmed:33852600" ; sc:description "miRGTF-net is a tool for construction of miRNA-gene-TF regulatory networks using both database-level and transcriptomics/miRNomics data. miRGTF-net uses graphml format to export networks and their weakly/strongly connected components." ; sc:featureList edam:operation_0314, edam:operation_0372, edam:operation_0463, edam:operation_3792, edam:operation_3799 ; sc:license "MIT" ; sc:name "miRGTF-net" ; sc:url "https://github.com/s-a-nersisyan/miRGTF-net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Retrieve the list of all available MIRIAM datatypes; retrieve information about a given datatype; resolve a given MIRIAM URN." ; sc:featureList edam:operation_2422 ; sc:name "MIRIAM Resources" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/miriam/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:35084791" ; sc:description "A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images." ; sc:featureList edam:operation_0314, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIRIAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Coffey-Lab/MIRIAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3071 ; sc:citation ; sc:description "Web Services which provide generation and resolving facilities for MIRIAM Annotations." ; sc:featureList edam:operation_2422 ; sc:name "MIRIAM WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/miriam/main/mdb?section=ws_help" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0659 ; sc:citation "pubmed:24794934" ; sc:description "Online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). It integrates microRNA regulations and PPIs with microRNA/mRNA expression data to identify the perturbed microRNA regulatory modules and reveals their functional roles in specific biological conditions." ; sc:featureList edam:operation_2497 ; sc:name "Mirin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://mirin.ym.edu.tw/tool.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Prediction of biological processes indirectly targeted by human microRNAs. miRinGO: Prediction of GO terms indirectly targeted by human microRNAs. This R Shiny application can be used to predict Gene Ontology (GO) terms indirectly targeted by human microRNAs. In contrast to direct targets which are predicted to have binding sites, indirect targets are regulated transcriptionally through transcription factors (TFs).""" ; sc:featureList edam:operation_0445, edam:operation_0463, edam:operation_3501, edam:operation_3792 ; sc:license "MIT" ; sc:name "miRinGO" ; sc:url "https://github.com/Fadeel/miRinGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description "Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "mirIntegrator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mirIntegrator.html" ; biotools:primaryContact "Diana Diaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3379, edam:topic_3697 ; sc:citation , "pmcid:PMC9010828", "pubmed:35432465" ; sc:description "A Distance-Based Microbiome Kernel Association Test With Multi-Categorical Outcomes.MiRKAT-MC" ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MiRKAT-MC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Zhiwen-Owen-Jiang/MiRKATMC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_1957, edam:format_3999 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3518 ; sc:description "miRkit is an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, can perform the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and is specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology." ; sc:featureList edam:operation_2436, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mirKit" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/miRkit" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3752 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0659, edam:topic_2269, edam:topic_3047, edam:topic_3512 ; sc:citation , "pmcid:PMC4696828", "pubmed:26716983" ; sc:description "Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses." ; sc:featureList edam:operation_0438, edam:operation_2497, edam:operation_3439, edam:operation_3664, edam:operation_3792 ; sc:license "GPL-2.0" ; sc:name "miRLAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRLAB.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:26694379" ; sc:description "Novel method  which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network." ; sc:featureList edam:operation_2495 ; sc:name "miRlastic" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://www.helmholtz-muenchen.de/icb/research/groups/computational-cell-maps/projects/mirlastic/index.html" ; biotools:primaryContact "Steffen Sass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Library", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0797, edam:topic_3071 ; sc:citation ; sc:description "Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources." ; sc:featureList edam:operation_0224, edam:operation_2422 ; sc:license "LGPL-2.1" ; sc:name "miRMaid" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:url "http://www.mirmaid.org/" ; biotools:primaryContact "Anders Jacobsen", "Morten Lindow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Provides comprehensive prediction of microRNA target repression strength. MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. Our resource enables to search precompiled and predict online miRNA targets with miRmap." ; sc:featureList edam:operation_2423 ; sc:name "miRmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://mirmap.ezlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3511 ; sc:citation "pubmed:25344330" ; sc:description "Site-level and UTR-level classifier for miRNA target prediction." ; sc:featureList edam:operation_0415 ; sc:name "MirMark" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mn.eng.hawaii.edu/~garmire/HTML/MirMark/" ; biotools:primaryContact "Lana Garmire" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170 ; sc:citation , "pubmed:33872372" ; sc:description "miRMaster 2 is a comprehensive analysis framework for sncRNA-seq data. Samples are directly preprocessed in the browser before being uploaded to our server." ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_3223, edam:operation_3792, edam:operation_3891 ; sc:name "miRMaster" ; sc:url "https://www.ccb.uni-saarland.de/mirmaster2" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:23300555" ; sc:description "MiRmat is a software designed to predict mature microRNA from pri-microRNA. This tool can be divided into two parts, one is for predicting Drosha processing site, which is based on energy distribution pattern along primary microRNA’s secondary structure; the other is for predicting Dicer processing site, which is based on precursor microRNA’s structure feature" ; sc:featureList edam:operation_0278 ; sc:name "MiRmat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mcube.nju.edu.cn/jwang/lab/soft/MiRmat/index.html" ; biotools:primaryContact "Chenfeng He (suggestions on online tool)", "Prof. J.Wang (Other)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "miRmine database is a collection of expression profiles from different publicly available miRNA-seq datasets, Panwar et al (2017) miRmine: A Database of Human miRNA Expression, prepared with this data package as RangedSummarizedExperiment." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRmine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRmine.html" ; biotools:primaryContact "Dusan Randjelovic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2640, edam:topic_3674 ; sc:citation ; sc:description "Binary classification of microsatellite instability using methylation and mutations." ; sc:featureList edam:operation_3225 ; sc:name "MIRMMR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ding-lab/MIRMMR" ; biotools:primaryContact "Li Ding", "Steven M Foltz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3168 ; sc:citation , "pmcid:PMC4662591", "pubmed:26623179" ; sc:description "miRMOD is a tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data." ; sc:featureList edam:operation_2403 ; sc:license "Other" ; sc:name "miRMOD" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.4" ; sc:url "http://bioinfo.icgeb.res.in/miRMOD/" ; biotools:primaryContact "Dinesh Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0749 ; sc:citation "pubmed:25527098" ; sc:description "Software tool for systematic discovery of miRNA modules from a set of predefined miRNA target sites. Given a sets of miRNA binding sites, miRModule efficiently identifies groups of miRNAs, whose binding sites significantly co-occur in the same set of target mRNAs, as putative miRNA modules." ; sc:featureList edam:operation_2423 ; sc:name "miRModule" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://hulab.ucf.edu/research/projects/miRNA/miRModule/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_0769, edam:topic_3512 ; sc:citation , "pmcid:PMC9039401", "pubmed:35495139" ; sc:description "Detecting miRNA-mRNA Regulatory Modules." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "miRModuleNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/malikyousef/miRModuleNet/" . a sc:SoftwareApplication ; 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sc:name "miRNA Digger" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfolab.cn/miRNA_Digger/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation ; sc:description "A Comprehensive Web Resource for Plant Pre-microRNA Classification." ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "miRNAFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mirnafinder.shyaman.me/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0659 ; sc:citation "pubmed:26130578" ; sc:description "Adaptive Lasso based method that integrates full spectrum of sequence features for microRNA target prediction." ; sc:featureList edam:operation_2423 ; sc:name "miRNALasso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nba.uth.tmc.edu/homepage/liu/miRNALasso/" ; biotools:primaryContact "Yin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation , "pubmed:27797767" ; sc:description "Package containing an S4 class for translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names." ; sc:featureList edam:operation_0224, edam:operation_0335 ; sc:license "Artistic-2.0" ; sc:name "miRNAmeConverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRNAmeConverter.html" ; biotools:primaryContact "Stefan J. Haunsberger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3115 ; sc:encodingFormat edam:format_3475 ; sc:name "Microarray metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659 ; sc:citation , "pmcid:PMC4333818", "pubmed:25745387" ; sc:description "This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "miRNApath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRNApath.html" ; biotools:primaryContact "James M. Ward" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3512 ; sc:citation , "pmcid:PMC7319542", "pubmed:32484556" ; sc:description """A webserver for comparative quality control of miRNA-seq data. mirnaQC will try to automatically detect protocol and species from your data but if you provide these, your job will run faster. mirnaQC provides several quality features that can help researchers identify issues in their samples. These features are provided as absolute values and ranked with a percentile calculated from a corpus of more than 36,000 samples.""" ; sc:featureList edam:operation_2428, edam:operation_3192, edam:operation_3891 ; sc:name "mirnaQC" ; sc:url "https://arn.ugr.es/mirnaqc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_2885, edam:topic_3512 ; sc:citation , "pubmed:32990748" ; sc:description """A comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets. Welcome to the miRNASNP -v3 database. microRNAs (miRNAs) are endogenous and regulatory non-coding RNAs by targeting mRNAs for cleavage or translational repression. SNPs in pre-miRNAs or target sites will affect miRNA expression or function. miRNASNP is a comprehensive resource of human miRNA-related SNPs, including their effects on target gain and loss.""" ; sc:featureList edam:operation_0463, edam:operation_3661, edam:operation_3792 ; sc:name "miRNASNP-v3" ; sc:url "http://bioinfo.life.hust.edu.cn/miRNASNP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_3474 ; sc:citation ; sc:description "Machine learning method specifically designed for pre-miRNA prediction. It takes advantage of unlabeled sequences to improve the prediction rates even when there are just a few positive examples, when the negative examples are unreliable or are not good representatives of its class." ; sc:featureList edam:operation_0463 ; sc:name "miRNAss" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "https://cran.r-project.org/web/packages/miRNAss/index.html" ; biotools:primaryContact "Cristian Yones" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_3033 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene ID (NCBI)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_2815, edam:topic_3168, edam:topic_3518 ; sc:citation ; sc:description "The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation)." ; sc:featureList edam:operation_2423, edam:operation_3436 ; sc:license "GPL-2.0" ; sc:name "miRNAtap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRNAtap.html" ; biotools:primaryContact "Maciej Pajak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_0749, edam:topic_3518, edam:topic_3794 ; sc:citation , "pubmed:31647101" ; sc:description """Updates to the experimentally validated microRNA-target interaction database. the experimentally validated microRNA-target interactions database. As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.""" ; sc:featureList edam:operation_0463, edam:operation_2428, edam:operation_3792 ; sc:name "miRNATarBase" ; sc:url "http://miRTarBase.cuhk.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC5046196", "pubmed:28185545" ; sc:description "A SOM-based miRNA-target interactions predictor." ; sc:featureList edam:operation_0463 ; sc:name "MiRNATIP" ; sc:operatingSystem "Linux" ; sc:url "http://tblab.pa.icar.cnr.it/public/miRNATIP/" ; biotools:primaryContact "Antonino Fiannaca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0634, edam:topic_0659, edam:topic_3300, edam:topic_3308 ; sc:citation , "pubmed:34570238" ; sc:description "A small noncoding RNA tissue atlas by determining the RNA expression for nine different types of sncRNAs. For the human atlas, the expression data is determined in 21 organs using 188 samples from six humans. For the mouse atlas, the expression data is determined in 7 organs using 59 samples from 37 mice." ; sc:featureList edam:operation_2422, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "miRNATissueAtlas2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ccb.uni-saarland.de/tissueatlas2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3500, edam:topic_3518 ; sc:citation "pubmed:22135287" ; sc:description "miRNEST: a comprehensive database of animal, plant and virus microRNAs." ; sc:featureList edam:operation_0346, edam:operation_0463, edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "miRNEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rhesus.amu.edu.pl/mirnest/copy/" ; biotools:primaryContact "miRNEST Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0602, edam:topic_0659 ; sc:citation , "pmcid:PMC4987881", "pubmed:27105848" ; sc:description "Tool with comprehensive support for statistical analysis and functional interpretation of data generated in miRNAs studies." ; sc:featureList edam:operation_0463, edam:operation_2497, edam:operation_3792 ; sc:name "miRNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mirnet.ca/" ; biotools:primaryContact "Jeff Xia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0622, edam:topic_0659, edam:topic_3299 ; sc:citation ; sc:description "miROrtho contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline." ; sc:featureList edam:operation_0224 ; sc:name "miROrtho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://cegg.unige.ch/mirortho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:25165094" ; sc:description "Enables rapid and simple browser-based miRNA homology detection and quantification." ; sc:featureList edam:operation_2423 ; sc:name "MIRPIPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformatics.mpi-bn.mpg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC4141084", "pubmed:25117656" ; sc:description "It extends miRDeep to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants." ; sc:featureList edam:operation_3695 ; sc:name "miRPlant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v4" ; sc:url "http://www.australianprostatecentre.org/research/software/mirplant" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3168 ; sc:citation "pubmed:23184675" ; sc:description "Tool for microRNA prediction from high-throughput sequencing data that requires only small RNA datasets as input." ; sc:featureList edam:operation_2423 ; sc:name "MiRPlex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/mirplex" ; biotools:primaryContact "Dr. Daniel Mapleson", "Dr. Simon Moxon," . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:32609318" ; sc:description """A partial linear structure identifier method for cancer subtyping using microRNAs. The R package for ‘mirPLS: a partial linear structure identifier method for cancer subtyping using MicroRNAs’. Run cv_mirPLS to determine the regularization parameters: lambda1 and lambda2. We suggest to search lambda1 and lambda2 in the ranges of (0, 1) and (0, 10), respectively. With lambda1 and lambda2, run mirPLS to select miRNAs linearly or non-linearly associated with disease outcomes. Finally, run sp_clustering to conduct spectral clustering on patients using the selected non-linearly associated miRNAs. In the whole process, cv_mirPLS are time consuming. It may take hours to run the whole process for a typical miRNA data from TCGA.""" ; sc:featureList edam:operation_0463, edam:operation_3432, edam:operation_3792 ; sc:name "mirPLS" ; sc:url "https://github.com/pfruan/mirPLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3518 ; sc:citation ; sc:description "Determines normalised expression levels of sRNAs matching known miRNAs in miRBase." ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MiRProf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://srna-workbench.cmp.uea.ac.uk/mirprof/" ; biotools:primaryContact "Vincent Moulton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , "pmcid:PMC4410649", "pubmed:25527833" ; sc:description "Database and a related web application which provides a powerful and intuitive interface to the researchers that want to search for publications related to particular microRNA molecules. It also provides useful information about the correlation of these microRNAs to any diseases, tissues and genes. It facilitates publication search by considering microRNA families and the history of the microRNA nomenclature." ; sc:featureList edam:operation_0306 ; sc:name "mirPub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=mirpub/index" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_1929 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation , , "pmcid:PMC3531190", "pubmed:23193287", "pubmed:28686301" ; sc:description "A pipeline for automated analyses of small RNAs in non-model plants" ; sc:featureList edam:operation_0361, edam:operation_2424 ; sc:isAccessibleForFree true ; sc:name "miRPursuit" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "v1.0" ; sc:url "https://github.com/forestbiotech-lab/miRPursuit" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3077, edam:topic_3810 ; sc:citation , "pmcid:PMC8271970", "pubmed:34283163" ; sc:description "A Modular and Cost-Effective Microclimate Monitoring System for Real-Time Remote Applications." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MIRRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/opieters/MIRRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0219, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC9045266", "pubmed:35352997" ; sc:description "Database and Tool for Metataxonomics with Long-Read Sequence." ; sc:featureList edam:operation_0579, edam:operation_3200, edam:operation_3460, edam:operation_3695, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MIrROR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mirror.egnome.co.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:17989254" ; sc:description "Computational procedure to identify miRNA genes conserved in more than one genome." ; sc:featureList edam:operation_0415 ; sc:name "MiRScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bartellab.wi.mit.edu/softwareDocs/MiRscan3/Introduction.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2229, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description "miRSCAPE -- to infer miRNA expression in a sample from its RNA-seq profile. We establish miRSCAPE's accuracy separately in 10 tissues comprising ~10,000 tumor and normal bulk samples and demonstrate that miRSCAPE accurately infers cell type-specific miRNA activities (predicted vs observed fold-difference correlation ~ 0.81) in two independent datasets where miRNA profiles of specific cell types are available (HEK-GBM, Kidney-Breast-Skin)." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_3432, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "miRSCAPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hannenhalli-lab/miRSCAPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2269, edam:topic_3512, edam:topic_3518 ; sc:author ; sc:citation , "pubmed:33822666" ; sc:description "miRSM is an R package to infer and analyse miRNA sponge modules in heterogeneous data." ; sc:featureList edam:operation_0463, edam:operation_3463, edam:operation_3557, edam:operation_3766, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "miRSM" ; sc:softwareHelp , ; sc:url "https://github.com/zhangjunpeng411/miRSM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3063, edam:topic_3518 ; sc:citation ; sc:description "This package provides several functions to study miRNA sponge, including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules." ; sc:featureList edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "miRsponge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/miRsponge.html" ; biotools:primaryContact "Junpeng Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3071, edam:topic_3168 ; sc:citation ; sc:description "The product of this pipeline creates a miRspring document, which essentiallyis a small HTML javascript file. Each miRspring document has been developed in such a way that it reproduces miRNA sequencing data from a BAM file. Additionally it provides unique analysis tools, and does not need internet connectivity for these processes." ; sc:featureList edam:operation_0335 ; sc:license "GPL-3.0" ; sc:name "MiRspring" ; sc:softwareHelp ; sc:url "https://github.com/davhum/miRspring" ; biotools:primaryContact "David T. Humphreys" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3360, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description """Detecting microRNA arm shift and switch events. This website uses Matomo Analytics and cookies. For more information, please refer to the privacy notice for our websites. Learn more I agree.""" ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3799 ; sc:name "miRSwitch" ; sc:url "https://www.ccb.uni-saarland.de/mirswitch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation , "pubmed:24894504" ; sc:description "Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion." ; sc:featureList edam:operation_0438 ; sc:license "GPL-2.0" ; sc:name "Mirsynergy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Mirsynergy.html" ; biotools:primaryContact "Yue Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0659 ; sc:citation ; sc:description "MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. miRSystem integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan." ; sc:featureList edam:operation_2423, edam:operation_2454 ; sc:name "miRSystem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20150312" ; sc:url "http://mirsystem.cgm.ntu.edu.tw/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC5389546", "pubmed:27903911" ; sc:description "Novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA–target interaction data." ; sc:featureList edam:operation_0463 ; sc:name "miRTar2GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://academic.oup.com/nar/article/45/6/e42/2605966" ; biotools:primaryContact "Gaurav Sablok", "Gyorgy Hutvagner", "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3518, edam:topic_3678 ; sc:citation "pubmed:21071411" ; sc:description "miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2428, edam:operation_2495 ; sc:name "miRTarBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://miRTarBase.mbc.nctu.edu.tw/" ; biotools:primaryContact "miRTarBase Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0659, edam:topic_2885, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC8728135", "pubmed:34850920" ; sc:description "The experimentally validated microRNA-target interactions database" ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "miRTarBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://miRTarBase.cuhk.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:26361498" ; sc:description "Visual analysis tool for miRNA-mRNA expression profile data." ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:name "mirTarVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hcil.snu.ac.kr/~rati/miRTarVis/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0204, edam:topic_0659 ; sc:citation "pubmed:26407127" ; sc:description "Text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature." ; sc:featureList edam:operation_0306 ; sc:name "miRTex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.bioinformatics.udel.edu/miRTex/" ; biotools:primaryContact "Gang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9438248", "pubmed:36050754" ; sc:description "Imputation via Rank-Transformation and Harmonization (MIRTH), a method to impute unmeasured metabolite abundances by jointly modeling metabolite covariation across datasets which have heterogeneous coverage of metabolite features." ; sc:featureList edam:operation_3436, edam:operation_3557, edam:operation_3799, edam:operation_3891 ; sc:license "Other" ; sc:name "MIRTH" ; sc:url "https://github.com/reznik-lab/MIRTH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3474 ; sc:citation "pubmed:19091027" ; sc:description "Machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRanda, PicTar and TargetScanS." ; sc:featureList edam:operation_3695 ; sc:name "MiRTif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mirtif.bii.a-star.edu.sg/" ; biotools:primaryContact "Kuo-Bin Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3063 ; sc:citation , "pubmed:32287029" ; sc:description """A miRNA Target Prediction Method Based on Matrix Completion Algorithm. miRNA target prediction based on matrix completion algorithm. This project includes the dataset and excuteable programs (both on Windows and Linux platform) of the paper "miRTMC: A miRNA target prediction method based on matrix completion algorithm", which is submitted to the Journal of Biomedical and Health Informatics.""" ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3927 ; sc:name "miRTMC" ; sc:url "https://github.com/hjiangcsu/miRTMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:20478827" ; sc:description "Web server for microRNA data analysis, profiling and discovery based on high-throughput sequencing." ; sc:featureList edam:operation_3198, edam:operation_3680, edam:operation_3792 ; sc:name "MirTools" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://centre.bioinformatics.zj.cn/mirtools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:22356618" ; sc:description "Web-based application to analyse the interactions between miRNAs and predicated target genes via their transcripts (mRNAs)." ; sc:featureList edam:operation_3439 ; sc:name "miRTrail" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://mirtrail.bioinf.uni-sb.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622 ; sc:citation "pubmed:25596308" ; sc:description "Web server to accurately detect de novo mutations (DNMs) based on Expectation-maximization (EM) model. mirTrios also surports identification of rare inherited mutations, known diagnostic variants, as well as the prioritisation of novel and promising candidate genes." ; sc:featureList edam:operation_3198, edam:operation_3202, edam:operation_3227 ; sc:name "MirTrios" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://centre.bioinformatics.zj.cn/mirTrios/" ; biotools:primaryContact "Huiqian Chen", "Jinchen Li", "Qing Xie", "Tao Wang", "Yi Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:15980567" ; sc:description "miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes." ; sc:featureList edam:operation_0464, edam:operation_2421, edam:operation_2454 ; sc:name "miRU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&Itemid=44" ; biotools:primaryContact "The Zhao Bioinformatics Laboratory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_3301 ; sc:citation , "pmcid:PMC6045920", "pubmed:30018852" ; sc:description "Performs digital 24-loci MIRU-VNTR typing for Mycobacterium tuberculosis." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "MIRU-profiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rahimrajwani/MIRU-profiler" ; biotools:primaryContact "Gilman Kit Hang Siu", "Rahim Rajwani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3068, edam:topic_3293 ; sc:citation "pubmed:18550737", "pubmed:20457747" ; sc:description "Allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information." ; sc:featureList edam:operation_0325, edam:operation_2429, edam:operation_3196 ; sc:name "MIRU-VNTRplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.miru-vntrplus.org" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_2640, edam:topic_3360 ; sc:citation "pubmed:23175189" ; sc:description "MIRUMIR is an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets." ; sc:featureList edam:operation_2998 ; sc:name "MIRUMIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.chemoprofiling.org/cgi-bin/GEO/MIRUMIR/web_run_MIRUMIR.V1.pl" ; biotools:primaryContact "AV Antonov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0203, edam:topic_0659, edam:topic_2885, edam:topic_3382 ; sc:citation , "pmcid:PMC4756848", "pubmed:26384425" ; sc:description """a tool to predict the impact of genetic variants on miRNAs. miRVaS is a program designed to predict the impact of genetic variants on miRNAs. Upload variant file (tab separated or vcf). or paste data in the field below (complete including header and with tabs). Cammaerts, S., Strazisar, M., Dierckx, J., Del Favero, J., De Rijk, P. (2015) miRVaS: a tool to predict the impact of genetic variants on miRNAs. Nucl. Acids Res., 10.1093/nar/gkv921.""" ; sc:featureList edam:operation_0331, edam:operation_0463, edam:operation_0570, edam:operation_2441, edam:operation_3226 ; sc:name "miRVaS" ; sc:url "http://mirvas.bioinf.be/analyse.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0204, edam:topic_0659, edam:topic_3308 ; sc:citation "pubmed:21602264" ; sc:description "miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM)." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0314, edam:operation_2495, edam:operation_3463 ; sc:name "miRvestigator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mirvestigator.systemsbiology.net" ; biotools:primaryContact "miRvestigator Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_3308 ; sc:citation , "pmcid:PMC5716067", "pubmed:29036674" ; sc:description "Robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs." ; sc:featureList edam:operation_2403 ; sc:name "miRvial" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/SystemsBiologyOfJianghanUniversity/miRvial" ; biotools:primaryContact "Weixiong Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC7319447", "pubmed:32319523" ; sc:description """A novel webserver application to visualize and interpret microRNA datasets. miRViz – visualizing microRNA data on networks. Overlay microRNA data (miR expression, differential expression, phenotypic score, etc.) on various microRNA networks (position on the genome, shared targets, shared seed). Compare different datasets on the same networks and/or compare the same datasets on different microRNA networks.""" ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3925 ; sc:name "miRViz" ; sc:url "http://mirviz.prabi.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0659, edam:topic_3518 ; sc:citation "pubmed:19468042" ; sc:description "Web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm." ; sc:featureList edam:operation_2489 ; sc:name "MirZ" ; sc:url "http://www.mirz.unibas.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_2885 ; sc:citation "pubmed:12589540" ; sc:description "Allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases." ; sc:featureList edam:operation_0415 ; sc:name "MISA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pgrc.ipk-gatersleben.de/misa/" ; biotools:primaryContact "Thomas Thiel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3305 ; sc:citation , "pmcid:PMC8122113", "pubmed:34026466" ; sc:description "MISCAN is an online modelling-based tool for informing breast, cervical, and colorectal cancer screening decisions in Europe." ; sc:featureList edam:operation_3435 ; sc:name "MISCAN" ; sc:url "https://miscan.eu-topia.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_2814, edam:topic_3120 ; sc:citation , "pmcid:PMC7319582", "pubmed:32402084" ; sc:description """MIssense variant to protein StruCture Analysis web SuiTe. MISCAST (MIssense variant to protein StruCture Analysis web SuiTe; http://miscast.broadinstitute.org/) is a web server to interactively visualize and analyze missense variants in protein sequence and structure space.""" ; sc:featureList edam:operation_0570, edam:operation_2406, edam:operation_3227 ; sc:name "MISCAST" ; sc:url "http://miscast.broadinstitute.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "MiscMetabar aims to facilitate the description, transformation, exploration and reproducibility of metabarcoding analysis using R. The development of MiscMetabar relies heavily on the R packages dada2 (Callahan et al. 2016), phyloseq (McMurdie and Holmes 2013) and targets (Landau 2021)." ; sc:name "MiscMetabar" ; sc:softwareHelp ; sc:url "https://adrientaudiere.github.io/MiscMetabar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7814713", "pubmed:33461500" ; sc:description """A framework for medical image segmentation with convolutional neural networks and deep learning. The open-source Python library MIScnn is an intuitive API allowing fast setup of medical image segmentation pipelines with state-of-the-art convolutional neural network and deep learning models in just a few lines of code.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "MIScnn" ; sc:url "https://github.com/frankkramer-lab/MIScnn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3339, edam:topic_3678, edam:topic_3697 ; sc:citation ; sc:description "Microbiome data simulator for power analysis" ; sc:featureList edam:operation_2939, edam:operation_3359, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MiSDEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pchlenski/misdeed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3303, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:35612011" ; sc:description "A Metric Library for Medical Image Segmentation Evaluation." ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MISeval" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/frankkramer-lab/miseval" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3572 ; sc:citation "pubmed:26573684" ; sc:description "Tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis." ; sc:featureList edam:operation_0310, edam:operation_3180 ; sc:name "misFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/hitbio/misFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "MISHIMA is a program for multiple DNA sequence alignment. 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MitoBreak provides a complete, quality checked and regularly updated list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially-duplicated (duplications) and linear mtDNAs." ; sc:featureList edam:operation_2421 ; sc:name "MITOBREAK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mitobreak.portugene.com/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3520 ; sc:citation , "pubmed:33174596" ; sc:description """An updated mitochondrial proteome now with sub-organelle localization and pathway annotations. An Inventory of Mammalian Mitochondrial Proteins and Pathways. MitoCarta3.0 is an inventory of 1136 human and 1140 mouse genes encoding proteins with strong support of mitochondrial localization, now with sub-mitochondrial compartment and pathway annotations. To generate this inventory, we performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy,.""" ; sc:featureList edam:operation_2436, edam:operation_2489, edam:operation_2942 ; sc:name "MitoCarta" ; sc:softwareVersion "3.0" ; sc:url "http://www.broadinstitute.org/mitocarta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_2229 ; sc:citation "pubmed:23282223" ; sc:description "Tool for counting mitochondrial DNA reads from Whole Genome Sequence," ; sc:featureList edam:operation_3799 ; sc:name "MitoCounter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mitocounter/?source=navbar" ; biotools:primaryContact "Cheng-Yan Kao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:35001369" ; sc:description "A machine learning approach for the accurate identification of cross-contamination-derived tumor mitochondrial DNA mutations." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "mitoDataclean" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/3150129019/mitoDataclean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_2229, edam:topic_3500 ; sc:citation , "pmcid:PMC3808866", "pubmed:23955518" ; sc:description "Mitochondrial genome database of fish with an accurate and automatic annotation pipeline." ; sc:featureList edam:operation_2421 ; sc:name "MitoFish" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mitofish.aori.u-tokyo.ac.jp/" ; biotools:primaryContact "Wataru Iwasaki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0659, edam:topic_3168 ; sc:citation , "pubmed:33605414" ; sc:description """An efficient, high-performance toolkit for animal mitogenome assembly, annotation, and visualization. MitoFlex is a Python3 based toolkit designated for mitochondrial genome assembling, it's inspired from MitoZ, but with improved performance and result quality. And also it implemented a both easy and flexible mechanism to extend the program feature. It accepts both single-end and pair-end data, and follows an already set workflow to output results. Working mechanism is highly flexible and can be easily reconfigured here.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3184, edam:operation_3216, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "MitoFlex" ; sc:url "https://github.com/Prunoideae/MitoFlex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_2229 ; sc:citation "pubmed:20118192" ; sc:description "Developed to assist in the annotation of genes and tRNAs in seed plant mitochondrial genomes." ; sc:featureList edam:operation_0362 ; sc:name "MITOFY" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://dogma.ccbb.utexas.edu/mitofy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:20833631" ; sc:description "Dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability. It integrates and establishes cross-comparisons between these data." ; sc:featureList edam:operation_0306, edam:operation_0310, edam:operation_0314, edam:operation_2409, edam:operation_2495 ; sc:name "MitoGenesisDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dsimb.inserm.fr/dsimb_tools/mitgene/" ; biotools:primaryContact "Claude JACQ", "Gaelle LELANDAIS", "Jean-Christophe GELLY", "Mickael ORGEUR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "Find, circularise and annotate mitogenome from PacBio assemblies" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_0525, edam:operation_2995 ; sc:license "MIT" ; sc:name "MitoHiFi" ; sc:softwareVersion "2.2" ; sc:url "https://github.com/marcelauliano/MitoHiFi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:34571248" ; sc:description "A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases." ; sc:featureList edam:operation_2422, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MitoLink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ab-openlab.csir.res.in/mitolink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_0634, edam:topic_3399, edam:topic_3520 ; sc:citation "pubmed:22121219" ; sc:description "MitoMiner integrates mitochondrial proteomics data for a range of organisms. You can run flexible queries, export results and analyse lists of data." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2436, edam:operation_3561 ; sc:name "MitoMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mitominer.mrc-mbu.cam.ac.uk/release-2.0/begin.do" ; biotools:primaryContact "MitoMiner Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3033 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3383, edam:topic_3523 ; sc:citation , "pmcid:PMC3827932", "pubmed:24131777" ; sc:description "The package contains the methods to fit a cell-cycle model on cell count data." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "mitoODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mitoODE.html" ; biotools:primaryContact , "Gregoire Pau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3047, edam:topic_3175, edam:topic_3407 ; sc:citation , "pmcid:PMC8050385", "pubmed:33889820" ; sc:description "MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito). It is a logically-framed tool for visualizing multiple mitochondrial pathways." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3695, edam:operation_3926 ; sc:license "GPL-3.0" ; sc:name "MitopatHs" ; sc:softwareHelp ; sc:url "https://web.math.unipd.it/mitopaths/" ; biotools:primaryContact "Saverio Marchi", "Silvia Crafa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2229, edam:topic_3293 ; sc:citation "pubmed:25721538" ; sc:description "New automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes." ; sc:featureList edam:operation_0324 ; sc:name "MitoPhAST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mht85/MitoPhAST" ; biotools:primaryContact "Tan Mun Hua" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_0654, edam:topic_3407 ; sc:citation , "pmcid:PMC8464050", "pubmed:34428295" ; sc:description "The MitoPhen database is a human phenotype ontology-based approach to identify mitochondrial DNA diseases." ; sc:featureList edam:operation_2998, edam:operation_3095, edam:operation_3196 ; sc:name "MitoPhen" ; sc:url "http://www.mitophen.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_0654, edam:topic_3407 ; sc:citation , "pmcid:PMC8464050", "pubmed:34428295" ; sc:description "A human phenotype ontology-based approach to identify mitochondrial DNA diseases." ; sc:featureList edam:operation_2998, edam:operation_3095, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "MitoPhen database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.7" ; sc:url "http://www.mitophen.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_0621, edam:topic_0736 ; sc:citation "pubmed:15037509", "pubmed:15215413" ; sc:description "Uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers." ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_3092 ; sc:name "MITOPRED" ; sc:url "http://bioinformatics.albany.edu/~mitopred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_2229 ; sc:citation "pubmed:8944766" ; sc:description "Calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site." ; sc:featureList edam:operation_2479 ; sc:name "MITOPROT II" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ihg.gsf.de/ihg/mitoprot.html" ; biotools:primaryContact "Manuel G. Claros", "Pierre Vincens" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_1929, edam:format_2305, edam:format_3003 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_3500, edam:topic_3673 ; sc:citation , "pubmed:22982435" ; sc:description "De novo metazoan mitochondrial genome annotation." ; sc:featureList edam:operation_0362 ; sc:name "MITOS" ; sc:softwareHelp ; sc:url "https://mitos.bioinf.uni-leipzig.de/index.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3168, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC8610268", "pubmed:34762648" ; sc:description "A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data." ; sc:featureList edam:operation_0292, edam:operation_0308, edam:operation_3227, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MitoScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/larryns/MitoScape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2229, edam:topic_3676 ; sc:description "Open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. It evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome." ; sc:featureList edam:operation_3182 ; sc:name "MitoSeek" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "https://github.com/riverlee/MitoSeek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7554024", "pubmed:33083756" ; sc:description """Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology. MitoSegNet_AccuracyTesting_Manuscript. Scripts used to generate quantitative figures shown in MitoSegNet manuscript. All scripts used to generate statistical and visual data shown in the MitoSegNet manuscript can be found here.""" ; sc:featureList edam:operation_3435, edam:operation_3552, edam:operation_3799 ; sc:name "MitoSegNet" ; sc:url "https://zenodo.org/search?page=1&size=20&q=mitosegnet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1493 ; sc:encodingFormat edam:format_2572 ; sc:name "RNA structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC10523499", "pubmed:37725654" ; sc:description "A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:name "mitoSplitter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lnscan/mitoSplitter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_1775 ; sc:citation ; sc:description "An algorithm for predicting the impact of novel mitochondrial tRNA mutations. The algorithm is available through MITOMAP" ; sc:featureList edam:operation_3202, edam:operation_3226, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "MitoTIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.mitomap.org/MITOMAP" ; biotools:primaryContact "Neal Sondheimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data." ; sc:featureList edam:operation_3660, edam:operation_3799, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MitoTNT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.mitotnt.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_2229, edam:topic_2815 ; sc:citation "pubmed:20933105" ; sc:description "Web-based bioinformatics platform, provides a convenient, user-friendly interface for handling human mtDNA sequence data." ; sc:featureList edam:operation_2478 ; sc:name "MitoTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mitotool.org/" ; biotools:primaryContact "Yong-Gang Yao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3500 ; sc:citation "pubmed:25655564" ; sc:description "Designed for data analysis of mitochondrial DNA of eight domestic animals, including cattle, chicken, dog, horse, goat, pig, sheep and yak." ; sc:featureList edam:operation_2478 ; sc:name "MitoToolPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mitotool.org/mp.html#intro" ; biotools:primaryContact "Long Fan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2229, edam:topic_2840, edam:topic_3336 ; sc:citation , "pmcid:PMC8283953", "pubmed:34266386" ; sc:description "A comprehensive mitochondrial toxicity database." ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "MitoTox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mitotox.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0199, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10298143", "pubmed:37372402" ; sc:description "Computational framework for analyzing mitochondrial variation in single-cell RNA sequencing data." ; sc:featureList edam:operation_0314, edam:operation_3185, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MitoTrace" ; sc:operatingSystem "Linux" ; sc:url "http://github.com/lkmklsmn/MitoTrace" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0654 ; sc:citation , "pubmed:35412583" ; sc:description "MitoVisualize is a tool for analysis of variants in human mitochondrial RNAs and DNA." ; sc:featureList edam:operation_0502, edam:operation_0570, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MitoVisualize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.mitovisualize.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3299 ; sc:citation ; sc:description "A curated mitochondrial genome database of metazoans for comparative genomics studies." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "MitoZoa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-CNR" ; sc:softwareHelp ; sc:url "http://srv00.recas.ba.infn.it/mitozoa/" ; biotools:primaryContact "Graziano Pesole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3339, edam:topic_3679 ; sc:citation "pubmed:16339140" ; sc:description "Web-server specifically trained to predict the proteins which are destined to localized in mitochondria in yeast and animals particularly." ; sc:featureList edam:operation_2489 ; sc:name "MitPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/mitpred/" ; biotools:primaryContact "G.P.S.Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation "pubmed:11262950" ; sc:description "Clustering algorithm based on a straightforward geometric principle. Initially it was designed to be a binary hierarchical clustering algorithm for gene expression analysis." ; sc:featureList edam:operation_2495, edam:operation_3432 ; sc:name "MITree" ; sc:operatingSystem "Windows" ; sc:url "http://www.snubi.org/software/MITree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:24931999" ; sc:description "Command line application for the discovery of transcription factor binding site (TFBS) motifs." ; sc:featureList edam:operation_0438 ; sc:name "MITSU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mitsu-motif/" ; biotools:primaryContact "Alastair M. Kilpatrick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_3407, edam:topic_3673 ; sc:citation ; sc:description """A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data. Technically you can run mity call and mity normalise separately, but since mity report requires a normalised vcf file, we recommend running mity call --normalise""" ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "mity" ; sc:url "https://github.com/KCCG/mity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:author "Alexis Groppi", "Florence Maurier", "Heissam Soueidan", "Macha Nikolski" ; sc:citation ; sc:description "Tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length." ; sc:featureList edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Mix" ; sc:operatingSystem "Linux" ; sc:provider "CBiB - Universite Victor Segalen Bordeaux, 146, rue Leo Saignat, 33076 Bordeaux, France", "CNRS / LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France", "NKI-AVL, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands", "u-bordeaux.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://github.com/cbib/MIX" ; biotools:primaryContact "Alexis Groppi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3055 ; sc:description "Designed for breeding value estimation. The aim is to offer a general and effective program for many kinds of data sets. One of the most important application is to solve large random regression test-day models for national dairy cattle evaluations. Nevertheless, the software is designed to be a general tool that is suited to fit many models." ; sc:featureList edam:operation_2238, edam:operation_3664 ; sc:license "Proprietary" ; sc:name "Mix99" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://portal.mtt.fi/portal/page/portal/mtt_en/mtt/about/researchunits/bel/biometricalgenetics/software/MiX99" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2269, edam:topic_3169, edam:topic_3173, edam:topic_3179 ; sc:citation ; sc:description """Efficient Detection and Classification of Epigenomic Changes Under Multiple Conditions. Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions. mixNBHMM is an R package for the detection of genomic regions exhibiting short and broad differential enrichment under multi-replicate, multi-condition settings. It is applicable to data from ChIP-seq, ATAC-seq, DNase-seq, and related experiments. mixNBHMM detects these regions using a three-state hidden Markov model (HMM) with a finite mixture of negative binomials as emission distribution in the HMM’s differential state. The HMM framework is particularly suitable for the detection of differential broad peaks and the mixture model allows the classification of differential combinatorial patterns of enrichment across conditions. Code to replicate the results from the mixNBHMM paper is available at https://github.com/plbaldoni/mixNBHMMPaper""" ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3435 ; sc:name "mixNBHMM" ; sc:url "https://github.com/plbaldoni/mixNBHMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3055 ; sc:description "Modern genetic evaluation system for all breeding organizations. It estimates genetic merit of individuals using observations and family relationships, given the components of variance." ; sc:featureList edam:operation_2238 ; sc:license "Proprietary" ; sc:name "Mixblup" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://www.mixblup.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3125, edam:topic_3169 ; sc:citation "pubmed:26703974" ; sc:description "Probabilistic method for identifying cell type specific TF binding sites from heterogeneous chromatin immunoprecipitation sequencing (ChIP-seq) data." ; sc:featureList edam:operation_0420 ; sc:name "MixChIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.ics.aalto.fi/csb/software/" ; biotools:primaryContact "Harri Lähdesmäki", "Sini Rautio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_2640 ; sc:citation ; sc:description "Comprehensive software package to study the subclonal structures of tumor genomes, including subclonal cellular prevalences estimation, allelic configuration estimation, absolute copy number estimation and a few visualization tools." ; sc:featureList edam:operation_0337, edam:operation_2480 ; sc:name "MixClone" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.4" ; sc:url "https://github.com/uci-cbcl/MixClone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "MixDB is a database search tool that able to identify mixture MS/MS spectra from more than one peptide." ; sc:featureList edam:operation_2421 ; sc:name "MixDB" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0r" ; sc:url "http://proteomics.ucsd.edu/software-tools/mixdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3697 ; sc:citation , "pmcid:PMC8916743", "pubmed:35280976" ; sc:description "The R package mixedCCA implements sparse canonical correlation analysis for data of mixed types: continuous, binary or zero-inflated (truncated continuous)." ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:license "Not licensed" ; sc:name "mixedCCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/irinagain/mixedCCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:25225354" ; sc:description "Computes the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%." ; sc:featureList edam:operation_3214 ; sc:name "MixGF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/software-tools/mixgf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC7788837", "pubmed:33407074" ; sc:description """A R package for statistical independence testing of loci in database of multi-locus genotypes. Genetics and Independence Testing of Mixed Genetic Panels. Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package. The goal of mixIndependR is to test the mutual independence of mixed genetic markers.""" ; sc:featureList edam:operation_0488, edam:operation_3196, edam:operation_3891, edam:operation_3920 ; sc:license "GPL-2.0" ; sc:name "mixIndependR" ; sc:url "https://cran.r-project.org/web/packages/mixIndependR/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3307, edam:topic_3391, edam:topic_3569 ; sc:citation , ; sc:description "Kernel-based methods are powerful methods for integrating heterogeneous types of data. mixKernel aims at providing methods to combine kernel for unsupervised exploratory analysis. Different solutions are provided to compute a meta-kernel, in a consensus way or in a way that best preserves the original topology of the data. mixKernel also integrates kernel PCA to visualize similarities between samples in a non linear space and from the multiple source point of view. Functions to assess and display important variables are also provided in the package." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mixKernel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.8" ; sc:url "http://mixkernel.clementine.wf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation." ; sc:featureList edam:operation_0487 ; sc:name "MIXMUL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.csjfann.ibms.sinica.edu.tw/eag/programlist/MIXMUL/MIXMUL.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation ; sc:description """A tool for calculating required masses and volumes for laboratory solutions. Simple calculator for weighing out components of media/buffers/etc. Mixology is a tool that makes it easy to calculate the ingredients needed for media, buffers, etc. First you enter the final volume of buffer at the top. Then on the left hand side you enter the concentrations desired, in any units (mg/ul, uM, % v/v, etc.). The amounts you need to measure out will appear on the right hand side, in the units that you enter there. Mixology automatically extracts molecular weights from ChEBI to make these calculations as smooth as possible.""" ; sc:featureList edam:operation_2422 ; sc:name "Mixology" ; sc:url "http://mixology.science" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3751 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3751 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0602, edam:topic_2269, edam:topic_3172, edam:topic_3308, edam:topic_3391, edam:topic_3474 ; sc:citation , ; sc:description "The tool offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mixomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp , ; sc:url "http://mixomics.org/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3390, edam:topic_3520 ; sc:citation , "pubmed:32479074" ; sc:description """Software for the Dereplication of Mixtures Based on 13C NMR Spectroscopy. 13C-NMR based dereplication software. MixONat allows the dereplication of natural products mixtures using 13C-NMR and DEPT data.""" ; sc:featureList edam:operation_0320, edam:operation_3629, edam:operation_3907 ; sc:name "MixONat" ; sc:url "https://sourceforge.net/projects/mixonat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0654, edam:topic_3303, edam:topic_3325, edam:topic_3673 ; sc:citation ; sc:description """Programmatic Detection of Diploid-Triploid Mixoploidy via Whole Genome Sequencing. Detection and visualization of 2n/3n mixoploidy from a VCF. This repo contains the scripts used to calculate ratios of diploid-triploid mixoploidy within a Whole Genome Sequencing (WGS) sample. The only input requirement is a tabix-indexed VCF file containing a trio (child, mother, father) with alleles depths (AD tag) and call quality (GQ tag). We have tested the scripts using VCF files from GATK3 on human samples.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3629 ; sc:name "mixoviz" ; sc:url "https://github.com/HudsonAlpha/mixoviz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3174, edam:topic_3697, edam:topic_3810 ; sc:citation , "pmcid:PMC9723553", "pubmed:37938691" ; sc:description "MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms." ; sc:featureList edam:operation_0362, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "MIxS-SA" ; sc:url "https://github.com/GenomicsStandardsConsortium/mixs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:21541012" ; sc:description "Software for disease scoring (combining case-only admixture and case-control SNP association signals) in Admixed Populations such as African Americans." ; sc:featureList edam:operation_2238 ; sc:name "MIXSCORE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bogdan.bioinformatics.ucla.edu/software/" ; biotools:primaryContact "Alkes L. Price", "Bogdan Pasaniuc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654 ; sc:citation ; sc:description "Probabilistic model for solving the single individual haplotyping (SIH) or haplotype assembly problem." ; sc:featureList edam:operation_0487 ; sc:name "MixSIH" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://sites.google.com/site/hmatsu1226/software/mixsih" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3293, edam:topic_3569 ; sc:citation "pubmed:25963975" ; sc:description "Mixture of Trees using Expectation Maximization is a species tree reconstruction method." ; sc:featureList edam:operation_3478 ; sc:name "MixTreEM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://prime.scilifelab.se/mixtreem/" ; biotools:primaryContact "Ikram Ullah Khattak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0632, edam:topic_0804, edam:topic_3518 ; sc:citation , "pubmed:33693483" ; sc:description "MixTwice is an R package for large-scale hypothesis testing for peptide arrays by variance mixing. Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local false discovery rate statistics and local false sign rate statistics when provided with data on estimated effects and estimated standard errors from all the measured peptides. As the name suggests, the MixTwice tool involves the estimation of two mixing distributions, one on underlying effects and one on underlying variance parameters" ; sc:featureList edam:operation_3435, edam:operation_3649 ; sc:license "GPL-2.0" ; sc:name "MixTwice" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=MixTwice" ; biotools:primaryContact "Michael A Newton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0797, edam:topic_3053 ; sc:citation "pubmed:19834152" ; sc:description "Multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene." ; sc:featureList edam:operation_2478 ; sc:name "MizBee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.utah.edu/~miriah/mizbee/Overview.html" ; biotools:primaryContact "Miriah Meyer", "Tamara Munzner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC9921313", "pubmed:36777398" ; sc:description "Automatic Polyp Segmentation with Multiple Kernel Dilated Convolution Network." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MKDCNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nikhilroxtomar/MKDCNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3489 ; sc:citation "pubmed:10404623" ; sc:description "Program we use routinely to build each new release of ProDom, Protein domain families automatically generated from protein databases. It relies on the assumption that the shortest amino acid sequence corresponds to a single domain, and may be used as a query to screen the database with the psi-blast program, in order to cluster homologous domains." ; sc:featureList edam:operation_0495 ; sc:name "mkdom" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://prodom.prabi.fr/prodom/xdom/welcome.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0736 ; sc:citation ; sc:description "Algorithm used to build each new release of ProDom. It can be run on any set of protein sequences in a fasta file." ; sc:featureList edam:operation_2403 ; sc:name "MkDom2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://prodom.prabi.fr/prodom/current/documentation/mkdom2.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1954, edam:format_2187 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3210 ; sc:name "Genome index" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:author "Robert Homann" ; sc:citation ; sc:description "Open source program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on our implementation of Manzini's lightweight Deep-Shallow algorithm [1], which can also utilize multiple CPUs/cores for some extra speed-up. The generated output is compatible with the output of mkvtree from the Vmatch package written by Stefan Kurtz." ; sc:featureList edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "mkESA" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bibiserv.cebitec.uni-bielefeld.de/mkesa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3056, edam:topic_3500, edam:topic_3512 ; sc:citation "pubmed:18515345" ; sc:description "Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection." ; sc:featureList edam:operation_0239, edam:operation_0554, edam:operation_3197 ; sc:name "MKT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mkt.uab.es" ; biotools:primaryContact "Antonio Barbadilla", "Raquel Egea", "Sonia Casillas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3047, edam:topic_3318 ; sc:citation , "pmcid:PMC7384070", "pubmed:32282082" ; sc:description """A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations. 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This repository accompanies our work "Machine Learning-Assisted Directed Evolution Navigates a Combinatorial Epistatic Fitness Landscape with Minimal Screening Burden".""" ; sc:featureList edam:operation_0331, edam:operation_2415, edam:operation_3216, edam:operation_3359 ; sc:name "MLDE" ; sc:url "https://github.com/fhalab/MLDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3308, edam:topic_3474 ; sc:citation "pubmed:24520154" ; sc:description "R package  for machine learning (ML)-based differential network analysis of transcriptimic data." ; sc:featureList edam:operation_2497 ; sc:name "mlDNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cmbb.arizona.edu/mlDNA/" ; biotools:primaryContact "Chuang Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32845847" ; sc:description """Multilevel Edge Features Guided Network for Image Denoising. This repository is an official PyTorch implementation of the paper ''Multi-level Edge Features Guided Network for Image Denoising''. (TNNLS 2020). The paper can be downloaded from MLEFGN. Image denoising is a challenging inverse problem due to the complex scenes and information loss.""" ; sc:featureList edam:operation_3443, edam:operation_3927 ; sc:name "MLEFGN" ; sc:url "https://github.com/MIVRC/MLEFGN-PyTorch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pmcid:PMC2732217", "pubmed:18635570" ; sc:description "An R package to analyze computer models of complex systems." ; sc:featureList edam:operation_2238 ; sc:name "mlegp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.1.4" ; sc:url "https://gdancik.github.io/bioinformatics/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC7355841", "pubmed:32392760" ; sc:description """Machine Learning-Based Analysis of Gaze Error Patterns in Consumer Eye Tracking Systems. A machine learning repository for pattern recognition of gaze errors in consumer eye trackers. The MLGaze repository contains python coding resources for gaze data processing such as data augmentation, outlier removal , creation of gaze features for training and machine learning algorithms for classification and modelling of gaze error patterns. The data used for implementing and testing the methods may be found in the Mendeley repository (link below).""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "MLGaze" ; sc:url "https://github.com/anuradhakar49/MLGaze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3336, edam:topic_3375, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC9235472", "pubmed:35758801" ; sc:description "A Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction." ; sc:featureList edam:operation_3660, edam:operation_3926, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MLGL-MP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dubingxue/MLGL-MP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3676 ; sc:description "Processing and analysis of high throughput, long-read (e.g. Roche 454) sequences generated from multiple loci and multiple biological samples. 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It compares the results of the experimental data with theoretic values included in the database. 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Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_3047, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:33675541" ; sc:description "ML-LPA (Machine Learning-assisted Lipid Phase Analysis) is a Python 3 library developed to analyse lipid membranes generated during molecular dynamics (MD) simulation runs in order to predict the phase of each lipid and map the local environment of the lipids in the bilayer." ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "MLLPA" ; sc:softwareHelp , ; sc:url "https://vivien-walter.github.io/mllpa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:35289352" ; sc:description "Drug repositioning based on multi-view learning with matrix completion." ; sc:license "Not licensed" ; sc:name "MLMC" ; sc:url "https://github.com/BioinformaticsCSU/MLMC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_2229, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8223360", "pubmed:34167457" ; sc:description "A web server for predicting multiple sub-cellular localization of mRNA" ; sc:featureList edam:operation_2489, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "mLoc-mRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cabgrid.res.in:8080/mlocmrna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_2229, edam:topic_3063, edam:topic_3068 ; sc:citation , "pubmed:33126250" ; sc:description """A manually curated database of the relations between membraneless organelles and diseases. Membraneless organelles (MLOs) play important roles in the temporal and spatial regulation of various biological processes, and emerging evidence supports that liquid-liquid phase separation (LLPS) is underlying the assembly of MLOs. Dysfunction of MLOs and LLPS are associated with various pathological processes. MloDisDB aims to gather MLOs and LLPS related diseases from the dispersed literature. Each entry was assigned with one of the three evidence levels based on original publication: Direct experiment, Indirect experiment, Clinical Investigation. The functional factors, changes of MLOs and changes of the factors were recorded, the components of MLOs and LLPS related predictions were integrated (go to About for detail).""" ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3454 ; sc:name "MloDisDB" ; sc:url "http://mlodis.phasep.pro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "Mean Log P Analysis." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "MLP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MLP.html" ; biotools:primaryContact "Tobias Verbeke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "mlPhaser is an R package for phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA." ; sc:featureList edam:operation_3454 ; sc:name "mlPhaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.01" ; sc:url "http://cran.r-project.org/web/packages/mlPhaser/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3305, edam:topic_3673 ; sc:author ; sc:citation , , "pmcid:PMC6321875", "pmcid:PMC7018651", "pubmed:30383524", "pubmed:32047136" ; sc:contributor ; sc:description """mlplasmids consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived. It currently classifies short-read contigs as chromosomes and plasmids for Enterococcus faecium, Escherichia coli and Klebsiella pneumoniae.""" ; sc:featureList edam:operation_0525, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mlplasmids" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "V1.0.0", "V2.0.0", "V2.1.0" ; sc:url "https://gitlab.com/sirarredondo/mlplasmids" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:33523131" ; sc:description """An R Package for Machine Learning in Survival Analysis. mlr3proba is a machine learning toolkit for making probabilistic predictions within the mlr3 ecosystem. It currently supports the following tasks:. Probabilistic Supervised Learning for mlr3. Core learners are implemented in mlr3proba, recommended common learners are implemented in mlr3learners, and many more are implemented in mlr3extralearners. Use the interactive search table to search for available learners and see the learner status page for their live status.""" ; sc:featureList edam:operation_0303, edam:operation_3659, edam:operation_3927 ; sc:license "LGPL-3.0" ; sc:name "mlr3proba" ; sc:url "https://github.com/mlr-org/mlr3proba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3518 ; sc:citation , "pmcid:PMC6612842", "pubmed:31510644" ; sc:description "Model-based optimization of subgroup weights for survival analysis | Toolbox for Bayesian Optimization and Model-Based Optimization in R | Model-based optimization with mlr | Issues, Requests and Bug Tracker" ; sc:featureList edam:operation_3659 ; sc:name "mlrMBO" ; sc:url "http://github.com/mlr-org/mlrMBO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3056, edam:topic_3127, edam:topic_3168 ; sc:citation "pubmed:20331786" ; sc:description "Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate." ; sc:featureList edam:operation_3658 ; sc:name "mlRho" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://guanine.evolbio.mpg.de/mlRho/" ; biotools:primaryContact "Haubold B" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3474 ; sc:citation ; sc:description "This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART, to RNA-Seq data." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "MLSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MLSeq.html" ; biotools:primaryContact "Gokmen Zararsiz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation , "pmcid:PMC3318499", "pubmed:22238442" ; sc:description "Multi Locus Sequence Typing from an assembled genome or from a set of reads." ; sc:featureList edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MLST" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.7" ; sc:url "http://cge.cbs.dtu.dk/services/MLST/" ; biotools:primaryContact "Mette Voldby Larsen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Chlamydia trachomatis multilocus sequence typing (MLST) database." ; sc:featureList edam:operation_0224 ; sc:name "MLST-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://mlstdb.bmc.uu.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3174, edam:topic_3324, edam:topic_3673 ; sc:citation , "pmcid:PMC6915855", "pubmed:31842753" ; sc:description """Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework. Deconvoluting the Diversity of Within-host Pathogen Strain in a MLST Framework.""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3629, edam:operation_3840 ; sc:name "MLST_F" ; sc:url "https://github.com/WGS-TB/MLST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2533, edam:topic_3474 ; sc:citation "pubmed:19840377" ; sc:description "Machine learning integration for predicting the effect of single amino acid substitutions on protein stability." ; sc:featureList edam:operation_0474 ; sc:name "MLSTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.prc.boun.edu.tr/appserv/prc/mlsta/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known." ; sc:featureList edam:operation_0547 ; sc:name "MLtree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www2.unil.ch/phylo/bioinformatics/mltree.html" ; biotools:primaryContact "MLtree Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0821, edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:20687950" ; sc:description "Tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments." ; sc:featureList edam:operation_0324 ; sc:name "MLTreeMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mltreemap.org/" ; biotools:primaryContact "http://mltreemap.org/treemap_cgi/treemap_input_page.pl?sessionId=pboNF1ki5uQW&userId=so9xq1rVittY" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3373 ; sc:citation , "pubmed:35953081" ; sc:description "Graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites." ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:name "MLysPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://47.100.136.41:8181" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_2275 ; sc:citation "pubmed:26605745" ; sc:description "Ultrafast and accurate scoring function for protein-protein and protein-ligand docking." ; sc:featureList edam:operation_0482, edam:operation_2464 ; sc:name "MM-ISMSA" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://ub.cbm.uam.es/software/mmismsa.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7255610", "pubmed:32463818" ; sc:description """Welcome to the mmannot Web page. For instance, suppose that you have sequenced your organism of interest with sRNA-Seq (RNA-Seq works too), and you want to know how many times you have sequenced miRNAs, rRNAs, tRNAs, etc. This is what mmannot does.""" ; sc:featureList edam:operation_0362, edam:operation_3192, edam:operation_3800 ; sc:name "mmannot" ; sc:url "https://github.com/mzytnicki/mmannot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0102, edam:topic_2885, edam:topic_3170 ; sc:citation ; sc:description "An analysis pipeline for mapping mutations using RNA-seq. It works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome." ; sc:featureList edam:operation_2429 ; sc:name "MMAPPR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.83" ; sc:url "http://yost.genetics.utah.edu/software.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475, edam:format_3752 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_2332 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2331 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_3343, edam:topic_3520, edam:topic_3524 ; sc:citation , , , "pubmed:18293430", "pubmed:20465224", "pubmed:26831710" ; sc:description "User-friendly and free software to view MS data in a range of formats." ; sc:featureList edam:operation_0366, edam:operation_2421, edam:operation_2929, edam:operation_3215, edam:operation_3435, edam:operation_3441, edam:operation_3627, edam:operation_3629, edam:operation_3631, edam:operation_3632, edam:operation_3646, edam:operation_3694, edam:operation_3695 ; sc:name "mMass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mmass.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2275 ; sc:citation "pubmed:21121048" ; sc:description "Previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient." ; sc:featureList edam:operation_2439 ; sc:name "MMB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://simtk.org/home/rnatoolbox" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1964 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1011 ; sc:encodingFormat edam:format_1964 ; sc:name "EC number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1005 ; sc:encodingFormat edam:format_1964 ; sc:name "HET group name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1705 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_1477, edam:format_3464 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0081 ; sc:description "REST API to access MMB-IRB data repo (PDB, Uniprot, Protein Variants, NA Features)" ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MMB-IRB Data Repository API" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mmb.irbbarcelona.org/api" ; biotools:primaryContact "Josep Ll. Gelpi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation "pubmed:19854940" ; sc:description "Method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays." ; sc:featureList edam:operation_0571 ; sc:name "MMBGX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bgx.org.uk/software/mmbgx.html" ; biotools:primaryContact "Sylvia Richardson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2533 ; sc:citation "pubmed:14511568" ; sc:description "Server of prediction of of MHC class I binders which can bind to wide range of MHC alleles with high affinity. This server has potential to develop sub-unit vaccine for large population." ; sc:featureList edam:operation_1777 ; sc:name "MMBPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/mmbpred/" ; biotools:primaryContact "Dr.G.P.S.Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects" ; sc:featureList edam:operation_0335, edam:operation_2429 ; sc:name "MMCIF Dictionary Suite" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.250" ; sc:url "http://sw-tools.rcsb.org/apps/MMCIF-DICT-SUITE/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0637, edam:topic_2640, edam:topic_3500 ; sc:citation , "pmcid:PMC10050155", "pubmed:36717674" ; sc:description "R package for consensus molecular subtyping of mouse colorectal cancer models." ; sc:featureList edam:operation_3196, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "MmCMS" ; sc:url "https://github.com/MolecularPathologyLab/MmCMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3308, edam:topic_3400, edam:topic_3934 ; sc:citation ; sc:description """The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data. It is distributed as a R package. .""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "mMCP-counter" ; sc:url "https://github.com/cit-bioinfo/mMCP-counter" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199 ; sc:citation , "pmcid:PMC8600011", "pubmed:34805992" ; sc:description "Accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity." ; sc:featureList edam:operation_0331, edam:operation_0420, edam:operation_0478, edam:operation_0480, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "mmCSM-NA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biosig.unimelb.edu.au/mmcsm_na" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation , "pubmed:33893812" ; sc:description "mmCSM-PPI is a tool for predicting the effects of multiple point mutations on protein-protein interactions." ; sc:featureList edam:operation_0331, edam:operation_2409, edam:operation_2492, edam:operation_3435 ; sc:name "mmCSM-PPI" ; sc:softwareHelp , ; sc:url "http://biosig.unimelb.edu.au/mmcsm_ppi" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0154, edam:topic_1317, edam:topic_2275 ; sc:citation "pubmed:12520055", "pubmed:22135289" ; sc:description "Database of molecular modelling of 3-D structures; experimentally determined structures only." ; sc:featureList edam:operation_0322, edam:operation_0346, edam:operation_0360, edam:operation_0477 ; sc:name "MMDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml" ; biotools:primaryContact "Stephen H. Bryant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0625, edam:topic_0659, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6920994", "pubmed:31652812" ; sc:description """A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Murine microbiome database (MMDB) contains 16S rRNA gene-based microbiome taxonomic profiles of the healthy mouse gut microbiota with manually curated metadata. Identify frequently found bacterial species in the gastrointestinal tract of healthy laboratory mice.""" ; sc:featureList edam:operation_3196, edam:operation_3460, edam:operation_3797 ; sc:name "MMDB_Mouse" ; sc:url "http://leb.snu.ac.kr/mmdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3169 ; sc:citation ; sc:description "This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD)." ; sc:featureList edam:operation_3501 ; sc:license "Artistic-2.0" ; sc:name "MMDiff2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MMDiff2.html" ; biotools:primaryContact "Gabriele Schweikert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_2269 ; sc:citation , "pubmed:34416654" ; sc:description "Mitochondrial mixture database and interpretation tool (MMDIT) is an open-source, interactive software for the probabilistic genotyping of mitochondrial DNA mixtures based on complete mitochondrial genomes (mtGenomes). MMDIT can perform both 'Mixture Deconvolution' and 'Mixture Analysis'." ; sc:featureList edam:operation_3454, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MMDIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.unthsc.edu/mmdit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:33130111" ; sc:description "Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis." ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3803 ; sc:name "MMEASE" ; sc:url "https://idrblab.org/mmease/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Enrique Blanco" ; sc:citation ; sc:description "mmeta is a program to produce and to align the TF-maps of multiple promoter regions. mmeta is very powerful to characterize promoter regions from multiple orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mmeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://big.crg.cat/services/mmeta" ; biotools:primaryContact "Enrique Blanco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3303, edam:topic_3678, edam:topic_3697 ; sc:citation , "pubmed:33768631" ; sc:description "Adaptive multi-marker meta-analysis (aMeta) is an R package provides facilities for multi-marker meta analysis (mMeta) and adaptive multi-marker meta-analysis (aMeta) which conduct meta-analyses to combine multiple studies throughout multiple related markers. The R package includes two core functions, mMeta.aMeta and mMeta.aMeta.plot, and one summary data set, HIV.Sum.Data." ; sc:featureList edam:operation_3435, edam:operation_3658, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "mMeta" ; sc:url "https://github.com/hk1785/mMeta" ; biotools:primaryContact , "Ni Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0637, edam:topic_0798, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:33074335" ; sc:description """A database for human metagenomic extrachromosomal mobile genetic elements. Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below)""" ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3460 ; sc:name "mMGE" ; sc:url "https://mgedb.comp-sysbio.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3384 ; sc:citation , "pubmed:35286257" ; sc:description "an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality" ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MMGL" ; sc:url "https://github.com/SsGood/MMGL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3071, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC7065671", "pubmed:32159764" ; sc:description """Database for the mulberry metabolome. The Mulberry Metabolome Database. Comprehensively, freely, and User-friendly.""" ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3803 ; sc:name "MMHub" ; sc:url "https://biodb.swu.edu.cn/mmdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:19420067" ; sc:description "Web server that integrates miRNA and mRNA expression data with predicted miRNA target information. It incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar)." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2454 ; sc:name "MMIA" ; sc:url "http://cancer.informatics.indiana.edu/mmia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC10262779", "pubmed:37306408" ; sc:description "A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm." ; sc:featureList edam:operation_3660, edam:operation_3891, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MMINP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YuLab-SMU/MMINP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3342, edam:topic_3423, edam:topic_3577 ; sc:citation , "pmcid:PMC9452637", "pubmed:36091046" ; sc:description "A mind mapping knowledgebase prototyping tool for precision medicine." ; sc:featureList edam:operation_0224, edam:operation_2429, edam:operation_3196 ; sc:license "Apache-2.0" ; sc:name "MMKP" ; sc:url "https://github.com/ZjuLiangsl/mmkp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:19908387" ; sc:description "Is a software to analyze haplotype polymorphisms in a real human population." ; sc:featureList edam:operation_0487 ; sc:name "MML" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/xlxlxlxinli/mml" ; biotools:primaryContact "Xin Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2269 ; sc:citation , "pmcid:PMC6612809", "pubmed:31510703" ; sc:description "Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors | Minimum Message Length (MML) based aligner of protein (amino acid) sequences | Dependencies: GNUMake or equivalent. A modern C++ compiler. seqMMLigner is known to build with g++ (GCC) >= 4.1.2. If these dependencies are met, follow these instructions:" ; sc:featureList edam:operation_3798 ; sc:name "MMLigner" ; sc:url "http://lcb.infotech.monash.edu.au/seqmmligner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172 ; sc:citation "pubmed:22139941" ; sc:description "Mouse Multiple Tissue Metabolome Database: metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_3561, edam:operation_3627 ; sc:name "MMMDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mmmdb.iab.keio.ac.jp/" ; biotools:primaryContact "Masahiro SUGIMOTO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3174, edam:topic_3305, edam:topic_3360, edam:topic_3837 ; sc:citation ; sc:description "mmmvi is a tool to identify potential SARS-CoV-2 Variants of Concern (VoC) in metagenomic samples." ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MMMVI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dorbarker/voc-identify/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3172, edam:topic_3301 ; sc:citation ; sc:description "This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "mmnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "https://www.rdocumentation.org/packages/mmnet/versions/1.10.2" ; biotools:primaryContact "Fei Li", "Yang Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3315, edam:topic_3382, edam:topic_3520, edam:topic_3524 ; sc:citation , "pmcid:PMC10375467", "pubmed:37490627" ; sc:description "A workflow framework to accelerate the development of experimental simulations." ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "mmodel" ; sc:softwareHelp ; sc:url "http://github.com/marohn-group/mmodel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0622, edam:topic_0637, edam:topic_1775, edam:topic_3174, edam:topic_3366, edam:topic_3387, edam:topic_3473, edam:topic_3697 ; sc:author , "MMP team" ; sc:citation , "pmcid:PMC5753341", "pubmed:29106641" ; sc:contributor ; sc:description "The Marine Metagenomics Portal (MMP) hosts the marine databases MarRef, MarDB, MarFun, and SalDB. These databases provide the marine scientific community with openly accessible, comprehensive microbial genomics and metagenomics resources, including high-quality, manually curated sequences. The user-friendly web interface allows visitors to easily navigate and refine searches within the contextual databases and offers additional BLAST searches, visualizations, downloads, and workflows (via META-pipe)." ; sc:featureList edam:operation_0224, edam:operation_0361, edam:operation_2945, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "CC-BY-ND-3.0" ; sc:name "Marine Metagenomics Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mmp.sfb.uit.no/" ; biotools:primaryContact "MMP team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3518 ; sc:citation ; sc:description "R package compendium for the analysis of murine palate miRNA two-color expression data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "MmPalateMiRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MmPalateMiRNA.html" ; biotools:primaryContact "Guy Brock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0593, edam:topic_0736, edam:topic_3315 ; sc:citation ; sc:description """A distance-assisted multimodal conformation sampling for de novo protein structure prediction. Distance-assisted multimodal conformation sampling for de novo protein structure prediction.""" ; sc:featureList edam:operation_0476, edam:operation_2415, edam:operation_2476 ; sc:name "MMpred" ; sc:url "https://github.com/iobio-zjut/MMpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170 ; sc:citation ; sc:description "Tool for computing gene expression, included duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes." ; sc:featureList edam:operation_0292, edam:operation_2429 ; sc:name "mmquant" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/mzytnicki/multi-mapping-counter" ; biotools:primaryContact "Matthias Zytnicki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0797, edam:topic_3168, edam:topic_3308 ; sc:citation "pubmed:26519503" ; sc:description "Infers optimal mapping locations from the coverage densities of other mapped reads in vicinity." ; sc:featureList edam:operation_2520 ; sc:name "MMR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://raetschlab.org/suppl/MMR" ; biotools:primaryContact "MSKCC – Computational Biology Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3379 ; sc:citation , "pubmed:33821961" ; sc:description "MMRFBiolinks isn R package that extends TCGABiolink package for integrative analysis with MMRF-COMMPASS data. IMMRFBiolinks extends TCGABiolink package for searching, downloading and analyzing MMRF-COMMPASS data available at the NCI’s Genomic Data Commons (GDC) Data Portal." ; sc:featureList edam:operation_0490, edam:operation_2422, edam:operation_3503 ; sc:name "MMRFBiolinks" ; sc:url "https://github.com/marziasettino/MMRFBiolinks" ; biotools:primaryContact "Mario Cannataro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3324, edam:topic_3500, edam:topic_3697 ; sc:citation , "pmcid:PMC8314026", "pubmed:34313795" ; sc:description "The NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA." ; sc:featureList edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MMRRC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://med.unc.edu/mmrrc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description """An R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides. The package mms2plot visualizes multiple tandem mass spectrometry (MS/MS or MS2) for modificated and/or non-modified peptides identified from the same raw MS files, annotated by peptide identification algorithms. It will output a mirror-style plots for two peptide-spectrum matches (PSMs) and an aligned plot for more than two PSMs. MMS2plot features a batch mode and generates the output images in vector graphics file format (i.e. PDF) that facilitate evaluation and publication of the PSM assignment.The output file width is recommended as 3.35 inch (single column) or 7 inch (double column).""" ; sc:featureList edam:operation_0337, edam:operation_3631, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "MMS2plot" ; sc:url "https://github.com/lileir/MMS2plot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation ; sc:description "Alternative web-oriented InChI-based normalization tool developed with the specific aim to efficiently analyze and remove chemical redundancy, minimizing all problems that might affect the performance and the usability of any chemical database." ; sc:featureList edam:operation_3564 ; sc:name "MMsDusty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://mms.dsfarm.unipd.it/MMsDusty/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation "pubmed:21310039" ; sc:description "Pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data." ; sc:featureList edam:operation_2495 ; sc:name "MMSEQ" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/eturro/mmseq" ; biotools:primaryContact "Ernest Turro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623 ; sc:citation ; sc:description "Software suite for very fast protein sequence searches and clustering of huge protein sequence data sets." ; sc:featureList edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MMseqs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/soedinglab/MMseqs" ; biotools:primaryContact "Johannes Söding" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3360, edam:topic_3676 ; sc:citation , "pmcid:PMC8007623", "pubmed:33782531" ; sc:description "mmsig is a tool for flexible and easily interpretable mutational signature analysis. mmsig was developed for hematological malignancies, but can be extended to any cancer with a well-known mutational signature landscape. mmsig is based on an expectation maximization algorithm for mutational signature fitting and applies cosine similarities for dynamic error suppression as well as bootstrapping-based confidence intervals and assessment of transcriptional strand bias." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3227 ; sc:license "Not licensed" ; sc:name "mmsig" ; sc:url "https://github.com/evenrus/mmsig" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3077, edam:topic_3382 ; sc:citation ; sc:description """An open toolbox for accessible structured illumination microscopy. Parent repository for the MMSIM framework which currently includes MMSIMPlugin and MMLiveFFT which are plugins for MicroManager. MMSIMPlugin modifies MicroManager to produce multiple frames per MicroManager "frame" for microscopy systems like SIM. MMLiveFFT provides a live Power frequency spectrum of the live image which is useful for system alignment and quality control.""" ; sc:featureList edam:operation_2428, edam:operation_3431, edam:operation_3552 ; sc:name "mmSIM" ; sc:url "https://github.com/ctr26/MMSIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation ; sc:description "Web-oriented database of commercially-available compounds for virtual screening and chemoinformatics applications. It contains over 4 million non-redundant chemical compounds in 3D formats." ; sc:featureList edam:operation_0224 ; sc:name "MMsINC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:url "http://mms.dsfarm.unipd.it/MMsINC/search/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258 ; sc:description "Web-oriented tool developed with the specific aim to calculate chemical similarity indexes between a query structure and a chemical database." ; sc:featureList edam:operation_3502 ; sc:name "MMsSimilarity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareVersion "1" ; sc:url "http://mms.dsfarm.unipd.it/ChemUtils/SimpleSimilarity/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_2275 ; sc:citation "pubmed:15099834" ; sc:description "Can be used for replica exchange calculations with sander. This package also facilitates other Amber tasks, such as dealing in a consistent way with an ensemble of conformations, massaging PDB files, and carrying out some common types of structural analysis." ; sc:featureList edam:operation_2406 ; sc:name "MMTSB toolset" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://blue11.bch.msu.edu/mmtsb/Main_Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "MMV_Im2Im is an open-source Python package for image-to-image transformation in bioimaging applications. MMV_Im2Im is designed with a generic image-to-image transformation framework that can be used for a wide range of tasks, including semantic segmentation, instance segmentation, image restoration, and image generation, etc.. Our implementation takes advantage of state-of-the-art machine learning engineering techniques, allowing researchers to focus on their research without worrying about engineering details." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MMV_Im2Im" ; sc:url "https://github.com/MMV-Lab/mmv_im2im" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2830, edam:topic_3379, edam:topic_3930, edam:topic_3966 ; sc:citation , "pmcid:PMC8533362", "pubmed:34679165" ; sc:description "Vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0560 ; sc:isAccessibleForFree true ; sc:name "MMVdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.mmvdb.dqweilab-sjtu.com/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3746 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_1915 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_1915 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3301 ; sc:citation ; sc:description "Neural networks for estimating microbe-metabolite interactions through their co-occurence probabilities." ; sc:featureList edam:operation_0337, edam:operation_3664 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "mmvec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biocore/mmvec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3452 ; sc:citation , "pmcid:PMC4853872", "pubmed:27140159" ; sc:description "MMX-I is a data-processing software for multimodal X-ray imaging and tomography." ; sc:featureList edam:operation_3443 ; sc:license "MIT" ; sc:name "MMX-I" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/antoinebergamaschi/mmx-i/overview" ; biotools:primaryContact "Antoine Bergamaschi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0634, edam:topic_0659, edam:topic_3068 ; sc:citation , "pubmed:32833025" ; sc:description """Mammal ncRNA-disease repository with increased coverage and annotation. Mammalian ncRNA-Disease Repository. MNDR v3.1: Mammal NcRNA-Disease Repository. MNDR (Mammalian ncRNA-Disease Repository) is a database that curated associations between ncRNA and disease. Here, we have updated the MNDR to version 3.1 by integrating experimentally supported and predicted ncRNA-disease associations curated from manual literatures and other resources. MNDR v3.1 currently contains more than one million ncRNA-disease entries, including 6,301 miRNAs, 39,880 lncRNAs, 20,256 circRNAs, 10,894 piRNAs and 521 snoRNAs with over 1,600 diseases, and an increase of species coverage to 11 mammals.""" ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_2489 ; sc:name "MNDR" ; sc:softwareVersion "3.0" ; sc:url "http://www.rna-society.org/mndr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3300, edam:topic_3384 ; sc:citation , "pmcid:PMC9390980", "pubmed:35990374" ; sc:description "Organizing electrophysiological data into the BIDS format and facilitating their analysis." ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MNE-BIDS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mne.tools/mne-bids/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3168, edam:topic_3316, edam:topic_3944 ; sc:citation , "pubmed:34100911" ; sc:description "MNHN Tree Tools are a set of programs to investigate a database of sequences, and its \"evolution\", with a plethora of options." ; sc:featureList edam:operation_0291, edam:operation_0292, edam:operation_0323 ; sc:isAccessibleForFree true ; sc:license "zlib-acknowledgement" ; sc:name "MNHN-Tree-Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.in2p3.fr/mnhn-tools/mnhn-tree-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3336 ; sc:citation "pubmed:17406508" ; sc:description "Algorithm to identify the gene targets of a drug treatment based on gene-expression data. In a typical use of the algorithm, a single expression profile, say obtained as a result of a treatment under study, is used as the test profile while a set of hundreds of expression profiles is used as the training set." ; sc:featureList edam:operation_3439 ; sc:name "MNI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dibernardo.tigem.it/softwares/mode-of-action-by-network-inference-mni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:33604806" ; sc:description """An Open-Source Tool for Computing Subtraction Ictal Single-Photon Emission CT Coregistered to MRI. MNI SISCOM is a Windows/Mac/Linux desktop and command line application for computing Subtraction ictal single-photon emission CT coregistered to MRI (SISCOM). The underlying Python library that implements the functionality of MNI SISCOM is also available on PyPi. Please cite the following paper if you use MNI SISCOM in a paper: [reference to come]. A simple command line tool and GUI for computing subtraction ictal SPECT coregistered to MRI (SISCOM). mnisiscom is exclusively intended for research use!.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:license "MPL-2.0" ; sc:name "MNI SISCOM" ; sc:url "https://github.com/jeremymoreau/mnisiscom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3520 ; sc:citation , "pmcid:PMC9941872", "pubmed:36824227" ; sc:description "Predicting human microbe-disease association via a method to minimize matrix nuclear norm." ; sc:featureList edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MNNMDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Haiyan-Liu666/MNNMDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9472403", "pubmed:36104797" ; sc:description "MntJULiP is a method for comprehensively and accurately quantifying splicing differences at intron level from collections of RNA-seq data." ; sc:featureList edam:operation_0264, edam:operation_0433, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MntJULiP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/splicebox/MntJulip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3308, edam:topic_3315, edam:topic_3336 ; sc:citation , "pmcid:PMC8275331", "pubmed:34252937" ; sc:description "Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding." ; sc:featureList edam:operation_3501, edam:operation_3928, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MoAble" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dmis-lab/moable" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_2830 ; sc:citation , "pubmed:34661627" ; sc:description "A multi-outcome interaction identification approach" ; sc:featureList edam:operation_3503 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MOAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/moaitool/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3794 ; sc:citation , "pmcid:PMC7071693", "pubmed:32171255" ; sc:description """Efficient software for detection of enriched regions of MeRIP-Seq. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) is a popular sequencing method for studying RNA modifications and, in particular, for N6-methyladenosine (m6A), the most abundant RNA methylation modification found in various species.""" ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3501 ; sc:name "MoAIMS" ; sc:url "https://github.com/rreybeyb/MoAIMS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined." ; sc:featureList edam:operation_0238 ; sc:name "MoAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://moan.binf.ku.dk/" ; biotools:primaryContact "Eivind Valen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3305, edam:topic_3360, edam:topic_3673 ; sc:citation , "pmcid:PMC7660255", "pubmed:32969786" ; sc:description """Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.""" ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_3431, edam:operation_3432 ; sc:name "MOB-suite" ; sc:url "https://github.com/phac-nml/mob-suite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0798, edam:topic_3174 ; sc:description """MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies The MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically if you do not specify an alternate database location.""" ; sc:name "mob_suite" ; sc:softwareVersion "3.1.7" ; sc:url "https://github.com/phac-nml/mob-suite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "Web server to detect and visualise flexible regions in NMR solved structures." ; sc:featureList edam:operation_2487 ; sc:name "Mobi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://protein.bio.unipd.it/mobi/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2007 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2331, edam:format_3464 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3538 ; sc:citation , , , , "pmcid:PMC7779018", "pubmed:22661649", "pubmed:25361972", "pubmed:29136219", "pubmed:33237329" ; sc:description "Database of protein disorder and mobility annotations." ; sc:featureList edam:operation_0224, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "MobiDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp , ; sc:softwareVersion "5" ; sc:url "https://mobidb.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2548, edam:format_3464 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation "pubmed:28453683" ; sc:description "MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions" ; sc:featureList edam:operation_2480, edam:operation_3092 ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "MobiDB-lite" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://protein.bio.unipd.it/mobidblite/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Plug-in" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:36765247" ; sc:description "Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "MoBIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mobie.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0798, edam:topic_3174 ; sc:citation , "pubmed:36036594" ; sc:description "A Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements." ; sc:featureList edam:operation_0427, edam:operation_0578, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "mobileOG-db" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mobileogdb.flsi.cloud.vt.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3277, edam:topic_3361 ; sc:citation , "pubmed:31898294" ; sc:description """A free user-friendly application for collecting experience sampling data. mobileQ is a free, open-source web dashboard and Android smartphone application developed by the research group of quantitative psychology and individual differences at KU Leuven to enable researchers to perform experience sampling or ecological momentary assessment (ESM/EMA) studies and interventions in an easy, intuitive, and accessible way.""" ; sc:name "mobileQ" ; sc:url "https://mobileQ.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:34898430" ; sc:description "Extremely Efficient RGB-D Salient Object Detection." ; sc:featureList edam:operation_3436, edam:operation_3454, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "MobileSal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yuhuan-wu/mobilesal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3172 ; sc:citation , "pubmed:35781328" ; sc:description "An R package for effective mobility transformation of CE-MS data." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "MobilityTransformR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/MobilityTransformR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3168, edam:topic_3336 ; sc:citation "pubmed:15640440", "pubmed:16414954", "pubmed:17537813" ; sc:description "Tool for high-throughput genomic island discovery." ; sc:featureList edam:operation_0238, edam:operation_0430, edam:operation_0452, edam:operation_3228, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "MobilomeFINDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://db-mml.sjtu.edu.cn/MobilomeFINDER/" ; biotools:primaryContact "Hong-Yu Ou", "Kumar Rajakumar", "Zixin Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3297, edam:topic_3500, edam:topic_3810 ; sc:citation , , "pmcid:PMC7401664", "pubmed:32645982" ; sc:description """A unifying concept of animal breeding programs. Simulation Study on the Integration of Health Traits in Horse Breeding Programs. Developed and optimized in Google Chrome. Added Sharing of projects between users (03/11/20). More convenient input for Manuel Select (selection of cohorts for BVE - 03/11/20).""" ; sc:featureList edam:operation_0282, edam:operation_0554, edam:operation_3196 ; sc:name "MoBPS-GC" ; sc:url "http://www.mobps.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3511 ; sc:citation "pubmed:25348035" ; sc:description "Used to detect novel (non-reference) Mobile Element Insertion (MEI) events in BAM files and uses both a discordant read pair method and a split-read method." ; sc:featureList edam:operation_0253 ; sc:name "Mobster" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mobster/" ; biotools:primaryContact "Jayne Y Hehir-Kwa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3056, edam:topic_3299, edam:topic_3673 ; sc:citation , "pmcid:PMC7672894", "pubmed:33203356" ; sc:description """The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. Model-based tumour subclonal deconvolution.""" ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3629 ; sc:name "mobster-R" ; sc:url "https://caravagnalab.github.io/mobster/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3068, edam:topic_3407 ; sc:citation , "pubmed:35876789" ; sc:description "A comprehensive Python library for simulating cancer development with Phase Field Models." ; sc:featureList edam:operation_2426, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "Mocafe" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioComputingUP/mocafe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2269 ; sc:citation "pubmed:20226024" ; sc:description "Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM." ; sc:featureList edam:operation_3658 ; sc:name "Mocapy++" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/mocapy/" ; biotools:primaryContact "Martin Paluszewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. 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We have built a set of pre-trained models called Generic Autodidactic Models, nicknamed Models Genesis, because they are created ex nihilo (with no manual labeling), self-taught (learned by self-supervision), and generic (served as source models for generating application-specific target models). We envision that Models Genesis may serve as a primary source of transfer learning for 3D medical imaging applications, in particular, with limited annotated data.""" ; sc:featureList edam:operation_0335, edam:operation_3443, edam:operation_3553 ; sc:name "Models-Genesis" ; sc:url "https://github.com/MrGiovanni/ModelsGenesis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3292, edam:topic_3407, edam:topic_3955 ; sc:citation ; sc:description """The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes. The ModelSEED is a resource for the reconstruction, exploration, comparison, and analysis of metabolic models.""" ; sc:featureList edam:operation_2421, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "ModelSEED" ; sc:url "https://modelseed.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0654, edam:topic_3293 ; sc:citation "pubmed:16845102", "pubmed:9918953" ; sc:description "Program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses." ; sc:featureList edam:operation_0550 ; sc:name "ModelTest" ; sc:url "http://darwin.uvigo.es/software/modeltest_server.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:22216865" ; sc:description "Computational tool that reconstructs gene regulatory networks from high throughput experimental data." ; sc:featureList edam:operation_3439 ; sc:name "ModEnt" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/modent/" ; biotools:primaryContact "Guy Karlebach" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2269, edam:topic_3169, edam:topic_3375 ; sc:citation , "pmcid:PMC7203737", "pubmed:31999322" ; sc:description """First-order Markov modeling and discovery of monomeric and dimeric binding motifs. MODER2 is implemented in C++ and has been tested in Linux platform. As the only external dependency, the MODER2 requires the Boost library, which is normally installed on Linux machines. Relatively recent version should be used.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "MODER2" ; sc:url "https://github.com/jttoivon/moder2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097 ; sc:citation ; sc:description "Program for comparative modeling of RNA 3D structures." ; sc:featureList edam:operation_2478, edam:operation_2481 ; sc:license "GPL-1.0" ; sc:name "ModeRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genesilico.pl/moderna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0625, edam:topic_3125 ; sc:citation , "pmcid:PMC4086063", "pubmed:24838561" ; sc:description "MODEST: A web-based tool for rapid and effective design of optimal multiplex automated genome engineering (MAGE) oligos based on simple input, to achieve any mutation possible with MAGE. The tool is useful in oligonucleotide-mediated genome engineering and recombineering." ; sc:featureList edam:operation_0308, edam:operation_0331, edam:operation_0451, edam:operation_3196 ; sc:name "MODEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://modest.biosustain.dtu.dk" ; biotools:primaryContact "MODDEST Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_2275 ; sc:citation ; sc:description "MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general." ; sc:featureList edam:operation_2479 ; sc:name "MODexplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://modorama.org/modexplorer/index/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2814 ; sc:citation , "pubmed:33972023" ; sc:description "The ModFlex server provides an interface with multiple options and tools, which make it possible to explore structural diversity in the available modeling templates and make an optimal choice. The server uses information from the previously developed PDBFlex database which is focused on structural flexibility and conformational diversity of proteins. The PDBFlex database contains structures that were extracted from the PDB and clustered based on sequence identity, such that each cluster represents an individual protein. The structures in each cluster were further grouped into subclusters based on structural similarity, such that each subcluster represents a distinct conformation of the protein. Thus, each cluster represents a protein, while each subcluster represents a specific conformation of that protein." ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_3767 ; sc:name "ModFlex" ; sc:url "https://modflex.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_1476 ; sc:name "Mathematical model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130 ; sc:citation , "pmcid:PMC5570241", "pubmed:28460136" ; sc:description "Global and local quality estimation of 3D protein models. It integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0321 ; sc:name "ModFOLD6" ; sc:softwareHelp ; sc:url "http://www.reading.ac.uk/bioinf/ModFOLD/" ; biotools:primaryContact "Dr Liam J. McGuffin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:23620298" ; sc:description "Webserver for the estimation of both global and local (per-residue) quality of 3D protein models. It produces both machine readable and graphical output." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0322, edam:operation_0331, edam:operation_0477 ; sc:name "ModFOLD4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.reading.ac.uk/bioinf/ModFOLD/" ; biotools:primaryContact "Dr Liam J. McGuffin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation "pubmed:16845006" ; sc:description "Tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide." ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3627, edam:operation_3645, edam:operation_3755 ; sc:name "MODi" ; sc:url "http://prix.uos.ac.kr/research.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3170, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:32271876" ; sc:description """An Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks. R package for robust disease module identification.""" ; sc:featureList edam:operation_3435, edam:operation_3625, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "MODifieR" ; sc:url "https://gitlab.com/Gustafsson-lab/MODifieR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2306 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:citation , ; sc:description "Extend or shrink a list of genomic coordinates." ; sc:featureList edam:operation_2409 ; sc:name "modifygenomiccoordinates" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080 ; sc:citation , ; sc:description "Extend or shring a list of sequences." ; sc:featureList edam:operation_0369, edam:operation_3436 ; sc:name "modifysequencelist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3295 ; sc:citation , "pubmed:36094338" ; sc:description "MODIG is a GAT-based model designed for generating gene repre-sentation from a multi-dimensional gene network for the identifica-tion of cancer driver genes, which mainly performed three steps to integrate multi-omics data and multiple gene associations." ; sc:featureList edam:operation_0314, edam:operation_0533, edam:operation_3927 ; sc:license "Not licensed" ; sc:name "MODIG" ; sc:url "https://github.com/zjupgx/modig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:19483690" ; sc:description "Mixture of Distributions Indel Locator, a novel method for finding medium sized indels from high throughput sequencing datasets." ; sc:featureList edam:operation_0279, edam:operation_0452, edam:operation_2478, edam:operation_3197 ; sc:name "MoDIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://compbio.cs.toronto.edu/modil/" ; biotools:primaryContact "MoDIL support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3305, edam:topic_3315 ; sc:citation , "pmcid:PMC9375249", "pubmed:35990010" ; sc:description "An automated online software for modeling epidemics." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "ModInterv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://fisica.ufpr.br/modinterv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0123, edam:topic_2830, edam:topic_3301 ; sc:citation ; sc:description "Package for the design, classification and visual representation of peptide data." ; sc:featureList edam:operation_3095, edam:operation_3482 ; sc:name "modlAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rossa-prod-ap11.ethz.ch/delivery/DeliveryManagerServlet?dps_pid=IE4903447" ; biotools:primaryContact "Gisbert Schneide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0654, edam:topic_0769, edam:topic_3169, edam:topic_3382 ; sc:citation , "pmcid:PMC9710047", "pubmed:36451166" ; sc:description "MoDLE is a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes." ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_2476, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MoDLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/paulsengroup/modle" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1218 ; sc:name "Protein sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0736 ; sc:author , "Oriol Fornes" ; sc:citation , "pmcid:PMC2687990", "pubmed:15883372", "pubmed:19357100" ; sc:description "A tool predicts protein fold domain and family by means of sequence similarity and a relevant number of similar interactions (the same partners or is potential homologs)." ; sc:featureList edam:operation_0474 ; sc:name "ModLink+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://sbi.imim.es/modlink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:24497192" ; sc:description "Tool for advanced analysis of biological networks. Given two biological networks, it seeks a set of modules, each representing strongly connected nodes in the first network, that are also strongly interconnected in the second network." ; sc:featureList edam:operation_3439 ; sc:name "ModMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://acgt.cs.tau.ac.il/modmap/" ; biotools:primaryContact "David Amar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation , "pmcid:PMC4133046", "pubmed:25122495" ; sc:description "MODMatcher is a multi-omics data matcher for integrative genomic analysis." ; sc:featureList edam:operation_0335, edam:operation_2945 ; sc:name "MODMatcher" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://research.mssm.edu/integrative-network-biology/Software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0821, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33835459" ; sc:description "MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes." ; sc:featureList edam:operation_2421, edam:operation_3432, edam:operation_3929 ; sc:name "MODOMICS" ; sc:url "http://www.genesilico.pl/modomics" ; biotools:primaryContact "Pietro Boccaletto" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0893 ; sc:name "Sequence-structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation , ; sc:description "At MODORAMA two applications can be run: MODexplorer, an integrated tool for exploring protein sequence, structure and function relationships, and MODalign, a rich alignment editor to improve target-template alignments" ; sc:featureList edam:operation_0474, edam:operation_0477, edam:operation_2089 ; sc:name "MODORAMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://modorama.org" ; biotools:primaryContact "Jan Kosinski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2258, edam:topic_2814 ; sc:citation ; sc:description "Fast ab initio structure prediction of protein-bound peptides." ; sc:featureList edam:operation_0474 ; sc:name "MODPEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/modpep/" ; biotools:primaryContact "Sheng-You Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_3510 ; sc:citation "pubmed:24872426" ; sc:description "New, easy-to-use webserver for the prediction of binding partners for modular protein domains. The server comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively." ; sc:featureList edam:operation_3760 ; sc:name "MoDPepInt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://modpepint.informatik.uni-freiburg.de/" ; biotools:primaryContact "Rolf Backofen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_0769, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc:description "ModPhred is an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. modPhred is a pipeline for detection, annotation and visualisation of DNA/RNA modifications from raw ONT data. The pipeline consists of four steps / modules: modEncode (Encoding modification probabilities in FastQ), modAlign (Build alignments keeping modification information in BAMs), modReport (Extraction of RNA modification information and QC reports), and modAnalysis (Plotting venn diagrams (mod_plot.py), co-occurrence of modifications and per-read clustering based on modification profiles)." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_0417 ; sc:license "MIT" ; sc:name "ModPhred" ; sc:softwareHelp ; sc:url "https://github.com/novoalab/modPhred" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601, edam:topic_3510 ; sc:citation "pubmed:24888500" ; sc:description "Software package and web tool that predicts up to 23 types of post-translational modifications." ; sc:featureList edam:operation_0417 ; sc:name "ModPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://montana.informatics.indiana.edu/ModPred/" ; biotools:primaryContact "Pejaver, V" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_2814 ; sc:citation "pubmed:17478500" ; sc:description "Server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides." ; sc:featureList edam:operation_0252, edam:operation_0321, edam:operation_0322, edam:operation_0477, edam:operation_0481 ; sc:name "MODPROPEP" ; sc:url "http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2275, edam:topic_2814 ; sc:citation ; sc:description "An algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field." ; sc:featureList edam:operation_0322 ; sc:name "ModRefiner" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "20111024" ; sc:url "http://zhanglab.ccmb.med.umich.edu/ModRefiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:25542927" ; sc:description "Program using modified screening and ranking algorithm to detect chromosome copy number variations. It is an optimal and accurate approach solving practical issues regarding CNV detection." ; sc:featureList edam:operation_2423 ; sc:name "modSaRa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://c2s2.yale.edu/software/modSaRa/" ; biotools:primaryContact "Feifei Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3293 ; sc:citation , "pmcid:PMC5860124", "pubmed:28453611" ; sc:description "modSaRa is an R package designed to perform copy number variants identification." ; sc:featureList edam:operation_0282 ; sc:license "GPL-2.0" ; sc:name "modSaRa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://publichealth.yale.edu/c2s2/software/modSaRa/" ; biotools:primaryContact "Heping Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3360, edam:topic_3399, edam:topic_3512 ; sc:citation "pubmed:20128910" ; sc:description "Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. A method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. These modular biomarkers are applied to assign novel aging-related functions to poorly characterized longevity genes." ; sc:featureList edam:operation_1781, edam:operation_2454, edam:operation_3463, edam:operation_3501 ; sc:name "Modular Subnetwork Biomarker Identification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.utoronto.ca/~juris/data/GB10/" ; biotools:primaryContact "Igor Jurisica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8336963", "pubmed:34348892" ; sc:description "ModTect is a tool for identifying sites of RNA modifications that disrupts base-pairing using typical RNA-sequencing datasets" ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ModTect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ktan8/ModTect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3170, edam:topic_3306, edam:topic_3308 ; sc:citation , "pmcid:PMC7992795", "pubmed:33761871" ; sc:description "ModularBoost is an efficient network inference algorithm based on module decomposition." ; sc:featureList edam:operation_2437, edam:operation_3625, edam:operation_3659, edam:operation_3891 ; sc:name "ModularBoost" ; sc:url "https://github.com/cosinalee/ModularBoost" ; biotools:primaryContact "Jianming Zhang", "Wei Zhang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation ; sc:description "An itemset mining framework for the detection of cis-regulatory modules." ; sc:featureList edam:operation_0438 ; sc:name "ModuleDigger" ; sc:operatingSystem "Linux" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Sun_2009_ModuleDigger/Index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3518 ; sc:citation "pubmed:19819296" ; sc:description "Novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs." ; sc:featureList edam:operation_0438, edam:operation_3659 ; sc:name "ModuleMaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/welcome_e.html" ; biotools:primaryContact "Andreas Zell", "Klaus Harter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Software package proposing a synthetic view of a set of DNA sequences by providing both a segmentation of them into domains and a classification on the basis of these domains." ; sc:featureList edam:operation_2403 ; sc:name "moduleorganizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.genouest.org/spip.php?page=outils&id_rubrique=113&lang=en" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2259 ; sc:citation "pubmed:21827286" ; sc:description "Software for finding cliques and near-cliques in a protein-protein interaction network." ; sc:featureList edam:operation_3439 ; sc:name "ModuleSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bclab.inha.ac.kr/ModuleSearch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0621, edam:topic_0622, edam:topic_3500 ; sc:citation , "pmcid:PMC8982048", "pubmed:35380657" ; sc:description "A web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses." ; sc:featureList edam:operation_2436, edam:operation_3559, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "MOET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rgd.mcw.edu/rgdweb/enrichment/start.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3306, edam:topic_3336, edam:topic_3375, edam:topic_3407 ; sc:citation ; sc:description "MOFA is a Multi-Objective Flux Analysis for the COBRA Toolbox." ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_4009 ; sc:license "GPL-2.0" ; sc:name "MOFA" ; sc:url "https://bbs.llnl.gov" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:name "Sequence motif (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:27898063" ; sc:description "A modest Feature Finder to extract features in MS1 Data." ; sc:featureList edam:operation_3092 ; sc:name "MoFF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/compomics/moFF" ; biotools:primaryContact "Lennart Martens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:citation , "pubmed:29624378" ; sc:description "MoFi annotates glycoprotein mass spectra by integrating hybrid data from the intact protein and glycopeptide level." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MoFi" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/cdl-biosimilars/mofi/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3172, edam:topic_3518 ; sc:citation , "pmcid:PMC7039010", "pubmed:31956905" ; sc:description """A workbench for interactive exploratory data analysis of large expression datasets. MetaOmGraph (MOG) is a Java software to interactively explore and visualize large datasets. MOG overcomes the challenges posed by big size and complexity of big datasets by efficient handling of data files by using a combination of data indexing and buffering schemes. By incorporating metadata, MOG adds another dimension to the analyses and provides flexibility in data exploration. MOG allows users to explore their own data on their local machines.""" ; sc:featureList edam:operation_2940, edam:operation_2943, edam:operation_3463, edam:operation_3891 ; sc:license "MIT" ; sc:name "MOG" ; sc:url "https://github.com/urmi-21/MetaOmGraph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170 ; sc:citation ; sc:description """A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks. MOGAMUN is a Multi Objective Genetic Algorithm to find active modules (i.e., highly connected subnetworks with an overall deregulation) in MUltiplex biological Networks. For a detailed description of MOGAMUN check out the preprint https://www.biorxiv.org/content/10.1101/2020.05.25.114215v1. All the expression datasets and networks that we used to obtain the results reported in our preprint are available in the GitHub repository https://github.com/elvanov/MOGAMUN-data.""" ; sc:featureList edam:operation_2495, edam:operation_3436, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "MOGAMUN" ; sc:url "https://github.com/elvanov/MOGAMUN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0804, edam:topic_2275 ; sc:citation "pubmed:26722115" ; sc:description "Useful tool for converting chromosomal contact data into 3D genome models to provide a better view into the spatial organization of genomes." ; sc:featureList edam:operation_2480 ; sc:name "MOGEN" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://calla.rnet.missouri.edu/mogen/" ; biotools:primaryContact "Cheng J" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3115 ; sc:encodingFormat edam:format_3033 ; sc:name "Microarray metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3391, edam:topic_3518 ; sc:citation ; sc:description "This package provide a method for doing gene set analysis based on multiple omics data." ; sc:featureList edam:operation_0571, edam:operation_3744 ; sc:license "GPL-2.0" ; sc:name "mogsa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mogsa.html" ; biotools:primaryContact "Chen Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC6816163", "pubmed:31660850" ; sc:description """Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues. Moiety Modeling implemented in Python. moiety_modeling package provides facilities for moiety model representation, model optimization and model selection. Welcome to moiety_modeling’s documentation! — moiety_modeling 1.0.3.2 documentation. The model selection results produced by moiety_modeling framework using the UDP-GlcNAc isotopologue datasets. ‘moiety_modeling’ runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following depencies and you are ready to go!. Welcome to moiety_modeling’s documentation!¶. 'moiety_modeling' runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following depencies and you are ready to go!.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3660 ; sc:license "BSD-3-Clause" ; sc:name "moiety_modeling" ; sc:softwareHelp ; sc:url "https://figshare.com/articles/moiety_modeling_framework/7886135" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3572 ; sc:citation ; sc:description "MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems." ; sc:featureList edam:operation_2409, edam:operation_2428, edam:operation_2945 ; sc:name "MOIRAI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20140528" ; sc:url "http://sourceforge.net/projects/moirai/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3398 ; sc:citation , "pmcid:PMC8136780", "pubmed:33956139" ; sc:description "MoiRNAiFold is a tool for complex in silico RNA design." ; sc:featureList edam:operation_0483 ; sc:name "MoiRNAiFold" ; sc:url "https://moiraibiodesign.com/design/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_2275, edam:topic_3299 ; sc:citation "pubmed:20529921" ; sc:description "Automated computational tool for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.)." ; sc:featureList edam:operation_2483 ; sc:name "MOITF-EM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ai.stanford.edu/~mitul/motifEM/" ; biotools:primaryContact "Mitul Saha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3173, edam:topic_3303, edam:topic_3308 ; sc:citation , "pmcid:PMC9235504", "pubmed:35758807" ; sc:description "A fast and universal method for integration of multimodal single-cell data." ; sc:featureList edam:operation_3435, edam:operation_3891, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MOJITOO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CostaLab/MOJITOO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC8022319", "pubmed:33596079" ; sc:description "Fast and Flexible Semisupervised Learning for Peptide Detection" ; sc:featureList edam:operation_3631, edam:operation_3767, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "mokapot" ; sc:url "https://github.com/wfondrie/mokapot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0749, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:34428290" ; sc:description "Mol2Context-vec provides a deep context aware molecular representation to drive the boundaries for drug discovery. It can integrate different levels of internal states to bring abundant molecular structure information." ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Mol2Context-vec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lol88/Mol2Context-vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC7454275", "pubmed:32778891" ; sc:description """A soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm. MolAICal is a drug design software combined by artificial intelligence and classical programming. MolAICal is freely for education, academic and other non-profit purposes. If you want to use MolAICal for any commercial purpose, you should contact with licensors (Email: molaical@yeah.net).""" ; sc:featureList edam:operation_2476, edam:operation_3899, edam:operation_3938 ; sc:name "MolAICal" ; sc:url "https://molaical.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "This is a tool for Molar Conversions." ; sc:name "Molar Conversions" ; sc:url "https://www.creativebiomart.net/resource/tools.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0166, edam:topic_0820, edam:topic_3518 ; sc:citation "pubmed:18448468" ; sc:description "The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output." ; sc:featureList edam:operation_0270, edam:operation_0384, edam:operation_0387, edam:operation_1816, edam:operation_3351 ; sc:name "MolAxis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinfo3d.cs.tau.ac.il/MolAxis" ; biotools:primaryContact "Eitan Yaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0176, edam:topic_3047 ; sc:citation , "pubmed:32931272" ; sc:description """A VMD Graphical User Interface Featuring Molecule Manipulation. Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks. For instance, translation or rotation of a selected molecule(s) or part(s) of a molecule, which are currently only can be achieved using tcl scripts. Here, we use tcl script develop a user-friendly GUI for VMD, named Molcontroller, which is featured by allowing users to quickly and conveniently perform various molecular manipulations. This GUI might be helpful for improving the modeling efficiency of VMD users.""" ; sc:featureList edam:operation_0337, edam:operation_0477, edam:operation_2476 ; sc:name "Molcontroller" ; sc:url "https://github.com/ChenchenWu-hub/Molcontroller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3324, edam:topic_3336, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description "Molecular Benchmark for Disease and Target Based Machine Learning." ; sc:featureList edam:operation_3216, edam:operation_3359, edam:operation_3937, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MolData" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Transilico/MolData" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_2275, edam:topic_3332 ; sc:citation "pubmed:10721501" ; sc:description "Package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format." ; sc:featureList edam:operation_2409 ; sc:name "MOLDEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cmbi.ru.nl/molden/molden.html" ; biotools:primaryContact "G.Schaftenaar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3520 ; sc:citation ; sc:description """Learning Mass Spectrometry Fragmentation of Small Molecules. MolDiscovery is a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by (i) utilizing an efficient algorithm to generate mass spectrometry fragmentations, and (ii) learning a probabilistic model to match small molecules with their mass spectra. A search of over six million spectra from global natural product social molecular networking infrastructure shows that our probabilistic model can identify nearly twice more small molecules than previous method.""" ; sc:featureList edam:operation_3647, edam:operation_3649, edam:operation_3801, edam:operation_3803, edam:operation_3860 ; sc:name "molDiscovery" ; sc:url "https://github.com/mohimanilab/molDiscovery" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2878 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Protein structural motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_0820, edam:topic_0821 ; sc:author "Martin Petrek" ; sc:citation , ; sc:contributor "Jaroslav Koča", "Karel Berka", "Michal Otyepka", "Radka Svobodová Vařeková", "Veronika Navrátilová" ; sc:description "Location and basic characterization of channels in molecular structures." ; sc:featureList edam:operation_0250, edam:operation_0570, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MOLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Masaryk University, Brno, Czech Republic", "Palacký University, Olomouc, Czech Republic" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://mole.chemi.muni.cz" ; biotools:primaryContact "David Sehnal", "Lukáš Pravda" . a sc:SoftwareApplication ; 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The model works by learning pKa related chemical patterns automatically and building reliable predictors with learned features." ; sc:featureList edam:operation_3927, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MolGpKa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://xundrug.cn/molgpka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0209 ; sc:citation , "pubmed:35695435" ; sc:description "A Web Server for Structure-Based Drug Design by Molecular Hybridization." ; sc:featureList edam:operation_0482, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MolHyb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://molhyb.xundrug.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3301 ; sc:author "Aurelien Barré" ; sc:citation , "pmcid:PMC308848", "pubmed:14681420" ; sc:contributor , "Pascal Sirand-Pugnet" ; sc:description "Database dedicated to the comparative genomics of bacteria belonging to the class Mollicutes. It provides annotated sequence data and analysis for 72 genomes belonging to 51 species. The database provides genome and genetic element pages, homology relationship defined by various methods, pre-computed statistics, metabolic pathways, and a huge collection of tools for exploring and comparing genomes." ; sc:featureList edam:operation_0362, edam:operation_3209 ; sc:isAccessibleForFree true ; sc:name "Molligen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Centre de Bioinformatique de Bordeaux (CBiB)", "u-bordeaux.fr" ; sc:softwareHelp , ; sc:softwareVersion "4" ; sc:url "https://services.cbib.u-bordeaux.fr/molligen4/" ; biotools:primaryContact "Aurélien Barré" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0166, edam:topic_3125, edam:topic_3534 ; sc:citation "pubmed:19465382" ; sc:description "Web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues." ; sc:featureList edam:operation_0387, edam:operation_2483, edam:operation_3351, edam:operation_3666 ; sc:name "MolLoc" ; sc:url "http://bcb.dei.unipd.it/MolLoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Plug-in" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0623, edam:topic_0821, edam:topic_3308 ; sc:citation , "pmcid:PMC8059625", "pubmed:33813885" ; sc:description "MolluscDB is a genome and transcriptome database for molluscs." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3258, edam:operation_3436 ; sc:license "Apache-2.0" ; sc:name "MolluscDB" ; sc:url "https://molluscdb.org" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation ; sc:description "A structured database that provides best practice-based protocols for molecular analyses." ; sc:featureList edam:operation_0224 ; sc:name "MolMeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://www.molmeth.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:36108142" ; sc:description "PharmaMind®-MolMiner is a rule-free OCSR (Optical Chemical Structure Recognition) learning system. It aims to transform the vectorization problem into object detection tasks. That means it is able to extract chemical elements in an object detection manner by training well-labelled datasets with atom and bond annotations." ; sc:featureList edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MolMiner" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/iipharma/pharmamind-molminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082, edam:topic_0097, edam:topic_0176 ; sc:citation "pubmed:12520056" ; sc:description "The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available." ; sc:featureList edam:operation_0244, edam:operation_0279, edam:operation_2406, edam:operation_2481 ; sc:name "MolMovDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molmovdb.org/" ; biotools:primaryContact "Bo Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0605, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:35849817" ; sc:description "A lightweight self-attention-based method focused on spatial structure of molecular graph for drug-drug interactions prediction." ; sc:featureList edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Molormer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/IsXudongZhang/Molormer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2275, edam:topic_3071 ; sc:description "PDB to POV file (POV-Ray) converter and molecular visualization tool for MS Windows.The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format." ; sc:featureList edam:operation_0335, edam:operation_0337 ; sc:name "MolPOV" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.0" ; sc:url "https://richardson.chem.ufl.edu/software/molpov-molecular-images/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:35961924" ; sc:description "MolPredictX is a web tool that allows the scientific community to obtain biological activities predictions of molecules. MolPredictX manages predictive models already published in indexed scientific articles and makes predictions of molecules the researcher wishes to investigate. It informs the qualitative prediction of the molecules, as well as a probability quantitative value of activity. 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It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0322, edam:operation_1844, edam:operation_2428 ; sc:name "MolProbity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molprobity.biochem.duke.edu/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0593, edam:topic_2828 ; sc:citation , "pmcid:PMC6933861", "pubmed:31724275" ; sc:description """CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. File Upload/Retrieval (more options). CCTBX, which powers this version of MolProbity (4.2), requires stricter adherence to PDB format. If you are having trouble with version 4.2 try using MolProbity4 legacy version 4.02 at http://rutile.biochem.duke.edu. Note that not all features are supported on legacy 4.02 and we suggest repairing your PDB format instead.""" ; sc:featureList edam:operation_0321, edam:operation_0479, edam:operation_3891 ; sc:name "MolProbity_3D" ; sc:url "http://molprobity.manchester.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1317, edam:topic_2814, edam:topic_2828 ; sc:citation ; sc:description "A program for automated molecular replacement in the case where a homologous structure has already been identified." ; sc:featureList edam:operation_0477, edam:operation_2406, edam:operation_3455 ; sc:isAccessibleForFree true ; sc:name "MolRep" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ccp4.ac.uk/html/molrep.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description """A Deep Representation Learning Library for Molecular Property Prediction. MolRep is a Python package for fairly measuring algorithmic progress on chemical property datasets. It currently provides a complete re-evaluation of 16 state-of-the-art deep representation models over 16 benchmark property datsaets.""" ; sc:featureList edam:operation_0310, edam:operation_3359, edam:operation_3659 ; sc:license "MIT" ; sc:name "MolRepp" ; sc:url "https://github.com/biomed-AI/MolRep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36971363" ; sc:description "Image-to-graph model that translates a molecular image to its chemical structure." ; sc:featureList edam:operation_0303, edam:operation_0394, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MolScribe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/thomas0809/MolScribe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC10097503", "pubmed:37056719" ; sc:description "Search-based multi-objective molecular generation and property optimization." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MolSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/illidanlab/MolSearch" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3603 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics." ; sc:featureList edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MolStar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "https://molstar.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0593, edam:topic_0602, edam:topic_0611, edam:topic_2828 ; sc:citation , "pubmed:33956157" ; sc:description "Mol* Viewer is web app for 3D visualization and analysis of large biomolecular structures. Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB)" ; sc:featureList edam:operation_0321, edam:operation_0337, edam:operation_2476, edam:operation_4009 ; sc:name "Molstar Viewer" ; sc:softwareHelp ; sc:url "https://molstar.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3047 ; sc:citation "pubmed:12824324" ; sc:description "Graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures." ; sc:featureList edam:operation_0570, edam:operation_2480 ; sc:name "MolSurfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://projects.h-its.org/dbase/molsurfer/index.html" ; biotools:primaryContact "Dirk Walther", "Rebecca Wade" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0982 ; sc:encodingFormat edam:format_1196 ; sc:name "Molecule identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1710 ; sc:encodingFormat edam:format_3814 ; sc:name "Structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3303, edam:topic_3318, edam:topic_3336 ; sc:citation , "pubmed:36939644" ; sc:description "A tool for the rapid generation of favorable tautomer in aqueous solution." ; sc:featureList edam:operation_0387 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MolTaut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://moltaut.xundrug.cn" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:33070179" ; sc:description """Molecular interaction transformer for drug target interaction prediction. Drug target interaction (DTI) prediction is a foundational task for in-silico drug discovery, which is costly and time-consuming due to the need of experimental search over large drug compound space.""" ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3938 ; sc:license "BSD-3-Clause" ; sc:name "MolTrans" ; sc:url "https://github.com/kexinhuang12345/moltrans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3047, edam:topic_3292 ; sc:citation , "pubmed:29464735" ; sc:description """molUP is a free VMD extension that allows you to open and save Gaussian files. This tool can be used to analyze results from Gaussian output files and prepare Gaussian input files. molUP provides also a set of tools to adjust bond lengths, rotate angles and dihedral angles directly on VMD. With molUP, it is possible to add and remove atoms or molecules using VMD.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:name "molUP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.7.0" ; sc:url "https://biosim.pt/molup/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1710 ; sc:name "Structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3314 ; sc:description "Chemical sketching and molecular modeling made easy" ; sc:featureList edam:operation_0337, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "MolView" ; sc:url "https://molview.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0769, edam:topic_3382, edam:topic_3500 ; sc:citation , "pubmed:32573714" ; sc:description """Streamlining the design and rendering of molecular movies. A Python script to automate the production of molecular movies in VMD. Molywood is there to make cool molecular movies for you. Specifically, molywood automatizes the most tedious steps in generation of these movies, i.e. scripting in TCL, rendering, generating overlays and combining frames, as well as merging frames into the final movie:.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3431 ; sc:name "Molywood" ; sc:url "http://gitlab.com/KomBioMol/molywood" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:19228804" ; sc:description "Short-read mapping" ; sc:featureList edam:operation_3198 ; sc:name "MOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hugheaves/MOM" ; biotools:primaryContact "H. L. Eaves" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Plug-in" ; sc:applicationSubCategory edam:topic_0204, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "Takes specific advantage of the geometry of the device to accurately segment and track cells using only phase-contrast images, and further provides a curation user interface with leveraged-editing, meaning that a set of related errors are often fixed with a single click." ; sc:featureList edam:operation_1781, edam:operation_3443 ; sc:name "MoMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fjug/MoMA" ; biotools:primaryContact "Florian Jug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_0176, edam:topic_0602 ; sc:citation "pubmed:23671332" ; sc:description "Web server for simulating protein-ligand unbinding. It computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms. The PDB file provided as input may contain several ligands." ; sc:featureList edam:operation_0322, edam:operation_0478, edam:operation_0482, edam:operation_2476 ; sc:name "MoMA-LigPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://moma.laas.fr" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2085 ; sc:encodingFormat edam:format_1476 ; sc:name "Structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_3277 ; sc:citation , "pubmed:34432000" ; sc:description "MoMA-LoopSampler is a method to exhaustively sample the conformational space of protein loops. It exploits structural information encoded in a large library of three-residue fragments, and enforces loop-closure using a closed-form inverse kinematics (IK) solver. A novel reinforcement-learning-based approach is applied to accelerate sampling while preserving diversity." ; sc:featureList edam:operation_0480, edam:operation_0481, edam:operation_3283 ; sc:isAccessibleForFree true ; sc:name "MoMA-LoopSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://moma.laas.fr/applications/LoopSampler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC7984561" ; sc:description "Momba is a Python framework for dealing with quantitative models centered around the JANI-model interchange format. Momba strives to deliver an integrated and intuitive experience to aid the process of model construction, validation, and analysis. It provides convenience functions for the modular construction of models effectively turning Python into a syntax-aware macro language for quantitative models. Momba's built-in exploration engine allows gaining confidence in a model, for instance, by rapidly prototyping a tool for interactive model exploration and visualization, or by connecting it to a testing framework. Finally, thanks to the JANI-model interchange format, several state-of-the-art model checkers and other tools are readily available for model analysis." ; sc:featureList edam:operation_3799, edam:operation_3891, edam:operation_3927 ; sc:license "MIT" ; sc:name "Momba" ; sc:softwareHelp ; sc:url "https://github.com/koehlma/momba" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382 ; sc:citation , "pubmed:32149637" ; sc:description """Multi-Objective Matrix Normalization for Fine-grained Visual Recognition. Bilinear pooling achieves great success in fine-grained visual recognition (FGVC). Recent methods have shown that the matrix power normalization can stabilize the second-order information in bilinear features, but some problems, e.g., redundant information and over-fitting, remain to be resolved. In this paper, we propose an efficient Multi-Objective Matrix Normalization (MOMN) method that can simultaneously normalize a bilinear representation in terms of square-root, low-rank, and sparsity. These three regularizers can not only stabilize the second-order information, but also compact the bilinear features and promote model generalization. In MOMN, a core challenge is how to jointly optimize three non-smooth regularizers of different convex properties. To this end, MOMN first formulates them into an augmented Lagrange formula with approximated regularizer constraints""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3935 ; sc:name "MOMN" ; sc:url "https://github.com/mboboGO/MOMN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0602 ; sc:citation , "pubmed:33165517" ; sc:description "Accurate Biological Network Alignment Through Optimal Neighborhood Matching Between Focal Nodes." ; sc:featureList edam:operation_0491, edam:operation_3094, edam:operation_3925 ; sc:name "MONACO" ; sc:url "https://github.com/bjyoontamu/MONACO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0623, edam:topic_3382 ; sc:citation ; sc:description "A novel Gene Ontology enrichment analysis visualisation system." ; sc:featureList edam:operation_2942, edam:operation_3501, edam:operation_3559 ; sc:license "GPL-3.0" ; sc:name "MonaGO" ; sc:url "http://monago.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0632, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6886866", "pubmed:31738756" ; sc:description """MoNaS is a pipeline to genotype mosquito's voltage-gated sodium channel genes using NGS data. (Mosquito Na+ channel mutation Search).""" ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3196, edam:operation_3216 ; sc:name "MoNaS" ; sc:url "https://github.com/ItokawaK/MoNaS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """An open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces. Note: This repository contains the scRNA-Seq analysis software. For other tools named Monet, see Disambiguation. This repository contains gene lists and the scRNA-Seq datasets using in the analyses presented in Monet paper (Wagner, 2020). Monet is an open-source Python package for analyzing and integrating scRNA-Seq data using PCA-based latent spaces. Datasets from the Monet paper (Wagner, 2020) can be found in a separate repository.""" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3432 ; sc:license "BSD-3-Clause" ; sc:name "Monet-RNA" ; sc:url "https://github.com/flo-compbio/monet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2885, edam:topic_3172, edam:topic_3360 ; sc:citation , "pubmed:34694378" ; sc:description "MoNET is an R package providing network analysis of -omics findings. It is built on top of an integrated network, including metabolite-protein interactions, protein interactions and relationships between genetic variations and transcription factor binding sites." ; sc:featureList edam:operation_0276, edam:operation_2437, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MoNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JW-Yan/MONET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:22689643" ; sc:description "Web server that can identify the modules, homologous modules (called module family), and MMI networks across multiple species for the query protein(s)." ; sc:featureList edam:operation_3439 ; sc:name "MoNetFamily" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://monetfamily.life.nctu.edu.tw/" ; biotools:primaryContact "Chun-Yu Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3365 ; sc:citation , "pmcid:PMC4797132", "pubmed:26987515" ; sc:description "Modular Network Generation and Visualization Platform with Knowledge Integration Environments (MONGKIE) is a software platform that integrates network visualization with omics data analysis tools." ; sc:featureList edam:operation_2422 ; sc:license "AGPL-3.0" ; sc:name "MONGKIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://yjjang.github.io/mongkie/" ; biotools:primaryContact "Yeongjun Jang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3407 ; sc:citation , "pmcid:PMC4205847", "pubmed:25291352" ; sc:description "MONGOOSE (MetabOlic Network GrOwth Optimization Solved Exactly) is a package for structural analysis and refinement of constraint-based metabolic networks. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results certifiably accurate" ; sc:featureList edam:operation_2425, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MONGOOSE" ; sc:softwareHelp ; sc:url "http://cb.csail.mit.edu/cb/mongoose/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:citation ; sc:description "A Pangenomics Index for Finding MEMs." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3198, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MONI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maxrossi91/moni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:15575972" ; sc:description "MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_0448 ; sc:name "MONKEY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://labs.csb.utoronto.ca/moses/monkey.html" ; biotools:primaryContact "Michael B Eisen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3419, edam:topic_3444 ; sc:citation , "pmcid:PMC7198896", "pubmed:32410977" ; sc:description """A Toolbox for Connectivity-Based Parcellation of Monkey Brain. MonkeyCBP (A toolbox for connectivity-based parcellation of monkey brain).""" ; sc:featureList edam:operation_0337, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MonkeyCBP" ; sc:url "https://github.com/bheAI/MonkeyCBP_CLI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0749, edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description """A Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins. Codes for "MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins". The benchmark dataset described in this paper can be found in ./data/, and the creation of this dataset can be reproduced by the protocol in ./create_dataset/.""" ; sc:featureList edam:operation_0272, edam:operation_0478, edam:operation_2492, edam:operation_3094 ; sc:name "MONN" ; sc:url "https://github.com/lishuya17/MONN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053 ; sc:citation "pubmed:18689846" ; sc:description "Finds meaningful partitions using semi-supervised class discovery." ; sc:featureList edam:operation_2436 ; sc:name "MonoClad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.cs.technion.ac.il/people/zohar/MonoClad/software.html" ; biotools:primaryContact "Tomer Shlomi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1213 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1713 ; sc:encodingFormat edam:format_2032 ; sc:name "Fate map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3519 ; sc:citation , , "pmcid:PMC5330805", "pubmed:28114287" ; sc:description "This tool performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. It also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well." ; sc:featureList edam:operation_3439, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "monocle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/monocle.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_0611 ; sc:citation "pubmed:29395788" ; sc:description "An automatic method for determing local resolution of 3D elecron microscopy maps. MonoRes is available via the Xmipp and Scipion software packages" ; sc:featureList edam:operation_2238, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MonoRes" ; sc:url "http://scipion.i2pc.es/" ; biotools:primaryContact "J.L. Vilas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2746 ; sc:name "MonosaccharideDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2313 ; sc:encodingFormat edam:format_2331 ; sc:name "Carbohydrate report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152 ; sc:citation ; sc:description "Information on the residues used in glycan databases." ; sc:featureList edam:operation_0224 ; sc:name "Monosaccharide database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.monosaccharidedb.org/" ; biotools:primaryContact "Thomas Lütteke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data. It takes a list of bam files as input and outputs a vcf file containing the detected SNVs." ; sc:featureList edam:operation_0484 ; sc:license "Not licensed" ; sc:name "Monovar" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/hamimzafar/monovar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation "pubmed:15215451" ; sc:description "MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site." ; sc:featureList edam:operation_0475 ; sc:license "Not licensed" ; sc:name "MONSTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://monster.northwestern.edu/" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3517, edam:topic_3676, edam:topic_3958 ; sc:citation , "pmcid:PMC7905641", "pubmed:33627065" ; sc:description "A new tool for high-throughput detection of mosaic copy number variation." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3961 ; sc:license "GPL-3.0" ; sc:name "Montage" ; sc:url "https://github.com/CAG-CNV/MONTAGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0209, edam:topic_0821, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:33982793" ; sc:description "MonteCarbo is a software to generate and dock multifunctionalized ring molecules. It is able to construct simple 5-, 6- and 7-membered ring multifunctionalized monosaccharides and nucleobases and to dock them into target glyco- and RNA DNA- active enzymes." ; sc:featureList edam:operation_2476, edam:operation_4009 ; sc:license "GPL-3.0" ; sc:name "MonteCarbo" ; sc:url "https://github.com/drsalonsogil/montecarbo" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC8461247", "pubmed:34567063" ; sc:description "MONTI is a tool for analyzing large multi-omics cancer cohort data in association with clinical featuers" ; sc:featureList edam:operation_3435, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MONTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/inukj/MONTI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0157 ; sc:citation , , ; sc:description "A suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions." ; sc:featureList edam:operation_0239 ; sc:license "GPL-3.0" ; sc:name "MOODS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.cs.helsinki.fi/group/pssmfind/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_2640 ; sc:citation , "pubmed:28456671" ; sc:description "The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role. We present an R/bioconductor package which returns a list of candidate driver genes for specific cancer types based on TCGA expression data. 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Bhalla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36723817" ; sc:description "Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores." ; sc:featureList edam:operation_3185, edam:operation_3258, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MoP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biocorecrg/MOP2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3315, edam:topic_3407 ; sc:citation ; sc:description """A Python package for metabolic modelling and topological analysis. Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, amongst others, differential equations based modeling of metabolic systems, constraint based modeling and topological analysis of metabolic networks. Most of these methods are well established and are implemented in numerous software packages, but these are scattered between different programming languages, packages and syntaxes. This complicates establishing straight forward pipelines integrating model construction and simulation""" ; sc:featureList edam:operation_2426, edam:operation_3660, edam:operation_3929 ; sc:name "moped" ; sc:url "https://gitlab.com/marvin.vanaalst/moped" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_2885, edam:topic_3172, edam:topic_3173 ; sc:citation ; sc:description "R-shiny application for the simulation and power calculation of multi-omics studies." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MOPower" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hsyed.shinyapps.io/MOPower/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3678 ; sc:citation ; sc:description "Identification and characterization of periodic fluctuations in time-series data." ; sc:featureList edam:operation_3565 ; sc:license "GPL-3.0" ; sc:name "MoPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MoPS.html" ; biotools:primaryContact "Philipp Eser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3335, edam:topic_3407, edam:topic_3411 ; sc:citation , "pmcid:PMC7016191", "pubmed:32051506" ; sc:description "Multimorbidity networks in adult general population. Analysis of type 2 diabetes mellitus comorbidity." ; sc:featureList edam:operation_3925 ; sc:name "MorbiNet" ; sc:url "https://morbinet.org/shiny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3366, edam:topic_3372, edam:topic_3473 ; sc:citation ; sc:description "Mobile client able to integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools." ; sc:featureList edam:operation_2409, edam:operation_3761, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mORCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "uma.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bitlab-es.com/morca/" ; biotools:primaryContact "Esteban Pérez-Wohlfeil" . a sc:SoftwareApplication ; 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sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "moreThanANOVA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hanchen.shinyapps.io/moreThanANOVA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC8957949", "pubmed:35350759" ; sc:description "A package for molecular recognition feature function prediction based on multi-label learning and ensemble learning" ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_1777, edam:operation_3904 ; sc:license "Not licensed" ; sc:name "MoRF-FUNCpred" ; sc:url "https://github.com/LiangYu-Xidian/MoRF-FUNCpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3510 ; sc:citation "pubmed:27174932" ; sc:description "New computational approach for a fast and accurate prediction of MoRFs(Molecular Recognition Features) in protein sequences." ; sc:featureList edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MoRFCHiBi" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.chibi.ubc.ca/faculty/joerg-gsponer/gsponer-lab/software/morf_chibi/" ; biotools:primaryContact "Nawar Malhis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "MORFEE (Mutation on Open Reading FramE annotation) is a tool (R package) that, from a VCF file, detects and annotates single nucleotide variants creating premature ATG codons." ; sc:featureList edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MORFEE" ; sc:url "https://daissi.github.io/MORFEE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3321 ; sc:citation , "pmcid:PMC4137093", "pubmed:25096057" ; sc:description "Meta-analysis based orthology finder using symmetrical best hits." ; sc:featureList edam:operation_2403 ; sc:name "morFeus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bio.biochem.mpg.de/morfeus/" ; biotools:primaryContact "BH Habermann", "M Volkmer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3064, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8451065", "pubmed:34494114" ; sc:description "MOrgAna (Machine-learning based Organoids Analysis) to segment and analyse 2D multi-channel images of organoids." ; sc:featureList edam:operation_3443, edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MOrgAna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LabTrivedi/MOrgAna.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC7744578", "pubmed:33328504" ; sc:description """Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors. MORLD is a molecule optimization method based on reinforcement learning and docking. This repository provides the source code of the main part of the MORLD software and its usage. Molecule Optimization by Reinforcement Learning and Docking. MORLD is a molecule optimization method based on reinforcement learning and docking.""" ; sc:featureList edam:operation_2489, edam:operation_3899, edam:operation_3938 ; sc:license "Apache-2.0" ; sc:name "MORLD" ; sc:url "http://morld.kaist.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:23204403" ; sc:contributor ; sc:description "Algorithm to associate candidate genes with a given target pathway. Unlike any other algorithm in plant sciences, this algorithm tests multiple combinations by learning how to choose among various forms of evidence (large scale data sets) to link genes to a specific target pathway." ; sc:featureList edam:operation_2497 ; sc:name "MORPH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/morph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3334, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "An open-source ImageJ plugin that automatizes the data extraction process of morphological features of single microglial cells." ; sc:featureList edam:operation_2409, edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MorphData" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/anabelacampos/MorphData" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3407 ; sc:citation , "pmcid:PMC5867296", "pubmed:29616063" ; sc:description """Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants. 1. MORPH bulk run command line interface. Get MORPH candidate gene predictions for your gene(s) of interest. 2. Install morph-bulk using Singularity (recommended). Get MORPH candidate gene predictions for your pathway or GO term of interest for your favourite organism(s). Make a MORPH network for your process of interest. 3. Install morph-bulk the classical way. Perform complex SPARQL queries on MORPH prediction data. rdf Generate RDF graph (for MorphDB).""" ; sc:featureList edam:operation_0224, edam:operation_2454, edam:operation_3463, edam:operation_3929 ; sc:name "MorphDB" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A proteomics search algorithm specifically designed for high-resolution tandem mass spectra." ; sc:featureList edam:operation_3646 ; sc:license "MIT" ; sc:name "Morpheus" ; sc:softwareHelp ; sc:url "https://cwenger.github.io/Morpheus/" ; biotools:primaryContact "Craig Wenger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3604 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3449 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Cell migration track image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3877, edam:format_3997 ; sc:name "Trajectory data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3870 ; sc:encodingFormat edam:format_3603, edam:format_3752 ; sc:name "Trajectory data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2259, edam:topic_2840, edam:topic_3064, edam:topic_3306, edam:topic_3376, edam:topic_3569, edam:topic_3895 ; sc:author , ; sc:citation , "pmcid:PMC3998129", "pubmed:24443380" ; sc:contributor ; sc:description "Morpheus is an open-source modeling and simulation framework for multi-scale and multicellular biological systems. The GUI allows to construct and simulate models from gene regulation, metabolism and signaling to tissue morphogenesis and their multi-scale feedbacks without the need to program. Morpheus is based on declarative modeling in biological terms and mathematical expressions and internally uses the domain-specific language MorpheusML, allowing for rapid model prototyping without extra code-compilation. Morpheus supports cell-based model formalisms, ODEs, PDEs, rule-based models, SBML models etc. (all freely coupled) as well as image-based modeling. It renders results in customizable 2D and 3D images or movies and offers analysis tools to extract features right during simulation. The plugin architecture makes it extensible. Binary installers are available for all major OS from the Morpheus homepage together with online courses, a public model repository and many more resources." ; sc:featureList edam:operation_2426, edam:operation_3926, edam:operation_3927 ; sc:funder "Deutsche Forschungsgemeinschaft (DFG)" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Morpheus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , ; sc:softwareVersion "2.2" ; sc:url "https://morpheus.gitlab.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_2229, edam:topic_3383, edam:topic_3474 ; sc:citation , "pubmed:32567069" ; sc:description """An automated tool for unbiased and reproducible cell morphometry. A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2. MORPHEUS is a Fiji ImageJ2 plugin for the automated evaluation of cell morphometry from cell cultures images acquired by fluorescence microscopy.""" ; sc:featureList edam:operation_3457 ; sc:name "MORPHEUS_IJ" ; sc:url "https://sourceforge.net/projects/morpheus-for-fiji/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_2259, edam:topic_2815 ; sc:citation "pubmed:24861622" ; sc:description "Web-based bioinformatics tool to study human diseases using model organism genes." ; sc:featureList edam:operation_3439 ; sc:name "MORPHIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.inetbio.org/morphin/" ; biotools:primaryContact "Sohyun Hwang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3500, edam:topic_3954 ; sc:citation , "pmcid:PMC8800241", "pubmed:35093113" ; sc:description "An unsupervised machine learning workflow to detect the activation of microglia and astrocytes." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MORPHIOUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jsilburt/Morphious" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0092, edam:topic_2229 ; sc:citation "pubmed:24132424" ; sc:description "Cross-platform, open-source application for the visualization and processing of 3D biological datasets." ; sc:featureList edam:operation_3443 ; sc:name "MorphoGraphX" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www.morphographx.org/" ; biotools:primaryContact "Richard Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3382 ; sc:citation "pubmed:27412086" ; sc:description "Library that proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins." ; sc:featureList edam:operation_3443, edam:operation_3695 ; sc:name "MorphoLibJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ijpb.github.io/MorphoLibJ/" ; biotools:primaryContact "Philippe Andrey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3315, edam:topic_3452 ; sc:citation , "pubmed:32865237" ; sc:description """An R package for long bone landmarking, cortical thickness, and cross-sectional geometry mapping. morphomap at each section extracts two sets of semilandmarks, cortical thickness, cortical area and the parameters useful for cross-sectional Geometry. morphomap returns also 2D and 3D cortical maps. The morphomap package from a single input (an oriented 3D mesh) is capable to produce the output suitable for thickness geometry, shape analysis and cross-sectional geometry. Morphometric Maps, Bone Landmarking and Cross Sectional Geometry. Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.""" ; sc:featureList edam:operation_2429 ; sc:license "GPL-2.0" ; sc:name "morphomap" ; sc:url "https://github.com/AProfico/morphomap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3064, edam:topic_3071, edam:topic_3307 ; sc:citation , , "pmcid:PMC6597584" ; sc:description "MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "MorphoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.1.3-35b3182" ; sc:url "https://morphonet.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0611 ; sc:citation ; sc:description """Transport-based interpolation between EM maps with UCSF ChimeraX. MorphOT is a plugin for ChimeraX, which allows users to directly interpolate multiple density maps. It relies on adapting and optimizing for EM maps some recent methods of shape interpolation based on optimal transport (OT), resulting in significant improvement in quality of morphing, compared with the standard command provided withChimeraX. For more details on the method, please see the appendix here and the paper accompanying the software.""" ; sc:featureList edam:operation_2429, edam:operation_3890 ; sc:name "MorphOT" ; sc:url "https://github.com/kdd-ubc/MorphOT.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269 ; sc:citation , "pubmed:35323864" ; sc:description "The package MorphoTools2 is intended for multivariate analyses of morphological data." ; sc:featureList edam:operation_2938, edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MorphoTools2" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://cran.r-project.org/package=MorphoTools2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3314 ; sc:description "Simulink realization of Morris-Lecar neuron model." ; sc:featureList edam:operation_3450 ; sc:isAccessibleForFree true ; sc:name "Morris-Lecar model MATLAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/20112-simulink-realization-of-morris-lecar-neuron-model" ; biotools:primaryContact "Guan Wenye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:19780815" ; sc:description "Software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone." ; sc:featureList edam:operation_3664 ; sc:name "mosaic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zoology.ubc.ca/prog/mosaic/" ; biotools:primaryContact "Leithen K. M’Gonigle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_0780, edam:topic_3068, edam:topic_3500 ; sc:citation , "pmcid:PMC10235418", "pubmed:37264011" ; sc:description "A unified trait database to complement structured population models." ; sc:featureList edam:operation_0324, edam:operation_2422, edam:operation_3283, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "MOSAIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mosaicdatabase.web.ox.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0804, edam:topic_3400 ; sc:citation "pubmed:17187074" ; sc:description "Will generate candidate vaccine protein cocktails that optimize the coverage, by a small set of mosaic proteins that could be included in a vaccine cocktail, of potential T-cell epitopes in a large diverse set of proteins." ; sc:featureList edam:operation_2430 ; sc:name "Mosaic Vaccine Designer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hiv.lanl.gov/content/sequence/MOSAIC/makeVaccine.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_2840, edam:topic_3292, edam:topic_3375 ; sc:citation , "pubmed:33982382" ; sc:description "The MOSAIC bioacc application is a turn-key web tool providing bioaccumulation factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3454 ; sc:name "MOSAICbioacc" ; sc:softwareHelp ; sc:url "https://mosaic.univ-lyon1.fr/bioacc" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0621, edam:topic_3382 ; sc:citation , "pmcid:PMC7953913", "pubmed:33763206" ; sc:description "MosaicExplorerJ is an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection." ; sc:featureList edam:operation_2409, edam:operation_3443, edam:operation_3552 ; sc:license "GPL-3.0" ; sc:name "MosaicExplorerJ" ; sc:softwareHelp ; sc:url "https://github.com/SebastienTs/MosaicExplorerJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169 ; sc:citation ; sc:description "This package provides functions for fitting MOSAiCS-HMM, an statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification." ; sc:featureList edam:operation_2478 ; sc:license "GPL-2.0" ; sc:name "mosaics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mosaics.html" ; biotools:primaryContact "Dongjun Chung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_3306 ; sc:citation , "pubmed:36333911" ; sc:description "A software suite for analysis of membrane structure and dynamics in simulated trajectories." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MOSAICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MOSAICS-NIH/MOSAICS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:citation , , "pmcid:PMC3944147", "pmcid:PMC4051166", "pubmed:24599324", "pubmed:24708189" ; sc:description "Reference guided aligner/assembler." ; sc:featureList edam:operation_0310 ; sc:license "GPL-2.0" ; sc:name "MOSAIK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wanpinglee/MOSAIK" ; biotools:primaryContact "Wan Ping Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2640, edam:topic_3172, edam:topic_3474 ; sc:citation ; sc:description "Multi-algorithm Ensemble Biclustering Method MoSBi (Molecular Signature Identification using Biclustering)" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "MoSBi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.lrz.de/lipitum-projects/mosbi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275, edam:topic_3047 ; sc:citation "pubmed:11885962" ; sc:description "Program to view atomic structures of protein molecules. Beyond its basic molecular graphics functions, extension modules provides custom functions for research works in structural biology and computational molecular biology." ; sc:featureList edam:operation_2480 ; sc:name "MOSBY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://staff.aist.go.jp/yutaka.ueno/mosby/index.html" ; biotools:primaryContact "Yutaka Ueno" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:encodingFormat edam:format_3620 ; sc:name "Map data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_2331 ; sc:name "Quality control report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_3475 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2711 ; sc:encodingFormat edam:format_1929 ; sc:name "Genome report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3603 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3174, edam:topic_3941 ; sc:author ; sc:citation ; sc:description "Meta-Omics Software for Community Analysis" ; sc:featureList edam:operation_0327, edam:operation_0362, edam:operation_0524, edam:operation_3192, edam:operation_3219, edam:operation_3282, edam:operation_3672, edam:operation_3800, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MOSCA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , , ; sc:softwareVersion "1.3.6" ; sc:url "https://github.com/iquasere/MOSCA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3168, edam:topic_3577 ; sc:citation ; sc:description "This code executes the Multi-Omic Single-Cell Analysis using TensOr regression (MOSCATO) method which uses multi-omic, single-cell data with two data types, X and G, and a univariate outcome which follows an exponential family distribution. In summary, it will estimate the similarity and perform tensor regression using the similarity as the predictor tensor. The features will be selected by applying an elastic net constraint on the coefficient vectors, and any non-zero coefficients will correspond to the features selected. In addition to applying MOSCATO, code to simulate multi-omic, single-cell data is also provided." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MOSCATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lorinmil/MOSCATO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0769, edam:topic_3315 ; sc:citation , "pubmed:33931885" ; sc:description "Molecular simulation design framework (MoSDeF) Cassandra is a complete Python interface for the Cassandra Monte Carlo software." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3893 ; sc:license "MIT" ; sc:name "MoSDeF Cassandra" ; sc:softwareHelp ; sc:url "https://github.com/MaginnGroup/mosdef_cassandra" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3315, edam:topic_3372 ; sc:citation , "pubmed:36791286" ; sc:description "Python Software for the Creation of Scientific Workflows for the Monte Carlo Simulation Engine GOMC." ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MoSDeF-GOMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GOMC-WSU/MoSDeF-GOMC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3572 ; sc:citation ; sc:description "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing." ; sc:featureList edam:operation_2478, edam:operation_3230 ; sc:license "MIT" ; sc:name "mosdepth" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/brentp/mosdepth" ; biotools:primaryContact "Brent Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0654, edam:topic_2269 ; sc:citation "pubmed:22868683" ; sc:description "Contains a lot of sequence analysis algorithms, including methods for motif statistics, exact motif discovery, analysis of pattern matching algorithms, etc." ; sc:featureList edam:operation_0238 ; sc:name "MoSDi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/tobiasmarschall/mosdi" ; biotools:primaryContact "Tobias Marschall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC7775580", "pubmed:33390943" ; sc:description """A Benchmarking Platform for Molecular Generation Models. Deep generative models are rapidly becoming popular for the discovery of new molecules and materials. Such models learn on a large collection of molecular structures and produce novel compounds. In this work, we introduce Molecular Sets (MOSES), a benchmarking platform to support research on machine learning for drug discovery. MOSES implements several popular molecular generation models and provides a set of metrics to evaluate the quality and diversity of generated molecules. With MOSES, we aim to standardize the research on molecular generation and facilitate the sharing and comparison of new models.""" ; sc:featureList edam:operation_3216, edam:operation_3435, edam:operation_3938 ; sc:license "MIT" ; sc:name "MOSES" ; sc:url "https://github.com/molecularsets/moses" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0937 ; sc:name "Protein X-ray crystallographic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275, edam:topic_3382 ; sc:citation ; sc:description "Program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used." ; sc:featureList edam:operation_3453 ; sc:isAccessibleForFree true ; sc:name "Mosflm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "7" ; sc:url "http://www.mrc-lmb.cam.ac.uk/harry/mosflm/index.html" ; biotools:primaryContact "Andrew G.W. Leslie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_0769, edam:topic_0780 ; sc:citation , "pubmed:33258916" ; sc:description """Modular Open-Source Genome Annotator. The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies.""" ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3436 ; sc:name "MOSGA" ; sc:url "https://gitlab.com/mosga/mosga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:35325043" ; sc:description "Multi-omic integration with Sparse Value Decomposition (MOSS), a free and open-source R package for integration and feature selection in multiple large omics datasets." ; sc:featureList edam:operation_0314, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MOSS" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://CRAN.R-project.org/package=MOSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:24227293" ; sc:description "Able to analyze all the traits jointly. The framework is flexible in that it can handle both continuous and binary traits, or a mixture of them. In addition, it can accommodate family data, can adjust for covariates (such as ancestry variables, age, gender, etc.), and can be combined efficiently across studies with different designs." ; sc:featureList edam:operation_2238 ; sc:name "MOST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dlin.web.unc.edu/software/MOST/" ; biotools:primaryContact "DANYU LIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:35657830" ; sc:description "Application in Single-shot T2 Mapping with Severe Head Motion Using Overlapping-echo Acquisition." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MOST-DL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/qinqinyang/MOST-DL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:description "MOST+ is a fast MOTIF finding tool(MOtif finding by Suffix tree and heterogeneous Tags). It extracts distribution features of nearby epigenomic markers, like histone modification or nucleosome occupancy, to help de novo find motif, thus rendering a higher level of accuracy on characterizing motif (cross-validated by ChIP-seq data) and more co-factors." ; sc:featureList edam:operation_0337 ; sc:name "MOST+" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://cbb.sjtu.edu.cn/~ccwei/pub/software/MOST/MOST.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2885, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description "Multi-Omic Strategies for Transcriptome-Wide Association Studies." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3232, edam:operation_3557, edam:operation_3791 ; sc:name "MOSTWAS" ; sc:url "https://bhattacharya-a-bt.github.io/MOSTWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:24607867" ; sc:description "Detects structural motifs containing β-strands." ; sc:featureList edam:operation_0303 ; sc:name "MotAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=motan" ; biotools:primaryContact "Eva Aksianov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382, edam:topic_3474, edam:topic_3500, edam:topic_3794 ; sc:citation ; sc:description """Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings. This repository is the backend library of our GUI based app - MOTHe-GUI. Mothe is a PYPI library to detect and track multiple animals in a heterogeneous environment. MOTHe is a python based repository and it uses Convolutional Neural Network (CNN) architecture for the object detection task. It takes a digital image as an input and reads its features to assign a category.""" ; sc:featureList edam:operation_3799, edam:operation_3925 ; sc:license "MIT" ; sc:name "MOTHe" ; sc:url "https://github.com/tee-lab/MOTHe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3174 ; sc:description "Converting mothur's taxonomy summaries into Krona-compatible XML files." ; sc:featureList edam:operation_0335, edam:operation_0337 ; sc:license "BSD-2-Clause" ; sc:name "mothur_krona" ; sc:url "https://github.com/accaldwell/mothur_krona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0637, edam:topic_3697 ; sc:citation ; sc:description "Open-source, platform-independent, community-supported software for describing and comparing microbial communities" ; sc:featureList edam:operation_0291, edam:operation_0324, edam:operation_0337, edam:operation_3200, edam:operation_3218, edam:operation_3460, edam:operation_3921 ; sc:license "GPL-3.0" ; sc:name "mothur" ; sc:softwareHelp , ; sc:url "http://mothur.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pubmed:33532840" ; sc:description """A Cell Type-Specific and Transcription Factor Centric Approach for Post-GWAS Prioritization of Causal Regulators. We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predic-tive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Genome-wide association studies (GWAS) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging.""" ; sc:featureList edam:operation_0239, edam:operation_0331, edam:operation_3226, edam:operation_3791 ; sc:license "AGPL-3.0" ; sc:name "Motif-Raptor" ; sc:url "https://github.com/pinellolab/MotifRaptor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_2269 ; sc:citation "pubmed:21901740" ; sc:description "Software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background." ; sc:featureList edam:operation_0253 ; sc:name "motif-x" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://motif-x.med.harvard.edu/motif-x.html" ; biotools:primaryContact "Daniel Schwartz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0160, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:12824320" ; sc:description "Protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures." ; sc:featureList edam:operation_0245, edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_2406 ; sc:name "Motif3D" ; sc:url "http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2330 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2330 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0160, edam:topic_0203, edam:topic_2269 ; sc:citation , "pmcid:PMC8449872", "pubmed:34537012" ; sc:description "Fast and exact quantification of motif occurrences in biological sequences." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "motif_prob" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/DataIntellSystLab/motif_prob" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3511 ; sc:citation ; sc:description "Tool for finding matches to degenerate sequence motifs in FASTA files." ; sc:featureList edam:operation_0239 ; sc:license "MIT" ; sc:name "Motif scraper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/RobersonLab/motif_scraper" ; biotools:primaryContact "Elisha D O Roberson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885, edam:topic_3511 ; sc:citation , "pmcid:PMC4653394", "pubmed:26272984" ; sc:description "Allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. It is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources. It can predict effects for novel or previously described variants in public databases." ; sc:featureList edam:operation_2404 ; sc:license "GPL-2.0" ; sc:name "motifbreakR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/motifbreakR.html" ; biotools:primaryContact "Simon Gert Coetzee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0160 ; sc:description "a MATLAB GUI platform for determination and evaluation of biologically significant motifs" ; sc:featureList edam:operation_0239, edam:operation_0445, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:name "MotifCatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32100-motifcatcher" ; biotools:primaryContact "Phillip Seitzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "The package is in particular useful for long motifs and/or relaxed choices of score thresholds, because the implemented algorithms efficiently bypass the need for enumerating a (potentially huge) set of DNA words that can give rise to a motif match." ; sc:featureList edam:operation_0361, edam:operation_2928 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "motifcounter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/motifcounter.html" ; biotools:primaryContact "Wolfgang Kopp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:16873465" ; sc:description "DNA motif-finding algorithm using a Maximum Density Subgraph." ; sc:featureList edam:operation_0238 ; sc:name "MotifCut 0.1 beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://motifcut.stanford.edu/" ; biotools:primaryContact "Serafim Batzoglou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3365, edam:topic_3511 ; sc:citation ; sc:description "More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms." ; sc:featureList edam:operation_3431 ; sc:license "Artistic-2.0" ; sc:name "MotifDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MotifDb.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0654 ; sc:citation "pubmed:16278946" ; sc:description "Designed to find motifs in multiple DNA sequences.The software uses the randomized algorithm to find good seeds and uses the improved EM algorithm to do local search." ; sc:featureList edam:operation_0238 ; sc:name "MotifDetector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.cityu.edu.hk/~lwang/software/motif/index.html" ; biotools:primaryContact "Lusheng Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0601 ; sc:citation , "pubmed:31622013" ; sc:description """An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. This is an R package for motifeR software. Shisheng Wang, Yue Cai, Jingqiu Cheng, Wenxue Li, Yansheng Liu and Hao Yang. "motifeR: An Integrated Web Software for Identification and Visualization of Protein Post‐Translational Modification Motifs." Proteomics (2019): 201900245. (DOI: 10.1002/pmic.201900245)""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0337, edam:operation_0417, edam:operation_3755 ; sc:name "motifeR" ; sc:url "https://www.omicsolution.org/wukong/motifeR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3169, edam:topic_3179 ; sc:citation , "pubmed:33999190" ; sc:description "MotifGenie is a Python command line tool for searching transcription factor binding motif sequences in merged ChIP-Seq binding sites. First, MotifGenie analyzes multiple ChIP-Seq samples simultaneously to identify shared binding regions for a locus of interest, then, searches the binding motif sequence of a given transcription factor in these shared binding regions." ; sc:featureList edam:operation_0232, edam:operation_0239, edam:operation_0445, edam:operation_3215 ; sc:name "MotifGenie" ; sc:url "https://github.com/ceragoguztuzun/MotifGenie" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749 ; sc:author "Kjetil Klepper" ; sc:citation , ; sc:contributor "Finn Drabløs", "Norwegian infrastructure for bioinformatics ELIXIR.no", "The National Programme for Research in Functional Genomics in Norway" ; sc:description "General workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. It can improve performance of binding site predictions by allowing users to integrate several motif discovery tools, as well as different types of data: phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, TF-TF interactions, TF-expression and target gene expression." ; sc:featureList edam:operation_0564 ; sc:funder "Norwegian infrastructure for bioinformatics ELIXIR.no", "The National Programme for Research in Functional Genomics in Norway" ; sc:isAccessibleForFree true ; sc:name "MotifLab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "NTNU" ; sc:softwareHelp , ; sc:softwareVersion "1.8" ; sc:url "http://www.motiflab.org" ; biotools:primaryContact "Finn Drabløs", "Kjetil Klepper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki." ; sc:featureList edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "motifmatchr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/motifmatchr.html" ; biotools:primaryContact "Alicia Schep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0654 ; sc:citation ; sc:description "MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions." ; sc:featureList edam:operation_3659 ; sc:name "MotifRegressor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.math.umass.edu/~conlon/mr.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "Tools for discriminative motif discovery using regression methods." ; sc:featureList edam:operation_0238, edam:operation_3659 ; sc:license "Artistic-2.0" ; sc:name "motifRG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/motifRG.html" ; biotools:primaryContact "Zizhen Yao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_2269 ; sc:citation ; sc:description "MotifSampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. In this implementation we focus on the use of higher-order background models to improve the robustness of the motif finding. At the moment the MotifSampler comes with background models for several organisms ." ; sc:featureList edam:operation_0239, edam:operation_2238, edam:operation_2423 ; sc:name "MotifSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2" ; sc:url "http://homes.esat.kuleuven.be/~sistawww/bioi/thijs/Work/MotifSampler.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "MotifScan is a non-parametric DNA motif scanning algorithm." ; sc:featureList edam:operation_0239 ; sc:name "MotifScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://motifscan.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3125 ; sc:citation ; sc:description "Motif Search allows you to specify several different criteria when searching for sites, such as a p-value or an approximate false-positive rate given a set of negative examples." ; sc:featureList edam:operation_0239, edam:operation_2421 ; sc:name "MotifSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "200502" ; sc:url "http://compbio.cs.princeton.edu/bindsites/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3511 ; sc:citation , "pmcid:PMC5610392", "pubmed:28632401" ; sc:description "Detecting similarity in a single or multiple DNA motif datasets." ; sc:featureList edam:operation_0240 ; sc:name "MOTIFSIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://motifsim.org/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1361 ; sc:encodingFormat edam:format_3033 ; sc:name "Position frequency matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053, edam:topic_3168, edam:topic_3169, edam:topic_3510, edam:topic_3511, edam:topic_3518 ; sc:citation ; sc:description "This package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors." ; sc:featureList edam:operation_0240 ; sc:license "GPL-2.0" ; sc:name "motifStack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/motifStack.html" ; biotools:primaryContact "Jianhong Ou" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation ; sc:description "Probabilistic motif detection." ; sc:featureList edam:operation_0238 ; sc:name "MotifSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/MotifSuite/Index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0166, edam:topic_0203, edam:topic_0749 ; sc:citation "pubmed:15215422" ; sc:description "MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0438, edam:operation_0445, edam:operation_3222 ; sc:name "MotifViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biowulf.bu.edu/MotifViz/" ; biotools:primaryContact "Yutao Fu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3303, edam:topic_3344, edam:topic_3474 ; sc:citation , "pmcid:PMC9287611", "pubmed:35856034" ; sc:description "A machine learning framework for automatic prediction of human sperm motility." ; sc:featureList edam:operation_3436, edam:operation_3659, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "motilitAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EIHW/motilitAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0203, edam:topic_3168 ; sc:citation ; sc:description """A significant discriminative sequence motif discovery algorithm with multiple testing correction. sudo apt-get install libgmp3-dev. Or see this URL. Notice that the build option "--enable-cxx" is necessary for configuration like this:. Execute MotiMul without distinguishing a sequence and its complementary strand if you use it for DNA sequences. -v.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_2238 ; sc:license "MIT" ; sc:name "MotiMul" ; sc:url "https://github.com/ko-ichimo-ri/MotiMul" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611 ; sc:citation ; sc:description "An algorithm for improving resolution of cryo-electron microscopy. It enables to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images" ; sc:featureList edam:operation_2425, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "MotionCor2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://msg.ucsf.edu/em/software/index.html" ; biotools:primaryContact "David Agard", "Shawn Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation ; sc:description "This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs." ; sc:featureList edam:operation_0240 ; sc:license "GPL-2.0" ; sc:name "MotIV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MotIV.html" ; biotools:primaryContact "Eloi Mercier", "Raphael Gottardo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1539 ; sc:name "Protein structural quality report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154 ; sc:author "David Sehnal" ; sc:citation ; sc:contributor "Crina-Maria Ionescu", "Deepti Jaiswal", "Lukáš Pravda", "Radka Svobodová Vařeková" ; sc:description """A web application for validation of annotation of ligands and residues.""" ; sc:featureList edam:operation_0336 ; sc:isAccessibleForFree true ; sc:name "MotiveValidator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "http://webchem.ncbr.muni.cz/Platform/MotiveValidator" ; biotools:primaryContact "David Sehnal", "Lukáš Pravda", "Primacy Contact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3382 ; sc:citation , "pmcid:PMC6910107", "pubmed:31844560" ; sc:description """An open-source R toolbox for time-domain motor unit analyses. Analyzing Paired Neuron Discharge Times for Time-Domain Synchronization. Using motoRneuron for motor unit synchronization. The temporal relationship between motor neurons can offer explanations for neural strategies. We combined functions to reduce neuron action potential discharge data and analyze it for short-term, time-domain synchronization. Even more so, motoRneuron combines most available methods for the determining cross correlation histogram peaks and most available indices for calculating synchronization into simple functions. See Nordstrom, Fuglevand, and Enoka (1992) for a more thorough introduction. The purpose of this document is to get you started using the motoRneuron package for analyzing motor unit data, even if you've never used R before! So we will show you how to install the toolbox through CRAN, access the functions, help files, and sample motor unit data""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3215, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "motoRneuron" ; sc:url "https://github.com/tweedell/motoRneuron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0203, edam:topic_3168, edam:topic_3315 ; sc:citation , "pmcid:PMC7536857", "pubmed:32816922" ; sc:description """Representing Motifs in Consensus Sequences with Minimum Information Loss. Represent motifs in consensus sequences. -- representing motifs in consensus sequences with minimum information loss. git clone https://github.com/MichaelMW/motto.git.""" ; sc:featureList edam:operation_0239, edam:operation_0564, edam:operation_3192 ; sc:name "Motto" ; sc:url "http://wanglab.ucsd.edu/star/motto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3293, edam:topic_3944 ; sc:citation , "pmcid:PMC9376867", "pubmed:35979445" ; sc:description "A robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation." ; sc:featureList edam:operation_0310, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mOTUlizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/moritzbuck/mOTUlizer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1931 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pubmed:24141494", "pubmed:30833550" ; sc:contributor ; sc:description "Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Metagenomic operational taxonomic units (mOTUs)" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "HD-HuB" ; sc:softwareHelp ; sc:softwareVersion "2.5.1" ; sc:url "https://motu-tool.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6813887", "pubmed:31542416" ; sc:description "MountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq | Citation: Cass AA and Xiao X. (2019). mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-Seq. Cell Systems | mountainClimber is a tool built for identifying alternative transcription start sites (ATS) and alternative polyadenylation sites (APA) from RNA-Seq by finding significant change points in read coverage. It is made up of three main steps which can be used in isolation:" ; sc:featureList edam:operation_3680, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "mountainClimber" ; sc:url "http://github.com/gxiaolab/mountainClimber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0199, edam:topic_0625, edam:topic_3500 ; sc:citation , "pmcid:PMC8633315", "pubmed:34870209" ; sc:description "Dimensional reduction of phenotypes from 53 000 mouse models reveals a diverse landscape of gene function." ; sc:featureList edam:operation_3559, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mouse-embeddings" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tkonopka/mouse-embeddings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0623, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC1311911", "pubmed:16352711" ; sc:description "A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "Mouse Atlas of Gene Expression" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mouseatlas.org/mouseatlas_index_html" ; biotools:primaryContact "Marco A. Marra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3376, edam:topic_3386 ; sc:citation ; sc:description "data about GPCR expression in different organ systems" ; sc:name "Mouse GPCRs and Human and Rat orthologs" ; sc:url "https://esbl.nhlbi.nih.gov/Databases/GPCRs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0621, edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:16615898" ; sc:description "Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0477, edam:operation_3232, edam:operation_3741 ; sc:name "Mouse Proteome Project" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tap.med.utoronto.ca/mts/" ; biotools:primaryContact "Thomas Kislinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0199, edam:topic_0625, edam:topic_3500 ; sc:citation "pubmed:19854936" ; sc:description "The database and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. It portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide value-added information." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_3227, edam:operation_3357 ; sc:name "Mousebook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mousebook.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2885 ; sc:citation "pubmed:22260749" ; sc:description "R package specifically designed to genotype the Mouse Diversity Genotyping Array, an Affymetrix mouse genotyping array similar to the human SNP 6.0. It contains functions which allow you to perform genotyping, identify probe sets potentially harboring a new mutation (Variable INtensity Oligonucleotide or VINO, here we call it a vinotyping) and perform CNV analysis." ; sc:featureList edam:operation_3196 ; sc:name "MouseDivGeno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cgd.jax.org/tools/mousedivgeno/" ; biotools:primaryContact "Jessica Seavey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0625, edam:topic_3500 ; sc:citation ; sc:description """In silico candidate variant and gene identification using inbred mouse strains. This repository contains the backend of the MouseFM tool including the scripts of the etl process and the webserver. The MouseFM client is available as an R package on Github (https://github.com/matmu/MouseFM) or on Bioconductor (https://bioconductor.org/packages/devel/bioc/html/MouseFM.html).""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "MouseFM" ; sc:url "https://github.com/matmu/MouseFM-Backend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0654, edam:topic_2885 ; sc:citation "pubmed:19933259" ; sc:description "Integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database currently includes polymorphisms identified from our alignment of whole-genome shotgun sequence traces from four laboratory mouse strains mapped against the reference C57BL/6J genome using GMAP." ; sc:featureList edam:operation_0224, edam:operation_2429, edam:operation_2871, edam:operation_3194, edam:operation_3196 ; sc:name "MouseIndelDB" ; sc:url "http://polybrowse.abcc.ncifcrf.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625 ; sc:citation , "pmcid:PMC4534495", "pubmed:26092688" ; sc:description "Data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer." ; sc:featureList edam:operation_0224 ; sc:name "MouseMine" ; sc:softwareHelp , ; sc:url "http://www.mousemine.org/mousemine/begin.do" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625 ; sc:citation , "pubmed:36762471" ; sc:description "Online search tool to search for variations in all protein-coding gene sequences of 36 sequenced mouse inbred strains, compared to the reference strain C57BL 6J, which could be linked to strain-specific phenotypes and modifier effects." ; sc:featureList edam:operation_2421, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "Mousepost" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://mousepost.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation ; sc:description "A user-friendly tool for rapid biological discovery from human or mouse transcriptional data." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "MouSR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mousr.qub.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC10197232", "pubmed:37208601" ; sc:description "Method for evaluating the pathogenicity of missense variants using AlphaFold2." ; sc:featureList edam:operation_0331, edam:operation_2454, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "MOVA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/yuya-hatano/MOVA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33258917" ; sc:description """Modeling and visualization of dynamics of alternative polyadenylation across biological samples. Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically.""" ; sc:featureList edam:operation_0337, edam:operation_0428, edam:operation_3799 ; sc:name "movAPA" ; sc:url "https://github.com/BMILAB/movAPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3500 ; sc:citation , "pmcid:PMC9290230", "pubmed:35843990" ; sc:description "MoveApps is a no-code analysis platform for animal tracking data hosted by the Max Planck Institute of Animal Behavior. The aim is to make sophisticated analytical tools accessible to a larger audience." ; sc:isAccessibleForFree true ; sc:name "MoveApps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.moveapps.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_2640, edam:topic_3577 ; sc:citation ; sc:description """An R package for multi-omics integration and visualization in cancer subtyping. Multi-Omics integration and VIsualization in Cancer Subtyping. The goal of MOVICS is to provide a unified interface for 10 state-of-the-art multi-omics clustering algorithms, and standardizes the output for each algorithm so as to form a pipeline for downstream analyses. MOVICS incorporates the most commonly used downstream analyses in cancer subtyping researches and enables creating feature rich customizable visualizations with minimal effort.""" ; sc:featureList edam:operation_0337 ; sc:name "MOVICS" ; sc:url "https://github.com/xlucpu/MOVICS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0176, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:15980488" ; sc:description "MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions." ; sc:featureList edam:operation_0244 ; sc:name "MovieMaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/moviemaker/" ; biotools:primaryContact "MovieMaker Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0081, edam:topic_0097, edam:topic_0154, edam:topic_0176 ; sc:citation "pubmed:15215475" ; sc:description "MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. 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Davuluri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0209, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC10289339", "pubmed:37352252" ; sc:description "A machine learning (ML) driven web-app for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists." ; sc:featureList edam:operation_0478, edam:operation_2476, edam:operation_3891, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Mpropred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://share.streamlit.io/nadimfrds/mpropred/Mpropred_app.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3071, edam:topic_3320, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC6282714", "pubmed:30118150" ; sc:description """Review and classification of published variants in the ARSB gene. 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About Next-Gen Sequence Databases. The databases and the web pages (with customized web interfaces) were devloped to handle and display 'next-gen' sequencing data for several organisms and related varieties (mainly plants). 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White" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0102, edam:topic_3474 ; sc:citation ; sc:description "Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo." ; sc:featureList edam:operation_3200 ; sc:name "mPTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mptp.h-its.org/#/tree" ; biotools:primaryContact "Alexandros Stamatakis", "Paschalia Kapli", "Tomas Flouri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:36124954" ; sc:description "Mutated Pathway Visible Neural Network (MPVNN) architecture, designed using prior signaling pathway knowledge and random replacement of known pathway edges using gene mutation data simulating signal flow disruption." ; sc:featureList edam:operation_2437, edam:operation_3928 ; sc:license "GPL-2.0" ; sc:name "MPVNN" ; sc:url "https://github.com/gourabghoshroy/MPVNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC10265443", "pubmed:37267150" ; sc:description "R package for comparing the performance of mass spectrometry-based proteomic workflows." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mpwR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://okdll.github.io/mpwR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3837 ; sc:citation ; sc:description """Quotient filters for efficient storage of k-mers with their counts and metadata. Benchmarking MQF vs CQF vs Countmin. Welcome to khmer: k-mer counting, filtering, and graph traversal FTW!. .""" ; sc:featureList edam:operation_0224, edam:operation_3192, edam:operation_3359, edam:operation_3472, edam:operation_3695 ; sc:license "BSD-3-Clause" ; sc:name "MQF" ; sc:url "https://github.com/dib-lab/2020-paper-mqf-benchmarks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:20529018" ; sc:description "Program which can be useful for parametric linkage analysis of quantitative traits on the base of large pedigrees without loops." ; sc:featureList edam:operation_0283 ; sc:name "MQscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mga.bionet.nsc.ru/soft/mqscore/" ; biotools:primaryContact "Tatiana Axenovich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2229, edam:topic_3308 ; sc:citation ; sc:description "MQuad (Mixture Model for Mitochondrial Mutation detection in single-cell omics data) is a tool that detects mitochondrial mutations that are informative for clonal substructure inference. 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Also compare portions of gray and white matter present." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "MRI Brain Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.5.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/4879-mri-brain-segmentation" ; biotools:primaryContact "Robert Bemis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3304, edam:topic_3306, edam:topic_3444 ; sc:description "Tool for brain tumor detection from MRI images using anisotropic filter and segmentation image processing. This image processing routine can detect tumors presence, location, area, and boundary." ; sc:featureList edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "MRI image brain tumor detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63792-brain-tumor-detection-from-mri-images-using-anisotropic-filter-and-segmentation-image-processing" ; biotools:primaryContact "Shazid Mahmood" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:description "Compute SNR for MRI parallel images using different reconstruction methods. There are three methods we used here to compute the SNR of MR images: ACR, SoS, and OPT." ; sc:featureList edam:operation_0268, edam:operation_0470, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "MRI parallel image SNR Computer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36325-compute-snr-for-mri-parallel-images-using-different-reconstruction-methods" ; biotools:primaryContact "Yingying Wang, Ph.D." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3304, edam:topic_3306, edam:topic_3444 ; sc:description "This code implements the MICO algorithm for MRI tissue segmentation and bias field correction." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "MRI segmentation and bias field correction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/59752-mri-segmentation-and-bias-field-correction" ; biotools:primaryContact "Chunming Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3512 ; sc:citation , "pubmed:34283296" ; sc:description "Brain imaging in a cross-sectional cohort of 1870 university students, in french." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MRi-Share" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.i-share.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC8236813", "pubmed:34194294" ; sc:description "A Matlab Toolbox for Mapping the Responses to Intracranial Electrical Stimulation." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MRIES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SunKaijia0065/MRIES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:34448358" ; sc:description "We introduce a new R package ‘MrIML’ (Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to map multi-locus genomic relationships, to identify loci of interest for future landscape genetics studies and to gain new insights into adaptation across environmental gradients. Relationships between genetic change and environment are often non-linear, interactive and autocorrelated. Our package helps capture this complexity and offers functions that construct, fit and conduct inference on a wide range of highly flexible models that are routinely used for single-locus landscape genetics studies but are rarely extended to estimate response functions for multiple loci" ; sc:featureList edam:operation_0282, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MrIML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nfj1380.github.io/mrIML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3372, edam:topic_3444 ; sc:citation , "pubmed:33817833" ; sc:description "MRIReco is a Julia packet for magnetic resonance imaging. It contains algorithms for the simulation and reconstruction of MRT data and is both easy to use and flexibly expandable." ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3443 ; sc:license "MIT" ; sc:name "MRIReco" ; sc:url "https://github.com/MagneticResonanceImaging/MRIReco.jl" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2269, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description """Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity. Code for analyses in MRLocus paper. MRLocus is a statistical method providing Mendelian Randomization analysis per locus, leveraging eQTL and GWAS summary statistics, for estimation of gene-to-trait effect size and dispersion.""" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3659, edam:operation_3791 ; sc:name "MRLocus" ; sc:url "https://mikelove.github.io/mrlocus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0602 ; sc:citation , "pmcid:PMC8041396", "pubmed:33683131" ; sc:description "A Comprehensive Resource for Targeted Proteomics Assays in the Community." ; sc:featureList edam:operation_2422, edam:operation_3630, edam:operation_3925 ; sc:name "MRMAssayDB" ; sc:url "http://mrmassaydb.proteincentre.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3172, edam:topic_3370, edam:topic_3520 ; sc:citation , "pubmed:32930575" ; sc:description """Automated Data Processing for Large-Scale Targeted Metabolomics Analysis. MRMkit: automated data processing for large-scale targeted mass spectrometry.""" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3799 ; sc:name "MRMkit" ; sc:url "https://github.com/MRMkit/MRMkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3361, edam:topic_3517 ; sc:citation , "pubmed:33346083" ; sc:description """An R Platform for Multi-locus Genome-wide Association Studies. Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface. Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) .""" ; sc:featureList edam:operation_3658 ; sc:license "GPL-2.0" ; sc:name "mrMLM" ; sc:softwareVersion "4.0" ; sc:url "https://bigd.big.ac.cn/biocode/tools/BT007077" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pubmed:14965900" ; sc:description "C program for selecting DNA substitution models using PAUP*" ; sc:featureList edam:operation_0550 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "mrmodeltest2" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/nylander/MrModeltest2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640 ; sc:citation "pubmed:26652794" ; sc:description "Freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays." ; sc:featureList edam:operation_2945 ; sc:name "MRMPlusGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/paiyetan/mrmplusgui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3374 ; sc:citation ; sc:description "mRMR Feature Selectionis a cross-platform version of mimimum-redundancy maximum-relevancy feature selection. It is using a mutual information computation" ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "mRMR Feature Selection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/14608-mrmr-feature-selection-using-mutual-information-computation" ; biotools:primaryContact "Hanchuan Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation "pubmed:23825369" ; sc:description "Contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with minimum Redundancy, Maximum Relevance (mRMR) and a new ensemble mRMR technique." ; sc:featureList edam:operation_2238 ; sc:name "mRMRe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pmgenomics.ca/bhklab/software/mrmre" ; biotools:primaryContact "Benjamin Haibe-Kains" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3512 ; sc:citation "pubmed:23325845" ; sc:description "Tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength." ; sc:featureList edam:operation_0278 ; sc:name "mRNA optimiser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/software/mrna-optimiser/" ; biotools:primaryContact "Paulo Gaspar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7319581", "pubmed:32421834" ; sc:description "A novel machine-learning based in-silico tool to predict mRNA subcellular localization." ; sc:featureList edam:operation_0372, edam:operation_0418, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "mRNALoc" ; sc:url "http://proteininformatics.org/mkumar/mrnaloc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:33823302" ; sc:description "mRNALocater is a comprehensive and advanced model to accuracy prtiction of eukaryotic mRNA subcellular localization.Three different machine learning models with relatively stable performance based on the optimal feature subset using algorithms including XGBoost, LightGBM and CatBoost are constructed. The mRNALocater is an integration of these three models, and it has better performance than the state-of-the-art mRNALoc for some subcellular localization predict. The independent testing datasets proves that mRNALocater is a comprehensive and advanced predictor." ; sc:featureList edam:operation_0418, edam:operation_2489, edam:operation_3936 ; sc:name "mRNALocater" ; sc:url "http://bio-bigdata.cn/mRNALocater" ; biotools:primaryContact "Wei Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0176, edam:topic_0601 ; sc:citation , "pubmed:32672967" ; sc:description """A Parametrizer of Post-Translationally Modified Residues. This program streamlines the process of post-translationally modified residue parameterization. MRP.py is designed to work with AmberTools and the Gaussian software package to handle molecular modeling and QM calculations, respectively. AmberTools15 or higher should be used in conjuction with this program.""" ; sc:featureList edam:operation_0387, edam:operation_0393, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "MRP_py" ; sc:url "https://github.com/pgsahrmann/mrp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC8120292", "pubmed:33995486" ; sc:description "MRPC is an R package for inference of Causal Graphs. MRPC builds on existing PC algorithms and learns a causal network with increased accuracy. The inferred causal network contains directed and undirected edges, with the direction indicating causality. For genomic data, MRPC determines edge direction under the principle of Mendelian randomization when genotype and molecular phenotype (e.g. gene expression) data are both available at the individual level. Nodes in the inferred network may be a genotype or a molecular phenotype." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3557, edam:operation_3766, edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "MRPC" ; sc:url "https://cran.r-project.org/package=MRPC" ; biotools:primaryContact "Audrey Qiuyan Fu", "Md. Bahadur Badsha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3318, edam:topic_3448 ; sc:citation , "pmcid:PMC7401789", "pubmed:32788907" ; sc:description """Automated execution of Pixel calculations via the Mercury interface. MrPIXEL is a program that enables the energetics of crystal packing to be analysed quickly and easy through a user interface, using PIXEL, Python scripts and the widely known visualiser, Mercury.""" ; sc:featureList edam:operation_0455, edam:operation_2950, edam:operation_3454 ; sc:name "MrPIXEL" ; sc:url "http://www.crystal.chem.ed.ac.uk/software/mrpixel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_3519 ; sc:citation "pubmed:27154272" ; sc:description "Server that performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, and ranks the resulting primers to return the top-1 best primers to the user." ; sc:featureList edam:operation_0308 ; sc:name "MRPrimerW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mrprimerw.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3383, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pubmed:33176026" ; sc:description """An open-source tool for quality control of MR imaging data. This tool takes MRI datasets in the file formats (.dcm, .nii, .nii.gz or .mha) as the input. Two Python scripts (QC.py and QCF.py) are used to generate several tags and noise/information measurements for quality assessment. These scripts save the calculated measures in a .tsv file as well as generate .png thumbnails for all images in a subject volume. These are then fed to .js scripts to create the user interface (index.html) output. A schematic illustrating the framework of the tool is as follows.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:license "BSD-3-Clause-Clear" ; sc:name "MRQy" ; sc:url "http://github.com/ccipd/MRQy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC6659377" ; sc:description "mrrobust—a tool for performing two-sample summary Mendelian randomization analyses | Stata package for two-sample Mendelian randomization analyses using summary data | Installing and updating mrrobust | Improved compatibility with the github package, i.e. mrrobust and its dependencies can be installed simply by issuing: gitget mrrobust , assuming that you have the github package installed. See below for instructions" ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "mrrobust" ; sc:url "https://github.com/remlapmot/mrrobust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation "pubmed:15980580" ; sc:description "MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set." ; sc:featureList edam:operation_2422 ; sc:name "MRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mrs.cmbi.ru.nl/" ; biotools:primaryContact "M.L. Hekkelman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0602, edam:topic_3172 ; sc:citation , "pmcid:PMC9420769", "pubmed:35775808" ; sc:description "A cloud-based spectral simulation tool “MRSCloud,” which allows MRS users to simulate a vendor-specific and sequence-specific basis set online in a convenient and time-efficient manner. This tool can simulate basis sets for GE, Philips, and Siemens MR scanners, including conventional acquisitions and spectral editing schemes with PRESS and semi-LASER localization at 3 T." ; sc:featureList edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MRSCloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://braingps.mricloud.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3277, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8874219", "pubmed:35065709" ; sc:description "A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease." ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_0433, edam:operation_3226, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MRSD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mcgm-mrsd.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , , "pmcid:PMC3115707", "pmcid:PMC3694458", "pubmed:20676076", "pubmed:23758764" ; sc:description "micro-read substitution-only Fast Alignment Search Tool. Short read mapper that optimizes cache usage to get higher performance." ; sc:featureList edam:operation_2429, edam:operation_3198 ; sc:license "BSD-3-Clause" ; sc:name "mrsFAST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sfu-compbio/mrsfast" ; biotools:primaryContact "Faraz Hach", "Iman Sarrafi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:24810850" ; sc:description "Cache oblivious mapper that is designed to map short reads to reference genome. It maps short reads with respect to user defined error threshold. In this manual, we will show how to choose the parameters and tune the tool with respect to the library settings." ; sc:featureList edam:operation_0525, edam:operation_3198 ; sc:name "mrsFAST-Ultra" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sfu-compbio.github.io/mrsfast/" ; biotools:primaryContact "Faraz Hach" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation "pubmed:7668300" ; sc:description "MRVTEST is a simple program which automates setting up likelihood calculations for combined linkage and association analysis using a variety of different transmission models. It consists of an adaptation of the earlier MFLINK program, which performs likelihood-based model-free linkage analysis." ; sc:featureList edam:operation_0283 ; sc:name "MRVTEST" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://www.davecurtis.net/dcurtis/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3056 ; sc:citation ; sc:description "A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models." ; sc:featureList edam:operation_2426 ; sc:license "Not licensed" ; sc:name "ms" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://home.uchicago.edu/~rhudson1/source/mksamples.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation "pubmed:11354471" ; sc:description "Specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra." ; sc:featureList edam:operation_0495 ; sc:name "MS-BLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetics.bwh.harvard.edu/msblast/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description """A feature-filtering approach to improve annotation rate in untargeted LC-MS based metabolomics. MS-CleanR: A package for cleaning and annotating LC-MS data. The MS-CleanR package provides functions for feature filtering and annotation of LC-MS data. MS-CleanR use as input MS-DIAL peak list processed in data dependent analysis (DDA) or data independent analysis (DIA) using either positive ionization mode (PI) or negative ionization mode (NI) or both.""" ; sc:featureList edam:operation_3629, edam:operation_3695, edam:operation_3891 ; sc:name "MS-CleanR" ; sc:url "https://github.com/eMetaboHUB/MS-CleanR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_0798, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7272069", "pubmed:32497070" ; sc:description """A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. This repository contains the analytical code necessary to reproduce the results described in the paper: "A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.".""" ; sc:featureList edam:operation_0417, edam:operation_3186, edam:operation_3206, edam:operation_3207, edam:operation_3919 ; sc:name "MS-DArT-seq" ; sc:url "https://github.com/wendelljpereira/ms-dart-seq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3684 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3247, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654, edam:format_3681, edam:format_3684, edam:format_3714, edam:format_3827 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3681 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3681, edam:format_3684, edam:format_3827 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3004 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3372, edam:topic_3520 ; sc:citation "pubmed:25910694" ; sc:description "The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources." ; sc:featureList edam:operation_0335, edam:operation_0336, edam:operation_1812, edam:operation_2409, edam:operation_2422, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ms-data-core-api" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.31" ; sc:url "https://github.com/PRIDE-Utilities/ms-data-core-api" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:35020790" ; sc:description "A user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides." ; sc:featureList edam:operation_0417, edam:operation_2421, edam:operation_3645, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS-Decipher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DICP-1809/MS-Decipher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph." ; sc:featureList edam:operation_3629 ; sc:name "MS-Deconv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.8.0.7370" ; sc:url "http://proteomics.ucsd.edu/software-tools/ms-deconv/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1056 ; sc:encodingFormat edam:format_2330 ; sc:name "Database name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1238 ; sc:encodingFormat edam:format_2330, edam:format_2548 ; sc:name "Proteolytic digest" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0137, edam:topic_3520 ; sc:description "Digests a protein sequence." ; sc:featureList edam:operation_0422 ; sc:name "MS-Digest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msdigest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_2332 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Peptide mass fingerpriting tool in the ProteinProspector suite." ; sc:featureList edam:operation_2929, edam:operation_3631, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767 ; sc:name "MS-Fit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msfitstandard" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1667 ; sc:encodingFormat edam:format_3247 ; sc:name "E-value" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1667 ; sc:encodingFormat edam:format_3247 ; sc:name "E-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3475 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1667 ; sc:encodingFormat edam:format_3475 ; sc:name "E-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation , "pubmed:18597511", "pubmed:25358478" ; sc:description "A tool which performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database." ; sc:featureList edam:operation_0335, edam:operation_3631, edam:operation_3643, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767 ; sc:name "MS-GF+" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://omics.pnl.gov/software/ms-gf" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3475 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:20829449" ; sc:description "Peptide identification using a combination of ''de novo'' and database search." ; sc:featureList edam:operation_3631, edam:operation_3643, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767 ; sc:name "MS-GFDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/ProteoSAFe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3304, edam:topic_3444 ; sc:citation , "pubmed:33942058" ; sc:description "MS-HBM is script for individual-specific areal-level parcellations improve functional connectivity prediction of behavior. A multi-session hierarchical Bayesian model (MS-HBM) for estimating high-quality individual-specific network-level parcellations. Here, we extend the model to estimate individual-specific areal-level parcellations. While network-level parcellations comprise spatially distributed networks spanning the cortex, the consensus is that areal-level parcels should be spatially localized, i.e., should not span multiple lobes. There is disagreement about whether areal-level parcels should be strictly contiguous or comprise multiple non-contiguous components, therefore we considered three areal-level MS-HBM variants spanning these range of possibilities: distributed MS-HBM (dMSHBM), contiguous MS-HBM (cMSHBM) and gradient-infused MS-HBM (gMSHBM)." ; sc:featureList edam:operation_3359, edam:operation_3659 ; sc:name "MS-HBM" ; sc:url "https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Kong2022_ArealMSHBM" ; biotools:primaryContact "B T Thomas Yeo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1957 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520, edam:topic_3524 ; sc:description "Calculates the isotopic distribution from a peptide sequence." ; sc:featureList edam:operation_3632 ; sc:name "MS-Isotope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msisotope" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071, edam:topic_3520 ; sc:citation , "pubmed:20058248" ; sc:description "Project that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data." ; sc:featureList edam:operation_2409 ; sc:name "Ms-lims" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "7.7.7" ; sc:url "https://github.com/compomics/ms-lims" ; biotools:primaryContact "Lennart Martens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3419, edam:topic_3473 ; sc:citation , "pmcid:PMC8688841", "pubmed:34949983" ; sc:description "Multisource Marginal Distribution Adaptation for Cross-Subject and Cross-Session EEG Emotion Recognition." ; sc:featureList edam:operation_0303, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MS-MDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/VoiceBeer/MS-MDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:description "Python library for large-cohort metabolomics (MS1) processing." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MINT (Metabolomics Integrator)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LewisResearchGroup/ms-mint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3314, edam:topic_3344, edam:topic_3520 ; sc:description "Function that align peaks from several files and gives a matrix as result." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "Multiple Peaks Alignment for Mass Spectrometry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/31635-multiple-peaks-alignment-for-mass-spectrometry" ; biotools:primaryContact "Andrea Padoan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Quantitiave analysis of multiple LC-MS(/MS) analyses in mzXML." ; sc:featureList edam:operation_3215, edam:operation_3634, edam:operation_3694, edam:operation_3704, edam:operation_3731, edam:operation_3744 ; sc:name "MS-Spectre" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ms-spectre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:36516971" ; sc:description "A Tool for the Analysis of Fragment Ions Generated from Intact Proteins." ; sc:featureList edam:operation_3629, edam:operation_3767, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MS-TAFI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kylejuetten/MSFIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC9913042", "pubmed:36702456" ; sc:description "MS1Connect is a tool that scores the similarity between a pair of mass spectrometry runs." ; sc:featureList edam:operation_3431, edam:operation_3627, edam:operation_3643, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MS1Connect" ; sc:url "https://github.com/bmx8177/MS1Connect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , , ; sc:description "DirectMS1 proteomics search engine for LC-MS1 spectra" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ms1searchpy" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/markmipt/ms1searchpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description """Automated repurposing of public peptide LC-MS data for machine learning applications. Liquid-chromatography mass-spectrometry (LC-MS) is the established standard for analyzing the proteome in biological samples by identification and quantification of thousands of proteins. Machine learning (ML) promises to considerably improve the analysis of the resulting data, however, there is yet to be any tool that mediates the path from raw data to modern ML applications.""" ; sc:featureList edam:operation_2422, edam:operation_3631, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "MS2AI" ; sc:url "https://gitlab.com/roettgerlab/ms2ai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3172, edam:topic_3374 ; sc:citation , "pubmed:34115523" ; sc:description "MS2Compound is a user-friendly compound identification tool for LC-MS/MS-based metabolomics data." ; sc:featureList edam:operation_3801, edam:operation_3803 ; sc:license "CC-BY-4.0" ; sc:name "MS2Compound" ; sc:url "https://github.com/beherasan/MS2Compound" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3343, edam:topic_3474, edam:topic_3520 ; sc:citation ; sc:description "MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. 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It is especially designed for high resolution and high accuracy tandem mass spectra." ; sc:featureList edam:operation_3645, edam:operation_3646, edam:operation_3755, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MS Amanda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ms.imp.ac.at/?action=ms-amanda" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0128, edam:topic_0130, edam:topic_0736 ; sc:author ; sc:citation , ; sc:description "MS Annika is a cross-linking search engine for use with cleavable cross-linkers and MS2 or MS2-MS3 spectra. It can deal with a wide variety of cleavable cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer." ; sc:featureList edam:operation_3631, edam:operation_3645, edam:operation_3646, edam:operation_3649, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "MS Annika" ; sc:operatingSystem "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "Proteome Discoverer 2.3: MS Annika v1.0.0", "Proteome Discoverer 2.4: MS Annika v1.0.0", "Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3", "Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4", "Proteome Discoverer 3.1: MS Annika 2.0 v1.2.0" ; sc:url "https://ms.imp.ac.at/?action=ms-annika" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "MS-DIAL was launched as a universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters)" ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3636, edam:operation_3803 ; sc:name "MS-DIAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://prime.psc.riken.jp/compms/msdial/main.html" ; biotools:primaryContact , "Makoto Arita" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:34264676" ; sc:description "A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides." ; sc:featureList edam:operation_3631, edam:operation_3639, edam:operation_3767, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MS_Piano" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://chemdata.nist.gov/dokuwiki/doku.php?id=peptidew:ms_piano" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1935, edam:format_1936, edam:format_1948, edam:format_1997 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1935, edam:format_1936, edam:format_1948, edam:format_1997 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1982, edam:format_1984 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1711 ; sc:encodingFormat edam:format_3547 ; sc:name "Sequence alignment image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1984 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2305 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_1929, edam:format_1982, edam:format_1997, edam:format_3508 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3168, edam:topic_3293 ; sc:author "Sebastian Wilzbach" ; sc:citation , "pubmed:26315911" ; sc:contributor "Benedikt Rauscher", "Google Summer of Code (GSoC) 2014", "Guy Yachdav", "Ian Sillitoe", "Tatyana Goldberg" ; sc:description "Display multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms." ; sc:featureList edam:operation_0492, edam:operation_0564 ; sc:funder "Google Summer of Code (GSoC) 2014" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "msa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioJS", "Technische Universität München" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "http://msa.biojs.net" ; biotools:primaryContact "Ulrich Bodenhofer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3299, edam:topic_3945 ; sc:description "R/Bioconductor package MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calcualtes pairwise IUPAC distances." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MSA2dist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0", "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MSA2dist.html" ; biotools:primaryContact "Kristian Ullrich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640 ; sc:citation , "pmcid:PMC8567580", "pubmed:34736398" ; sc:description "Mutational signature attribution with confidence based on simulations" ; sc:featureList edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/s.senkin/MSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_3316 ; sc:citation ; sc:description """Reproducible mutational signature attribution with confidence based on simulations. Mutational signature attribution with confidence based on simulations.""" ; sc:featureList edam:operation_0552, edam:operation_3227, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "MSAP" ; sc:url "https://gitlab.com/s.senkin/MSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Multiple alignment algorithm for protein sequences." ; sc:featureList edam:operation_0492 ; sc:name "MSAprobs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://msaprobs.sourceforge.net/homepage.htm#latest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3316 ; sc:citation , "pubmed:33289885" ; sc:description """Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI. Parallel and accurate multiple sequence alignment. MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. MSAProbs-MPI is a parallelization of MSAProbs (v0.9.7) using MPI for distributed-memory systems.""" ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_0496 ; sc:name "MSAProbs-MPI" ; sc:url "http://msaprobs.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:21585724" ; sc:description "Python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types)." ; sc:featureList edam:operation_0253, edam:operation_0308 ; sc:name "msatcommander" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/msatcommander/" ; biotools:primaryContact "Brant C. 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It uses a set of identified peptides (or peptides with scores in a MS/MS search), peptide detectability, and a protein database to provide probabilities of protein identifications." ; sc:featureList edam:operation_3658 ; sc:name "MSBayesPro" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://darwin.informatics.indiana.edu/yonli/proteininfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation "pubmed:17090578" ; sc:description "Tool for the analysis of gene expression data using a new bi-clustering method. It can find constant bi-clusters and additive bi-clusters." ; sc:featureList edam:operation_0313 ; sc:name "MSBE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.cityu.edu.hk/~lwang/software/msbe/" ; biotools:primaryContact "Lusheng Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3336, edam:topic_3377, edam:topic_3379 ; sc:citation , "pubmed:33147616" ; sc:description """Computational drug repositioning based on multi-similarities bilinear matrix factorization. Based on multiple similarities of drug and disease, we propose a Multi-Similarities Bilinear Matrix Factorization algorithm to identify potential novel indications for known or novel drugs. The code of MSBMF in this package is implemented in Matlab2014a. An international forum for researchers and educators in the life sciences, covering genetic studies of phenotypes and genotypes, DNA sequencing, expression prof.""" ; sc:featureList edam:operation_0303, edam:operation_3196, edam:operation_3799 ; sc:name "MSBMF" ; sc:url "https://github.com/BioinformaticsCSU/MSBMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_2269, edam:topic_3293 ; sc:citation , "pubmed:30391518" ; sc:description "Tree-level bootstrap and jackknife resampling for gene-tree datasets in multispecies coalescent analysis." ; sc:featureList edam:operation_0544, edam:operation_0552 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "msc_tree_resampling" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/dbsloan/msc_tree_resampling" ; biotools:primaryContact "Daniel Sloan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3169 ; sc:citation , "pubmed:33522829" ; sc:description "mscDPB is a tool that uses Chou's 5-step rule to predict DNA-protein binding with nulti-scale complementary feature." ; sc:featureList edam:operation_0253, edam:operation_0445, edam:operation_3092 ; sc:name "mscDPB" ; sc:url "http://121.5.71.120/mscDPB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation ; sc:description "Algorithm for accurately inferring transcription factor binding sites using chromatin accessibility data." ; sc:featureList edam:operation_0445 ; sc:license "MIT" ; sc:name "msCentipede" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rajanil/msCentipede" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0659, edam:topic_3168 ; sc:citation , "pmcid:PMC8285884", "pubmed:34271851" ; sc:description "Inferring circRNA functional similarity based on multiple data sources." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MSCFS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CJNabla/MultiSourcCFS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0140, edam:topic_2640, edam:topic_3474 ; sc:citation ; sc:description """Median-supplement model-based classification tool for automated knowledge discovery. MSclassifier classifies instances using median-supplement machine learning methods.""" ; sc:featureList edam:operation_2489, edam:operation_3359, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "MSclassifier" ; sc:url "https://nweb.gimpa.edu.gh/schools/school-of-technology/software/MSclassifier/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3179 ; sc:description "MSCLtoolbox (The MSCL Analyst’s Toolbox) includes a set of scripts accessible as either a customized menu item (Windows) or as stand alone scripts (Mac) for the analysis of Affymetrix gene chip data. The scripts are run in the JMP statistical package, see below. 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For that it uses a fragment ion indexing method." ; sc:featureList edam:operation_3646, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:name "MSFragger" ; sc:url "http://www.nesvilab.org/software" ; biotools:primaryContact "Alexey Nesvizhskii" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0625, edam:topic_0821 ; sc:citation ; sc:description "Pipeline for the anaysis of a MS-GBS experiment." ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "msgbsR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/msgbsR.html" ; biotools:primaryContact "Benjamin Mayne" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converter from MS-GFDB output to pepXML." ; sc:featureList edam:operation_0335, edam:operation_0398 ; sc:license "GPL-3.0" ; sc:name "msgfdb2pepxml" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ms-utils.org/msgfdb2pepxml/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3365, edam:topic_3678 ; sc:citation ; sc:description "This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current results to another R session so the user can seamlessly integrate the gui into other workflows." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "MSGFgui" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MSGFgui.html" ; biotools:primaryContact "Thomas Lin Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_3520 ; sc:citation ; sc:description "This package contains function to perform peptide identification using MS-GF+." ; sc:featureList edam:operation_3631 ; sc:license "GPL-2.0" ; sc:name "MSGFplus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MSGFplus.html" ; biotools:primaryContact "Thomas Lin Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3344 ; sc:citation "pubmed:24463184" ; sc:description "This R package (multinomial sparse group lasso) fits multinomial models for e.g. multiclass classification with a sparse group lasso penalty." ; sc:featureList edam:operation_2426 ; sc:name "msgl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.math.ku.dk/~richard/msgl/" ; biotools:primaryContact "Vincent M" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3475 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3466 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "An MS-DOS program to visualize LC-MS data in 2D and 3D (converter from mzXML available)." ; sc:featureList edam:operation_1812, edam:operation_3203, edam:operation_3441, edam:operation_3694 ; sc:name "MSGraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://msgraph.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3056 ; sc:citation ; sc:description "This addition to ms, called msHOT, allows for implementation of multiple crossover hotspots and/or multiple gene conversion hotspots in the simulated genetic region. Crossover hotspots may overlap with gene conver-sion hotspots, but crossover hotspots may not overlap with each other and gene conversion hotspots may not overlap with each other." ; sc:featureList edam:operation_2426 ; sc:license "Not licensed" ; sc:name "msHOT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://uchicago.app.box.com/s/l3e5uf13tikfjm7e1il1eujitlsjdx13" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_2259 ; sc:citation "pubmed:18442405" ; sc:description "Ongoing project aimed at the development of software for the computational simulation of spatial processes in immunity. The software is an open source development project; there are several options for acquiring the program, including the complete source code, or just pre-built binaries." ; sc:featureList edam:operation_2426 ; sc:name "MSI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cs.duke.edu/~emonson/MSI_Site/index.html" ; biotools:primaryContact "Faheem Mitha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:33583182" ; sc:description """Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals. Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data. This repository contains the python script performing the recalibration of mass spectrometry images (MSI) from the associated paper Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data.""" ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3649, edam:operation_3860 ; sc:license "Apache-2.0" ; sc:name "MSI-R" ; sc:url "https://github.com/LaRoccaRaphael/MSI_recalibration" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0637, edam:topic_3301, edam:topic_3520, edam:topic_3673 ; sc:citation , "pmcid:PMC8552640", "pubmed:34378957" ; sc:description "Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry." ; sc:featureList edam:operation_3215, edam:operation_3431, edam:operation_3627, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MSI_mass_spectrometry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://msi.happy-dev.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC8042960", "pubmed:33845765" ; sc:description "MSIFinder is a python package for detecting Microsatellite instability (MSI) status using random forest classifier. Microsatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite lengths owing to the deficiency in the mismatch repair system. Based on the degree, MSI can be classified as microsatellite instability-high (MSI-H) and microsatellite stable (MSS). MSI is a predictive biomarker for immunotherapy efficacy in advanced/metastatic solid tumors, especially in colorectal cancer patients. Several computational approaches based on target panel sequencing data have been used to detect MSI; however, they are considerably affected by the sequencing depth and panel size." ; sc:featureList edam:operation_3198, edam:operation_3219, edam:operation_3222 ; sc:name "MSIFinder" ; sc:url "https://github.com/861934367/MSIFinder" ; biotools:primaryContact "Feng Lou", "Haijun Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description "MSight: An image analysis software for liquid chromatography-mass spectrometry. MSight is a tool specifically developed for the representation of mass spectra along with data from a separation step. It provides simple ways to navigate through very large volumes of data, with the ability to display small regions for closer scrutiny." ; sc:featureList edam:operation_3443, edam:operation_3630 ; sc:name "MSight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/MSight/" ; biotools:primaryContact "MSight Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3710 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3591, edam:format_3603, edam:format_3682 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3383, edam:topic_3391, edam:topic_3520 ; sc:citation ; sc:description "Generate images from WIFF data and export to imzML." ; sc:featureList edam:operation_0335 ; sc:name "MSImageView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ms-imaging.org/wp/msimageview/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A software platform for rapidly creating computational tools for mass spectrometry-based proteomics." ; sc:featureList edam:operation_3214 ; sc:name "msInspect" ; sc:url "https://github.com/dhmay/msInspect" ; biotools:primaryContact "Martin McIntosh" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3244, edam:format_3654, edam:format_3682 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_3244, edam:format_3654, edam:format_3682 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547, edam:format_3620 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3547, edam:format_3620 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3383, edam:topic_3520 ; sc:citation "pubmed:23536269" ; sc:description "Vendor-neutral MATLAB program to view analyze mass spectrometry imaging data." ; sc:featureList edam:operation_0337, edam:operation_3214, edam:operation_3215, edam:operation_3443, edam:operation_3627, edam:operation_3695 ; sc:license "BSD-3-Clause" ; sc:name "MSiReader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www4.ncsu.edu/~dcmuddim/msireader.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640 ; sc:citation "pubmed:24371154" ; sc:description "C++ program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples." ; sc:featureList edam:operation_0415 ; sc:name "MSIsensor" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ding-lab/msisensor" ; biotools:primaryContact "Beifang Niu", "Kai Ye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3360, edam:topic_3474 ; sc:citation , "pubmed:33461213" ; sc:description """Microsatellite instability detection using cfDNA sequencing data. MSIsensor-ct is a novel method based machine learning, which can accurately determine the MSI status of cfDNA sequencing data with ultra-low ctDNA content. In practice, we recommend aiming for a minimum of 30 valid microsatellites to classify the MSI status using MSIsensor-ct. MSIsensor (https://github.com/niu-lab/msisensor) is a viable option if paired tumor and normal sequencing data are available, and MSIsensor2 (https://github.com/niu-lab/msisensor2) is effective for tumor-only samples.""" ; sc:featureList edam:operation_0337, edam:operation_0346, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "MSIsensor-ct" ; sc:url "https://github.com/niu-lab/MSIsensor-ct" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_2885, edam:topic_3676 ; sc:citation ; sc:description """Fast, accurate and matched-normal-sample-free detection of microsatellite instability. MSIsensor-pro is an updated version of msisensor. MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples.""" ; sc:featureList edam:operation_2422, edam:operation_3222, edam:operation_3435 ; sc:name "MSIsensor-pro" ; sc:url "https://github.com/xjtu-omics/msisensor-pro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_2269 ; sc:citation "pubmed:20399855" ; sc:description "Program designed to analyse structural data of liganded and unliganded proteins." ; sc:featureList edam:operation_2479 ; sc:name "MSITE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://biocomp.chem.uw.edu.pl/tools/msite" ; biotools:primaryContact "Wanda Sicinska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC7745203", "pubmed:33317272" ; sc:description """A General Approach to Mass Alignment in Mass Spectrometry Imaging. MSIWarp is a flexible tool to perform mass alignment of Mass Spectrometry Imaging (MSI) spectra. A key feature of MSIWarp is its compatibility with centroid spectra.""" ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3694, edam:operation_3803, edam:operation_3860 ; sc:license "MIT" ; sc:name "MSIWarp" ; sc:url "https://github.com/horvatovichlab/MSIWarp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3172, edam:topic_3295, edam:topic_3337, edam:topic_3407 ; sc:citation , "pubmed:32777102" ; sc:description """Making Omics Data Useful to the Broader Scientific Community. Metabolic Disorders Knowledge Portal. ||| CORRECT NAME OF TOOL COULD ALSO BE 'MSK-KP'""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3928 ; sc:name "MSK-KP" ; sc:url "http://mskkp.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_2640, edam:topic_3070 ; sc:description "Functions for retrieving data from the Cancer Genomics Data Server (CGDS) at MSKCC cBio." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "MSKCC CGDS Cancer Genomics Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.5.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/31297-mskcc-cgds-cancer-genomics-toolbox" ; biotools:primaryContact "Erik Larsson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description "Mining Scientific Literature. Automatic and physical analysis of published scientific literature in PDF format It allows the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on the different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied OCR." ; sc:featureList edam:operation_0306, edam:operation_3443 ; sc:license "AFL-3.0" ; sc:name "MSL" ; sc:operatingSystem "Windows" ; sc:url "https://zenodo.org/record/30941#.W3FRsC1kjfZ" ; biotools:primaryContact "Zeeshan Ahmed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_3301, edam:topic_3336, edam:topic_3339 ; sc:citation , "pmcid:PMC10284384", "pubmed:37289843" ; sc:description "Microbial synthetic lethal and rescue database." ; sc:featureList edam:operation_0292, edam:operation_2421, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "Mslar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://guolab.whu.edu.cn/Mslar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3336 ; sc:author "Chao Li" ; sc:citation , "pubmed:33657798" ; sc:description "MSLDOCK is a multi-swarm optimization docking program for flexible ligand docking and virtual screening." ; sc:featureList edam:operation_0244, edam:operation_3899, edam:operation_3938 ; sc:name "MSLDOCK" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/lcmeteor/MSLDOCK" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC8822486", "pubmed:35042333" ; sc:description "Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics." ; sc:featureList edam:operation_3630, edam:operation_3633, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MSLibrarian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MarcIsak/MSLibrarian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2269, edam:topic_2275 ; sc:citation , "pmcid:PMC5232355", "pubmed:28076801" ; sc:description "Statistical Models for Biomolecular Dynamics." ; sc:featureList edam:operation_2476 ; sc:license "GPL-2.0" ; sc:name "MSMBuilder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/msmbuilder/msmbuilder" ; biotools:primaryContact "Robert T. 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Applications include power studies, analytical comparisons, approximated Bayesian computation among others." ; sc:featureList edam:operation_2426 ; sc:license "LGPL-3.0" ; sc:name "msms" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.mabs.at/ewing/msms/index.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3365, edam:topic_3520, edam:topic_3572 ; sc:citation ; sc:description "Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors." ; sc:featureList edam:operation_0531, edam:operation_3214, edam:operation_3432, edam:operation_3627 ; sc:license "GPL-2.0" ; sc:name "msmsEDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/msmsEDA.html" ; biotools:primaryContact "Josep Gregori" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3365, edam:topic_3520, edam:topic_3572 ; sc:citation ; sc:description "Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. 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Marcotte" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520, edam:topic_3524 ; sc:citation ; sc:description "Simulates peptide retention times and chromatographic profiles." ; sc:featureList edam:operation_2426, edam:operation_3633 ; sc:license "Other" ; sc:name "mspire-simulator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/princelab/mspire-simulator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3244 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3244, edam:format_3655 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:18930952" ; sc:description "MS data processing in Ruby, including mzML reader/writer/converter, ''in-silico'' digestion, isotopic pattern calculation etc." ; sc:featureList edam:operation_0335, edam:operation_0366, edam:operation_3633 ; sc:name "mspire_mspire-sequest" ; sc:url "http://mspire.rubyforge.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation ; sc:description "M-SPLIT is a spectral-library search tool for identification of mixture spectra of up to two peptides." ; sc:featureList edam:operation_2421 ; sc:name "MSPLIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://proteomics.ucsd.edu/software-tools/msplit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0622, edam:topic_3315, edam:topic_3360 ; sc:citation , "pmcid:PMC6953292", "pubmed:31918677" ; sc:description """Multiset sparse partial least squares path modeling for high dimensional omics data analysis. 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3524 ; sc:citation ; sc:description """Phylogeny inference under the general Markov model using MST-backbone. Phylogeny inference via maximum likelihood is NP-hard. Current methods make simplifying assumptions such as stationarity, homogeneity, and time-reversibility for computational ease. The stationarity assumption is violated by empirical observations of GC content evolution, and might systematically bias phylogeny inference.""" ; sc:featureList edam:operation_0324, edam:operation_3435, edam:operation_3625 ; sc:license "GPL-3.0" ; sc:name "MST-backbone-GM" ; sc:url "https://github.com/prabhavk/mst-backbone-sem-gm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3572, edam:topic_3678 ; sc:citation ; sc:description "It is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool builds the genetic linkage map by first constructing a Minimum Spanning Tree, and hence the name MSTMap. The algorithm implemented in MSTMap is very efficient and can handle ultra-dense maps of up to 10,000~100,000 markers." ; sc:featureList edam:operation_2429 ; sc:name "MSTMap" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://alumni.cs.ucr.edu/~yonghui/mstmap.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_3520 ; sc:citation , "pmcid:PMC9441560", "pubmed:36072432" ; sc:description "A tool to proteome-widely predict the translatable circRNAs based on mass spectrometry" ; sc:featureList edam:operation_3501, edam:operation_3631, edam:operation_3767 ; sc:license "Not licensed" ; sc:name "MStoCIRC" ; sc:url "https://github.com/QUMU00/mstocirc-master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3320, edam:topic_3520 ; sc:citation , "pubmed:34818005" ; sc:description "A Tool for the Visualization of Mass Shifts in Deconvoluted Top-Down Proteomics Data for the Database-Independent Detection of Protein Modifications." ; sc:featureList edam:operation_0417, edam:operation_3215, edam:operation_3629, edam:operation_3633, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "MSTopDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PhilippKaulich/MSTopDiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC8398219", "pubmed:34436433" ; sc:description "MStractor is an R workflow package for non-targeted processing of LC-MS data." ; sc:featureList edam:operation_0337, edam:operation_3629, edam:operation_3891, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MStractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MetabolomicsSA/MStractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3315, edam:topic_3520 ; sc:citation , "pmcid:PMC7259675", "pubmed:32365209" ; sc:description """A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow. MStree: A model-flexible approach for estimating parameters during speciation with gene flow. MStree is an open-source software for estimating ancestral population sizes and species divergence times during speciation with gene flow.""" ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "mstree" ; sc:url "https://github.com/liujunfengtop/MStree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056 ; sc:citation "pubmed:19363128" ; sc:description "Software for detection of population structure in the presence of admixing and mutations from multi-locus genotype data. It is a mixed membership model (also referred to as an admixture model) which incorporates a mutation process on the observed genetic markers." ; sc:featureList edam:operation_3197 ; sc:name "mStruct" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=399" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3384, edam:topic_3444, edam:topic_3954 ; sc:citation , "pmcid:PMC7928319", "pubmed:33679900" ; sc:description "MSU-Net is a tool for multi-scale U-net for 2D medical image segmentation. Aiming at the limitation of the convolution kernel with a fixed receptive field and unknown prior to optimal network width in U-Net, multi-scale U-Net (MSU-Net) is proposed by us for medical image segmentation. First, multiple convolution sequence is used to extract more semantic features from the images. Second, the convolution kernel with different receptive fields is used to make features more diverse. The problem of unknown network width is alleviated by efficient integration of convolution kernel with different receptive fields. In addition, the multi-scale block is extended to other variants of the original U-Net to verify its universality. Five different medical image segmentation datasets are used to evaluate MSU-Net. A variety of imaging modalities are included in these datasets, such as electron microscopy, dermoscope, ultrasound, etc" ; sc:featureList edam:operation_3443 ; sc:name "MSU-Net" ; sc:url "https://github.com/CN-zdy/MSU_Net" ; biotools:primaryContact "Jinhuai Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3365, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC7691389", "pubmed:33294868" ; sc:description """A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit. Msuite: Multi-mode DNA methylation data analysis suite. Msuite is written in Perl and R for Linux/Unix platform. To run Msuite you need a Linux/Unix machine with Bash 4 (or higher), Perl 5.10 (or higher) and R 2.10 (or higher) installed.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3186, edam:operation_3196, edam:operation_3919 ; sc:name "Msuite" ; sc:url "https://github.com/hellosunking/Msuite/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3474 ; sc:citation , "pubmed:34843978" ; sc:description "A centralized online platform for predicting the m6A methylation degree of mRNA and the SNP-related traits in Maize." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "msup6 supA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/maize" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2814 ; sc:citation ; sc:description "Database of human missense variants mapped to 3D protein structures." ; sc:featureList edam:operation_2406, edam:operation_3197 ; sc:name "MSV3d" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://decrypthon.igbmc.fr/msv3d/cgi-bin/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:28636386" ; sc:description "Supports manual validation of post-translational modifications (PTMs) and their relative quantitation in small- and medium-size experiments. Thanks to its interactive interface MsViz can display peptide spectrum matches, sequence coverage information, or tandem mass spectrometry (MS/MS) spectra and extracted ion chromatograms. It allows easy and comprehensive visualization of small and medium bottom-up proteomics datasets." ; sc:featureList edam:operation_3630, edam:operation_3637, edam:operation_3649, edam:operation_3694, edam:operation_3704 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MsViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0.1" ; sc:url "http://msviz-public.vital-it.ch" ; biotools:primaryContact "Roman Mylonas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3391 ; sc:citation "pubmed:26504141" ; sc:description "Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions." ; sc:featureList edam:operation_2426 ; sc:name "MT-HESS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Bayesian-Omics/CHESS" ; biotools:primaryContact "Leonardo Bottolo", "Sylvia Richardson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0637, edam:topic_2885, edam:topic_3384 ; sc:citation , "pmcid:PMC7355274", "pubmed:32657360" ; sc:description """Identifying diagnosis-specific genotype-phenotype associations via joint multitask sparse canonical correlation analysis and classification. Multi-task sparse canonical correlation analysis and logistic regression. 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Systematically analyze mutations affecting cancer drug sensitivity based on individual genomic profiles. 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The first is for fast database search with one input structure. The second is for multiple structure alignment with two or more input structures. After the search is done, a multiple structure alignment is performed automatically with the top 10 structure, using the second module. 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sc:softwareHelp ; sc:url "https://docs.scvi-tools.org/en/stable/user_guide/models/multivi.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3473 ; sc:citation ; sc:description "Software package for multiview pattern recognition methods." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "BSD-4-Clause" ; sc:name "multiview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://b2slab.upc.edu/software-and-tutorials/multiview-package-multiview-clustering-dimensionality-reduction-methods/" ; biotools:primaryContact "Samir Kanaan-Izquierdo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3334 ; 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3572 ; sc:citation "pubmed:20377452" ; sc:description "Program used to generate the empirical results on the missing data problem for an arbitrary, but fixed (at input) number of states." ; sc:featureList edam:operation_2409 ; sc:name "multperf" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://csiflabs.cs.ucdavis.edu/~gusfield/software.html" ; biotools:primaryContact "Dan Gusfield" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "This extension includes non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). 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Basically it is a ultra-fast alignment of large-scale DNA and protein sequences" ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "MUMmer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "4" ; sc:url "http://mummer.sourceforge.net/" ; biotools:primaryContact "Help list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:citation "pubmed:18070356" ; sc:description "MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by HTS." ; sc:featureList edam:operation_0292 ; sc:name "MUMmerGPU" ; sc:softwareHelp ; sc:url "https://github.com/rmtheis/mummergpu/tree/master/mummergpu-2.0" ; biotools:primaryContact "Michael C Schatz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3318 ; sc:citation , "pmcid:PMC6768458", "pubmed:31568526" ; sc:description """Mathematical modelling of collective behaviour without the maths. Multiscale Modelling Tool - mathematical modelling without the maths. MuMoT: Multiscale Modelling Tool. MuMoT (Multiscale Modelling Tool) is a tool designed to allow sophisticated mathematical modelling and analysis, without writing equations - the class of models that can be represented is broad, ranging from chemical reaction kinetics to demography and collective behaviour - by using a web-based interactive interface with minimal coding, rapid development and exploration of models is facilitated - the tool may also be particularly useful for pedagogical demonstrations""" ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "MuMoT" ; sc:url "http://github.com/DiODeProject/MuMoT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169 ; sc:citation "pubmed:19605420" ; sc:description "Probabilistically reincorporates multi-mapping tags into mapped short read data." ; sc:featureList edam:operation_2429 ; sc:license "MIT" ; sc:name "MuMRescueLite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.gsc.riken.jp/osc/english/software/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:citation ; sc:description "Rapid standardisation and quality control of summary statistics from GWAS" ; sc:featureList edam:operation_0335, edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "MungeSumstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://neurogenomics.github.io/MungeSumstats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3338, edam:topic_3500 ; sc:citation , "pmcid:PMC5939957", "pubmed:28472651" ; sc:description "Mouse Ultrasonic Profile ExTraction: A signal processing tool for rapid and unsupervised analysis of ultrasonic vocalizations." ; sc:featureList edam:operation_3450 ; sc:license "Apache-2.0" ; sc:name "MUPET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sail.usc.edu/mupet/" ; biotools:primaryContact "Pat Levitt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0654, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:15980531" ; sc:description "Tool to assist in the design of multiplex PCR assays. It takes a set of DNA sequences and other experimental information as input and provides a set of multiplex PCR assays intended to cover as many of the user-supplied sequences as possible." ; sc:featureList edam:operation_0307, edam:operation_0308, edam:operation_0484, edam:operation_3196 ; sc:name "MuPlex" ; sc:url "http://apps.diatomsoftware.com/muplex/html/MuPlex.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:17109407" ; sc:description "Protein secondary structure and solvent accessibility prediction server based on a novel framework." ; sc:featureList edam:operation_0267, edam:operation_0384 ; sc:name "MUPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://digbio.missouri.edu/mupred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2533, edam:topic_3120, edam:topic_3474 ; sc:citation "pubmed:16372356" ; sc:description "Set of machine learning programs to predict how single-site amino acid mutation affects protein stability. We developed two machine learning methods: Support Vector Machines and Neural Networks." ; sc:featureList edam:operation_0331 ; sc:name "MUpro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mupro.proteomics.ics.uci.edu/" ; biotools:primaryContact "Jianlin Cheng", "Paul Rigor", "Pierre Baldi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0780, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description "A deep learning-based framework for estimating fine-scale germline mutation rates." ; sc:featureList edam:operation_3227, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MuRaL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CaiLiLab/MuRaL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC8317383", "pubmed:34320923" ; sc:description "A robust and multi-reference approach of RNA-seq transcript normalization." ; sc:featureList edam:operation_3192, edam:operation_3223, edam:operation_3435, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MUREN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/hippo-yf/MUREN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "MUSA (Motif finding using an UnSupervised Approach) is a new algorithm that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders." ; sc:featureList edam:operation_0238, edam:operation_2421 ; sc:name "MUSA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.5.6" ; sc:url "http://kdbio.inesc-id.pt/~ndm/software/musa.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3366, edam:topic_3572, edam:topic_3577 ; sc:citation , "pmcid:PMC7811020", "pubmed:33452365" ; sc:description "a graphical user interface for multi-OMICs data integration in radiogenomic studies." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3891 ; sc:name "MuSA-r" ; sc:url "https://gitlab.com/Zanfardino/musa" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1935, edam:format_1936, edam:format_1948, edam:format_1997 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1935, edam:format_1936, edam:format_1948, edam:format_1997 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_1947, edam:format_1982, edam:format_1997, edam:format_2331 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Robert Edgar" ; sc:citation , , , , "pmcid:PMC390337", "pubmed:15034147" ; sc:description "This tool performs multiple sequence alignments of nucleotide or amino acid sequences." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "MUSCLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "5" ; sc:url "https://www.drive5.com/muscle/" ; biotools:primaryContact "Robert Edgar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3954 ; sc:description "Implementation of an optical flow algorithm to track muscle length changes imaged with ultrasound." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Muscle fascicle tracking - Ultrasound" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32770-muscle-fascicle-tracking-ultrasound" ; biotools:primaryContact "Glen Lichtwark" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Robert Edgar" ; sc:citation , ; sc:description "Sequence alignment using the Multiple Sequence Comparison by Log-Expectation (MUSCLE) method" ; sc:featureList edam:operation_0492 ; sc:name "MUSCLE (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/muscle" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Multiple sequence algnment tool." ; sc:featureList edam:operation_0492 ; sc:name "Muscle WS (jabaws)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.compbio.dundee.ac.uk/jabaws" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC7747357", "pubmed:33338203" ; sc:description """A web service for studying gene expression in human skeletal muscle. MuscleAtlasExplorer(BETA)2.""" ; sc:featureList edam:operation_0571, edam:operation_3463 ; sc:name "MuscleAtlasExplorer" ; sc:url "https://mae.crc.med.lu.se/mae2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation , "pubmed:11524378" ; sc:description "Multi-query Sequence Blast Output Examination is a program designed for multi-query sequence BLAST output examination. It examines the BLAST output, extracts the informative parameters of BLAST hits, and saves them in tabular form in either text or HTML format. The hit tables are optionally further analyzed with the program to produce subsets of BLAST hits according to user-specified criteria." ; sc:featureList edam:operation_0224 ; sc:name "MuSeqBox" ; sc:operatingSystem "Linux" ; sc:softwareVersion "20131003" ; sc:url "http://brendelgroup.org/bioinformatics2go/MuSeqBox.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3173 ; sc:citation ; sc:description "MuSERA (Multiple Sample Enriched Region Assessment) is a broadly useful stand-alone tool for both interactive and batch analysis of combined evidence from enriched regions in multiple ChIP-seq or DNase-seq sample replicates, with a user-friendly graphical interface." ; sc:name "MuSERA" ; sc:operatingSystem "Windows" ; sc:url "http://www.bioinformatics.deib.polimi.it/MuSERA/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0654, edam:topic_3053, edam:topic_3321 ; sc:citation , "pubmed:26355961" ; sc:description "Designed to analyze (aligned) gene libraries, in particular in case that codon directed mutagenesis was applied to them. The program generates several tables providing information about trinucleotide characteristics, deletions, substitutions and amino acids distributions." ; sc:featureList edam:operation_0258 ; sc:name "MuSi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gobics.de/ingo/musi/musi.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3125, edam:topic_3534 ; sc:citation "pubmed:22210894" ; sc:description "Tool for uncovering multiple peptides and nucleic acids binding specificities from sequence data. MUSI provides a simple interface for processing short peptides or nucleic acid sequence data. Starting from a set of sequences observed to bind to a given target, it automatically generates an optimal number of motifs based on the different specificity patterns present in the data." ; sc:featureList edam:operation_2423 ; sc:name "MUSI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.kimlab.org/software/musi" ; biotools:primaryContact "David Gfeller", "Marc Tyndel", "Philip M. Kim", "TaeHyung Simon Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640 ; sc:citation ; sc:description "Mutational Signatures in Cancer is a shiny-based web application aimed to visualize the somatic mutational profile of a series of provided samples (different formats are allowed) and to extract the contribution of the reported mutational signatures on their variation profile. It is mainly based on the MutationalPatterns R package." ; sc:featureList edam:operation_2945 ; sc:license "MIT" ; sc:name "MuSiCa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html" ; biotools:primaryContact "Sergi Castellví-Bel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:20479877" ; sc:description "Assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ~800 human full-length cDNA clones." ; sc:featureList edam:operation_0310 ; sc:name "MuSICA 2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://musica.gi.k.u-tokyo.ac.jp/" ; biotools:primaryContact "Masahiro Kasahara", "Reginaldo Kuroshu", "Shin-ichi Morishita", "Yutaka Suzuki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC8639789", "pubmed:34625425" ; sc:description "The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "musicatk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://camplab.net/musicatk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0121, edam:topic_0625, edam:topic_3360 ; sc:citation , "pubmed:36076312" ; sc:description "An R package for detecting multiple signatures with similar predictive performance." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "muSignAl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ShuklaLab/muSignAl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0601, edam:topic_3474 ; sc:citation , "pmcid:PMC7319475", "pubmed:32324217" ; sc:description """A deep-learning based webserver for protein post-translational modification site prediction and visualization. MusiteDeep is a deep-learning based webserver for protein post-translational modification site (PTM) prediction and visualization. The MusiteDeep web server is available at http://www.musite.net. This repository contains the stand-alone tools in python to run MusiteDeep on a local machine:.""" ; sc:featureList edam:operation_0415, edam:operation_0417, edam:operation_0480, edam:operation_3755 ; sc:license "MIT" ; sc:name "MusiteDeep" ; sc:url "https://www.musite.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654 ; sc:citation ; sc:description "It is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. It is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time." ; sc:featureList edam:operation_0310, edam:operation_0525 ; sc:name "Musket" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://musket.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation ; sc:description "Database of standardized mouse morphology data for morphometric meta-analyses." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MusMorph" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.facebase.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0798 ; sc:citation "pubmed:19393167" ; sc:description "Improved de novo detection program for recently active miniature inverted repeat transposable elements (MITEs)." ; sc:featureList edam:operation_0427 ; sc:name "MUST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.healthinformaticslab.org/supp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3382 ; sc:citation ; sc:description """Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation. Mustache (Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation) is a tool by Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi and Ferhat Ay (ferhatay@lji.org).""" ; sc:featureList edam:operation_0481, edam:operation_3222, edam:operation_3435 ; sc:license "MIT" ; sc:name "Mustache" ; sc:url "https://github.com/ay-lab/mustache" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation "pubmed:16736488" ; sc:description "Softwear for the alignment of multiple protein structures." ; sc:featureList edam:operation_0295 ; sc:name "MUSTANG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.csse.monash.edu.au/~karun/Site/mustang.html" ; biotools:primaryContact "Arun Konagurthu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7289789", "pubmed:32528107" ; sc:description """Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci. MuStARD - autoMated SmAll Rna Detection.""" ; sc:featureList edam:operation_0443, edam:operation_3222, edam:operation_3792 ; sc:license "MIT" ; sc:name "MuStARD" ; sc:url "http://gitlab.com/RBP_Bioinformatics/mustard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623, edam:topic_3168 ; sc:citation ; sc:description "Multiple structure-guided sequence alignment of protein families." ; sc:featureList edam:operation_0492 ; sc:name "Mustguseal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://biokinet.belozersky.msu.ru/mustguseal" ; biotools:primaryContact "Vytas K Švedas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3400 ; sc:citation , "pmcid:PMC7439739" ; sc:description """Minimal Unsatisfiable Subsets Enumeration Tool. MUST is a tool for online enumeration of minimal unsatisfiable subsets (MUSes) of a given unsatisfiable set of constraints. The tool currently implements three online MUS enumeration algorithms: MARCO [9], TOME [2], and ReMUS [3], and supports MUS enumeration in three constraint domains: SAT, SMT, and LTL. A paper [1] describing MUST will be presented at TACAS 2020.""" ; sc:license "MIT" ; sc:name "MUSTool" ; sc:url "https://github.com/jar-ben/mustool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3321 ; sc:citation , "pmcid:PMC4739551", "pubmed:26840129" ; sc:description "Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics." ; sc:featureList edam:operation_0361, edam:operation_3202 ; sc:name "MutAid" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/mutaid/" ; biotools:primaryContact "Ram Vinay Pandey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3173 ; sc:citation , "pubmed:29790943" ; sc:description "MUTation AnaLyIS toolKit. Comprehensive analysis of somatic DNA mutations with genome regulation elements and DNA sequence contexts." ; sc:featureList edam:operation_0438, edam:operation_3227, edam:operation_3501 ; sc:name "mutalisk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mutalisk.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3325, edam:topic_3577 ; sc:citation , "pubmed:26231427" ; sc:description "Tool that checks, analyzes and corrects descriptions of sequence variants according to the standard human sequence variant nomenclature of the Human Genome Sequence Variation Society (HGVS)." ; sc:featureList edam:operation_2428, edam:operation_3197, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Mutalyzer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://mutalyzer.nl" ; biotools:primaryContact "Vis JK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0085 ; sc:description "Checks sequence variant nomenclature according to the guidelines of the Human Genome Variation Society." ; sc:featureList edam:operation_2403 ; sc:name "Mutalyzer WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://mutalyzer.nl/soap-api" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3519, edam:topic_3572 ; sc:citation "pubmed:27044645" ; sc:description "Online tool for assessing the mutational spectrum of epPCR (error-prone PCR) libraries with poor sampling." ; sc:featureList edam:operation_2403 ; sc:name "Mutanalyst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mutanalyst.com/" ; biotools:primaryContact "Matteo P. Ferla" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_0625, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC7845113", "pubmed:33514395" ; sc:description """A computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. My Personal Mutanome: A Personalized Cancer Medicine Platform for Searching Network Perturbing Alleles Linking Somatic Genotype to Phenotype. A pharmacogenomics database for prioritizing actionable mutations for personalized cancer treatments.""" ; sc:featureList edam:operation_0417, edam:operation_2492, edam:operation_3196 ; sc:license "MIT" ; sc:name "Mutanome" ; sc:url "https://mutanome.lerner.ccf.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_0769, edam:topic_3068, edam:topic_3325, edam:topic_3673 ; sc:citation ; sc:description """A Pipeline for Identifying Saccharomyces cerevisiae Mutations. A bioinformatics pipeline for identification and characterization of mutations in Saccharomyces cerevisiae. MutantHuntWGS compares data, input in FASTQ format, from a mutant strain to a wild-type strain to identify high confidence sequence variants present only in the mutant. This pipeline was designed to be as user friendly as possible.""" ; sc:featureList edam:operation_0331, edam:operation_3196, edam:operation_3227 ; sc:name "MutantHuntWGS" ; sc:url "https://github.com/mae92/MutantHuntWGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pubmed:32875562" ; sc:description """A platform linking gene expression changes and mutation status in solid tumors. connect mutation status to gene expression changes in solid tumours. muTarget is a cancer biomarker / target discovery tool with two major functions.""" ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3223 ; sc:name "muTarget" ; sc:url "http://www.mutarget.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0199, edam:topic_3170 ; sc:citation , "pmcid:PMC7319544", "pubmed:32392303" ; sc:description """Analysis and visualization of mutation-induced changes in RNA structure. MutaRNA (Mutational Analysis of RNAs) predicts and visualizes the mutation-induced structure changes of a single-nucleotide polymorphism (SNP) in an RNA sequence. This covers changes in the accessibility (single-strandedness) of the molecule, its intra-molecular base pairing potential and its the base pairing probabilities. Combined with evaluation results of tools like remuRNA and RNAsnp, MutaRNA enables a detailed evaluation of a mutation's effects on RNA structure formation.""" ; sc:featureList edam:operation_0490, edam:operation_0570, edam:operation_2441 ; sc:name "MutaRNA" ; sc:url "http://rna.informatik.uni-freiburg.de/MutaRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2640 ; sc:description "Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations." ; sc:featureList edam:operation_3227 ; sc:name "Mutascope" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/mutascope/" ; biotools:primaryContact "Shawn Yost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3053 ; sc:citation , "pmcid:PMC4833594", "pubmed:26841357" ; sc:description "A functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures." ; sc:featureList edam:operation_2454 ; sc:name "mutation3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mutation3d.org/" ; biotools:primaryContact "Haiyuan Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:31746978" ; sc:description """Prediction of Mutation Effects using a Deep Temporal Convolutional Network. This is the code for the paper Prediction of Mutation Effects using a Deep Temporal Convolutional Network. https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz873/5634146. The code is compatible with tensorflow-gpu=1.10.0 and python=2.7""" ; sc:featureList edam:operation_0292, edam:operation_0331, edam:operation_3439 ; sc:name "mutationTCN" ; sc:url "https://github.com/ha01994/mutationTCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168, edam:topic_3299, edam:topic_3314 ; sc:citation ; sc:description """Open Source Oligo Design Platform for Protein Engineering. Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins. Mutation Maker, An Open Source Oligo Design Software For Mutagenesis and De Novo Gene Synthesis Experiments.""" ; sc:featureList edam:operation_0308, edam:operation_0337, edam:operation_3237 ; sc:license "GPL-3.0" ; sc:name "Mutation Maker" ; sc:url "https://github.com/Merck/Mutation_Maker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3063, edam:topic_3316, edam:topic_3325, edam:topic_3473, edam:topic_3512 ; sc:citation , , "pubmed:20676075", "pubmed:24681721" ; sc:description "It evaluates the pathogenic potential of DNA sequence alterations. It is designed to predict the functional consequences of amino acid substitutions as well as intronic and synonymous alterations, short insertion and/or deletion mutations and variants spanning intron-exon borders." ; sc:featureList edam:operation_0367, edam:operation_0452, edam:operation_2409, edam:operation_3197, edam:operation_3202, edam:operation_3439, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "MutationTaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mutationtaster.org" ; biotools:primaryContact "Dominik Seelow", "Jana Marie Schwarz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2533, edam:topic_2640 ; sc:citation , "pmcid:PMC4702822", "pubmed:26590264" ; sc:description "This enables you to explore mutation hotspots identified in protein domains from more than 5000 patients across 22 cancer types." ; sc:featureList edam:operation_0224 ; sc:name "MutationAligner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.mutationaligner.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution data." ; sc:featureList edam:operation_0337, edam:operation_3202 ; sc:license "MIT" ; sc:name "MutationalPatterns" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html" ; biotools:primaryContact "Francis Blokzijl", "Roel Janssen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0203, edam:topic_3168, edam:topic_3325 ; sc:citation , "pubmed:31106342" ; sc:description "Make the analysis of Next-Generation Sequencing data simple. Depending on your background and interest, it offers various modes with optimised settings: Clinical (HPO), Clinical (Gene Panels), Gene Function and Basic Search." ; sc:featureList edam:operation_2495, edam:operation_3227, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "MutationDistiller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://www.mutationdistiller.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation ; sc:description """The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome. MutationExplorer is a lightweight web application for exploring somatic mutations in cancer datasets. It is based on R and the Shiny framework. MutationExplorer is currently most usable for breast cancer samples, since the relevant biomarkers for patient selection (e.g. clinical status of ER and PgR) are hardcoded.""" ; sc:featureList edam:operation_0331, edam:operation_2495, edam:operation_3227 ; sc:license "BSD-2-Clause" ; sc:name "MutationExplorer" ; sc:url "http://oncogenomics.bmc.lu.se/MutationExplorer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2294 ; sc:name "Sequence variation ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "MutationInfo is a python package to extract the position, the reference and the alternative sequence of a genomic variant. It accepts variants in dbSNP rs format or in HGVS format." ; sc:featureList edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MutationInfo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3" ; sc:url "https://www.epga.gr/MutationInfo/" ; biotools:primaryContact "Alexandros Kanterakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "This library provides capabilities for analysis of mutation properties. Two different analysis approaches are supported: (1) log-linear analysis of neighbourhood base influences on mutation coupled with a sequence logo like representation of influences; (2) log-linear analysis of mutation spectra, the relative proportions of different mutation directioons from a starting base. A logo-like visualisation of the latter is also supported." ; sc:featureList edam:operation_2945 ; sc:name "MutationMotif" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bitbucket.org/pycogent3/mutationmotif" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199 ; sc:description "Identifying potential mutations across target gene sequences." ; sc:featureList edam:operation_0564 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Mutations-Meta-Analyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/Mutations-Meta-Analyser" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_1775 ; sc:citation ; sc:description "Employs a Bayes classifier to eventually predict the disease potential of an alteration. The Bayes classifier is fed with the outcome of all tests and the features of the alterations and calculates probabilities for the alteration to be either a disease mutation or a harmless polymorphism." ; sc:featureList edam:operation_0253 ; sc:license "Not licensed" ; sc:name "MutationTaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mutationtaster.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0199, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:37105446" ; sc:description "A tool to identify disease-prone sites in cancer using deep learning." ; sc:featureList edam:operation_0267, edam:operation_0451, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:name "MutBLESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/MutBLESS/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0199, edam:topic_3512, edam:topic_3922 ; sc:citation , "pmcid:PMC7355298", "pubmed:32657416" ; sc:description """Identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search. MutCombinator - Combinatorial mutation search. MutCombinator enables us to practically identify mutated peptides from tandem mass spectra allowing combinatorial mutations during the database search. It uses an upgraded version of a variant graph, keeping track of frame information. The variant graph is indexed by nine nucleotides for fast access. Combinations of point mutations are considered, and also it can be practically applied together with a large mutation database such as COSMIC.""" ; sc:featureList edam:operation_0398, edam:operation_3227, edam:operation_3643, edam:operation_3644, edam:operation_3646 ; sc:name "MutCombinator" ; sc:url "https://prix.hanyang.ac.kr/download/mutcombinator.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_0821, edam:topic_2830 ; sc:citation , "pmcid:PMC8993498", "pubmed:35421792" ; sc:description "A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2." ; sc:featureList edam:operation_0252, edam:operation_0478, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MutCov" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://jianglab.org.cn/MutCov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0114, edam:topic_0199, edam:topic_2814 ; sc:citation "pubmed:14512363", "pubmed:15980479" ; sc:description "Database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers." ; sc:featureList edam:operation_0320, edam:operation_0331, edam:operation_0339, edam:operation_0346, edam:operation_3202 ; sc:name "MutDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mutdb.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1921 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2032 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3676 ; sc:citation "pubmed:23396013" ; sc:description "A method for identification of somatic point mutations in next generation sequencing data of cancer genomes." ; sc:featureList edam:operation_0484, edam:operation_2238, edam:operation_3227, edam:operation_3695 ; sc:name "MuTect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.broadinstitute.org/cancer/cga/mutect" ; biotools:primaryContact "MuTect Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC7393734", "pubmed:32736515" ; sc:description """A flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. Author: Anthony R. Soltis (anthony.soltis.ctr@usuhs.edu, anthonyrsoltis@gmail.com). Institution: Uniformed Services University of the Health Sciences, Bethesda, MD. MutEnricher is a flexible toolset that performs somatic mutation enrichment analysis of both protein-coding and non-coding genomic loci from whole genome sequencing (WGS) data, implemented in Python and usable with Python 2 and 3. License: MIT License, see License.""" ; sc:featureList edam:operation_3227, edam:operation_3435, edam:operation_3501 ; sc:name "MutEnricher" ; sc:url "https://github.com/asoltis/MutEnricher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3344 ; sc:citation , "pmcid:PMC4590705", "pubmed:26427375" ; sc:description "Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Australia." ; sc:featureList edam:operation_2423 ; sc:name "MutExSL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v1" ; sc:url "https://sites.google.com/site/mutexsl/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3053, edam:topic_3534 ; sc:citation , "pmcid:PMC5210621", "pubmed:27907895" ; sc:description "Mutated ligand binding site gene DataBase." ; sc:featureList edam:operation_2421 ; sc:name "mutLBSgeneDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinfo.uth.edu/mutLBSgeneDB/" ; biotools:primaryContact "Zhongming Zha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation ; sc:description "MutPred is a web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, it predicts molecular cause of disease." ; sc:featureList edam:operation_2479 ; sc:name "MutPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://mutpred.mutdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0780, edam:topic_3308, edam:topic_3407 ; sc:citation , "pmcid:PMC7659623", "pubmed:33240618" ; sc:description """An R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. Transcriptomic data can uncover complex biological processes in part through the improved understanding of gene coexpression patterns.""" ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3463, edam:operation_3929 ; sc:name "MutRank" ; sc:url "https://github.com/eporetsky/MutRank" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3053 ; sc:citation ; sc:description "Draws a Needle-Plot for mutation data (stacked)." ; sc:featureList edam:operation_0337 ; sc:name "muts-needle-plot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioJS" ; sc:softwareHelp ; sc:softwareVersion "0.4.0" ; sc:url "https://github.com/bbglab/muts-needle-plot" ; biotools:primaryContact "Michael P Schroeder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0769, edam:topic_3676 ; sc:citation , "pmcid:PMC10236832", "pubmed:37264470" ; sc:description "Flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data." ; sc:featureList edam:operation_0337, edam:operation_3197, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mutscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fmicompbio/mutscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_2640, edam:topic_3360, edam:topic_3673 ; sc:citation , "pmcid:PMC8559159", "pubmed:34734182" ; sc:description "An analytical toolkit for probing the mutational landscape in cancer genomics." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MutScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/anitalu724/MutScape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:16845093" ; sc:description "Human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations." ; sc:featureList edam:operation_0308, edam:operation_2419, edam:operation_3672 ; sc:name "MutScreener" ; sc:url "http://bioinfo.bsd.uchicago.edu/MutScreener.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2269 ; sc:citation ; sc:description """An R package to map spectra to mutational signatures based on shot-noise modeling. R package mutSigMapper aims to resolve a critical shortcoming of existing software for mutational signature analysis, namely that of finding parsimonious and biologically plausible exposures. By implementing a shot-noise-based model to generate spectral ensembles, this package addresses this gap and provides a quantitative, non-parametric assessment of statistical significance for the association between mutational signatures and observed spectra.""" ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "mutSigMapper" ; sc:url "https://github.com/juliancandia/mutSigMapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640 ; sc:citation ; sc:description """An R Package for Extraction and Analysis of Cancer Mutational Signatures. mutSignatures R package - dev version - 2.1. Decipher Mutational Signatures from Somatic Mutational Catalogs. Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes.""" ; sc:featureList edam:operation_2422, edam:operation_3227 ; sc:license "GPL-2.0" ; sc:name "mutSignatures" ; sc:url "https://CRAN.R-project.org/package=mutSignatures" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3295, edam:topic_3452, edam:topic_3673 ; sc:citation , "pmcid:PMC7355300", "pubmed:32657413" ; sc:description """Cancer mutational signatures representation by large-scale context embedding. MutSpace is a method aiming to address the computational challenge to consider large-scale sequence context for mutational signatures.""" ; sc:featureList edam:operation_0363, edam:operation_3435, edam:operation_3891 ; sc:license "MIT" ; sc:name "MutSpace" ; sc:url "https://github.com/ma-compbio/MutSpace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3168 ; sc:citation "pubmed:24689688" ; sc:description "Application to next-generation sequencing based RNA structure probing." ; sc:featureList edam:operation_2439 ; sc:name "MutualFold" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/MutualFold/" ; biotools:primaryContact "Cuncong Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0769 ; sc:citation , "pubmed:33689914" ; sc:description "MutVis is an automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains. MutVis is an open-source, user-friendly, automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains, regardless the number, origin or species. The current framework integrates various opensource tools and is scripted using Python, R programming and Snakemake workflow management software. MutVis supports variant calling, processing of VCF files, transition and transversion graphical representation, generation of mutational count matrix, graphical visualization of basepair substitution spectrum (BPS) and mutation signatures." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3461 ; sc:license "MIT" ; sc:name "MutVis" ; sc:url "https://github.com/AkshathaPrasanna/MutVis" ; biotools:primaryContact "Vidya Niranjan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2885, edam:topic_3056, edam:topic_3299, edam:topic_3943 ; sc:citation ; sc:description """Assigning and summarizing mutation types for analyzing germline mutation spectra. A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs. See documentation for install and usage information. Ancestral \\(k\\)-mer Mutation Types for SNP Data — mutyper documentation. Pairs well with the package mushi, which performs mutation spectrum history inference. Ancestral k-mer mutation types for SNP data.""" ; sc:featureList edam:operation_0484, edam:operation_3436, edam:operation_3661 ; sc:license "MIT" ; sc:name "mutyper" ; sc:url "https://harrispopgen.github.io/mutyper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3305, edam:topic_3390 ; sc:citation ; sc:description """An end-to-end workflow for statistical analysis and inference of large-scale biomedical datasets. muvis is a visualization and analysis toolkit for multivariate datasets. To use this package, you will need the R statistical computing environment (version 3.0 or later).""" ; sc:featureList edam:operation_0337, edam:operation_3557, edam:operation_3658, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "MUVIS" ; sc:url "https://github.com/bAIo-lab/muvis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_0780, edam:topic_0798 ; sc:citation , "pubmed:34586393" ; sc:description "Mutant-seq library analysis and annotation." ; sc:featureList edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MuWU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tgstoecker/MuWU" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:18189342" ; sc:description "Multiplexed quantitiave proteomics using differential stable isotope labeling." ; sc:featureList edam:operation_3630, edam:operation_3632, edam:operation_3635, edam:operation_3705, edam:operation_3715 ; sc:license "GPL-3.0" ; sc:name "muxQuant" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.ms-utils.org/muxQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , ; sc:description "This repository contains a software mvBIMBAM, a version of BIMBAM for multivariate association analysis, implementing a Bayesian approach for genetic association analysis of multiple related phenotypes. We adapted source codes in BIMBAM to deal with multiple related phenotypes." ; sc:featureList edam:operation_2945 ; sc:license "GPL-3.0" ; sc:name "mvBIMBAM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/heejungshim/mvBIMBAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , "pmcid:PMC4448275", "pubmed:25962835" ; sc:description "R package for multi-view genomic data simulator. It is a tool in R to generate synthetic datasets from ordinary differential equations (ODE)-based models with known parameters." ; sc:featureList edam:operation_0337 ; sc:name "MVBioDataSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SALERNO" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://elixir-italy.org/salerno/en/archives/servizi/mvbiodatasim" ; biotools:primaryContact , "Paola Galdi", "Roberto Tagliaferri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Creates classes used in model-view-controller (MVC) design." ; sc:featureList edam:operation_2990 ; sc:license "GPL-3.0" ; sc:name "MVCClass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MVCClass.html" ; biotools:primaryContact "Elizabeth Whalen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:author "Angela Serra" ; sc:citation , "pmcid:PMC4539887", "pubmed:26283178" ; sc:description "R package for multi-view genomic data integration methodology. It is a tool in R that combines different types of measurements (such as mRNA expression, miRNA expression, DNA methylation, clinical data, etc) for a given set of samples (e.g. patients). The aim is to combine dimension reduction, variable selection, clustering (for each available data type) and data integration methods to find patient subtypes." ; sc:featureList edam:operation_2409 ; sc:name "MVDA" ; sc:provider "ELIXIR-ITA-SALERNO" ; sc:softwareVersion "1" ; sc:url "http://neuronelab.unisa.it/a-multi-view-genomic-data-integration-methodology/" ; biotools:primaryContact , "Paola Galdi", "Roberto Tagliaferri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:34499148" ; sc:description "A novel multi-view graph convolutional network (MVGCN) framework for link prediction in biomedical bipartite networks." ; sc:featureList edam:operation_3436, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MVGCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fuhaitao95/MVGCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0089 ; sc:citation ; sc:description "Platform-independent tools to identify GO terms that are differentially active in multiple contrasts of interest. Given a matrix of one-sided p-values, it uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify them as significantly more active, less active, or not significantly differentially active in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile of differential activity." ; sc:featureList edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "mvGST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mvGST.html" ; biotools:primaryContact "John R. Stevens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3174, edam:topic_3474, edam:topic_3520, edam:topic_3697 ; sc:citation , "pmcid:PMC9022840", "pubmed:35404958" ; sc:description "Microbiome-based disease prediction with multimodal variational information bottlenecks." ; sc:featureList edam:operation_3359, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MVIB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nec-research/microbiome-mvib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Normalization tests for shoulder electromyographic signals" ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "MVIC Combination Generator" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/56054-mvic_combination_generator" ; biotools:primaryContact "Fabien" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Re-format the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout." ; sc:featureList edam:operation_0492 ; sc:name "Mview API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/mview_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1948, edam:format_1982 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_1948, edam:format_1982 ; sc:name "Sequence search results" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071 ; sc:author "Nigel Brown" ; sc:citation , ; sc:description "Reformat the results of a sequence database search (BLAST, FASTA) or a multiple alignment adding optional HTML markup to control colouring and web page layout." ; sc:featureList edam:operation_0335 ; sc:name "MView (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/msa/mview" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169, edam:topic_3170, edam:topic_3320, edam:topic_3794 ; sc:citation , "pmcid:PMC8689837", "pubmed:34718748" ; sc:description "MVIP provides a large number of available multi-omics data under viral infection in various species." ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "MVIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mvip.whu.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3517, edam:topic_3974 ; sc:citation , "pmcid:PMC10484060", "pubmed:37243672" ; sc:description "Leveraging the genetic correlation between traits to detect epistasis in genome-wide association studies." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mvMAPIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lcrawlab/mvMAPIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2275 ; sc:description "Mainly for the illustration and processing of structure-related information which is useful in structure prediction." ; sc:featureList edam:operation_2409, edam:operation_2423, edam:operation_2480 ; sc:name "MVP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/MVP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3512, edam:topic_3520 ; sc:citation ; sc:description """An extensible Galaxy plug-In for multi-omics data visualization and exploration. The Galaxy MVP visualization plugin enables viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data.""" ; sc:featureList edam:operation_0337, edam:operation_3631, edam:operation_3695 ; sc:name "MVP_A" ; sc:url "https://github.com/galaxyproteomics/mvpapplication-git.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC7287158", "pubmed:32581662" ; sc:description """A Classification and Regression Toolbox for Multi-Dimensional Data. Matlab toolbox for classification and regression of multi-dimensional data. This is the companion repository of the MVPA-Light paper.""" ; sc:featureList edam:operation_3359, edam:operation_3659, edam:operation_3891 ; sc:license "MIT" ; sc:name "MVPA-Light" ; sc:url "http://github.com/treder/mvpa-light" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3361, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "MVPAlab is a MATLAB-based and very flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data. The MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contribution analyses. This toolbox has been designed to include an easy-to-use and very intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for those users with few or no previous coding experience. However, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner." ; sc:featureList edam:operation_3435, edam:operation_3658, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MVPAlab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/dlopezg/mvpalab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:35940520" ; sc:description "A highly efficient and sensitive pathogenicity prediction tool for missense variants." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "mvPPT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.mvppt.club" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0625 ; sc:citation , "pmcid:PMC5701343", "pubmed:29169342" ; sc:description "CIM QTL mapping via multivariate statistical method in an outbred full-sib family." ; sc:featureList edam:operation_0282, edam:operation_3232 ; sc:name "MVQTLCIM" ; sc:softwareHelp ; sc:url "https://github.com/tongchf/mvqtlcim" ; biotools:primaryContact "Chunfa Tong", "Fenxiang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3315, edam:topic_3697 ; sc:citation , "pmcid:PMC7202302", "pubmed:32391139" ; sc:description """An R-package that estimates a climate-driven mosquito-borne viral suitability index. Estimator of climate-driven, mosquito-borne viral suitability index. Understanding how climate dictates the timing and potential of mosquito-borne viral transmission is essential for preparedness of public health systems and design of control strategies. We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. The package estimates a suitability index based on a climate-driven mathematical expression for the basic reproductive number (R0) of a well established mathematical model for the transmission dynamics of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, suitability can be estimated for specific and viral species, as well as different regions of the globe.""" ; sc:featureList edam:operation_3946 ; sc:license "GPL-3.0" ; sc:name "MVSE" ; sc:url "http://sourceforge.net/projects/mvse/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:citation , "pmcid:PMC8351779", "pubmed:34373856" ; sc:description "A toolset for quantifying and designing multivalent interactions." ; sc:featureList edam:operation_2492, edam:operation_3799, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "MVsim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sarkarlab.github.io/MVsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_2258, edam:topic_2259, edam:topic_3172 ; sc:citation ; sc:description "It provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results." ; sc:featureList edam:operation_2428 ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "MWASTools" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/MWASTools.html" ; biotools:primaryContact "Andrea Rodriguez-Martinez", "Rafael Ayala" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find weights common to multiple molecular weights files." ; sc:featureList edam:operation_0398 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mwcontam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/mwcontam.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Filter noisy data from molecular weights file." ; sc:featureList edam:operation_0398 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mwfilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/mwfilter.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:34320315" ; sc:description "An Algorithm for Context-Based Annotation of Liquid Chromatography-Mass Spectrometry Features through Diffusion in Graphs." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mWISE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/b2slab/mWISE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC6683425", "pubmed:31382962" ; sc:description "Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms | maximum weighted merger method" ; sc:featureList edam:operation_3432, edam:operation_3766, edam:operation_3792 ; sc:name "MWMM" ; sc:url "https://github.com/BaiLab/MWMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3277 ; sc:citation ; sc:description "MWT computes FDR based on a moderated version of the Welch test. It’s particularly suited for small samples comparisons exprecially with unequal variances" ; sc:featureList edam:operation_2495 ; sc:name "MWT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.2.7" ; sc:url "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC8000456", "pubmed:33808985" ; sc:description "mwTab is a Python library for RESTful access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository. The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_2428, edam:operation_3431 ; sc:license "BSD-3-Clause" ; sc:name "mwTab" ; sc:softwareHelp , ; sc:url "https://github.com/MoseleyBioinformaticsLab/mwtab" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "Mann-Whitney-Wilcoxon non parametric test for two unpaired groups." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "mwwtest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/25830-mwwtest" ; biotools:primaryContact "Giuseppe Cardillo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:author "Giorgos Athineou", "Ioannis Tsamardinos", "Vincenzo Lagani" ; sc:citation ; sc:description "Mens per Machina. Flexible feature selection, cross-validation and Bayesian Networks for large datasets." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "MXM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1.3.9" ; sc:url "https://cran.r-project.org/web/packages/MXM/index.html" ; biotools:primaryContact "Michail Tsagris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_3293 ; sc:citation "pubmed:18665426" ; sc:description "Java program for computing a phylogenetic network from a collection of phylogenetic trees." ; sc:featureList edam:operation_0323 ; sc:name "MY-CLOSURE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/my-closure" ; biotools:primaryContact "Qiong Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3512, edam:topic_3697 ; sc:citation , "pmcid:PMC6602519", "pubmed:31049585" ; sc:description "Server for identification and characterization of diversity-generating retroelements." ; sc:featureList edam:operation_2422, edam:operation_3092, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "myDGR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://omics.informatics.indiana.edu/myDGR" ; biotools:primaryContact "Yuzhen Ye" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3511 ; sc:citation ; sc:description "Analysis of forensic DNA profiles." ; sc:featureList edam:operation_3504 ; sc:name "My Forensic Loci queries" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://github.com/beukueb/myflq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0623, edam:topic_0780, edam:topic_3293 ; sc:citation , "pmcid:PMC8933966", "pubmed:35305581" ; sc:description "This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new transcriptome of genome assemblies." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3258, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MYB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bpucker/MYB_annotator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3295, edam:topic_3304, edam:topic_3334, edam:topic_3419 ; sc:citation , , , , ; sc:description "MyBrain-Seq is a Compi pipeline for performing full analyses of miRNA-Seq data, with particular interest on neuropsychiatric data. It can automatically identify differentially expressed microRNAs (DE miRNAs) between two conditions using two differential expression analysis software, namely DESeq2 and EdgeR, and is able to offer an integrated result suitable for experimental validation. Additionally, a functional analysis module puts biological meaning behind the list of DE miRNAs and eases the process of biomarker identification." ; sc:featureList edam:operation_0531, edam:operation_2436, edam:operation_2478, edam:operation_2938, edam:operation_3187, edam:operation_3218, edam:operation_3792, edam:operation_3800, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "myBrain-Seq" ; sc:softwareHelp , ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/sing-group/my-brain-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3179 ; sc:citation "pubmed:17537814" ; sc:description "MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445, edam:operation_2575 ; sc:name "MYBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bits.iis.sinica.edu.tw/~mybs/" ; biotools:primaryContact "MYBS team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3837 ; sc:description "MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication" ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "mycc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/sb2nhri/files/MyCC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC6727546", "pubmed:31484491" ; sc:description "high-throughput analysis of Streptomyces mycelium live cell imaging data | To quickly get a grasp what results can be generated with mycelyso, please take a look at the static demo page of mycelyso Inspector generated with the example dataset" ; sc:featureList edam:operation_3431 ; sc:license "BSD-2-Clause" ; sc:name "mycelyso" ; sc:url "https://github.com/modsim/mycelyso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0736, edam:topic_2269, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:34023906" ; sc:description "MyCLADE is an accurate multi-source domain annotation server designed for a fast exploration of genomic and metagenomic sets of sequences. MyCLADE performs a multi-source domain annotation strategy based on a library of probabilistic domain models associated to each domain." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_0362, edam:operation_2422 ; sc:name "MyCLADE" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/myclade" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3299, edam:topic_3373 ; sc:citation , "pubmed:32615035" ; sc:description """Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. mycoCSM: identifying safe potent hits against Mycobacteria. Douglas E. V. Pires & David B. Ascher.""" ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3799 ; sc:name "mycoCSM" ; sc:url "http://biosig.unimelb.edu.au/myco_csm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820, edam:topic_3301 ; sc:citation "pubmed:23000219" ; sc:description "A sequence-based predictor for identifying mycobacterial membrane proteins and their types." ; sc:featureList edam:operation_0269 ; sc:name "MycoMemSVM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/MycoMemSVM" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "MycoPrint is a web interface for exploration of the interactome of Mycobacterium tuberculosis H37Rv (Mtb) predicted by \"Domain Interaction Mapping\" (DIM) method." ; sc:featureList edam:operation_2945 ; sc:name "mycoprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/mycoprint/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3305, edam:topic_3316, edam:topic_3673 ; sc:citation , "pubmed:35674957" ; sc:description "A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris." ; sc:featureList edam:operation_0484, edam:operation_3192, edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MycoSNP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/CDCgov/mycosnp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3301 ; sc:citation "pubmed:25437899" ; sc:description "This web-server was used to predict the subcellular localizations of mycobacterial proteins based on optimal tripeptide compositions." ; sc:featureList edam:operation_2489 ; sc:name "Mycosub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/Mycosub" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3407, edam:topic_3500, edam:topic_3810 ; sc:citation , "pubmed:37145977" ; sc:description "A data-driven platform for investigating masked forms of mycotoxins." ; sc:isAccessibleForFree true ; sc:name "MycotoxinDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.mycotoxin-db.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_0781, edam:topic_3305, edam:topic_3519 ; sc:citation ; sc:description """Partial RdRp sequences offer a robust method for Coronavirus subgenus classification. MyCoV is an R package that allows the prediction of coronavirus subgenus based on partial RdRp data. The ‘MyCoV’ package will currently only work in a linux environment. Essentially it is a wrapper script for nucleotide BLAST, and therefore requires a local installation of BLAST+.""" ; sc:featureList edam:operation_0567, edam:operation_2421, edam:operation_3460 ; sc:license "MIT" ; sc:name "MyCoV" ; sc:url "https://github.com/dw974/MyCoV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_2229, edam:topic_2259, edam:topic_3299 ; sc:citation , "pmcid:PMC9358437", "pubmed:35958127" ; sc:description "MycoWiki is organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae." ; sc:featureList edam:operation_0362, edam:operation_0477, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MycoWiki" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mycowiki.uni-goettingen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3500 ; sc:citation , "pmcid:PMC8298095", "pubmed:34193510" ; sc:description "A Semi-Automated Software for Myelin g-Ratio Quantification" ; sc:featureList edam:operation_3450, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MyelTracer" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/HarrisonAllen/MyelTracer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0091, edam:topic_0602, edam:topic_0769, edam:topic_3068 ; sc:citation "pubmed:20501605" ; sc:description "Online research environment that supports the social sharing of bioinformatics workflows." ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:name "myExperiment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.myexperiment.org" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene ID (NCBI)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:encodingFormat edam:format_3033 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3321 ; sc:citation ; sc:description "This package provides simple-to-use REST web services to query/retrieve gene annotation data." ; sc:featureList edam:operation_2422, edam:operation_3282 ; sc:license "Artistic-2.0" ; sc:name "mygene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mygene.html" ; biotools:primaryContact "Chunlei Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0769, edam:topic_3053, edam:topic_3500 ; sc:citation , "pmcid:PMC10481249", "pubmed:37070209" ; sc:description "An interactive and programmatic platform for community-curated and user-created collections of genes." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "MyGeneset.info" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://MyGeneset.info" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pmcid:PMC5408841", "pubmed:28011789" ; sc:description "Web-based environment that provides biologists with a way to build, query and share their genome browsers." ; sc:featureList edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "CECILL-B" ; sc:name "myGenomeBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736 ; sc:citation "pubmed:15215405", "pubmed:17545200" ; sc:description "The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. 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Co-expression analyses will help muscle researchers to delineate the tissue-, cell-, and pathology-specific elements of muscle protein interactions, cell signaling and gene regulation. Changes in co-expression between pathologic and healthy tissue may suggest new disease mechanisms and therapeutic targets. 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Rosenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3673 ; sc:citation ; sc:description "It is an easy-to-use application to build and publish websites for synteny block analyses by using users’ own genome sequences or synteny block definitions." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "mySyntenyPortal" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jkimlab/mySyntenyPortal" ; biotools:primaryContact "Jaebum Kim" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_3016 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3016 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_3033 ; sc:name "Database cross-mapping" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_3033 ; sc:name "ID list" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3120 ; sc:citation ; sc:description "A wrapper for querying MyVariant.info services." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3504 ; sc:license "Artistic-2.0" ; sc:name "myvariant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/myvariant.html" ; biotools:primaryContact "Chunlei Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3168, edam:topic_3321 ; sc:citation ; sc:description "Desktop application for high-throughput mutations data management." ; sc:featureList edam:operation_2403 ; sc:name "myVCF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://apietrelli.github.io/myVCF/" ; biotools:primaryContact "Alessandro Pietrelli" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3834 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts mzData files to MGF." ; sc:featureList edam:operation_0335 ; sc:name "mz2mgf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ce4csb.org/software.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts analysis.baf files from Bruker into mzXML files. This software requires the CDAL library from Bruker." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "mzBruker" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:mzBruker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3710 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "mzWiff is a command-line program to convert Analyst native acquisition (.wiff) files to mzXML and mzML." ; sc:featureList edam:operation_0335, edam:operation_1812 ; sc:license "LGPL-2.1" ; sc:name "mzWiff" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:mzWiff" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3653 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts mzXML and mzML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files. Comes with the current version of TPP." ; sc:featureList edam:operation_0335, edam:operation_1812 ; sc:license "LGPL-2.0" ; sc:name "mzXML2Search" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:MzXML2Search" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:36414245" ; sc:description "A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "MZA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PNNL-m-q/mza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "A new algorithm that enables untargeted metabolomics integration of samples that are measured with high resolution LC-MS." ; sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "mzExtract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NL" ; sc:softwareVersion "1" ; sc:url "https://github.com/NetherlandsMetabolomicsCentre/mzextract-website" ; biotools:primaryContact "Christoph M. Becker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "mzID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mzID.html" ; biotools:primaryContact "Thomas Lin Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , "pubmed:34718406" ; sc:description "Variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys." ; sc:featureList edam:operation_2238, edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "MZINBVA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liudoubletian/MZINBVA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3651 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:contributor "SIB Swiss Institute of Bioinformatics" ; sc:description "Library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments." ; sc:featureList edam:operation_0366, edam:operation_1812 ; sc:name "MzJava" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mzjava.expasy.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3682, edam:format_3839 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3370, edam:topic_3382 ; sc:citation ; sc:description "Mzkit is an open source raw data file toolkit for mass spectrometry data visualization and analysis, provides by the BioNovoGene. The features of mzkit inlcudes: raw data file content viewer(XIC/TIC/Mass spectrum plot), MS-imaging, ms-spectrum tree analysis, build molecule network, formula de-novo search and de-novo annotation." ; sc:featureList edam:operation_3694 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mzkit" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "v1.0.0.1-beta", "v1.0.0.2-beta" ; sc:url "https://mzkit.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3365, edam:topic_3520 ; sc:citation "pubmed:21401061" ; sc:description "Modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data." ; sc:featureList edam:operation_3214 ; sc:name "mzMatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mzmatch.sourceforge.net/" ; biotools:primaryContact "Rainer Breitling" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654, edam:format_3712 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654, edam:format_3712 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2332, edam:format_3681, edam:format_3752, edam:format_3788 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation "pubmed:16026613" ; sc:description "Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML." ; sc:featureList edam:operation_0531, edam:operation_0570, edam:operation_3203, edam:operation_3215, edam:operation_3432, edam:operation_3435, edam:operation_3441, edam:operation_3628, edam:operation_3629, edam:operation_3631, edam:operation_3646, edam:operation_3694, edam:operation_3695, edam:operation_3803 ; sc:name "MZmine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mzmine.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:26037908" ; sc:description "XML-based format that captures extensive information from quantitative proteomics experiments.This library project intends to develop a set of easy-to-use post-processing APIs/applications to facilitate utilizing the standard in the field." ; sc:featureList edam:operation_2409 ; sc:name "mzqLibrary" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:url "http://www.psidev.info/mzquantml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071, edam:topic_3520 ; sc:citation , "pmcid:PMC2732273", "pubmed:18606607" ; sc:description "Provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS." ; sc:featureList edam:operation_0335 ; sc:license "Artistic-2.0" ; sc:name "mzR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/mzR.html" ; biotools:primaryContact "Bernd Fischer", "Laurent Gatto", "Qiang Kou", "Steffen Neumann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:33826687" ; sc:description "mzRAPP is a tool for reliability assessment of data pre-processing in non-targeted metabolomics. The goal of mzRAPP is to allow reliability assessment of non-targeted data pre-processing (NPP; XCMS, XCMS3, MetaboanalystR 3.0, XCMS-online, MZmine 2, MS-DIAL, OpenMS, El-MAVEN,..) in the realm of liquid chromatography high-resolution mass spectrometry (LC-HRMS). mzRAPPs approach is based on the increasing popularity of merging non-targeted with targeted metabolomics meaning that both types of data evaluation are often performed on the same dataset." ; sc:featureList edam:operation_0337, edam:operation_3215, edam:operation_3628 ; sc:license "GPL-3.0" ; sc:name "mzRAPP" ; sc:url "https://github.com/YasinEl/mzRAPP" ; biotools:primaryContact , "Gunda Koellensperger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:33538780" ; sc:description "Recalibrate mass spectrometry datasets using peptides identified by MS/MS" ; sc:featureList edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "mzRecal" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/524D/mzrecal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3518, edam:topic_3524, edam:topic_3678 ; sc:citation ; sc:description """Simulation-based comprehensive study of batch effects in metabolomics studies. batch effect simulation and correction for GC/LC-MS based data. The goal of mzrtsim is to make batch effects simulation for LC/GC-MS based peaks list data""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:name "mzrtsim" ; sc:url "https://github.com/yufree/mzrtsim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3489 ; sc:citation ; sc:description "GIS Methods and Tools for Seismic Microzonation Mapping." ; sc:featureList edam:operation_0310, edam:operation_2429 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "MzS Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://plugins.qgis.org/plugins/MzSTools/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3710 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3654 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation ; sc:description "Converts SCIEX/ABI Analyst format (WIFF) to mzXML." ; sc:featureList edam:operation_0335 ; sc:name "mzStar" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/mzStar.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071 ; sc:description "Convert proteomics data files into a SQLite database" ; sc:featureList edam:operation_3434, edam:operation_3646 ; sc:name "mzToSQLite" ; sc:url "https://github.com/galaxyproteomics/mzToSQLite" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3016 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622 ; sc:author ; sc:citation "pubmed:30175587" ; sc:description "MzVar is a Java tool allowing the compilation of customized variant protein and peptide databases in the FASTA format for database searching of MS/MS data, using a VCF file as variant input and a FASTA file as transcript input. The tool is compatible with transcript sequences retrieved from either Ensembl or the UCSC Table Browser." ; sc:featureList edam:operation_2479, edam:operation_3197, edam:operation_3214, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "MzVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/sib-pig/mzvar-public/src/master/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3520 ; sc:description "MZViewer is a lightweight viewer for mzData mass spec files. 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Hurley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3517 ; sc:citation "pubmed:26243017" ; sc:description "R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods." ; sc:featureList edam:operation_0283 ; sc:name "NAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/NAM/index.html" ; biotools:primaryContact "Alencar Xavier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC6734308", "pubmed:31500563" ; sc:description "Using machine learning to assess the quality of atomic force microscopy-enabled nano-indentation data | Loading, fitting, and rating AFM force-indentation data | Documentation — nanite 1.2.4 documentation | The documentation, including the code reference and examples, is available at nanite.readthedocs.io | Loading, fitting, and rating AFM force-distance data | Free document hosting provided by Read the Docs" ; sc:featureList edam:operation_1812, edam:operation_3799, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "nanite" ; sc:softwareHelp ; sc:url "https://github.com/AFM-Analysis/nanite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pubmed:23966634" ; sc:description "This database provide several way to access to the genomic data, as a blast search page, a genome browser and a direct link to download the data." ; sc:featureList edam:operation_0224 ; sc:name "Nannocholopsis gaditana Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:url "http://www.nannochloropsis.org/" ; biotools:primaryContact "Andrea Telatin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3047, edam:topic_3170, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC7545145", "pubmed:32887688" ; sc:description """Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. 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biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_3168, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC9520466", "pubmed:36186464" ; sc:description "An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "NanoCoV19" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/ncov/?lang=en" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3127, edam:topic_3299 ; sc:citation , "pubmed:36174880" ; sc:description "A pipeline that detecting recombinant crossover using ONT sequencing data." ; sc:featureList edam:operation_0451 ; sc:license "Other" ; sc:name "NanoCross" ; sc:url "https://github.com/zuoquanchen/NanoCross" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3174, edam:topic_3295, edam:topic_3674, edam:topic_3697 ; sc:citation , "pmcid:PMC8107137", "pubmed:33820988" ; sc:description "nanodisco is a toolbox for de novo discovery of all the three types (6mA, 5mC and 4mC) of DNA methylation from individual bacteria and microbiomes using nanopore sequencing. For microbiomes, nanodisco also supports the use of DNA methylation patterns as natural epigenetic barcodes to facilitate high resolution metagenomic binning. Specifically, nanodisco can be used to De novo discover DNA methylation motifs, identify specific type (6mA, 5mC or 4mC, namely typing) of a methylation motif, and identify which specific position within the motif is methylated (namely fine mapping), performing metagenomic binning based on microbial DNA methylation pattern by constructing and clustering a methylation profile matrix, and to integrate the two functionalities above together for de novo methylation motif discovery from microbiomes, and metagenomic analysis." ; sc:featureList edam:operation_0238, edam:operation_0310, edam:operation_0417, edam:operation_3204, edam:operation_3644 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "nanodisco" ; sc:url "https://github.com/fanglab/nanodisco" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0601, edam:topic_0749, edam:topic_3474 ; sc:citation ; sc:description """RNA modification detection using Nanopore raw reads with Deep One-Class Classification. RNA modification detection using Nanopore raw reads with Deep One Class classification. This software requires In vitro unmodified RNA raw read and Native RNA raw read to process.""" ; sc:featureList edam:operation_0484, edam:operation_3432, edam:operation_3755 ; sc:license "GPL-3.0" ; sc:name "nanoDoc" ; sc:url "https://github.com/uedaLabR/nanoDoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0621, edam:topic_3168, edam:topic_3174 ; sc:citation , "pmcid:PMC8973472", "pubmed:35368340" ; sc:description "An integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology." ; sc:featureList edam:operation_0310, edam:operation_3185, edam:operation_3192, edam:operation_3196, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoForms" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nanoforms.tech" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769 ; sc:description "A collection of best practice and popular ONT-oriented tools are integrated (and are expanding) in this custom Galaxy instance." ; sc:name "NanoGalaxy" ; sc:url "https://nanopore.usegalaxy.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3382, edam:topic_3400, edam:topic_3520 ; sc:citation , "pmcid:PMC7655149", "pubmed:33191949" ; sc:description """A high-performance open-source super-resolution microscopy toolbox. NanoJ-Core is an open-source ImageJ and Fiji plugin that provide the base high-performance computing engine that other NanoJ plugins need to run: NanoJ-SRRF, NanoJ-SQUIRREL, NanoJ-VirusMapper and NanoJ-Fluidics. Super-Resolution Radial Fluctuations (SRRF) - ImageJ Plugin.""" ; sc:featureList edam:operation_3435, edam:operation_3457, edam:operation_3799 ; sc:license "MIT" ; sc:name "NanoJ" ; sc:softwareHelp ; sc:url "https://github.com/HenriquesLab/NanoJ-Core" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3385, edam:topic_3572 ; sc:citation ; sc:description "An analytical approach for quantifying image quality in super-resolution microscopy." ; sc:featureList edam:operation_2428, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "NanoJ-SQUIRREL" ; sc:softwareHelp ; sc:url "https://bitbucket.org/rhenriqueslab/nanoj-squirrel/wiki/Home" ; biotools:primaryContact "Sian Culley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:27162186" ; sc:description "System for benchmarking DNA assembly tools, based on 3rd generation sequencers." ; sc:featureList edam:operation_0310 ; sc:name "NanoMark" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/kkrizanovic/NanoMark" ; biotools:primaryContact "Ivan Sović" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275, edam:topic_3368, edam:topic_3520 ; sc:citation , "pmcid:PMC8752518", "pubmed:34871001" ; sc:description "CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems." ; sc:featureList edam:operation_0337, edam:operation_0480, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:name "Nanomaterial Modeler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.charmm-gui.org/demo/nanomaterial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3295, edam:topic_3512, edam:topic_3674 ; sc:citation ; sc:description """An R/Bioconductor package for visualizing long-read methylation data. Visualise methlation data from Oxford Nanopore sequencing. NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3206, edam:operation_3436, edam:operation_3919 ; sc:license "Apache-2.0" ; sc:name "NanoMethViz" ; sc:url "https://bioconductor.org/packages/NanoMethViz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2258, edam:topic_2840, edam:topic_3500 ; sc:citation , "pubmed:35713578" ; sc:description "A web-based tool for predicting cytotoxicity of TiO2-based multicomponent nanomaterials toward Chinese hamster ovary (CHO-K1) cells." ; sc:isAccessibleForFree true ; sc:name "NanoMixHamster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nanomixhamster.cloud.nanosolveit.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC7200061", "pubmed:32065578" ; sc:description """Accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples. Accurate multilocus sequence typing using Oxford Nanopore MinION with dual-barcode approach to multiplex large numbers of samples.""" ; sc:featureList edam:operation_3431, edam:operation_3695, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "nanoMLST" ; sc:url "https://github.com/jade-nhri/nanoMLST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0196, edam:topic_3297 ; sc:citation , "pubmed:36795071" ; sc:description "A Tool for Modeling and Engineering Functional Nanoparticles at a Coarse-Grained Resolution." ; sc:featureList edam:operation_1812, edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "NanoModeler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nanomodeler.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2830, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC9411858", "pubmed:36032123" ; sc:description "Rapid and accurate end-to-end nanobody modeling by deep learning." ; sc:featureList edam:operation_0416, edam:operation_0479, edam:operation_0480, edam:operation_0481 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NanoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dina-lab3D/NanoNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0622 ; sc:citation , "pmcid:PMC4681994", "pubmed:26382197" ; sc:description "A tool for comprehensive analysis of Oxford Nanopore MinION sequence data." ; sc:featureList edam:operation_0292, edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "NanoOK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.earlham.ac.uk/nanook" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3168 ; sc:citation , "pubmed:29547981" ; sc:description "Visualizing and processing long-read sequencing data." ; sc:featureList edam:operation_0564, edam:operation_2403 ; sc:name "NanoPack" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1.0" ; sc:url "https://github.com/wdecoster/nanopack" ; biotools:primaryContact "Wouter De Coster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3168, edam:topic_3170, edam:topic_3174 ; sc:citation , "pubmed:34270680" ; sc:description "Nanopanel2 (np2) is a somatic variant caller for Nanopore panel sequencing data. Np2 works directly on basecalled FAST5 files and outputs VCF and TSV files containing variant calls and associated statistics. It also produces haplotype map TSV and PDF files that inform about haplotype distributions of called (PASS) variants." ; sc:featureList edam:operation_0487, edam:operation_3185, edam:operation_3227, edam:operation_3431, edam:operation_3454, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Nanopanel2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/popitsch/nanopanel2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0769, edam:topic_3384, edam:topic_3385, edam:topic_3398 ; sc:citation ; sc:description """A workflow for characterizing nanoparticle monolayers for biosensors. A persistent challenge in materials science is the characterization of a large ensemble of heterogeneous nanostructures in a set of images. This often leads to practices such as manual particle counting, and sampling bias of a favorable region of the “best” image. Herein, we present the open-source software, imaging criteria and workflow necessary to fully characterize an ensemble of SEM nanoparticle images. Such characterization is critical to nanoparticle biosensors, whose performance and characteristics are determined by the distribution of the underlying nanoparticle film.""" ; sc:featureList edam:operation_3431, edam:operation_3436, edam:operation_3443 ; sc:name "workflow characterizing nanoparticle monolayers biosensors" ; sc:url "https://github.com/hugadams/imgproc_supplemental" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3374, edam:topic_3375 ; sc:citation , "pmcid:PMC4386773", "pubmed:25848269" ; sc:description "SimBiology model and code to perform CI and NCA analyses, and optimization using parallel computing." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "Nanoparticle PBPK model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/64988-nanoparticle-pbpk-model" ; biotools:primaryContact "Baojian Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC7502021", "pubmed:32948196" ; sc:description """An easy-to-use user interface for nanoparticle dosimetry with the 3DSDD model. The Nano Particle Administration Sedimentation Simulator (NanoPASS) is a package which intends to simulate the sedimentation process of nano particles in a cell culture well. By simulating this process the experimentator can estimate the effective dose over time the cells are exposed to. Also, this gives an idea on at which time point the cells are exposed to the calculated concentration of sedimenting particles.""" ; sc:name "NanoPASS" ; sc:url "https://github.com/falfren/NanoPASS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1207, edam:format_2546 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:citation , "pmcid:PMC6061794", "pubmed:29547981" ; sc:description "NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences" ; sc:featureList edam:operation_2940, edam:operation_2943 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoPlot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wdecoster/NanoPlot" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_1929 ; sc:name "Data reference" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_2269, edam:topic_3168 ; sc:citation ; sc:description "A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data." ; sc:featureList edam:operation_0310, edam:operation_2238, edam:operation_2429, edam:operation_3197, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nanopolish" ; sc:softwareHelp ; sc:url "https://github.com/jts/nanopolish" ; biotools:primaryContact "Jared Simpson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3168 ; sc:description """NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files. It is a companion package for Nanopolish.""" ; sc:featureList edam:operation_3204, edam:operation_3791 ; sc:license "MIT" ; sc:name "NanopolishComp" ; sc:url "https://a-slide.github.io/NanopolishComp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_0654, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """Overcoming high nanopore basecaller error rates for DNA storage via basecaller-decoder integration and convolutional codes. DNA storage for nanopore sequencing using convolutional coding and basecaller-decoder integration. In many of the scripts, you need to set the path for the corresponding data directories as well as the encoding parameters. The current paths assume that the data is stored in ../nanopore_dna_storage_data/.""" ; sc:featureList edam:operation_0363, edam:operation_3185, edam:operation_3195 ; sc:name "nanopore" ; sc:url "https://github.com/shubhamchandak94/nanopore_dna_storage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3173, edam:topic_3175, edam:topic_3512 ; sc:citation , "pmcid:PMC8640597", "pubmed:34901902" ; sc:description "Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era." ; sc:featureList edam:operation_0310, edam:operation_0452, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Nanopore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jts/nanopore-paper-analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC10435370", "pubmed:37549052" ; sc:description "User-friendly tool for nanopore-seq real-time transcriptional analysis." ; sc:featureList edam:operation_0337, edam:operation_3185, edam:operation_3223, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "NanopoReaTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AnWiercze/NanopoReaTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3474, edam:topic_3673 ; sc:citation ; sc:description """An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm. Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. However, the nanopore sequencing reads are susceptible to a fairly high error rate owing to the difficulty in identifying the DNA bases from the complex electrical signals. Here we proposed a DNA basecalling reviser, NanoReviser, based on a deep learning algorithm to correct the basecalling errors introduced by current basecallers provided by default. In our module, we re-segmented the raw electrical signals based on the basecalled sequences provided by the default basecallers. By employing convolution neural networks (CNNs) and bidirectional long short-term memory (Bi-LSTM) networks, we took advantage of the information from the raw electrical signals and the basecalled sequences from the basecallers.""" ; sc:featureList edam:operation_3185, edam:operation_3195, edam:operation_3219 ; sc:name "NanoReviser" ; sc:url "https://github.com/pkubioinformatics/NanoReviser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_3752 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174 ; sc:author , "Laura Ciuffreda" ; sc:contributor , "Laura Ciuffreda" ; sc:description """NanoRTax is a taxonomic and diversity analysis pipeline built originally for Nanopore 16S rRNA data with real-time analysis support in mind. It combines state-of-the-art classifiers such as Kraken2, Centrifuge and BLAST with downstream analysis steps to provide a framework for the analysis of in-progress sequencing runs. NanoRTax retrieves the final output files in the same structure/format for every classifier which enables more comprehensive tool/database comparison and better benchmarking capabilities. Additionally, NanoRTax includes a web application (./viz_webapp/) for visualizing complete or partial pipeline outputs. The NanoRTax pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with conda environments and docker containers making installation trivial and results highly reproducible.""" ; sc:featureList edam:operation_2478, edam:operation_3460, edam:operation_3731, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NanoRtax" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/genomicsITER/NanoRtax" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0611, edam:topic_2229, edam:topic_2640, edam:topic_3067 ; sc:citation , "pmcid:PMC8245131", "pubmed:34191720" ; sc:description "A first person exploration of a cancer cell deep in the human body, featuring a highly detailed simulation of cellular anatomy and processes based on the latest scientific research." ; sc:featureList edam:operation_0269, edam:operation_0337, edam:operation_2422, edam:operation_2426, edam:operation_2476, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "Nanoscape" ; sc:operatingSystem "Windows" ; sc:url "https://store.steampowered.com/app/1654050/Nanoscape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3524 ; sc:citation ; sc:description "Nanopore sequence read simulator based on statistical characterization." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "NanoSim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/nanosim" ; biotools:primaryContact "Inanç Birol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC9822538", "pubmed:36548365" ; sc:description "A progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3185, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NanoSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/huangnengCSU/NanoSNP.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3305, edam:topic_3316, edam:topic_3324, edam:topic_3837 ; sc:citation , "pmcid:PMC7319573", "pubmed:32442274" ; sc:description """A scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline. Scalable, Portable, and Cloud compatible pipeline analysing Nanopore metagenomic sequencing data. NanoSPC is a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data. It can identify potentially pathogenic viruses and bacteria simultaneously to provide comprehensive characterization of individual samples. It can also detect single nucleotide variants and assemble high quality complete consensus genome sequences.""" ; sc:featureList edam:operation_0525, edam:operation_3227, edam:operation_3933 ; sc:name "NanoSPC" ; sc:url "https://nanospc.mmmoxford.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Accurate identification of splice junctions using Oxford Nanopore sequencing." ; sc:featureList edam:operation_0232, edam:operation_0433, edam:operation_3185 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NanoSplicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/shimlab/NanoSplicer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3174, edam:topic_3500 ; sc:citation ; sc:description "Tool for compression of nanopore genomic reads in FASTQ format (gzipped input also supported)." ; sc:featureList edam:operation_0310, edam:operation_3185, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NanoSpring" ; sc:url "https://github.com/qm2/NanoSpring" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC9889824", "pubmed:36743210" ; sc:description "A method for detection of target short tandem repeats based on nanopore sequencing data." ; sc:featureList edam:operation_0379, edam:operation_0452, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NanoSTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/langjidong/NanoSTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. It incorporates size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized." ; sc:featureList edam:operation_3664 ; sc:license "GPL-3.0" ; sc:name "NanoStringDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NanoStringDiff.html" ; biotools:primaryContact "hong wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:22513995" ; sc:description "Set of tools for normalizing, diagnostics and visualization of NanoString nCounter data." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "NanoStringNorm" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/NanoStringNorm/" ; biotools:primaryContact "Paul Boutros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3175, edam:topic_3511 ; sc:citation ; sc:description "Pre-processing of NanoString CNV data." ; sc:featureList edam:operation_3219, edam:operation_3233 ; sc:name "NanoStringNormCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://labs.oicr.on.ca/boutros-lab/software/nanostringnormcnv" ; biotools:primaryContact "Paul C Boutros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "This tool provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data, i.e. to identify outlier probes and outlier samples. 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Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology)." ; sc:featureList edam:operation_0310, edam:operation_2423, edam:operation_2425 ; sc:name "NanoTiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://binkley2.ncifcrf.gov/users/bshapiro/software.html" ; biotools:primaryContact "Bruce A. Shapiro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3474 ; sc:citation ; sc:description """Development of a parsimonious in silico model for toxicity assessment of metal-oxide nanoparticles using physicochemical features. 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Nanomaterials Image Analysis Tool Powered by Enalos Cloud Platform. Computation User Guide Download demo image. Statistically processed image end result.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3935 ; sc:name "NanoXtract" ; sc:url "http://enaloscloud.novamechanics.com/EnalosWebApps/NanoXtract/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3324, edam:topic_3360, edam:topic_3411 ; sc:citation , "pmcid:PMC8454682", "pubmed:34546657" ; sc:description "A new modelling tool for estimating HIV epidemic indicators at the district level in sub-Saharan Africa." ; sc:featureList edam:operation_3436, edam:operation_3658, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Naomi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jeffeaton/naomi-model-paper/tree/master/naomi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3512 ; sc:citation ; sc:description "Nucleotide Amino Acid Alignment is a Java interface to the nap C program. The NAP program computes an optimal global alignment of a DNA sequence and a protein sequence without penalizing terminal gaps. NAP handles frameshifts and long introns in the DNA sequence. It delivers the alignment in linear space, so long sequences can be aligned. The experimental results demonstrate that NAP is a sensitive and powerful tool for finding genes by DNA-protein sequence homology." ; sc:featureList edam:operation_0496 ; sc:name "NAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://athena.bioc.uvic.ca/virology-ca-tools/nap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3170, edam:topic_3474, edam:topic_3930 ; sc:citation ; sc:description """Bioinformatic pipeline to predict MHC-I-restricted T cell epitopes in mice. 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NAP-CNB uses variant calling methods with models trained on recurrent neuronal networks (RNN) to produce a list of putative neoantigens.""" ; sc:featureList edam:operation_0252, edam:operation_3227, edam:operation_3927 ; sc:name "NAP-CNB" ; sc:url "http://biocomp.cnb.csic.es/NeoantigensApp/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3591, edam:format_3603, edam:format_3604 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196 ; sc:author , "Alexandr Dibrov" ; sc:contributor ; sc:description "A plugin to estimate chromosome sizes from karyotype images." ; sc:featureList edam:operation_3180, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "napari-kics" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.0.3.rc2" ; sc:url "https://github.com/mpicbg-csbd/napari-kics" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3511 ; sc:citation "pubmed:21984475" ; sc:description "Nucleic Acid Phylogenetic Profile Database: classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes." ; sc:featureList edam:operation_0279, edam:operation_0314, edam:operation_0415, edam:operation_0475, edam:operation_2436 ; sc:name "NAPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://napp.u-psud.fr/" ; biotools:primaryContact "NAPP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0154, edam:topic_3125, edam:topic_3534 ; sc:citation "pubmed:20478832" ; sc:description "Web server for the prediction of specific residues involved in nucleic acid-binding proteins binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted." ; sc:featureList edam:operation_0279, edam:operation_0415, edam:operation_0420, edam:operation_0475, edam:operation_2575 ; sc:name "NAPS" ; sc:url "http://proteomics.bioengr.uic.edu/NAPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC4378019", "pubmed:25853185" ; sc:description "The package applies a functional version of principal component analysis to postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks) and to analyse differential variation between multiple ChIP-seq samples with replicates." ; sc:featureList edam:operation_2939 ; sc:license "Artistic-2.0" ; sc:name "NarrowPeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NarrowPeaks.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:37356907" ; sc:description "Nascent RNA profiling data analysis platform." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:name "nASAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://grobase.top/nasap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2814 ; sc:citation "pubmed:21706248" ; sc:description "Automated program for side-chain resonance assignment and nuclear Overhauser effect (NOE) assignment from NOESY data. It does not require data from TOCSY experiments.NASCA casts the assignment problem into a Markov Random Field (MRF), and extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data." ; sc:featureList edam:operation_2406 ; sc:name "NASCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.duke.edu/donaldlab/software/nasca/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0637 ; sc:citation "pubmed:19707301" ; sc:description "Completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein interaction network modeling through gene-name mapping, and outputs the resulting network in graphical form and also in computer-readable graph-forms, directly applicable by popular network modeling software." ; sc:featureList edam:operation_2464 ; sc:name "Nascent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nascent.pitgroup.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_3170, edam:topic_3174, edam:topic_3308 ; sc:citation , "pmcid:PMC7322916", "pubmed:32600310" ; sc:description """A web-based platform for high-throughput sequencing data analysis and visualization. NASQAR (Nucleic Acid SeQuence Analysis Resource):. A web-based portal for High-throughput data analysis & visualization. This portal hosts a number of web-based Bioinformatics analysis and visualization apps. https://github.com/nasqar/nasqar.""" ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_2478, edam:operation_3891 ; sc:name "NASQAR" ; sc:url "http://nasqar.abudhabi.nyu.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0166, edam:topic_3511 ; sc:citation "pubmed:22661578" ; sc:description "The NASSAM webserver searches for 3D patterns in nucleic acid structures. Motifs and formations of nucleic acid bases in 3D space within nucleic acid PDB formatted structures. The searches are based on distances between the bases which are represented as pseudoatom vectors. This search is independent of the base sequence order." ; sc:featureList edam:operation_0279, edam:operation_0475, edam:operation_2481, edam:operation_2518 ; sc:name "NASSAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mfrlab.org/grafss/nassam/" ; biotools:primaryContact "NASSAM Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0632, edam:topic_0749, edam:topic_3168 ; sc:citation "pubmed:12912825", "pubmed:16845035" ; sc:description "Multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea." ; sc:featureList edam:operation_0258, edam:operation_0292, edam:operation_0492 ; sc:name "NAST" ; sc:url "http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3168 ; sc:description "The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "NAST-iEr" ; sc:url "http://microbiomeutil.sourceforge.net/#A_NASTiEr" ; biotools:primaryContact "Brian Haas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2535 ; sc:encodingFormat edam:format_2548 ; sc:name "Sequence tag profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2548 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "To identify cis-NATs using ssRNA-seq, a new computational method was developed based on model comparison that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries." ; sc:featureList edam:operation_0253 ; sc:name "NASTIseq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation ; sc:description "A Simple Method for Extracting Antimicrobial Resistance Information from metagenomic sequencing data." ; sc:featureList edam:operation_3482 ; sc:license "MIT" ; sc:name "NastyBugs" ; sc:softwareHelp ; sc:url "https://github.com/NCBI-Hackathons/MetagenomicAntibioticResistance" ; biotools:primaryContact "Greg Fedewa", "Steve Tsang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0736 ; sc:citation , "pmcid:PMC3998945", "pubmed:24690407" ; sc:description "A web server for protein-protein interaction network querying." ; sc:featureList edam:operation_2464 ; sc:name "NatalieQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/natalieq/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:33126245" ; sc:description """Identification of pan-cancer Ras pathway activation with deep learning. ##The identification of hidden responders are often the essential challenges in precision oncology.""" ; sc:featureList edam:operation_3928, edam:operation_3935 ; sc:name "NatDRAP" ; sc:url "https://github.com/lixt314/NatDRAP1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3053, edam:topic_3372 ; sc:citation ; sc:description "A relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NAToRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ldgh/NAToRA_Public" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3572 ; sc:citation ; sc:description """A package to classify occurrence records in levels of confidence in species identification. naturaList package for R. version 0.2.0.""" ; sc:featureList edam:operation_3460, edam:operation_3695 ; sc:name "naturaList" ; sc:url "https://github.com/avrodrigues/naturaList" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_3520 ; sc:citation , "pubmed:34145888" ; sc:description "NaViA is a web tool created to augmend the analysis of complex mass spectra obtained from native mass spectrometry." ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3694, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "NaViA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://navia.ms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:21349867" ; sc:description "Developed as an interactive, multi-scale navigation tool for large and complicated biological networks." ; sc:featureList edam:operation_2497 ; sc:name "NaviCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://navicluster.cb.k.u-tokyo.ac.jp/" ; biotools:primaryContact "Thanet Praneenararat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0749, edam:topic_0820, edam:topic_3382 ; sc:citation , "pmcid:PMC9580940", "pubmed:36304314" ; sc:description "A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Naview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.icb.ufmg.br/naview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_3382 ; sc:citation "pubmed:19837718" ; sc:description "NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR is a powerful graphing application for 2D and 3D visualization of biological networks. Tools for manual and automated annontation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs." ; sc:featureList edam:operation_0276, edam:operation_0337, edam:operation_2497, edam:operation_2935, edam:operation_3083 ; sc:name "NAViGaTOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ophid.utoronto.ca/navigator/" ; biotools:primaryContact "Jurisica Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3120 ; sc:author "Jan-Simon Baasner" ; sc:citation ; sc:contributor "Boas Pucker" ; sc:description "Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence at once when predicting the functional consequences. This is relevant if (independent) sequence variants compensate each other effects." ; sc:featureList edam:operation_0331 ; sc:name "Neighborhood-Aware Variant Impact Predictor" ; sc:url "https://github.com/bpucker/NAVIP" ; biotools:primaryContact "Boas Pucker", "Jan-Simon Baasner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3173, edam:topic_3307 ; sc:citation , "pmcid:PMC5461685", "pubmed:28587674" ; sc:contributor ; sc:description "User-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are navigated through a graphic user interface." ; sc:featureList edam:operation_0415, edam:operation_2403 ; sc:name "NaviSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/navise-superenhancer/" ; biotools:primaryContact "Ander Izeta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC7195715", "pubmed:32357831" ; sc:description """Negative binomial additive model for RNA-Seq data analysis. Negative Binomial Additive Model for RNA-Seq Data. High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.""" ; sc:featureList edam:operation_3223, edam:operation_3659, edam:operation_3664, edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "NBAMSeq" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NBAMSeq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0199, edam:topic_0203, edam:topic_0654, edam:topic_2640 ; sc:citation , "pmcid:PMC10320089", "pubmed:37224529" ; sc:description "Non-B DNA burden explorer in cancer." ; sc:featureList edam:operation_0224, edam:operation_0239, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "NBBC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kowalski-labapps.dellmed.utexas.edu/NBBC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3676 ; sc:citation , "pmcid:PMC9329447", "pubmed:35896555" ; sc:description "A versatile method for differential analysis of multiple types of RNA-seq data." ; sc:featureList edam:operation_0264, edam:operation_3223, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NBBt-test" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=NBBttest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:21062764" ; sc:description "Uses a method similar to that used in many email spam filters to score a genetic sample against different genomes, to possibly identify the closest match." ; sc:featureList edam:operation_2990 ; sc:name "NBC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/EESI/nbc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC7060280", "pubmed:32144346" ; sc:description """A network-based integrative analysis framework. With the explosion of high-throughput data, effective integrative analyses are needed to decipher the knowledge accumulated in biological databases. Existing meta-analysis approaches in systems biology often focus on hypothesis testing and neglect real expression changes, i.e. effect sizes, across independent studies. In addition, most integrative tools completely ignore the topological order of gene regulatory networks that hold key characteristics in understanding biological processes. Here we introduce a novel meta-analysis framework, Network-Based Integrative Analysis (NBIA), that transforms the challenging meta-analysis problem into a set of standard pathway analysis problems that have been solved efficiently""" ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3928 ; sc:name "NBIA" ; sc:url "http://bioconductor.org/packages/release/bioc/html/BLMA.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_2830, edam:topic_3071 ; sc:citation , "pubmed:33359127" ; sc:description """A dedicated database of non-B cell derived immunoglobulin variable region. Non-B cell derived ImmunoGlobulin Variable region Database. Welcome to NBIGV, a database dedicated to organizing and characterizing non-B cell derived immunoglobulins.""" ; sc:featureList edam:operation_0338, edam:operation_3431, edam:operation_3936 ; sc:name "NBIGV-DB" ; sc:url "http://nbigv.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "A snakemake workflow for metagenomics" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nbis-meta" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/NBISweden/nbis-meta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3067, edam:topic_3304 ; sc:citation ; sc:description """Network-based R-statistics for (unbalanced) longitudinal samples. Index of /web/packages/NBR/vignettes. Here are the scripts and preprocessed data to illustrate the R package NBR using the dataset SWU-SLIM. Network-Based R-Statistics using Mixed Effects Models.""" ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "NBR" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=NBR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0780, edam:topic_3489, edam:topic_3500 ; sc:citation "pubmed:19934255" ; sc:description "System for collecting, preserving and providing bioresources for use as experimental materials for life science research." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "NBRP resources" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nbrp.jp/index.jsp" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3444, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:34610435" ; sc:description "NBS-Predict aims to provide a fast way to identify neuroimaging-based biomarkers with high generalizability by combining machine learning with graph theory in a cross-validation structure." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NBS-Predict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eminSerin/NBS-Predict" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3534 ; sc:citation "pubmed:26656003" ; sc:description "Support vector machine-based high throughput pipeline for plant resistance protein NBSLRR (nucleotide binding site-leucine-rich repeats) prediction." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "NBSPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://soilecology.biol.lu.se/nbs/" ; biotools:primaryContact "Sandeep Kushwaha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_3068, edam:topic_3168 ; sc:citation , "pmcid:PMC10091358", "pubmed:37042467" ; sc:description "New thermostability database for nanobodies." ; sc:featureList edam:operation_0305, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "NbThermo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://valdes-tresanco-ms.github.io/NbThermo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2269, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:31904815" ; sc:description """Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data. NBZIMM: Negative Binomial and Zero-Inflated Mixed Models, with Applications to Microbiome Data Analysis.""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:name "NBZIMM" ; sc:url "http://github.com//nyiuab//NBZIMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3173, edam:topic_3308, edam:topic_3360 ; sc:citation , "pmcid:PMC7033623", "pubmed:32117995" ; sc:description """A Curated ncRNAomics Knowledgebase for Bridging Basic and Clinical Research in Eye Diseases. Nc2Eye, a literature-mined resource of experimentally validated non-coding RNAs in eye diseases. Eye diseases (EDs) represent the disorders affecting visual system, such as retinoblastoma, diabetic retinopathy, etc. Non-coding RNAs (ncRNAs), as a large category of functional RNA molecules, have been reported to play a crucial role in EDs. Here, we developed the Nc2Eye database, which contains 7088 experimentally validated ncRNA-ED associations. It covers 4363 ncRNAs involved in 104 kinds of EDs across 8 species through a comprehensive review of more than 2400 published papers. Nc2Eye also gathered 91 high-throughput transcriptome datasets in EDs and normal controls.""" ; sc:featureList edam:operation_2422, edam:operation_2939, edam:operation_3891 ; sc:name "Nc2Eye" ; sc:url "http://nc2eye.bio-data.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3170 ; sc:citation , "pubmed:31410488" ; sc:description "A database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types | Numerous studies indicate that ncRNAs have critical functions across biological processes, and single nucleotide polymorphisms (SNPs) could contribute to diseases or traits through influencing ncRNA expression" ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3792 ; sc:name "ncRNA-eQTL" ; sc:softwareHelp ; sc:url "http://ibi.hzau.edu.cn/ncRNA-eQTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3373, edam:topic_3375, edam:topic_3379 ; sc:citation , "pmcid:PMC8728186", "pubmed:34648031" ; sc:description "A comprehensive and curated portal for translational research." ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "NCATS Inxight Drugs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://drugs.ncats.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3174, edam:topic_3293, edam:topic_3489 ; sc:citation , "pubmed:33326008" ; sc:description """Collecting and managing taxonomic data with NCBI-taxonomist. ncbi-taxonomist handles and manages phylogenetic data from NCBI. Its primary use is to use taxonomic data to find and link related metadata from other Entrez databases, e.g. fetching data for metagenomic data-sets for specific or diverse group of org. Toolbox to manage NCBI taxonomical data.""" ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_2422, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "NCBI-taxonomist" ; sc:softwareHelp ; sc:url "https://cloud.sylabs.io/library/jpb/ncbi-taxonomist" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:15367931" ; sc:description "Links publically available assembly information with the NCBI Trace Archive's raw sequence data." ; sc:featureList edam:operation_0310, edam:operation_0523, edam:operation_0524, edam:operation_0525 ; sc:name "NCBI Assembly Archive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/projects/assembly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3297, edam:topic_3303, edam:topic_3344 ; sc:citation , "pmcid:PMC3531209", "pubmed:23203889" ; sc:description "Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2422, edam:operation_3431 ; sc:name "NCBI Bookshelf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books" ; biotools:primaryContact "Marilu A. Hoeppner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface." ; sc:featureList edam:operation_0338, edam:operation_2409, edam:operation_2422 ; sc:name "NCBI Datasets" ; sc:softwareVersion "13.29.1" ; sc:url "https://www.ncbi.nlm.nih.gov/datasets/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2719 ; sc:name "dbProbe ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2717 ; sc:encodingFormat edam:format_2331 ; sc:name "Oligonucleotide probe annotation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0607 ; sc:citation ; sc:description "Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities." ; sc:featureList edam:operation_0224 ; sc:name "NCBI dbProbe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/probe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3173, edam:topic_3295 ; sc:citation "pubmed:21075792" ; sc:description "Resource for whole-genome epigenetic data sets. 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Sayers" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:name "NCBI taxonomy ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2331 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0625, edam:topic_0637 ; sc:citation , , "pmcid:PMC3245000", "pubmed:10592169", "pubmed:10592170", "pubmed:22139910" ; sc:description "Curated classification and nomenclature for all of the organisms in the public sequence databases. 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In which multi-label learning framework and sequence labeling model were employed. It improved performance of nucleic acid binding residue prediction whlie maintaining a low cross-prediction rate, which is an important complement to existing methods. The framework and working process of NCBRPred are shown in Fig. 1. For more information please refer to our paper.""" ; sc:featureList edam:operation_0267, edam:operation_3095, edam:operation_3900, edam:operation_3901, edam:operation_4009 ; sc:name "NCBRPred" ; sc:url "http://bliulab.net/NCBRPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:description "nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. 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The method fully exploits the heterogeneous biological interactions of the mRNA-miRNA-lncRNA composite network, which was constructed by integrating experimentally validated interactions (protein-protein , miRNA-target and miRNA-lncRNA interactions). The identified ncRNAs may be targeted to overcome drug resistance and help realize individual treatment.""" ; sc:featureList edam:operation_0463, edam:operation_3792, edam:operation_3925 ; sc:name "ncDRMarker" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/ncDRMarker/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0219, edam:topic_0634, edam:topic_0659 ; sc:citation , "pubmed:32105730" ; sc:description """A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. More and more evidences have shown that non-coding RNAs (ncRNAs), such as lncRNAs, circRNAs and primary miRNAs, could encode proteins or peptides. ncEP is a database for collecting ncRNA-encoded proteins or peptides, which have been validated by low-throughput experiments from published papers. ncEP contains features of the proteins or peptides encoded by ncRNAs, including their names, sequences, species, genomic locations, tissues or cell lines, experimental methods, data source and other detailed information.""" ; sc:featureList edam:operation_0463, edam:operation_2428 ; sc:name "ncEP" ; sc:url "http://www.jianglab.cn/ncEP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3179, edam:topic_3308, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:34050762" ; sc:description "ncFANs v2.0 is an integrative platform for functional annotation of non-coding RNAs. 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This code is related to our recently proposed method called NCMHap. This method can solve single individual haplotype problem for diploid organisms.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3432 ; sc:name "NCMHap" ; sc:url "https://github.com/Fatemeh-Zamani/NCMHap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3172, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC9580955", "pubmed:36304309" ; sc:description "A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NCMW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/manuelgloeckler/ncmw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:description "The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5." ; sc:license "BSD-3-Clause" ; sc:name "NCO toolkit" ; sc:softwareHelp , ; sc:url "http://nco.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation ; sc:description """A multi-class SVM classification to distinguish between non-coding RNAs in Viridiplantae. Prediction model for non-coding RNA. Computational Structural Biology Lab. NCodR : A multi-class SVM classifier using single sequence repeat signatures to distinguish between ncRNA types.""" ; sc:featureList edam:operation_0463, edam:operation_3472, edam:operation_3695 ; sc:name "NCodR" ; sc:url "http://www.csb.iitkgp.ac.in/applications/NCodR/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation , "pubmed:2031185" ; sc:description "Prediction of coiled-coil secondary structure elements." ; sc:featureList edam:operation_0470 ; sc:name "ncoils" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.predictprotein.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0621, edam:topic_0659, edam:topic_3293 ; sc:citation , "pmcid:PMC10359484", "pubmed:37260093" ; sc:description "Efficient and reliable identification of miRNA orthologs." ; sc:featureList edam:operation_0337, edam:operation_0463, edam:operation_3478, edam:operation_3663, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ncOrtho" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/BIONF/ncortho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3324, edam:topic_3400, edam:topic_3930 ; sc:citation ; sc:description """Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV). Information on COVID-19, the infectious disease caused by the most recently discovered coronavirus.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0477, edam:operation_3663 ; sc:name "nCoV" ; sc:url "https://www.who.int/emergencies/diseases/novel-coronavirus-2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3305, edam:topic_3379 ; sc:citation , "pmcid:PMC8199916", "pubmed:34178436" ; sc:description "An R package for exploring COVID-19 statistics." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "nCov2019" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YuLab-SMU/nCov2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC10320176", "pubmed:37194703" ; sc:description "Docking server to predict the binding modes between COVID-19 targets and its potential ligands." ; sc:featureList edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "nCoVDock2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ncovdock2.schanglab.org.cn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "To identify non-coding RNA (ncRNA) signals within genomic regions, a classification tool was developed based on a hybrid random forest (RF) with a logistic regression model to efficiently discriminate short ncRNA sequences as well as long complex ncRNA sequences." ; sc:featureList edam:operation_2423 ; sc:name "NCpred" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "KMUTT" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://ncrna-pred.com/HLRF.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC7509369", "pubmed:33005306" ; sc:description """An integrated computational tool for identifying non-coding RNA promoters in multiple species. The promoter is located near the transcription start sites and regulates transcription initiation of the gene. Accurate identification of promoters is essential for understanding the mechanism of gene regulation. Since experimental methods are costly and ineffective, developing efficient and accurate computational tools to identify promoters are necessary. Although a series of methods have been proposed for identifying promoters, none of them is able to identify the promoters of non-coding RNA (ncRNA). In the present work, a new method called ncPro-ML was proposed to identify the promoter of ncRNA in Homo sapiens and Mus musculus, in which different kinds of sequence encoding schemes were used to convert DNA sequences into feature vectors. To test the length effect, for each species, datasets including sequences with different lengths were built""" ; sc:featureList edam:operation_0440, edam:operation_3936 ; sc:name "ncPro-ML" ; sc:url "http://www.bio-bigdata.cn/ncPro-ML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32890916" ; sc:description """Non-coding RNA classification with convolutional neural network. ncRDeep: Non coding RNA classification with convolutional neural network.""" ; sc:featureList edam:operation_0267, edam:operation_0502 ; sc:name "ncRDeep" ; sc:url "http://home.jbnu.ac.kr/NSCL/ncRDeep.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_3474 ; sc:citation , "pubmed:34242708" ; sc:description "A novel computational approach for classification of non-coding RNA family by deep learning." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "ncRDense" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nsclbio.jbnu.ac.kr/tools/ncRDense/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7059790", "pubmed:32180792" ; sc:description """Noncoding Ribonucleic Acid Prediction Based on a Deep Resident Network of Ribonucleic Acid Sequences. NCResNet: Noncoding RNA Prediction Based on a Deep Resident Network of RNA Sequences. A deep learning-based method to predict noncoding RNAs of RNA sequences.""" ; sc:featureList edam:operation_2441, edam:operation_3092, edam:operation_3927 ; sc:name "NCResNet" ; sc:url "https://github.com/abcair/NCResNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32224462" ; sc:description """A novel end-to-end method for non-coding RNAs family prediction based on Deep Learning. ncRNAs family classification.""" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2441 ; sc:name "ncRFP" ; sc:url "https://github.com/linyuwangPHD/ncRFP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_3170, edam:topic_3324, edam:topic_3518 ; sc:citation , "pmcid:PMC7268337", "pubmed:32487016" ; sc:description """A manually curated database for experimentally validated non-coding RNAs in inflammation. Non-coding RNAs in Inflammation (ncRI) provides a manually curated database for experimentally validated non-coding RNAs in inflammatary disease. Recently, inflammation is considered to be central to the onset, progression, and outcome of infectious and noninfectious diseases, especially believed as a hallmark of cancer. In addition, the inflammatory agents, such as cytokine and chemokines, can regulate the behavior of the immune system and involve in the immunotherapy.""" ; sc:featureList edam:operation_2421, edam:operation_2428 ; sc:name "ncRI" ; sc:url "http://www.jianglab.cn/ncRI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC1781251", "pubmed:17169980" ; sc:description "Non-translatable RNA transcripts that appear to work at the RNA level." ; sc:featureList edam:operation_0314, edam:operation_0372, edam:operation_0438, edam:operation_0483, edam:operation_2441 ; sc:name "Non-Coding RNA database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biobases.ibch.poznan.pl/ncRNA/" ; biotools:primaryContact "Non-Coding RNA database team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_3360 ; sc:citation , "pubmed:33275967" ; sc:description """A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. Jun 1, 2018: Startup of the ncRNAVar project.... Sep 10, 2019: The variant mapping was developed...""" ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3925 ; sc:name "ncRNAVar" ; sc:url "http://www.liwzlab.cn/ncrnavar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "NONCODE database integrates expression and functional long noncoding RNAs (lncRNA) data." ; sc:featureList edam:operation_2422 ; sc:name "ncRNAwsdl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.noncode.org/index.php" ; biotools:primaryContact "Runsheng Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0659, edam:topic_3360, edam:topic_3517 ; sc:citation , "pmcid:PMC7549653", "pubmed:32122231" ; sc:description """a comprehensive database platform for identification and validation of disease related noncoding RNAs. Mar 26, 2020: ncRPheno was published on the journal of RNA Biology... ncRPheno is a comprehensive database that provides experimentally supported associations between noncoding RNAs (ncRNAs, including miRNA, lncRNA, circRNA, snoRNA and piRNA etc.) and disease phenotypes across 11 species (including Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Sus scrofa, Pan troglodytes, Marmoset, Gallus gallus, Canis familiaris, Zebrafish and Rabbit). ncRNAs have been experimentally validated as a novel class of biomarkers and potential drug targets for disease diagnosis, therapy and prognosis. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/starbase (SYSU.EDU.CN)""" ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3792 ; sc:name "ncRPheno" ; sc:url "http://lilab2.sysu.edu.cn/ncrpheno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3277 ; sc:citation , "pubmed:34726689" ; sc:description "A method to evaluate circadian clock robustness in population scale data." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "nCV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gangwug/nCV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:description "Ncview is a netCDF visual browser." ; sc:featureList edam:operation_0337 ; sc:license "GPL-1.0" ; sc:name "Ncview" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://cirrus.ucsd.edu/ncview/" ; biotools:primaryContact "Robert W. McMullen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3360 ; sc:citation , "pubmed:34826297" ; sc:description "A Bidirectional LSTM Network with Attention for Y RNA and short non-coding RNA classification." ; sc:featureList edam:operation_0335, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NCYPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.gpea.uem.br/ncypred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0157, edam:topic_3511 ; sc:citation "pubmed:1384741" ; sc:description "NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids." ; sc:featureList edam:operation_0279, edam:operation_0475, edam:operation_2403, edam:operation_2481, edam:operation_2518 ; sc:name "Nucleic Acid Database (NDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ndbserver.rutgers.edu/" ; biotools:primaryContact "NDB Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0157, edam:topic_3511 ; sc:citation "pubmed:11345429", "pubmed:12824344", "pubmed:1384741" ; sc:description "The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures." ; sc:featureList edam:operation_0279, edam:operation_0475, edam:operation_2403, edam:operation_2481 ; sc:name "NDB Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ndbserver.rutgers.edu/ndbmodule/services/index.html" ; biotools:primaryContact "NDB Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0634, edam:topic_3305, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC9481935", "pubmed:36100329" ; sc:description "A risk factor knowledgebase for personalized prevention of neurodegenerative diseases." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3907 ; sc:license "Other" ; sc:name "NDDRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sysbio.org.cn/NDDRF/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2259, edam:topic_3303 ; sc:citation , "pmcid:PMC8544027", "pubmed:34570431" ; sc:description "NDEx, the Network Data Exchange, is a collaborative software infrastructure for storing, sharing and publishing biological network knowledge." ; sc:featureList edam:operation_3501, edam:operation_3926, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "NDEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ndexbio.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3382 ; sc:citation ; sc:description "Data-dependent visualization of biological networks in the web-browser with NDExEdit." ; sc:featureList edam:operation_2429, edam:operation_3096, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NDExEdit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://frankkramer-lab.github.io/NDExEdit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_3077 ; sc:citation ; sc:description "This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation." ; sc:featureList edam:operation_0224 ; sc:name "ndexr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioconductor.org/packages/release/bioc/html/ndexr.html" ; biotools:primaryContact "Alex Ishkin", "Dexter Pratt", "Florian Auer", "Frank Kramer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3300, edam:topic_3304, edam:topic_3382 ; sc:citation ; sc:description """A platform-independent data interface and database for neuroscience physiology and imaging experiments. Neuroscience Data Interface - A means of specifying and accessing neuroscience data. Available at https://github.com/VH-Lab/NDI-matlab. It is assumed that the function ndi_Init.m is run at startup. Please add this to your startup.m file. (If you use the http://github.com/VH-Lab/vhlab_vhtools distribution, it will be run automatically.).""" ; sc:featureList edam:operation_3435, edam:operation_3436 ; sc:name "NDI" ; sc:url "http://github.com/VH-Lab/NDI-matlab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:36409808" ; sc:description "Spacewise Multiscale Representation Learning via Neighbor Decoupling for Real-Time Driving Scene Parsing." ; sc:featureList edam:operation_1812, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NDNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LiShuTJ/NDNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC7738244", "pubmed:33323107" ; sc:description """A method for the quality assessment of single-cell RNA-Seq preprocessing data. A R package for selecting the best way for RNA-Seq data pretreatment.""" ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "NDRindex" ; sc:url "https://github.com/zeromakerlovesmiku/NDRindex" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pmcid:PMC3913712", "pubmed:24505344", "pubmed:24574290" ; sc:description "Phylogenic tree from reads using nucleotide difference method." ; sc:featureList edam:operation_0323 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NDtree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cge.cbs.dtu.dk/services/NDtree/" ; biotools:primaryContact "Ole Lund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3418 ; sc:citation , "pmcid:PMC8800139", "pubmed:35085870" ; sc:description "Neonatal EEG Artifact Removal, an automated pipeline for pre-processing." ; sc:featureList edam:operation_0321, edam:operation_3237, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NEAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vpKumaravel/NEAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3308, edam:topic_3512, edam:topic_3534, edam:topic_3794 ; sc:citation ; sc:description """A flexible pipeline characterizing protein binding to local RNA structure. nearBynding is an R package that discerns RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. Input CLIP protein-binding data can either be in aligned BAM or peak-called BED/bedGraph formats. RNA structure can either be internally calculated via CapR or can be provided by the user as a BED/bedGraph. RNA structure binding profiles can be visually and mathematically compared between proteins across multiple formats.""" ; sc:featureList edam:operation_0570, edam:operation_2441, edam:operation_2495, edam:operation_3216, edam:operation_3902 ; sc:license "Artistic-2.0" ; sc:name "nearBynding" ; sc:url "https://bioconductor.org/packages/nearBynding/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622 ; sc:citation , "pmcid:PMC5374688", "pubmed:28361684" ; sc:description "Performs network enrichment analysis against functional gene sets. Benchmarks networks. 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This project is maintained by imatge-upc. NeAT (Neuroimaging Analysis Toolbox) is a command-line toolbox written in Python that provides the tools to analyze the linear and nonlinear dynamics of a particular tissue and study the statistical significance of such dynamics at the voxel level.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:name "NeATB" ; sc:url "https://imatge-upc.github.io/neat-tool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC8969107", "pubmed:35290737" ; sc:description "NeatMS is an open source python package for untargeted LCMS signal labelling and filtering. NeatMS enables automated filtering of false positive MS peaks reported by commonly used LCMS data processing pipelines. NeatMS relies on neural network based classification." ; sc:featureList edam:operation_3215, edam:operation_3695, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NeatMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://anaconda.org/bioconda/neatms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_0821, edam:topic_2885, edam:topic_3295 ; sc:citation "pubmed:12824395" ; sc:description "NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb." ; sc:featureList edam:operation_0369, edam:operation_0431, edam:operation_2429, edam:operation_2944 ; sc:name "NEBcutter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://tools.neb.com/NEBcutter/index.php3" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3169, edam:topic_3365 ; sc:citation "pubmed:22829625" ; sc:description "Web service powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data." ; sc:featureList edam:operation_0389 ; sc:name "Nebula" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nebula.curie.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3175, edam:topic_3673 ; sc:citation , "pubmed:33503255" ; sc:description """Ultra-efficient mapping-free structural variant genotyper. Nebula is an ultra-efficient mapping-free structural variation genotyper based on kmer counting. Nebula is a mapping-free approach for accurate and efficient genotyping of SVs. Nebula is a two-stage approach and consists of a kmer extraction phase and a genotyping phase. Given as input a set of SV coordinates (BED/VCF), the reference assembly (FASTA), and a set of mapped samples on which the genotype of these SVs is already known, Nebula extracts a collection of kmers that represent the input SVs (kmer extraction phase) and these extracted kmers will then be used to genotype the same set of SVs on any new WGS sample(s) without the need to map the reads to the reference genome (genotyping phase). This is done by counting the kmers in the WGS reads of the new sample(s) and predicting genotypes using a likelihood model.""" ; sc:featureList edam:operation_0484, edam:operation_0524, edam:operation_3196, edam:operation_3454, edam:operation_3472 ; sc:name "Nebula-kmer" ; sc:url "https://github.com/Parsoa/Nebula" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Nebulosa recovers single cell gene expression signals by kernel density estimation. Due to the sparsity observed in single-cell data (e.g. RNA-seq, ATAC-seq), the visualization of cell features (e.g. gene, peak) is frequently affected and unclear, especially when it is overlaid with clustering to annotate cell types. Nebulosa is an R package to visualize data from single cells based on kernel density estimation. It aims to recover the signal from dropped-out features by incorporating the similarity between cells allowing a “convolution” of the cell features.""" ; sc:featureList edam:operation_0571, edam:operation_2939 ; sc:name "Nebulosa" ; sc:url "http://www.github.com/powellgenomicslab/Nebulosa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3474, edam:topic_3957 ; sc:citation ; sc:description """Network-based cancer gene relationship prediction method reveals perturbations in the cancer gene network. NEtwork-based CAncer gene RElationship prediciton. NECARE is a network-based algrithom which use Relational Graph Convolutional Network (R-GCN) to predict genes inetraction in cancer. The feature NECARE used include:1) knowledge-based feature OPA2Vec; 2)cancer specific feature which means mutation and expression profile of each gene from TCGA.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_2454 ; sc:license "MIT" ; sc:name "NECARE" ; sc:url "https://github.com/JiajunQiu/NECARE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads." ; sc:featureList edam:operation_0524 ; sc:name "NECAT" ; sc:softwareHelp , ; sc:url "https://github.com/xiaochuanle/NECAT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3315, edam:topic_3318 ; sc:citation , "pubmed:32716189" ; sc:description """N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods. FCIQMC code developed by George Booth and Ali Alavi, 2013.""" ; sc:license "GPL-3.0" ; sc:name "NECI" ; sc:url "https://github.com/ghb24/NECI_STABLE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Combine reference and assembled transcriptomes for RNA-Seq analysis." ; sc:featureList edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "Necklace" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Oshlack/necklace/wiki" ; biotools:primaryContact "Alicia Oshlack", "Nadia M Davidson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2640 ; sc:citation ; sc:description """A node embedding algorithm for multiplex heterogeneous networks. NECo is a node embedding tool that utilizes multiplex heterogeneous gene phenotype network. NECo allows multi-layer gene and phenotype networks. NECo generates gene embeddings using Gene-Gene, Gene-Phenotype, Phenotype-Gene and Phenotype-Phenotype neibhorhood spaces, using the random walk with restart rankings as node sequences.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3196 ; sc:name "NECo" ; sc:url "https://github.com/bozdaglab/NECo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3172, edam:topic_3297, edam:topic_3407 ; sc:citation , "pubmed:33315094" ; sc:description "Predicting Nash equilibria for microbial metabolic interactions." ; sc:featureList edam:operation_2426, edam:operation_3660, edam:operation_3929 ; sc:name "NECom" ; sc:url "https://github.com/Jingyi-Cai/NECom.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0634, edam:topic_3336, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC7495830", "pubmed:32938396" ; sc:description """A network embedding based method for predicting drug-disease associations. NEDD is an novel computational method, which utilizes heterogeneous information based on the idea of meta path to identify potential novel indications for a given drug.""" ; sc:featureList edam:operation_3927, edam:operation_3935 ; sc:name "NEDD" ; sc:url "http://bioinformatics.csu.edu.cn/resources/softs/DrugRepositioning/n_Web/NEDD.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0634, edam:topic_2269 ; sc:citation , "pmcid:PMC7290059", "pubmed:32581647" ; sc:description """Identify Lysine Neddylation Sites Using Bi-profile Bayes Feature Extraction via the Chou's 5-steps Rule and General Pseudo Components. Neddylation is a highly dynamic and reversible post-translational modification. The abnormality of neddylation has previously been shown to be closely related to some human diseases. The detection of neddylation sites is essential for elucidating the regulation mechanisms of protein neddylation. As the detection of the lysine neddylation sites by the traditional experimental method is often expensive and time-consuming, it is imperative to design computational methods to identify neddylation sites.""" ; sc:featureList edam:operation_0417, edam:operation_3755, edam:operation_3937 ; sc:name "NeddPred" ; sc:url "http://123.206.31.171/NeddPred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3336, edam:topic_3407 ; sc:citation , "pmcid:PMC8617287", "pubmed:34824199" ; sc:description "Network medicine for disease module identification and drug repurposing with the NeDRex platform." ; sc:featureList edam:operation_3431, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NeDRex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; 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sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/needle.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Pairwise sequence alignment of DNA or protein sequences using Needleman-Wunsch global alignment." ; sc:featureList edam:operation_0491 ; sc:name "needle-api (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_needle_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Needleman-Wunsch global alignment of two sequences." ; sc:featureList edam:operation_0491, edam:operation_0496 ; sc:name "needle (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/psa/emboss_needle/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "This program uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length." ; sc:featureList edam:operation_2403 ; sc:name "needle WS (husar)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; 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The database currently contains experimentally supported non-interacting protein pairs derived from two distinct sources: by manual curation of literature and by analyzing protein complexes with known 3D structure. It can be used to evaluate protein and domain interactions from new experiments and improve the training of interaction prediction algorithms." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_2492, edam:operation_2949, edam:operation_3439 ; sc:name "Negatome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.helmholtz-muenchen.de/proj/ppi/negatome" ; biotools:primaryContact "Dmitrij Frishman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:31985434" ; sc:description """Drug-target interaction prediction based on ensemble learning and logistic regression. This is the repository containing the source code for research, namely NegStacking: drug-target interaction prediction based on ensemble learning and logistic regression.""" ; sc:featureList edam:operation_3659 ; sc:name "NegStacking" ; sc:url "https://github.com/Open-ss/NegStacking" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0625, edam:topic_3517, edam:topic_3974 ; sc:citation , "pubmed:33514929" ; sc:description """Incorporating neighbor genotypic identity into genome-wide association studies of field herbivory. R source codes, accession list, and phenotype data used in "Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory on Arabidopsis thaliana" by Yasuhiro Sato, Eiji Yamamoto, Kentaro K. Shimizu and Atsushi J. Nagano""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3557, edam:operation_3659, edam:operation_3791 ; sc:license "GPL-3.0" ; sc:name "neighbor GWAS" ; sc:url "https://cran.r-project.org/package=rNeighborGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2830, edam:topic_3308, edam:topic_3318 ; sc:citation , "pubmed:35536255" ; sc:description "Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq." ; sc:featureList edam:operation_3200, edam:operation_3435, edam:operation_3436, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Neighbor-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sjdlabgroup/Neighborseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:35679376" ; sc:description "A Self-Supervised Framework for Deep Image Denoising." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Neighbor2Neighbor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TaoHuang2018/Neighbor2Neighbor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_3517 ; sc:citation ; sc:description """An interval mapping method for quantitative trait loci underlying plant neighborhood effects. Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects. To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2020) .""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "neighbor_QTL" ; sc:url "https://cran.r-project.org/package=rNeighborQTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749, edam:topic_3277 ; sc:citation , "pubmed:34355556" ; sc:description "A User-Friendly and Open-Source Implementation of Tree-Based Complex Refractive Index Analysis for Terahertz Spectroscopy." ; sc:featureList edam:operation_2422, edam:operation_3359, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Nelly" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YaleTHz/nelly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web service", "Workbench" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071, edam:topic_3307, edam:topic_3365, edam:topic_3366 ; sc:author "ELIXIR Norway" ; sc:citation , "pmcid:PMC6137412", "pubmed:30271575" ; sc:description "Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data. 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It takes as input a set of pathway components, which were perturbed, and a phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy." ; sc:featureList edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "nem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/nem.html" ; biotools:primaryContact "Holger Froehlich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3316, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC9650770", "pubmed:36367313" ; sc:description "An open access data, tools and compute resource operating on neuroelectromagnetic data." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "NEMAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://NEMAR.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0623, edam:topic_3308, edam:topic_3336, edam:topic_3512 ; sc:citation "pubmed:12584125", "pubmed:14681449", "pubmed:15543149", "pubmed:15571632" ; sc:description "Resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_0560, edam:operation_2871 ; sc:name "NEMBASE4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nematodes.org/nembase4/" ; biotools:primaryContact "John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0623, edam:topic_2269, edam:topic_3473 ; sc:citation "pubmed:19025691" ; sc:description "Recognises gene and protein names in biomedical text." ; sc:featureList edam:operation_3092, edam:operation_3280, edam:operation_3501 ; sc:name "NEMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://text0.mib.man.ac.uk/~sasaki/bootstrep/nemine.html" ; biotools:primaryContact "Yutaka Sasaki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3300, edam:topic_3306 ; sc:citation ; sc:description """Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation. Neuron Modeling for TMS (NeMo-TMS) toolbox is for multi-scale modeling of the effects of Transcranial Magnetic Stimulation on single neuron activity. The instructions and open-source codes provided here enable users with a different levels of expertese to investigate the neuronal behavior under TMS.""" ; sc:featureList edam:operation_2426, edam:operation_3450, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "NeMo-TMS" ; sc:url "https://github.com/OpitzLab/NeMo-TMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3173, edam:topic_3303, edam:topic_3304, edam:topic_3308 ; sc:citation , "pmcid:PMC9825473", "pubmed:36318260" ; sc:description "A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "NeMO Archive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nemoarchive.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0769, edam:topic_3336 ; sc:citation ; sc:description """A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. Source code and data repository associated with the study disclosed in manuscript:. Zahoranszky-Kohalmi et al., A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. Network analysis for therapeutic insights.""" ; sc:featureList edam:operation_2422, edam:operation_3927, edam:operation_3938 ; sc:license "MIT" ; sc:name "Neo4COVID19" ; sc:url "https://neo4covid19.ncats.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC7036241", "pubmed:32087727" ; sc:description """An integrated tool for identification of potential neoantigens. neoANT-HILL is a python toolkit that integrates several pipelines for fully automated identification of potential neoantigens (pNeoAgs) which could be used in personalized immunotherapy due to their ability to elicit and boosting T-cell immune response. It is available as a Docker pre-built image and allows the analysis of single- or multiple samples. As input files is required RNA sequencing reads and/or somatic DNA mutations derived from Next Generating Sequencing.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3629, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "neoANT-HILL" ; sc:url "https://github.com/neoanthill/neoANT-HILL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3512 ; sc:citation ; sc:description """A multifunctional R package for identification of tumor-specific neoantigens. Abstract It is known that some mutated peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T-cells on the surface of a tumor cell. These peptides are termed neoantigen and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions, and structural variants.""" ; sc:featureList edam:operation_0252, edam:operation_2495, edam:operation_3227 ; sc:name "neoantigen" ; sc:url "https://github.com/hase62/Neoantimon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3512 ; sc:citation , "pmcid:PMC7750962", "pubmed:33123738" ; sc:description """A multifunctional R package for identification of tumor-specific neoantigens. It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants""" ; sc:featureList edam:operation_0252, edam:operation_3227, edam:operation_3695 ; sc:name "Neoantimon" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=33123738" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3307, edam:topic_3372 ; sc:description "NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman." ; sc:featureList edam:operation_0292, edam:operation_0491, edam:operation_0495 ; sc:name "NeoBio 1.0 pre-alpha" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://neobio.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3930 ; sc:citation , "pmcid:PMC10263465", "pubmed:37311149" ; sc:description "Comprehensive neoantigen database and discovery platform for cancer immunotherapy." ; sc:featureList edam:operation_0252, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Neodb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://liuxslab.com/Neodb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:encodingFormat edam:format_3752 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3930, edam:topic_3948 ; sc:citation , "pmcid:PMC8299600", "pubmed:34301201" ; sc:description "A novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival." ; sc:featureList edam:operation_0252, edam:operation_0337, edam:operation_0560, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "neoDL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhangjbig/neoDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3068, edam:topic_3930 ; sc:citation , "pubmed:33970219" ; sc:description "NeoFox (NEOantigen Feature tOolboX) is a toolbox for annotating neoantigen candidates with neoantigen features. NeoFox annotates neoantigen candidate sequences with published neo-epitope descriptors." ; sc:featureList edam:operation_0305, edam:operation_0335, edam:operation_0416 ; sc:license "GPL-3.0" ; sc:name "NeoFox" ; sc:softwareHelp ; sc:url "https://github.com/TRON-Bioinformatics/neofox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC5428739", "pubmed:28503667" ; sc:description "Neopeptide discovery in proteomics data." ; sc:featureList edam:operation_3214 ; sc:license "MIT" ; sc:name "Neopeptide Analyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PGB-LIV/neo-pep-tool/releases/" ; biotools:primaryContact "Mandy Peffers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3360, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC9247272", "pubmed:35784189" ; sc:description "A Neonatal Resting State fMRI Data Preprocessing Pipeline." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NeoRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/venguix/NeoRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3170, edam:topic_3320, edam:topic_3520 ; sc:citation , "pmcid:PMC9154024", "pubmed:35669345" ; sc:description "A bioinformatics method for prediction of splice variant neoantigens." ; sc:featureList edam:operation_0252, edam:operation_0264, edam:operation_0433, edam:operation_0526, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NeoSplice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Benjamin-Vincent-Lab/NeoSplice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3297, edam:topic_3336, edam:topic_3376 ; sc:citation , "pmcid:PMC4086065", "pubmed:24782517" ; sc:description "Epitope prediction based on antibody neutralization of viral strains with diverse sequences." ; sc:featureList edam:operation_3092 ; sc:name "NEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformatics.niaid.nih.gov/nep/#home" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_2830, edam:topic_3068, edam:topic_3930 ; sc:citation , "pmcid:PMC8078594", "pubmed:33927717" ; sc:description "NEPdb is a database of T-cell experimentally-validated neoantigens and pan-cancer predicted neoepitopes for cancer immunotherapy. It contains more than 17,000 validated human immunogenic and non-immunogenic neoepitope entries with human leukocyte antigens (HLAs) and T cell information, curated from published literatures." ; sc:featureList edam:operation_0224, edam:operation_0252, edam:operation_0416, edam:operation_3659 ; sc:name "NEPdb" ; sc:url "http://nep.whu.edu.cn/" ; biotools:primaryContact "Lei Yin", "Yu Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_1775, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "NIAID, a cloud based tool for microbiome or metagenomics data analysis. Nephele allows you to process and analyze 16S raw data using pipelines based on QIIME and mothur. It also facilitates WGS functional analyses using bioBakery tools such as MetaPhlAn, HUMMAnN and metagenomic assembly using the a5-miseq/UDBA-UD." ; sc:featureList edam:operation_3460 ; sc:name "Nephele" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nephele.niaid.nih.gov" ; biotools:primaryContact "Nephele Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3474 ; sc:citation , "pubmed:29048594" ; sc:description "Locate genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies." ; sc:featureList edam:operation_2478 ; sc:name "Neptune" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://phac-nml.github.io/neptune/" ; biotools:primaryContact "Eric Marinier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0769, edam:topic_3303, edam:topic_3489, edam:topic_3958 ; sc:citation ; sc:description """An environment for the delivery of genomic medicine. Genomic medicine holds great promise for improving healthcare, but integrating searchable and actionable genetic data into electronic health records remains a challenge. Here, we describe Neptune, a system for managing the interaction between a clinical laboratory and an electronic health record system.

Methods< h4> We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis and EHR integration.

Results< h4> Neptune enabled the analysis of data for generation of and delivery to EHR systems of over 15,000 clinical genomic reports. These projects demanded customizable clinical reports that contained a variety of genetic data types including SNVs, CNVs, pharmacogenomics and polygenic risk scores""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "Neptune-med" ; sc:url "https://gitlab.com/bcm-hgsc/neptune" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3063, edam:topic_3168, edam:topic_3303, edam:topic_3379, edam:topic_3574 ; sc:citation , "pubmed:34257418" ; sc:description "An environment that enables users to identify and report known disease-causing variants in gene sets of interest, to gather curations for potential novel pathogenic variants from an external review system, and to share and update structured genomic knowledge with EHR systems and collaborators." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Neptune" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/bcm-hgsc/neptune" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3336, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:32077475" ; sc:description """A web portal providing access to in silico tools for drug discovery. New E-Resource for Drug Discovery. Regioselectivity prediction for phase 1 and phase 2 metabolism.""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3803, edam:operation_3929 ; sc:name "NERDD" ; sc:url "https://nerdd.zbh.uni-hamburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_3053, edam:topic_3067, edam:topic_3452 ; sc:citation , "pmcid:PMC10129873", "pubmed:37004189" ; sc:description "Biomedical corpus for nested named entity recognition." ; sc:featureList edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:name "NEREL-BIO" ; sc:url "https://github.com/nerel-ds/NEREL-BIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0659, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:37075604" ; sc:description "A negative data generation framework for machine learning applications of noncoding RNAs." ; sc:featureList edam:operation_0303, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NeRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Mehmeteminorhan/NegativeRNA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0893 ; sc:name "Sequence-structure alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0622, edam:topic_3172 ; sc:author ; sc:description "Nerpa is a tool for linking biosynthetic gene clusters (BGCs) to known nonribosomal peptides (NRPs). BGCs are predicted in genome sequences (FASTA or GBK) with antiSMASH. Known NRPs are accepted in the SMILES format and processed with rBAN." ; sc:featureList edam:operation_0292, edam:operation_0361, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Nerpa" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://cab.spbu.ru/software/nerpa/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3334, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36435056" ; sc:description "Corneal confocal microscope images stitching with neural networks." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NerveStitcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LiTianYu6/NerveStitcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_3300, edam:topic_3304, edam:topic_3361 ; sc:citation , "pmcid:PMC8777234", "pubmed:35069167" ; sc:description "Software Tool to Manage Experimental Data and Its Provenance." ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "NES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/neuromat/nes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3293 ; sc:description "High-throughput sequencing data analysis toolset." ; sc:featureList edam:operation_0292 ; sc:name "Nesoni" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/Victorian-Bioinformatics-Consortium/nesoni" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0625, edam:topic_3295, edam:topic_3500 ; sc:citation ; sc:description """Finding human gene-disease associations using a Network Enhanced Similarity Search (NESS) of multi-species heterogeneous functional genomics data. Network Enhanced Similarity Search (NESS). NESS aggregates and harmonizes heterogeneous graph types including ontologies and their annotations, biological networks, and bipartite representations of experimental study results across species. The tool employs diffusion metrics, specifically a random walk with restart (RWR), to estimate the relations among entities in the graph and to make data-driven comparisons.""" ; sc:featureList edam:operation_0335, edam:operation_2421, edam:operation_3226, edam:operation_3436 ; sc:name "NESS" ; sc:url "https://github.com/treynr/ness" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3524 ; sc:citation , "pmcid:PMC3790878", "pubmed:24124490" ; sc:description "A Next-Generation Sequencing Simulator for Metagenomics." ; sc:featureList edam:operation_2426 ; sc:name "NeSSM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3334 ; sc:citation ; sc:description "Simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. It is ideal for networks of spiking neurons of any size, for example: 1. Models of information processing e.g. in the visual or auditory cortex of mammals, 2. Models of network activity dynamics, e.g. laminar cortical networks or balanced random networks, 3. Models of learning and plasticity." ; sc:featureList edam:operation_3562 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "NEST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.12.0" ; sc:url "http://www.nest-simulator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26518695" ; sc:description "Designed to predict the gene essentiality based on protein interaction network and gene expression or CRISPR screen results." ; sc:featureList edam:operation_2454 ; sc:name "NEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nest.dfci.harvard.edu/" ; biotools:primaryContact "Peng Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3304, edam:topic_3524 ; sc:citation , "pmcid:PMC8638679", "pubmed:34764188" ; sc:description "Construct neuronal networks and explore network dynamics" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3927 ; sc:license "MIT" ; sc:name "NEST Desktop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ebrains.eu/service/nest-desktop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0621, edam:topic_0798, edam:topic_3299 ; sc:citation , "pmcid:PMC7755421", "pubmed:32663247" ; sc:description """structure-based detection of LTR retrotransposons and their nesting. Software to recursively identify TEs or other inserted sequences and cut them out to enable discovery of similar underlying older sequences.""" ; sc:featureList edam:operation_0369, edam:operation_0427, edam:operation_0525 ; sc:name "nested" ; sc:url "http://gitlab.fi.muni.cz/lexa/nested" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2332 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2343 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Pathway ID (KEGG)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1155 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Pathway ID (reactome)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1176 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "GO concept ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1775 ; sc:author "Samuele Bovo" ; sc:citation , "pmcid:PMC4480278", "pubmed:26110971" ; sc:description "Network-based enrichment analysis of gene sets." ; sc:featureList edam:operation_3083, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "NET-GE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://net-ge.biocomp.unibo.it/" ; biotools:primaryContact , "Pier Luigi Martelli", "Samuele Bovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:26699225" ; sc:description "Software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation." ; sc:featureList edam:operation_0314 ; sc:name "Net-RSTQ" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.umn.edu/Net-RSTQ/" ; biotools:primaryContact "Rui Kuang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:description """".NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included.\"""" ; sc:featureList edam:operation_0335, edam:operation_2403 ; sc:name ".NET BIO" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bio.codeplex.com/" ; biotools:primaryContact "Nigel Dalaney" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:15539450" ; sc:description "Prediction of substrates of N-acetyltransferase A (NatA)." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetAcet" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/NetAcet/" ; biotools:primaryContact "Henrik Nielsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:32726427" ; sc:description """Semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling. netAE: network-enhanced autoencoder. Network-enhanced autoencoder (netAE) is a semi-supervised dimensionality reduction method. It was specifically designed to facilitate cell labeling of single cell RNA-sequencing data. This repository was created by Zhengyang (Leo) Dong.""" ; sc:featureList edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:license "MIT" ; sc:name "netAE" ; sc:url "https://github.com/LeoZDong/netAE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_2275 ; sc:citation "pubmed:22618871" ; sc:description "Network alignment tool that allows the identification of conserved protein complexes and pathways across organisms. Predictions to fill missing interaction networks is based on likely conserved interactions based on evolutionary distance. Seven model organisms are included." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:name "NetAligner" ; sc:url "http://netaligner.irbbarcelona.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2830 ; sc:citation , "pmcid:PMC10603389", "pubmed:37901344" ; sc:description "NetAllergen-1.0 is a predictive model based on the random forest algorithm. 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NetCleave maps reported IEDB peptides to protein sequences in UniProt/UniParc. After the identification of the C-terminal cleavage site, amino acid sequences are coded using QSAR descriptors, including steric, electrostatic and hydrophobic properties. 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NetCoMi (Network Comparison for Microbiome data) provides functions for constructing, analyzing, and comparing networks suitable for the application on microbial compositional data. The package includes existing methods for zero handling, normalization, estimating associations between OTU/taxa as well as dissimilarities between samples. 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It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms’ niches." ; sc:featureList edam:operation_3660 ; sc:license "GPL-2.0" ; sc:name "NetCooperate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://elbo.gs.washington.edu/software_netcooperate.html" ; biotools:primaryContact "Anat Kreimer", "Elhanan Borenstein", "Rogan Carr", "Roie Levy", "Shiri Freilich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625, edam:topic_2640, edam:topic_3517 ; sc:citation , "pmcid:PMC7515737", "pubmed:32735660" ; sc:description """A network propagation approach using node coreness. 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sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3512 ; sc:citation , "pmcid:PMC146109", "pubmed:8811101" ; sc:description "Neural network predictions of splice sites in human, C. elegans and A. thaliana DNA." ; sc:featureList edam:operation_0433 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetGene2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/NetGene2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3053, edam:topic_3293, edam:topic_3474 ; sc:citation , "pmcid:PMC8495214", "pubmed:34630517" ; sc:description "A Database of Essential Genes Predicted Using Features From Interaction Networks." ; sc:featureList edam:operation_2421, edam:operation_2437, edam:operation_2454, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:name "NetGenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rbc-dsai-iitm.github.io/NetGenes/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3467 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:16762979" ; sc:description "Prediction of glycation of amino groups of lysines in mammalian proteins." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetGlycate" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/NetGlycate/" ; biotools:primaryContact "Morten Bo Johansen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3168, edam:topic_3517 ; sc:citation , "pubmed:32083639" ; sc:description """R-Shiny package for network-integrated pathway enrichment analysis. netGO is an R/Shiny package for network-integrated pathway enrichment analysis. netGO provides user-interactive visualization of enrichment analysis results and related networks. and returns a data frame of gene-sets, their p-values, q-values derived from netGO+, Fisher’s exact test and netGO (optional) as well as the scores for the network interaction and overlap.""" ; sc:featureList edam:operation_2436, edam:operation_3925, edam:operation_3928 ; sc:license "MIT" ; sc:name "netGOR" ; sc:url "https://github.com/unistbig/netGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC8221786", "pubmed:34115744" ; sc:description "Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data." ; sc:featureList edam:operation_3501, edam:operation_3925, edam:operation_3926 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NetGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/netgsa/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. We provide code for formal two-sample testing in Gaussian graphical models (Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (Stadler and Mukherjee, 2013)." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "nethet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/nethet.html" ; biotools:primaryContact "Frank Dondelinger", "Nicolas Staedler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3299, edam:topic_3400, edam:topic_3930 ; sc:citation , "pubmed:36303017" ; sc:description "The Bayesian Hierarchical Model named Neoantgien-T cell interaction estimation (Netie) is developed to investigate the neoantigens observed in the patient tumors to estimate the history of the impact of the host immune pressure on the evolution of the tumor clones. The estimation results will reveal whether the host immune system has been conferring strong or weaker selection pressure on the tumor clones over the time of tumor development. This may give us a peak into the future of how the mutations and clones will evolve for that patient. The model is based on pyclone/sciclone/phylowgs estimation results." ; sc:featureList edam:operation_0252, edam:operation_0314, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "netie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tianshilu/Netie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0659, edam:topic_3335 ; sc:citation , , "pubmed:32687354", "pubmed:33900090" ; sc:description "A Web Server for Prediction of Targets and Therapeutic and Adverse Effects via Network-Based Inference Methods." ; sc:featureList edam:operation_0269, edam:operation_2489, edam:operation_3094 ; sc:name "NetInfer" ; sc:url "http://lmmd.ecust.edu.cn/netinfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3304, edam:topic_3384 ; sc:citation , "pmcid:PMC7006875", "pubmed:32043044" ; sc:description """Bridging global and local topology in whole-brain networks using the network statistic jackknife. Tools for Working with Samples of Networks. Tools for managing large sets of network data and performing whole network analysis. This package is focused on the network based statistic jackknife method, and implements a framework that can be extended to other network manipulations and analyses.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "netjack" ; sc:url "https://cran.r-project.org/package=netjack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3068 ; sc:citation , "pmcid:PMC5568436", "pubmed:28832598" ; sc:description "Linguistic analysis of corpora by means of complex networks." ; sc:featureList edam:operation_0306 ; sc:license "GPL-3.0" ; sc:name "Netlang" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lluisbc/Netlang-Software" ; biotools:primaryContact "Lluís Barceló-Coblijn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344 ; sc:description "Agent-based modeling extension linking MATLAB and NetLogo." ; sc:isAccessibleForFree true ; sc:name "NetLogo-Matlab Extension" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/40474-netlogo-matlab-extension" ; biotools:primaryContact "Matt Biggs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3337, edam:topic_3577 ; sc:citation ; sc:description """A humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS. Given genetic associations from a Phenome-Wide Association Study (PheWAS), a disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between pheno-types. To improve the accessibility of the visualization of shared genetic components across pheno-types, we developed the humaN-disEase phenoType MAp GEnerator (NETMAGE), a web-based tool that produces interactive phenotype network visualizations from summarized PheWAS results.""" ; sc:featureList edam:operation_0282, edam:operation_3282, edam:operation_3925 ; sc:license "MIT" ; sc:name "NETMAGE" ; sc:url "https://hdpm.biomedinfolab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:17277332" ; sc:description "NetMatch: a Cytoscape plugin for searching biological networks. 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Bader" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749 ; sc:citation , "pmcid:PMC4642848", "pubmed:26594341" ; sc:description "Find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models." ; sc:featureList edam:operation_0224, edam:operation_3660 ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "NetMatchStar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2" ; sc:url "https://alpha.dmi.unict.it/netmatchstar/netmatchstar.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602, edam:topic_0769, edam:topic_3473 ; sc:citation , "pmcid:PMC8733431", "pubmed:35013714" ; sc:description "On-the-fly knowledge network construction from biomedical literature." ; sc:featureList edam:operation_3349, edam:operation_3625, edam:operation_3907, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NETME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://netme.click/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3390, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC7356744", "pubmed:32503277" ; sc:description """A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Please cite Tal, O.; Selvaraj, G.; Medina, S.; Ofaim, S.; Freilich, S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020, 8, 840. Genome files include species-specific enzymatic reaction content in their EC format. Environment files include lists of metabolites in their KEGG accessions.""" ; sc:featureList edam:operation_3461, edam:operation_3660, edam:operation_3929 ; sc:name "NetMet" ; sc:url "https://freilich-lab-tools.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC2323871", "pubmed:12717023", "pubmed:14962912", "pubmed:18413329" ; sc:description "Prediction of binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs)." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHC" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "3.4" ; sc:url "http://cbs.dtu.dk/services/NetMHC/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pubmed:22009319" ; sc:description "Predict binding of peptides to any known MHC class I molecule." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHCcons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.cbs.dtu.dk/services/NetMHCcons/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC2753847", "pubmed:19765293" ; sc:description "Predict binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHCII" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.2" ; sc:url "http://www.cbs.dtu.dk/services/NetMHCII/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:author "Edita Karosiene" ; sc:citation , "pmcid:PMC3809066", "pubmed:23900783" ; sc:description "Predict binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHCIIpan" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://www.cbs.dtu.dk/services/NetMHCIIpan/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pmcid:PMC2686430", "pubmed:19002680" ; sc:contributor ; sc:description "Predict binding of peptides to any known MHC molecule using artificial neural networks (ANNs)." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHCpan" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.8" ; sc:url "http://www.cbs.dtu.dk/services/NetMHCpan/" ; biotools:primaryContact "Morten Nielsen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3534 ; sc:citation , "pubmed:23927693" ; sc:description "Predict the stability of peptide binding to a number of different MHC molecules using artificial neural networks (ANNs)." ; sc:featureList edam:operation_0416, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NetMHCstab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.cbs.dtu.dk/services/NetMHCstab/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """A network-structured mixture model for reduced-bias estimation of altered subnetworks. NetMix is an algorithm for identifying altered subnetworks with node scores that are distributed differently from other nodes in the network. NetMix improves upon current methods by using a Gaussian Mixture Model to find a less biased estimate of the size of an altered subnetwork. 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It constructs networks from KGML, SBML and BioPAX files, providing three network representations: metabolic, reactiomic and genic. It finds active paths and applies machine learning methods to summarize found paths for easy interpretation. 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Wild" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3053 ; sc:citation ; sc:description "A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts." ; sc:featureList edam:operation_3562 ; sc:license "GPL-3.0" ; sc:name "netprioR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/netprioR.html" ; biotools:primaryContact "Fabian Schmich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description "Mapping transcription factor networks by exploiting scalable data resources." ; sc:featureList edam:operation_0282 ; sc:name "NetProphet" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/yiming-kang/NetProphet_2.0" ; biotools:primaryContact "Michael R Brent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_3474, edam:topic_3957 ; sc:citation , "pubmed:33576802" ; sc:description """Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity. 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sc:license "MIT" ; sc:name "nf-core-eager" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.1.0", "2.2.0", "2.2.1", "2.2.2", "2.3.0", "2.3.1", "2.3.2", "2.3.3", "2.3.4", "2.3.5", "2.4.0" ; sc:url "https://nf-co.re/eager" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769 ; sc:author ; sc:citation , "pubmed:32055031" ; sc:description "This pipeline is based on the HiC-Pro workflow. It was designed to process Hi-C data from raw FastQ files (paired-end Illumina data) to normalized contact maps. The current version supports most protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C. 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It comes with docker containers making installation trivial and results highly reproducible.""" ; sc:featureList edam:operation_0361, edam:operation_3227, edam:operation_3731 ; sc:license "MIT" ; sc:name "nf-core-sarek" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:softwareVersion "2.5", "2.5.1", "2.5.2", "2.6", "2.6.1", "2.7", "2.7.1", "2.7.2", "3.0", "3.0.1", "3.0.2", "3.1", "3.1.1", "3.1.2", "3.2.0", "3.2.1", "3.2.2", "3.2.3" ; sc:url "https://nf-co.re/sarek" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_3475 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_3864 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3327 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:author , , , "Chuan Wang" ; sc:citation , "pubmed:32055031" ; sc:description "nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline used for small RNA sequencing data." ; sc:featureList edam:operation_0463, edam:operation_3223, edam:operation_3680, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core-smrnaseq" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:softwareVersion "1.0.0" ; sc:url "https://nf-co.re/smrnaseq" ; biotools:primaryContact , , , , "Chuan Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, produces standardised output tables." ; sc:name "nf-core-taxprofiler" ; sc:softwareVersion "1.0.0", "1.0.1" ; sc:url "https://nf-co.re/taxprofiler/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929, edam:format_3975 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3327 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_2331 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_0769, edam:topic_0781, edam:topic_3168, edam:topic_3796 ; sc:author , , ; sc:citation , "pubmed:32055031" ; sc:description "nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports short-read Illumina sequencing data from both shotgun (e.g. sequencing directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based)." ; sc:featureList edam:operation_0292, edam:operation_0346, edam:operation_0525, edam:operation_3197, edam:operation_3227, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core-viralrecon" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:softwareVersion "1.0.0", "1.1.0", "2.0", "2.1", "2.2", "2.3", "2.3.1", "2.4", "2.4.1" ; sc:url "https://nf-co.re/viralrecon" ; biotools:primaryContact , , , , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9875403", "pubmed:36694127" ; sc:description "Portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs." ; sc:featureList edam:operation_0264, edam:operation_0463, edam:operation_3223, edam:operation_3792, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core circrna" ; sc:url "https://nf-co.re/circrna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10199315", "pubmed:36961337" ; sc:description "Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing." ; sc:featureList edam:operation_0362, edam:operation_3192, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core isoseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nf-co.re/isoseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC8808542", "pubmed:35118380" ; sc:description "nf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3460, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-core mag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nf-core/mag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:37417926" ; sc:description "nf-encyclopedia is a NextFlow pipeline specifically designed to analyze DIA proteomics experiment that leverage chromatogram libraries; however it is perfectly suited to analyze DIA proteomics experiments without chromatogram libraries as well. The nf-encyclopedia connects three open-source tools---MSconvert, EncyclopeDIA, and MSstats---to go from mass spectra to quantified peptides and proteins." ; sc:featureList edam:operation_3454, edam:operation_3630 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "nf-encyclopedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TalusBio/nf-encyclopedia" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1930 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308 ; sc:description "A Nextflow pipeline for obtaining raw read counts from RNA-seq data using a given reference genome and annotation." ; sc:featureList edam:operation_3198, edam:operation_3218, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-rnaSeqCount" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/phelelani/nf-rnaSeqCount" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1930 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2331 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308 ; sc:citation ; sc:description "A Nextflow pipeline for the identification and taxonomic classification of foreign/microbial reads reads from high throughput RNA-seq sequencing data" ; sc:featureList edam:operation_3198, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nf-rnaSeqMetagen" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/phelelani/nf-rnaSeqMetagen" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC4489258", "pubmed:25940629" ; sc:description "Combine experimental gene expression profiles and data from publicly available databases to identify conditions or experiments that induce similar or opposite gene expression patterns." ; sc:featureList edam:operation_0571, edam:operation_2421 ; sc:name "NFFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nffinder.cnb.csic.es/" ; biotools:primaryContact "A. Pascual-Montano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3697 ; sc:citation , "pmcid:PMC8404037", "pubmed:34216888" ; sc:description "NFnetFU (Neuro Fuzzy network Fusion) is a modularised integrative pipeline for microbiome data analysis and diseases specific prioritisation for targeted research which addresses problems surrounding collinearity, sparsity and effect size in data.." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3460, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NFnetFU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/VartikaBisht6197/NFnetFu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0610, edam:topic_3053 ; sc:citation , "pmcid:PMC5322572", "pubmed:28280740" ; sc:description "Characterizing and Comparing of Annotated Biological Networks." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "NFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.99.2" ; sc:url "https://cran.r-project.org/web/packages/NFP/index.html" ; biotools:primaryContact "Yang Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0749 ; sc:citation , "pmcid:PMC7671351", "pubmed:33575618" ; sc:description """Next-generation Circos for data visualization and interpretation. NG-Circos - interactive circos for biological data. Circos plots are widely used to display multi-dimensional next-generation genomic data, but existing implementations of Circos are not interactive or can incorporate only limited types of data. Here, we developed Next-Generation Circos (NG-Circos), a flexible JavaScript-based circular genome visualization tool for designing highly interactive Circos plots using 21 functional modules with various data types.""" ; sc:featureList edam:operation_0337 ; sc:name "NG-Circos" ; sc:url "https://wlcb.oit.uci.edu/NG-Circos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0625, edam:topic_2830, edam:topic_3673 ; sc:citation , "pubmed:33411920" ; sc:description "Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions." ; sc:featureList edam:operation_0337, edam:operation_3482, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "NG-STAR" ; sc:url "https://ngstar.canada.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "nGauge is a Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology. The library structure makes automation of data analysis pipelines easier, leading to faster and more reproducible results." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3450, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "nGauge" ; sc:url "https://github.com/Cai-Lab-at-University-of-Michigan/nGauge" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0780, edam:topic_3175, edam:topic_3299 ; sc:citation , "pmcid:PMC10027429", "pubmed:36883694" ; sc:description "Tool for publication-ready visualization of syntenic relationships across multiple genomes." ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NGenomeSyn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.5281/zenodo.7645148" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1710 ; sc:encodingFormat edam:format_3603 ; sc:name "Structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Web application for molecular visualization. It is employed to display molecules like proteins and DNA/RNA with a variety of representations." ; sc:featureList edam:operation_0570 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NGL VIewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "weirdbyte.de" ; sc:softwareHelp ; sc:softwareVersion "0.7.1a" ; sc:url "https://github.com/arose/ngl" ; biotools:primaryContact "Alexander Rose" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621 ; sc:citation , "pmcid:PMC3532370", "pubmed:22780965" ; sc:description "An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 85.3% to 91.4% across species." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "ngLOC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://genome.unmc.edu/ngLOC/index.html" ; biotools:primaryContact , "Babu Guda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_0166, edam:topic_2814 ; sc:citation ; sc:description "Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer." ; sc:featureList edam:operation_0570, edam:operation_2406 ; sc:license "MIT" ; sc:name "NGLview" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/arose/nglview" ; biotools:primaryContact "Alexander S Rose" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A resource of gene and protein expression in NGLY1 deficient patient-derived cell lines. Currently the dataset comprises bulk gene and protein expression data dervied from 31 donors (14 NGLY1-deficient children, 17 parent controls) representing 4 different cell types." ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_3196, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "NGLY1 browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://apps.embl.de/ngly1browser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3168 ; sc:citation , "pmcid:PMC7869453", "pubmed:33557755" ; sc:description """An automated library building tool to align highly divergent HIV envelope sequences. Verify that version 9.8 (R2020a) of the MATLAB Runtime is installed. NGlyAlignApp_v1.exe -MCRInstaller.exe Note: if end users are unable to download the MATLAB Runtime using the instructions in the previous section, include it when building your component by clicking the "Runtime included in package" link in the Deployment Tool. -This readme file.""" ; sc:featureList edam:operation_0238, edam:operation_0292, edam:operation_0323, edam:operation_0510, edam:operation_3081 ; sc:license "GPL-3.0" ; sc:name "NGlyAlign" ; sc:url "https://github.com/UNSW-Mathematical-Biology/NGlyAlign_v1.0" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_1929 ; sc:name "Data reference" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence alignment (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3175 ; sc:citation ; sc:description "An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation." ; sc:featureList edam:operation_0292, edam:operation_2520, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NGMLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/philres/ngmlr" ; biotools:primaryContact "Philipp Rescheneder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0780, edam:topic_3542 ; sc:citation , "pubmed:33189829" ; sc:description """Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa. NGOME-Lite is a fast algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. NGOME-Lite does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Just protein sequences in FASTA or multi-FASTA format is needed to run NGOME-Lite. Prediction of spontaneous asparagine deamidation at a proteomic scale.""" ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_3904 ; sc:name "NGOME-Lite" ; sc:url "https://ngome.proteinphysiologylab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0749, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC6929330", "pubmed:31874633" ; sc:description """Classification of adaptor proteins using recurrent neural networks and PSSM profiles. Adaptor proteins are carrier proteins that play a crucial role in signal transduction. We collected all the proteins from UniProt with GO molecular function annotations related to adaptor proteins.""" ; sc:featureList edam:operation_0303, edam:operation_0417, edam:operation_1777, edam:operation_3439 ; sc:name "ngphubinh" ; sc:url "https://github.com/ngphubinh/adaptors" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC7678096", "pubmed:33213365" ; sc:description """An efficient tool for combining multiple NGS data tracks using minimum Bayes' factors. NGS Integrator Tool (NGS-Integrator) is a Java-based tool that integrates multiple genome-wide NGS data via the minimum Bayes' Factor from density of sequence reads mapped on the genome. To integrate multiple NGS data, homogeneous replicates or heterogeneous NGS data can be integrated into the single data track based on the complements of the minimum Bayes factor (cMBF) (range: 0-1) calculated from signal-to-background noise ratios as a function of genomic position. NGS-Integrator is a Java-based commandline tool that integrates multiple genome-wide NGS data via the minimum Bayes' Factor from density of sequence reads mapped on the genome.""" ; sc:featureList edam:operation_0438, edam:operation_3222, edam:operation_3359, edam:operation_3436, edam:operation_3799 ; sc:license "MIT" ; sc:name "NGS-Integrator" ; sc:url "https://hpcwebapps.cit.nih.gov/ESBL/NGS-Integrator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3175, edam:topic_3577 ; sc:description "Complete solution for human re-sequencing projects." ; sc:featureList edam:operation_0361, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Ngs-pipeline" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:url "http://code.google.com/p/ngs-pipeline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3168, edam:topic_3512, edam:topic_3519 ; sc:citation ; sc:description """High-throughput primer design for multiplex polymerase chain reactions. NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design. It includes four Python-scripts:. NGS-PrimerPlex can be run as a Docker image. In this way you only need to install Docker (for windows 7 users this install steps should be performed). If you have "VD-x, VD-t error", you need to turn on virtualization in BIOS CPU section.""" ; sc:featureList edam:operation_0308, edam:operation_0346, edam:operation_3192, edam:operation_3196, edam:operation_3237 ; sc:license "GPL-3.0" ; sc:name "NGS-PrimerPlex" ; sc:url "https://github.com/aakechin/NGS-PrimerPlex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3572 ; sc:citation ; sc:description "Comparative analysis between ChIP-seq and other enrichment-related NGS datasets requires prior characterization of their degree of technical similarity. The Galaxy tool NGS-QC Generator is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile. Such information is then used for comparative purposes and for defining strategies to improve the quality of sample-derived datasets." ; sc:featureList edam:operation_3218 ; sc:license "GPL-2.0" ; sc:name "NGS-QC Generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ngs-qc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3120 ; sc:citation , "pmcid:PMC3150039", "pubmed:21697123" ; sc:description "Collection of command-line scripts for providing annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl." ; sc:featureList edam:operation_0361, edam:operation_3197 ; sc:license "Not licensed" ; sc:name "NGS-SNP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.ualberta.ca/~stothard/downloads/NGS-SNP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC3633008", "pubmed:23815181" ; sc:description "Next Generation Sequencing Transcriptome profile explorer." ; sc:featureList edam:operation_2495, edam:operation_3258 ; sc:name "NGS-Trex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ngs-trex.disit.unipmn.it/Trex/cms/" ; biotools:primaryContact "Flavio Mignone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC6488770", "pubmed:31042285" ; sc:description "Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding." ; sc:featureList edam:operation_0302, edam:operation_1812, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ngsRelateV2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ANGSD/ngsRelate" ; biotools:primaryContact , , "Ida Moltke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3489 ; sc:citation , "pubmed:31841127" ; sc:description """A Bioconductor package for managing FastQC reports and other NGS related log files. The shiny app that accompanies the ngsReports R package""" ; sc:featureList edam:operation_0337 ; sc:name "ngsReports" ; sc:url "https://github.com/UofABioinformaticsHub/shinyNgsreports" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descriptions." ; sc:featureList edam:operation_0310, edam:operation_3198 ; sc:license "AGPL-3.0" ; sc:name "Ngs backbone" ; sc:operatingSystem "Linux" ; sc:url "http://bioinf.comav.upv.es/ngs_backbone/index.html" ; biotools:primaryContact "Ngs backbone team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3168, edam:topic_3572 ; sc:citation , ; sc:description "This tool simulates an Illumina run and provides plots of false positives and false negatives. It allows for a range of simulation parameters to be set." ; sc:featureList edam:operation_0230, edam:operation_2426, edam:operation_3218 ; sc:name "ngs_simulation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation , "pubmed:24578402" ; sc:description "Tool to assess the efficiency of targeted enrichment sequencing." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ngsCAT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://ngscat.clinbioinfosspa.es/ngscat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170, edam:topic_3572, edam:topic_3673 ; sc:citation , "pmcid:PMC5499645", "pubmed:28369524" ; sc:description "Checking sample matching for NGS data." ; sc:featureList edam:operation_3218 ; sc:license "MIT" ; sc:name "NGSCheckMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/parklab/NGSCheckMate" ; biotools:primaryContact "Peter J. Parkcorresponding author3,5" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "RNA-seq analysis of non-model species using cloud computing." ; sc:featureList edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "NGScloud" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GGFHF/NGScloud/" ; biotools:primaryContact "Unai López de Heredia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:33822850" ; sc:description "ngsComposer is an automated pipeline for empirically based NGS data quality filtering." ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3200, edam:operation_3219, edam:operation_3933 ; sc:license "Apache-2.0" ; sc:name "ngsComposer" ; sc:url "https://github.com/ryandkuster/ngsComposer" ; biotools:primaryContact "Bode A Olukolu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation ; sc:description "Provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer." ; sc:featureList edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "NGScopy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NGScopy.html" ; biotools:primaryContact "Xiaobei Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description "Multicomponent pipeline for NGS using a set of versioned, modular and reusable container building blocks." ; sc:featureList edam:operation_0292, edam:operation_0361, edam:operation_2403, edam:operation_3197, edam:operation_3227 ; sc:license "GPL-2.0" ; sc:name "NGSeasy" ; sc:softwareHelp ; sc:softwareVersion "1.0-r001" ; sc:url "https://github.com/KHP-Informatics/ngseasy" ; biotools:primaryContact "Dr Amos Folarin", "Dr Stephen J Newhouse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC10514575", "pubmed:37745626" ; sc:description """Population genetic analysis of next-generation DNA sequencing data with Julia language. Templates and functions in Julia language to process next-generation sequencing (NGS) data for population genetic analysis. ngsJulias receives NGS data files as input and provides routines and functions to parse files, perform data filtering and implement custom population genetic analyses.""" ; sc:featureList edam:operation_0484, edam:operation_1812, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ngsJulia" ; sc:url "https://github.com/mfumagalli/ngsJulia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0749, edam:topic_3168, edam:topic_3295, edam:topic_3674 ; sc:citation "pubmed:20965971" ; sc:description "Database that contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. The database is currently populated with human, mouse and Arabidopsis data." ; sc:featureList edam:operation_0430, edam:operation_2422, edam:operation_3204 ; sc:name "NGSmethDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo2.ugr.es/NGSmethDB/gbrowse/" ; biotools:primaryContact "Michael Hackenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3307 ; sc:citation , "pubmed:35085089" ; sc:description "A medium for the representation and exchange of NGS data." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NGSML" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.sysbio.org.cn/NGSML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24603986" ; sc:description "R package to estimate the optimal window size in the analysis of very low coverage next-generation sequence data." ; sc:featureList edam:operation_2403 ; sc:name "NGSoptwin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www1.maths.leeds.ac.uk/~arief/R/win/" ; biotools:primaryContact "Arief Gusnanto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:26323718" ; sc:description "Used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes." ; sc:featureList edam:operation_2451 ; sc:name "NgsRelate" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.popgen.dk/software/index.php/NgsRelate" ; biotools:primaryContact "Ida Moltke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3168 ; sc:citation ; sc:description """A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data. Estimating relatedness coefficients from admixed populations. It can take called genotypes in PLINK format and genotype likelihoods in a beagle format. The method is implemented in an R package and as a commandline based C++ program embeded in the R package.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227 ; sc:name "NGSremix" ; sc:url "https://github.com/KHanghoj/NGSremix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:22290614" ; sc:description "Tool for researchers concerned with target enrichment issues in next-generation sequencing. It evaluates the target enrichment performance of target regions given in BED format and outputs summary statistics, visualizations, and some additional files giving details on the analysis." ; sc:featureList edam:operation_2436 ; sc:name "NGSrich" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ngsrich/" ; biotools:primaryContact "Dr. Peter Frommolt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3168 ; sc:citation "pubmed:24458950" ; sc:description "Collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data." ; sc:featureList edam:operation_2478 ; sc:name "ngsTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mfumagalli/ngsTools" ; biotools:primaryContact "Matteo Fumagalli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:citation "pubmed:23314324" ; sc:description "NGSUtils is a suite of software tools for working with next-generation sequencing datasets" ; sc:featureList edam:operation_0335, edam:operation_3187, edam:operation_3218, edam:operation_3219, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "NGSUtils" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://ngsutils.org" ; biotools:primaryContact "Marcus Breese (Primary developer)", "Yunlong Liu (PI)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:19855106" ; sc:description "High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView, a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API." ; sc:featureList edam:operation_3184 ; sc:name "NGSView" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://ngsview.sourceforge.net/" ; biotools:primaryContact "Erik Arner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_0749, edam:topic_3068, edam:topic_3673 ; sc:citation , "pmcid:PMC9029197", "pubmed:35448733" ; sc:description "An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis." ; sc:featureList edam:operation_0308, edam:operation_2421, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "NHCCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tbir.njau.edu.cn/NhCCDbHubs/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_2640, edam:topic_3512 ; sc:description "Protocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available)." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3223, edam:operation_3463 ; sc:name "NHGRI Micorarray Project" ; sc:softwareHelp ; sc:url "http://research.nhgri.nih.gov/microarray/index.html" ; biotools:primaryContact "Javed Khan", "Paul S. Meltzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:34002774" ; sc:description "nhKcr is a bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identification of Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and expensive when compared with computational approaches. To date, several predictors for Kcr site prediction have been developed, most of which are capable of predicting crotonylation sites on either histones alone or mixed histone and nonhistone proteins together. These methods exhibit high diversity in their algorithms, encoding schemes, feature selection techniques and performance assessment strategies. However, none of them were designed for predicting Kcr sites on nonhistone proteins." ; sc:featureList edam:operation_0303, edam:operation_0417, edam:operation_2575, edam:operation_3755 ; sc:name "nhKcr" ; sc:softwareHelp ; sc:url "https://nhkcr.erc.monash.edu/" ; biotools:primaryContact "Guoguang Ying", "Jiangning Song", "Zhen Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0804, edam:topic_3510 ; sc:citation "pubmed:17426378" ; sc:description "Allows to predict binding peptide for 67 MHC Class I alleles. This also allow to predict the proteasome cleavage site and binding peptide that have cleavage site at C terminus (potential T cell epitopes)." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "nHLAPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/nhlapred/" ; biotools:primaryContact "Dr G P S Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation ; sc:description """U-Net Model for Brain Extraction on Non-human Primates. U-Net model and PRIME-DE skull-stripped brain masks (pre-release). This is a pre-release of skull-stripped brian masks of T1w images for 136 macaque monkeys (20 sites) from PRIME-DE. The masks are created from a convolutional network - UNet model, initially trained on a human sample and upgraded with macaque data.""" ; sc:featureList edam:operation_3096, edam:operation_3907, edam:operation_3927 ; sc:name "NHP" ; sc:url "https://github.com/HumanBrainED/NHP-BrainExtraction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:17060197" ; sc:description "Program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998)." ; sc:featureList edam:operation_0323 ; sc:name "nhPhyML" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://doua.prabi.fr/software/nhphyml" ; biotools:primaryContact "Bastien Boussau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:24947751" ; sc:description "Implements a method for deffining causal networks corrected for the problem of interference between dynamically similar regulators within the context of a sparse linear auto-regression model." ; sc:featureList edam:operation_3439 ; sc:name "NIACS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software" ; biotools:primaryContact "Nigel J. Burroughs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC9933847", "pubmed:36727493" ; sc:description "Network-informed adaptive positive-unlabeled learning for disease gene identification." ; sc:featureList edam:operation_2454, edam:operation_3501, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NIAPU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AndMastro/NIAPU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3292 ; sc:citation "pubmed:27494258" ; sc:description "Server to help the analysis of the conformational preferences of amino acid residues in proteins." ; sc:featureList edam:operation_2406 ; sc:name "NIAS-Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbcb.inf.ufrgs.br/npas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053, edam:topic_3500 ; sc:citation "pubmed:20952407" ; sc:description "Genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database has plant and microorganism search systems to provide information on research materials, including passport and evaluation data for genetic resources with the desired properties. A database of plant diseases in Japan has been developed based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan." ; sc:featureList edam:operation_0224, edam:operation_0282, edam:operation_2421, edam:operation_2422, edam:operation_3197 ; sc:name "NIASGBdb" ; sc:softwareHelp ; sc:url "http://www.gene.affrc.go.jp/databases_en.php" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_2640 ; sc:citation , "pubmed:33677485" ; sc:description "NIBNA is a network-based node importance approach for identifying breast cancer drivers. 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This application predicts likelihood of home discharge following craniotomy for meningioma resection.""" ; sc:featureList edam:operation_3659 ; sc:name "NLP" ; sc:url "http://nlp-home.insds.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3416, edam:topic_3421, edam:topic_3474 ; sc:citation , "pubmed:35412473" ; sc:description "Natural Language Processing Algorithm for Detection of Incidental Durotomy in Operative Notes." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "NLP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sorg-apps.shinyapps.io/nlp_incidental_durotomy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3077, edam:topic_3365 ; sc:citation , "pmcid:PMC7148103" ; sc:description """Exploring the Universe of NLP Papers. Understanding the current research trends, problems, and their innovative solutions remains a bottleneck due to the ever-increasing volume of scientific articles. In this paper, we propose NLPExplorer, a completely automatic portal for indexing, searching, and visualizing Natural Language Processing (NLP) research volume. NLPExplorer presents interesting insights from papers, authors, venues, and topics.""" ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "NLPExplorer" ; sc:url "http://nlpexplorer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0218, edam:topic_3474 ; sc:citation "pubmed:15215466" ; sc:description "NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases." ; sc:featureList edam:operation_3429 ; sc:name "NLProt" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://rostlab.org/owiki/index.php/NLProt" ; biotools:primaryContact "Sven Mika" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_0780 ; sc:citation "pubmed:25586514" ; sc:description "Tool to rapidly annotate the NLR (nucleotide-binding leucine-rich repeat) complement from sequenced plant genomes." ; sc:featureList edam:operation_0226, edam:operation_2479 ; sc:name "NLR-parser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/steuernb/NLR-Parser" ; biotools:primaryContact "Steuernagel B" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0203, edam:topic_0780, edam:topic_3474 ; sc:citation , "pmcid:PMC9519389", "pubmed:36186050" ; sc:description "Bundle of machine learning motif predictors-Reveals motif stability underlying plant Nod-like receptors diversity." ; sc:featureList edam:operation_0239, edam:operation_0303, edam:operation_2422, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NLRexpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nlrexpress.biochim.ro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0623, edam:topic_0637, edam:topic_0780, edam:topic_3293 ; sc:citation , "pmcid:PMC9825502", "pubmed:36350627" ; sc:description "NLRscape is an interactive atlas of plant NLRs equipped with a collection of easy, ready to use bioinformatic tools aimed for the exploration of the complex sequence landscape of this class of receptors in plants." ; sc:featureList edam:operation_0291, edam:operation_0303, edam:operation_2844, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "NLRscape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nlrscape.biochim.ro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_3314, edam:topic_3384 ; sc:citation "pubmed:19563654" ; sc:description "Simple Hidden Markov Model for nuclear localization signal prediction." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0331, edam:operation_3092 ; sc:name "NLStradamus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.moseslab.csb.utoronto.ca/NLStradamus/" ; biotools:primaryContact "Alan M Moses" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3382 ; sc:citation , "pubmed:33502985" ; sc:description """Modeling the Domain Shift for Crowd Counting. PyTorch implementations of the paper: "Neuron Linear Transformation: Modeling the Domain Shift for Crowd Counting (T-NNLS, 2021).".""" ; sc:name "NLT" ; sc:url "https://github.com/taohan10200/NLT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "Predicting 2’-O-Methylation (Nm) Sites in Nanopore RNA Sequencing Data." ; sc:featureList edam:operation_2436, edam:operation_3185, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Nm-Nano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Janga-Lab/Nm-Nano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3512 ; sc:citation ; sc:description "Tool for systematic classification of nonsense mediated decay (NMD) events." ; sc:featureList edam:operation_2990 ; sc:name "NMD classifier" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/transcriptome-analysis/" ; biotools:primaryContact "Feng-Chi Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0634, edam:topic_3336, edam:topic_3374, edam:topic_3474 ; sc:citation , "pmcid:PMC8825773", "pubmed:34875000" ; sc:description "A Network-Based Drug Repurposing Method Via Non-Negative Matrix Factorization." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NMF-DR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sshaghayeghs/NMF-DR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071, edam:topic_3307 ; sc:citation "pubmed:25887585" ; sc:description "Implements the Non-negative Matrix Factorization (NMF) algorithm by making use of Graphics Processing Units (GPUs)." ; sc:featureList edam:operation_2409 ; sc:name "NMF-mGPU" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo-cnb.github.io/bionmf-gpu/" ; biotools:primaryContact "Alberto Pascual-Montano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3345, edam:topic_3382, edam:topic_3452 ; sc:citation "pubmed:15033365" ; sc:description "The theory and methods behind NMFF are based on searching along a few lowest frequency normal mode vectors, constructed from a multi-resolution elastic network representation of the atomic structure of interest, to maximize the correlation between the computed electron density for the flexible model and the experimental density." ; sc:featureList edam:operation_0337 ; sc:name "NMFF" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.mmtsb.org/software/nmff.html" ; biotools:primaryContact "Charles Brooks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3295, edam:topic_3407 ; sc:citation ; sc:description """NMFNA: a non-negative matrix factorization network analysis method for identifying communities and characteristic genes from pancreatic cancer data. we have provided demo data and Pancreatic Cancer data for NMFNA, if you want to run NMFNA method, please run the script "Demo.m" directly.""" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3927 ; sc:name "NMFNA" ; sc:url "https://github.com/CDMB-lab/NMFNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3474 ; sc:citation ; sc:description """High-throughput morphological screening of neuromuscular junctions identifies subtle changes in mouse neuromuscular disease models. NMJ-Analyser requires NMJs to be separated by at least 20um. Images which contain superimposed NMJs are not ideal for analysis. The NMJ Analyser takes as input directories where jpg or png files have been stored.""" ; sc:featureList edam:operation_2939, edam:operation_3359, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "NMJ-Analyser" ; sc:url "https://github.com/csudre/NMJ_Analyser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2737 ; sc:name "FIG ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0797 ; sc:citation ; sc:description "Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma." ; sc:featureList edam:operation_0224 ; sc:name "National microbial pathogen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nmpdr.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0623, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC10767849", "pubmed:37811892" ; sc:description "Database of novel protein families from microbial metagenomes and metatranscriptomes." ; sc:featureList edam:operation_0303, edam:operation_2422, edam:operation_3216, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "NMPFamsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nmpfamsdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3047, edam:topic_3172, edam:topic_3474 ; sc:citation ; sc:description """De Novo Molecule Identification from NMR Spectra. Molecule identification from NMR spectrum using de novo molecule generator. This code is for reference only as it requires MPI and Gaussian environment which is hard to ensure among different clusters. Also, for the NMR spectrum prediction part, we have used a Gaussain encapsulation package which we can not make public for now. Replacing this part by a traditional Gaussian code or other NMR spectrum prediction method would solve the problem.""" ; sc:featureList edam:operation_3215, edam:operation_3860, edam:operation_3891 ; sc:name "NMR-TS" ; sc:url "https://github.com/tsudalab/NMR-TS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3444 ; sc:citation "pubmed:20513646" ; sc:description "NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom." ; sc:featureList edam:operation_2945 ; sc:name "NMR Constraints Analyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molsim.sci.univr.it/bioinfo/tools/constraint/" ; biotools:primaryContact "Alejandro Giorgetti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_1317, edam:topic_2814 ; sc:citation ; sc:description "Cloud-based virtual machine loaded with NMR software." ; sc:featureList edam:operation_3214 ; sc:name "NMRbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.nmrbox.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:26504145" ; sc:description "Provides a simple and fast NMR protein structure refinement." ; sc:featureList edam:operation_0322 ; sc:name "NMRe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://psb.kobic.re.kr/nmre/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:34850821" ; sc:description "Identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences." ; sc:featureList edam:operation_0250, edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "NmRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lab.malab.cn/~acy/NmRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_3520 ; sc:citation , "pmcid:PMC4393527", "pubmed:25505092" ; sc:description "Enhanced software for biomolecular NMR spectroscopy." ; sc:featureList edam:operation_3215 ; sc:name "NMRFAM-SPARKY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pine.nmrfam.wisc.edu/download_packages.html" ; biotools:primaryContact "Dr. Woonghee Lee" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:name "NMR spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:encodingFormat edam:format_3825 ; sc:name "NMR spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0593, edam:topic_3172, edam:topic_3366, edam:topic_3370 ; sc:author "Daniel Jacob" ; sc:citation ; sc:description "This tool is used to support the nmrML data standard for nuclear magnetic resonance raw data in metabolomics. It converts native Bruker, Jeol and Agilent vendor formats into the open access nmrML data standard that is used by an ever-so growing number of small molecule NMR repositories." ; sc:featureList edam:operation_3434 ; sc:name "nmrML converter" ; sc:softwareVersion "1.2" ; sc:url "http://nmrml.org/" ; biotools:primaryContact "Daniel Jacob", "Daniel Schober" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0593, edam:topic_3474 ; sc:citation ; sc:description "Deep learning approach to automated peak picking of protein NMR spectra (part of a Dumpling software)." ; sc:featureList edam:operation_3214, edam:operation_3215 ; sc:name "NMRNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dumpling.bio/" ; biotools:primaryContact "Adam Gonczarek", "Michał J Walczak", "Piotr Klukowski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:name "NMR spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "An interactive 1D NMR spectra processing tool dedicated to metabolomics. This open source software provides a complete set of tools for processing and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2928, edam:operation_3214, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NMRProcFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://nmrprocflow.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0593, edam:topic_1317 ; sc:citation , "pmcid:PMC5356280", "pubmed:28302053" ; sc:description "ibrary for reading, writing, and accessing BMRB entries in NMR-STAR and JSONized NMR-STAR formats." ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "nmrstarlib" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinformatics.cesb.uky.edu/Main/SoftwareDevelopment#nmrstarlib" ; biotools:primaryContact "Andrey Smelter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_2814, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC9913044", "pubmed:36723167" ; sc:description "An online platform for automated biomolecular NMR spectra analysis." ; sc:featureList edam:operation_0320, edam:operation_3215, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "NMRtist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nmrtist.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_0602, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:22669906" ; sc:description "Webserver for modeling biologically relevant protein conformational changes. The approach has been shown to reproduce experimentally observed conformational variabilities in the case of domain and loop motions and is able to generate meaningful pathways of conformational transitions." ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_0480, edam:operation_0481, edam:operation_2476 ; sc:name "NMSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nmsim.de" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3360, edam:topic_3474 ; sc:citation ; sc:description """Prediction of breast cancer proteins using molecular descriptors and artificial neural networks. neural-networks-for-breast-cancer-proteins. Machine Learning for breast cancer protein screening. This project is a collaboration from different institutions:.""" ; sc:featureList edam:operation_2436, edam:operation_3439, edam:operation_3901 ; sc:license "MIT" ; sc:name "NN-breastcancerproteins" ; sc:url "https://github.com/muntisa/neural-networks-for-breast-cancer-proteins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2640, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "Neural network-based model for prediction of mRNA sub-cellular localization using distance-based sub-sequence profiles." ; sc:featureList edam:operation_0314, edam:operation_2489, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NN-RNALoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NeginBabaiha/NN-RNALoc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330, edam:format_3033 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2830 ; sc:citation ; sc:description "Discovering sequence motifs in quantitative peptide data. It allows generating artificial neural network models of receptor-ligand interactions. It takes as input a set of ligand sequences with target values; it returns a sequence alignment, a binding motif of the interaction, and a model that can be used to scan for occurrences of the motif in other sequences." ; sc:featureList edam:operation_0245 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NNAlign" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/NNAlign/" ; biotools:primaryContact "Massimo Andreatta", "Morten Nielsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_0130, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:19420062" ; sc:description "Using 2D-recursive neural networks, it is a web server for predicting protein contact maps." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0392, edam:operation_0474, edam:operation_2429 ; sc:name "NNcon" ; sc:url "http://casp.rnet.missouri.edu/nncon.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:19880381" ; sc:description "The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. Also covered are parameters for predicting RNA folding free energy and enthalpy changes." ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_0475, edam:operation_0483 ; sc:name "NNDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.urmc.rochester.edu/NNDB" ; biotools:primaryContact "David Mathews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC9196133", "pubmed:35712677" ; sc:description "Mean-Field Based Analysis Tools for Neuronal Network Models." ; sc:featureList edam:operation_3454, edam:operation_3860, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NNMT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/INM-6/nnmt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Nearest Neighbor Networks is a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated." ; sc:featureList edam:operation_3432 ; sc:name "NNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.01" ; sc:url "http://genomics-pubs.princeton.edu/nnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "nnNorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/nnNorm.html" ; biotools:primaryContact "Adi Laurentiu Tarca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3053, edam:topic_3334 ; sc:citation "pubmed:12914569" ; sc:description "Neural network program for analysing case-control multi-locus genotype data using a permutation test." ; sc:featureList edam:operation_2945 ; sc:name "NNPERM" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.davecurtis.net/bvnorth/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC8305591", "pubmed:34303360" ; sc:description "A neural network-based method for polypharmacy side effects prediction." ; sc:featureList edam:operation_3891, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "NNPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/raziyehmasumshah/NNPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3308 ; sc:citation , "pmcid:PMC10333391", "pubmed:37429865" ; sc:description "nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes." ; sc:featureList edam:operation_3435, edam:operation_3695, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nnSVG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioconductor.org/packages/nnSVG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33288961" ; sc:description """nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. In 3D biomedical image segmentation, dataset properties like imaging modality, image sizes, voxel spacings, class ratios etc vary drastically. In current research practice, segmentation pipelines are designed manually and with one specific dataset in mind.""" ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "nnU-Net" ; sc:url "https://github.com/MIC-DKFZ/nnUNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7363192" ; sc:description """The Neural Network Verification Tool for Deep Neural Networks and Learning-Enabled Cyber-Physical Systems. This paper presents the Neural Network Verification (NNV) software tool, a set-based verification framework for deep neural networks (DNNs) and learning-enabled cyber-physical systems (CPS). The crux of NNV is a collection of reachability algorithms that make use of a variety of set representations, such as polyhedra, star sets, zonotopes, and abstract-domain representations. NNV supports both exact (sound and complete) and over-approximate (sound) reachability algorithms for verifying safety and robustness properties of feed-forward neural networks (FFNNs) with various activation functions. F""" ; sc:featureList edam:operation_3927 ; sc:name "NNV" ; sc:url "https://github.com/verivital/nnv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2259 ; sc:citation , ; sc:description "The NOA (Network Ontology Analysis) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges." ; sc:featureList edam:operation_3501 ; sc:name "NOA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://nrnb.org/tools/noa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_0621, edam:topic_3168 ; sc:citation , "pmcid:PMC8521201", "pubmed:34704076" ; sc:description "Protocol for using NoBadWordsCombiner to merge and minimize \"bad words\" from BLAST hits against multiple eukaryotic gene annotation databases." ; sc:featureList edam:operation_2421, edam:operation_3092, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "NoBadWordsCombiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hsdfinder.com/combiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0602, edam:topic_0659, edam:topic_3318 ; sc:citation "pubmed:18449469" ; sc:description "Facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules." ; sc:featureList edam:operation_0438, edam:operation_2441, edam:operation_3457, edam:operation_3458 ; sc:name "NOBAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.manet.uiuc.edu/nobai/nobai.php" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "NoD is a predictor of nucleolar localization sequences (NoLSs) in proteins. NoLSs are short basic motifs that localize proteins to the nucleolus, a sub-compartment of the nucleus. You can search the set of NoLSs predicted in 9531 human proteins out of the 43534 human proteins considered (from IPI version 3.40)." ; sc:featureList edam:operation_2421, edam:operation_2423, edam:operation_2479 ; sc:name "NoD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.compbio.dundee.ac.uk/www-nod/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3474 ; sc:citation ; sc:description "Predicting protein subcellular location using learned distributed representations from a protein-protein network | Predicting protein subcellular location using node embedding | we present a deep learning based method, node2loc, to predict protein subcellular location. node2loc first learns distributed representations of proteins in a protein-protein network, which acquires representations from unlabeled data for downstream tasks. Then the learned representations are further fed into a recurrent neural network (RNN) to predict subcellular locations | To identify the functions of a protein, we first need know where this protein is located. Interacting proteins tend to locate in the same subcellular location. Thus, it is imperative to take the protein-protein interactions into account for computational identification of protein subcellular locations" ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_3439 ; sc:name "node2loc" ; sc:url "https://github.com/xypan1232/node2loc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC9891245", "pubmed:36688699" ; sc:description "Accurately modeling biased random walks on weighted networks using node2vec+." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "node2vec+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/krishnanlab/node2vecplus_benchmarks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3335 ; sc:citation ; sc:description """Network-Oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. Rapid development of high-throughput technologies has permitted the identification of an increasing number of disease-associated genes (DAGs), which are important for understanding disease initiation and developing precision therapeutics. However, DAGs often contain large amounts of redundant or false positive information, leading to difficulties in quantifying and prioritizing potential relationships between these DAGs and human diseases. Here, a network-oriented gene entropy approach (NOGEA) is proposed for accurately inferring master genes that contribute to specific diseases by quantitatively calculating their perturbation abilities on directed disease-specific gene networks.""" ; sc:featureList edam:operation_2454, edam:operation_3435, edam:operation_3799 ; sc:name "NOGEA" ; sc:url "https://github.com/guozihuaa/NOGEA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove mark-up (e.g. HTML tags) from an ASCII text file." ; sc:featureList edam:operation_0335 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "nohtml" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/nohtml.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description """Effects of technical noise on bulk RNA-seq differential gene expression inference. Abstract Motivation Inconsistent, analytical noise introduced either by the sequencing technology or by the choice of read-processing tools can bias bulk RNA-seq analyses by shifting the focus to the variation in expression of low-abundance transcripts; as a consequence these highly-variable genes are often included the differential expression (DE) call and impact the interpretation of results. Results To illustrate the effects of “noise”, we present simulated datasets following closely the characteristics of a H.sapiens and a M.musculus dataset, respectively, highlighting the extent of technical-noise in both a high inter-individual variability ( H. sapiens ) and reduced variability ( M. Musculus ) setup.""" ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3800 ; sc:name "noiseDetection_mRNA" ; sc:url "https://github.com/yry/noiseAnalysis/tree/master/noiseDetection_mRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC4666377", "pubmed:26184878" ; sc:description "Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions." ; sc:featureList edam:operation_3680 ; sc:license "Artistic-2.0" ; sc:name "NOISeq" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NOISeq.html" ; biotools:primaryContact "Sonia Tarazona" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3466 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Cleaning aligned sequences." ; sc:featureList edam:operation_3081 ; sc:name "noisy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5.12.1" ; sc:url "http://www.bioinf.uni-leipzig.de/Software/noisy/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32997627" ; sc:description """Learning Self-supervised Denoising from Corrupted Image. PyTorch Code for "Noisy-As-Clean: Learning Self-supervised Denoising from Corrupted Image", TIP 2020. To reproduce the results in the NAC paper:. Training and test for Set12 at the same time.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3927 ; sc:name "Noisy-As-Clean" ; sc:url "https://github.com/csjunxu/Noisy-As-Clean" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3466 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "Cleaning aligned sequences." ; sc:featureList edam:operation_0258 ; sc:name "noisy_oneclick" ; sc:softwareVersion "1.5.12.1" ; sc:url "http://www.bioinf.uni-leipzig.de/Software/noisy/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8373073", "pubmed:34076236" ; sc:description "Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output." ; sc:featureList edam:operation_0314, edam:operation_2437, edam:operation_3557, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "noisyR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=noisyr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A decoy-free approach to the identification of peptides." ; sc:featureList edam:operation_2479 ; sc:license "Apache-2.0" ; sc:name "Nokoi" ; sc:operatingSystem "Linux" ; sc:provider "ugent.be" ; sc:softwareVersion "1" ; sc:url "http://genesis.ugent.be/files/costore/Nokoi_utilities.zip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3315, edam:topic_3318, edam:topic_3520 ; sc:citation , "pmcid:PMC9263366", "pubmed:35811996" ; sc:description "NoLiTiA is a free, open-source Matlab toolbox for nonlinear time series analysis. It incorporates methods from dynamical systems theory, recurrence quantification analysis and information theory." ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "NoLiTiA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nolitia.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_0602, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:12126621", "pubmed:15096585", "pubmed:16087736", "pubmed:16845062" ; sc:description "Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions." ; sc:featureList edam:operation_0244, edam:operation_0322, edam:operation_0477, edam:operation_0478 ; sc:name "NOMAD-Ref" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lorentz.immstr.pasteur.fr/nomad-ref.php" ; biotools:primaryContact "Marc Delarue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major Mycobacterium tuberculosis lineages." ; sc:featureList edam:operation_2422 ; sc:name "Nomenclature WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.miru-vntrplus.org/MIRU/help/helpSOAP.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0196, edam:topic_3520 ; sc:citation "pubmed:26743511" ; sc:description "Homolgy-driven assembly tool to create a NOn-redundant protEin Sequence Set for mass spectrometry." ; sc:featureList edam:operation_0310 ; sc:name "NOmESS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.biochem.mpg.de/5116134/others" ; biotools:primaryContact "Prof. Jürgen Cox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description """Quantifying morphometric deviation from normality over the lifetime in the adult human brain. NOrmative Morphometry Image Statistics. NOMIS is a free tool to compute normative morphometric values for FreeSurfer 6 developed by the MEDICS laboratory at the CERVO Brain Research Centre / Universite Laval, Quebec, Canada.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "BSD-3-Clause" ; sc:name "NOMIS" ; sc:url "https://github.com/medicslab/NOMIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3399, edam:topic_3421, edam:topic_3577 ; sc:citation , "pmcid:PMC6724291", "pubmed:31481021" ; sc:description "Dynamic prediction of long-term survival in patients with primary gastric diffuse large B-cell lymphoma | BACKGROUND:This study investigated a large number of patients to develop a predictive nomogram for survival and a web-based survival rate calculator that can dynamically predict the long-term survival of patients with primary gastric diffuse large B-cell lymphoma. METHODS:A total of 2647 patients diagnosed with primary gastric diffuse large B-cell lymphoma from 1998 to 2014 were extracted from the SEER database. We used the Lasso Cox regression model to identify independent risk factors for long-term survival and to develop a predictive nomogram for survival and a web-based survival rate calculator. RESULTS:The median (mean) follow-up time was 30 months (52.8 months). Cancer-specific survival rates decreased with time, while the 5-year conditional survival increased with time" ; sc:featureList edam:operation_3503, edam:operation_3659 ; sc:name "nomogram" ; sc:url "https://linjuli1991.shinyapps.io/dynnomapp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:37314949" ; sc:description "An open-source python package for processing high resolution mass spectrometry data on natural organic matter." ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NOMspectra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NOMspectra/NOMspectra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0199, edam:topic_0654, edam:topic_2885 ; sc:citation "pubmed:21097885" ; sc:description "It is a non-canonical (non-B) structure database database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats, mirror repeats and direct repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively." ; sc:featureList edam:operation_0224, edam:operation_0237, edam:operation_0253, edam:operation_0429, edam:operation_2442 ; sc:name "Non-B DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://nonb-abcc.ncifcrf.gov/apps/nBMST/default/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3304, edam:topic_3474 ; sc:citation , "pubmed:1546119" ; sc:description "The code simulates magnocellular cells in Retina and lateral geniculate nucleus." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "Non-directional transient cells" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/25837-non-directional-transient-cells" ; biotools:primaryContact "Massimiliano Versace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "A statistical non-parametric multivariable test based on the Fisher's method for combination of partial tests." ; sc:isAccessibleForFree true ; sc:name "Non-parametric Multivariate Permutation Test" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/69764-non-parametric-multivariate-permutation-test" ; biotools:primaryContact "Juliano Pierezan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3408 ; sc:citation , "pubmed:31568041" ; sc:description """Prediction of Thiopurine Metabolite Levels Based on Haematological and Biochemical Parameters. Absolute number of lymphocytes [x10^9/l]. Imuputed absolute number of lymphocytes data:.""" ; sc:name "nonadherence" ; sc:url "https://hradskyo.shinyapps.io/Non_adherence/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3510 ; sc:citation , "pubmed:33245691" ; sc:description """Robust and efficient prediction of non-classically secreted proteins by integrating subset-specific optimal models of imbalanced data. Nonclassically secreted proteins (NCSPs) are proteins that are located in the extracellular environment although the lack of known signal peptides or secretion motifs. In this work, a new computational predictor was developed for NCSP prediction of gram-positive bacteria. The subset-specific optimal feature combination process was adopted to characterize the original data from different aspects, and all subdataset based models were integrated into a unified model NonClasGP-Pred, which achieved an excellent performance and outperformed state-of-the-art available toolkits. Prediction of non-classically secreted proteins of Gram-positive bacteria.""" ; sc:featureList edam:operation_3936 ; sc:name "NonClasGP-Pred" ; sc:url "http://lab.malab.cn/~wangchao/softwares/NonClasGP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0654, edam:topic_0659 ; sc:citation "pubmed:22135294" ; sc:description "Database of all kinds of noncoding RNAs (except tRNAs and rRNAs). It also provides an efficient search option, allowing recovery of sequence, related publications and other information." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_2422, edam:operation_3092 ; sc:name "NONCODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.noncode.org" ; biotools:primaryContact "Runsheng Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC3592461", "pubmed:23012263" ; sc:description "Exon array-based detection of long non-coding RNAs." ; sc:featureList edam:operation_0314 ; sc:name "Noncoder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://noncoder.mpi-bn.mpg.de/" ; biotools:primaryContact "Thomas Braun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC7048090", "pubmed:32111231" ; sc:description """A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that aim to potentially provide a high-quality data resource for exploring drug sensitivity resistance-related ncRNAs in various human cancers. ncRNA are RNA molecular that do not encode proteins, but are involved in gene regulation and cellular functions in variety of human diseases, including neurodegenerative diseases and cancers. Here, we developed NoncoRNA which contained 8233 entries between 5568 ncRNAs and 154 drugs in 134 cancers. Each entry in the NoncoRNA contains detailed information on the ncRNAs, drugs, and cancers, the ncRNA expression pattern and experimental detection techniques, drug response and other targets, literature references, and other information""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3792 ; sc:name "NoncoRNA" ; sc:url "http://www.ncdtcdb.cn:8080/NoncoRNA/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3033 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3519 ; sc:citation , "pmcid:PMC4133581", "pubmed:24764462" ; sc:description "Methods to model and impute non-detects in the results of qPCR experiments." ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3566 ; sc:license "GPL-3.0" ; sc:name "nondetects" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/nondetects.html" ; biotools:primaryContact "Valeriia Sherina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "Correct nonlinear drift distortions in scanning probe images." ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "Nonlinear Drift Correction from Scanning Probe Microscopy (SPM) Orthogonal Image Pairs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51941-nonlinear-drift-correction-from-scanning-probe-microscopy-spm-orthogonal-image-pairs" ; biotools:primaryContact "Colin Ophus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3374 ; sc:description "Computes Michaelis-Menten model parameters" ; sc:isAccessibleForFree true ; sc:name "Nonlinear Fit of Michaelis-Menten model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/13424-nonlinear-fit-of-michaelis-menten-model" ; biotools:primaryContact "Housam Binous" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_3475 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:author "Luis M Rodriguez-R" ; sc:citation ; sc:description "Estimate metagenomic coverage and sequence diversity" ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "nonpareil" ; sc:softwareHelp ; sc:softwareVersion "3.4.1" ; sc:url "http://enve-omics.ce.gatech.edu/nonpareil/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3371 ; sc:citation ; sc:description "Software for design of hard-to-synthesize structures." ; sc:featureList edam:operation_0322 ; sc:license "GPL-3.0" ; sc:name "Nonpher" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/lich-uct/nonpher" ; biotools:primaryContact "Daniel Svozil" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "R function for compound, adducts and ion series detection using isotopic distributions." ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3694 ; sc:name "nontarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/nontarget/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0203, edam:topic_3169 ; sc:citation , "pubmed:32991679" ; sc:description """k-mer based motif discovery in ChIP-Seq data without peak calling. NoPeak: Binding Motif Discovery from ChIP-Seq Data without Peak calling. Binding motif discovery through Chromatin immunoprecipitation with high-throughput DNA sequencing (ChIP-Seq) data is an important tool for understanding regulatory processes. The NoPeak Software uses the integration profile of k-mers based on mapped reads.""" ; sc:featureList edam:operation_0238, edam:operation_3215, edam:operation_3222, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "NoPeak" ; sc:url "https://github.com/menzel/nopeak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8170991", "pubmed:34078267" ; sc:description "Non-coding RNA Sets Cis Enrichment Tool (NoRCE) performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out by using the functional annotations of the coding genes located proximally to the input ncRNAs. NoRCE allows incorporating other biological information such as the topologically associating domain (TAD) regions, co-expression patterns, and miRNA target information." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3463, edam:operation_3501, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NoRCE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rpubs.com/golgun/649085" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_2269 ; sc:citation , "pmcid:PMC8371904", "pubmed:34404355" ; sc:description "NOREC4DNA is an all-in-one Suite for analyzing, testing and converting Data into DNA-Chunks to use for a DNA-Storage-System using integrated DNA-Rules as well as the MOSLA DNA-Simulation-API." ; sc:featureList edam:operation_2422, edam:operation_3359, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "NOREC4DNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/umr-ds/NOREC4DNA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove carriage return from ASCII files." ; sc:featureList edam:operation_0335 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "noreturn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/noreturn.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation , "pmcid:PMC5570188", "pubmed:28525573" ; sc:description "NORmalization and EVAluation of MS-based metabolomics data. Enables performance evaluation of various normalization methods from multiple perspectives. In particular, it integrates 5 well-established criteria, each with a distinct underlying theory, to ensure a more comprehensive evaluation than any single criterion. Moreover, it provides various available and popular normalization methods, with a unique feature of allowing quality control based correction sequentially followed by data normalization." ; sc:featureList edam:operation_3435 ; sc:name "NOREVA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://server.idrb.cqu.edu.cn/noreva/" ; biotools:primaryContact "Dr. Bo Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC7849405", "pubmed:33468550" ; sc:description "A platform for curated products from novel open reading frames prompts reinterpretation of disease variants." ; sc:featureList edam:operation_0436, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "nORFs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nORFs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation ; sc:description "NORMA is a handy tool for interactive network annotation, visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Annotations and/or node groups can be precomputed or automatically calculated and users can combine several networks and groupings they are interested in. Annotated networks can be visualized using both pie-chart nodes and shaded convex hulls and can be shown using several layouts while users can isolate the groups of interest interactively. In addition, NORMA is suitable for direct comparison of topological features between one or more networks." ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "NORMA" ; sc:softwareVersion "1" ; sc:url "http://bib.fleming.gr:3838/NORMA/" ; biotools:primaryContact "Georgios Pavlopoulos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3176 ; sc:citation ; sc:description "NOrMAL (NucleOsome Mapping ALgorithm) is a command line tool for accurate placing of the nucleosomes. It was designed to resolve overlapping nucleosomes and extract extra information (“fuzziness”, probability, etc.) of nucleosome placement." ; sc:featureList edam:operation_2429 ; sc:name "NOrMAL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.cs.ucr.edu/~polishka/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3306, edam:topic_3576 ; sc:description "To calculate NTCP models for rectal and bladder toxicity based on DVHs" ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "Normal Tissue Complication Probability" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/34760-normal-tissue-complication-probability" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_3518 ; sc:citation , "pmcid:PMC4354407", "pubmed:25806048" ; sc:description "This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "BSD-4-Clause" ; sc:name "normalize450K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/normalize450K.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation "pubmed:24766612" ; sc:description "A tool for overviewing the effects of different normalisation methods on omics data." ; sc:featureList edam:operation_3435 ; sc:name "Normalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://quantitativeproteomics.org/normalyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203 ; sc:citation , "pubmed:30277078" ; sc:description "A tool for analysis of normalisation effects on quantitative omics data and for subsequent differential expression analysis. The tool provides multiple normalisation methods and access to different statistical tests and generates reports and data matrices" ; sc:featureList edam:operation_2495, edam:operation_3219, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "NormalyzerDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.quantitativeproteomics.org/normalyzerde" ; biotools:primaryContact "Jakob Willforss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2840, edam:topic_3370, edam:topic_3520 ; sc:citation , "pmcid:PMC9587084", "pubmed:36284750" ; sc:description "Facilitating European and Worldwide Collaboration on Suspect Screening in High Resolution Mass Spectrometry." ; sc:featureList edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "NORMAN-SLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.norman-network.com/nds/SLE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3365 ; sc:citation , "pmcid:PMC6936146", "pubmed:31888469" ; sc:description """An R package to remove systematic biases in genome architecture mapping data. normGAM is an R package for normalizing genome architecture mapping (GAM) data. It implements five normalization methods, including normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), iterative correction and eigenvector decomposition (ICE), and Knight-Ruiz 2-norm (KR2). The normalization procedure can remove known and unknown systematic biases, the known biases including window detection frequency, fragment length, mappability, and GC content.""" ; sc:featureList edam:operation_3435 ; sc:name "normGAM" ; sc:url "http://dna.cs.miami.edu/normGAM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_3360, edam:topic_3519 ; sc:citation , "pmcid:PMC7523363", "pubmed:32993488" ; sc:description """Tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies. GitLab is a single application for the entire software development lifecycle. 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The Natural Product Atlas MAP4 TMAP colored by fungal (in magenta) or bacterial (in green) origin. a first jupyter lab notebook containing the code to reproduce this work NPAtlas.ipynb;. The Natural Products Atlas Network views of chemical space.""" ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3216, edam:operation_3891, edam:operation_3935 ; sc:name "NPAtlas" ; sc:url "https://tm.gdb.tools/map4/npatlas_map_tmap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3047, edam:topic_3071, edam:topic_3314 ; sc:citation , "pmcid:PMC7731925", "pubmed:33306802" ; sc:description """A chemical data resource with relational data between natural products and biological sources. NPBS Database of Shanghai Institute of Organic Chemistry.""" ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3938 ; sc:name "NPBS" ; sc:url "http://www.organchem.csdb.cn/scdb/NPBS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description "A new PacBio sequencing simulator is developed for producing CLR reads. It simulator firstly samples the read sequences according to the read length logarithmic normal distribution, and choses different base quality values with different proportions. 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We typitcally will deploy this locally. To bring everything up. CC1C(O)CC2C1C(OC1OC(COC(C)=O)C(O)C(O)C1O)OC=C2C(O)=O. We pass through tensorflow serving at this url:. 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Nearest-neighbor Projected-Distance Regression (NPDR) detects network interactions and controls for confounding and multiple testing. 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These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. 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FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. For more details, please read the associated manuscript -- "Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution" (Current Biology 2011, 21(1), pp.1-11). 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Furthermore, it continuously reports assembly quality during the experiment so that users can terminate the sequencing when an assembly of sufficient quality and completeness is obtained." ; sc:featureList edam:operation_0525, edam:operation_3180, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "npScarf" ; sc:softwareHelp ; sc:url "https://github.com/mdcao/npScarf" ; biotools:primaryContact "Minh Duc Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:22127579" ; sc:description "R package for the significance analysis of sequencing data.  The statistic used is exactly the same as that in SAM 4.0. The only difference is that our tool uses symmetric cutoffs, while SAM uses asymmetric cutoffs. 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In this paper, we present NQontrol, a digital feedback-control solution based on the ADwin platform that delivers eight simultaneous feedback loops running with 200 kHz sampling frequency and offers five second-order filtering sections per channel for flexible shaping of the feedback loop. With this system, we demonstrate a Pound-Drever-Hall lock of an optical resonator and compare its performance to an analog reference implementation. A comprehensive support package written in Python, together with a web-based graphical user interface, makes the system quick to setup and easy to use, while maintaining the full flexibility of open-source platforms""" ; sc:featureList edam:operation_3695 ; sc:name "NQontrol" ; sc:url "https://gitlab.com/las-nq/nqontrol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3343, edam:topic_3474 ; sc:citation , "pmcid:PMC9116378", "pubmed:35383362" ; sc:description "Predicting the binding of small molecules to nuclear receptors using machine learning." ; sc:featureList edam:operation_0478, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "NR-ToxPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://nr-toxpred.cchem.berkeley.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:name "Map data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:name "Map data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3050, edam:topic_3855 ; sc:author , ; sc:citation ; sc:description "The ArcGIS National Responsibility Assessment Tool (NRA-Tool) can be used to create hierarchical lists of national responsibilities and priorities for global species conservation. Our tool will allow conservationists to prioritize conservation efforts and to focus limited resources on relevant species and regions. We showcase our tool with data on 258 bird species and various biophysical regions, including Environmental Zones in 58 Asian countries and regions. Our tool provides a decision support system for conservation policy with attractive and easily interpretable visual outputs illustrating national responsibilities and priorities for species conservation. 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We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING)." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0336, edam:operation_2428, edam:operation_3431 ; sc:name "NRG-CING" ; sc:url "http://nmr.cmbi.ru.nl/NRG-CING/HTML/index.html" ; biotools:primaryContact "Geerten W. Vuister", "Gert Vriend", "Jurgen F. Doreleijers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_0601, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:33742655" ; sc:description "NRGTEN (Najmanovich Research Group Toolkit for Elastic Networks) is an extensible Python toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes." ; sc:featureList edam:operation_0244, edam:operation_0478, edam:operation_3435, edam:operation_3927 ; sc:license "MIT" ; sc:name "NRGTEN" ; sc:softwareHelp ; sc:url "https://github.com/gregorpatof/nrgten_package/" ; biotools:primaryContact "Rafael Najmanovich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3306, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9832141", "pubmed:36627356" ; sc:description "An application to streamline biophysical modeling of synaptic integration using NEURON." ; sc:featureList edam:operation_2238, edam:operation_3450, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "NRN-EZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/scimemia/NRN-EZ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0204, edam:topic_0749, edam:topic_2229 ; sc:citation "pubmed:15039428" ; sc:description "SVM based tool for the classification of nuclear receptors on the basis of amino acid composition or dipeptide composition. 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We appreciate your interest in nubeam-dedup. If you use nubeam-dedup, please kindly cite:.""" ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3227 ; sc:license "BSD-3-Clause" ; sc:name "Nubeam-dedup" ; sc:url "https://haplotype.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621 ; sc:citation , "pmcid:PMC7035700", "pubmed:32085722" ; sc:description """Location of structural errors in a genome assembly by using paired-end Illumina reads. NucBreak detects structural errors in assemblies and structural variants between pairs of genomes when only a genome of one organism and Illumina paired-end reads from another organism are available. It is able to detect insertions, deletions, different inter- and intra-chromosomal translocations, and inversions. However, the types of detected breakpoints are not specified. It was written in Python and uses Bowtie2 for reads alignment. 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MacCallum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0749, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC9249596", "pubmed:35832617" ; sc:description "A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences." ; sc:featureList edam:operation_0267, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:name "Nucpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csb.iitkgp.ac.in/applications/Nucpred/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3053 ; sc:citation "pubmed:16451620" ; sc:description "Program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers." ; sc:featureList edam:operation_0283 ; sc:name "nucular" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mlemire.freeshell.org/nucular.README" ; biotools:primaryContact "Mathieu Lemire" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_3125 ; sc:citation "pubmed:25296770" ; sc:description "Bioinformatic tool that generates nucleosome occupation maps." ; sc:featureList edam:operation_0432 ; sc:name "NUCwave" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://nucleosome.usal.es/nucwave/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)." ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "nudge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/nudge.html" ; biotools:primaryContact "N. Dean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products." ; sc:featureList edam:operation_3963 ; sc:name "NuDup" ; sc:url "https://github.com/tecangenomics/nudup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation "pubmed:23304815" ; sc:description "NulceiHomo is a hybrid morphological reconstruction for pre-processing of nuclei image." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "NulceiHomo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47423-nulceihomo-zip" ; biotools:primaryContact "Cheng Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622 ; sc:author "Torsten Seemann" ; sc:contributor "A Goncalves da Silva", "BP Howden", "DM Bulach", "JC Kwong", "MB Schultz" ; sc:description "Pipeline to generate complete public health microbiology reports from isolates sequenced with Illumina paired-end sequencing." ; sc:featureList edam:operation_0323, edam:operation_0362, edam:operation_0415, edam:operation_0524, edam:operation_0567, edam:operation_3192, edam:operation_3208, edam:operation_3218, edam:operation_3227, edam:operation_3472, edam:operation_3504 ; sc:license "GPL-2.0" ; sc:name "nullarbor" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Melbourne, Australia", "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/tseemann/nullarbor" ; biotools:primaryContact "Australia", "Torsten Seemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Creates Random Coding Sequences with specified GC content and Amino Acid usage." ; sc:featureList edam:operation_0364 ; sc:name "NullSeq" ; sc:url "https://github.com/amarallab/NullSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "The fundamental package for scientific computing with Python" ; sc:featureList edam:operation_2409, edam:operation_3438 ; sc:license "BSD-3-Clause" ; sc:name "NumPy" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "https://numpy.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_2269 ; sc:citation , "pmcid:PMC10697733", "pubmed:37966918" ; sc:description "Optimally partitioning data into piece-wise linear segments." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "nunchaku" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/nunchaku" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0654 ; sc:citation "pubmed:7583696" ; sc:description "Program for analysis of sequence dependent variations in nucleic apdb_id (DNA & RNA) double helices." ; sc:featureList edam:operation_2403 ; sc:name "NUPARM-Plus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nucleix.mbu.iisc.ernet.in/nuparm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3176, edam:topic_3511 ; sc:citation ; sc:description "R package for Nucleosome Positioning Prediction. This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available." ; sc:featureList edam:operation_0432 ; sc:license "GPL-2.0" ; sc:name "NuPoP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/NuPoP.html" ; biotools:primaryContact "Ji-Ping Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_2840, edam:topic_3384 ; sc:citation , "pubmed:32961130" ; sc:description """A curated dataset of nuclear receptor modulators. Nuclear receptors (NRs) are key regulators of human health and constitute a relevant target for medicinal chemistry applications as well as for toxicological risk assessment. Several open databases dedicated to small molecules that modulate NRs exist; however, depending on their final aim (i.e., adverse effect assessment or drug design), these databases contain a different amount and type of annotated molecules, along with a different distribution of experimental bioactivity values. Stemming from these considerations, in this work we aim to provide a unified dataset, NURA (NUclear Receptor Activity) dataset, collecting curated information on small molecules that modulate NRs, to be intended for both pharmacological and toxicological applications""" ; sc:featureList edam:operation_3216, edam:operation_3907 ; sc:name "NURA" ; sc:url "https://doi.org/10.5281/zenodo.3991561" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:23837734" ; sc:description "Efficient and reliable tool for estimating the isoform expression level. Given the reads mapping result and gene annotation file, it will output the expression estimation result." ; sc:featureList edam:operation_3680 ; sc:name "NURD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo.au.tsinghua.edu.cn/software/NURD/" ; biotools:primaryContact "Xuegong Zhan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , , ; sc:description "NuST is a set of tools and data sets that can be used to analyze the aggregation of a set of genes along the genome coordinate, at different scales of observation." ; sc:featureList edam:operation_3436 ; sc:name "NuST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/nust/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC7472695", "pubmed:32973479" ; sc:description """A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. Nutil simplifies and streamlines the pre-and-post processing of 2D brain image data from mouse and rat.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Nutil" ; sc:url "https://www.nitrc.org/projects/nutil/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC7478146", "pubmed:32982658" ; sc:description """Open Source Software for M/EEG Source Reconstruction. NUTMEG (Neurodynamic Utility Toolbox for Magnetoencephalography) is an open-source MATLAB toolbox for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. .""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "NUTMEG" ; sc:url "http://nitrc.org/projects/nutmeg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3318, edam:topic_3390, edam:topic_3399 ; sc:citation , "pubmed:31858107" ; sc:description """Dietary Intakes of Vegetable Protein, Folate, and Vitamins B-6 and B-12 Are Partially Correlated with Physical Functioning of Dutch Older Adults Using Copula Graphical Models. Structure Learning with Copula Graphical Model. Statistical tool for learning the structure of direct associations among variables for continuous data, discrete data and mixed discrete-continuous data. The package is based on the copula graphical model in Behrouzi and Wit (2017) """ ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "nutriNetwork" ; sc:url "https://cran.r-project.org/web/packages/nutriNetwork" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_1196 ; sc:name "Compound name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1150 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1082 ; sc:encodingFormat edam:format_2333 ; sc:name "Pathway or network identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3390 ; sc:citation , ; sc:description "Database generated by text mining of 21 million MEDLINE abstracts, with information that links plant-based foods with their small molecule components and human disease phenotypes." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "NutriChem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:url "http://www.cbs.dtu.dk/services/NutriChem-1.0" ; biotools:primaryContact "Irene Kouskoumvekaki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3316 ; sc:description "NVBIO is a library of reusable components designed by NVIDIA Corporation to accelerate bioinformatics applications using CUDA." ; sc:license "BSD-3-Clause" ; sc:name "NVBIO" ; sc:softwareHelp , ; sc:url "http://nvlabs.github.io/nvbio/index.html" ; biotools:primaryContact "Jacopo Pantaleoni", "Nuno Subtil" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:name "Feature table" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation ; sc:description "An R package for the assessment of RNA-Seq normalization methods." ; sc:featureList edam:operation_3223 ; sc:name "NVT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/Edert/NVT" ; biotools:primaryContact "CUBE-AT", "Thomas Eder" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1910, edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , , , "pmcid:PMC2464588", "pubmed:18577231" ; sc:description "Display a phylogenetic tree as SVG." ; sc:featureList edam:operation_0567 ; sc:name "nwdisplay" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6" ; sc:url "http://cegg.unige.ch/newick_utils" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0654, edam:topic_0749, edam:topic_3125, edam:topic_3176 ; sc:citation "pubmed:16845070" ; sc:description "Finds potential nucleosome-free regions of DNA sequences. It can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function." ; sc:featureList edam:operation_0432, edam:operation_2454 ; sc:name "NXSensor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.sfu.ca/~ibajic/NXSensor/" ; biotools:primaryContact "Ivan V. Bajic", "Peter Luykx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25661542" ; sc:description "Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location." ; sc:featureList edam:operation_2425, edam:operation_3192 ; sc:name "NxTrim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sequencing/NxTrim" ; biotools:primaryContact "Anthony J. Cox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3444 ; sc:description "Phase guided method for Nyquist ghost correction in 3D EPSI data" ; sc:featureList edam:operation_3443, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "Nyquist artifact correction in 3D Echo Planar Spectroscopic Imaging (EPSI) data" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/56658-nyquist-artifact-correction-in-3d-echo-planar-spectroscopic-imaging-epsi-data" ; biotools:primaryContact "Ti Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3572 ; sc:citation ; sc:description "An R package to import, clean and update data from the New Zealand Freshwater Fish Database." ; sc:featureList edam:operation_0224, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "nzffdr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/flee598/nzffdr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0634, edam:topic_2640 ; sc:citation ; sc:description "A Database of Experimentally Identified O-GlcNAc Sites and Proteins." ; sc:featureList edam:operation_0306, edam:operation_0417, edam:operation_3755 ; sc:name "O-GlcNAcAtlas" ; sc:url "https://oglcnac.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0601, edam:topic_3120, edam:topic_3510 ; sc:citation ; sc:description "Integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique." ; sc:featureList edam:operation_3092 ; sc:name "O-GlcNAcPRED-II" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://121.42.167.206/OGlcPred/" ; biotools:primaryContact "Cangzhi Jia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0749, edam:topic_0804, edam:topic_0821, edam:topic_3292 ; sc:citation , "pubmed:34611872" ; sc:description "A Formal-Language-Based Generator of O-Glycosylation Networks." ; sc:featureList edam:operation_0416, edam:operation_0417, edam:operation_3896 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "O-Glycologue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://glycologue.org/o/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_3308, edam:topic_3365, edam:topic_3391 ; sc:citation "pubmed:22600742" ; sc:description "Webserver that automates the analysis and annotation of complex -omics data. Specifically deals with genomics and transcriptomics data." ; sc:featureList edam:operation_0306, edam:operation_0314, edam:operation_3501 ; sc:name "O-miner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.o-miner.org" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC9201625", "pubmed:35720715" ; sc:description "A Novel Framework With Deep Fusion of CNN and Transformer for Simultaneous Segmentation and Classification." ; sc:featureList edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "O-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ortonwang/O-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """Reconstructing who-infected-whom from routinely collected surveillance data. o2geosocial: Integrating geographical and social contact data to reconstruct transmission chains. o2geosocial was developed to infer probabilistic transmission trees from routinely-collected epidemiological data. It combines the age group, location, onset date and genotype of cases to infer their import status, and their likely infector. o2geosocial is based upon the R package "outbreaker2" (https://github.com/reconhub/outbreaker2), it is designed to study datasets that do not include genetic sequences but genotype of the cases. o2geosocial clusters cases from different genotypes in different trees, without computing the genetic distance between cases.""" ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3907, edam:operation_3942 ; sc:license "MIT" ; sc:name "o2geosocial" ; sc:url "https://CRAN.R-project.org/package=o2geosocial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3308, edam:topic_3407, edam:topic_3512 ; sc:citation , "pubmed:31724725" ; sc:description """A database of putative RNA binding protein target sites in the transcriptomes of model species. Dashboard - Overview of the database. Welcome to oRNAment - o RNA motifs enrichment in complete transcriptomes. Here, we developed a computational tool to enable the global mapping of putative RBP target motifs across full transcriptomes, including messenger RNAs (mRNAs) and non-coding RNAs, in multiple species. The oRNAment database provides a user-friendly interface to parse the motif scan data. See tutorial for further detail""" ; sc:featureList edam:operation_0239, edam:operation_3695, edam:operation_3795, edam:operation_3902 ; sc:name "oRNAment" ; sc:url "http://rnabiology.ircm.qc.ca/oRNAment/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:37156312" ; sc:description "Prediction of human O-linked threonine glycosites using multi-feature fusion." ; sc:featureList edam:operation_0417, edam:operation_3755, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "O-GlyThr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbcb.cdutcm.edu.cn/O-GlyThr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9670740", "pubmed:36394419" ; sc:description "The Pedunculate oak (Quercus robur) root database (OakRootRNADB) consolidates information currently available on RNA-seq research conducted on both coding and non-coding RNA. The database contains the sequences of genes, transcripts, proteins, and microRNA obtained from the meristematic and elongation zones of both taproot and lateral roots of Q. robur." ; sc:featureList edam:operation_0308, edam:operation_0314, edam:operation_2421, edam:operation_3431, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "OakRootRNADB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://oakrootrnadb.idpan.poznan.pl/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3016, edam:format_3464, edam:format_3475, edam:format_3620, edam:format_3752 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0199, edam:topic_0622 ; sc:description "OakVar is a Python-based genomic variant analysis platform. It is a fork of OpenCRAVAT and further developed with newer visions." ; sc:featureList edam:operation_0362, edam:operation_3661, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OakVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://oakvar.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3360, edam:topic_3517 ; sc:citation , "pmcid:PMC9254640", "pubmed:35788653" ; sc:description "Multi-omics molecular biomarkers and database of osteoarthritis." ; sc:featureList edam:operation_2422, edam:operation_3207, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "OAOB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ibi.zju.edu.cn/oaobdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2830, edam:topic_3374, edam:topic_3500, edam:topic_3930 ; sc:citation , "pmcid:PMC8740823", "pubmed:34655133" ; sc:description "A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "OAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://opig.stats.ox.ac.uk/webapps/oas/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3181 ; sc:name "Sequence assembly report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3673 ; sc:citation , "pubmed:22368243" ; sc:description "De novo transcriptome assembler designed to produce transcripts from short read sequencing technologies. It uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms." ; sc:featureList edam:operation_3258, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Oases" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dzerbino/oases" ; biotools:primaryContact "Daniel Zerbino", "Marcel Schulz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation ; sc:description "It is a web application that allows for the fast and flexible online analysis of small-RNA-seq data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data, and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis generates downloadable interactive web reports for easy visualization, exploration, and analysis of data on a local system." ; sc:featureList edam:operation_3198 ; sc:name "Oasis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://oasis.dzne.de" ; biotools:primaryContact "Oasis Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3172, edam:topic_3517 ; sc:citation ; sc:description "OASIS (Omics Analysis, Search & Information System) is an information system for analyzing, searching, and visualizing associations between phenotypes, genotypes, and other types of omics data (such as transcriptomics, metabolomics, etc.). It is designed to enable discovery by connecting to the thought processes of biological researchers in a way that allows them to search results from an initial GWAS (or other association study), ask follow-up questions, and get answers in real-time. OASIS accomplishes this with a web-based search system and a variety of real-time analysis tools including conditional & multi-covariate analysis, and real-time linkage disequilibrium (LD) calculations. On-demand visualizations are provided in the form of boxplots, histograms, LocusZoom & Haploview plots. The OASIS search reports contain a broad spectrum of annotation from Annovar and WGSA plus a variety of links to external resources such as gnomAD, GTEx, HaploReg, Roadmap, UCSC and NCBI." ; sc:featureList edam:operation_0488, edam:operation_2421, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "OASIS" ; sc:url "http://edn.som.umaryland.edu/OASIS/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3335, edam:topic_3384 ; sc:citation , "pubmed:37020156" ; sc:description "A verified and validated moving domain computational fluid dynamics solver with applications to cardiovascular flows." ; sc:featureList edam:operation_2426, edam:operation_2428, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OasisMove" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KVSlab/OasisMove/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_3299 ; sc:citation "pubmed:26585518" ; sc:description "Uses OrthoANI to measure overall similarity between two genome sequences." ; sc:featureList edam:operation_3209 ; sc:name "OAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ezbiocloud.net/sw/oat" ; biotools:primaryContact "Jongsik Chun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_2275 ; sc:citation "pubmed:16808918" ; sc:description "Method to assess the likelihood that a protein will succeed in a high-throughput crystallography experiment." ; sc:featureList edam:operation_3435 ; sc:name "OB Score" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/obscore/" ; biotools:primaryContact "Geoffrey J. Barton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_0769, edam:topic_3520 ; sc:citation ; sc:description """One-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data. obaDIA takes a FASTA fromat protein sequence file and a fragment-level, peptide-level or protein-level abundance matrix file from data-independent acquisition (DIA) mass spectrometry experiment, and performs differential protein expression analysis, functional annotation and enrichment analysis in a completely automated way.""" ; sc:featureList edam:operation_2436, edam:operation_3741, edam:operation_3799 ; sc:name "obaDIA" ; sc:url "https://github.com/yjthu/obaDIA.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC7413081", "pubmed:32832259" ; sc:description """OBAMA for Bayesian amino-acid model averaging. A BEAST2 package for amino acid/protein site model averaging.""" ; sc:featureList edam:operation_0324, edam:operation_0477, edam:operation_0550 ; sc:license "LGPL-2.1" ; sc:name "OBAMA" ; sc:url "https://github.com/rbouckaert/obama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_2229, edam:topic_3382 ; sc:citation "pubmed:19746416" ; sc:description "Software we designed to perform organelle-based colocalisation analysis from multi-fluorophore microscopy 2D, 3D and 4D cell imaging." ; sc:featureList edam:operation_2489, edam:operation_3443, edam:operation_3552 ; sc:name "OBCOL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://obcol.imb.uq.edu.au/" ; biotools:primaryContact "Nicholas A. Hamilton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3337 ; sc:citation , "pubmed:33135050" ; sc:description """An identical-by-descent mapping tool based on SNP streak. obelisc (Observational linkage scan) is an identical-by-descent (IBD) mapping tool based on the SNP streak approach. obelisc is a command line tool to perform two effective nonparametric linkage analyses (i.e., SNP streak-based IBD mapping and runs of homozygosity (ROH) mapping). obelisc also supports an intuitive visualization of the analytical results.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3454 ; sc:name "Obelisc" ; sc:url "https://github.com/qsonehara/Obelisc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0769, edam:topic_3299, edam:topic_3966 ; sc:citation , "pmcid:PMC9334345", "pubmed:35910305" ; sc:description "A computational tool for the analysis and systematization of the positive selection in proteins." ; sc:featureList edam:operation_0324, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OBI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://anaconda.org/jcalvento/obi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:16944896" ; sc:description "Aligns multiple LC-MS(/MS) datasets in retention time by dynamic time warping." ; sc:featureList edam:operation_3628 ; sc:name "OBI-Warp" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://obi-warp.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3379, edam:topic_3384, edam:topic_3474, edam:topic_3954 ; sc:citation , "pubmed:37806555" ; sc:description "An open biomedical imaging archive." ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "OBIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/obia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3298, edam:topic_3308 ; sc:citation ; sc:description """Omics-Based Interaction Framework – a systems model to reveal molecular drivers of synergy. OBIF Package in R includes the analytical components of the Omics-Based Interaction Framework. This framework and package are used to discover molecular drivers of non-additive phenotypes (synergistic or angatonistic responses) from single- or multi-Omics data.""" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3501 ; sc:name "OBIF" ; sc:url "http://www.github.com/evanslaboratory/OBIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25959493" ; sc:description "Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding." ; sc:featureList edam:operation_2403 ; sc:name "OBITools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://git.metabarcoding.org/obitools/obitools/wikis/home" ; biotools:primaryContact "Eric Coissac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3383, edam:topic_3489 ; sc:citation ; sc:description "OMERO-based integrated workflow for annotating microbes in the cloud." ; sc:featureList edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ObiWan-Microbi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hip-satomi/ObiWan-Microbi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3464, edam:format_3475, edam:format_3620, edam:format_3750, edam:format_3752 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3464, edam:format_3475, edam:format_3604, edam:format_3620, edam:format_3750, edam:format_3752 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3365, edam:topic_3366, edam:topic_3572 ; sc:description """ObjTables is a toolkit for creating re-usable datasets that are both human and machine-readable, combining the ease of spreadsheets (e.g., Excel workbooks) with the rigor of schemas (classes, their attributes, the type of each attribute, and the possible relationships between instances of classes). ObjTables consists of a format for describing schemas for spreadsheets, numerous data types for science, a syntax for indicating the class and attribute represented by each table and column in a workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. ObjTables is ideal for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.""" ; sc:featureList edam:operation_0335, edam:operation_0336, edam:operation_0337, edam:operation_1812, edam:operation_2424, edam:operation_2928, edam:operation_2945, edam:operation_3096, edam:operation_3359, edam:operation_3434, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ObjTables" ; sc:softwareHelp , , , ; sc:softwareVersion "1.0.0" ; sc:url "https://www.objtables.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071 ; sc:citation , "pmcid:PMC8546234", "pubmed:34697637" ; sc:description "Community development of interoperable ontologies for the biological sciences" ; sc:featureList edam:operation_2422, edam:operation_3352 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "OBO Foundry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://obofoundry.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC9019955", "pubmed:35443717" ; sc:description "A unified framework to integrate and analyze single-cell RNA-seq data." ; sc:featureList edam:operation_3223, edam:operation_3436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OCAT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/bowang-lab/OCAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3068, edam:topic_3673 ; sc:citation ; sc:description "occAssess is an R package for assessing potential biases in species occurrence data." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3891 ; sc:license "MIT" ; sc:name "occAssess" ; sc:url "https://github.com/robboyd/occAssess" ; biotools:primaryContact "Rob J. Boyd" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_3033 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3033 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2794 ; sc:encodingFormat edam:format_3033 ; sc:name "ORF ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3301 ; sc:citation ; sc:description "Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries." ; sc:featureList edam:operation_0436, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "occugene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/occugene.html" ; biotools:primaryContact "Oliver Will" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3169 ; sc:citation , "pmcid:PMC4061025", "pubmed:24936875" ; sc:description "ChIP-Seq Peak Calling Based on Internal Background Modelling." ; sc:featureList edam:operation_3222 ; sc:name "OccuPeak" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.hartfaalcentrum.nl/index.php?main=files&fileName=ManualOccuPeak_V2.pdf&description=Occupeak%20manual&sub=ManualOccuPeak_V2" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_2830 ; sc:citation ; sc:description "OCD is a command-line tool for the calculation of immunoglobulin inter-domain orientations. The OCD tool automatically creates a reasonable coordinate system for the characterization of inter-domain orientations based on a user-provided reference structure." ; sc:featureList edam:operation_0244, edam:operation_0295, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "OCD" ; sc:url "https://github.com/liedllab/OCD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_3168, edam:topic_3277, edam:topic_3941 ; sc:citation , "pubmed:33434383" ; sc:description """A web service to explore the biodiversity and biogeography of marine organisms. - "Community ecological analysis" allows one to search for a taxon in a metabarcoding database in order to obtain. ecological analyses (alpha and beta diversity) using graphical representations (NMDS, boxplot..). - "Sequence based query" allows one to interrogate a metabarcoding database in order to obtain the abundance,.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3200 ; sc:name "Ocean-Barcode-Atlas" ; sc:softwareHelp ; sc:url "http://oba.mio.osupytheas.fr/ocean-atlas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0622 ; sc:citation ; sc:description "Mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks." ; sc:featureList edam:operation_0282 ; sc:license "CC-BY-4.0" ; sc:name "OCEAN-C" ; sc:softwareHelp ; sc:url "https://github.com/ChengLiLab/OCEAN-C/" ; biotools:primaryContact "Cheng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description "Exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools | resistome on TARA ocean samples" ; sc:featureList edam:operation_3482, edam:operation_3891 ; sc:name "Ocean-resistome" ; sc:url "https://github.com/rcuadrat/ocean_resistome" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3579, edam:format_3603, edam:format_3604 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3752 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3174, edam:topic_3387, edam:topic_3941 ; sc:citation , "pubmed:38413777" ; sc:contributor ; sc:description "The « Ocean Read Atlas » web service allows to search one or several sequences across all of Tara Oceans metagenomic raw sequencing data using kmindex, a new tool that performs indexing and queries using orders of magnitudes with less resources. It enables the visualization of the results on a geographic map and their correlation with each of the 56 environmental variables collected during the circumnavigation campaign. This server enables to perform instant searches on a large and complex dataset, providing new perspectives on the deep exploitation of Tara Oceans resources." ; sc:featureList edam:operation_0292, edam:operation_3211, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Ocean Read Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ora.mio.osupytheas.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2828, edam:topic_3372 ; sc:citation , "pubmed:34241085" ; sc:description "An infrastructure for data-driven research to discover and design crystalline organic semiconductors." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "OCELOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://oscar.as.uky.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3407, edam:topic_3518 ; sc:citation ; sc:description "oCEM is a tool for automatic detection and analysis of overlapping co-expressed gene modules." ; sc:featureList edam:operation_3463, edam:operation_3766, edam:operation_3891 ; sc:license "MIT" ; sc:name "oCEM" ; sc:url "https://github.com/huynguyen250896/oCEM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_1775 ; sc:citation "pubmed:22080466" ; sc:description "Creates an overlapping class system from an unweighted simple graph G = (V,E).OCG is essentially a hierarchical ascending algorithm. By default, it will fuse the initial classes until further fusions do not increase the modularity but other options are available." ; sc:featureList edam:operation_3432 ; sc:name "OCG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tagc.univ-mrs.fr/tagc/index.php/software/17" ; biotools:primaryContact "Brun C" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2851 ; sc:encodingFormat edam:format_1196 ; sc:name "Drug structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3332 ; sc:citation , "pmcid:PMC3131510", "pubmed:21660515" ; sc:description "\"The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records.\"" ; sc:featureList edam:operation_3664 ; sc:name "Online Chemical Modeling Environment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v.2.4.98" ; sc:url "http://www.ochem.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_0634, edam:topic_3067 ; sc:citation , "pmcid:PMC8404035", "pubmed:34139439" ; sc:description "An ontology for ocular immune-mediated inflammatory diseases" ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "OcIMIDo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sap218/ocimido" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3299, edam:topic_3305 ; sc:citation ; sc:description """Generation and application of river network analogues for use in ecology and evolution. 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Please input protein name or PDB ID. To map allosteric communications, we use percolation theory to identify connections throughout a protein and search for paths between any of its two sites. 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Post-database search is a key procedure in peptide identification with tandem mass spectrometry (MS MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although many statistical and machine learning-based methods have been developed to improve the accuracy of peptide identification, the challenge remains on large-scale datasets and datasets with a distribution of unbalanced PSMs.""" ; sc:featureList edam:operation_2929, edam:operation_3631, edam:operation_3767 ; sc:name "OLCS-Ranker" ; sc:url "http://161.6.5.181:8000/olcs-ranker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170 ; sc:citation , , "pmcid:PMC3664805", "pmcid:PMC5792058", "pubmed:23571760", "pubmed:27941783" ; sc:description "Designed for de novo spliced mapping of mRNA-seq reads. It adopts a seeding and extension scheme, and does not rely on a separate external. It achieves high sensitivity of junction detection by using very small seeds, efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "OLego" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://zhanglab.c2b2.columbia.edu/index.php/OLego" ; biotools:primaryContact "Chaolin Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0749 ; sc:citation , "pubmed:34469532" ; sc:description "OlfactionBase is a manually-curated comprehensive database that incorporates multidimensional facets of major components involved in the olfaction process, i.e., odors, chemicals (both odorants and odourless), Olfactory Receptors (ORs), odorant-OR interaction, and other associated proteins (odorant-binding proteins (OBPs), pheromone binding proteins (PBPs), and chemosensory proteins)." ; sc:featureList edam:operation_0269 ; sc:isAccessibleForFree true ; sc:name "OlfactionBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioserver.iiita.ac.in/olfactionbase/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_1929 ; sc:name "Text" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3673 ; sc:citation ; sc:description "Automated multiplex oligonucleotide design. Performs primer and different hybridization probe designs as well as specificity and cross dimer checks in a single run." ; sc:featureList edam:operation_2419 ; sc:name "Oli2go" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://oli2go.ait.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0632 ; sc:citation ; sc:description "OliCheck is a program designed to test the validity of potential microarray probes by considering the possibility of cross-hybridization with non-target coding sequences. This analysis can be performed within a single genome or between several different strains/organisms." ; sc:featureList edam:operation_2495 ; sc:name "OliCheck" ; sc:operatingSystem "Windows" ; sc:url "http://www.genomic.ch/software.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3068, edam:topic_3325, edam:topic_3407 ; sc:citation , "pmcid:PMC9216476", "pubmed:35411390" ; sc:description "OLIDA is a curated database of oligogenic diseases and the variants in genes that have been published as causing these diseases. 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It is a graphical user interface to draw complex oligosaccharides, store linear notations and produce the corresponding MS/MS theoretical spectra." ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3860 ; sc:license "BSD-3-Clause" ; sc:name "Oligator" ; sc:softwareHelp ; sc:url "https://github.com/vlollier/oligator" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC2944196", "pubmed:20688976" ; sc:description "A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files)." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "oligo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/oligo.html" ; biotools:primaryContact "Benilton Carvalho" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1353 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3510, edam:topic_3511 ; sc:citation "pubmed:10648794", "pubmed:12824373", "pubmed:25904632", "pubmed:9719638" ; sc:description "Compute k-mer frequencies (oligonucleotides or oligopeptides) and various statistics to discover exceptional motifs (over-represented or under-represented). Typical applications include discovery of transcription factor binding motifs, restriction sites in bacterial genomes, RNA termination and polyadenylation signals, detection of motifs associated with replication origins, analysis of oligopeptide frequencies in protein sequences." ; sc:featureList edam:operation_0238, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT oligo-analysis" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "RSAT" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://teaching.rsat.eu/oligo-analysis_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0632, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:12799432" ; sc:description "OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequenced genome can be found at http://berry.engin.umich.edu/oligoarraydb/index.html" ; sc:featureList edam:operation_0308, edam:operation_0309, edam:operation_2419, edam:operation_3198 ; sc:name "OligoArray" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://berry.engin.umich.edu/oligoarray2_1/" ; biotools:primaryContact "Jean-Marie Rouillard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "OligoArrayAux is an auxilliary package designed for use with the OligoArray software.  The package consists of several C programs and Perl scripts for performing energy minimization calculations on nucleic acid sequences.  OligoArrayAux is a subset of the UNAFold package, which calculates partition functions as well as minimum energies for a full ensemble of species for one or two nucleic acid sequences." ; sc:featureList edam:operation_2495 ; sc:name "OligoArrayAux" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.8-1" ; sc:url "http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0601, edam:topic_0654, edam:topic_3318 ; sc:citation "pubmed:17452344" ; sc:description "OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation." ; sc:featureList edam:operation_0250, edam:operation_0398, edam:operation_0455 ; sc:name "OligoCalc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.basic.northwestern.edu/biotools/OligoCalc.html" ; biotools:primaryContact "Warren A. Kibbe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632 ; sc:citation ; sc:description "This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages." ; sc:featureList edam:operation_2990, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "oligoClasses" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/oligoClasses.html" ; biotools:primaryContact "Benilton Carvalho", "Robert Scharpf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3174, edam:topic_3511 ; sc:citation "pubmed:19161433" ; sc:description "Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example from metagenomics) to a sequenced genome." ; sc:featureList edam:operation_0253 ; sc:name "OligoCounter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webhost1.mh-hannover.de/davenport/oligocounter/index.html" ; biotools:primaryContact "Davenport, C. F" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0632 ; sc:citation "pubmed:18440971" ; sc:description "Online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically." ; sc:featureList edam:operation_0292, edam:operation_2478, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "OligoHeatMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinfomed.fr/__Tools/ohm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168 ; sc:citation "pubmed:18158128" ; sc:description "Program for fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences. Optimal performance is achieved at about 500000 query sequences." ; sc:featureList edam:operation_2421 ; sc:name "Oligomap" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.mirz.unibas.ch/software.php" ; biotools:primaryContact "Mihaela Zavolan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0621, edam:topic_0632, edam:topic_0654, edam:topic_3474 ; sc:citation , "pmcid:PMC7319443", "pubmed:32313927" ; sc:description "A web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment." ; sc:featureList edam:operation_0455, edam:operation_0475, edam:operation_2419 ; sc:license "MIT" ; sc:name "OligoMinerApp" ; sc:url "http://oligominerapp.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0632, edam:topic_0654 ; sc:citation "pubmed:18446650" ; sc:description "Web-based tool for evaluating the propensity of primers to hybridize to similar sequences throughout the genome." ; sc:featureList edam:operation_2419 ; sc:name "Oligonucleotide Search" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://compbio.med.wayne.edu/software/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3475 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3475 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:encodingFormat edam:format_1964 ; sc:name "Phenotype name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:encodingFormat edam:format_1964 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3464 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3464 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3325 ; sc:author ; sc:description "Oligopipe is a Python package for the discovery of candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction developed at the Interuniveristy Institute of Bioinformatics in Brussels." ; sc:featureList edam:operation_0331, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "oligopipe - Python package for Oligogenic Variant Analysis pipelines" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Interuniversity Institute of Bioinformatics in Brussels" ; sc:softwareHelp , ; sc:url "https://pypi.org/project/oligopipe/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0607, edam:topic_0632, edam:topic_3071, edam:topic_3168 ; sc:citation , "pmcid:PMC8442484", "pubmed:34539193" ; sc:description "An Information System for Oligonucleotide Management." ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OligoPrime" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OligoPrime" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3047, edam:topic_3318, edam:topic_3520 ; sc:citation , "pmcid:PMC10308331", "pubmed:37310448" ; sc:description "Native HDX/MS data processing application dedicated to oligonucleotides." ; sc:featureList edam:operation_2409, edam:operation_3629, edam:operation_3632 ; sc:isAccessibleForFree true ; sc:name "OligoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ghcr.io/ericlarg4/oligor:master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:18490376" ; sc:description "OligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides binding to a target RNA." ; sc:featureList edam:operation_0465, edam:operation_2008 ; sc:name "OligoWalk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.urmc.rochester.edu/servers/oligowalk" ; biotools:primaryContact "David Mathews" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3365 ; sc:citation , ; sc:description "Intelligent design of oligonucleotides for DNA microarrays." ; sc:featureList edam:operation_0309 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "OligoWiz" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://cbs.dtu.dk/services/OligoWiz/" ; biotools:primaryContact "Henrik Bjorn Nielsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3321, edam:topic_3518 ; sc:citation , "pubmed:15585527" ; sc:description "Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "OLIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OLIN.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation , "pubmed:15585527" ; sc:description "Graphical user interface for the OLIN package." ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "OLINgui" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OLINgui.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3810 ; sc:citation , "pmcid:PMC10053119", "pubmed:36986964" ; sc:description "Gene expression atlas tool for Olea europaea. OliveAtlas includes data for most of the main organs of the olive tree variety Picual, and multiple responses to biotic and abiotic stresses." ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "OliveAtlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.oliveatlas.uma.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:author "Samples, Phenotypes and Ontologies Team", "Simon Jupp" ; sc:citation , , ; sc:contributor "CORBEL", "DIACHRON", "EMBL-EBI" ; sc:description "Repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Users can browse the ontologies through the web interface and programatic access is provided via a RESTful API." ; sc:featureList edam:operation_3282, edam:operation_3559 ; sc:funder "CORBEL", "DIACHRON", "EMBL-EBI" ; sc:license "Apache-2.0" ; sc:name "Ontology Lookup Service" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "ebi.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "3" ; sc:url "http://www.ebi.ac.uk/ols/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3344 ; sc:citation ; sc:description "Java front end to the ontology lookup service (OLS)." ; sc:featureList edam:operation_2421 ; sc:name "Ols-dialog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "3.4.3" ; sc:url "http://compomics.github.io/projects/ols-dialog.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0219, edam:topic_3053 ; sc:citation "pubmed:20078892" ; sc:description "Java front end to the Ontology Lookup Service allowing easy access to an extensive list of biomedical ontologies." ; sc:featureList edam:operation_2422 ; sc:name "OLS Dialog" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/ols-dialog/" ; biotools:primaryContact "Harald Barsnes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3301, edam:topic_3324 ; sc:citation "pubmed:23796450" ; sc:description "Automated hybrid clustering method in the field of time series gene expression analysis." ; sc:featureList edam:operation_2945, edam:operation_3432 ; sc:name "OLYMPUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosignal.med.upatras.gr/wordpress/?page_id=173" ; biotools:primaryContact "Prof. Anastasios Bezerianos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3299 ; sc:citation , "pmcid:PMC4383958", "pubmed:25399418" ; sc:description "Project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind." ; sc:featureList edam:operation_2423 ; sc:name "OMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB" ; sc:softwareHelp ; sc:url "http://omabrowser.org/oma/home/" ; biotools:primaryContact "Christophe Dessimoz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0797, edam:topic_1775, edam:topic_3053 ; sc:description "A package for the orthology prediction data download from OMA database." ; sc:featureList edam:operation_0226, edam:operation_1777 ; sc:license "GPL-2.0" ; sc:name "OmaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OmaDB.html" ; biotools:primaryContact "Adrian Altenhoff", "Klara Kaleb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0623, edam:topic_3500 ; sc:citation ; sc:description """Tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. OMAmer is a novel alignment-free protein family assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. It is based on an innovative method using subfamily-informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, it has provided better and quicker subfamily-level assignments than a method based on closest sequences (using DIAMOND).""" ; sc:featureList edam:operation_0224, edam:operation_0495, edam:operation_3211, edam:operation_3460, edam:operation_3472 ; sc:name "OMAmer" ; sc:url "https://github.com/DessimozLab/omamer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2259, edam:topic_3068, edam:topic_3500 ; sc:citation ; sc:description "OMAMO is a tool that suggests the best model organism to study a biological process based on orthologous relationship between a species and human." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMAMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DessimozLab/omamo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2269 ; sc:description "Proteome quality assessment software" ; sc:featureList edam:operation_3180, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "OMArk" ; sc:softwareVersion "0.3.0" ; sc:url "https://github.com/DessimozLab/OMArk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3293, edam:topic_3517, edam:topic_3697 ; sc:citation , "pmcid:PMC8900191", "pubmed:35265838" ; sc:description "OMARU (Omnibus metagenome-wide association study with robustness) is a new end-to-end analysis workflow that covers a wide range of microbiome analysis from phylogenetic and functional profiling to case-control metagenome-wide association studies (MWAS)." ; sc:featureList edam:operation_0324, edam:operation_2436, edam:operation_3216, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "OMARU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/toshi-kishikawa/OMARU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3372, edam:topic_3383, edam:topic_3474 ; sc:citation , "pmcid:PMC8648559", "pubmed:34845388" ; sc:description "A next-generation file format for expanding bioimaging data-access strategies." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "OME-NGFF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngff.openmicroscopy.org/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3172, edam:topic_3174 ; sc:citation , "pubmed:33974004" ; sc:description "omeClust is a clustering method that detects clusters of features using omics data and scores metadata (resolution score) based on their influences in clustering. The similarity of features within each cluster can be different (different resolution). Resolution of similarity score takes to account not only similarity between measurements and also the structure in a hierarchical structure of data and number of features which group together." ; sc:featureList edam:operation_2937, edam:operation_2938, edam:operation_3432 ; sc:license "MIT" ; sc:name "omeClust" ; sc:url "http://github.com/omicsEye/omeClust" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174 ; sc:citation "pubmed:24947750" ; sc:description "Software for assembling and scaffolding Illumina sequencing data of microbial communities." ; sc:featureList edam:operation_0525 ; sc:name "Omega" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://omega.omicsbio.org/" ; biotools:primaryContact "Chongle Pan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3315, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:33588401" ; sc:description """open-source emission tomography software. Open-source MATLAB/GNU Octave Emission Tomography Software. The purpose of OMEGA is twofold. First it is designed to allow easy, fast and efficient reconstruction of any positron emission tomography (PET) data, including simulated GATE data. Secondly, it is intended for easy algorithmic development as it allows easy matrix-free implementation of the forward (A * x) and backward (A' * y) projections.""" ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "OMEGA-m" ; sc:url "https://github.com/villekf/OMEGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0203, edam:topic_3315, edam:topic_3318 ; sc:citation , "pmcid:PMC7671739", "pubmed:33240741" ; sc:description """A molecular dynamics simulation engine for virtual-system coupled sampling. myPresto/omegagene is a Molecular Dynamics package (more description here).""" ; sc:featureList edam:operation_2476, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "omegagene" ; sc:url "https://github.com/kotakasahara/omegagene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2269, edam:topic_3474 ; sc:citation , "pubmed:35552634" ; sc:description "Network-based Driver Gene Identification using Mutual Exclusivity." ; sc:featureList edam:operation_3435, edam:operation_3695, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OMEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.github.com/DriesVanDaele/OMEN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3382 ; sc:citation "pubmed:26476368" ; sc:description "Client-server Java software for visualisation, management and analysis of biological microscope images." ; sc:featureList edam:operation_3443 ; sc:name "OMERO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.openmicroscopy.org/omero/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3071, edam:topic_3384, edam:topic_3385, edam:topic_3452 ; sc:citation ; sc:description """Efficient data management infrastructure for the integration of imaging and omics data in life science research. Abstract As technical developments in omics and biomedical imaging drive the increase in quality, modality, and throughput of data generation in life sciences, the need for information systems capable of integrative, long-term storage and management of these heterogeneous digital assets is also increasing. Here, we propose an approach based on principles of Service Oriented Architecture design, to allow the integrated management and analysis of multi-omics and biomedical imaging data. The proposed architecture introduces an interoperable image management system, the OMERO server, into the backend of qPortal, a FAIR-compliant web-based platform for omics data management.""" ; sc:featureList edam:operation_0224, edam:operation_3443, edam:operation_3760 ; sc:name "OMERO-lib" ; sc:url "https://github.com/qbicsoftware/omero-lib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3277, edam:topic_3382, edam:topic_3489 ; sc:citation , "pmcid:PMC9171289", "pubmed:35685190" ; sc:description "Easing batch image processing from OMERO." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "OMERO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GReD-Clermont/omero_batch-plugin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , "pmcid:PMC1347514", "pubmed:16381939" ; sc:description "A catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 233 animal species (other than human and mouse and rats, which have their own resources)." ; sc:featureList edam:operation_2422 ; sc:license "Not licensed" ; sc:name "OMIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://omia.angis.org.au/home/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , "pmcid:PMC4329600", "pubmed:25717363" ; sc:description "It allows rapid mixed-model based genome-wide association analysis; it efficiently handles large datasets, and both single trait and multiple trait (\"omics\") analysis." ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "OmicABEL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.genabel.org/packages/OmicABEL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1637, edam:format_1638, edam:format_1639 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_2229, edam:topic_3303, edam:topic_3391, edam:topic_3518 ; sc:citation , "pmcid:PMC4053266", "pubmed:24884486" ; sc:contributor ; sc:description "Multiple co-inertia analysis of omics datasets." ; sc:featureList edam:operation_2938, edam:operation_2942, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "omicade4" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/omicade4.html" ; biotools:primaryContact "Chen Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:19528066" ; sc:description "OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset." ; sc:featureList edam:operation_0362, edam:operation_3208 ; sc:name "OmicBrowse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sourceforge.net/projects/omicbrowse/" ; biotools:primaryContact "Tetsuro Toyoda" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2060, edam:format_3033 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2060, edam:format_3033 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2060, edam:format_3033 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:encodingFormat edam:format_2060, edam:format_3033 ; sc:name "Map data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Heat map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3391 ; sc:citation ; sc:description "R package for generating high-quality circular plots for omics data." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_3208 ; sc:license "GPL-2.0" ; sc:name "OmicCircos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OmicCircos.html" ; biotools:primaryContact "Ying Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3308 ; sc:citation "pubmed:24799323" ; sc:description "Method which emphasizes the use of a wide variety of systems-level data, such as those increasingly made available by comprehensive surveys of the genome, transcriptome and epigenome, for complex trait prediction." ; sc:featureList edam:operation_2423 ; sc:name "OmicKriging" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.scandb.org/newinterface/tools/OmicKriging.html" ; biotools:primaryContact "Hae Kyung Im" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3520 ; sc:citation , "pmcid:PMC7931979", "pubmed:33663372" ; sc:description "OmicLoupe is a software used for interactive exploration of omics-datasets. It provides an extensive set of visualizations designed to explore quality issues and biological and technical trends rapidly. It also provides visualizations aiming to make it easy to compare how gene products behave across multiple datasets." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3891 ; sc:license "MIT" ; sc:name "OmicLoupe" ; sc:url "http://quantitativeproteomics.org/omicloupe" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3174, edam:topic_3308, edam:topic_3697 ; sc:description "A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata." ; sc:featureList edam:operation_0337, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "omicplotR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/omicplotR.html" ; biotools:primaryContact "Daniel Giguere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0204, edam:topic_2269, edam:topic_3295, edam:topic_3308 ; sc:author ; sc:citation , , "pmcid:PMC9678903", "pubmed:31243429", "pubmed:36411288" ; sc:description "It systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA)." ; sc:featureList edam:operation_0337, edam:operation_2424, edam:operation_3223, edam:operation_3659, edam:operation_3809 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "omicRexposome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/omicRexposome.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3077 ; sc:description """The Omics Data Paper Generator is an R Shiny app, installable as a golem, which imports (gen)omics metadata from EMBL's ENA and associated records from ArrayExpress and BioSamples into a data paper manuscript according to Pensoft's Biodiversity Data Journal omics data paper manuscript template. The manuscript can be downloaded as HTML or JATS XML. The goal of the tool is to enable (gen)omic data sharing and reuse through facilitating the authoring of genomics data papers. The workflow implemented in the Omics Data Paper Generator has been integrated inside Pensoft's ARPHA platform for authoring and reviewing scholarly articles. There, via this workflow, genomic data papers manuscripts can be generated by providing an ENA Study of Project identifier. Authors are then encouraged to improve their manuscripts through additional metadata and narrative. In addition to running this tool to use the workflow, it can be used via a web application: https://mdmtrv.shinyapps.io/Omics_data_paper/""" ; sc:featureList edam:operation_0336, edam:operation_2421, edam:operation_3436, edam:operation_3908 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Omics Data Paper Generator" ; sc:softwareHelp ; sc:url "https://github.com/pensoft/omicsdatapaper" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3382, edam:topic_3518 ; sc:citation , "pmcid:PMC7671354", "pubmed:33575569" ; sc:description """A comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data. Omics Playground: Explore Omics Data Freely. Omics Playground is a comprehensive self-service analytics platform for the visualization, analytics and exploration of Big Omics Data. It allows biologists to apply a multitude of state-of-the-art analysis tools to their own data to explore and discover underlying biology without coding.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3891 ; sc:name "Omics Playground" ; sc:softwareHelp ; sc:url "https://github.com/bigomics/omicsplayground" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3360 ; sc:citation ; sc:description """Reproducible Research using R Shiny and Alexa. Omics BioAnalytics is a Shiny app that perform common bioinformatics analyses such as descriptive analyses of demographics variables, exploratory data analysis, differential expression analysis and biomarker discovery analysis. The can either use the provided sample data to run through the various analyses of the app or upload their own data (demographics variables, omics data).""" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3744 ; sc:name "Omics BioAnalytics" ; sc:url "https://amritsingh.shinyapps.io/omicsBioAnalytics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3173, edam:topic_3391 ; sc:citation "pubmed:27096930" ; sc:description "Package comprised of command-line tools designed to integrate high-throughput datasets such as gene expression, phospho-proteomic data and the results from genetic screens." ; sc:featureList edam:operation_2424 ; sc:name "Omics Integrator" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://fraenkel-nsf.csbi.mit.edu/omicsintegrator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3391 ; sc:citation "pubmed:25637560" ; sc:description "Open-source, modular computational platform that automates best practice multi-omics data analysis pipelines published in Nature Protocols and other commonly used pipelines, such as GATK." ; sc:featureList edam:operation_2945, edam:operation_3760 ; sc:name "Omics Pipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sulab.org/tools/omics-pipe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0769, edam:topic_3315, edam:topic_3520 ; sc:citation , "pubmed:34019646" ; sc:description "OmicsAnalyst is a comprehensive web-based platform for visual analytics of multi-omics data. It is used for navigating complex landscapes of multi-omics data integration via intuitive visual analytics." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3925, edam:operation_3935 ; sc:name "OmicsAnalyst" ; sc:softwareHelp , ; sc:url "https://www.omicsanalyst.ca" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0091, edam:topic_0196, edam:topic_0199, edam:topic_0769, edam:topic_1775, edam:topic_3168, edam:topic_3174, edam:topic_3517, edam:topic_3941 ; sc:description """OmicsBox is a desktop application which allows to analyse NGS data analysis of genomes, transcriptomes, and metagenomes and its functional interpretation. The software is structured in different modules, each with a specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results. The functional analysis module, which includes the popular Blast2GO annotation methodology makes OmicsBox particularly suited for non-model organism research.""" ; sc:featureList edam:operation_0495 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "OmicsBox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "https://www.biobam.com/omicsbox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation ; sc:description """A database for exploring functional networks of plant pathogens. Integration of biological networks and omicsdata across species. 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Phan", "May D. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_2229, edam:topic_3297, edam:topic_3407 ; sc:citation , "pmcid:PMC9176753", "pubmed:35617352" ; sc:description "Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers." ; sc:featureList edam:operation_3435, edam:operation_3565 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "omniplate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://swainlab.bio.ed.ac.uk/software/omniplate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9636021", "pubmed:36253643" ; sc:description "Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. 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It simplifies creation and deployment of (meta)data transformation processes, emphasizing FAIRification, executable metadata crosswalks and data brokering. Omnipy aids generic data tasks like extraction from multiple sources, (meta)data mapping and systematic data model transformations. Embracing a \"parse, don't validate\" approach, omnipy uses Python type hints and pydantic for data consistency and adherence to specific models. Highly modular, it allows integration of (meta)data transformation steps dependent on software like pandas and R. The architecture supports pluggable execution engines like Prefect, a highly interoperable industry-developed Open Source data flow orchestration engine. Envisioned as a community effort, omnipy aims to offer various import formats and data models (both hierarchical and tabular representations), as well as ontology mapping and semiautomatic data cleaning." ; sc:featureList edam:operation_0335, edam:operation_0336, edam:operation_1812, edam:operation_2422, edam:operation_2428, edam:operation_2429, edam:operation_3096, edam:operation_3357, edam:operation_3359, edam:operation_3435, edam:operation_3436, edam:operation_3695, edam:operation_3763 ; sc:funder "The Research Council of Norway" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "omnipy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider , "ELIXIR Norway", "University of Oslo" ; sc:softwareHelp ; sc:softwareVersion "0.10.4" ; sc:url "https://fairtracks.net/fair/#fair-07-transformation" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:26508754" ; sc:description "A shape similarity search service for 3D structures of macromolecules. 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Yip", "Ting-Fung Chan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:27454532" ; sc:description "Tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii." ; sc:featureList edam:operation_0525 ; sc:name "OMWare" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sharpa/OMWare" ; biotools:primaryContact "Aaron R. Sharp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "OMWSA (optimized moving window spectral analysis) is a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis." ; sc:featureList edam:operation_2423, edam:operation_3214 ; sc:name "OMWSA" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.hy8.com/bioinformatics.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089 ; sc:description "A package that allows the annotation of text with ontology terms (mainly from OBO ontologies) and the computation of semantic similarity measures based on the structure of the ontology between different annotated samples." ; sc:featureList edam:operation_0226, edam:operation_0360, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "Onassis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Onassis.html" ; biotools:primaryContact "Eugenia Galeota" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3337, edam:topic_3676 ; sc:citation , "pmcid:PMC9417173", "pubmed:36026442" ; sc:description "OncMTR stands for missense tolerance ratio specific for cancer-driving mutations. 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There is support for GRCh37 and GRCh38 human reference genome builds." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "oncoanalyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "5.34" ; sc:url "https://github.com/nf-core/oncoanalyser/tree/dev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC9120235", "pubmed:35615022" ; sc:description "Human 51 672 molecular pathways database with tools for activity calculating and visualization." ; sc:featureList edam:operation_0533, edam:operation_3926, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "OncoboxPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://open.oncobox.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0634, edam:topic_2640, edam:topic_3335, edam:topic_3421 ; sc:citation , "pmcid:PMC10167979", "pubmed:37159238" ; sc:description "Public and curated database of molecular information in onco-cardiology/cardio-oncology." ; sc:featureList edam:operation_0224, edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "OncoCardioDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biodb.uv.es/oncocardio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25016581" ; sc:description "Package to detect copy number changes in Deep Sequencing data developed by OncoDNA." ; sc:featureList edam:operation_3435 ; sc:name "ONCOCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://oncocnv.curie.fr/" ; biotools:primaryContact "Valentina Boeva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2640, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC8728272", "pubmed:34718715" ; sc:description "An interactive online database for analysis of gene expression and viral infection in cancer." ; sc:featureList edam:operation_3207, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "OncoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://oncodb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:23884480" ; sc:description "identify genes whose mutations are biased towards a large spatial clustering. 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The package leverages an extensive amount of prior molecular knowledge for geneset interpretation along multiple dimensions. oncoEnrichR is primarily intended for exploratory analysis and prioritization of a gene list from high-throughput cancer biology experiments, e.g. genetic screens (siRNA/CRISPR), protein proximity labeling, or transcriptomics (differential expression). The tool queries a number of high-quality data resources in order to assemble useful gene annotations and analyses in an interactive report.""" ; sc:featureList edam:operation_0276, edam:operation_0531, edam:operation_2436, edam:operation_2437, edam:operation_3282, edam:operation_3463, edam:operation_3672, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "oncoEnrichR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1.0.9" ; sc:url "https://github.com/sigven/oncoEnrichR" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640 ; sc:description "Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation." ; sc:featureList edam:operation_0253, edam:operation_0331 ; sc:name "Oncofuse" ; sc:url "https://github.com/mikessh/oncofuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3299 ; sc:citation ; sc:description """Software for Investigating Tumor Variants From Multiple Biopsies With Integrated Cancer Annotations. OncoGEMINI is an adaptation of GEMINI intended for the improved identification of biologically and clincally relevant tumor variants from multi-sample and longitudinal tumor sequencing data. Using a GEMINI-compatible database (generated from an annotated VCF file), OncoGEMINI is able to filter tumor variants based on included genomic annotations and various allele frequency signatures.""" ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:license "MIT" ; sc:name "OncoGEMINI" ; sc:url "https://github.com/fakedrtom/oncogemini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168 ; sc:citation , "pubmed:30071882" ; sc:description "The widespread incorporation of next-generation sequencing into clinical oncology has yielded an unprecedented amount of molecular data from thousands of patients. A main current challenge is to find out reliable ways to extrapolate results from one group of patients to another and to bring rationale to individual cases in the light of what is known from the cohorts. We present OncoGenomic Landscapes, a framework to analyze and display thousands of cancer genomic profiles in a 2D space. Our tool allows users to rapidly assess the heterogeneity of large cohorts, enabling the comparison to other groups of patients, and using driver genes as landmarks to aid in the interpretation of the landscapes. In our web-server, we also offer the possibility of mapping new samples and cohorts onto 22 predefined landscapes related to cancer cell line panels, organoids, patient-derived xenografts, and clinical tumor samples." ; sc:name "OncogenomicLandscapes" ; sc:url "https://oglandscapes.irbbarcelona.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168 ; sc:citation ; sc:description "This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "oncomix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/oncomix.html" ; biotools:primaryContact "Daniel Pique" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_0622, edam:topic_2640, edam:topic_3345, edam:topic_3366, edam:topic_3473 ; sc:author ; sc:description """oncoPharmaDB - Targeted and non-targeted anticancer drugs and drug regimens. This R package provides a dataset and method to query targeted and non-targeted cancer drugs, including comprehensive annotations per target, drug mechanism-of-action, approval dates, clinical trial phases for various indications etc.""" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "oncoPharmaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "0.7.2" ; sc:url "https://github.com/sigven/oncoPharmaDB" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_2640 ; sc:citation , "pubmed:36058206" ; sc:description "A platform for oncology publication mining." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:name "OncoPubMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://oncopubminer.chosenmedinfo.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3068 ; sc:citation ; sc:description "Tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3625 ; sc:license "GPL-3.0" ; sc:name "OncoScore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OncoScore.html" ; biotools:primaryContact "Daniele Ramazzotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0218, edam:topic_0602, edam:topic_2640 ; sc:citation , "pmcid:PMC4086113", "pubmed:24813447" ; sc:description "Cancer gene search engine with literature evidence." ; sc:featureList edam:operation_0305, edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:name "OncoSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://oncosearch.biopathway.org" ; biotools:primaryContact "Jong C. Park1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3722 ; sc:encodingFormat edam:format_2330 ; sc:name "Physiology parameter" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3547 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3056, edam:topic_3524 ; sc:citation , "pmcid:PMC4339747", "pubmed:25879190" ; sc:description "Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Also included are functions for simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other tumor progression models, and for plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling, as well as functions for plotting the true phylogenetic relationships of the clones." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "OncoSimulR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OncoSimulR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3320, edam:topic_3512 ; sc:citation , , "pubmed:31391553", "pubmed:34554251" ; sc:description "OncoSplicing is a database to systematically study clinically relevant alternative splicing in 33 TCGA cancers and 31 GTEx tissues." ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "OncoSplicing" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.oncosplicing.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2533, edam:topic_2640, edam:topic_2815 ; sc:citation "pubmed:25703262" ; sc:description "Web application to annotate point mutations and indels with functional data relevant to cancer researchers. Annotations include gene names, functional consequence (e.g. Missense), PolyPhen-2 predictions, and cancer-specific annotations from resources such as COSMIC, Tumorscape, and published MutSig results." ; sc:featureList edam:operation_0361 ; sc:name "Oncotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.broadinstitute.org/oncotator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0605, edam:topic_0622, edam:topic_2640 ; sc:citation , "pmcid:PMC8275328", "pubmed:34252935" ; sc:description "visualization of large-scale longitudinal cancer molecular data." ; sc:featureList edam:operation_0337, edam:operation_3282, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OncoThreads" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://oncothreads.gehlenborglab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC7577240", "pubmed:32597311" ; sc:description """An online resource for exploration of tRNA-derived fragments in human cancers. a comprehensive database for tRNA-derived RNA fragments in human cancer research. 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Other key features include visualisation of ontologies in hierarchical/graph format, advanced search capabilities, peer review/approval workflow and web service access to data." ; sc:featureList edam:operation_2422, edam:operation_2429, edam:operation_3436, edam:operation_3559 ; sc:funder "Innovative Medicines Initiative (IMI)" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "OntoBrowser" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://github.com/Novartis/ontobrowser" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_1775 ; sc:citation ; sc:description "This package provides a simple interface to ontologies described in widely used standard formats, stored locally in the filesystem or accessible online." ; sc:featureList edam:operation_0337 ; sc:license "Apache-2.0" ; sc:name "ontoCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ontoCAT.html" ; biotools:primaryContact "Natalja Kurbatova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3068, edam:topic_3303 ; sc:citation , "pubmed:34270699" ; sc:description "Ontoclick is a web browser extension to facilitate biomedical knowledge curation. 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sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontocount.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3067, edam:topic_3168, edam:topic_3293 ; sc:citation ; sc:description "ontoFAST is an R package for interactive and semi-automatic annotation of characters with biological ontologies. ontoFAST aids annotating characters and character matrices with biological ontologies." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3559, edam:operation_3745 ; sc:license "GPL-2.0" ; sc:name "ontoFAST" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ontoFAST/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology term(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontoget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontoget.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get common ancestor for terms." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetcommon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetcommon.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology term(s) by parent id." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetdown" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetdown.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology ontology terms." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetobsolete" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetobsolete.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology root terms by child identifier." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetroot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetroot.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology term(s) by id with common parent." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetsibs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetsibs.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology term(s) by id of child." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontogetup" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontogetup.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2223 ; sc:name "Ontology metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Report whether an ontology term id is obsolete." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontoisobsolete" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontoisobsolete.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "A Tool for Statistical Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology." ; sc:featureList edam:operation_2495 ; sc:name "Ontologizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ontologizer.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3324, edam:topic_3325, edam:topic_3474 ; sc:citation , "pmcid:PMC6958746", "pubmed:31931870" ; sc:description """Combining lexical and context features for automatic ontology extension. This repository contains script which were used to build and train the prediction models together with the scripts for evaluating their performance.""" ; sc:featureList edam:operation_3280, edam:operation_3778, edam:operation_3935 ; sc:license "BSD-2-Clause" ; sc:name "ontology extension" ; sc:url "https://github.com/bio-ontology-research-group/ontology-extension" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3298 ; sc:citation , "pmcid:PMC9547537", "pubmed:36208225" ; sc:description "A toolkit for building, maintaining and standardizing biomedical ontologies." ; sc:featureList edam:operation_2428, edam:operation_3431, edam:operation_3435, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Ontology Development Kit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/INCATools/ontology-development-kit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0602, edam:topic_0634, edam:topic_3063 ; sc:citation , "pmcid:PMC7787442", "pubmed:33406098" ; sc:description "Use of a modular ontology and a semantic annotation tool to describe the care pathway of patients with amyotrophic lateral sclerosis in a coordination network." ; sc:featureList edam:operation_3280, edam:operation_3778, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "OntoPaRON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioportal.bioontology.org/ontologies/ONTOPARON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089 ; sc:description "Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ontoProc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ontoProc.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071 ; sc:description "Download a NIF ontology file." ; sc:featureList edam:operation_2422 ; sc:name "OntoQuest WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071, edam:topic_3473 ; sc:description "Search terms starting for the query used for auto-complete service." ; sc:featureList edam:operation_2422 ; sc:name "OntoQuestMain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain#OntoQuestMain-%28updatedon03%2F10%2F2010%29" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0966 ; sc:name "Ontology term" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get ontology term(s) original full text." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ontotext" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/ontotext.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3324 ; sc:citation , "pmcid:PMC10237395", "pubmed:37267413" ; sc:description "3D visualization of application ontology class hierarchies." ; sc:featureList edam:operation_0570, edam:operation_3280, edam:operation_3559, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OntoTrek" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genepio.org/ontotrek/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9148541", "pubmed:35579517" ; sc:description "A dashboard to visualize gene expression during Drosophila oogenesis suggests meiotic entry is regulated post-transcriptionally." ; sc:featureList edam:operation_0313, edam:operation_0571, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "Oo-site" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ranganlab.com/Oo-site" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC9159682", "pubmed:35669063" ; sc:description "Generative model-enhanced human motion prediction." ; sc:featureList edam:operation_0244, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OoD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bouracha/OoDMotion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0128 ; sc:citation "pubmed:25244105" ; sc:description "Novel computational tool designed to inform compound design by combining structural and activity data. It uses 3D matched molecular pairs to contextualise both activity and inactivity data in its relevant protein environment." ; sc:featureList edam:operation_2406, edam:operation_2430 ; sc:name "OOMMPPAA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/" ; biotools:primaryContact "Anthony Bradley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3518 ; sc:citation "pubmed:25380958" ; sc:description "Object-oriented microarray and proteomics analysis library implemented in R using S4 classes and compatible with BioConductor." ; sc:featureList edam:operation_2945 ; sc:name "OOMPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/OOMPA:Overview" ; biotools:primaryContact "Kevin R. Coombes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_2269, edam:topic_3063, edam:topic_3325 ; sc:citation , "pubmed:30407490" ; sc:description """Combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Ontologies Plus Annotations to Vectors: OPA2Vec. OPA2Vec is a tool that can be used to produce feature vectors for biological entities from an ontology. OPA2Vec uses mainly metadata from the ontology in the form of annotation properties as the main source of data. It also uses formal ontology axioms as well as entity-concept associations as sources of information. This document provides instructions on how to run OPA2Vec as a tool and contains also a detailed documentation of the implementation of OPA2Vec for users willing to change the code according to their needs which is quite easy.""" ; sc:featureList edam:operation_0303, edam:operation_2492, edam:operation_3778 ; sc:license "GPL-3.0" ; sc:name "OPA2Vec" ; sc:url "https://github.com/bio-ontology-research-group/opa2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16845117" ; sc:description "Tool for investigating structural neighbors that can calculate a structural alignment for two protein structures." ; sc:featureList edam:operation_0250, edam:operation_0295, edam:operation_2487, edam:operation_2488 ; sc:name "OPAAS" ; sc:url "http://opaas.ibms.sinica.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0736, edam:topic_2814 ; sc:citation ; sc:description "Prediction of MoRF regions in intrinsically disordered protein sequences." ; sc:featureList edam:operation_0245 ; sc:isAccessibleForFree true ; sc:name "OPAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.alok-ai-lab.com/tools/opal/" ; biotools:primaryContact "Alok Sharma", "Ashwini Patil" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3068, edam:topic_3303, edam:topic_3344 ; sc:citation "pubmed:20529877" ; sc:description "Opal Web Services for Biomedical Applications is a production web server. Powered by Opal, it allows users to use scientific applications easily as web services without any modification to the scientific codes." ; sc:featureList edam:operation_0482, edam:operation_3432, edam:operation_3760, edam:operation_3761, edam:operation_3762 ; sc:name "Opal Web Services for Biomedical Applications" ; sc:operatingSystem "Linux" ; sc:url "https://sourceforge.net/projects/opaltoolkit/files/" ; biotools:primaryContact "Luca Clementi", "Nadya Williams", "Sriram Krishnan", "Wilfred Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3337, edam:topic_3384 ; sc:citation , "pubmed:33522661" ; sc:description """Informing research participants and obtaining consent to share brain imaging data. Make open data sharing a no-brainer for ethics committees. The ideology of open and reproducible science makes its way into various fields of science. Flexibility in the interpretation of original regulations established in the past century, decentralization of those committees, and lack of a "community" influence over them created the problem: for neuroimaging studies, there was no commonly accepted version of a Consent form template that would allow for collected imaging data to be shared as openly as possible while providing adequate guarantees for research participants' privacy.""" ; sc:featureList edam:operation_0310, edam:operation_3283, edam:operation_3431 ; sc:name "Open Brain Consent" ; sc:url "https://open-brain-consent.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0769, edam:topic_2640, edam:topic_3175 ; sc:citation , "pmcid:PMC7113103", "pubmed:32228266" ; sc:description "OpenCRAVAT is a new open source, scalable decision support system to support variant and gene prioritization. It offers a dynamic GUI, allowing users to easily, download tools from an extensive resource catalog, create customized pipelines, run jobs at speeds that exceed current variant annotation API services, and explore results in a richly detailed viewing environment. OpenCRAVAT is distinguished from similar tools by the amount and diversity of data resources and computational prediction methods available, which span germline, somatic, common, rare, coding and non-coding variants. We have designed the OpenCRAVAT resource catalog to be open and modular to maximize community and developer involvement, and as a result the catalog is being actively developed and growing larger every month." ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "open-cravat" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://opencravat.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation , "pubmed:34009953" ; sc:description "Open Specy is a web application and R package for for microplastic spectral classification." ; sc:featureList edam:operation_2422, edam:operation_3214, edam:operation_3221 ; sc:license "CC-BY-4.0" ; sc:name "Open Specy" ; sc:url "http://www.openspecy.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description "A modular Python library for t-SNE dimensionality reduction and embedding | Extensible, parallel implementations of t-SNE | openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE), a popular dimensionality-reduction algorithm for visualizing high-dimensional data sets. openTSNE incorporates the latest improvements to the t-SNE algorithm, including the ability to add new data points to existing embeddings, massive speed improvements, enabling t-SNE to scale to millions of data points and various tricks to improve global alignment of the resulting visualizations" ; sc:featureList edam:operation_0337 ; sc:license "BSD-3-Clause" ; sc:name "openTSNE" ; sc:url "https://github.com/pavlin-policar/openTSNE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3292, edam:topic_3314 ; sc:citation ; sc:description "Chemical toolbox designed to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_3431 ; sc:name "Open Babel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://openbabel.org/wiki/Main_Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3361, edam:topic_3678 ; sc:citation , "pubmed:35233751" ; sc:description "A web application for running and sharing online experiments." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Open Lab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://open-lab.online" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2258, edam:topic_3325, edam:topic_3336 ; sc:citation ; sc:description "It is a resource for pharmacological data. The platform has been developed to reduce barriers to drug discovery in industry, academia and for small businesses." ; sc:featureList edam:operation_2422, edam:operation_2497, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Open PHACTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.openphacts.org/" ; biotools:primaryContact "Open PHACTS foundation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3332, edam:topic_3336, edam:topic_3343 ; sc:citation , ; sc:contributor "Innovative Medicines Initiative (IMI)" ; sc:description "Open PHACTS Discovery Platform brings together data from multiple publicly available sources of pharmacological and physicochemical information, in order to streamline research and drug discovery processes. The data is integrated into a consolidated triple store, which can be accessed via applications or workflow tools which make use of the Open PHACTS API." ; sc:featureList edam:operation_0360, edam:operation_2421, edam:operation_2422 ; sc:funder "Innovative Medicines Initiative (IMI)" ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "Open PHACTS API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Open PHACTS Foundation", "cs.manchester.ac.uk" ; sc:softwareHelp , , ; sc:softwareVersion "2.1" ; sc:url "https://dev.openphacts.org/docs/2.1" ; biotools:primaryContact "Open PHACTS contact", "Open PHACTS support portal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2258, edam:topic_3336 ; sc:citation ; sc:contributor "Innovative Medicines Initiative (IMI)" ; sc:description "Database of compounds registered in the Open PHACTS platform, with structure similarity search. Look up chemical properties (SMILES)." ; sc:featureList edam:operation_0360, edam:operation_0570, edam:operation_2422 ; sc:funder "Innovative Medicines Initiative (IMI)" ; sc:isAccessibleForFree true ; sc:name "Open PHACTS Chemistry Registry System" ; sc:provider "Royal Society of Chemistry", "cs.manchester.ac.uk" ; sc:softwareHelp , , ; sc:url "http://ops.rsc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2258, edam:topic_3336 ; sc:author "Ian Dunlop" ; sc:citation ; sc:contributor "Innovative Medicines Initiative (IMI)" ; sc:description "Interface to the Open PHACTS Discovery Platform and is built to answer the critical pharmacology questions defined by eight major pharmaceutical companies." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:funder "Innovative Medicines Initiative (IMI)" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Open PHACTS Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Open PHACTS Foundation", "University of Manchester", "cs.manchester.ac.uk" ; sc:softwareHelp , , ; sc:softwareVersion "1.5.0" ; sc:url "http://www.openphacts.org/explorer" ; biotools:primaryContact "Open PHACTS Explorer issue tracker", "Open PHACTS support portal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3336, edam:topic_3574 ; sc:citation , , "pmcid:PMC7611956", "pmcid:PMC7778936", "pubmed:33045747", "pubmed:34711957" ; sc:description """Open Targets Genetics is a robust tool highlighting variant-centric statistical evidence to allow both prioritisation of candidate causal variants at trait-associated loci and identification of potential drug targets. The portal aggregates and merges genetic associations curated from both literature and newly-derived loci from UK Biobank, which contains functional genomics data (e.g. chromatin conformation, chromatin interactions) and quantitative trait loci (eQTLs and pQTLs). Statistical fine-mapping methods are applied across thousands of trait-associated loci to resolve association signals and to link each variant to its proximal and distal target gene(s), using a single evidence score. Integrated cross-trait colocalisation analyses and linking to detailed pharmaceutical compounds extend the capability of Open Targets Genetics to explore drug repositioning opportunities and shared genetic architecture.""" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Open Targets Genetics" ; sc:softwareHelp , , , ; sc:url "https://genetics.opentargets.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "It is a public toxicogenomics database based on the Japanese Toxicogenomics Projects (TGP and TGP2), developed so that a wider community of researchers could utilize the fruits of this research. This API provides access to the RNA microarray (Affymetrix) samples from Open TG-GATEs. Rat data, as well as human data is provided, for repeat and single doses.\"," ; sc:featureList edam:operation_2422 ; sc:name "Open TG-GATEs API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://toxico.nibiohn.go.jp/english/" ; biotools:primaryContact "Hiroshi Yamada" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing. OpenABM-Covid19: Agent-based model for modelling the Covid-19 epidemic.""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "OpenABM-Covid19" ; sc:url "https://github.com/BDI-pathogens/OpenABM-Covid19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_1317 ; sc:citation "pubmed:24925323" ; sc:description "Open source project primarily aimed at the plant research community.It is a distributed collaborative effort to develop Python libraries and tools which address the needs of current and future work in Plant Architecture modeling. Includes modules to represent, analyse, and model the functioning and growth of plant architecture." ; sc:featureList edam:operation_2426 ; sc:name "OpenAlea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://openalea.gforge.inria.fr/" ; biotools:primaryContact "guillaume.garin@itkweb.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3277, edam:topic_3295, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:33999180" ; sc:description "OpenAnnotate is a web server to annotate the chromatin accessibility of genomic regions. The construction of the OpenAnnotate backend requires great efforts and can hardly be deployed on an ordinary server or workstation. Briefly, in order to construct the OpenAnnotate backend, one needs 1) elaborate chromatin accessibility data preprocessing for high-frequency data read operation, 2) sophisticated multithreaded program tailored to the preprocessed data, and 3) high-performance computer to maximize the program efficiency." ; sc:featureList edam:operation_0441, edam:operation_2422, edam:operation_3219 ; sc:license "MIT" ; sc:name "OpenAnnotate" ; sc:url "http://health.tsinghua.edu.cn/openannotate/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336, edam:topic_3388 ; sc:citation "pubmed:12825620" ; sc:description "Java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page or as a desktop application." ; sc:featureList edam:operation_0570 ; sc:name "OpenAstexViewer 3.0" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://openastexviewer.net/web/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0736, edam:topic_3306, edam:topic_3892 ; sc:citation ; sc:description """a fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM. A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA in OpenMM. The OpenAWSEM code is currently being tested. Use at your own risk. And let us know what you find. :-).""" ; sc:featureList edam:operation_0471, edam:operation_0480, edam:operation_1850, edam:operation_2415, edam:operation_2476 ; sc:license "MIT" ; sc:name "OpenAWSEM" ; sc:url "https://github.com/npschafer/openawsem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3474 ; sc:citation , "pubmed:32339214" ; sc:description """A benchmarking framework for large-scale biomedical link prediction. OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data. It contains benchmark datasets as well as tools for creating custom benchmarks and training and evaluating models.""" ; sc:featureList edam:operation_3359, edam:operation_3927 ; sc:license "MIT" ; sc:name "OpenBioLink" ; sc:url "https://github.com/OpenBioLink/OpenBioLink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Breast image processing" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "OpenBreast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.5" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71615-openbreast" ; biotools:primaryContact "Said Pertuz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3344 ; sc:citation ; sc:description "openCARP is an open cardiac electrophysiology simulator for in-silico experiments. Its source code is public and the software is freely available for academic purposes. openCARP is easy to use and offers single cell as well as multiscale simulations from ion channel to organ level. Additionally, openCARP includes a wide variety of functions for pre- and post-processing of data as well as visualization. The python-based CARPutils framework enables the user to develop and share simulation pipelines, i.e. automating in-silico experiments including all modeling/simulation steps." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "openCARP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0-5.0" ; sc:url "https://www.openCARP.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0621, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description "OpenCell is a tool for proteome-scale endogenous tagging enables the cartography of human cellular organization." ; sc:featureList edam:operation_2429, edam:operation_2492, edam:operation_3799 ; sc:name "OpenCell" ; sc:url "http://opencell.czbiohub.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_3332, edam:topic_3474 ; sc:citation ; sc:description """A Deep Learning Toolkit for Computational Chemistry and Drug Design. OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.""" ; sc:featureList edam:operation_3431, edam:operation_3659, edam:operation_3938 ; sc:license "MIT" ; sc:name "OpenChem" ; sc:url "https://github.com/Mariewelt/OpenChem" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_1637, edam:format_3244, edam:format_3650, edam:format_3654, edam:format_3712, edam:format_3752 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3244, edam:format_3620, edam:format_3650, edam:format_3752 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation "pubmed:20673335" ; sc:description "Open source tool for mass spectrometry and chromatography." ; sc:featureList edam:operation_2424, edam:operation_3203, edam:operation_3214, edam:operation_3215, edam:operation_3436, edam:operation_3629, edam:operation_3694, edam:operation_3695 ; sc:name "OpenChrom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.openchrom.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3398, edam:topic_3569 ; sc:citation "pubmed:21762717" ; sc:description "Mathematical modelling environment that enables the application of finite element analysis techniques to a variety of complex bioengineering problems." ; sc:featureList edam:operation_2426 ; sc:name "OpenCMISS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://physiomeproject.org/software/opencmiss/" ; biotools:primaryContact "ChrisBradley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3393, edam:topic_3572 ; sc:citation , "pubmed:33576798" ; sc:description "A web-based application for detecting microbial contaminants in next-generation sequencing data. OpenContami: Open Cell Microbial Contaminants by High-throughput Sequencing." ; sc:featureList edam:operation_0338, edam:operation_3198, edam:operation_3219, edam:operation_3799 ; sc:name "OpenContami" ; sc:url "https://openlooper.hgc.jp/opencontami/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3361 ; sc:citation , "pmcid:PMC4148203", "pubmed:25167361" ; sc:description "This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy." ; sc:featureList edam:operation_3799 ; sc:license "Artistic-2.0" ; sc:name "openCyto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/openCyto.html" ; biotools:primaryContact "Mike Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3315, edam:topic_3384 ; sc:citation , "pmcid:PMC7539649", "pubmed:32169912" ; sc:description """Open-Access Resource for Nuclear Medicine Dosimetry. If you wish to receive the OpenDose newsletter, send an email to this link. You will receive shortly a confirmation email for your registration.""" ; sc:featureList edam:operation_3431 ; sc:name "OpenDose" ; sc:url "http://www.opendose.org" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0958 ; sc:encodingFormat edam:format_2376, edam:format_3464, edam:format_3475 ; sc:name "Tool metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3071, edam:topic_3344 ; sc:citation ; sc:description "OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. OpenEBench is part of the ELIXIR Tools platform and its development is led by the Barcelona Supercomputing Center (BSC) in collaboration with partners within ELIXIR and beyond. OpenEBench, holds a specific infrastructure to monitor software quality. In an initial analysis phase BSC has put together a series of quality metrics taken from a number of sources. The source of such metrics includes documents by the Software Sustainability Institute, recommendations for open source software development, or for software quality metrics. 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It also provides supporting evidence for each protein, such as mass-spectrometry and ribosome profiling detection, protein homology and predictions of funtional domains.""" ; sc:featureList edam:operation_0303, edam:operation_0436, edam:operation_2422 ; sc:name "OpenProt" ; sc:softwareHelp ; sc:url "https://openprot.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3305, edam:topic_3418, edam:topic_3421, edam:topic_3575 ; sc:citation ; sc:description "OpenSAFELY is a secure analytics platform for electronic health records in the NHS, delivering analyses across more than 58 million patients’ records anddeliver urgent results during the global COVID-19 emergency." ; sc:featureList edam:operation_3283, edam:operation_3454 ; sc:name "OpenSAFELY" ; sc:url "https://opensafely.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2815, edam:topic_3068 ; sc:citation , "pubmed:35500997" ; sc:description "A model for estimating lower back kinetics in gait." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OpenSim" ; sc:url "https://simtk.org/projects/emg_opt_tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_2269, edam:topic_3892 ; sc:citation ; sc:description "Beginning with SMOG v2.4, it is possible to create force fields that are written specifically for use with OpenMM. 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SMOG 2 and OpenSMOG have been co-designed for integrated use." ; sc:featureList edam:operation_2415, edam:operation_2476, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OpenSMOG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://smog-server.org/smog2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3574 ; sc:citation , "pubmed:24647222" ; sc:description "openSNP allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results by getting the latest primary literature on their variations, and help scientists find new associations." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "openSNP" ; sc:softwareVersion "v1.0" ; sc:url "https://www.opensnp.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3385 ; sc:citation "pubmed:23749304" ; sc:description "Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM)." ; sc:featureList edam:operation_3552 ; sc:name "OpenSPIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://openspim.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3421, edam:topic_3577 ; sc:citation "pmcid:PMC10114931", "pubmed:37082565" ; sc:description "OpenSRH contains data from the most common brain tumors diagnoses, full pathologic annotations, whole slide tumor segmentations, raw and processed optical imaging data for end-to-end model development and validation." ; sc:featureList edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OpenSRH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://opensrh.mlins.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2269 ; sc:citation ; sc:description """A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput Phenotypic Data. A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association.""" ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3664 ; sc:license "GPL-2.0" ; sc:name "OpenStats" ; sc:url "http://www.bioconductor.org/packages/OpenStats" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_1957 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:33724840" ; sc:description "Open and Easy Access to timsTOF Raw Data." ; sc:featureList edam:operation_3704 ; sc:name "OpenTIMS" ; sc:url "http://www.github.com/michalsta/opentims" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0637, edam:topic_3050, edam:topic_3293, edam:topic_3944 ; sc:citation , "pubmed:33970279" ; sc:description "opentree is a Python package for accessing and analyzing data from the Open Tree of Life. This package is a python library designed to make it easier to work with web services and data resources associated with the Open Tree of Life project." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3460, edam:operation_3907 ; sc:license "BSD-2-Clause" ; sc:name "opentree" ; sc:softwareHelp , , ; sc:url "https://github.com/OpenTreeOfLife/python-opentree" ; biotools:primaryContact "Emily Jane Mctavish" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_3379 ; sc:citation ; sc:description "OpenTrials is a collaboration between Open Knowledge International and Dr Ben Goldacre from the University of Oxford DataLab. It aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally." ; sc:featureList edam:operation_2422 ; sc:name "OpenTrials API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://opentrials.net/" ; biotools:primaryContact "Ben Goldacre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC8741824", "pubmed:34996963" ; sc:description "An open-source, low-cost device for fallow weed detection." ; sc:featureList edam:operation_2428, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OpenWeedLocator OWL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/geezacoleman/OpenWeedLocator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0602, edam:topic_0749, edam:topic_2885 ; sc:citation , "pmcid:PMC10320191", "pubmed:37158276" ; sc:description "Web-server update for genomic summary data interpretation." ; sc:featureList edam:operation_0282, edam:operation_3095, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OpenXGR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.openxgr.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:21929371" ; sc:description "Sequence assembly program. It uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads." ; sc:featureList edam:operation_0310 ; sc:name "Opera" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/operasf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies." ; sc:featureList edam:operation_3216 ; sc:license "Not licensed" ; sc:name "OPERA-LG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/operasf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_2258, edam:topic_3306, edam:topic_3371 ; sc:citation ; sc:description "Command line application providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties and environmental fate endpoints." ; sc:featureList edam:operation_0322 ; sc:license "MIT" ; sc:name "OPERA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/kmansouri/OPERA" ; biotools:primaryContact "Kamel Mansouri" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_1632 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_1775, edam:topic_2229 ; sc:citation ; sc:description "This flexible R package deals with the data generated by PerkinElmer's Opera High Content Screening System. Its functions include the data importing, normalization and quality control, hit detection and function analysis." ; sc:featureList edam:operation_2409, edam:operation_2428, edam:operation_3435, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "OperaMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OperaMate.html" ; biotools:primaryContact "Chenglin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0749, edam:topic_3297, edam:topic_3300 ; sc:citation , "pubmed:37356898" ; sc:description "A deep learning-based web server for accurate prediction of prokaryotic operons." ; sc:featureList edam:operation_0435, edam:operation_0579, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Operon Finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.iitg.ac.in/spkanaujia/operonfinder.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0780, edam:topic_3308, edam:topic_3474, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data." ; sc:featureList edam:operation_0435, edam:operation_0579, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "OperonSEQer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sandialabs/OperonSEQer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3297, edam:topic_3837 ; sc:citation , "pmcid:PMC9017871", "pubmed:35445164" ; sc:description "A Python package for identifying gene clusters in large genomics and metagenomics data sets." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Opfi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/wilkelab/Opfi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3489 ; sc:citation , "pubmed:31583635" ; sc:description """A Focus on the Integrated Interactions Database (IID). Integrated Interactions Database. tissue specific PPI networks across species.""" ; sc:featureList edam:operation_2422, edam:operation_2492, edam:operation_3083 ; sc:name "ophid" ; sc:url "http://ophid.utoronto.ca/iid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2269 ; sc:citation ; sc:description "Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "OPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=OPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:21890895" ; sc:description "Orientations of Proteins in Membranes (OPM) database: curated resource, provides spatial positions of membrane-bound peptides and proteins of known 3D structure, together with their structural classification, topology and intracellular localization. Data can be searched and retrieved, database offers downloadable coordinates. Protein images and visualization tools provided." ; sc:featureList edam:operation_0270, edam:operation_0320, edam:operation_2422, edam:operation_2996 ; sc:name "Orientations of Proteins in Membranes database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://opm.phar.umich.edu/" ; biotools:primaryContact "Andrei Lomize" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation , "pubmed:26063839" ; sc:description "This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "oposSOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/oposSOM.html" ; biotools:primaryContact "Henry Loeffler-Wirth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3308, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC7574456", "pubmed:33076824" ; sc:description """An interactive tool to explore omics data landscapes in health science. The new oposSOM-Browser extends this toolkit and introduces the interactive browsing of single gene and function set profiles, of their mapping into the molecular ‘portrait landscape’, of phenotype diversity and associated survival differences, and of cellular signaling pathway activation patterns. Further, individual signature gene list can be mapped and evaluated regarding diagnostic quality. oposSOM is a comprehensive data analysis software combining diversity analyses, biomarker selection, functional information mining, and visualization to the machine learning based ‘high-dimensional data portraying’.""" ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_3935 ; sc:name "oposSOM-Browser" ; sc:url "http://www.izbi.uni-leipzig.de/opossom-browser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:15933209", "pubmed:17576675" ; sc:description "oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445, edam:operation_2575, edam:operation_3222 ; sc:name "oPOSSUM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cisreg.ca/oPOSSUM/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053 ; sc:citation , "pmcid:PMC3553066", "pubmed:23216803" ; sc:description "The R implementation of mCOPA package. This package provides methods for Cancer Outlier Profile Analysis. Although initially developed to detect outlier genes in cancer studies, its methods can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis." ; sc:featureList edam:operation_2454 ; sc:license "GPL-2.0" ; sc:name "oppar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/oppar.html" ; biotools:primaryContact "Soroor Hediyeh zadeh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3574 ; sc:citation "pubmed:16761918" ; sc:description "Optimal algorithm for perfect phylogeny haplotyping.The perfect phylogeny haplotyping (PPH) problem is one of the many computational approaches to the haplotype inference (HI)  problem. This algorithm is one of the first O(nm) algorithms presented for the PPH problem." ; sc:featureList edam:operation_0487 ; sc:name "opph" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://vlsi.cs.ucf.edu/nsf/software/opph/" ; biotools:primaryContact "Ravi VijayaSatya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:35802238" ; sc:description "A MATLAB Package for Comprehensive Pathway Analysis of lncRNA-miRNA-mRNA in Humans." ; sc:featureList edam:operation_0314, edam:operation_3792, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "opplncRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HangZhouSheep/opplncRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:36205845" ; sc:description "Omics Pilot Platform of Ontology (oppOntology) is a kind of enrichment analysis tool for omics data with a graphical user interface (GUI), founded on the architecture of MATLAB AppDesigner. oppOntology supports the enrichment calculation of GO (Gene Ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), HPO (Human Phenotype Ontology), COG (Clusters of Orthologous Groups), MsigDB (Molecular Signatures Database) and Function (custom functions)." ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "oppOntology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HangZhouSheep/oppOntology" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3383, edam:topic_3385, edam:topic_3474 ; sc:citation ; sc:description """Open source Python framework for collaborative instance segmentation of bioimages. Various pre-trained deep-learning models for the segmentation of biomedical images have been made available to users with little to no knowledge in machine learning. However, testing these tools individually is tedious and success is uncertain. Here, we present OpSeF, a Python framework for deep-learning based semantic segmentation that was developed to promote the collaboration of biomedical user with experienced image-analysts.""" ; sc:featureList edam:operation_2940, edam:operation_3552, edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "OpSeF" ; sc:url "https://github.com/trasse/OpSeF-IV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_0804, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6882880", "pubmed:31780669" ; sc:description """Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets. Parallel opt-SNE implementation with Python wrapper. opt-SNE is a modified version of t-SNE that enables high-quality embeddings in the optimal amount of compute time without having to empirically tune algorithm parameters. For thorough background and discussion on this work, please read the paper. opt-SNE is a modified version of t-SNE that enables high-quality embeddings in the optimal amount of compute time without having to tune algorithm parameters. opt-SNE was developed to solve two fundamental problems with t-SNE. The first is the tendency of large datasets to fail to produce useful embeddings. The second is the need to empirically search the algorithm parameter space to find optimal settings""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3695 ; sc:license "BSD-3-Clause" ; sc:name "opt-SNE" ; sc:url "http://www.omiq.ai/opt-SNE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """Optimized sgRNA Design by Deep Learning to Balance the Off-Target Effects and On-Target Activity of CRISPR/Cas9. A user-friendly tool for single-guide RNA (sgRNA) design of CRISPR-Cas system. The CRISPR Cas9 system is currently considered as the most advanced tool used for numerous areas of biological study in which it is useful to target or modify specific DNA sequences.""" ; sc:featureList edam:operation_3659, edam:operation_3927 ; sc:name "OPT-sgRNA" ; sc:url "https://github.com/Jie-lan/OPT-sgRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3307, edam:topic_3569 ; sc:citation , "pmcid:PMC5450252", "pubmed:28584451" ; sc:description "Cluster analysis using statistical and biological validation measures for both continuous and count data." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "optCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/optCluster/index.html" ; biotools:primaryContact "Michael Sekula", "Somnath Datta", "Susmita Datta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7502308" ; sc:description """An optimized convolutional neural network for an automatic diagnosis of COVID-19. 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Predictions of protein backbone torsion angles (ϕ and ψ) and secondary structure from sequence are crucial subproblems in protein structure prediction. With the development of deep learning approaches, their accuracies have been significantly improved. 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Data mining through visual programming or Python scripting. Components for machine learning. Add-ons for bioinformatics and text mining. 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It extends Orange by providing common functionality for basic tasks in bioinformatics. It also provides widgets for Orange Canvas, which enable users who are not programmers to manage microarray and genomic data flow and to customize their analysis by combining common data analysis tools to fit their needs." ; sc:featureList edam:operation_2495 ; sc:name "Orange-Bioinformatics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.5.40" ; sc:url "http://pythonhosted.org/Orange-Bioinformatics/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2330 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2330 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3473, edam:topic_3474 ; sc:author "Jernej Kernc" ; sc:description "A network analysis extension for a data mining software Orange. Network add-on includes components for network generation, network analysis, clustering and access to SNAP network database. All features can be combined with powerful visualizations, bioinformatics tools and data mining techniques from the core Orange data mining framework." ; sc:featureList edam:operation_1781, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Orange Network" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-SI-hackathon", "Laboratory for Bioinformatics, University of Ljubljana" ; sc:softwareHelp ; sc:softwareVersion "1.1.2" ; sc:url "http://orange.biolab.si" ; biotools:primaryContact "Blaž Zupan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3303, edam:topic_3382 ; sc:citation , "pubmed:33513032" ; sc:description "A Real-Time, Open Platform for Knowledge-Based Quality Control of Radiotherapy Treatment Planning." ; sc:featureList edam:operation_2428 ; sc:name "ORBIT-RT" ; sc:url "https://www.orbit-rt.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation ; sc:description "An online genome annotation resource offering users the necessary tools and information to validate and correct gene annotation." ; sc:featureList edam:operation_0362 ; sc:name "ORCAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/orcae/" ; biotools:primaryContact "Yves Van de Peer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0199, edam:topic_2640, edam:topic_3474 ; sc:citation ; sc:description "Novel management, annotation, and machine learning framework for analyzing cancer mutations." ; sc:featureList edam:operation_0224, edam:operation_3197, edam:operation_3661 ; sc:name "Orchid" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/wittelab/orchid" ; biotools:primaryContact "John S Witte" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2332, edam:format_3464 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3345 ; sc:citation ; sc:description "ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized." ; sc:featureList edam:operation_2422 ; sc:name "Orcid API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://orcid.org/" ; biotools:primaryContact "Laurel L. HAAK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25536966" ; sc:description "ORCOM (Overlapping Reads COmpression with Minimizers) is a compressor of sequencing reads. 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It integrates a classification of rare diseases, relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ORDO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Inserm US14" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://www.ebi.ac.uk/ols/ontologies/ordo" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3318, edam:topic_3372, edam:topic_3382 ; sc:citation , "pubmed:34241315" ; sc:description "A Python package for data analysis with permutation entropy and ordinal network methods." ; sc:featureList edam:operation_0455 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ordpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/arthurpessa/ordpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0204, edam:topic_0749 ; sc:citation "pubmed:16397004", "pubmed:18006570" ; sc:description "Collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations." ; sc:featureList edam:operation_0438, edam:operation_0445 ; sc:name "ORegAnno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.oreganno.org/" ; biotools:primaryContact "S. J. M. Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_1775, edam:topic_3512 ; sc:citation "pubmed:18463135" ; sc:description "EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. 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The ORFhunteR package is a R and C++ library for an automatic identification and annotation of open reading frames (ORFs) in a large set of RNA molecules.""" ; sc:featureList edam:operation_0436, edam:operation_2995, edam:operation_3435 ; sc:license "Artistic-2.0" ; sc:name "ORFhunteR" ; sc:url "http://orfhunter.bsu.by" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3168, edam:topic_3170 ; sc:description "Tools for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CageSeq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for the whole genomes and many more." ; sc:featureList edam:operation_2928 ; sc:license "MIT" ; sc:name "ORFik" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ORFik.html" ; biotools:primaryContact "Kornel Labun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3170, edam:topic_3308, edam:topic_3316 ; sc:citation ; sc:description """A fast and flexible tool for extracting ORFs. orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. 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Please read the preprint here.""" ; sc:featureList edam:operation_0436, edam:operation_0524, edam:operation_2421, edam:operation_3258 ; sc:license "MIT" ; sc:name "orfipy" ; sc:url "https://anaconda.org/bioconda/orfipy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3512 ; sc:citation , "pubmed:33970232" ; sc:description "ORFLine is a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes." ; sc:featureList edam:operation_0416, edam:operation_0436, edam:operation_3192, edam:operation_3216 ; sc:name "ORFLine" ; sc:url "https://github.com/boboppie/ORFLine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation , "pmcid:PMC5013905", "pubmed:27153669" ; sc:description "A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences." ; sc:featureList edam:operation_0436 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "orfm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wwood/OrfM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "ORForise is a Prokaryote Genome Annotation Comparison and Analysis Platform." ; sc:featureList edam:operation_0362, edam:operation_0436, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "ORForise" ; sc:url "https://github.com/NickJD/ORForise" ; biotools:primaryContact "Nicholas J. Dimonaco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:15980561" ; sc:description "OrfPredictor is designed for prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences." ; sc:featureList edam:operation_0436, edam:operation_0489, edam:operation_0526 ; sc:name "OrfPredictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ysu.edu/tools/OrfPredictor.html" ; biotools:primaryContact "X. (Jack) Min" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32601440" ; sc:description """Quantification of translation uncovers the functions of the alternative transcriptome. An R package for Splice-aware quantification of translation using Ribo-seq data. ORFquant is an R package that aims at detecting and quantifiying ORF translation on complex transcriptomes using Ribo-seq data. This package uses syntax and functions present in Bioconductor packages like GenomicFeatures, rtracklayer or BSgenome. ORFquant aims at quantifying translation at the single ORF level taking into account the presence of multiple transcripts expressed by each gene. To do so, the ORFquant pipeline consists of transcript filtering, de-novo ORF finding, ORF quantification and ORF annotation. 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OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying. Data sources include proteomes from arthropods, fungi, vertebrates and basal metazoans." ; sc:featureList edam:operation_2414, edam:operation_3672 ; sc:name "OrthoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://www.orthodb.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1150 ; sc:name "Disease ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634 ; sc:citation ; sc:description "A database of disease gene orthologs." ; sc:featureList edam:operation_0224 ; sc:name "Orthodisease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://orthodisease.sbc.su.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0194, edam:topic_0621, edam:topic_0623 ; sc:citation , "pmcid:PMC8496211", "pubmed:34544141" ; sc:description "Orthofisher conducts automated and high-throughout identification of a predetermined set of orthologs, which can be used for phylgenomics, gene family copy number determination and more!" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "orthofisher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/JLSteenwyk/orthofisher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC5312442", "pubmed:28209129" ; sc:description "Applies reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data." ; sc:featureList edam:operation_0495, edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "Orthograph" ; sc:softwareHelp ; sc:url "https://mptrsen.github.io/Orthograph/" ; biotools:primaryContact "Malte Petersen", "Oliver Niehuis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:25273105" ; sc:description "Software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species." ; sc:featureList edam:operation_2423 ; sc:name "OrthoInspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lbgi.igbmc.fr/orthoinspector/" ; biotools:primaryContact "Odile Lecompte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293 ; sc:citation , "pmcid:PMC3531125", "pubmed:23203876" ; sc:description "Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. Also contains reciprocal best hit-based ortholog predictions, in-paralog predictions (recently duplicated genes) and proposed ortholog groups." ; sc:featureList edam:operation_0324, edam:operation_0327, edam:operation_0438 ; sc:name "OrtholugeDB" ; sc:softwareHelp , ; sc:url "http://www.pathogenomics.sfu.ca/ortholugedb/" ; biotools:primaryContact "Brinkman lab at Simon Fraser University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0623, edam:topic_3512 ; sc:citation "pubmed:19491309" ; sc:description "Web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0797, edam:topic_3053, edam:topic_3796 ; sc:citation , "pmcid:PMC4489293", "pubmed:25964301" ; sc:description "Web platform for comparison and annotation of orthologous gene clusters among multiple species." ; sc:featureList edam:operation_3731 ; sc:name "OrthoVenn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfogenome.net/OrthoVenn/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3343, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:34508259" ; sc:description "Orthrus is an R package for scoring combinatorial CRISPR screening data." ; sc:featureList edam:operation_3096, edam:operation_3219, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Orthrus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/csbio/Orthrus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0084, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:9614272" ; sc:description "BLAST a protein sequence then perform automated phylogenetic analysis to detect orthologous sequences." ; sc:featureList edam:operation_0499, edam:operation_0544, edam:operation_2479 ; sc:name "Orthologue Search Service" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dove.embl-heidelberg.de/Blast2e/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3168, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC8500227", "pubmed:34580179" ; sc:description "Prediction of microbial interactions in complex communities" ; sc:featureList edam:operation_0362, edam:operation_3432, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "OrtSuite" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mdsufz/OrtSuite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_3172, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description "A Fully-Automated Open-Source Software for Three-Dimensional Proton Magnetic Resonance Spectroscopic Imaging Data Analysis." ; sc:featureList edam:operation_1812, edam:operation_2429, edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Oryx-MRSI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/sevimcengiz/Oryx-MRSI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC1326027", "pubmed:16403737" ; sc:description "Integrated rice genetic map and mutant database at the National Institute of Genetics in Japan." ; sc:featureList edam:operation_0224, edam:operation_2422 ; sc:license "Not licensed" ; sc:name "Oryzabase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shigen.nig.ac.jp/rice/oryzabase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0780, edam:topic_2258, edam:topic_3071, edam:topic_3303 ; sc:citation , "pubmed:36512929" ; sc:description "An online structural and analytics based database for herbs of India." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "OSADHI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://neist.res.in/osadhi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3375, edam:topic_3518 ; sc:citation , "pmcid:PMC5197943", "pubmed:27669316" ; sc:contributor ; sc:description "OSAnalyzer is a software tool able to compute the overall survival (OS) and progression-free survival (PFS) of cancer patients and evaluate their association with ADME gene variants." ; sc:featureList edam:operation_3503 ; sc:license "Other" ; sc:name "OSAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/overallsurvivalanalyzer/" ; biotools:primaryContact "Giuseppe Agapito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3678 ; sc:citation ; sc:description "A sizable genomics study often involves the use of multiple batches. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. This tool is developed to facilitate the allocation of samples to different batches. It produces setup that optimizes the even distribution of samples in groups of biological interest into batches, reducing the confounding or correlation between batches and variables." ; sc:featureList edam:operation_2430 ; sc:license "Artistic-2.0" ; sc:name "OSAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OSAT.html" ; biotools:primaryContact "Li Yan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6932997", "pubmed:31921624" ; sc:description """A Web Server for Breast Cancer Prognostic Biomarker Investigation With Massive Data From Tens of Cohorts. Potential prognostic mRNA biomarkers are exploited to assist in the clinical management and treatment of breast cancer, which is the first life-threatening tumor in women worldwide. However, it is technically challenging for untrained researchers to process high dimensional profiling data to screen and validate the potential prognostic values of genes of interests in multiple cohorts. Our aim is to develop an easy-to-use web server to facilitate the screening, developing, and evaluating of prognostic biomarkers in breast cancers""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3503 ; sc:name "OSbrca" ; sc:url "http://bioinfo.henu.edu.cn/BRCA/BRCAList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3399, edam:topic_3518 ; sc:citation "pubmed:17545194" ; sc:description "Platform for cluster analysis of microarray data." ; sc:featureList edam:operation_0313, edam:operation_2495, edam:operation_3432 ; sc:name "OSCAR" ; sc:url "http://biocomp.bioen.uiuc.edu/oscar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC7445923", "pubmed:32838730" ; sc:description """Inferring oscillatory gene networks. Bootstrap-based OscoNet method: Method to infer sinusoidal oscillations in single cell data. This software reproduces the approach presented in 'OscoNet: inferring oscillatory gene networks' by Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu & Magnus Rattray.""" ; sc:featureList edam:operation_2238, edam:operation_2437, edam:operation_3432 ; sc:license "MIT" ; sc:name "OscoNet" ; sc:url "https://github.com/alexisboukouvalas/OscoNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_3170 ; sc:citation ; sc:description "Statistical pipeline developed to identify and recover the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. It includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group." ; sc:featureList edam:operation_2238, edam:operation_2495 ; sc:license "Artistic-2.0" ; sc:name "Oscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Oscope.html" ; biotools:primaryContact "Ning Leng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3749 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3314 ; sc:citation ; sc:description "Access to organic compound spectral data" ; sc:featureList edam:operation_2422 ; sc:name "OSDB API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://osdb.info" ; biotools:primaryContact "Stuart J. Chalk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3063, edam:topic_3360 ; sc:citation , "pmcid:PMC7067743", "pubmed:32211334" ; sc:description "Online consensus Survival analysis web server for Esophageal Adenocarcinoma (OSeac) is an online survival analysis tool for esophageal adenocarcinoma." ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "OSeac" ; sc:url "http://bioinfo.henu.edu.cn/EAC/EACList.jsp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC8965707", "pubmed:35371973" ; sc:description "A Web Portal to Assess the Performance of Prognostic Biomarkers in Gastric Cancer." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_3503 ; sc:isAccessibleForFree true ; sc:name "OSgc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.henu.edu.cn/GC/GCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3444 ; sc:citation ; sc:description "OsiriX is an image processing software dedicated to DICOM images (“.dcm” / “.DCM” extension) produced by imaging equipment (MRI, CT, PET, PET-CT, SPECT-CT, Ultrasounds, …). It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or imaging modality (C-STORE SCP/SCU, and Query/Retrieve : C-MOVE SCU/SCP, C-FIND SCU/SCP, C-GET SCU/SCP, WADO) ." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_3443 ; sc:name "OsiriX" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:softwareVersion "6.5.1" ; sc:url "http://www.osirix-viewer.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC7381343", "pubmed:32775301" ; sc:description """An Online Prognostic Biomarker Analysis Tool for Low-Grade Glioma. Glioma is the most frequent primary brain tumor that causes high mortality and morbidity with poor prognosis. There are four grades of gliomas, I to IV, among which grade II and III are low-grade glioma (LGG). Although less aggressive, LGG almost universally progresses to high-grade glioma and eventual causes death if lacking of intervention. Current LGG treatment mainly depends on surgical resection followed by radiotherapy and chemotherapy, but the survival rates of LGG patients are low. Therefore, it is necessary to use prognostic biomarkers to classify patients into subgroups with different risks and guide clinical managements. Using gene expression profiling and long-term follow-up data, we established an Online consensus Survival analysis tool for LGG named OSlgg. OSlgg is comprised of 720 LGG cases from two independent cohorts""" ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_3503 ; sc:name "OSlgg" ; sc:url "http://bioinfo.henu.edu.cn/LGG/LGGList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC7298068", "pubmed:32587519" ; sc:description """An Online Prognostic Biomarker Analysis Tool for Hepatocellular Carcinoma. Liver hepatocellular carcinoma (LIHC) is one of the most common malignant tumors in the world with an increasing number of fatalities. Identification of novel prognosis biomarker for LIHC may improve treatment and therefore patient outcomes. The availability of public gene expression profiling data offers the opportunity to discover prognosis biomarkers for LIHC. We developed an online consensus survival analysis tool named OSlihc using gene expression profiling and long-term follow-up data to identify new prognosis biomarkers. OSlihc consists of 637 cases from four independent cohorts. As a risk assessment tool, OSlihc generates the Kaplan-Meier survival plot with hazard ratio (HR) and p value to evaluate the prognostic value of a gene of interest""" ; sc:featureList edam:operation_2495, edam:operation_3503 ; sc:name "OSlihc" ; sc:url "http://bioinfo.henu.edu.cn/LIHC/LIHCList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:32386152" ; sc:description """Deep Small-Sample Classification with an Orthogonal Softmax Layer. Code release for OSLNet: Deep Small-Sample Classification with an Orthogonal Softmax Layer (TIP2020) DOI.""" ; sc:license "MIT" ; sc:name "OSLNet" ; sc:url "https://github.com/dongliangchang/OSLNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3063, edam:topic_3360 ; sc:citation , "pmcid:PMC7264384", "pubmed:32528519" ; sc:description """An Interactive Web Server to Evaluate Prognostic Biomarkers for Lung Cancer. Biomedical Informatics Institute. OSluca ( Online consensus Survival for Lung Cancer) encompasses 35 expression datasets, provides 4 types of survival terms for 5741 patients of lung cancer.""" ; sc:featureList edam:operation_2495, edam:operation_3503, edam:operation_3659 ; sc:name "OSluca" ; sc:url "http://bioinfo.henu.edu.cn/LUCA/LUCAList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3534 ; sc:citation "pubmed:25730499" ; sc:description "Query-driven dynamic machine learning model for predicting protein-ligand binding sites." ; sc:featureList edam:operation_2575 ; sc:name "OSML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn:8080/OSML/" ; biotools:primaryContact "Dong-Jun" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC8773055", "pubmed:35053021" ; sc:description "An Interactive Web Server to Evaluate Prognostic Biomarkers for Ovarian Cancer." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3503 ; sc:name "OSov" ; sc:url "https://bioinfo.henu.edu.cn/OV/OVList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3063, edam:topic_3360 ; sc:citation , "pubmed:31912599" ; sc:description "An online tool to perform survival analysis by integrating gene expression profiling and long-term follow-up data of 1319 pancreatic carcinoma patients." ; sc:featureList edam:operation_2495, edam:operation_3359, edam:operation_3503 ; sc:name "OSpaad" ; sc:url "http://bioinfo.henu.edu.cn/PAAD/PAADList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3421, edam:topic_3474 ; sc:citation ; sc:description "Machine learning to predict 5-year survival among pediatric Acute Myeloid Leukemia patients and development of OSPAM-C online survival prediction tool." ; sc:featureList edam:operation_3503, edam:operation_3659, edam:operation_3927 ; sc:name "OSPAM-C" ; sc:url "https://ashis-das.shinyapps.io/ospam/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2640, edam:topic_3308, edam:topic_3360 ; sc:citation , "pubmed:36587732" ; sc:description "A web server for online survival analysis using proteome of pan-cancers, including TCGA (The Cancer Genome Atlas) RPPAs (Reverse-Phase Protein Arrays) data and CPTAC (the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium) mass spectrometry data, and provides 5 types of survival terms for about 8,000 patients of 33 distinct malignancies." ; sc:featureList edam:operation_2940, edam:operation_3223, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:name "OSppc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.henu.edu.cn/Protein/OSppc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC9067362", "pubmed:35467964" ; sc:description "A Digital Health Aid for Rapid Predictive Analysis of Correlations Between Early End Points and Overall Survival in Non-Small-Cell Lung Cancer Clinical Trials." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "OSPred tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AstraZeneca/OSPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_2814 ; sc:citation "pubmed:24931991" ; sc:description "Suite of programs for computational structure-based protein design. It is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.)." ; sc:featureList edam:operation_2430 ; sc:name "OSPREY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cs.duke.edu/donaldlab/osprey.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0769, edam:topic_3172, edam:topic_3304, edam:topic_3444 ; sc:citation ; sc:description """Open-Source Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data. Osprey is an all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data. Download the latest Osprey code from its GitHub repository, then extract and add the entire folder (with subfolders) to your MATLAB path. Make sure to regularly check for updates, as we frequently commit new features, bug fixes, and improved functions.""" ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3799 ; sc:license "MIT" ; sc:name "Osprey-M" ; sc:url "https://github.com/schorschinho/osprey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_3318, edam:topic_3382 ; sc:citation "pubmed:12620107" ; sc:description "Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:name "The Osprey Network Visualization System" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://biodata.mshri.on.ca/osprey" ; biotools:primaryContact "Biogrid Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3277, edam:topic_3325, edam:topic_3678 ; sc:description "Online Sample Size Estimator (OSSE) provides a convenient way to estimate sample size for case-control association studies. The base values are set for the conventionally used significance level of 5% at 80% power, with minor allele frequencies of 15% and 7% in cases and controls, respectively. This estimates the necessary sample size in the setting of a pilot study, with unknown actual minor allele frequencies." ; sc:featureList edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "OSSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://osse.bii.a-star.edu.sg/index.php" ; biotools:primaryContact "Adrian Mondry", "Marie Loh", "Zhuo Shaowei (IT enquiries)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3063, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation , "pmcid:PMC7236197", "pubmed:32467670" ; sc:description "An online survival analysis webserver for skin cutaneous melanoma based on 1085 transcriptomic profiles." ; sc:featureList edam:operation_2495, edam:operation_3503, edam:operation_3659 ; sc:name "OSskcm" ; sc:url "http://bioinfo.henu.edu.cn/Melanoma/MelanomaList.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC9718079", "pubmed:36474475" ; sc:description "A web-based gene and non-coding RNA expression database." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3792, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "OsteoDIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ophid.utoronto.ca/OsteoDIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:author "WurmLab" ; sc:description "Provides quick and simple Docker based virtual environments on Macs and compute clusters alike for reproducible bioinformatics." ; sc:featureList edam:operation_3760 ; sc:isAccessibleForFree true ; sc:name "oswitch" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.2.6" ; sc:url "https://github.com/wurmlab/oswitch" ; biotools:primaryContact "Anurag Priyam", "Yannick Wurm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_2229, edam:topic_3295 ; sc:citation ; sc:description "Optimal Transport improves cell-cell similarity inference in single-cell omics data. This Jupyter Notebook will walk you trough the code to replicate the experiments from our research on applying Optimal Transport as a similarity metric in between single-cell omics data." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "OT-scOmics" ; sc:url "https://github.com/ComputationalSystemsBiology/OT-scOmics" ; biotools:primaryContact , "Geert-Jan Huizing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3053, edam:topic_3373 ; sc:citation , "pmcid:PMC10394122", "pubmed:37467069" ; sc:description "GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "otargen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://amirfeizi.github.io/otargen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2259 ; sc:author "OTP Development Team" ; sc:description "Automation platform for managing next generation sequencing (NGS) data. The application provides support in all steps of this process including data transfer from temporary to final storage, execution of data quality monitoring programs and alignment of reads to the reference genome using BWA based pipeline." ; sc:featureList edam:operation_0292, edam:operation_3218, edam:operation_3661 ; sc:name "One Touch Pipeline (OTP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EilsLabs", "German Cancer Research Center (DKFZ)", "hdhub" ; sc:softwareHelp ; sc:url "https://otp.dkfz.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3318, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC7556463", "pubmed:33052977" ; sc:description """Python package for the optical analysis of solar-thermal collectors and photovoltaic cells with arbitrary geometry. OTSun is a python package that uses the Monte Carlo Forward Ray Tracing for the optical analysis of Solar Thermal Collectors and Solar Cells.""" ; sc:featureList edam:operation_0399, edam:operation_3435, edam:operation_3928 ; sc:license "MIT" ; sc:name "OTSun" ; sc:softwareHelp ; sc:url "http://otsun.uib.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC9992663", "pubmed:36882394" ; sc:description "TWAS framework leveraging summary-level reference data." ; sc:featureList edam:operation_0244, edam:operation_3196, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OTTERS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/daiqile96/OTTERS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3336, edam:topic_3342, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC10516341", "pubmed:37594310" ; sc:description "Automated classification tool for translational drug discovery from omics data." ; sc:featureList edam:operation_0306, edam:operation_3223, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "OTTM" ; sc:url "http://otter-simm.com/ottm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3365 ; sc:citation ; sc:description "Provides a platform for Operational Taxonomic Unit based analysis." ; sc:featureList edam:operation_0337 ; sc:license "Artistic-2.0" ; sc:name "OTUbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OTUbase.html" ; biotools:primaryContact "Daniel Beck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "OTUreporter is a modular automated pipeline for the analysis and report of amplicon data." ; sc:name "OTUreporter" ; sc:softwareHelp , , , ; sc:url "https://bitbucket.org/xvazquezc/otureporter/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3746, edam:format_3751 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A set of tools to work with OTU tables (and feature tables) generated by amplicon sequencing experiments" ; sc:featureList edam:operation_0336 ; sc:name "otusfocus" ; sc:url "https://github.com/quadram-institute-bioscience/otusfocus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3385 ; sc:citation , "pmcid:PMC4752901", "pubmed:26538279" ; sc:description "Oufti is an open-source software package designed for analysis of microscopy data." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "Oufti" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.oufti.org/" ; biotools:primaryContact "Christine Jacobs-Wagner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3758 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Collects Sequest and TurboSequest *.out files to HTML for use with INTERACT." ; sc:featureList edam:operation_0335 ; sc:name "Out2Summary" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/out2summary.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3500 ; sc:citation , "pmcid:PMC8264965", "pubmed:34238385" ; sc:description "OUTBREAK facilitates surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak" ; sc:isAccessibleForFree true ; sc:name "outbreak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://outbreak.sysbio.tools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3305, edam:topic_3379 ; sc:citation , , "pmcid:PMC10399614", "pubmed:36823331", "pubmed:36823332" ; sc:description "A standardized, searchable platform to discover and explore COVID-19 resources. Scalable and dynamic surveillance of SARS-CoV-2 variants and mutations." ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_2421, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Outbreak.info" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://Outbreak.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3324 ; sc:citation ; sc:description "Phone application for rehydration calculator for diarrheal disease management in a resource-limited setting." ; sc:featureList edam:operation_2409, edam:operation_2423 ; sc:name "Outbreak Responder" ; sc:softwareHelp ; sc:url "https://play.google.com/store/apps/developer?id=Outbreak+Responder&hl=en" ; biotools:primaryContact "Eric Jorge Nelson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_3168 ; sc:citation ; sc:description "This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data." ; sc:featureList edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "OutlierD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/OutlierD.html" ; biotools:primaryContact "Sukwoo Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382 ; sc:citation , "pmcid:PMC5346729", "pubmed:27825131" ; sc:description "OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes." ; sc:featureList edam:operation_3443 ; sc:license "Other" ; sc:name "OutLyzer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/EtieM/outLyzer" ; biotools:primaryContact "Laurent Castéra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """A statistical method for detecting aberrantly expressed genes in RNA sequencing data. OUTRIDER is a tool to find aberrantly expressed genes in RNA-seq samples. The method is published in the AJHG and available through Bioconductor. We will use BiocManager to install the package and its dependencies. If you want to install the devel version of OUTRIDER, please install it with devtools from GitHub directly (see below).""" ; sc:featureList edam:operation_3196, edam:operation_3563, edam:operation_3695 ; sc:license "MIT" ; sc:name "OUTRIDER" ; sc:url "https://i12g-gagneurweb.in.tum.de/public/paper/OUTRIDER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC10089674", "pubmed:36945891" ; sc:description "Detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "OutSingle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/esalkovic/outsingle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_1775 ; sc:citation "pubmed:26272982" ; sc:description "Online variant filtering and prioritisation application. Ontology Variant Analysis Tool can filter your VCF files on a wide array of criteria. Remaining genes are prioritisated based on their functional and phenotypic profile similarity to a user supplied phenotype." ; sc:featureList edam:operation_3197 ; sc:name "OVA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dna2.leeds.ac.uk:8080/OVA/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:10738528" ; sc:description "Program to assess the overall Linkage Disequilibrium (LD) over several markers and assess the LD between groups of markers." ; sc:featureList edam:operation_0488 ; sc:name "Overall LD" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Population_Genetics" ; biotools:primaryContact "Hongyu Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3305 ; sc:citation , "pmcid:PMC7929412", "pubmed:33432321" ; sc:description """Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2. The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has created an unprecedented threat to public health. The pandemic has been sweeping the globe, impacting more than 200 countries, with more outbreaks still lurking on the horizon. To tide over COVID-19, the web portal OverCOVID is provided to share bioinformatics resources and information that may contribute to research advances. Various layers of interactions among the viruses and human hosts.""" ; sc:featureList edam:operation_0224, edam:operation_2421 ; sc:name "OverCOVID" ; sc:url "http://bis.zju.edu.cn/overcovid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077 ; sc:author "Sarah Djebali" ; sc:description "Program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set (basic mode, however more and more precise information can be retrieved)." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "overlap" ; sc:operatingSystem "Linux" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "3.1" ; sc:url "http://big.crg.cat/services/overlap" ; biotools:primaryContact "Sarah Djebali" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1742 ; sc:name "PDB residue number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2700 ; sc:name "CATH identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0736, edam:topic_3542 ; sc:citation , "pubmed:35674374" ; sc:description """OverProt creates an overview of secondary structure elements in protein families. For each protein family from the CATH database, a secondary structure consensus is available, showing the characteristic helices and β-sheets of the family. A consensus for an arbitrary subset of a family can be computed using User-defined queries.""" ; sc:featureList edam:operation_0468, edam:operation_0570, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "OverProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://overprot.ncbr.muni.cz/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:32838931" ; sc:description "OvirusTdb is a resource to explore the therapeutic potential of oncolytic viruses." ; sc:featureList edam:operation_2945 ; sc:name "ovirustdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ovirustdb/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0114, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC7319551", "pubmed:32392343" ; sc:description """A web-based platform for interactive cancer genomics data visualization. Powerful solution to data visualization. Platform for Cancer Genomics Data Visualization. Oviz is a component-based data visualization framework written in TypeScript that runs in browsers or NodeJS. In Oviz, you mainly describe the structure of a graph using its visualization language and write optional JavaScript or TypeScript code for complicated logic. Oviz is designed to be capable of visualizing anything.""" ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Oviz-Bio" ; sc:url "https://bio.oviz.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3520 ; sc:citation "pubmed:20198638" ; sc:description "Application designed to facilitate the analysis of data obtained by mass spectrometry in proteomic approaches. Indeed, it assists the experts in their analysis." ; sc:featureList edam:operation_2945 ; sc:name "OVNIp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwwappli.nantes.inra.fr:8180/OVNIp/" ; biotools:primaryContact "Dominique Tessier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25244564" ; sc:description "Ordered Subset – Variable Threshold – Pedigree Disequilibrium Test, a family-based association test using both common and rare variants and accounting for directions of effects for sequencing data." ; sc:featureList edam:operation_2478 ; sc:name "OVPDT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ovpdt/" ; biotools:primaryContact "Ren-Hua Chung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pubmed:34260700" ; sc:description "OWAS is an R implementation of a computational approach, Openness Weighted Association Studies(OWAS), which leverages and aggregates predictions of chromosome accessibility in personal genomes to prioritize GWAS signals." ; sc:featureList edam:operation_3196, edam:operation_3216, edam:operation_3226, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "OWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shuangsong0110/OWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0091, edam:topic_0160, edam:topic_3303 ; sc:citation , "pubmed:37301337" ; sc:description "A tool for identifying oxalate-binding domain(s)/motif(s) in protein(s)." ; sc:featureList edam:operation_0303, edam:operation_0477 ; sc:isAccessibleForFree true ; sc:name "OxaBIND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.stonemod.org/oxabind.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "OXBench includes data and software to evaluate the accuracy of protein multiple sequence alignments.  It is a benchmark suite for multiple alignment algorithms that includes a large set of test alignments and software to aid in analysis of a method’s performance or relative performance." ; sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "OXBench" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.compbio.dundee.ac.uk/software.html#msa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC2683861", "pubmed:19405962" ; sc:description "OxDBase: A Database of Biodegradative Oxygenases" ; sc:featureList edam:operation_2945 ; sc:name "oxdbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/oxdbase/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0176, edam:topic_0654, edam:topic_3306, edam:topic_3316 ; sc:citation , "pubmed:34009383" ; sc:description "oxDNA.org is a public webserver for coarse-grained simulations of DNA and RNA nanostructures. The goal is to facilitate development of more advanced and complex designs in the fields of DNA and RNA nanotechnology by facilitating non-experts to run simple simulations. This server uses oxDNA and oxRNA models to simulate DNA and RNA nanostructures to verify and prototype novel designs. The simulations this server supports are equilibrium sampling of assembled designs, meant to assist users to test in silico their designs before taking them to the lab. The server is provided for free for anyone." ; sc:featureList edam:operation_0244, edam:operation_0570, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "oxDNA.org" ; sc:url "http://OxDNA.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation "pubmed:18267306" ; sc:description "Predict the Oxygen Binding Proteins, Which is carrying Erythrocruorin, Hemoglobin, Myoglobin, Hemerithrin, Leghemoglobin and Hemocyanin." ; sc:featureList edam:operation_2995 ; sc:name "Oxypred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/oxypred/" ; biotools:primaryContact "Dr Gajendra P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3534 ; sc:citation "pubmed:25059323" ; sc:description "Tool for predicting the binding sites on pair of given proteins." ; sc:featureList edam:operation_2575 ; sc:name "P-Binder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/guofeics/p-binder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0621, edam:topic_0659, edam:topic_3174, edam:topic_3512 ; sc:citation , "pmcid:PMC7191817", "pubmed:32349659" ; sc:description """Genomic and metagenomic annotation of RNase P RNA gene (rnpB). P Finder is a GUI software application for the fast identification of RNase P RNA in prokaryotes.""" ; sc:featureList edam:operation_0362, edam:operation_0502, edam:operation_3469 ; sc:name "P-Finder" ; sc:url "https://github.com/JChristopherEllis/P-Finder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15980505" ; sc:description "Transcription factor binding site identification tool that increases its accuracy by combining weight matrix and pattern matching approaches. Registration at the site is free and is required." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575 ; sc:name "P-Match" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:26382195" ; sc:description "Web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants." ; sc:featureList edam:operation_3095 ; sc:name "P-SAMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://p-sams.carringtonlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation "pubmed:10820484" ; sc:description "Software of Peak quantification using Statistical Comparative ANalysis." ; sc:featureList edam:operation_3222, edam:operation_3799 ; sc:name "P-SCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://abs.cit.nih.gov/pscan/" ; biotools:primaryContact "L. Young", "P. J. Munson", "V. V. Prabhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3168, edam:topic_3337 ; sc:citation , "pmcid:PMC9245627", "pubmed:35785021" ; sc:description "P-smoother is an efficient method to correct recent mutations and genotyping errors in biobank-scale haplotype panels. Utilizing P-smoother to \"smooth\" a panel allows for downstream haplotype matching tasks to be error tolerant and more accurate. The input data for P-smoother is phased genotype data (in VCF format)." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "P-smoother" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/ZhiGroup/P-smoother" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3300, edam:topic_3304, edam:topic_3520 ; sc:citation ; sc:description "P-sort is an open-source, Python-based, cross-platform software with an intuitive GUI. It has been designed to address the challenges of cerebellar neurophysiology, specifically, sorting cerebellar Purkinje cells." ; sc:featureList edam:operation_3432, edam:operation_3802, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "P-sort" ; sc:url "https://github.com/esedaghatnejad/psort" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3577 ; sc:citation , "pubmed:32422654" ; sc:description """Disease characterization using a partial correlation-based sample-specific network. Construct the single-sample network based on partial correlation(P-SSN).""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3927 ; sc:name "P-SSN" ; sc:url "https://github.com/hyhRise/P-SSN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation ; sc:description "It is a free and new open source software that automatically recognizes, from numeric images, the structure of a panicle and the seeds on the panicle. The software processes and quantifies several traits related to the structures of the panicles, detects and counts the grains, and measures their shape parameters. It offers both efficient results and friendly environment for users to perform their experiments. Manual processing is not repeatable because dry panicles are vulnerable to damage." ; sc:featureList edam:operation_2409 ; sc:name "P-TRAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.mpl.ird.fr/index.php?option=com_content&view=article&id=102&Itemid=2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_0621, edam:topic_0623, edam:topic_3174 ; sc:citation "pubmed:21051349" ; sc:description "Database for prokaryotic two-component systems (TCSs). It annotates and classifies TCS proteins from completely sequenced prokaryotic genomes and metagenomes. TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users)." ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_0362, edam:operation_3432 ; sc:name "P2CS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.p2cs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_1317, edam:topic_2258, edam:topic_3510 ; sc:citation ; sc:description "Novel machine learning-based method for prediction of ligand binding sites from protein structure." ; sc:featureList edam:operation_2575 ; sc:license "MIT" ; sc:name "P2Rank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://siret.ms.mff.cuni.cz/p2rank" ; biotools:primaryContact "David Hoksza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0621, edam:topic_0749 ; sc:citation , "pmcid:PMC3637814", "pubmed:23601859" ; sc:description "Web server which provide a platform for regulatory protein (RP) prediction. The program can perform several types of analyses depending on the type of request, and provide detailed annotation of each RP gene including classification, sequence features, as well as functional domains. Data can be outputted for download in a variety of specified formats." ; sc:featureList edam:operation_0438 ; sc:name "Predicted Prokaryotic Regulatory Proteins (P2RP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.p2rp.org/index.php?PHPSESSID=a025bb831c57e0ec4c48933ac0685725" ; biotools:primaryContact "P2RP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885 ; sc:description "P2S is a small utility program to convert formats from plink to sumstat and vice versa.The plink program uses the LINKAGE input format, which is a widely used format in genetic linkage and association analysis. The sumstat suite of programs has been developed using a different input format. Specifically, it lists each SNP on a separate input line (row) rather than an input column." ; sc:featureList edam:operation_0335, edam:operation_2945 ; sc:name "P2S" ; sc:operatingSystem "Windows" ; sc:softwareVersion "20150226" ; sc:url "http://www.jurgott.org/linkage/p2s.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0121, edam:topic_0154 ; sc:citation , "pmcid:PMC5570244", "pubmed:28482090" ; sc:description "Peptidomes for Phylogenies. Bacterial strain classification based on peptide datasets." ; sc:featureList edam:operation_0323, edam:operation_2929 ; sc:name "P4P" ; sc:softwareHelp , ; sc:url "http://sing-group.org/p4p" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "P53 mutation browser." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "p53" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:url "http://persson-group.scilifelab.se/p53/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_2229, edam:topic_2640 ; sc:citation "pubmed:26986515" ; sc:description "First online tool for statistical validation of hypotheses regarding the effect of p53 mutational status on gene regulation in cancer." ; sc:featureList edam:operation_2428 ; sc:name "p53MutaGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.chemoprofiling.org/cgi-bin/GEO/tp53/web_run_tp53.V1.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0654, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC7038560", "pubmed:32093759" ; sc:description """Identification of DNA N6-methyladenine sites by integration of sequence features. p6mA is a N^6-methyladenine predictor which is trained by multiple species' data. There are 6 built-in models and you can choose a proper one. If your data is some species not included in the 4 species (O. sativa, C. elegans, D. melanogaster and H. sapiens), you can choose the Compre or Compre2 model. Compre model is trained by comprehensive samples without redunction of dedundancy and Compre2 model is trained by non-redundant comprehensive dataset.""" ; sc:featureList edam:operation_0417, edam:operation_0432, edam:operation_3936 ; sc:name "p6mA" ; sc:url "https://github.com/Konglab404/p6mA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "A database of paralogs and single copy genes in Arabidopsis thaliana. Database of single copy and duplicated genes in the Arabidopsis genome. It is a collection that integrates comparative results at genomic level to identify any form of gene duplication in the genome. It makes accessible single genes with specific classifications." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "pATsi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cab.unina.it/athparalog/main2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:31364357" ; sc:description "An Algorithm To Preprocess High-Resolution Tandem Mass Spectra for Database Searching | pClean: a tool for MS/MS spectrum preprocessing | pClean is a powerful tool to preprocess high-resolution tandem mass spectra prior to database searching, and aimed at filtering out extraneous peaks with/without specific-feature, which integrated three modules, removal of label-associated ions, isotope peak reduction and charge deconvolution, and a graph-based network approach. pClean is supportive to a wide array of instruments with all types of MS data, and incorporative into most data analysis pipelines" ; sc:featureList edam:operation_3627, edam:operation_3629, edam:operation_3646 ; sc:name "pClean" ; sc:url "https://github.com/AimeeD90/pClean_release" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC6667459", "pubmed:31363125" ; sc:description "A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides." ; sc:featureList edam:operation_2929, edam:operation_3649 ; sc:name "pLink" ; sc:url "http://pfind.ict.ac.cn/software/pLink/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3399, edam:topic_3474 ; sc:citation , "pubmed:30569871" ; sc:description "Predict Subcellular Localization of Eukaryotic Proteins by General PseAAC and Quasi-balancing Training Dataset." ; sc:featureList edam:operation_2489, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "pLoc_bal-mEuk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/pLoc_bal-mEuk/" ; biotools:primaryContact "Xuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3673 ; sc:citation , "pmcid:PMC6612832", "pubmed:31510687" ; sc:description "pNovo 3 is a precise de novo peptide sequencing using a learning-to-rank framework." ; sc:featureList edam:operation_3202, edam:operation_3644, edam:operation_3646 ; sc:name "pNovo 3" ; sc:url "http://pfind.ict.ac.cn/software/pNovo/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3416, edam:topic_3452 ; sc:citation , "pubmed:31848038" ; sc:description "pQCT is a tool for identifying and assessing Inter-Muscular Fat at the Distal Diaphyseal Femur Measured by Peripheral Quantitative Computed Tomography (pQCT)." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:license "BSD-2-Clause" ; sc:name "pQCT" ; sc:url "https://github.com/tjrantal/pQCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC6385978", "pubmed:30573468" ; sc:description "polyploid Sequence Based Virtual Breeding (pSBVB) - versatile simulation tool to evaluate genomic selection in polyploid species." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "pSBVB" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lauzingaretti/pSBVB" ; biotools:primaryContact "Laura Zingaretti", "M Pérez-Enciso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2269 ; sc:citation , "pubmed:31086978" ; sc:description "R package for computing probabilistic distances between species tree models under the multispecies coalscent." ; sc:featureList edam:operation_0544, edam:operation_0555, edam:operation_0557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "pSTDistanceR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/radamsRHA/pSTDistanceR/" ; biotools:primaryContact "Todd A. Castoe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3306, edam:topic_3314, edam:topic_3316, edam:topic_3892 ; sc:citation ; sc:description """a high-performance simulator for intracellular reaction-diffusion systems. a lattice-based particle simulator. Lattice-based stochastic particle simulator. Spatiocyte — A lattice-based particle simulator. Simulate with mass action, Gillespie Next-Reaction and lattice-based particle diffusion and reaction algorithms simultaneously. Three-dimensional diffusion and reaction in a cubic volume. Parallel version of Spatiocyte (pSpatiocyte): Github""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3891 ; sc:name "pSpatiocyte" ; sc:url "https://spatiocyte.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_3168 ; sc:citation , "pmcid:PMC6511130", "pubmed:31077131" ; sc:description "Tool to trim primers of multiplex deep sequencing data." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pTrimmer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DMU-lilab/pTrimmer" ; biotools:primaryContact "Jun Chen", "Zhiguang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3360, edam:topic_3676 ; sc:citation , "pmcid:PMC6822339", "pubmed:31666118" ; sc:description """prioritizing tumor neoantigens from next-generation sequencing data. pTuneos: prioritizing Tumor neoantigen from next-generation sequencing data. pTuneos is the state-of-the-art computational pipeline for identifying personalized tumor neoantigens from next-generation sequencing data. With raw whole-exome sequencing data and/or RNA-seq data, pTuneos calculates five important immunogenicity features to construct a machine learning-based classifier (Pre&RecNeo) to predict and prioritize neoantigens recognized by T cell, followed by an efficient score scheme (RefinedNeo) to ealuate naturally processed, MHC presented and T cell recognized probability of a predicted neoepitope""" ; sc:featureList edam:operation_0252, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "pTuneos" ; sc:url "https://github.com/bm2-lab/pTuneos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:31397839" ; sc:description "> HOMEPAGE MISSING! | > CORRECT NAME OF TOOL COULD ALSO BE 'omicssimla' | a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions | MOTIVATION:DNA methylation plays an important role in regulating gene expression. DNA methylation is commonly analyzed using bisulfite sequencing (BS-seq)-based designs, such as whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and oxidative bisulfite sequencing (oxBS-seq). Furthermore, there has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e., methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i.e., allele-specific methylation or ASM), and the differentially methylated regions (DMRs) among different cell types" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3207 ; sc:name "pWGBSSimla" ; sc:url "https://omicssimla.sourceforge.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3474, edam:topic_3500 ; sc:citation "pubmed:14990451", "pubmed:15215412" ; sc:description "This tool can be used to predict the subcellular localization of proteins using established machine learning techniques." ; sc:featureList edam:operation_0267, edam:operation_1777, edam:operation_2489, edam:operation_3092 ; sc:name "PA-SUB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.ualberta.ca/~bioinfo/PA/Sub/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:name "Raw microarray data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_3475 ; sc:name "Text" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_3475 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3591, edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3360, edam:topic_3518 ; sc:author ; sc:citation , "pmcid:PMC4866526", "pubmed:26803161" ; sc:contributor "Martin Eisenacher" ; sc:description "It imports single color (protein) microarray data that has been saved in gpr file format. After preprocessing univariate feature preselection is performed. Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Thereto, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. It provides a complete toolbox of analysis tools including several different plots for results examination and evaluation." ; sc:featureList edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PAA - Protein Array Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioInfra.Prot", "Ruhr-Universitaet Bochum, Medizinisches Proteom-Center (MPC)", "This work is supported by de.NBI, a project of the BMBF [FKZ 031 A 534A].", "This work was supported by P.U.R.E., a project of Nordrhein-Westfalen, a federal state of Germany." ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://bioconductor.org/packages/PAA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allows you to predict the residue-residue contact in proteins from its amino acid sequence." ; sc:featureList edam:operation_2945 ; sc:name "paaint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/paaint/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3299, edam:topic_3382 ; sc:citation , "pubmed:32845497" ; sc:description """Addressing Pitfalls in Phase-Amplitude Coupling Analysis with an Extended Modulation Index Toolbox. - direct PAC estimate - calculates the direct PAC estimate (Ozkurt and Schnitzler 2011) for a given data and saves the results in the localization indicated by the user. The results consists of images summarizing the analysis, MAT structure containing the results and MAT structure containing the configuration parameters. It requires several parameters as an input - check documentation for details (pop_dPAC_calc.m).""" ; sc:featureList edam:operation_3435, edam:operation_3454 ; sc:name "PAC" ; sc:url "https://github.com/GabrielaJurkiewicz/ePAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_2885, edam:topic_3170 ; sc:citation , "pmcid:PMC10311332", "pubmed:37387170" ; sc:description "Scalable sequence database search using partitioned aggregated Bloom comb trees." ; sc:featureList edam:operation_0524, edam:operation_2421, edam:operation_3211, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Malfoy/PAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description """PACAS is a tool for pairwise comparisons of aligned subsequences. PACAS consists of three files: Pacas.py, Pacas_FB.pl, and Pacas_CP.pl. In the current version, these all need to present in the same directory as the data files. The input files consist of a fasta file that contains the accession numbers for protein sequences, and the sequences themselves. The sequences need to be properly aligned, on a single line, and of equal length. It also requires an *.out file identically named to the *.fasta file, which indicates the low complexity regions of interest. These can be created as the output of programs such as seg, or manually.""" ; sc:featureList edam:operation_0259, edam:operation_0491, edam:operation_0492 ; sc:name "PACAS" ; sc:url "https://github.com/BlabOaklandU/PACAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "Python scripts for Exploratory Data Analysis of Pacific Biosciences sequence data" ; sc:featureList edam:operation_0495, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "PacBioEDA" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/TomSkelly/PacBioEDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2640, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7319576", "pubmed:32402082" ; sc:description "A web service for interpretable anticancer compound sensitivity prediction." ; sc:featureList edam:operation_0337, edam:operation_3927, edam:operation_3938 ; sc:name "PaccMann" ; sc:url "https://ibm.biz/paccmann-aas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_2275 ; sc:citation , "pmcid:PMC9610523", "pubmed:36296477" ; sc:description "A Web Server for Positional Distance-Based and Interaction-Based Analysis of Docking Results." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_3432, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PacDOCK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pegasus.lbic.unibo.it/pacdock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3170, edam:topic_3174, edam:topic_3324 ; sc:citation ; sc:description """A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting viral sequences.""" ; sc:featureList edam:operation_0308, edam:operation_0363, edam:operation_2409 ; sc:license "MIT" ; sc:name "PACIFIC" ; sc:url "https://github.com/pacific-2020/pacific" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176 ; sc:citation , "pmcid:PMC6084522", "pubmed:30055754" ; sc:description "A bioinformatic tool that performs a topographic analysis of lipid bilayer surfaces from various molecular dynamics simulations." ; sc:featureList edam:operation_2476 ; sc:license "Unlicense" ; sc:name "PackMem" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://packmem.ipmc.cnrs.fr/index.html" ; biotools:primaryContact "Romain Gautier" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2305 ; sc:name "Nucleic acid report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3508, edam:format_3603 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Generates publication quality images of methylated motifs counts, locations and non-methylated locations, on one or both strands of the DNA. The user can apply several filters on the gff data to avoid bad quality modifications or low coverage, for example. The optional filters are the IPDratio, the coverage and the identification quality value (idqv). This web page requires upload of a bacterial full or draft genome, together with the motifs.gff file of a PacBio sequencing analysis." ; sc:featureList edam:operation_0337 ; sc:name "PACMAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareVersion "1" ; sc:url "http://www.unifr.ch/bugfri/pacman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC8633639", "pubmed:34524450" ; sc:description "Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning." ; sc:featureList edam:operation_3625 ; sc:isAccessibleForFree true ; sc:name "PACNN+RL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://112.74.48.115:9000/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830 ; sc:citation "pubmed:21666259" ; sc:description "PAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes." ; sc:featureList edam:operation_0252, edam:operation_0487, edam:operation_3767 ; sc:name "PAComplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://PAcomplex.life.nctu.edu.tw" ; biotools:primaryContact "Jinn-Moon Yang", "Yu-Shu Lo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0199 ; sc:citation , "pubmed:35311953" ; sc:description "A program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment." ; sc:featureList edam:operation_0292, edam:operation_3198, edam:operation_3200, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PacRAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dunhamlab/PacRAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_2814, edam:topic_3489 ; sc:citation "pubmed:22903636" ; sc:description "Relational database management system that integrates information from the Protein Database Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database." ; sc:featureList edam:operation_0339 ; sc:name "PACSY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pacsy.nmrfam.wisc.edu/" ; biotools:primaryContact "Woonghee Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_0769, edam:topic_2640, edam:topic_3316 ; sc:citation , "pmcid:PMC10415172", "pubmed:37549060" ; sc:description "Pipeline for analysis of circulating tumor DNA." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ChrisMaherLab/PACT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC7245912", "pubmed:32448146" ; sc:description """plastome assembly coverage visualization in R. 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By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates." ; sc:featureList edam:operation_0264, edam:operation_0487, edam:operation_0488, edam:operation_3196, edam:operation_3436 ; sc:license "MIT" ; sc:name "PAIRADISE" ; sc:url "https://github.com/Xinglab/PAIRADISE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation ; sc:description "Pairagon is a pair-HMM based cDNA-to-genome alignment program." ; sc:featureList edam:operation_3182 ; sc:name "Pairagon" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.1" ; sc:url "http://mblab.wustl.edu/software.html#pairagonLink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "The Paircoil2 program predicts coiled-coil domains in protein sequences by using pairwise residue correlations obtained from a coiled-coil database. The original Paircoil program is still available for use." ; sc:featureList edam:operation_2479 ; sc:name "Paircoil2" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://groups.csail.mit.edu/cb/paircoil2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3678 ; sc:citation ; sc:description "This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "paircompviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/paircompviz.html" ; biotools:primaryContact "Michal Burda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """Gaussian process modeling of longitudinal data from paired multi-condition studies. PairGP, a non-stationary Gaussian process method to compare gene expression timeseries across several conditions that can account for paired longitudinal study designs and can identify groups of conditions that have different gene expression dynamics.""" ; sc:featureList edam:operation_2426, edam:operation_3565, edam:operation_3800 ; sc:name "PairGP" ; sc:url "https://github.com/michelevantini/PairGP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_2269, edam:topic_3365 ; sc:citation "pubmed:24016862" ; sc:description "Tool to compare two heatmaps and discover patterns within and across groups." ; sc:featureList edam:operation_0531 ; sc:name "pairheatmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/pairheatmap/index.html" ; biotools:primaryContact "Xiaoyong Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:34978573" ; sc:description "1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates" ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pairix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/4dn-dcic/pairix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2814 ; sc:citation "pubmed:24243399" ; sc:description "Partner specific protein-protein interaction site predictor that can make accurate predictions of whether a pair of residues from two different proteins interact or not." ; sc:featureList edam:operation_2464 ; sc:name "PAIRPred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://combi.cs.colostate.edu/supplements/pairpred/" ; biotools:primaryContact "Asa Ben-Hur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation , "pubmed:34978573" ; sc:description "A file format and a tool for efficient storage and retrieval for Hi-C read pairs." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pairs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/4dn-dcic/pairsqc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description """Fast reconstruction of cancer evolutionary history using pairwise mutation relationships. Pairtree infers the phylogeny underlying a cancer using genomic mutation data. Pairtree is particularly suited to settings with multiple tissue samples from each cancer, providing separate estimates of subclone frequency from each sample that constrain the set of consistent phylogenies.""" ; sc:featureList edam:operation_0337, edam:operation_3454, edam:operation_3557 ; sc:name "Pairtree" ; sc:url "https://www.github.com/morrislab/pairtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "PairwiseStatSig estimates the pairwise statistical significance of a pairwise local alignment of two protein sequences independent of any database using censored Maximum Likelihood Fitting." ; sc:featureList edam:operation_0495, edam:operation_2479 ; sc:name "PairwiseStatSig" ; sc:operatingSystem "Linux" ; sc:softwareVersion "20110801" ; sc:url "http://brendelgroup.org/bioinformatics2go/PairwiseStatSig.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:35831615" ; sc:description "Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq." ; sc:featureList edam:operation_0428, edam:operation_3192, edam:operation_3200 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PAIso-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Lulab-IGDB/PAIso-seq_scripts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3322 ; sc:citation , "pmcid:PMC7120348", "pubmed:32224838" ; sc:description """prediction of avian influenza virus subtype. In order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end-users.""" ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3219, edam:operation_3227 ; sc:name "PAIVS" ; sc:url "http://ircgp.com/paivs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:18549303" ; sc:description "Implementation of an efficient algorithm to compute an optimal structural alignment of an RNA sequence against a genomic substring." ; sc:featureList edam:operation_2423 ; sc:name "PAL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/PAL/" ; biotools:primaryContact "Shaojie Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0203, edam:topic_0654, edam:topic_3512 ; sc:citation "pubmed:16845082" ; sc:description "PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0550, edam:operation_2479 ; sc:name "PAL2NAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bork.embl.de/pal2nal/" ; biotools:primaryContact "Mikita Suyama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_3174 ; sc:citation ; sc:description "Protein alignment for functional profiling whole metagenome shotgun data." ; sc:featureList edam:operation_0292 ; sc:name "PALADIN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/twestbrookunh/paladin" ; biotools:primaryContact "Anthony Westbrook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3407 ; sc:citation "pubmed:19507283" ; sc:description "Software of alignment of metabolic pathways without abstraction." ; sc:featureList edam:operation_0334, edam:operation_2497, edam:operation_3478 ; sc:name "palAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.cise.ufl.edu/palAlign.html" ; biotools:primaryContact "Tamer Kahveci" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:citation "pubmed:26677963" ; sc:description "Java program that supports both online palindrome pattern matching and online multiple palindrome pattern matching." ; sc:featureList edam:operation_0292 ; sc:name "PalCheck" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://toc.yonsei.ac.kr/OMPPM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3673 ; sc:citation "pubmed:24722405" ; sc:description "User-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling." ; sc:featureList edam:operation_0484, edam:operation_2478, edam:operation_3192 ; sc:name "PALEOMIX" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://geogenetics.ku.dk/publications/paleomix" ; biotools:primaryContact "Ludovic Orlando", "Mikkel Schubert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0081 ; sc:citation "pubmed:18388951" ; sc:description "Software for analysis of residual dipolar couplings. Its main component is the Prediction of ALignmEnt from Structure simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute’s (protein/nucleic acid/oligosaccharide) three-dimensional shape." ; sc:featureList edam:operation_2423 ; sc:name "PALES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_pales.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_3174, edam:topic_3175, edam:topic_3697 ; sc:citation , "pmcid:PMC10132078", "pubmed:36897935" ; sc:description "Palindromic Detection of Insertion Sequences. The tool is based upon identifying inverted terminal repeats (ITRs) using paired-end, short-read metagenomic data/mixed microbial genomes." ; sc:featureList edam:operation_0224, edam:operation_0427, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PaliDIS4" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/blue-moon22/palidis4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:25273103" ; sc:description "Predicts RNA secondary structures for fixed RNA multiple sequence alignments, with special attention for pseudoknotted structures." ; sc:featureList edam:operation_0278 ; sc:name "pAliKiss" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bibiserv2.cebitec.uni-bielefeld.de/palikiss" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find inverted repeats in nucleotide sequence(s)." ; sc:featureList edam:operation_0278, edam:operation_0379 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "palindrome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/palindrome.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """Penalized mAximum LikeLihood and pArticle Swarms for Inference of Gene Regulatory Networks from Time Series Data. A Python package for inference of gene regulatory networks from noisy gene expression data.""" ; sc:featureList edam:operation_1781, edam:operation_3435, edam:operation_3925 ; sc:name "PALLAS" ; sc:url "https://github.com/yukuntan92/PALLAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3512, edam:topic_3517 ; sc:citation , "pmcid:PMC9950853", "pubmed:36744920" ; sc:description "A powerful and adaptive latent model for prioritizing risk variants with functional annotations." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3659, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PALM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YangLabHKUST/PALM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:17537755" ; sc:description "A novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, this algorithm tunes the parameters of the model such that true alignments score higher than other alignments." ; sc:featureList edam:operation_0292 ; sc:name "PALMA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.fml.tuebingen.mpg.de/raetsch/suppl/palma" ; biotools:primaryContact "Uta Schulze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:21154708" ; sc:description "A tool for aligning RNA-Seq reads. It is designed to compute both unspliced and spliced alignments." ; sc:featureList edam:operation_0292, edam:operation_2238, edam:operation_3198, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "PALMapper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper" ; biotools:primaryContact "Andre Kahles", "Gunnar Rätsch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_2259, edam:topic_2640, edam:topic_3407 ; sc:citation , "pmcid:PMC7532116", "pubmed:33008309" ; sc:description """Improving pathway annotation based on the biomedical literature mining with a constrained latent block model. PALMER: A Constrained Biclustering Algorithm to Improve Pathway Annotation Based on the Biomedical Literature Mining.""" ; sc:featureList edam:operation_0306, edam:operation_3432, edam:operation_3778, edam:operation_3928 ; sc:name "PALMER" ; sc:url "https://dongjunchung.github.io/palmer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10041512", "pubmed:36973282" ; sc:description "A comprehensive platform for analyzing longitudinal multi-omics data." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3223, edam:operation_3436, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PALMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/aifimmunology/PALMO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC7766988", "pubmed:33352643" ; sc:description "Platform for Analysis and Labeling of Medical Time Series." ; sc:featureList edam:operation_3215, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "PALMS" ; sc:url "https://github.com/PALMS-gui/PALMS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3382 ; sc:citation "pubmed:25362091" ; sc:description "Platform designed for the visualization and analysis of single-molecule localization microscopy data. It includes interactive browsing, filtering and analysis, plus the ability to extend its functionality through plugins." ; sc:featureList edam:operation_3443 ; sc:name "PALMsiever" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PALMsiever/palm-siever/wiki" ; biotools:primaryContact "Thomas Pengo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9272793", "pubmed:35642896" ; sc:description "Spatially-aware color palette optimization for single-cell and spatial data." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Palo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Winnie09/Palo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0623, edam:topic_0634, edam:topic_2640, edam:topic_3407 ; sc:citation "pubmed:18467422" ; sc:description "The tool highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome." ; sc:featureList edam:operation_0533, edam:operation_2497, edam:operation_3501, edam:operation_3672, edam:operation_3695 ; sc:name "PaLS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pals.bioinfo.cnio.es" ; biotools:primaryContact "A. Alibés" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pmcid:PMC7916825", "pubmed:33670102" ; sc:description "PALS (Pathway Activity Level Scoring) is a complete tool that performs database queries of pathways, decomposes activity levels in pathways via the PLAGE method, as well as presents the results in a user-friendly manner. The results are found to be more robust to noise and missing peaks compared to the alternatives (ORA, GSEA). This is particularly important for metabolomics peak data, where noise and missing peaks are prevalent." ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3929 ; sc:license "MIT" ; sc:name "PALS" ; sc:url "https://pals.glasgowcompbio.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0780, edam:topic_3172, edam:topic_3407 ; sc:citation ; sc:description """Decomposing metabolite set activity levels with PALS. Pathway analysis is an important task in understanding complex metabolomic data. Here we introduce PALS (Pathway Activity Level Scoring), a complete tool that performs database queries of pathways, decomposes activity levels in pathways via the PLAGE method, as well as presents the results in a user-friendly manner. The results are found to be more robust to noise and missing peaks compared to the alternatives (ORA, GSEA). This is particularly important for metabolomics peak data, where noise and missing peaks are prevalent.""" ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3803, edam:operation_3929 ; sc:name "PALS-V" ; sc:url "https://pals.glasgowcompbio.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "Predictive Assignment of Linear Secondary Structure Elements is a software that delineates secondary structure elements from protein Cα coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and β-strand, typically those that can be well approximated by vectors." ; sc:featureList edam:operation_2479 ; sc:name "PALSSE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20090521" ; sc:url "http://prodata.swmed.edu/palsse/palsse.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3303, edam:topic_3379, edam:topic_3676 ; sc:citation , "pmcid:PMC6596890", "pubmed:30445488" ; sc:description """Fast model-based optimization of treatment/case-control matches. 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This includes functions for importing and visualising any or all of these sensor data, formatting the data for analysis (with some functions already setup for birds), deriving classifications (using cluster analysis or hidden markove models), and finally for comparing classification accuracy between different models." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "pamlr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kiranlda.github.io/PAMLrManual/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2229, edam:topic_3308, edam:topic_3315, edam:topic_3940 ; sc:citation ; sc:description "Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona." ; sc:featureList edam:operation_0496, edam:operation_3435, edam:operation_3891 ; sc:license "MIT" ; sc:name "Pamona" ; sc:url "https://github.com/caokai1073/Pamona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3050 ; sc:description "PAMPA tool suite for biodiversity" ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:name "PAMPA" ; sc:url "https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game." ; sc:featureList edam:operation_3436 ; sc:name "Pan-Tetris" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9" ; sc:url "http://it.inf.uni-tuebingen.de/?page_id=920" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3321 ; sc:citation ; sc:description "Computational Tool to Improve the Accuracy of Pan-Genomic Analysis Using Draft Genomes." ; sc:featureList edam:operation_2403 ; sc:license "CC-BY-4.0" ; sc:name "Pan4Draft" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.computationalbiology.ufpa.br/pan4drafts" ; biotools:primaryContact "Rommel Ramos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3053 ; sc:citation , "pmcid:PMC6020400", "pubmed:29945570" ; sc:description "Suite of PERL scripts that allows for visualization of prokaryotic pan-chromosomes, including core and variable regions." ; sc:featureList edam:operation_0564 ; sc:license "GPL-2.0" ; sc:name "PanACEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/JCVenterInstitute/PanACEA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654 ; sc:citation ; sc:description "Panache (Pangenome analyzer with chromosomal exploration) is a web-based interface designed for the visualization of linearized pangenomes. 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Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0114, edam:topic_0610, edam:topic_0621 ; sc:citation ; sc:description "Panakeia is a python-based tool for prokaryotic pangenome analysis. Panakeia uses graph-based representations of the input genomes to build a complete pangenome graph. It then utilises graph algorithms on this pangenome graph to detect shared patterns of insertions, deletions, rearrangement and variants between groups of genomes in the pangenome. 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Koche" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3173, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC9701218", "pubmed:36435816" ; sc:description "PandaOmics provides a unique opportunity to both explore the unknown of OMICs data and interpret it in the context of all the scientific data generated by the scientific community." ; sc:featureList edam:operation_0337, edam:operation_3216, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "PandaOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://insilico.com/pandaomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC3669401", "pubmed:23741402" ; sc:description "Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources." ; sc:featureList edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "pandaR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pandaR.html" ; biotools:primaryContact "Dan Schlauch", "Joseph N. Paulson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "Pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language." ; sc:featureList edam:operation_2409, edam:operation_3438 ; sc:license "BSD-3-Clause" ; sc:name "Pandas" ; sc:softwareHelp , ; sc:softwareVersion "1.5.3" ; sc:url "https://pandas.pydata.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3174 ; sc:citation ; sc:description "Paired-end Assembler for DNA sequences (PANDAseq) is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence." ; sc:featureList edam:operation_0232, edam:operation_0310, edam:operation_3237, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "PANDAseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/neufeld/pandaseq" ; biotools:primaryContact "Josh D Neufeld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2640, edam:topic_3315, edam:topic_3517 ; sc:citation , "pmcid:PMC10161511", "pubmed:37142970" ; sc:description "Python package for easy retrieval of GWAS catalog data." ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_2422, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pandasGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://caotianze.github.io/pandasgwas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3299, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC9029369", "pubmed:35457649" ; sc:description "Monitoring the COVID-19 Pandemic in Catalonia, Spain." ; sc:featureList edam:operation_2429, edam:operation_2940, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PandemonCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.udg.edu/pandemoncat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC7579968", "pubmed:33087120" ; sc:description """Pan-cancer analysis of differential DNA methylation patterns. Pan-cancer differential methylation (DM) analysis investigates aberrant DNA methylation patterns in multiple distinct cancer types. PanDM is a statistical model for such comprehensive study. By jointly modeling DNA methylation profiles from various cancer types, PanDM is able to learn the pan-cancer commonalities and differences of DM patterns. PanDM works on the summary statistics from the individual DM analyses for each cancer type. Thus, it can be easily integrated with existing DM calling methods. Furthermore, the same framework can also be applied to pan-cancer analyses of other functional genomic profiles, such as transcriptomes.""" ; sc:featureList edam:operation_3204, edam:operation_3432, edam:operation_3435 ; sc:name "PanDM" ; sc:url "http://www.sta.cuhk.edu.hk/YWei/PanDM.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0623, edam:topic_3520 ; sc:citation "pubmed:20444873" ; sc:description "The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides." ; sc:featureList edam:operation_2403, edam:operation_2406, edam:operation_3224, edam:operation_3501, edam:operation_3741 ; sc:name "PANDORA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pandora.cs.huji.ac.il" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0804, edam:topic_2275, edam:topic_3966 ; sc:citation , "pmcid:PMC9127323", "pubmed:35619705" ; sc:description "A Fast, Anchor-Restrained Modelling Protocol for Peptide." ; sc:featureList edam:operation_0224, edam:operation_0478, edam:operation_0481, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PANDORA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/X-lab-3D/PANDORA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3373 ; sc:citation ; sc:description """Generating antiviral peptides using Generative Adversarial Network. Antiviral peptide predictions using GAN.""" ; sc:featureList edam:operation_0418, edam:operation_3631, edam:operation_4009 ; sc:license "MIT" ; sc:name "PandoraGAN" ; sc:url "https://pandora-gan.herokuapp.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_3016 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1621 ; sc:name "Pharmacogenomic test report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0622, edam:topic_2533, edam:topic_2640 ; sc:author "SING Research Group. Informatics Department. University of Vigo" ; sc:citation "pmcid:PMC5977747", "pubmed:29848362" ; sc:description "PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique compounds." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PanDrugs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BU_CNIO", "CNIO" ; sc:softwareHelp , ; sc:softwareVersion "2018.06.18", "2021.04.27" ; sc:url "https://www.pandrugs.org/" ; biotools:primaryContact , "Fatima Al-Shahrour" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0625, edam:topic_3120, edam:topic_3517 ; sc:citation , "pmcid:PMC10881103", "pubmed:38337024" ; sc:description "A pan-genome visualization tool for variant effects in maize." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0331, edam:operation_1812, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PanEffect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.maizegdb.org/effect/maize/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3303, edam:topic_3325, edam:topic_3577, edam:topic_3676 ; sc:description "Genomics England PanelApp is a publically-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes to be added or reviewed by experts throughout the worldwide scientific community, providing an opportunity for the standardisation of gene panels, and a consensus on which genes have sufficient evidence for disease association." ; sc:featureList edam:operation_2990, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "PanelApp" ; sc:url "https://panelapp.genomicsengland.co.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3168, edam:topic_3421 ; sc:citation , "pmcid:PMC8478415", "pubmed:34406119" ; sc:description "Multi-syndrome, multi-gene risk modeling for individuals with a family history of cancer with the novel R package PanelPRO." ; sc:featureList edam:operation_3196, edam:operation_3920 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PanelPRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://projects.iq.harvard.edu/bayesmendel/panelpro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3308, edam:topic_3407, edam:topic_3473 ; sc:citation , "pmcid:PMC7006390", "pubmed:32028885" ; sc:description "Pathway Network Visualizer (PaNeV) is an R package for a pathway-based network visualization. Based on information available on KEGG, it maps and visualizes genes within a network of upstream and downstream-connected pathways (from 1 to n levels). The graph helps to interpret functional profiles of cluster of genes." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3925, edam:operation_3926 ; sc:name "PANEV" ; sc:url "https://github.com/vpalombo/PANEV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3299, edam:topic_3382 ; sc:citation , "pmcid:PMC9477528", "pubmed:35916725" ; sc:description "A web-based tool for exploratory analysis and visualization of bacterial pan-genomes." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PanExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://panexplorer.southgreen.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3301 ; sc:citation "pubmed:26409790" ; sc:description "This software is a tool to predict functional composition of microbial communities based on communities survey data which builds a pangenome for each OTU and assigns the pangenome’s functional profile to the OTU." ; sc:featureList edam:operation_2423, edam:operation_2995 ; sc:name "PanFP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/srjun/PanFP" ; biotools:primaryContact "Andrey A. Gorin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3071, edam:topic_3314, edam:topic_3318 ; sc:description "This information system is operated as an Open Access library aimed at archiving, publishing and distributing georeferenced data from earth system research. The system guarantees long-term availability of its content through a commitment of the hosting institutions." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "PANGAEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pangaea.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0769 ; sc:citation ; sc:description """A modular and extensible collection of tools for mining context-dependent gene relationships from the biomedical literature. The tool extracts gene relations from PubMed abstracts and outputs the results in both CSV and JSON format.""" ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3625 ; sc:name "Pangaea" ; sc:softwareHelp ; sc:url "https://github.com/ss-lab-cancerunit/pangaea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:19442283" ; sc:description "Tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology." ; sc:featureList edam:operation_0495, edam:operation_2495, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "PanGEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kofler.or.at/bioinformatics/PanGEA" ; biotools:primaryContact "Robert Kofler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_2333, edam:format_3975 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1211 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_2333, edam:format_3975 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1333 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0797 ; sc:author ; sc:citation , "pubmed:33532821" ; sc:description "PLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a \"seed-and-extend approach\" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes." ; sc:featureList edam:operation_0227, edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bielefeld University", "Genome Informatics" ; sc:softwareHelp ; sc:softwareVersion "0.0.1-0.2.0" ; sc:url "https://github.com/tischulz1/plast" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description """A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection. The bioinformatics pipeline leverages BWA/Minimap2 to identify ‘where’ reads belong to provides taxonomy identification specific to strain-level. Other than community profiling, PanGIA uses two approaches to obtain a metric of confidence, one that relies on uniqueness of sequences and the other one that relies on comparing test samples with control samples (organism-basis).""" ; sc:featureList edam:operation_2422, edam:operation_3198, edam:operation_3200, edam:operation_3460, edam:operation_3472 ; sc:name "PanGIA" ; sc:url "https://github.com/LANL-Bioinformatics/PanGIA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3016, edam:format_3752 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC9022248", "pubmed:35449021" ; sc:description "Pangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_3196, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pangolin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tkzeng/Pangolin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:encodingFormat edam:format_3751 ; sc:name "Taxonomic classification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781 ; sc:author "Áine O'Toole" ; sc:citation ; sc:description "Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages" ; sc:featureList edam:operation_0499, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pangolin" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "v4.0 - v4.3.1" ; sc:url "https://cov-lineages.org/resources/pangolin.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3332, edam:topic_3336 ; sc:citation ; sc:description "PanGPCR docks the compound of interest to a library of 36 experimentally determined crystal structures comprising of 46 docking sites for human GPCRs, and a ranked list is generated from the docking studies to assess all GPCRs and their binding affinities. Users can determine a given compound’s GPCR targets and its repurposing potential accordingly. Moreover, potential side effects collected from the SIDER (Side-Effect Resource) database and mapped to 45 tissues and organs are provided by linking predicted off-targets and their expressed sequence tag profiles. With PanGPCR, multiple targets, repurposing potential and side effects can be determined by simply uploading a small ligand." ; sc:name "PanGPCR" ; sc:url "https://gpcrpanel.cmdm.tw/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168, edam:topic_3299, edam:topic_3301, edam:topic_3794 ; sc:citation , "pmcid:PMC7371109", "pubmed:32213253" ; sc:description """Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software. panISa is a software identifying insertion sequence (IS) on resequencing data (bam file) in bacterial genomes. The panISa software searches for Insertion Sequences on NGS data ab initio (i.e. with a database-free approach) in bacterial genomes from short read data. Briefly, the software identifies a signature of insertion in the alignment by counting clipped reads on the start and end positions of the potential IS. These clipped reads overlap the direct repeats due to IS insertion. Finally, using a reconstruction of the beginning of both sides of the IS (IRL and IRR), panISa validates the IS by searching for inverted repeat regions.""" ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_2428, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "panISa" ; sc:url "https://github.com/bvalot/panISa" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1084 ; sc:encodingFormat edam:format_2330 ; sc:name "Data resource definition ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:encodingFormat edam:format_2330 ; sc:name "Species name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3621 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3489 ; sc:citation ; sc:description "Processing annotation data from public data repositories and building protein-centric annotation data packages." ; sc:featureList edam:operation_0361, edam:operation_2422, edam:operation_3561 ; sc:license "GPL-2.0" ; sc:name "PAnnBuilder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PAnnBuilder.html" ; biotools:primaryContact "Li Hong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168, edam:topic_3301 ; sc:citation "pubmed:24065654" ; sc:description "Automated pipeline for the annotation of closely related genomes well suited for pangenome studies." ; sc:featureList edam:operation_0226 ; sc:name "PANNOTATOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bnet.egr.vcu.edu/pannotator/pannotator.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_1775 ; sc:citation "pubmed:25653249" ; sc:description "Fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE), EC numbers and GO classes." ; sc:featureList edam:operation_0226 ; sc:name "PANNZER" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://ekhidna.biocenter.helsinki.fi/pannzer" ; biotools:primaryContact "Patrik Koskinen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2200 ; sc:name "Text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:29741643" ; sc:description "Protein ANNotation with Z-scoRE. Fully automated functional annotation of prokaryotic and eukaryotic proteins of unknown function. Designed to predict the functional description (DE) and GO classes." ; sc:featureList edam:operation_0224, edam:operation_0226, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "pannzer2" ; sc:softwareHelp ; sc:url "http://ekhidna2.biocenter.helsinki.fi/sanspanz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """Identification of SNP Targeted Pathways From Genome-wide Association Study (GWAS) Data. Abstract The identification of the variants that explain familial risk of a specific disease is important since it enables the development of genetic risk prediction tests, diagnosis tools and therapeutical applications. One possible reason of multifactorial diseases is the alterations in the activity of biological pathways, where a series of mutations occur in distinct genes. While each of these variations extends slightly the likelihood of having the disease, they work together to give birth to the perturbations in normal biological processes. We provide a protocol \\(termed PANOGA, Pathway and Network Oriented GWAS \\(Genome-wide association study) Analysis) to devise functionally important pathways through the identification of genes within these pathways, where these genes are targeted by single nucleotide polymorphisms \\(SNPs) obtained from the GWAS analysis ||| HOMEPAGE BROKEN!""" ; sc:featureList edam:operation_3196, edam:operation_3920, edam:operation_3928 ; sc:name "PANOGA" ; sc:url "http://akademik.bahcesehir.edu.tr/~bbgungor/panoga_protocol.zip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_2640, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC7452437", "pubmed:32904262" ; sc:description "Panomicon (formerly Toxygates) is a web application for user-friendly analysis of multi-omics data (presently focusing on mRNA and mRNA-miRNA interaction data). It was originally developed for the Open TG-GATEs dataset but is now being used for more general purposes." ; sc:featureList edam:operation_0224, edam:operation_3096, edam:operation_3925 ; sc:license "GPL-2.0" ; sc:name "Panomicon" ; sc:url "https://toxygates.nibiohn.go.jp/panomicon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2640, edam:topic_3308, edam:topic_3922 ; sc:citation ; sc:description "PANOPLY is a platform for applying state-of-the-art statistical and machine learning algorithms to transform multi-omic data from cancer samples into biologically meaningful and interpretable results." ; sc:featureList edam:operation_0417, edam:operation_2436, edam:operation_3639 ; sc:name "PANOPLY" ; sc:softwareHelp , , ; sc:url "https://app.terra.bio/#workspaces/broad-firecloud-cptac/PANOPLY_Production_Pipelines_v1_0" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:encodingFormat edam:format_2032 ; sc:name "Workflow metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_4006 ; sc:name "Protocol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3519 ; sc:description "Monitor computational workflows in real-time" ; sc:featureList edam:operation_3636 ; sc:name "panoptes" ; sc:softwareVersion "0.1.1" ; sc:url "https://github.com/panoptes-organization/panoptes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC4156235", "pubmed:25102069" ; sc:description "A web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments." ; sc:featureList edam:operation_0224, edam:operation_3801 ; sc:name "Panorama" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://panoramaweb.org/project/home/begin.view?" ; biotools:primaryContact "Brendan MacLean" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3388, edam:topic_3423, edam:topic_3444 ; sc:citation , "pubmed:28453651" ; sc:description "The massive molecular profiling of thousands of cancer patients has led to the identification of many tumor type specific driver genes. However, only a few (or none) of them are present in each individual tumor and, to enable precision oncology, we need to interpret the alterations found in a single patient. Cancer PanorOmics (http://panoromics.irbbarcelona.org) is a web-based resource to contextualize genomic variations detected in a personal cancer genome within the body of clinical and scientific evidence available
for 26 tumor types, offering complementary cohort and patient-centric views. Additionally, it explores the cellular environment of mutations by mapping them on the human interactome and providing quasiatomic structural details, whenever available. This ‘PanorOmic’ molecular view of individual tumors should contribute to the identification of actionable alterations ultimately guiding the clinical decision-making process." ; sc:featureList edam:operation_1781 ; sc:name "PanorOmics" ; sc:url "https://panoromics.irbbarcelona.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:description "PANOW (Poisson Approximation for the Number of Occurrences of Words)is a software dedicated to the search of rare words in biological sequences (over- or under-represented words in DNA or protein sequences)." ; sc:featureList edam:operation_2421 ; sc:name "PANOW" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.math-evry.cnrs.fr/logiciels/panow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3321 ; sc:citation ; sc:description "A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. It is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date." ; sc:featureList edam:operation_2454 ; sc:license "GPL-2.0" ; sc:name "panp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.44.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/panp.html" ; biotools:primaryContact "Peter Warren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3299 ; sc:citation , "pubmed:35289871" ; sc:description "PANPROVA is a computational tool for simulating pangenomic evolution by evolving the complete genomic sequence of an ancestral isolate. In this way, the possibility of operating at the pre-assembly stage is enabled. 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It queries protein dynamics and structural conservation to identify pockets that may exert a regulatory effect upon binding of a small-molecule ligand." ; sc:featureList edam:operation_3092 ; sc:name "PARS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.uab.cat/cgi-bin/pars-cgi/pars.pl" ; biotools:primaryContact "Xavier Daura" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3337, edam:topic_3517, edam:topic_3958 ; sc:citation , "pubmed:36316489" ; sc:description "Efficient sequencing tool for copy number variation genome-wide association studies." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ParseCNV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CAG-CNV/ParseCNV2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_3053 ; sc:description "Function goal is to parse TAB delimited Gene Ontology [GO] file and return GO structure" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "ParseFiles-GoFiles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/66451-mayagalili-parsefiles-gofiles" ; biotools:primaryContact "Maya Galili" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:24470570" ; sc:description "Statistical approach for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts." ; sc:featureList edam:operation_0438 ; sc:name "Parseq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/parseq/" ; biotools:primaryContact "Bogdan Mirauta", "Hugues Richard", "Pierre Nicolas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation "pubmed:12824424" ; sc:description "Tool for the analysis of polymorphisms in genes." ; sc:featureList edam:operation_0477, edam:operation_0484, edam:operation_2479, edam:operation_3202 ; sc:name "PARSESNP" ; sc:url "http://www.proweb.org/parsesnp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3372, edam:topic_3474, edam:topic_3517, edam:topic_3673 ; sc:citation , "pmcid:PMC7244787", "pubmed:32444882" ; sc:description "High Performance Computing tool for the genome-wide detection of pathogenic variants." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:license "GPL-3.0" ; sc:name "parSMURF" ; sc:url "https://github.com/AnacletoLAB/parSMURF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0123, edam:topic_2814, edam:topic_3510 ; sc:citation ; sc:description "Sequence-based protein solubility prediction using gradient boosting machine." ; sc:featureList edam:operation_0409 ; sc:name "PaRSnIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RedaRawi/PaRSnIP" ; biotools:primaryContact "Gwo-Yu Chuang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2885, edam:topic_3293 ; sc:description "Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees." ; sc:featureList edam:operation_0484, edam:operation_3182 ; sc:license "BSD-3-Clause" ; sc:name "Parsnp" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "https://github.com/marbl/parsnp" ; biotools:primaryContact "Maryland Bioinformatics Labs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC9931301", "pubmed:36812603" ; sc:description "Privacy-aware multi-institutional time-to-event studies." ; sc:featureList edam:operation_3283, edam:operation_3436, edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Partea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://partea.zbh.uni-hamburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3169, edam:topic_3173, edam:topic_3308, edam:topic_3320 ; sc:citation ; sc:description "Easy to use software providing A to Z analysis for all Next Generation Sequencing and Microarray data." ; sc:featureList edam:operation_3800 ; sc:name "Partek Genomics Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.partek.com" ; biotools:primaryContact "Partek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3344 ; sc:description "Partest is a MATLAB for calculating the performance of a clinical test based on the Bayes theorem." ; sc:isAccessibleForFree true ; sc:name "Partest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/12705-partest" ; biotools:primaryContact "Giuseppe Cardillo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0654, edam:topic_3382, edam:topic_3940 ; sc:citation ; sc:description "A Particle Swarm Optimization Algorithm for Chromosome and Genome 3D Structure Prediction from Hi-C Data." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_0475 ; sc:name "ParticleChromo3D" ; sc:url "https://github.com/OluwadareLab/ParticleChromo3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269 ; sc:citation "pubmed:20542911" ; sc:description "Web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects." ; sc:featureList edam:operation_0337, edam:operation_3457 ; sc:name "ParticleStats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ParticleStats.com" ; biotools:primaryContact "Russell Hamilton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0654 ; sc:citation "pubmed:26589276" ; sc:description "Designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms." ; sc:featureList edam:operation_2403 ; sc:name "ParTIES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/oarnaiz/ParTIES" ; biotools:primaryContact "Linda Sperling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0820 ; sc:citation "pubmed:24766258" ; sc:description "Software to investigate the folding landscape of TMBs (Transmembrane Beta-barrel Proteins)." ; sc:featureList edam:operation_0292, edam:operation_0303 ; sc:name "partiFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://partifold.csail.mit.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_3512 ; sc:citation "pubmed:15608203" ; sc:description "Database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data." ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_0525, edam:operation_0526 ; sc:name "PartiGeneDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.partigenedb.org/" ; biotools:primaryContact "Dr. John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:19337306" ; sc:description "Model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms." ; sc:featureList edam:operation_3432 ; sc:name "Partition" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.genetix.univ-montp2.fr/partition/partition.html" ; biotools:primaryContact "K.J. Dawson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3360, edam:topic_3697 ; sc:citation , "pubmed:31504178" ; sc:description "A surjective mapping approach for dimensionality reduction | Agglomerative Partitioning Framework for Dimension Reduction | A fast and flexible framework for agglomerative partitioning. 'partition' uses an approach called Direct-Measure-Reduce to create new variables that maintain the user-specified minimum level of information. Each reduced variable is also interpretable: the original variables map to one and only one variable in the reduced data set. 'partition' is flexible, as well: how variables are selected to reduce, how information loss is measured, and the way data is reduced can all be customized" ; sc:featureList edam:operation_0337, edam:operation_3891, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Partition_R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=partition" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation ; sc:description "Partitioning R2 in generalized linear mixed models." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:name "partR2" ; sc:url "https://github.com/mastoffel/partR2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0611, edam:topic_0625, edam:topic_3383, edam:topic_3452 ; sc:citation ; sc:description "PartSeg is a tool for Quantitative Feature Extraction From 3D Microscopy Images." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3891 ; sc:license "BSD-3-Clause" ; sc:name "PartSeg" ; sc:softwareHelp ; sc:url "https://4dnucleome.cent.uw.edu.pl/PartSeg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3125, edam:topic_3297, edam:topic_3511 ; sc:citation ; sc:description "Integrated tool for optimizing and sharing synthetic biology parts." ; sc:featureList edam:operation_2430 ; sc:name "PartsGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://parts.synbiochem.co.uk/#" ; biotools:primaryContact "Neil Swainston" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3520 ; sc:citation , "pmcid:PMC7861515", "pubmed:33493161" ; sc:description """Proteomic analysis of serum antibodies web server. PASA allows generating quantitative and qualitative molecular measurements related to serum antibody repertoire from high-resolution proteomic data. PASA is applicable for researchers at all levels that are interested in addressing basic questions related to B cell development and differentiation, as well as an application focused tool for vaccine development, immunodiagnostic discovery and monoclonal antibody engineering. The web server accepts proteomics spectral files (in '.raw' format), and requires (at least) two technical replicates of each fraction (elution and flow-through). See running example input and output. PASA web server allows generating quantitative molecular measurements related to serum antibody repertoire from high-resolution proteomic data. Proteomics Analysis of Serum Antibodies web server. ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/PASA""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "PASA" ; sc:url "https://pasa.tau.ac.il" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3517 ; sc:citation , "pmcid:PMC6813133", "pubmed:31651322" ; sc:description """a biological insight into the novel associated genes. BACKGROUND:Attention-Deficit Hyperactivity Disorder (ADHD) is a complex neurodevelopmental disorder (NDD) which may significantly impact on the affected individual's life. ADHD is acknowledged to have a high heritability component (70-80%). Recently, a meta-analysis of GWAS (Genome Wide Association Studies) has demonstrated the association of several independent loci. Our main aim here, is to apply PASCAL (pathway scoring algorithm), a new gene-based analysis (GBA) method, to the summary statistics obtained in this meta-analysis. PASCAL will take into account the linkage disequilibrium (LD) across genomic regions in a different way than the most commonly employed GBA methods (MAGMA or VEGAS (Versatile Gene-based Association Study)).""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3501 ; sc:name "PASCAL" ; sc:url "https://www2.unil.ch/cbg/index.php?title=Pascal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC10185402", "pubmed:37137228" ; sc:description "Python library for GWAS gene and pathway enrichment tests." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "PascalX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bergmannlab.github.io/PascalX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3393 ; sc:citation , "pmcid:PMC5829578", "pubmed:29186545" ; sc:description "Quality control for single cell whole-genome sequencing data using power spectral density estimation." ; sc:featureList edam:operation_3218 ; sc:name "PaSD-qc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/parklab/PaSDqc" ; biotools:primaryContact "Maxwell Sherman", "Peter Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3295 ; sc:citation "pubmed:21092284" ; sc:description "Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-seq and methylome mapping by whole-genome bisulfite sequencing" ; sc:featureList edam:operation_0292, edam:operation_3186 ; sc:name "PASH" ; sc:url "http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml" ; biotools:primaryContact "Aleksandar Milosavljevic", "Elke Norwig-Eastaugh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "It is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, it has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources." ; sc:featureList edam:operation_0310, edam:operation_0524 ; sc:name "PASHA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.10" ; sc:url "http://pasha.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3407, edam:topic_3569 ; sc:citation "pubmed:27174940" ; sc:description "Web-based platform for predicting, modelling and analysing metabolic systems. It is a non-commercial and user-friendly tool for assisting non-experts in mathematical modelling, computing or programming to work on computational biology." ; sc:featureList edam:operation_2497, edam:operation_3439 ; sc:name "PASMet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pasmet.riken.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , "pmcid:PMC4051166", "pubmed:19218350", "pubmed:23162053", "pubmed:24708189" ; sc:description "PASS: a program to align short sequences" ; sc:featureList edam:operation_0292 ; sc:license "Other" ; sc:name "PASS" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "2.25" ; sc:url "http://pass.cribi.unipd.it/cgi-bin/pass.pl" ; biotools:primaryContact "Davide Campagna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081, edam:topic_0736 ; sc:citation "pubmed:22123743" ; sc:description "Database of structure-based sequence alignments of structural domain superfamilies." ; sc:featureList edam:operation_0292, edam:operation_0294, edam:operation_0303, edam:operation_2479 ; sc:name "PASS2" ; sc:softwareHelp ; sc:url "http://caps.ncbs.res.in/pass2/" ; biotools:primaryContact "Prof. R. Sowdhamini" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0160, edam:topic_0218, edam:topic_3474 ; sc:citation , "pmcid:PMC9581018", "pubmed:36303767" ; sc:description "Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks." ; sc:featureList edam:operation_0224, edam:operation_0291, edam:operation_0361 ; sc:isAccessibleForFree true ; sc:name "PASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pass.eecs.wsu.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3336, edam:topic_3373, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:37561047" ; sc:description """Prediction of Allosteric Sites Server. To approach this problem, PASSer is designed for accurate allosteric sites prediction. Ensemble learning, consisting of eXtreme gradient boosting and graph convolutional neural network, is used to learn the physical properties and topology information. Allostery is the process by which proteins transmit perturbations caused by the binding effect at one site to another distal site. Allosteric process is fundamental in regulation of activity. The identification of allosteric sites is important for allosteric drug development and has attracted a wide range of interests.""" ; sc:featureList edam:operation_2476, edam:operation_3092, edam:operation_3891, edam:operation_3938 ; sc:license "MIT" ; sc:name "PASSer" ; sc:url "https://passer.smu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3678 ; sc:citation ; sc:description """PASSIM (The Patient and Sample System for Information Management)is an open source software system for managing information in biomedical studies. The data submission form is brief, thus making the system simple to use and customize for any biomedical study easily. The PASSIM consists of the two parts:""" ; sc:featureList edam:operation_3431 ; sc:name "PASSIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://passim.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32426818" ; sc:description "PASSION is an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs." ; sc:featureList edam:operation_3902, edam:operation_3936 ; sc:name "PASSION" ; sc:softwareHelp ; sc:url "http://flagship.erc.monash.edu/PASSION/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16844992" ; sc:description "Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids." ; sc:featureList edam:operation_0245, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2487 ; sc:name "PAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://past.in.tum.de/" ; biotools:primaryContact "HANJO TÄUBIG" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3556 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128 ; sc:citation , "pmcid:PMC4086119", "pubmed:24848016" ; sc:description "A web server predictor for amyloid aggregation propensity from protein sequences." ; sc:featureList edam:operation_2492 ; sc:name "PASTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA", "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://protein.bio.unipd.it/pasta2/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "PASTAQ (Pipelines And Systems for Threshold Avoiding Quantification) provides a set of tools for high-performance pre-processing of LC-MS/MS data. Avoiding the use of arbitrary intensity thresholds in early stages of the pipeline can aid in the detection of important biological low intensity signals common in metabolomics and proteomics experiments." ; sc:featureList edam:operation_3215, edam:operation_3629, edam:operation_3631, edam:operation_3799 ; sc:license "MIT" ; sc:name "PASTAQ" ; sc:url "https://pastaq.horvatovichlab.com" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Insert one sequence into another." ; sc:featureList edam:operation_0232 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pasteseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pasteseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3174, edam:topic_3510, edam:topic_3837 ; sc:citation ; sc:description """Automatic protein partitioning and validation using conserved residues. Post-homology search validation and partitioning of specific sequences of interest. An automated pipeline for protein active site validation.""" ; sc:featureList edam:operation_0321, edam:operation_0447, edam:operation_3192 ; sc:license "MIT" ; sc:name "PASV" ; sc:softwareHelp ; sc:url "https://github.com/mooreryan/pasv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3297, edam:topic_3400 ; sc:citation "pubmed:27039071" ; sc:description "Web server that can efficiently identify target molecules for antibodies." ; sc:featureList edam:operation_0474 ; sc:name "PAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kimlab.org/software/pat" ; biotools:primaryContact "Philip M. Kim" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:name "Gene ID (NCBI)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0749, edam:topic_2830, edam:topic_3068 ; sc:citation , "pubmed:36243963" ; sc:description "A comprehensive database of prokaryotic antimicrobial toxins." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "PAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.qd.sdu.edu.cn/PAT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:16005138" ; sc:description "Pattern-matching software. It was developped in order to: allow large-scale searches on a bank without to use too much memory, implement the “block without error” option." ; sc:featureList edam:operation_0278 ; sc:name "PatBank" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://wwwabi.snv.jussieu.fr/research/publi/small_ncRNA/" ; biotools:primaryContact "M.Boccara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0821 ; sc:citation "pubmed:26422234" ; sc:description "Resource for researchers in the field of P-Type ATPases which aims to aid researchers by giving them access to easy-to-use, efficient and up-to-date computational tools for the prediction of the subtype of P-Type ATPase sequences." ; sc:featureList edam:operation_0267 ; sc:name "PATBox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://services.birc.au.dk/patbox/" ; biotools:primaryContact "Dan Søndergaard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Patch-seq is powerful technique that allows for multimodal characterization of individual neurons – electrophysiological, morphological and transcriptomic. At the Allen Institute we have optimized this technique to efficiently collect high-quality data. On this GitHub repo we provide links to the manuscript describing this optimized technique and associated data, a detailed protocol, Allen Institute manuscripts that have utilized this technique, and links to Allen Institute resources and software. In addition, this repo includes an R package of Patch-seq tools for quality control and cell typing of Patch-seq cells." ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3450 ; sc:name "Patch-seq" ; sc:url "https://github.com/AllenInstitute/patchseqtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2814 ; sc:citation "pubmed:25359888" ; sc:description "Method used to predict the binding ligand for a protein. The method used the 3 Dimensional Zernike Descriptor (3DZD) and Approximate Patch Position (APP) to describe the features of different patches of the protein pocket." ; sc:featureList edam:operation_2492 ; sc:name "Patch-Surfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kiharalab.org/patchsurfer2.0/" ; biotools:primaryContact "Daisuke Kihara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2814 ; sc:citation "pubmed:19768681" ; sc:description "Calculates Information statistics for protein sequence alignments to find coevolving residues." ; sc:featureList edam:operation_2928, edam:operation_2945 ; sc:name "PatchD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwwlabs.uhnresearch.ca/tillier/PatchDWEB/PatchDWEP.php" ; biotools:primaryContact "Elisabeth R. M. Tillier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation , "pubmed:12784375", "pubmed:15215437", "pubmed:15980490" ; sc:description "PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. 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The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, low tumor cell content or are aneuploid. The first takes BAM files as input whereas CG takes input from CompleteGenomics files." ; sc:featureList edam:operation_2945 ; sc:name "Patchwork" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://patchwork.r-forge.r-project.org/" ; biotools:primaryContact "Sebastian Dilorenzo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0601 ; sc:citation , "pubmed:35438792" ; sc:description "patcHwork is a user-friendly web-server that identifies amino acids of proteins that undergo a charge-shift when the pH assumes two user-defined values. For sequence functionality, users may submit a FASTA file with up to ten thousand amino acid sequences (max 20MB). For structure functionality, users may submit a single 3D structure (PDB) file or a zip file with multiple PDB files (max 20MB) for batch processing." ; sc:featureList edam:operation_0272, edam:operation_0337, edam:operation_0394, edam:operation_1839 ; sc:isAccessibleForFree true ; sc:name "patcHwork" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://patchwork.biologie.uni-freiburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_3297, edam:topic_3489 ; sc:citation "pubmed:19884134" ; sc:description "Collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents." ; sc:featureList edam:operation_0338, edam:operation_0346, edam:operation_0349, edam:operation_3092 ; sc:name "EBI patent sequence database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ebi.ac.uk/patentdata/nr/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:description "Facilitates the creation of sequence listings for inclusion in patent applications sequences. It accepts data about the sequences validates the data, creates a sequence listing file and a mechanism for printing out and saving to removable medium for submission." ; sc:featureList edam:operation_0335, edam:operation_2403 ; sc:name "PatentIn" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.5.1" ; sc:url "http://www.uspto.gov/patents-getting-started/patent-basics/types-patent-applications/utility-patent/checker/patentin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:1587248" ; sc:description "Computer program for the calculation of paternity probabilities from the multilocus DNA profiles of trios, comprising mother, child and putative father." ; sc:featureList edam:operation_0346 ; sc:name "PATERN" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/patern.txt" ; biotools:primaryContact "Michael Krawczak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3315 ; sc:citation , "pmcid:PMC8389186", "pubmed:34457037" ; sc:description "An interactive web platform for analysis of time-course high-dimensional genomic data." ; sc:featureList edam:operation_0337, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PATH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ouyanglab.shinyapps.io/PATH/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2259 ; sc:citation ; sc:description "Branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG, BioCarta, MetaCyc, PID and SABIO-RK." ; sc:featureList edam:operation_2421 ; sc:license "Apache-2.0" ; sc:name "Path2Models" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/biomodels-main/path2models" ; biotools:primaryContact "Nicolas Le Novère" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26733452" ; sc:description "Package to predict pathway specific protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available." ; sc:featureList edam:operation_3439 ; sc:name "PATH2PPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/release/bioc/html/Path2PPI.html" ; biotools:primaryContact "Oliver Philipp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_0659, edam:topic_3500 ; sc:citation , "pubmed:31733064" ; sc:description """An extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. Search Genes Search miRNAs Search Pathways API Download Statistics Documentation Publications Team Contact. pathDIP is an annotated database of signaling cascades in human and non-human organisms, comprising core pathways from major curated pathways databases, and pathways predicted based on orthology, and by using physical protein interactions. Data integration and predictions increase coverage of pathway annotations for human proteome to 92%. pathDIP annotates 122,131 unique proteins in 6,401 pathways in 17 organisms (including 18,454 human proteins), annotates 36,216 pathway orphans (including 5,366 human proteins), and provides multiple query, analysis and output options.""" ; sc:featureList edam:operation_0277, edam:operation_2421, edam:operation_3083, edam:operation_3439, edam:operation_3501 ; sc:name "pathDIP" ; sc:url "http://ophid.utoronto.ca/pathDIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3360 ; sc:citation , "pmcid:PMC10303868", "pubmed:37380943" ; sc:description "Pathway level survival enquiry for immuno-oncology and drug repurposing." ; sc:featureList edam:operation_2436, edam:operation_3211, edam:operation_3629, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PATH-SURVEYOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://shawlab-moffitt.shinyapps.io/path_surveyor_fileprep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33066841" ; sc:description "The essential set of tools to start with whole slide analysis. A simple way to experience computer-assisted WSI." ; sc:featureList edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Pathadin" ; sc:url "https://gitlab.com/Digipathology/Pathadin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice." ; sc:featureList edam:operation_2422 ; sc:name "PathBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.pathbase.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3407 ; sc:citation "pubmed:19811683" ; sc:description "Unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules." ; sc:featureList edam:operation_0306 ; sc:name "PathBinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.metnetdb.org/MetNet_PathBinder.htm" ; biotools:primaryContact "Lifeng Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0130, edam:topic_0602, edam:topic_3557 ; sc:citation "pubmed:15215356" ; sc:description "Tool for cross-species comparison of protein interaction networks. It takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user." ; sc:featureList edam:operation_0276, edam:operation_3083, edam:operation_3439 ; sc:name "PathBLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pathblast.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3168 ; sc:citation ; sc:description "Powerful differential expression analysis incorporating network topology for next-generation sequencing data." ; sc:featureList edam:operation_3741 ; sc:name "pathDESeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MalathiSIDona/pathDESeq" ; biotools:primaryContact "Agus Salim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_2640, edam:topic_3474 ; sc:citation ; sc:description """Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity. Predict the drug sensitivity to cancer cells.""" ; sc:featureList edam:operation_0533, edam:operation_3927, edam:operation_3929 ; sc:name "pathDNN" ; sc:url "http://pathdnn.denglab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0634, edam:topic_3324 ; sc:citation "pubmed:19843611" ; sc:description "It is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses." ; sc:featureList edam:operation_2422, edam:operation_2436, edam:operation_3196, edam:operation_3431, edam:operation_3461 ; sc:name "Pathema" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pathema.jcvi.org" ; biotools:primaryContact "Lauren Brinkac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3407, edam:topic_3577 ; sc:citation , "pmcid:PMC8363825", "pubmed:34429851" ; sc:description "PathExNET is a web service that allows the creation of pathway expression networks that hold the over- and under-expression information obtained from differential gene expression analyses." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3223, edam:operation_3926, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PathExNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformatics.cing.ac.cy/PathExNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "PathExpand is a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and expanding them to include densely interconnected interaction partners." ; sc:featureList edam:operation_2429 ; sc:name "PathExpand" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pathexpand.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0821, edam:topic_3407, edam:topic_3518 ; sc:citation "pubmed:17586825", "pubmed:19474337" ; sc:description "Tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment." ; sc:featureList edam:operation_0314, edam:operation_0533, edam:operation_2495, edam:operation_3223 ; sc:name "PathExpress" ; sc:url "http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3172, edam:topic_3308, edam:topic_3315 ; sc:citation ; sc:description """PathExt is a general framework for path-based mining of omics-integrated biological networks. We provide a computational tool - PathExt, which identifies differentially active paths when a control is available, and most active paths otherwise, in an omics-integrated biological network. The sub-network comprising such paths, referred to as the TopNet, captures the most relevant genes and processes underlying the specific biological context. The TopNet forms a well-connected graph, reflecting the tight orchestration in biological systems. Two key advantages of PathExt are (i) it can extract characteristic genes and pathways even when only a single sample is available, and (ii) it can be used to study a system even in the absence of an appropriate control.""" ; sc:featureList edam:operation_1781, edam:operation_3223, edam:operation_3501, edam:operation_3660 ; sc:name "PathExt" ; sc:url "https://github.com/NarmadaSambaturu/PathExt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0121, edam:topic_0623, edam:topic_0736, edam:topic_3174 ; sc:citation , "pmcid:PMC8442362", "pubmed:34521345" ; sc:description "Statistical detection of pathogen-associated protein domains." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_3461, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PathFams" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pathfams.uwaterloo.ca" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:encodingFormat edam:format_3166 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3753 ; sc:name "Over-representation data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_0602, edam:topic_3053 ; sc:author , ; sc:citation , ; sc:description "Pathway enrichment analysis enables researchers to uncover mechanisms underlying the phenotype. pathfindR is a tool for pathway enrichment analysis utilizing active subnetworks. It identifies active subnetworks in a protein-protein interaction network using user-provided a list of genes. It performs pathway enrichment analyses on the identified subnetworks. pathfindR also offers functionalities to cluster enriched pathways and identify representative pathways, visualize analysis results and to score the pathways per sample." ; sc:featureList edam:operation_0276, edam:operation_0337, edam:operation_2436, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pathfindR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.4.0, 1.4.1, 1.4.2" ; sc:url "https://github.com/egeulgen/pathfindR" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_2269, edam:topic_2640, edam:topic_3168 ; sc:citation ; sc:description """PathFinder is a method that infers cell migration routes accurately by using principles of Bayesian molecular phylogenetics in cancer cell genomes. Bayesian inference of clone migration histories in cancer. PathFinder is a python script developed in a Windows 64-bit architecture, and does not need to be compiled prior to usage. To use PathFinder, the following python packages need to be installed.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3478 ; sc:name "PathFinder" ; sc:url "https://github.com/SayakaMiura/PathFinder" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3477 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Cytoscape plug-in that identifies path motifs in integrated networks and arranges them in a modular structure." ; sc:featureList edam:operation_2497 ; sc:name "Pathicular" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/Pathicular" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "Algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample." ; sc:featureList edam:operation_2497 ; sc:license "Artistic-1.0" ; sc:name "pathifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pathifier.html" ; biotools:primaryContact "Assif Yitzhaky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269, edam:topic_2830, edam:topic_3518 ; sc:citation "pubmed:23748960" ; sc:description "PATHiWAYS is a web tool for the interpretation of the consequences of the combined changes in expression levels of genes in the context of signaling pathways. Specifically, this tool allows the user to identify the stimulus-response subpathways that are significantly activated or deactivated in the typical case/control experiment." ; sc:featureList edam:operation_0314, edam:operation_0533, edam:operation_2436, edam:operation_2495, edam:operation_3223 ; sc:name "PATHiWAYS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pathiways.babelomics.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3071 ; sc:citation ; sc:description "Web server which integrates pathway-related annotations from several public sources (Reactome, KEGG, Biocarta, etc) making easier the understanding of gene lists of interest." ; sc:featureList edam:operation_2422 ; sc:name "PathJam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.pathjam.org/server/api/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0769, edam:topic_3376, edam:topic_3452, edam:topic_3520 ; sc:citation , "pmcid:PMC9455941", "pubmed:36076268" ; sc:description "Pathling is a set of tools that make it easier to use clinical terminology and FHIR® within health data analytics. It is built on Apache Spark, and includes both language libraries and a server implementation." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Pathling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "5.4.0" ; sc:url "https://pathling.csiro.au" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC7161108", "pubmed:32299344" ; sc:description "PathME is a pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data." ; sc:featureList edam:operation_0533, edam:operation_3432, edam:operation_3935 ; sc:name "PathME" ; sc:url "https://github.com/AminaLEM/PathME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0634, edam:topic_3303, edam:topic_3316, edam:topic_3382, edam:topic_3391, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC9127877", "pubmed:34880124" ; sc:description """Tools for computational pathology. PathML objective is to lower the barrier to entry to digital pathology. Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. PathML is publicly available at www.pathml.org -- 🚀 The fastest way to get started? docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml""" ; sc:featureList edam:operation_0227, edam:operation_0337, edam:operation_2409, edam:operation_2428, edam:operation_2429, edam:operation_2945, edam:operation_2990, edam:operation_3429, edam:operation_3432, edam:operation_3438 ; sc:license "GPL-2.0" ; sc:name "PathML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://pathml.org" ; biotools:primaryContact "Massimo Loda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3172 ; sc:author ; sc:citation , "pmcid:PMC6997860", "pubmed:32058961" ; sc:description "PathModel is a prototype to infer new biochemical reactions and new metabolite structures." ; sc:isAccessibleForFree true ; sc:name "Pathmodel" ; sc:softwareVersion "0.1.9." ; sc:url "https://github.com/pathmodel/pathmodel" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation , "pmcid:PMC3563509", "pubmed:23006764" ; sc:description "This tool uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression." ; sc:featureList edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "PathNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PathNet.html" ; biotools:primaryContact "Jason B. Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data." ; sc:featureList edam:operation_2454, edam:operation_3461, edam:operation_3482 ; sc:name "PathoFact" ; sc:url "https://git-r3lab.uni.lu/laura.denies/PathoFact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7913958", "pubmed:33557152" ; sc:description """An Open-Source AI Framework for Recognition of Pathomorphological Features and Mapping of Immunohistochemical Data. A deep learning based framework for recognition and fusion of multimodal histopathological images.""" ; sc:featureList edam:operation_0531, edam:operation_3443, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "PathoFusion" ; sc:url "https://github.com/guoqingbao/Pathofusion" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2200 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3324 ; sc:citation ; sc:description "Prediction of a bacteria's pathogenicity towards human hosts." ; sc:featureList edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PathogenFinder" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://cge.cbs.dtu.dk/services/PathogenFinder/" ; biotools:primaryContact "Mette Voldby Larsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3336 ; sc:citation , "pubmed:34515762" ; sc:description "PATHOME-Drug is a web-based interfarce that implements network-aware statistical test for expression dataset, based on KEGG pathways." ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PATHOME-Drug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://statgen.snu.ac.kr/software/pathome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3315, edam:topic_3382, edam:topic_3388, edam:topic_3474 ; sc:citation , "pmcid:PMC8055887", "pubmed:33875676" ; sc:description "PathoNet introduced as a deep neural network backend for evaluation of Ki-67 and tumor-infiltrating lymphocytes in breast cancer." ; sc:featureList edam:operation_3454, edam:operation_3659, edam:operation_3799 ; sc:license "MIT" ; sc:name "PathoNet" ; sc:url "https://github.com/SHIDCenter/PathoNet" ; biotools:primaryContact "Amirreza Dehghanian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3174, edam:topic_3837 ; sc:citation ; sc:description "Pathogen Detection in RNA-Seq Data with Pathonoia." ; sc:featureList edam:operation_3436, edam:operation_3460, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Pathonoia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kepsi/Pathonoia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "PATHOQC is a quality control and preprocessing standalone program for a high-throughput dataset. PATHOQC combines three commonly-used quality control programs (FastQC, cutadapt, and prinseq-lite) into one package that can handle a variety type of NGS dataset in a parallel computation." ; sc:featureList edam:operation_2428 ; sc:name "PATHOQC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jlab.bu.edu/software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0654, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:25225611" ; sc:description "Takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm." ; sc:featureList edam:operation_2403 ; sc:name "Pathoscope" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/pathoscope/" ; biotools:primaryContact "Changjin Hong", "William Evan Johnson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3300, edam:topic_3382, edam:topic_3385 ; sc:citation ; sc:description "Computational tool for the automatic identification of glomerular lesions in histological images of kidneys." ; sc:featureList edam:operation_3443 ; sc:name "PathoSpotter-K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/geogob/PathoSpotter-K" ; biotools:primaryContact "George Oliveira Barros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. This tool provides various functionalities including relative abundance charts, diversity estimates and plots, tests of differential abundance, time series visualization, and core OTU analysis." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "PathoStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PathoStat.html" ; biotools:primaryContact "Solaiappan Manimaran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3343, edam:topic_3407 ; sc:citation "pubmed:20435670" ; sc:description "Enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pathways of environmental compounds and biosynthesis pathways of secondary metabolites are predicted." ; sc:featureList edam:operation_0224, edam:operation_0474, edam:operation_3439, edam:operation_3660 ; sc:name "PathPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.jp/tools/pathpred/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC3971351", "pubmed:23890051" ; sc:description "Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a 'pathway fingerprint', a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways." ; sc:featureList edam:operation_3465 ; sc:license "GPL-1.0" ; sc:name "pathprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.4" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pathprint.html" ; biotools:primaryContact "Sokratis Kariotis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Build graphs from pathway databases, render them by Rgraphviz." ; sc:featureList edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "pathRender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.42.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pathRender.html" ; biotools:primaryContact "Vince Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation , "pmcid:PMC4436019", "pubmed:25982732" ; sc:description "A web-based tool for exploration of ortholog and expression data in biological pathways." ; sc:featureList edam:operation_3083 ; sc:name "PathRings" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://raven.anr.udel.edu/~sunliang/PathRings/" ; biotools:primaryContact "Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3518 ; sc:citation "pubmed:21143778" ; sc:description "A novel network model and a reconstruction approach PATTERN are proposed for reconstructing the context specific time varying regulatory networks by integrating microarray gene expression profiles and existing knowledge of pathways and transcription factors." ; sc:featureList edam:operation_3439 ; sc:name "PathRNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compgenomics.utsa.edu/tvnet.html" ; biotools:primaryContact "Jia Meng", "Shou-Jiang Gao", "Yidong Chen", "yufei.huang@utsa.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2533, edam:topic_2640 ; sc:citation "pubmed:27503224" ; sc:description "Quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients." ; sc:featureList edam:operation_3202 ; sc:name "PathScore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pathscore.publichealth.yale.edu/" ; biotools:primaryContact "Gaffney SG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:33198455" ; sc:description """A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes. PATHcre8 is an open-access online tool for heterologous biosynthesis pathway search. Given the starting compound, the target product, and the heterologous host, PATHcre8 explores biosynthesis routes and ranks them.""" ; sc:featureList edam:operation_2421, edam:operation_3660, edam:operation_3929 ; sc:name "PATHsupcre8" ; sc:url "https://www.cbrc.kaust.edu.sa/pathcre8/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation ; sc:description "This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability." ; sc:featureList edam:operation_0277 ; sc:license "GPL-2.0" ; sc:name "pathVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pathVar.html" ; biotools:primaryContact "Samuel Zimmerman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC3268235", "pubmed:22123829" ; sc:description "PathVar, a web-application to study how the variance of expression levels across genes/proteins in cellular pathways changes under different experimental conditions, and to extract patterns for sample clustering and classification." ; sc:name "PathVar" ; sc:softwareHelp ; sc:url "http://pathvar.embl.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259 ; sc:citation , "pmcid:PMC3702256", "pubmed:23740750" ; sc:description "Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis." ; sc:featureList edam:operation_2497, edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "pathview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pathview.html" ; biotools:primaryContact "Weijun Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation , "pmcid:PMC5570256", "pubmed:28482075" ; sc:description "User friendly pathway visualization and data integration." ; sc:featureList edam:operation_3083 ; sc:name "Pathview Web" ; sc:softwareHelp ; sc:url "https://pathview.uncc.edu/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3325 ; sc:citation , "pmcid:PMC4338111", "pubmed:25706687" ; sc:description "Free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PathVisio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "3.3.0" ; sc:url "http://www.pathvisio.org/" ; biotools:primaryContact "Chris T. Evelo", "Martina Kutmon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3325 ; sc:citation "pubmed:26298294" ; sc:description "A XML-RPC interface for the pathway analysis tool PathVisio. It allows you to use PathVisio functions to create pathways and visualise and analyse data on pathways in your familiar analytical environment (R, Python, Perl, C++, so on …)" ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3096 ; sc:license "Apache-2.0" ; sc:name "PathVisioRPC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://projects.bigcat.unimaas.nl/pathvisiorpc/" ; biotools:primaryContact "Anwesha Bohler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0634, edam:topic_3407, edam:topic_3697 ; sc:citation , "pmcid:PMC7332569", "pubmed:32369599" ; sc:description "PathWalks is a random walk based algorithm, developed in R, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study." ; sc:featureList edam:operation_0533, edam:operation_3927, edam:operation_3929 ; sc:name "PathWalks" ; sc:url "https://github.com/vagkaratzas/PathWalks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0605, edam:topic_3172, edam:topic_3407 ; sc:citation , "pubmed:31813964" ; sc:description """Software for pathway/genome informatics and systems biology. The Pathway Tools software performs computational genomics, metabolic reconstruction and modeling, and analysis of gene-expression and metabolomics data. Pathway Tools is a comprehensive systems biology software system that is associated with the BioCyc database collection. The software has been licensed by more than 10,000 groups and powers a number of websites for biological databases. Pathway Tools integrates a broad set of capabilities that span genome informatics, pathway informatics, regulatory informatics, and omics data analysis. The software supports multiple use cases in bioinformatics and systems biology:.""" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3660 ; sc:name "pathway" ; sc:url "http://pathwaytools.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:24006871" ; sc:description "Uses the framework of Pedigree Disequilibrium Test (PDT) for general family data, to perform pathway analysis." ; sc:featureList edam:operation_2497 ; sc:name "Pathway-PDT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/pathway-pdt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0602, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:33305310" ; sc:description "Leveraging heterogeneous network embedding for metabolic pathway prediction." ; sc:featureList edam:operation_0533, edam:operation_3660, edam:operation_3929 ; sc:name "pathway2vec" ; sc:url "https://github.com/hallamlab/pathway2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Collection of publicly available pathways from multiple organisms." ; sc:featureList edam:operation_2422 ; sc:name "Pathway Commons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.pathwaycommons.org/pc/webservice.do?cmd=help" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3168 ; sc:citation "pubmed:15980551" ; sc:description "Tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP." ; sc:featureList edam:operation_0314, edam:operation_0533, edam:operation_2497, edam:operation_3562 ; sc:name "Pathway Explorer" ; sc:url "https://pathwayexplorer.genome.tugraz.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:15980483", "pubmed:19281817", "pubmed:20228128" ; sc:description "This tool is a part of the network analysis tool suite (NeAT). Given a metabolic network, the tool extracts a subnetwork that connects a list of input compounds, reactions, EC numbers or enzyme-coding genes. Three metabolic networks (KEGG LIGAND, KEGG RPAIR and MetaCyc) are preloaded, but custom networks can be submitted as well." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3439, edam:operation_3562, edam:operation_3660 ; sc:name "Pathway extraction" ; sc:url "http://rsat.bigre.ulb.ac.be/rsat/index_neat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0621, edam:topic_3407 ; sc:citation "pubmed:15572476" ; sc:description "Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite." ; sc:featureList edam:operation_2497, edam:operation_3083, edam:operation_3439, edam:operation_3562, edam:operation_3660 ; sc:name "Pathway Hunter Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pht.tu-bs.de/" ; biotools:primaryContact "Syed Asad Rahman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "Web application helping researchers to find patterns of expression in complex RNAseq experiments." ; sc:featureList edam:operation_2495 ; sc:name "Pathway Inspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Department of Molecular Medicine, University of Padua", "FEM Research and Innovation Center" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://pathwayinspector.dmm.unipd.it/" ; biotools:primaryContact "Stefano Toppo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:15145817" ; sc:description "Tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses." ; sc:featureList edam:operation_0314, edam:operation_2497, edam:operation_3083, edam:operation_3439 ; sc:name "Pathway Miner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biorag.org/pathway.html" ; biotools:primaryContact "Ritu Pandey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description """Automating parameter selection to avoid implausible biological pathway models. Parameter advising for biological pathway creation algorithms. Pathway parameter advising is described in the following preprint:. Pathway parameter advising was written and tested using Python 3.6 and requires the packages networkx and numpy. The runPPA.sh and setupPGD.sh scripts require git. These scripts have only been tested in a Linux environment initially""" ; sc:featureList edam:operation_0277, edam:operation_0533, edam:operation_3439, edam:operation_3562 ; sc:license "MIT" ; sc:name "pathway parameter advising" ; sc:url "https://github.com/gitter-lab/pathway-parameter-advising" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:19907644" ; sc:description "This tool was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities." ; sc:featureList edam:operation_2429 ; sc:name "Pathway Projector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.g-language.org/PathwayProjector/" ; biotools:primaryContact "Nobuaki Kono" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3407 ; sc:citation "pubmed:19955237" ; sc:description "Supports creation, editing, querying, visualization, and analysis of PGDBs. The software also allows users to publish a PGDB on the Web for access by the scientific community. A PGDB is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signalling pathways, and of the regulatory network." ; sc:featureList edam:operation_2497 ; sc:name "Pathway Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ai.sri.com/ptools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0804, edam:topic_3308, edam:topic_3407, edam:topic_3421 ; sc:citation , "pmcid:PMC10080220", "pubmed:37033947" ; sc:description "An integrated platform for deciphering the systems-level signaling pathways." ; sc:featureList edam:operation_3501, edam:operation_3926, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "PathwayKO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/allenaigit/pathwayko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:20211756" ; sc:description "In silico pathway analysis tool, enabling pharmaceutical R&D to reach their target decisions faster and with higher accuracy." ; sc:featureList edam:operation_2497 ; sc:name "PathwayLab" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.garuda-alliance.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26361499" ; sc:description "Presents novel methods to visualize and interact with representations of signaling pathways. It provides visual anayltics tools that allow systems biologists and cancer researchers to find patterns in the relationships and reactions between proteins and protein complexes." ; sc:featureList edam:operation_3083 ; sc:name "PathwayMatrix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CreativeCodingLab/PathwayMatrix" ; biotools:primaryContact "Angus Graeme Forbes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2640 ; sc:citation , "pmcid:PMC7677175", "pubmed:32430990" ; sc:description """pathwayPCA an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection. With the advance in high-throughput technology for molecular assays, multi-omics datasets have become increasingly available. However, most currently available pathway analysis software do not provide estimates on sample-specific pathway activities, and provide little or no functionalities for analyzing multiple types of omics data simultaneously. To address these challenges, we present pathwayPCA, a unique integrative pathway analysis software that utilizes modern statistical methodology on principal component analysis (PCA) and gene selection.""" ; sc:featureList edam:operation_3659, edam:operation_3891, edam:operation_3928 ; sc:name "pathwayPCA" ; sc:url "https://gabrielodom.github.io/pathwayPCA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "Unbiased pathway analysis of alternative splicing in RNA-Seq data." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_2499, edam:operation_3659 ; sc:license "LGPL-2.0" ; sc:name "PathwaySplice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/PathwaySplice.html" ; biotools:primaryContact "Aimin Yan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:26400039" ; sc:description "Provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents." ; sc:featureList edam:operation_2497 ; sc:name "PathwaysWeb" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/PathwaysWeb:Overview" ; biotools:primaryContact "Melott JM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3325, edam:topic_3366 ; sc:citation , , "pmcid:PMC4343077", "pmcid:PMC4572507", "pubmed:25725061", "pubmed:26119816" ; sc:description "A platform developed by Kinghorn Center of Clinical Genomics (KCCG) for managing, sharing and discussing patient cases (clinical and genomic information)." ; sc:featureList edam:operation_3096, edam:operation_3280, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "KCCG Patient Archive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.4" ; sc:url "http://patientarchive.org/#/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web API" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3263, edam:topic_3303 ; sc:citation ; sc:description "PatientMatcher is a customizable Python-based open-source tool for matching undiagnosed rare disease patients via the MatchMaker Exchange network." ; sc:featureList edam:operation_3196 ; sc:license "MIT" ; sc:name "PatientMatcher" ; sc:url "https://github.com/Clinical-Genomics/patientMatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622 ; sc:citation "pubmed:18467344" ; sc:description "Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes." ; sc:featureList edam:operation_0492, edam:operation_0496, edam:operation_2422, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PatMaN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinf.eva.mpg.de/patman/" ; biotools:primaryContact "Kay Pruefer", "Udo Stenzel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:15980466" ; sc:description "PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns." ; sc:featureList edam:operation_0235, edam:operation_2421, edam:operation_2479 ; sc:name "PatMatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl" ; biotools:primaryContact "PatchMatch Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Search protein sequences with a sequence motif." ; sc:featureList edam:operation_0338, edam:operation_3092 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "patmatdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/patmatdb.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Scan a protein sequence with motifs from the PROSITE database." ; sc:featureList edam:operation_3092 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "patmatmotifs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/patmatmotifs.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3293, edam:topic_3301 ; sc:citation ; sc:description """Pangenome Analysis Toolkit. PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species. It allows to analyze the core-genome, accessory genome and whole genome, the population structure, and the horizontal gene transfer dynamics. PATO uses, as core software, MASH , MMSeq2, Minimap2 and R.""" ; sc:featureList edam:operation_3227, edam:operation_3478, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "PATO" ; sc:url "https://github.com/irycisBioinfo/PATO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0659, edam:topic_3168 ; sc:citation , "pmcid:PMC10049783", "pubmed:36924420" ; sc:description "Genome-wide prediction of lncRNA-DNA triple helices." ; sc:featureList edam:operation_0468, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UDC-GAC/pato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0621, edam:topic_3520 ; sc:citation , "pmcid:PMC9933831", "pubmed:36744907" ; sc:description "Patpat stands for Proteomics Aiders Telescope, a public proteomics dataset search framework that simply passes in protein identifiers to search for relevant datasets and returns metadata to aid your research." ; sc:featureList edam:operation_2421, edam:operation_3767, edam:operation_3801 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Patpat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/henry-leo/Patpat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:16388682" ; sc:description "Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances." ; sc:featureList edam:operation_0557 ; sc:name "Patristic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/patristic/" ; biotools:primaryContact "Fourment Mathieu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0204, edam:topic_0621, edam:topic_0659, edam:topic_2885 ; sc:citation "pubmed:19906729" ; sc:description "Compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation." ; sc:featureList edam:operation_0484, edam:operation_2454, edam:operation_3196, edam:operation_3232, edam:operation_3439 ; sc:name "Patrocles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.patrocles.org" ; biotools:primaryContact "Carole Charlier", "Denis Baurain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3343, edam:topic_3520, edam:topic_3855 ; sc:citation ; sc:description """Open source software platform for environmental mass spectrometry based non-target screening. patRoon aims to provide a solution for comprehensive mass spectrometry based non-target analysis (NTA) workflows for environmental analysis. The name is derived from a Dutch word that means pattern and may also be an acronym for hyPhenated mAss specTROmetry nOn-target aNalysis. This R package contains example to test and demonstrate the patRoon R package. The data is used in the package vignette to demonstrate the various functionalities of patRoon regarding mass spectrometry based non-target analysis.""" ; sc:featureList edam:operation_2422, edam:operation_3629, edam:operation_3860, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "patRoon" ; sc:softwareHelp ; sc:url "https://rickhelmus.github.io/patRoon/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3473 ; sc:citation ; sc:description "Highly interactive web interface to the powerful generic pattern search tool PatScan. The complex PatScan-patterns are created in a drag-and-drop aware interface allowing researchers to do rapid prototyping of the often complicated patterns useful to identifying features of interest." ; sc:featureList edam:operation_0238, edam:operation_0239 ; sc:license "AGPL-3.0" ; sc:name "PatScanUI" ; sc:softwareHelp ; sc:url "https://patscan.secondarymetabolites.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3168, edam:topic_3542 ; sc:citation "pubmed:12824377" ; sc:description "A pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices." ; sc:featureList edam:operation_0267, edam:operation_2439, edam:operation_2487, edam:operation_2488 ; sc:name "PatSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "C.N.R. - Institute of Biomedical Technology", "ELIXIR-ITA-CNR" ; sc:softwareHelp ; sc:url "http://itbtools.ba.itb.cnr.it/patsearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Pattern clustering is a tool to cluster a set of DNA patterns onto smaller and more representative set of DNA patterns.Most pattern enumeration tools, such as POCO, report patterns overlapping. Therefore after discovering a set of statistically significant nucleotide patterns, it is useful to cluster the overlapping patterns into representative patterns." ; sc:featureList edam:operation_3432 ; sc:name "PATTERN CLUSTERING" ; sc:operatingSystem "Linux" ; sc:softwareVersion "20060220" ; sc:url "http://ekhidna.biocenter.helsinki.fi/poxo/cluster" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1477, edam:format_2033 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_2033 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0166, edam:topic_1317, edam:topic_3510 ; sc:citation ; sc:description "A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time." ; sc:featureList edam:operation_0245, edam:operation_0250, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "PatternQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "http://ncbr.muni.cz/PatternQuery" ; biotools:primaryContact "David Sehnal", "Lukáš Pravda", "Primary Contact" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3244, edam:format_3712 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:18644148" ; sc:description "Suite of pattern recognition software for interpretation of quantiative proteomics data." ; sc:featureList edam:operation_3203, edam:operation_3634, edam:operation_3635, edam:operation_3647, edam:operation_3694 ; sc:name "PatternLab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pcarvalho.com/patternlab/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1477 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_1477, edam:format_2033 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_2033 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_0166, edam:topic_1317, edam:topic_3510 ; sc:author "David Sehnal" ; sc:citation ; sc:contributor "Crina-Maria Ionescu", "Lukáš Pravda", "Radka Svobodová Vařeková" ; sc:description "A web application to define, extract, and analyze structural patterns or biomolecular complexes in real-time." ; sc:featureList edam:operation_0245, edam:operation_0250, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "PatternQuery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "http://ncbr.muni.cz/PatternQuery" ; biotools:primaryContact "David Sehnal", "Lukáš Pravda", "Primary Contact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation , "pubmed:18428704" ; sc:description "PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods" ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "paup" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://paup.phylosolutions.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3361, edam:topic_3474, edam:topic_3678 ; sc:citation ; sc:description """An Interpretable Risk Prediction Model for Healthcare with Pattern Attention. Pattern Attention Model with Value Embedding (PAVE).""" ; sc:featureList edam:operation_0303, edam:operation_3435, edam:operation_3557 ; sc:name "PAVE" ; sc:url "https://github.com/yinchangchang/PAVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3174 ; sc:citation ; sc:description "Web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. Researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams." ; sc:featureList edam:operation_0226, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Pavian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/pavian/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0632, edam:topic_0769, edam:topic_3518 ; sc:citation , "pmcid:PMC7499988", "pubmed:32942983" ; sc:description "paweR is an R package for analysing protein microarray data via web exploreR." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3435 ; sc:name "PAWER" ; sc:url "https://biit.cs.ut.ee/pawer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0204, edam:topic_0602, edam:topic_3407 ; sc:citation , "pubmed:34128961" ; sc:description "A Python library for large-scale regulation network analysis using BIOPAX." ; sc:featureList edam:operation_3695, edam:operation_3896, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PAX2GRAPHML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://pax2graphml.genouest.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:description "PaxDb contains estimated abundance values for a large number of proteins in several different species. Furthermore, it contains information about inter-species variation of protein abundances." ; sc:featureList edam:operation_3630 ; sc:name "PaxDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pax-db.org/" ; biotools:primaryContact "Milan Simonovic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2229 ; sc:description "Parser for PaxDB-file which contains the proteins level of genes in the cell" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "PaxDB Parser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/65589-mayagalili-parsefiles-paxdb" ; biotools:primaryContact "Maya Galili" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26685306" ; sc:description "Java library specially designed for accessing and manipulating data in BioPAX format. This Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software." ; sc:featureList edam:operation_2497 ; sc:name "Paxtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biopax.org/paxtools.php" ; biotools:primaryContact "Luna A" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3156 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3619, edam:format_3692 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229 ; sc:citation , "pmcid:PMC4824129", "pubmed:26685306" ; sc:description "The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC." ; sc:featureList edam:operation_0335, edam:operation_1781, edam:operation_2421, edam:operation_3083, edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "paxtoolsr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html" ; biotools:primaryContact "Augustin Luna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:17916232" ; sc:description "Open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of gene expression." ; sc:featureList edam:operation_0224, edam:operation_0438, edam:operation_3431 ; sc:name "PAZAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pazar.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3292, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:32416316" ; sc:description """Automatic peak integration by sequential deep learning for multiple reaction monitoring. PeakBoundaryNet: a sequential neural network for peak boundary detection and peak area integration. Predictions by sequential and reference-based PB-Nets are respectively stored in test_preds.pkl and test_preds_ref.pkl, as a list of numpy arrays representing peak start/end probabilities (in the same order as input). These predictions can also be generated through run.py, based on the pre-trained models. The data used for test is stored in test_input.pkl as a list of peak instances, each instance is a tuple of (X, y, metainfo, sample name & peak name).""" ; sc:featureList edam:operation_3215, edam:operation_3636 ; sc:license "GPL-3.0" ; sc:name "PB-Net" ; sc:url "https://github.com/miaecle/PB-net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:26231429" ; sc:description "Pipeline for file processing and quality control of pedigree data with dense genetic markers." ; sc:featureList edam:operation_2945 ; sc:name "PBAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://faculty.washington.edu/wijsman/software.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121 ; sc:citation ; sc:description "A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment." ; sc:featureList edam:operation_2479 ; sc:license "GPL-3.0" ; sc:name "Pbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Pbase.html" ; biotools:primaryContact "Laurent Gatto", "Sebastian Gibb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation "pmcid:PMC3525120", "pubmed:15814068" ; sc:description "PBAT is an interactive software package for the design of genetic family-based association studies. It provides analytical power calculations for family-based association tests." ; sc:featureList edam:operation_2238 ; sc:license "Not licensed" ; sc:name "PBAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.hsph.harvard.edu/pbat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3321 ; sc:citation ; sc:description "Package that characterizes uncertainty assessment on gene expression classifiers (molecular signatures), based on a permutation test. To achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice." ; sc:featureList edam:operation_0315, edam:operation_2428 ; sc:license "GPL-2.0" ; sc:name "pbcmc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pbcmc.html" ; biotools:primaryContact "Cristobal Fresno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:11025540", "pubmed:15996119", "pubmed:16844973" ; sc:description "This tool uses a structural alphabet of short structural motifs to compare protein structures. It uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database." ; sc:featureList edam:operation_0245, edam:operation_0295, edam:operation_0477, edam:operation_2488 ; sc:name "PBE" ; sc:url "http://bioinformatics.univ-reunion.fr/PBE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0166, edam:topic_0602, edam:topic_0736, edam:topic_3318 ; sc:citation "pubmed:18508808" ; sc:description "PBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential." ; sc:featureList edam:operation_0248, edam:operation_0384, edam:operation_0387, edam:operation_2950 ; sc:name "PBEQ-Solver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.charmm-gui.org/?doc=input/pbeqsolver" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331, edam:format_2376, edam:format_3752 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "SPARQL endpoint", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0780, edam:topic_0797 ; sc:author ; sc:citation , , ; sc:contributor , ; sc:description "Linked Data platform for Plant Breeding & Genomics" ; sc:featureList edam:operation_0224, edam:operation_0361, edam:operation_3282, edam:operation_3436 ; sc:license "Apache-2.0" ; sc:name "pbg-ld" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://www.research-software.nl/software/pbg-ld" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3168, edam:topic_3301 ; sc:citation , "pubmed:34232887" ; sc:description "PBGI is an effective approach and automatic bioinformatics pipeline for bacterial genome identification, performing automatedly and customized bioinformatics analysis using short-reads or long-reads sequencing data produced by multiple platforms such as Illumina, PacBio and Oxford Nanopore." ; sc:isAccessibleForFree true ; sc:name "PBGI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lyotvincent/PBGI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0097, edam:topic_0157, edam:topic_3511 ; sc:citation "pubmed:12824334" ; sc:description "Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses." ; sc:featureList edam:operation_0279, edam:operation_2451, edam:operation_2478 ; sc:name "PBIL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prabi.ibcp.fr/htm/site/web/home" ; biotools:primaryContact "Gilbert DELEAGE", "Raphael TERREUX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC9283883", "pubmed:35860413" ; sc:description "Evaluating statistical significance in a meta analysis by using numerical integration." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Pbine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Yinchun-Lin/Pbine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6334396", "pubmed:30646844" ; sc:description "Multithread blat algorithm speeding up aligning sequences to genomes." ; sc:featureList edam:operation_0302, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "pblat" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/icebert/pblat" ; biotools:primaryContact "M. Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation , ; sc:description "PBM Analysis Suite provides the in-house tools and the procedural methods used in the analysis of universal protein binding microarrays (PBMs) synthesized by Agilent Techonologies" ; sc:featureList edam:operation_2495 ; sc:name "PBM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR." ; sc:featureList edam:operation_0491, edam:operation_3802 ; sc:license "BSD-3-Clause-Clear" ; sc:name "pbmm2" ; sc:softwareVersion "1.4.0" ; sc:url "https://github.com/PacificBiosciences/pbmm2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602, edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:25535244" ; sc:description "GPU based tool for parallel permutation tests in genome-wide association studies." ; sc:featureList edam:operation_2478 ; sc:name "PBOOST" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ust.hk/" ; biotools:primaryContact "Ling Sing Yung", "Weichuan Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3375 ; sc:description "Provides a PBPK and a Renin-Angiotensin system model for SimBiology" ; sc:isAccessibleForFree true ; sc:name "Physiologically-based Pharmacokinetic (PBPK) model for SimBiology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/37132-physiologically-based-pharmacokinetic-pbpk-model-for-simbiology" ; biotools:primaryContact "Sven Mesecke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0622, edam:topic_0625, edam:topic_0634 ; sc:citation , "pmcid:PMC6022555", "pubmed:29452392" ; sc:description """Gene prioritization by correlating functional and phenotypic annotations through integrative data fusion. pBRIT : Gene prioritization tool. pBRIT candiate gene prioritization. pBRIT stands for priortization of candidate genes using Bayesian Ridge Regression and Information Theoretic Model. It is an adaptive and scalable prioritzation tool that integrates Pubmed Abstracts, Gene Ontology, Pathways (Biocarta, EHMN, HumanCyc, INOH, KEGG, NetPath, PharmGKB, PID, Reactome, Signalink, SMPDB, WikiPathways), Protein-Protein Interactions (PhosphoPOINT, PDZBase, NetPath, PINdb, BIND, CORUM, Biogrid, InnateDB, MIPS-MPPI, Spike, Manual upload, MatrixDB, DIP, IntAct, MINT, PDB, HPRD), Protein sequence similarities (BLAST), Mouse Phenotype Ontologies (MPO), Human Phenotype Ontology (HPO), Disease Ontology (DO), Genetic association database (GAD), HuGe. pBRIT is available as web-interface for single exome prioritization or as an API for >1000 exomes in batch mode.""" ; sc:featureList edam:operation_2422, edam:operation_3659, edam:operation_3672 ; sc:name "pBRIT" ; sc:url "http://biomina.be/apps/pbrit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:citation , "pmcid:PMC5605237", "pubmed:28100700" ; sc:description "A web-based platform for real-time collaborative exploration of genomic data." ; sc:featureList edam:operation_2403, edam:operation_3208 ; sc:license "BSD-2-Clause" ; sc:name "PBrowse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pbrowse.victorchang.edu.au/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. This tool simulates those PacBio reads by using either a model-based or sampling-based simulation." ; sc:featureList edam:operation_0310 ; sc:name "PBSIM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "https://code.google.com/p/pbsim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3168, edam:topic_3314 ; sc:citation , "pubmed:32976553" ; sc:description """pbsim2 is a simulator for long read sequencers with a novel generative model of quality scores. When a coverage depth is 100x and a length of reference sequence is about 10M, PBSIM generates simulated dataset in several minutes. The runtime is roughly proportional to the coverage depth and the length of reference sequence. PBSIM requires memory of the length of reference sequence plus several mega bytes.""" ; sc:featureList edam:operation_2426, edam:operation_3185, edam:operation_3198 ; sc:license "GPL-2.0" ; sc:name "PBSIM2" ; sc:url "https://github.com/yukiteruono/pbsim2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275, edam:topic_3534 ; sc:citation , "pubmed:34270697" ; sc:description "Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions." ; sc:featureList edam:operation_0478, edam:operation_2464, edam:operation_2492, edam:operation_2575, edam:operation_3897 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PBSP" ; sc:operatingSystem "Linux" ; sc:url "http://web.pkusz.edu.cn/wu/PBSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3125, edam:topic_3336, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:22689645" ; sc:description "Web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database." ; sc:featureList edam:operation_0224, edam:operation_0478, edam:operation_2575, edam:operation_3222 ; sc:name "PBSword" ; sc:url "http://pbs.rnet.missouri.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3071 ; sc:description "This package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets." ; sc:featureList edam:operation_2945, edam:operation_3431 ; sc:name "PBWT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/richarddurbin/pbwt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0736, edam:topic_1317, edam:topic_2814 ; sc:citation , "pmcid:PMC5700758", "pubmed:29177113" ; sc:description """PBxplore is a suite of tools dedicated to Protein Block (PB) analysis. Protein Blocks are structural prototypes defined by de Brevern et al. (Proteins, 2000, PMID: 11025540). The 3-dimensional local structure of a protein backbone can be modelled as an 1-dimensional sequence of PBs. In principle, any conformation of any amino acid could be represented by one of the sixteen available Protein Blocks.""" ; sc:featureList edam:operation_2480 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PBxplore" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.3.8", "1.4.0" ; sc:url "https://github.com/pierrepo/PBxplore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3307 ; sc:citation , "pubmed:36168679" ; sc:description "R scripts to preform perform principal components regression based on the dot product theory on different frameworks" ; sc:featureList edam:operation_2939, edam:operation_3659 ; sc:license "Not licensed" ; sc:name "PC-DOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SUNHAO-JLU/Genome_Prediction-PC_DOT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3056, edam:topic_3517 ; sc:citation "pubmed:24788602" ; sc:description "Calculates GWAS association statistics using a data-adaptive GRM that improves power over standard mixed models while simultaneously avoiding confounding from population stratification." ; sc:featureList edam:operation_3438 ; sc:name "PC-select" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/gjtucker/PC-Select" ; biotools:primaryContact "Bonnie Berger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0621, edam:topic_3474, edam:topic_3957 ; sc:citation , "pubmed:33416831" ; sc:description """PC2P is a network clustering algorithm that can be used to find protein complexes from protein-protein interaction networks(PPINs). There is an implementation with Jupiter, in which I put some examples. In these examples, you can find the original network and the predicted clusters after applying PC2P along with the total number of removed edges to obtain these clusters.""" ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3925 ; sc:name "PC2P" ; sc:url "https://github.com/SaraOmranian/PC2P" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0153, edam:topic_0154, edam:topic_0749, edam:topic_3342 ; sc:citation , "pmcid:PMC10533498", "pubmed:37758874" ; sc:description "A signature-driven predictor of chemical compounds for cellular transition." ; sc:featureList edam:operation_0310, edam:operation_0314, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "PC3T" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pc3t.idrug.net.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174, edam:topic_3293, edam:topic_3305, edam:topic_3474 ; sc:citation , "pmcid:PMC10193333", "pubmed:37202721" ; sc:description "A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes." ; sc:featureList edam:operation_0495, edam:operation_2995, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "PC-mer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SAkbari93/PC-mer_Corona" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:35662456" ; sc:description "Prediction of Binding Free Energy Change Upon Missense Mutation in Protein-carbohydrate Complexes." ; sc:featureList edam:operation_0475, edam:operation_2488, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PCA-MutPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/pcamutpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3383 ; sc:citation "pubmed:24278197" ; sc:description "Uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture." ; sc:featureList edam:operation_3443 ; sc:name "PCaAnalyser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cs.uno.edu/~tamjid/Software.html" ; biotools:primaryContact "Vicky M. Avery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:24899666" ; sc:description "Software to detect footprints of local adaptation in population genetics data set." ; sc:featureList edam:operation_2403 ; sc:name "PCAdapt" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://membres-timc.imag.fr/Nicolas.Duforet-Frebourg/PCAdapt.html" ; biotools:primaryContact "Michael Blum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3299 ; sc:citation , "pubmed:32343802" ; sc:description """Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4. Using pcadapt to detect local adaptation. Keurcien Luu, Florian Privé, Michael G.B. Blum. pcadapt has been developed to detect genetic markers involved in biological adaptation. pcadapt provides statistical tools for outlier detection based on Principal Component Analysis (PCA).""" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:name "pcadapt" ; sc:softwareVersion "4.0" ; sc:url "https://bcm-uga.github.io/pcadapt/articles/pcadapt.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts." ; sc:featureList edam:operation_2939, edam:operation_3223, edam:operation_3431, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "PCaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.jialab-ucr.org/PCaDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3053 ; sc:citation ; sc:description "Method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.  The method considers data chromosome by chromosome." ; sc:featureList edam:operation_2939, edam:operation_3745 ; sc:name "PCAdmix" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://sites.google.com/site/pcadmix/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis." ; sc:featureList edam:operation_2939 ; sc:license "MIT" ; sc:name "pcaExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pcaExplorer.html" ; biotools:primaryContact "Federico Marini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3125, edam:topic_3518 ; sc:citation , "pmcid:PMC3288097", "pubmed:22384239" ; sc:description "This package contains functions to ease the analyses of DNA micro arrays. 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It integrates possible lifestyles and lifestyle-related factors included foods, nutrients, habits, social factors, environment, associated genes, physiological and biochemical indexes together with the corresponding diseases or drugs. It provides a Lifestyle-Wide Association Studies of PCa (PCa_LWAS), seeking to identify the systematic and deep-seated studies between lifestyles and PCa, and to study the profound benefits achievable with lifestyle changes and to tell people “what to do”, “how to do” and to continue developing ways to encourage choices that promote human health. The ultimate goal is to accelerate the translation of LWAS discoveries into results that are closer to clinical applications, to obtain the accurate predictive models for prostate cancer prevention based on evidence-based personalized lifestyle-related data.""" ; sc:featureList edam:operation_3891 ; sc:name "PCaLiStDB" ; sc:url "http://www.sysbio.org.cn/pcalistdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3517, edam:topic_3518 ; sc:citation , "pubmed:32926120" ; sc:description """PCAmatchR is a flexible R package for optimal case-control matching using weighted principal components. PCAmatchR optimally matches a set of population-based controls to cases. PCAmatchR converts user-provided principal components (PC) into a Mahalanobis distance metric for selecting a set of well-matched controls for each case. Matches cases to controls based on genotype principal components (PC). In order to produce better results, matches are based on the weighted distance of PCs where the weights are equal to the % variance explained by that PC. A weighted Mahalanobis distance metric is used to determine matches.""" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3891 ; sc:license "MIT" ; sc:name "PCAmatchR" ; sc:url "https://github.com/machiela-lab/PCAmatchR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269 ; sc:citation ; sc:description "This tool provides BPCA, PPCA and NipalsPCA that can be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure to provide a common interface to the PCA results." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "pcaMethods" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.66.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pcaMethods.html" ; biotools:primaryContact "Henning Redestig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3053 ; sc:citation , "pmcid:PMC5142268", "pubmed:27923364" ; sc:description "Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors)." ; sc:featureList edam:operation_0277, edam:operation_2451 ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "PCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PCAN.html" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0154, edam:topic_0749, edam:topic_2830, edam:topic_3534 ; sc:citation , "pubmed:33313775" ; sc:description """Prediction of protein-carbohydrate complex binding affinity using structural features. 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This technique offers a good compression ratio at the expense of losing some precision in the trajectory." ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:name "PCASuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mmb.pcb.ub.edu/software/pcasuite/" ; biotools:primaryContact "Institute for Research in Biomedicine Barcelona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3379 ; sc:citation ; sc:description "PDX for Childhood Cancer Therapeutics. An integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models." ; sc:featureList edam:operation_3463 ; sc:name "PCAT" ; sc:url "http://pcat.zhenglab.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:14691953" ; sc:description "Software that performs tSNP selection using principal component analysis (PCA)." ; sc:featureList edam:operation_2939, edam:operation_2945, edam:operation_3661 ; sc:name "PCAtag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-genepi.med.utah.edu/PCAtag/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0176, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:21097895" ; sc:description "Database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structures could be considered as different instances of protein dynamism. As a measure of the conformational diversity we use the maximum RMSD obtained comparing the structures deposited for each domain. The redundant structures were extracted following CATH classification and cross linked." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_2996, edam:operation_3431 ; sc:name "PCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pcdb.unq.edu.ar" ; biotools:primaryContact "Gustavo D. Parisi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_0821, edam:topic_1317 ; sc:citation "pubmed:21071417" ; sc:description "The Protein Circular Dichroism Data Bank is a public repository for circular dichroism and synchrotron radiation CD spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files." ; sc:featureList edam:operation_0224, edam:operation_0319, edam:operation_2428, edam:operation_3431 ; sc:name "PCDDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pcddb.cryst.bbk.ac.uk" ; biotools:primaryContact "PCDDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166 ; sc:citation "pubmed:15980492" ; sc:description "Interface to electrostatic potentials and pKa calculations using the MEAD package." ; sc:featureList edam:operation_0245, edam:operation_0250, edam:operation_0387, edam:operation_0400 ; sc:name "PCE" ; sc:url "http://bioserv.rpbs.jussieu.fr/Help/PCE.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0123, edam:topic_2814 ; sc:citation , "pubmed:26391627" ; sc:description "A pDynamo-based Toolkit for Protonation State Calculations in Proteins" ; sc:featureList edam:operation_0250 ; sc:name "Pcetk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mfx9/pcetk" ; biotools:primaryContact "Mikolaj Feliks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_0602, edam:topic_0623, edam:topic_2275 ; sc:citation "pubmed:20511590" ; sc:description "The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins." ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_0477, edam:operation_3767 ; sc:name "PCFamily" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pcfamily.life.nctu.edu.tw" ; biotools:primaryContact "PCFamily Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0203, edam:topic_3172, edam:topic_3474 ; sc:citation ; sc:description """PCfun (Protein Complex Function). Towards a systematic characterization of protein complex function. Fast and accurate tool for the functional annotation of protein complex queries built upon hybrid unsupervised and supervised machine learning on PubMed Central full-text word embeddings.""" ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3799 ; sc:license "MIT" ; sc:name "PCfun" ; sc:url "https://github.com/sharmavaruns/PCfun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3295, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC9252750", "pubmed:35639771" ; sc:description "A comprehensive web server for phenotype-cell-gene association analysis." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PCGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pmglab.top/pcga" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3475 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3464 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0092, edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3175, edam:topic_3374, edam:topic_3577 ; sc:author ; sc:citation , "pmcid:PMC5946881", "pubmed:29272339" ; sc:contributor ; sc:description "The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for translation of individual tumor genomes for precision cancer medicine. PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations, and produces interactive HTML reports intended for clinical interpretation." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PCGR - Personal Cancer Genome Reporter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , , ; sc:softwareVersion "1.0.2" ; sc:url "https://github.com/sigven/pcgr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3055 ; sc:citation "pubmed:17922480" ; sc:description "Principal Component of Heritability Association Test" ; sc:featureList edam:operation_2939 ; sc:name "PCHAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wpicr.wpic.pitt.edu/WPICCompGen/PCHAT/PCHAT.htm" ; biotools:primaryContact "Bert Klei" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Multiple-enzyme ''in silico'' digester for experimental design." ; sc:featureList edam:operation_0366 ; sc:name "PChopper" ; sc:url "http://pchopper.lifesci.dundee.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0654, edam:topic_3050, edam:topic_3299 ; sc:citation "pubmed:23390499" ; sc:description "Calculates the barcode gap probability of correct identification (PCI) of species." ; sc:featureList edam:operation_2403, edam:operation_3221 ; sc:name "PCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/software/program.html?uid=17" ; biotools:primaryContact "John L. Spouge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3542 ; sc:citation ; sc:description "PCI-SS is a method of predicting protein secondary structure using a PCI-based classifier and also a consensus method to combine PCI with PSIPRED." ; sc:featureList edam:operation_2423, edam:operation_2479, edam:operation_2488 ; sc:name "PCI-SS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinf.sce.carleton.ca/PCISS/start.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_0781, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC8025556", "pubmed:33823910" ; sc:description "Pooled CRISPR Inverse PCR sequencing (PCIP-seq) is a method that leverages selective cleavage of circularized DNA fragments carrying proviral DNA with a pool of CRISPR guide RNAs, followed by inverse long-range PCR and multiplexed sequencing on the Oxford Nanopore MinION platform." ; sc:featureList edam:operation_0308, edam:operation_3185, edam:operation_3192, edam:operation_3227, edam:operation_3933 ; sc:name "PCIP-seq" ; sc:url "https://github.com/GIGA-AnimalGenomics-BLV/PCIP" ; biotools:primaryContact , "Keith Durkin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7789375", "pubmed:33407069" ; sc:description "PCirc is a pipeline to predict plant circular RNA (CircRNA) which based on Python3. It can identify circRNA from a given RNA-seq data by high-throughput. The pipeline can alignment RNA_seq and extract features ,then based on Random Forest classification, the final circRNA will be predicted. 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PeaKO takes in paired wild-type/knockout BAM files in addition to several reference files, as input. It returns a file of ranked motifs (see our paper for more details) | PeaKO finding transcription factor binding motifs using knockout controls | Denisko D, Viner C, Hoffman MM. Motif elucidation in ChIP-seq datasets with a knockout control. BioRxiv 10.1101/721720 [Preprint]. 2019. Available from: https://doi.org/10.1101/721720 | PeaKO identifies motifs relevant to ChIP-seq experiments by combining two differential analysis approaches. 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It uses local-maxima in the LC-HRMS dataset each of which is then exported as a standarized two-dimensional area (rt x mz), which is used as the input for a machine-learning CNN model that reports whether the local-maxima is a chromatographic peak with left/right isomeric compounds or a signal of the background." ; sc:featureList edam:operation_3215, edam:operation_3799, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "PeakBot" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/christophuv/PeakBot_example" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305, edam:format_2330, edam:format_2572, edam:format_2573, edam:format_3003, edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation , , ; sc:description "Peak Finder/Analysis application for the ChIP-Seq." ; sc:featureList edam:operation_3215 ; sc:name "peakcalling_findpeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.0.9.2" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3334, edam:topic_3474, edam:topic_3518, edam:topic_3958 ; sc:citation , "pmcid:PMC9478359", "pubmed:36147666" ; sc:description "A multi-feature ranking algorithm-based tool for genome-wide copy number variation-association study." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PeakCNV" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://rdrr.io/github/mahdieh1/PeakCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3179, edam:topic_3656 ; sc:citation ; sc:description "PeakFinder program was developed to find cohesin binding sites represented by the peaks in yeast chromatin immunoprecipitation (ChIP) microarray data, but can be applied to plot any measurement against a parameter such as genome coordinate, to interactively analyze the measurement plot, and to annotate the peaks on the basis of local properties of the curve." ; sc:featureList edam:operation_2495 ; sc:name "PeakFinder" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://research.stowers-institute.org/gertonlab/peakfinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0593, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9197906", "pubmed:35699774" ; sc:description "A multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3801, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PeakForest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://peakforest.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3277 ; sc:description "PeakHeights is a powerful tool for measuring signal intensities of selected peaks within ABI electropherograms and exporting the data into spreadsheets for easy manipulation. Large batches of samples can be processed at once." ; sc:featureList edam:operation_3443 ; sc:name "PeakHeights" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130408" ; sc:url "http://dna.leeds.ac.uk/peakheights/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3534, edam:topic_3794 ; sc:citation , "pmcid:PMC8796379", "pubmed:34734974" ; sc:description "Peakhood is a tool that takes a set of CLIP-seq peak regions, and for each region individually extracts the most likely site context (transcript or genomic)." ; sc:featureList edam:operation_3215, edam:operation_3222, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Peakhood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BackofenLab/Peakhood" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3473, edam:topic_3520 ; sc:citation "pubmed:24813213" ; sc:description "Uses information in both the time and frequency domain as inputs to a non-linear support vector machine (SVM) classifier. The PL algorithm first removes candidate corresponding peaks with excessively large elution time shifts, then calculates the correlation between a pair of candidate peaks after removing noise. Then a SVM classifier is trained and applied for differentiating corresponding and non-corresponding peptide peaks." ; sc:featureList edam:operation_3215 ; sc:name "PeakLink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compgenomics.utsa.edu/zgroup/PeakLink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3172, edam:topic_3474 ; sc:citation , "pubmed:31841624" ; sc:description """Deep Learning for the Precise Peak Detection in High-Resolution LC-MS Data. peakonly is a novel approach written in Python (v3.5) for peaks (aka features) detection in raw LC-MS data. The main idea underlying the approach is the training of two subsequent artificial neural networks to firstly classify ROIs (regions of interest) into three classes (noise, peaks, uncertain peaks) and then to determine boundaries for every peak to integrate its area. Current approach was developed for the high-resolution LC-MS data for the purposes of metabolomics, but can be applied with several adaptations in other fields that utilize data from high-resolution GC- or LC-MS techniques""" ; sc:featureList edam:operation_3215, edam:operation_3431, edam:operation_3629 ; sc:license "MIT" ; sc:name "peakonly" ; sc:url "https://github.com/arseha/peakonly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3407, edam:topic_3520 ; sc:citation , "pubmed:34125879" ; sc:description "R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets." ; sc:featureList edam:operation_3215, edam:operation_3803, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "peakPantheR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phenomecentre.github.io/peakPantheR.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:22909347" ; sc:description "Serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface." ; sc:featureList edam:operation_3630, edam:operation_3637 ; sc:name "PeakQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ruhr-uni-bochum.de/mpc/software/PeakQuant/index.html.de" ; biotools:primaryContact "Martin Eisenacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation "pubmed:21554709" ; sc:description "A multi-purpose, ultrafast ChIP Seq peak caller" ; 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sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3169, edam:topic_3173 ; sc:citation , "pmcid:PMC9878872", "pubmed:36698077" ; sc:description "An R package for ChIP-seq peak saturation analysis." ; sc:featureList edam:operation_3218, edam:operation_3222, edam:operation_3230, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Peaksat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/FrietzeLabUVM/peaksat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation ; sc:description "PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments." ; sc:featureList edam:operation_3222 ; sc:name "PeakSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://info.gersteinlab.org/PeakSeq" ; biotools:primaryContact "Arif Harmanci", "Joel Rozowsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Alternative basecaller for improving the quality and read length of Sanger DNA sequencing traces. The basecaller works with trace files produced by the ABI 310, 3700, 3100, 3130, 3730, and 3500 DNA sequencers. MegBACE sequencers are also supported." ; sc:featureList edam:operation_3185 ; sc:name "PeakTrace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.peaktrace.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation ; sc:description "Identify transcription factor binding sites from ChIP-seq data at high resolution." ; sc:featureList edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Peakzilla" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/steinmann/peakzilla" ; biotools:primaryContact "Anaïs Bardet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0780 ; sc:description "The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. An ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Plant Experimental Assay Ontology (PEAO)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/PlantExpAssay/ontology" ; biotools:primaryContact "Inês Chaves" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC3933873", "pubmed:24142950" ; sc:description "Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results." ; sc:featureList edam:operation_0232 ; sc:license "CC-BY-NC-1.0" ; sc:name "PEAR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sco.h-its.org/exelixis/web/software/pear/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_2885, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC10325485", "pubmed:37410918" ; sc:description "Multiomics database for pear (Pyrus) genomics, genetics and breeding study." ; sc:featureList edam:operation_0308, edam:operation_0314, edam:operation_2421, edam:operation_2422, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PearMODB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.peardb.org.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:21565121" ; sc:description "Provides the average user who is working on SNP data the basic analysis tools, and make it possible to analysis large SNP data set for those people who do not write programs. It focuses on population genetic analysis of SNP data and most commonly used SNP data operations." ; sc:featureList edam:operation_2478 ; sc:name "PEAS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.picb.ac.cn/PGG/resource.php" ; biotools:primaryContact "Li Jin", "Shuhua Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804, edam:topic_2830, edam:topic_3336 ; sc:citation "pubmed:25432167" ; sc:description "Automated tool for predicting the epitope for a given antigen structure and an antibody sequence." ; sc:featureList edam:operation_0416, edam:operation_2423 ; sc:name "PEASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ofranlab.org/PEASE" ; biotools:primaryContact "Ofran Y" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_1637, edam:format_1638, edam:format_1639, edam:format_3475 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_2331, edam:format_3033, edam:format_3475 ; sc:name "Processed microarray data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_2331, edam:format_3033, edam:format_3475 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3518, edam:topic_3520 ; sc:citation ; sc:description "Calculates Probe-level Expression Change Averages to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively." ; sc:featureList edam:operation_3223, edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "PECA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PECA.html" ; biotools:primaryContact "Tomi Suomi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation "pubmed:18849524" ; sc:description "Alignment method practical for large genomic sequences." ; sc:featureList edam:operation_0292 ; sc:name "PECAN" ; sc:softwareHelp ; sc:url "https://github.com/benedictpaten/pecan" ; biotools:primaryContact "Benedict Paten" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "PECAN (PEptide-Centric Analysis) is a tool for peptide detection directly from DIA data without the need of a spectral library. PECAN takes a list of peptide sequences and query each peptide against the DIA data (in centroid mzML format) and reports the best evidence of detection for each peptide. The PECAN report is designed for Percolator to separate correct from incorrect matches with false discovery rate (FDR) control." ; sc:featureList edam:operation_0224, edam:operation_3215, edam:operation_3631, edam:operation_3649, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PECAN (PEptide-Centric Analysis)" ; sc:softwareHelp ; sc:url "https://bitbucket.org/maccosslab/pecan" ; biotools:primaryContact "Michael MacCoss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """PecanPy: A parallelized, efficient, and accelerated node2vec in Python. Learning low-dimensional representations (embeddings) of nodes in large graphs is key to applying machine learning on massive biological networks. Node2vec is the most widely used method for node embedding. PecanPy is a fast, parallelized, memory efficient, and cache optimized Python implementation of node2vec. It uses cache-optimized compact graph data structures and precomputing/parallelization to result in fast, high-quality node embeddings for biological networks of all sizes and densities.""" ; sc:featureList edam:operation_0337, edam:operation_3927 ; sc:license "BSD-3-Clause" ; sc:name "PecanPy" ; sc:url "https://github.com/krishnanlab/pecanpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "The Personalized Cancer Network Explorer (PeCaX) as a visual analytics tool to support molecular tumor boards." ; sc:featureList edam:operation_3197, edam:operation_3226, edam:operation_3227, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PeCaX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KohlbacherLab/PeCaX-docker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_3168, edam:topic_3360, edam:topic_3958 ; sc:citation , "pmcid:PMC9487654", "pubmed:36056740" ; sc:description "Scripts for accurate and efficient detection of copy number variations of various lengths." ; sc:featureList edam:operation_3219, edam:operation_3435, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PEcnv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Sherwin-xjtu/PEcnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623, edam:topic_3299 ; sc:citation "pubmed:12217925" ; sc:description "This server offers a new way to examine positional conservation in protein sequences." ; sc:featureList edam:operation_0253, edam:operation_0292 ; sc:name "PeCoP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/pecop/" ; biotools:primaryContact "Friedberg I" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0820, edam:topic_3512 ; sc:citation , , "pubmed:33325715" ; sc:description """PeCorA is short for "Peptide Correlation Analysis", which is an R package that enables detection of discordant peptide quantities in shotgun proteomics data. The package also contains a number of published proteomics datasets processed with different processing tools to demonstrate the workflow. Peptide correlation analysis (PeCorA). Detection of Discordant Peptide Quantities in Shotgun Proteomics Data by Peptide Correlation Analysis (PeCorA).""" ; sc:featureList edam:operation_0418, edam:operation_3630, edam:operation_3645, edam:operation_3646, edam:operation_3767 ; sc:license "Apache-2.0" ; sc:name "PeCorA" ; sc:url "https://github.com/jessegmeyerlab/PeCorA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3391 ; sc:citation "pubmed:20959292", "pubmed:21666272" ; sc:description "Repository for pancreatic-derived -omics data. It includes easurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports on a broad range of specimen and experimental types." ; sc:featureList edam:operation_0224, edam:operation_0313, edam:operation_0314, edam:operation_0315, edam:operation_2422 ; sc:name "Pancreatic Expression Database (PED)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pancreasexpression.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3053, edam:topic_3382 ; sc:citation , "pmcid:PMC7727153", "pubmed:33297934" ; sc:description """pedigree drawing with ease. A simple python script to draw (complex and multi generation!) pedigrees with graphviz. ped_draw reads in a ped file (from a specified file or from /dev/stdin) and generates a dot file (to stdout). The subsequent dot output can be piped directly to dot/graphviz to generate png, svg, pdf, ps, or any other image option available in the graphviz documentation.""" ; sc:featureList edam:operation_0573, edam:operation_1812 ; sc:license "MIT" ; sc:name "ped_draw" ; sc:url "https://peddraw.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:21565058" ; sc:description "Windows program that simulates population dynamics at the individual level, allows for heritability and selection of traits, records individual genotype and pedigree information, and allows for several types of errors to manifest in the output which can be formatted for 57 existing software programs." ; sc:featureList edam:operation_2426 ; sc:name "PEDAGOG" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://bcrc.bio.umass.edu/pedigreesoftware/node/5" ; biotools:primaryContact "Jason Coombs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "PedCheck is a program for identification of genotype incompatibilities in linkage analysis.It  will assist researchers in identifying all Mendelian inconsistencies in pedigree data and will provide them with useful and detailed diagnostic information to help resolve the errors." ; sc:featureList edam:operation_0283 ; sc:name "Pedcheck" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.00" ; sc:url "http://watson.hgen.pitt.edu/register/docs/pedcheck.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3574 ; sc:citation "pubmed:18301450" ; sc:description "Program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size." ; sc:featureList edam:operation_0283, edam:operation_0335 ; sc:name "PedCut" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mga.bionet.nsc.ru/soft/index.html" ; biotools:primaryContact "Tatyana I. Axenovich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3574 ; sc:citation "pubmed:9521925" ; sc:description "Software package that facilitates creation and verification of pedigrees within large genealogies." ; sc:featureList edam:operation_0283 ; sc:name "PedHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html" ; biotools:primaryContact "Alejandro Schäffer", "Richa Agarwala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:21923410" ; sc:description "Infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction." ; sc:featureList edam:operation_0487 ; sc:name "PEDIBD" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/xlxlxlxinli/pedibd" ; biotools:primaryContact "Jing Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2815, edam:topic_3053, edam:topic_3175 ; sc:citation , "pmcid:PMC4466794", "pubmed:26073932" ; sc:description "An online gene resource for pediatric cancers with literature evidence." ; sc:featureList edam:operation_0224 ; sc:name "Pedican" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pedican.bioinfo-minzhao.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3055, edam:topic_3056 ; sc:description "Fortran software suited to the analysis of very large populations (up to several tens of million individuals). It is a set of independent programs to: manipulate pedigree information : extract and recode pedigree information, search for errors in the pedigree, extract common ancestors. Characterize the quality of pedigree information. Calculate probabilities of gene origin, relationship coefficients, inbreeding coefficients" ; sc:featureList edam:operation_2238 ; sc:license "Not licensed" ; sc:name "pedig" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=53&Itemid=57" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3500 ; sc:citation "pubmed:14986440" ; sc:description "Pedigraph is able to draw pedigrees with complex inbreeding structures over multiple generations in a population with a large number of individuals, as is common in animal populations." ; sc:name "Pedigraph" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://animalgene.umn.edu/pedigraph/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "It is a software that provides for creation, editing and drawing of pedigrees, or family trees, of human or non-human extended family lineages. It was developed originally for use in analyzing population data gathered for biomedical and genetic research. The program can be used to collect and edit biographical data found in the course of family history research, as well as pictures of family members, and display or print those data in hierarchical diagrams suitable for publication." ; sc:featureList edam:operation_3096 ; sc:name "Pedigree-Draw" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:softwareVersion "6" ; sc:url "http://www.pedigree-draw.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3293 ; sc:citation ; sc:description "Interactive graphical pedigree editor written in JavaScript, which uses standard pedigree nomenclature." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "pedigreejs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccge-boadicea.github.io/pedigreejs/" ; biotools:primaryContact "Tim Carver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0625, edam:topic_0634 ; sc:citation ; sc:description "A new web server for two-way interactive pedigree drawing." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "PedigreeOnline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ig.zju.edu.cn/PedigreeOnline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:15575512" ; sc:description "Program for working with large pedigrees. Some times it is required to get chart only of some shapes of such pedigrees. This tool was made for drawing shapes of pedigrees using step-by-step algorithm." ; sc:featureList edam:operation_3429 ; sc:name "PedigreeQuery" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://mga.bionet.nsc.ru/soft/pedquery/pedigreequery.html" ; biotools:primaryContact "Kirichenko AV." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:23013469" ; sc:description "Software that generates simulated genetic marker data of individuals in pedigreed populations. A population can consist of either diploid or tetraploid individuals. It can simulate meioses with or without chiasma interference, and in tetraploids it can simulate meioses with two bivalents or one quadrivalent per set of hom(oe)ologous chromosomes." ; sc:featureList edam:operation_2426 ; sc:name "PedigreeSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.wageningenur.nl/en/show/Software-PedigreeSim.htm" ; biotools:primaryContact "Roeland E Voorrips" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3053 ; sc:citation "pubmed:23087384" ; sc:description "Software designed to graphically present genetic information in pedigrees. This information can include phenotypic data, observed marker alleles, calculated Identity by Descent (IBD) probabilities, and (to be added) QTL (Quantitative Trait Loci) allele probabilities." ; sc:featureList edam:operation_0337 ; sc:name "Pedimap" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.wageningenur.nl/en/show/Pedimap.htm" ; biotools:primaryContact "Roeland E. Voorrips" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:23462161" ; sc:description "Fortran program for rapid haplotype construction and genotype imputation for whole genome SNP panels in general pedigrees dominated by medium to large half-sib families as in dairy cattle data." ; sc:featureList edam:operation_0487 ; sc:name "PedImpute" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dekoppel.eu/pedimpute/" ; biotools:primaryContact "E.L.Nicolazzi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:19761602" ; sc:description "Designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data from a pedigree of two generations: two parents with two or more children. I" ; sc:featureList edam:operation_2945 ; sc:name "pediSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://pevsnerlab.kennedykrieger.org/pediSNP/" ; biotools:primaryContact "Jonathan Pevsner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3053 ; sc:citation "pubmed:15829728" ; sc:description "Software package to recursively analyse plant pedigree data which is arranged in a simple-single table database structure." ; sc:featureList edam:operation_2945 ; sc:name "Peditree" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.softsea.com/review/PediTree.html" ; biotools:primaryContact "ralph.vanberloo@wur.nl." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0218, edam:topic_0602, edam:topic_3474 ; sc:citation , "pmcid:PMC7355289", "pubmed:32657389" ; sc:description "PEDL is a method for predicting protein-protein assocations from text. extracting protein-protein associations using deep language models and distant supervision." ; sc:featureList edam:operation_3280, edam:operation_3625, edam:operation_3928 ; sc:name "PEDL" ; sc:url "https://github.com/leonweber/pedl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:32393981" ; sc:description """PedMiner is a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data. The advance in Next Generation Sequencing technology has revolutionized the field of disease research. ( PedMiner offers a default filtration process to prioritize the candidate variants ). Inheritance Pattern: Autosomal recessive.""" ; sc:featureList edam:operation_0283, edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:name "PedMiner" ; sc:url "https://mcg.ustc.edu.cn/bsc/pedminer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:17500037" ; sc:description "Prepares pedigree data for calculation of Elston-Stewarts’ likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays." ; sc:featureList edam:operation_2238, edam:operation_2409 ; sc:name "PedPeel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mga.bionet.nsc.ru/soft/pedpeel/" ; biotools:primaryContact "Nadezhda Belonogova" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:19507288" ; sc:description "Suite of computer programs for haplotype inference from genotypes on pedigree data. It consists of several different algorithms that are designed based on a combinatorial formulation of haplotype inference, namely the minimum-recombinant haplotype configuration (MRHC) problem, and are effective for different types of data." ; sc:featureList edam:operation_0487 ; sc:name "PedPhase" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://engr.case.edu/li_jing/haplotyping.html" ; biotools:primaryContact "Jing Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3518, edam:topic_3520, edam:topic_3676 ; sc:citation "pubmed:12610571", "pubmed:15073025" ; sc:description "Software and schemata for modelling, capturing and disseminating proteomics experimental data" ; sc:featureList edam:operation_0477, edam:operation_2409, edam:operation_2428, edam:operation_2495, edam:operation_3561 ; sc:name "PEDRo" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pedrodownload.man.ac.uk/" ; biotools:primaryContact "Kevin Garwood (Support)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3053 ; sc:description "Handy tool for quick validation and summary of any pair of pedigree (.ped) and data (.dat) files. It produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets." ; sc:featureList edam:operation_2428, edam:operation_2429 ; sc:name "PEDSTATS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.12" ; sc:url "http://www.sph.umich.edu/csg/abecasis/PedStats/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3473 ; sc:description "Database system developed as a specialized tool for management of genetic, pedigree and demographic data." ; sc:featureList edam:operation_2409 ; sc:license "Other" ; sc:name "PEDSYS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pedsys.txbiomedgenetics.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3510 ; sc:author "Tatyana Goldberg" ; sc:citation ; sc:contributor "Alexander von Humboldt foundation through the German Federal Ministry for Education and Research", "Burkhard Rost", "Ernst Ludwig Ehrlich Studienwerk", "Yana Bromberg" ; sc:description "Prediction of type III effector proteins from protein sequence." ; sc:featureList edam:operation_1777 ; sc:funder "Alexander von Humboldt foundation through the German Federal Ministry for Education and Research", "Ernst Ludwig Ehrlich Studienwerk" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "pEffect" ; sc:operatingSystem "Linux" ; sc:provider "RostLab", "Rutgers University", "Technical University of Munich" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://rostlab.org/services/peffect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3372, edam:topic_3512 ; sc:citation "pubmed:15096276" ; sc:description "Pegasys is a a flexible, modular and customizable software system that coordinates the execution of multiple biological sequence analysis tools and facilitates the integration of their output. The software allows users to create analysis workflows using a graphical user interface. Adaptors are included for various software tools." ; sc:featureList edam:operation_2403, edam:operation_2409, edam:operation_3695 ; sc:name "Pegasys" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioextract.org/query/index.jsp" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_0821, edam:topic_3168, edam:topic_3511 ; sc:citation ; sc:description "pegFinder: pegRNA designer for CRISPR prime editing." ; sc:featureList edam:operation_0308, edam:operation_0363, edam:operation_3096 ; sc:license "MIT" ; sc:name "pegFinder" ; sc:url "http://pegfinder.sidichenlab.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2554 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0632, edam:topic_3047, edam:topic_3512, edam:topic_3912 ; sc:citation , "pmcid:PMC8265180", "pubmed:34060619" ; sc:description "pegIT facilitates rapid and effective design of pegRNAs for prime editing based on simple inputs." ; sc:featureList edam:operation_0308, edam:operation_0479, edam:operation_2422, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "pegIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pegit.giehmlab.dk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3173, edam:topic_3292 ; sc:citation ; sc:description "Platform for Epigenomic and Genomic Research (PEGR) is a web service platform that logs metadata for samples and sequencing experiment, manages the data processing workflows, and provides reporting and visualization." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3216, edam:operation_3431, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PEGR" ; sc:operatingSystem "Mac" ; sc:url "https://github.com/seqcode/pegr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:name "Sequence cluster" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2085 ; sc:encodingFormat edam:format_3003 ; sc:name "Structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3003 ; sc:name "Count matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:name "Statistical estimate score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3173 ; sc:citation , "pmcid:PMC8406447", "pubmed:34504687" ; sc:description "PEGS (Peak-set Enrichment of Gene-Sets) is a Python bioinformatics utility for calculating enrichments of gene cluster enrichments from peak data at different genomic distances." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PEGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pegs.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0176, edam:topic_0602 ; sc:citation "pubmed:23729469" ; sc:description "Model the all-atom protein-ligand dynamical interactions." ; sc:featureList edam:operation_0477, edam:operation_0478, edam:operation_0480, edam:operation_0482, edam:operation_2476 ; sc:name "PELE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pele.bsc.es" ; biotools:primaryContact "Joan Gilabert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:19236709" ; sc:description "The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from the ‘novel’ genome. Subsequent analysis with PEMer workflow on the simulated reads can facilitate parameterize PEMer workflow." ; sc:featureList edam:operation_3228 ; sc:name "PEMer" ; sc:operatingSystem "Linux" ; sc:url "http://sv.gersteinlab.org/pemer/" ; biotools:primaryContact "Mark Gerstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0128, edam:topic_0199, edam:topic_3315, edam:topic_3318 ; sc:citation , "pmcid:PMC8084330", "pubmed:33872313" ; sc:description "PEMPNI (Predictors for Effects of Mutations on PNIs) is a computational method that could effectively predict the effects of missense mutations on protein-DNA and protein-RNA interactions. This algorithm includes an energy module and a nonenergy module. The former is based on the novel geometric partition-based energy features, and the latter is based on the structural and sequence features. The integration of multifaceted information could generate more robust predictions." ; sc:featureList edam:operation_0331, edam:operation_0420, edam:operation_3659, edam:operation_3900, edam:operation_3901 ; sc:name "PEMPNI" ; sc:url "http://liulab.hzau.edu.cn/PEMPNI" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3305, edam:topic_3336 ; sc:citation , "pmcid:PMC9805556", "pubmed:36322820" ; sc:description "A patent enrichment tool for drug discovery." ; sc:featureList edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PEMT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Fraunhofer-ITMP/PEMT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2099 ; sc:name "Name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3512, edam:topic_3922 ; sc:citation , "pmcid:PMC8405889", "pubmed:34504668" ; sc:description "Protein-gene Expression Nexus (PEN), which consolidates an extensive dataset of paired proteomics and genomics studies. PEN present a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy number alterations, transcriptomic differences, peptide expressions, and modifications. As a freely available resource, PEN provide new insights into the proteogenomic landscape cancer cells, allowing more detailed study of oncogenesis and cancer treatment. A search using PEN can produce quantitative comparisons of proteogenomic analysis results, as following feature." ; sc:featureList edam:operation_0417, edam:operation_3638, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "PEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://combio.snu.ac.kr/pen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3577 ; sc:citation , "pmcid:PMC7274464", "pubmed:32392248" ; sc:description "An R package that performs personalized differential analysis of omics data. The penda package provide different methods to perform differential analysis and rank-based method for personalized differential analysis." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3891 ; sc:name "PenDA" ; sc:url "https://github.com/bcm-uga/penda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "Penguin is a tool for predicting pseudouridine sites in direct RNA nanopore sequencing data. The penguin tool needs as input a fast5 path and if you don't provide a sam file you have to provide a reference genome to align to so the tool can create the sam file. If no bed file is provided a default one is included and will be used. The tool will then id all fast5 files and create coordinate file with ids of files that are modified." ; sc:featureList edam:operation_3185, edam:operation_3359, edam:operation_3937 ; sc:name "Penguin" ; sc:url "https://github.com/Janga-Lab/Penguin" ; biotools:primaryContact "Sarath Chandra Janga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3175 ; sc:citation ; sc:description "Free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "PennCNV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://penncnv.openbioinformatics.org/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3063, edam:topic_3175 ; sc:citation , "pmcid:PMC3834792", "pubmed:24021380" ; sc:description "A C++ software package for detection of copy number alterations on tumor samples from SNP arrays and NGS data." ; sc:featureList edam:operation_2480 ; sc:license "Not licensed" ; sc:name "PennCNV2" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/WGLab/PennCNV2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "PennSeq is a statistical method that allows each isoform to have its own non-uniform read distribution." ; sc:featureList edam:operation_0314, edam:operation_3799 ; sc:name "PennSeq" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://sourceforge.net/projects/pennseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2275, edam:topic_3047 ; sc:citation "pubmed:19728739" ; sc:description "Advanced software tool for obtaining alignment-independent 3D quantitative structure-activity relationships. The program starts from a set of structures, computing highly relevant 3D maps of interaction energies between the molecule and chemical probes (GRID based Molecular Interaction Fields, or MIFs)." ; sc:featureList edam:operation_0272 ; sc:name "Pentacle" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.moldiscovery.com/login.php" ; biotools:primaryContact "Manuel Pastor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC8976968", "pubmed:35366792" ; sc:description "A tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments." ; sc:featureList edam:operation_2939, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pentad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/magnitov/pentad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Pentaho is business intelligence (BI) software that provides data integration, OLAP services, reporting, information dashboards, data mining and extract, transform, load (ETL) capabilities." ; sc:featureList edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "Pentaho" ; sc:softwareVersion "Stable release 9.2.0.0-290 June 2, 2021;" ; sc:url "https://github.com/pentaho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_3520, edam:topic_3538, edam:topic_3542 ; sc:citation , "pmcid:PMC8924573", "pubmed:35294674" ; sc:description "The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins." ; sc:featureList edam:operation_0272, edam:operation_0468, edam:operation_0469, edam:operation_0470, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "PentUnFOLD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://3.17.12.213/pent-un-fold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0780, edam:topic_3170 ; sc:citation , "pubmed:38050352" ; sc:description "Comparative transcriptomic database for 103 Archaeplastida." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_2942, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "PEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://expression.plant.tools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0621, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. Pipeline results reporting package. Project metadata manager for PEPs in Python. python interface reporting postgresql pipelines results reproducibility. PEP, or Portable Encapsulated Projects, is a community effort to make sample metadata reusable. PEPs decouple metadata from analysis by providing:. An open structure and toolkit for organizing large-scale, sample-intensive biological research projects. A PEP is written using a familiar yaml + csv format that can be read by our R and Python packages, and well as by workflow frameworks. PEP is your metadata solution for sample-intensive research projects.""" ; sc:featureList edam:operation_1812, edam:operation_2428, edam:operation_3435 ; sc:name "PEP" ; sc:url "http://pep.databio.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation "pubmed:19433514", "pubmed:22581768", "pubmed:26588162", "pubmed:27131374" ; sc:description "PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides." ; sc:featureList edam:operation_0476 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PEP-FOLD" ; sc:softwareHelp ; sc:softwareVersion "2.0", "3.5" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD3" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3322, edam:topic_3335, edam:topic_3474 ; sc:citation , "pubmed:35358751" ; sc:description "A web server for prediction of highly specific peptides targeting voltage-gated Na+ channels using machine learning techniques." ; sc:featureList edam:operation_3454, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "PEP-PRED Na+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://peppredna.herokuapp.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3534 ; sc:citation "pubmed:24803671", "pubmed:28236231" ; sc:description "PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces." ; sc:featureList edam:operation_0476, edam:operation_3897 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PEP-SiteFinder" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-SiteFinder" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_3299 ; sc:citation , "pubmed:35598299" ; sc:description "Evolution Guided Design of Inhibitory Peptides" ; sc:featureList edam:operation_0482, edam:operation_2492, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Pep-Whisperer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo3d.cs.tau.ac.il/PepWhisperer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "Peptide Secondary Structure Prediction server that allows users to predict regular secondary structure in their peptides." ; sc:featureList edam:operation_2945 ; sc:name "pep2d" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pep2d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0634, edam:topic_3520 ; sc:citation , "pubmed:35924633" ; sc:description "A standalone tool to analyse proteolytic cleavages by proteases from gel-based mass spectrometry data." ; sc:featureList edam:operation_0372 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Pep2Graph" ; sc:operatingSystem "Mac", "Windows" ; sc:url "http://www.mathivananlab.org/Pep2Graph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0196 ; sc:citation , "pmcid:PMC4154637", "pubmed:25188327" ; sc:description "Automate the identification of biosynthetic gene clusters for peptides analyzed by tandem MS approaches, by matching mass shift sequences from mass spectra to the gene clusters that most likely encode the corresponding peptide." ; sc:featureList edam:operation_2929, edam:operation_3643, edam:operation_3803 ; sc:license "GPL-3.0" ; sc:name "Pep2Path" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.0" ; sc:url "http://pep2path.sourceforge.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0942 ; sc:encodingFormat edam:format_3603 ; sc:name "2D PAGE image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15228367" ; sc:description "Plots LC-MS and LC-MS/MS data in a 2D ''m''/''z'' vs time plot." ; sc:featureList edam:operation_3203, edam:operation_3441, edam:operation_3694 ; sc:name "Pep3D" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/Pep3D.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_0769, edam:topic_3697 ; sc:citation ; sc:description """pepFunk is a tool for peptide-centric functional analysis in metaproteomic human gut microbiome studies. It is a metaproteomic peptide-centric functional enrichment workflow. pepFunk allows you to complete a peptide-focused functional enrichment workflow for gut microbiome metaproteomic studies. This workflow uses KEGG annotation for pathway enrichment, alongside Gene Set Variation Analysis (GSVA) adapted for peptide data. By completing analysis on peptides, rather than proteins, we lose less information and retain more statistical power. We curated peptide database specific to human gut microbiome studies for computational speed.""" ; sc:featureList edam:operation_3501, edam:operation_3755, edam:operation_3891 ; sc:name "pepFunk" ; sc:url "https://shiny.imetalab.ca/pepFunk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Meta-Search peptide identification platform for tandem mass spectra" ; sc:featureList edam:operation_3631 ; sc:name "PepArML" ; sc:url "https://edwardslab.bmcb.georgetown.edu/pymsio/" ; biotools:primaryContact "Nathan J. Edwards" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769 ; sc:citation ; sc:description """An optimized ATAC-seq pipeline with serial alignments. PEPATAC is a pipeline designed to process ATAC-seq data. For more information see: http://pepatac.databio.org/. PEPATAC is an ATAC-seq pipeline. It trims adapters, maps reads, calls peaks, and creates bigwig tracks, TSS enrichment files, and other outputs. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches. An open structure and toolkit for organizing large-scale, sample-intensive biological research projects. PEP, or Portable Encapsulated Projects, is a community effort to make sample metadata reusable. PEPs decouple metadata from analysis-""" ; sc:featureList edam:operation_1812, edam:operation_3180, edam:operation_3192, edam:operation_3222 ; sc:license "BSD-2-Clause" ; sc:name "PEPATAC" ; sc:url "https://pepatac.databio.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:35604077" ; sc:description "Predicting protein-peptide binding residues via interpretable deep learning." ; sc:featureList edam:operation_0272, edam:operation_0482, edam:operation_3092, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PepBCL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://server.wei-group.net/PepBCL/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1929 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_1317, edam:topic_2258, edam:topic_3510 ; sc:citation , "pmcid:PMC3760854", "pubmed:24019881" ; sc:description "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database." ; sc:featureList edam:operation_0477 ; sc:name "PepBindPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1929 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_1317, edam:topic_2258, edam:topic_3510 ; sc:citation , "pmcid:PMC3760854", "pubmed:24019881" ; sc:description "PepBindPred is for users interested in identifying peptide binding regions within a protein sequence, which may bind to a know protein structure. PepBindPred was trained on a set of non-redundant protein sequences containing known peptide binding regions sourced from the ELM database." ; sc:featureList edam:operation_0477 ; sc:name "PepBonPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/pepbindpred.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:15215449" ; sc:description "Tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format." ; sc:featureList edam:operation_0570, edam:operation_2416, edam:operation_2488 ; sc:name "PepBuild" ; sc:url "http://www.imtech.res.in/bvs/pepbuild/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0123, edam:topic_0154, edam:topic_3047 ; sc:citation , "pmcid:PMC7097909", "pubmed:32226857" ; sc:description """a Tool for Generating Peptide Combinations. A tool for generating all the possible combinations that a particular peptide sequence can acquire owing to its physiochemical properties. Peptide combination generator (PepCoGen), a web server for generating all the possible combinations of peptides by varying the amino acids having similar physiochemical properties at a particular position. It also predicts other properties of the peptides including molecular weight, charge, solubility, hydrophobic plot, and isoelectric point, and random three-dimensional models for each generated combination.""" ; sc:featureList edam:operation_0398, edam:operation_0407, edam:operation_0418, edam:operation_3631 ; sc:name "PepCoGen" ; sc:url "https://www.bicfri.in/pepcogen/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Predict coiled coil regions in protein sequences." ; sc:featureList edam:operation_0268 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepcoil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepcoil.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Report on protein proteolytic enzyme or reagent cleavage sites." ; sc:featureList edam:operation_0422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepdigest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepdigest.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154 ; sc:citation "pubmed:22623377" ; sc:description "Software designed to validate the peptide identifications obtained from MASCOT search results." ; sc:featureList edam:operation_2428 ; sc:name "PepDistiller" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.bprc.ac.cn/PepDistiller/" ; biotools:primaryContact "Fuchu He", "Ning Li", "Yunping Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC4159663", "pubmed:24878498" ; sc:contributor ; sc:description "PepExplorer – Statistically Filtering and Organising de novo Sequencing Results" ; sc:featureList edam:operation_2479, edam:operation_3644, edam:operation_3695 ; sc:name "PepExplorer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0.78" ; sc:url "http://proteomics.fiocruz.br/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33843206" ; sc:description "PepFormer is a end-to-end Siamese network coupled with a hybrid architecture of a Transformer and gated recurrent units that is able to predict the peptide detectability based on peptide sequences only." ; sc:featureList edam:operation_3092, edam:operation_3767, edam:operation_3927 ; sc:license "MIT" ; sc:name "PepFormer" ; sc:url "https://github.com/WLYLab/PepFormer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_2258, edam:topic_2830 ; sc:citation , "pmcid:PMC8002403", "pubmed:33809815" ; sc:description "PepFun is a compilation of bioinformatics and chemoinformatics functionalities that are easy to implement and personalize for studying peptides at different levels: sequence, structure and large datasets. The package has been created under the python scripting language based on built-in functions and methods available in the open source projects BioPython and RDKit. Some of the prediction and characterization tools were tested with two datasets of peptide binders of known protein systems, the MHC class II and the Granzyme B protease." ; sc:featureList edam:operation_0252, edam:operation_0394, edam:operation_0418, edam:operation_3631, edam:operation_3938 ; sc:license "MIT" ; sc:name "PepFun" ; sc:url "https://github.com/rochoa85/pepfun" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0637, edam:topic_2269 ; sc:citation , "pmcid:PMC10182852", "pubmed:37129543" ; sc:description "A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores." ; sc:featureList edam:operation_3435, edam:operation_3649, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "PepGM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BAMeScience/PepGM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "pephub is a biological metadata server that lets you view, store, and share your sample metadata in form of PEPs. It has 3 components: 1) a database where PEPs are stored; 2) an API to programmatically read and write PEPs in the database; and 3) a web-based user interface to view and manage these PEPs via a front-end." ; sc:name "pephub" ; sc:url "https://pephub.databio.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1506 ; sc:name "Amino acid index (hydropathy)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1502 ; sc:name "Amino acid index (chemical classes)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Plot amino acid properties of a protein sequence in parallel." ; sc:featureList edam:operation_0250 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepinfo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepinfo.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0123 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Plot amino acid properties of a protein sequence in parallel." ; sc:featureList edam:operation_0250 ; sc:name "pepinfo (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/seqstats/emboss_pepinfo/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:27224861" ; sc:description "Pipeline that is dedicatedly developed for Polygenic, specifically, Epistatic QTL mapping." ; sc:featureList edam:operation_2429 ; sc:name "PEPIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.noble.org/PolyGenic_QTL/" ; biotools:primaryContact "Patrick X. Zhao", "Shizhong Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC5098197", "pubmed:27819351" ; sc:description "PEPlife is a manually curated database of experimentally validated therapeutic peptides and their half-lives." ; sc:featureList edam:operation_2945 ; sc:name "peplife" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/peplife/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_3557 ; sc:citation , ; sc:description "PepMapper is a web-based mapping tool developed for the purpose of epitope prediction using a collection of affinity selected peptides (mimotopes) derived from phage display experiments." ; sc:featureList edam:operation_2423, edam:operation_2429, edam:operation_2479 ; sc:name "PepMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://informatics.nenu.edu.cn/PepMapper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258 ; sc:citation ; sc:description "Web-oriented tool that, given a peptide three-dimensional structure, is able to automate a multi-conformers three-dimensional similarity search among 17 million of conformers calculated from 3.9 million of commercially available chemicals collected in the MMsINC database." ; sc:featureList edam:operation_2421 ; sc:name "pepMMsMIMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://mms.dsfarm.unipd.it/pepMMsMIMIC/" ; biotools:primaryContact "Stefano Moro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2163 ; sc:name "Helical net" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw a helical net for a protein sequence." ; sc:featureList edam:operation_0319, edam:operation_2574 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepnet.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3653, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15858974" ; sc:description "\"De novo\" sequencing using probabilistic network modeling." ; sc:featureList edam:operation_2238, edam:operation_3631, edam:operation_3644 ; sc:name "PepNovo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/ProteoSAFe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_3053 ; sc:citation , "pmcid:PMC7605250", "pubmed:33055096" ; sc:description """Accurate reconstruction of bacterial pan- and core genomes with PEPPAN. PEPPAN (Phylogeny Enhanced Pipeline for PAN-genome) is a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPAN implements a combination of tree- and synteny-based approaches to identify and exclude paralogous genes, as well as similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes. There are two final output files for PEPPAN:. This file includes all pan-genes predicted by PEPPAN in GFF3 format. Intact CDSs are labeled as "CDS", disrupted genes (potential pseudogenes) are labeled as "pseudogene" and suspicious annotations ignored in the pipeline are labeled as "misc_feature" entries.""" ; sc:featureList edam:operation_0553, edam:operation_3478, edam:operation_3663, edam:operation_3797, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "PEPPAN" ; sc:softwareHelp ; sc:url "https://github.com/zheminzhou/PEPPAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:25138169" ; sc:description "Plugin which finds meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization." ; sc:featureList edam:operation_2949 ; sc:name "Pepper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.issb.genopole.fr/Technology/pepper-cytoscape-app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation ; sc:description "PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant." ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "P.E.P.P.E.R. and DeepVariant" ; sc:softwareHelp , ; sc:url "https://github.com/kishwarshafin/pepper" ; biotools:primaryContact "Kishwar Shafin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0769, edam:topic_3474 ; sc:citation , "pmcid:PMC8897833", "pubmed:35662463" ; sc:description "Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning." ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PEPPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanggroup.org/PEPPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """Quality control and processing of nascent RNA profiling data. PEPPRO is a pipeline for nascent RNA sequencing data. It can process PRO-seq, GRO-seq, and ChRO-seq data and is optimized on unique features of nascent RNA to be fast and accurate. It performs variable-length UMI adapter removal, read deduplication, trimming, mapping, QC, and signal tracks (bigWig) for plus and minus strands using mappability-scaled or unscaled read counts.""" ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3192, edam:operation_3472 ; sc:license "BSD-2-Clause" ; sc:name "PEPPRO" ; sc:url "https://peppro.databio.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_2330 ; sc:name "ID list" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:name "Evidence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3308 ; sc:author "Olivier Sallou", "Thomas Darde" ; sc:citation ; sc:contributor "Lydie Lane", "Olivier Collin", "Paula P. Duek" ; sc:description "A gene expression-based prioritization system to help investigators to determine in which human tissues they should look for an unseen protein." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "PepPSy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://peppsy.genouest.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3652, edam:format_3653 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0622, edam:topic_2640, edam:topic_3520 ; sc:citation "pubmed:23614390" ; sc:description "A software that identifies new proteins and aberrant protein forms withing proteomic data." ; sc:featureList edam:operation_0362, edam:operation_0366, edam:operation_3631, edam:operation_3646, edam:operation_3648, edam:operation_3649, edam:operation_3767 ; sc:name "Peppy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.geneffects.com/peppy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "peppy is the official python package for reading Portable Encapsulated Projects or PEPs in python." ; sc:name "peppy" ; sc:softwareVersion "0.31.1" ; sc:url "http://peppy.databio.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:36474016" ; sc:description "A Comprehensive Data Source and Information Platform for Peptide Quantitative Structure–Activity Relationships." ; sc:featureList edam:operation_3659, edam:operation_3664, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "PepQSAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/PQsarDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3169, edam:topic_3511 ; sc:citation "pubmed:24894502" ; sc:description "Analysis pipeline for ChIP-Seq experiments with biological replicates, written and available as python scripts." ; sc:featureList edam:operation_3222 ; sc:name "PePr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sartorlab.ccmb.med.umich.edu/node/6" ; biotools:primaryContact "Maureen A. Sartor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "pepr is the official R package for reading Portable Encapsulated Projects or PEPs in R." ; sc:name "pepr" ; sc:softwareVersion "0.4.0" ; sc:url "http://code.databio.org/pepr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_3168 ; sc:citation , "pubmed:35192366" ; sc:description "Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization." ; sc:featureList edam:operation_0292, edam:operation_0564, edam:operation_3096, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PepSeA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Merck/PepSeA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation "pubmed:21572105" ; sc:description "Web server for peptide analysis, clustering and visualization." ; sc:featureList edam:operation_2479, edam:operation_3432 ; sc:name "PepServe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserver-1.bioacademy.gr/Bioserver/PepServe/" ; biotools:primaryContact "George M. Spyrou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0166, edam:topic_0209, edam:topic_2275 ; sc:citation , "pubmed:32324992" ; sc:description """Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes. A benchmark consisting of 185 protein-peptide complexes with peptide length ranging from 5 to 20 residues.""" ; sc:featureList edam:operation_0482, edam:operation_2575, edam:operation_3899 ; sc:name "PepSet" ; sc:url "http://cadd.zju.edu.cn/pepset/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:name "Protein structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121 ; sc:citation ; sc:description "Visualization of conformational proteomics data." ; sc:featureList edam:operation_2479 ; sc:name "Pepshell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "0.9" ; sc:url "https://github.com/compomics/pepshell" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_0749, edam:topic_2830 ; sc:citation , "pubmed:34478497" ; sc:description "pepsickle is an open-source command line tool for proteasomal cleavage prediction. pepsickle is designed with flexibility in mind allows for the use of either direct amino acid sequences or the use of FASTA files. Predictions can also be determined based on a variety of available models including those trained on: in-vivo epitope data (default), in-vitro constitutive proteasome data, or in-vitro immunoproteasome data." ; sc:featureList edam:operation_0416, edam:operation_0418, edam:operation_0422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pepsickle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pdxgx/pepsickle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_0602 ; sc:citation "pubmed:22600738" ; sc:description "PepSite webserver predicts binding of a given peptide onto a protein structure, enabling users to better understand the details of the interaction of interest." ; sc:featureList edam:operation_0387, edam:operation_0474, edam:operation_2464, edam:operation_2492, edam:operation_3439 ; sc:name "PepSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pepsite2.russelllab.org" ; biotools:primaryContact "PepSite Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:17768164" ; sc:description "Cache-optimized search algorithm." ; sc:featureList edam:operation_3647 ; sc:name "PepSplice" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/buotex/BICEPS/tree/master/libs/pepsplice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_3518 ; sc:citation ; sc:description "Statistical analysis of peptide microarrays." ; sc:featureList edam:operation_0418 ; sc:license "Artistic-2.0" ; sc:name "pepStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pepStat.html" ; biotools:primaryContact "Gregory C Imholte" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1505 ; sc:name "Amino acid index (molecular weight)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1502 ; sc:name "Amino acid index (chemical classes)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Calculate statistics of protein properties." ; sc:featureList edam:operation_0250 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepstats.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0123 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Calculate statistics of protein properties." ; sc:featureList edam:operation_0250 ; sc:name "pepstats (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/seqstats/emboss_pepstats" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:17897087" ; sc:description "The Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the methods uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns." ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0469, edam:operation_0470, edam:operation_0474 ; sc:name "PepStr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/pepstr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allows you to predict the 3D structure of peptides from its amino acid sequence." ; sc:featureList edam:operation_2945 ; sc:name "pepstr2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pepstr2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "The PEPstrMOD server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues." ; sc:featureList edam:operation_2945 ; sc:name "pepstrmod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pepstrmod/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0122, edam:topic_0601 ; sc:citation ; sc:description "Manual annotation of MS data for intact glycopeptides. It displays an interactive map of all theoretical glycopeptides that match the molecular masses of queried precursor ions. Ion matching can be performed in two modes: simple when the search space spans the combination of all tryptic peptides including N-glycosites in the human proteome, and advanced when the search space is custom-built by specifying peptides and glycans." ; sc:featureList edam:operation_0417 ; sc:name "PepSweetener" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://glycoproteome.expasy.org/pepsweetener/app/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3303, edam:topic_3375 ; sc:citation , "pubmed:33647438" ; sc:description "PepTherDia is a database and tool for structural composition analysis of approved peptide therapeutics and diagnostics. Manually curated database containing a searchable list of approved peptide drugs and diagnostic agents. On these compounds, we have performed a detailed analysis of the structural features and collected information on their physicochemical and pharmacokinetic properties, indication, route of administration, production methodologies, marketing authorisation and origin of their design. The final purpose of this database is to aid the scientific community to more successfully design or pre-screen candidates at an early stage of the peptide drug discovery process." ; sc:featureList edam:operation_4009 ; sc:name "PepTherDia" ; sc:url "http://peptherdia.herokuapp.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:25574629" ; sc:description "Interpretation of proteomics identification results." ; sc:featureList edam:operation_2479 ; sc:name "Peptide-shaker" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.7.1" ; sc:url "http://compomics.github.io/projects/peptide-shaker.html" ; biotools:primaryContact "Lennart Martens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157 ; sc:citation ; sc:description "Quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms." ; sc:featureList edam:operation_0236, edam:operation_2479 ; sc:name "Peptide Match" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://research.bioinformatics.udel.edu/peptidematch/docs/userguide.htm#single_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2398 ; sc:name "Ensembl protein ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2398 ; sc:name "Ensembl protein ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:name "Protein identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2398 ; sc:name "Ensembl protein ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2398 ; sc:name "Ensembl protein ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2384 ; sc:name "IPI protein ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2331 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2332 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation ; sc:description "A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences." ; sc:featureList edam:operation_0224 ; sc:name "PeptideAtlas peptide database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.peptideatlas.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1056 ; sc:encodingFormat edam:format_2330 ; sc:name "Database name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1238 ; sc:encodingFormat edam:format_2330, edam:format_2548 ; sc:name "Proteolytic digest" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0137, edam:topic_3520 ; sc:description "Another web based protein digestion applet." ; sc:featureList edam:operation_0422 ; sc:name "PeptideCutter" ; sc:url "http://www.expasy.ch/tools/peptidecutter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0154 ; sc:citation "pubmed:23505299" ; sc:description "For users interested in identifying bioactive peptides within a protein sequence. PeptideLocator was trained on a set of non-redundant protein sequences conatining known bioactive peptides." ; sc:featureList edam:operation_2479 ; sc:name "PeptideLocator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioware.ucd.ie/~compass/biowareweb/Server_pages/biopred.php" ; biotools:primaryContact "Denis C. Shields" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3510, edam:topic_3512 ; sc:citation "pubmed:9150918" ; sc:description "Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides." ; sc:featureList edam:operation_0366, edam:operation_0417, edam:operation_0418, edam:operation_2929, edam:operation_3755 ; sc:name "PeptideMass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://us.expasy.org/tools/peptide-mass.html" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_3655 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:12403597" ; sc:description "Validation of peptide identifications by MS/MS and database searches." ; sc:featureList edam:operation_3631, edam:operation_3649, edam:operation_3664, edam:operation_3675 ; sc:name "PeptideProphet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://peptideprophet.sourceforge.net/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:citation "pubmed:20201590" ; sc:description "Optimization-based peptide quantification tool. It is designed to take two challenges in peptide abundance estimation: peptide overlapping and peak intensity variation." ; sc:featureList edam:operation_3630 ; sc:name "Peptidequant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ust.hk/PeptideQuant/peptidequant.htm" ; biotools:primaryContact "Weichuan Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:36701129" ; sc:description "An R package to optimize synthetic peptide selection for mass spectrometry applications." ; sc:featureList edam:operation_2929, edam:operation_3643, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "PeptideRanger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rr-2/PeptideRanger/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154 ; sc:citation "pubmed:22350209" ; sc:description "Includes three peptide reranking methods: PPMRanker, PPIRanker, and MIRanker. PPMRanker only uses Protein-Peptide Map (PPM) information from the protein database, PPIRanker only uses Precursor Peak Intensity (PPI) information, and MIRanker employs both PPM information and PPI information." ; sc:featureList edam:operation_2990 ; sc:name "PeptideReranking" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ust.hk/pepreranking/" ; biotools:primaryContact "Chao Yang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:encodingFormat edam:format_3579, edam:format_3604 ; sc:name "Protein structure image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_3547 ; sc:name "Sequence image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:encodingFormat edam:format_2330 ; sc:name "GO-term enrichment data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0644, edam:topic_3520 ; sc:citation ; sc:description "PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data" ; sc:featureList edam:operation_0570, edam:operation_2428, edam:operation_3501, edam:operation_3631, edam:operation_3694, edam:operation_3755, edam:operation_3767 ; sc:license "Apache-2.0" ; sc:name "PeptideShaker" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BioInfra.Prot" ; sc:softwareHelp ; sc:softwareVersion "1.13.6" ; sc:url "http://compomics.github.io/projects/peptide-shaker.html" ; biotools:primaryContact "Dominik Kopczynsk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pmcid:PMC8650087", "pubmed:34709836" ; sc:description "A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data." ; sc:featureList edam:operation_0337, edam:operation_3644, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PeptideShaker Online" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/barsnes-group/peptide-shaker-online" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154 ; sc:citation , "pmcid:PMC7564585", "pubmed:32825686" ; sc:description """Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. PeptideWitch is designed to take raw spectral counting data and produce high-stringency data for easy quantitation.""" ; sc:featureList edam:operation_3435, edam:operation_3637, edam:operation_3767, edam:operation_3891 ; sc:name "PeptideWitch" ; sc:url "http://peptidewitch.online" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3300, edam:topic_3360, edam:topic_3520 ; sc:citation ; sc:description "Peptimetric is a tool for quantifying and visualizing differences in peptidomic data." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3630, edam:operation_3646 ; sc:license "MIT" ; sc:name "Peptimetric" ; sc:url "https://peptimetric.herokuapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0804, edam:topic_3398, edam:topic_3474 ; sc:citation , "pmcid:PMC8415426", "pubmed:34478499" ; sc:description "A user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach." ; sc:featureList edam:operation_0310, edam:operation_0418, edam:operation_3646 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Peptipedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ProteinEngineering-PESB2/peptipedia" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:18667410" ; sc:description "Automating manual validation of MS/MS search results." ; sc:featureList edam:operation_2479 ; sc:name "Peptizer" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp , ; sc:softwareVersion "1.8.4" ; sc:url "https://github.com/compomics/peptizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830 ; sc:citation "pubmed:15980443" ; sc:description "PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity." ; sc:featureList edam:operation_0252, edam:operation_0465, edam:operation_2575 ; sc:name "PEPVAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imed.med.ucm.es/PEPVAC/" ; biotools:primaryContact "PEPVAC Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2162 ; sc:name "Helical wheel" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw a helical wheel diagram for a protein sequence." ; sc:featureList edam:operation_0267 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepwheel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepwheel.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1501 ; sc:name "Amino acid index" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw a hydropathy plot for a protein sequence." ; sc:featureList edam:operation_2574 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepwindow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepwindow.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0123 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Draw a hydropathy plot for a protein sequence." ; sc:featureList edam:operation_2574 ; sc:name "pepwindow (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/jdispatcher/seqstats/emboss_pepwindow/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Draw a hydropathy plot for protein sequences." ; sc:featureList edam:operation_2574 ; sc:name "pepwindow (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/seqstats/emboss_pepwindow" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1501 ; sc:name "Amino acid index" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:name "Sequence alignment (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:name "Protein sequence hydropathy plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw Kyte-Doolittle hydropathy plot for a protein alignment." ; sc:featureList edam:operation_2574 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pepwindowall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pepwindowall.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0130, edam:topic_0154, edam:topic_0602 ; sc:citation "pubmed:19880386" ; sc:description "Exhaustive data set of all protein-peptide complexes available in the PDB with peptide lengths up to 35 residues. Complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. Each complex is annotated with both biological and structural information. Peptides are also annotated with naturally occurring backbone variations using fragment clusters from the BriX database to aid peptide design." ; sc:featureList edam:operation_0477, edam:operation_3432, edam:operation_3646 ; sc:name "PepX" ; sc:url "http://pepx.switchlab.org/pepx/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3468 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description "Converts output from PeptideProphet to protein level information in Excel." ; sc:featureList edam:operation_0335, edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "pepXML2Excel" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.ms-utils.org/pepXML2Excel.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation ; sc:description "Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "pepXMLTab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pepXMLTab.html" ; biotools:primaryContact "Xiaojing Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:20576625" ; sc:description "A probabilistic framework to predict the alignment of each transcript fragment to a reference genome for each PER (RNA-seq paired-end read). 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The database includes phylogenetic trees and tools to capture kinetic information from Brenda, CheBI and Sabio-RK databases and selected bibliographic references." ; sc:featureList edam:operation_0324, edam:operation_0477, edam:operation_0554, edam:operation_3092, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PeroxisomeDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.peroxisomeDB.org" ; biotools:primaryContact "Agatha Schlüter", "Aurora Pujol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_2269 ; sc:citation "pubmed:23176165" ; sc:description "Software package for shotgun proteomics data analysis, which helps researchers to extract biologically meaningful information from their MaxQuant output such as post-translational modifications." ; sc:featureList edam:operation_2945 ; sc:name "Perseus" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.biochem.mpg.de/en/rg/cox" ; biotools:primaryContact "Jürgen Cox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640 ; sc:citation ; sc:description "A Method for the Identification and Prioritization of Personalized Cancer Drivers." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PersonaDrive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/abu-compbio/PersonaDrive" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3016, edam:format_3464, edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0092, edam:topic_0622, edam:topic_2640, edam:topic_3473, edam:topic_3577 ; sc:citation , "pmcid:PMC5946881", "pubmed:29272339" ; sc:contributor ; sc:description "The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for translation of individual tumor genomes for precision cancer medicine. PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations, and produces interactive HTML reports intended for clinical interpretation" ; sc:featureList edam:operation_0331, edam:operation_2422, edam:operation_3225, edam:operation_3226, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Personal Cancer Genome Reporter (PCGR)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , , , ; sc:softwareVersion "1.0.2" ; sc:url "https://github.com/sigven/pcgr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3053, edam:topic_3175 ; sc:citation , "pmcid:PMC4086072", "pubmed:24799434" ; sc:description "This tool allows on to visualize functions of genetic variants." ; sc:featureList edam:operation_3197, edam:operation_3208, edam:operation_3226, edam:operation_3227 ; sc:name "Personal Genome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pgbrowser.org/" ; biotools:primaryContact "Yadong Wang*" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:31900722" ; sc:description """A Toolbox for ICA Map Classification and Individualized ROI Definition. Personode is a MATLAB toolbox designed for regions-of-interest (ROI) individualization based on fMRI spatial independent component analysis (ICA) maps after a semi-automatic classification into resting-state networks (RSNs). Personode is a user-friendly, open-source MatLab toolbox that semi-automatically guides through ICA components classification into resting-state networks (RSN), alleviating the selection process, and allows the robust definition of either group- or subject-specific ROIs derived from RSN, which could make network analysis more accurate and individually specific.""" ; sc:featureList edam:operation_2429, edam:operation_3432, edam:operation_3891 ; sc:name "Personode" ; sc:url "http://www.nitrc.org/projects/personode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2885, edam:topic_3175, edam:topic_3673 ; sc:citation , , "pmcid:PMC9380391", "pubmed:35974382" ; sc:description "perSVade runs structural variation (SV), small variant (SNPs and IN/DELs) and read depth-based Copy Number Variation (CNV) calling and annotation for WGS datasets." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3227, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "perSVade" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v1.02.7" ; sc:url "https://github.com/Gabaldonlab/perSVade" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "perturbatr does stage-wise analysis of large-scale genetic perturbation screens for integrated data sets consisting of multiple screens. For multiple integrated perturbation screens a hierarchical model that considers the variance between different biological conditions is fitted. The resulting list of gene effects is then further extended using a network propagation algorithm to correct for false negatives." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "perturbatr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/perturbatr.html" ; biotools:primaryContact "Simon Dirmeier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC7584257", "pubmed:33095769" ; sc:description """Learning gene networks underlying clinical phenotypes using SNP perturbation. 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PERUNPDB is the first version of a collection of more than 200 compounds of Peruvian origin where 95% of the compounds come from plants and 5% from animals." ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "PeruNPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://perunpdb.com.pe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3335, edam:topic_3409, edam:topic_3697 ; sc:citation , "pubmed:33080028" ; sc:description """Peryton is a manual collection of experimentally supported microbe-disease associations. Peryton constitutes a novel resource of experimentally supported microbe-disease associations, currently hosting more than 7,900 entries linking 43 diseases and 1,396 microorganisms. Peryton’s content is exclusively sustained by manual curation of biomedical articles. Importantly, diseases and microorganisms are provided in a systematic, standardized manner using reference resources to create database dictionaries. Information about the experimental design, study cohorts and the applied high- or low-throughput techniques are meticulously annotated and catered to users.""" ; sc:featureList edam:operation_0224 ; sc:name "Peryton" ; sc:url "https://dianalab.e-ce.uth.gr/peryton/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "As a user or developer you can use the PESI webservice to feed your own application with standard PESI taxonomy." ; sc:featureList edam:operation_2422 ; sc:name "PESI WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.eu-nomen.eu/portal/webservices.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3489 ; sc:citation ; sc:description """A near-real-time, open-source monitoring and analytics system for small-scale fisheries. 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sc:featureList edam:operation_0384, edam:operation_0387, edam:operation_3799 ; sc:name "PESUCA" ; sc:url "https://pesuca.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3452 ; sc:citation , "pubmed:33882476" ; sc:description "PET-ABC is an R package for fully Bayesian likelihood-free inference for kinetic models." ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3659 ; sc:name "PET-ABC" ; sc:url "https://github.com/cgrazian/PETabc" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation ; sc:description "An extension to the brain imaging data structure for positron emission tomography." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "PET-BIDS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://openneuro.org/search/modality/pet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "PET-Tool is a mySQL-based muti-component software package specifically designed for processing the sequences generated from PET (Paired-End diTag) technology." ; sc:featureList edam:operation_2409 ; sc:name "PET-Tool" ; sc:operatingSystem "Linux" ; sc:softwareVersion "3.0" ; sc:url "http://www.gis.a-star.edu.sg/PET_Tool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360, edam:topic_3372 ; sc:citation , "pubmed:33325491" ; sc:description """PETAL (ParallEl paThways AnaLyzer): a python tool for deep analysis of biological pathways. PETAL software is written in the Python 3 programming language. It contains a set of tools for pathway analysis and discovery of novel therapeutic targets. The approach allows you to scan and perform a in-depth search of the biological pathway to analyze less recurrent pathways, detect nodes that are far from the initial target nodes and showing the pathway of origin from which it was taken the gene.""" ; sc:featureList edam:operation_3925, edam:operation_3928 ; sc:name "PETAL" ; sc:url "https://github.com/Pex2892/PETAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_2275 ; sc:citation ; sc:description "Construction of small-world, scale-free networks." ; sc:featureList edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "petalNet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/julipetal/petalNet" ; biotools:primaryContact "Juli Petereit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0602, edam:topic_0659 ; sc:citation "pubmed:21609960" ; sc:description "The PETfold and PETcofold web servers for the analysis of multiple RNA sequences for common RNA structure and for RNA-RNA interaction sites. 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Benchmark existing placement software and compare placement accuracy on different reference trees. PEWO compiles a set of workflows dedicated to the evaluation of phylogenetic placement algorithms and their software implementation. It focuses on reporting placement accuracy under different conditions and associated computational costs.""" ; sc:featureList edam:operation_0224, edam:operation_0415 ; sc:license "MIT" ; sc:name "PEWO" ; sc:url "https://github.com/phylo42/PEWO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3293 ; sc:citation "pubmed:25948716" ; sc:description "R package that permits measurement, modelling, and simulation of phylogenetic structure in ecological data." ; sc:featureList edam:operation_0324, edam:operation_2426 ; sc:name "pez" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/willpearse/pez" ; biotools:primaryContact "Pearse WD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0601, edam:topic_3068, edam:topic_3474 ; sc:citation , "pubmed:35753700" ; sc:description "A machine learning-based phosphorylation sites prediction tool for Plasmodium proteins." ; sc:featureList edam:operation_0417, edam:operation_2492, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "Pf-Phospho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nii.ac.in/pfphospho.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Scripts for sequence file handling." ; sc:name "pf1-tools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@pf1-tools@0.1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:name "Sequence accession (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1138 ; sc:name "Pfam accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1138 ; sc:name "Pfam accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2758 ; sc:name "Pfam clan ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_0160, edam:topic_0623, edam:topic_0736 ; sc:citation , , , "pmcid:PMC3965110", "pmcid:PMC4702930", "pmcid:PMC7779014", "pubmed:24288371", "pubmed:26673716", "pubmed:33125078", "pubmed:9223186" ; sc:description "Database which contains information about protein domains and families. 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The experiments on the benchmark datasets from DREAM challenge as well as the E.coli datasets show that PFBNet achieves significantly better performance than other state-of-the-art methods (HiDi, iRafNet and BiXGBoost).""" ; sc:featureList edam:operation_2437, edam:operation_3454, edam:operation_3659 ; sc:name "PFBNet" ; sc:url "https://github.com/ddche/PFBNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "PFClust is a partitioning-based clustering algorithm capable, unlike many widely-used clustering algorithms, of automatically proposing an optimal number of clusters for the data." ; sc:featureList edam:operation_3432 ; sc:name "PFClust" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://chemistry.st-andrews.ac.uk/staff/jbom/group/PFClust.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3307 ; sc:citation , "pubmed:36251780" ; sc:description "Pfeature is a web server for computing wide range of protein and peptides features from their amino acid sequence. Following are main menus for computing features; i) Composition-based features, ii) Binary profile of sequences, iii) evolutionary information based features, iv) structural descriptors, v) pattern based descriptors, and vi) model building, for a group of protein/peptide sequences. Additionally, users will also be able to generate these features for sub-parts of protein/peptide sequences. Pfeature be helpful to annotate structure, function and therapeutic properties of proteins/peptides." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pfeature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pfeature/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation , "pubmed:11893514" ; sc:description "Mask out (i.e. replace amino acid characters with Xs) regions of low complexity, coiled-coil regions and regions with extremely biased amino acid compositions. For compositional biased regions,only the overrepresented amino acids are masked." ; sc:featureList edam:operation_2479, edam:operation_3695 ; sc:name "pfilt" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.5" ; sc:url "http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:17702057", "pubmed:23272783", "pubmed:24799117" ; sc:description "Computational platform for mass spectrometry-based proteomics, including pFind , pNovo and pQuant." ; sc:featureList edam:operation_0335, edam:operation_3630, edam:operation_3631, edam:operation_3694 ; sc:license "Proprietary" ; sc:name "pFind Studio" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://pfind.ict.ac.cn/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0176, edam:topic_0736 ; sc:citation "pubmed:18477634" ; sc:description "Protein Flexibility Analyzer (pFlexAna) detects and displays conformational changes in remotely related proteins, without using sequence homology information. Rather than detecting regions of structural similarity, pFlexAna detects regions exhibiting structural change." ; sc:featureList edam:operation_0244, edam:operation_0477, edam:operation_2487, edam:operation_3432 ; sc:name "pFlexAna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bigbird.comp.nus.edu.sg/pmwiki/farm/motion/index.php?n=Site.ProteinFlexibility" ; biotools:primaryContact "David Hsu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3324, edam:topic_3474 ; sc:citation "pubmed:19908123" ; sc:description "Developed for predicting mitochondrial proteins of malaria parasite Plasmodium falciparum . All models were trained and tested on 175 proteins (40 mitochondrial & 135 non-mitochondrial proteins) and evaluated using five-fold cross validation." ; sc:featureList edam:operation_2423 ; sc:name "PFMpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/pfmpred/" ; biotools:primaryContact "Dr.G.P.S.Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0623, edam:topic_1775, edam:topic_3474 ; sc:citation , "pubmed:35366467" ; sc:description "A novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods." ; sc:featureList edam:operation_0477, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PFmulDL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/idrblab/PFmulDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "RNA 2nd structure prediction from a multiple alignment of RNA sequences." ; sc:featureList edam:operation_0278 ; sc:name "Pfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.daimi.au.dk/~compbio/pfold/" ; biotools:primaryContact "Zsuzsanna Sukosd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0166, edam:topic_1317, edam:topic_3534 ; sc:citation "pubmed:17537808" ; sc:description "Web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces." ; sc:featureList edam:operation_2406 ; sc:name "PFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pfp.technion.ac.il/index.html" ; biotools:primaryContact "Inbal Paz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_1317, edam:topic_3299 ; sc:citation "pubmed:18996396" ; sc:description "Web server of predicting protein fold pattern with functional domain and sequential evolution information" ; sc:featureList edam:operation_0303 ; sc:name "PFP-FunDSeqE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/PFP-FunDSeqE/" ; biotools:primaryContact "Hong-Bin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_1775 ; sc:citation "pubmed:25273111" ; sc:description "Sequence similarity-based protein function prediction server designed to predict GO annotations for a query sequence beyond what can be found by conventional database search such as BLAST." ; sc:featureList edam:operation_1777 ; sc:name "PFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kiharalab.org/web/pfp.php" ; biotools:primaryContact "Daisuke Kihara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0623, edam:topic_0736, edam:topic_1775 ; sc:citation , "pmcid:PMC9556876", "pubmed:36246645" ; sc:description "Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms." ; sc:featureList edam:operation_0303, edam:operation_2489, edam:operation_2492, edam:operation_2575, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:name "PFP-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sites.google.com/view/pfp-go/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "PFP-Pred is an ensemble classifier for protein fold pattern recognition" ; sc:featureList edam:operation_0303, edam:operation_2423, edam:operation_2479 ; sc:name "PFP-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/PFP-Pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_3382 ; sc:citation ; sc:description """A computational platform for siRNA and antisense oligonucleotides design. PFRED Restful Service Implementation. Jersey based RESTful service implementation for PFRED;. This is a repository for the Dockerfile and file dependencies for the RESTful-PFRED service that is compiled as a .war file (see pfred-rest-service). Note that this process will setup the pfredservice environment and install all needed dependencies. Process might take up to 10 mins in a regular modern laptop.""" ; sc:featureList edam:operation_0337, edam:operation_2008, edam:operation_3198 ; sc:license "MIT" ; sc:name "PFRED" ; sc:url "https://github.com/pfred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0218 ; sc:citation , "pubmed:36794913" ; sc:description "An attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships." ; sc:featureList edam:operation_1777, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PFresGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioColLab/PFresGO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0736 ; sc:citation "pubmed:23505298" ; sc:description "Replaces the original pfsearch program distributed with the pftools. It uses modern CPU instructions to exploit the capabilities of multicore processors and a new heuristic filter to rapidly score and select possible candidate matches." ; sc:featureList edam:operation_2421 ; sc:name "pfsearch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://web.expasy.org/pftools/#pfsearchV3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_2269 ; sc:description "PFSTATS is a set of programs and scripts devoted to analyze protein families using simple statistics." ; sc:featureList edam:operation_2479 ; sc:name "PFSTATS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.biocomp.icb.ufmg.br/biocomp/?page_id=119" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0160, edam:topic_0166, edam:topic_0736 ; sc:citation , "pubmed:23505298" ; sc:description "The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model." ; sc:featureList edam:operation_0239 ; sc:license "GPL-2.0" ; sc:name "pftools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sib-swiss/pftools3" ; biotools:primaryContact "pftools team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3407, edam:topic_3577 ; sc:citation , "pubmed:31841030" ; sc:description "PG-Hacker is a tool for the prediction of major adverse cardiac, cerebrovascular events in patients with diabetes after acute coronary syndrome." ; sc:featureList edam:operation_3503 ; sc:name "PG-HACKER" ; sc:url "http://medicalc.github.io/pghacker" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2306, edam:format_3003, edam:format_3016 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0219, edam:topic_3170, edam:topic_3366, edam:topic_3489, edam:topic_3520, edam:topic_3571 ; sc:citation , "pmcid:PMC4912784", "pubmed:27316337" ; sc:description "This package provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data." ; sc:featureList edam:operation_3431, edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "PGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PGA.html" ; biotools:primaryContact , "Shaohang Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3055, edam:topic_3517 ; sc:citation , "pubmed:33738486" ; sc:description "pgainsim is an R-package to assess the mode of inheritance for quantitative trait loci in GWAS. After performing genome-wide association studies under an additive, recessive and dominant model for a quantitative trait the pgainsim package allows to determine study specific critical values when one of the three models is more informative than the other ones for a quantitative trait locus. First, study specific p-gain values are simulated. Second, based on the simulated values quantiles of the empirical density of the p-gain are computed. Finally, the quantiles are exported or interpolated and the critical values are obtained." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3799 ; sc:name "pgainsim" ; sc:url "https://github.com/genepi-freiburg/pgainsim" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654 ; sc:citation ; sc:description "PGAP (pan-genome analysis pipeline) can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters." ; sc:featureList edam:operation_3197, edam:operation_3501 ; sc:name "PGAP" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.12" ; sc:url "http://sourceforge.net/projects/pgap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC5451011", "pubmed:28562641" ; sc:description "Protein Group Code Algorithm is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs are called \"connected\" groups." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "pgca" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pgca.html" ; biotools:primaryContact "Gabriela Cohen-Freue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_2885, edam:topic_3174, edam:topic_3293, edam:topic_3301 ; sc:citation ; sc:description "Build a Bioinformatic Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics." ; sc:featureList edam:operation_0323, edam:operation_0525, edam:operation_3216 ; sc:name "PGCGAP" ; sc:url "https://github.com/liaochenlanruo/pgcgap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7180314", "pubmed:32362739" ; sc:description """Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes. This tool is for gap-closing in the genome using long-reads or contigs. PGcloser contains 7 modules: SplitFa, ExtrGap, BwtBuilt, CompGap, ClsGap, MergFa and GetCls.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216 ; sc:name "PGcloser" ; sc:softwareVersion "1.0" ; sc:url "http://software.tobaccodb.org/software/pgcloser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation , "pmcid:PMC2808862", "pubmed:19906726" ; sc:description "This tool enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. It is valuable for assessing the uniqueness of observed conformational or geometric features in protein structure as well as discovering novel features and principles of protein structure." ; sc:featureList edam:operation_0245, edam:operation_0249, edam:operation_0474, edam:operation_0479, edam:operation_1844 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "The Protein Geometry Database (PGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pgd.cgrb.oregonstate.edu/" ; biotools:primaryContact "Dale Tronrud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0780, edam:topic_3068 ; sc:citation "pubmed:26258475" ; sc:description "System specifically designed for plant gene normalization. This website enables user search gene normalization information by keywords, a list of PMIDs, or UniProt ACs in the database. The results (Gene names and corresponding UniProt ACs) are displayed in sortable tables with text evidence and downloadable for further research." ; sc:featureList edam:operation_0306 ; sc:name "pGenN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biotm.cis.udel.edu/gn/" ; biotools:primaryContact "BioNLP and Text Mining Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3292, edam:topic_3520 ; sc:citation , "pmcid:PMC8478412", "pubmed:34579805" ; sc:description "Analysis pipeline for the consistent, reproducible and high-resolution structural analysis of bacterial peptidoglycans." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "PGfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Mesnage-Org/PGFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC9825418", "pubmed:36321663" ; sc:description "Toward understanding the diversity of major histocompatibility complexes in human populations" ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PGG MHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.pggmhc.org/pggmhc/#/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168, edam:topic_3175, edam:topic_3518 ; sc:citation , "pubmed:36243989" ; sc:description "A whole-genome-sequencing-based structural variant resource and data analysis platform." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PGG SV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Shuhua-Group/PGGSVpipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3169 ; sc:citation , "pmcid:PMC5384132", "pubmed:28388874" ; sc:description "Manipulation of Hi-C peak and other chromatin interaction data." ; sc:featureList edam:operation_2403, edam:operation_3222 ; sc:license "BSD-3-Clause" ; sc:name "Pgltools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/billgreenwald/pgltools" ; biotools:primaryContact "William W. Greenwald" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3176, edam:topic_3569 ; sc:citation , "pmcid:PMC5384132", "pubmed:28388874" ; sc:description "Pgltools is a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data." ; sc:featureList edam:operation_2403 ; sc:license "BSD-3-Clause" ; sc:name "pgltools" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/billgreenwald/pgltools" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0621, edam:topic_3520 ; sc:citation ; sc:description "Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3755 ; sc:name "pGlyco3" ; sc:url "https://github.com/pFindStudio/pGlyco3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3360, edam:topic_3520 ; sc:citation ; sc:description "pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation." ; sc:featureList edam:operation_3223, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "pGlycoQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/expellir-arma/pGlycoQuant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0154, edam:topic_0621 ; sc:citation ; sc:description "The PGM Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data." ; sc:featureList edam:operation_2429 ; sc:name "PGM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.agbase.msstate.edu/tools/pgm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC7734255", "pubmed:33329748" ; sc:description """Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data. Linux operation system with python3.x.""" ; sc:featureList edam:operation_3198, edam:operation_3461, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "PGMicroD" ; sc:url "https://github.com/BDanalysis/PGMicroD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation "pubmed:23761451" ; sc:description "PGMRA is a web server for phenotype-genotype relationship detection." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3197 ; sc:name "PGMRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phop.ugr.es/fenogeno" ; biotools:primaryContact "Igor Zwir", "Javier Arnedo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3170, edam:topic_3922 ; sc:citation , "pmcid:PMC10000440", "pubmed:36899918" ; sc:description "Proteogenomics-based pipeline to predict neoantigens in noncoding regions." ; sc:featureList edam:operation_0252, edam:operation_3227, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PGNneo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tanxiaoxiu/PGNneo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , ; sc:contributor "Astrid Junker", "European Commission within the transPlant project", "German Federal Ministry of Education and Research within the German-Plant-Phenotyping Network", "Leibniz Institute of Plant Genetics and Crop Plant Research as infrastructural service", "Uwe Scholz" ; sc:description "Plant Genomics and Phenomics Research Data Repository (e!DAL-PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents. PGP is registered as research data repository at BioSharing.org, re3data.org and OpenAIRE as valid EU Horizon 2020 open data archive. Above features, the programmatic interface and the support of standard metadata formats, enable PGP to fulfil the FAIR data principles - findable, accessible, interoperable, reusable." ; sc:featureList edam:operation_3431 ; sc:funder "European Commission within the transPlant project", "German Federal Ministry of Education and Research within the German-Plant-Phenotyping Network", "Leibniz Institute of Plant Genetics and Crop Plant Research as infrastructural service" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Plant Genomics and Phenomics Research Data Repository (PGP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", "ipk" ; sc:softwareHelp , ; sc:url "https://edal-pgp.ipk-gatersleben.de/" ; biotools:primaryContact "Daniel Arend", "Matthias Lange" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474 ; sc:citation "pubmed:21501515" ; sc:description "Software tool in particular for analyzing gene expression time courses. It allows its user to interactively define linear HMM queries on time course data using rectangular graphical widgets called probabilistic time boxes. The analysis is fully interactive and the graphical display shows the time courses along with the graphical query. 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Pseudogenome-based Read Compressor (PgRC) is an in-memory algorithm for compressing the DNA stream of FASTQ datasets, based on the idea of building an approximation of the shortest common superstring over high-quality reads.""" ; sc:featureList edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:name "PgRC" ; sc:url "https://github.com/kowallus/PgRC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0622 ; sc:citation ; sc:description "Web-based tool to design distance independent paired-gRNA." ; sc:featureList edam:operation_0231 ; sc:name "pgRNAFinder" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/xiexiaowei/pgRNAFinder" ; biotools:primaryContact "Zhiming Dai", "Zhou Songyang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2269 ; sc:citation "pubmed:24947752" ; sc:description "Penalized regression model incorporating grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures." ; sc:featureList edam:operation_3659, edam:operation_3792 ; sc:name "PGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/feizhe/PGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3334, edam:topic_3335, edam:topic_3517 ; sc:citation ; sc:description """PGS Catalog is an open database for reproducibility and systematic evaluation. 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It allows to ask for presence of k-mers in the reads." ; sc:featureList edam:operation_0525, edam:operation_3202 ; sc:name "PgSA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=pgsa&subpage=about" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3321 ; sc:citation ; sc:description "Parametric Analysis of Gene Set Enrichment." ; sc:featureList edam:operation_2436 ; sc:license "GPL-2.0" ; sc:name "PGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PGSEA.html" ; biotools:primaryContact "Karl Dykema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:11331236" ; sc:description "Software to find motifs using random projections." ; sc:featureList edam:operation_0292, edam:operation_3209 ; sc:name "PGT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www1.cse.wustl.edu/~jbuhler/pgt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0202, edam:topic_0769, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC8592507", "pubmed:34598320" ; sc:description "Reproducible cleaning of bio-medical laboratory data using methods of visualization,error correction and transformation implemented as interactive R-notebooks." ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pguIMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/pguIMP/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0780, edam:topic_0797, edam:topic_3175 ; sc:citation , "pmcid:PMC8520301", "pubmed:34656081" ; sc:description "Reference-agnostic representation and visualization of pan-genomes." ; sc:featureList edam:operation_0490, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PGV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ucrbioinfo/PGV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3168, edam:topic_3520 ; sc:citation "pubmed:26638927" ; sc:description "Proteogenomic intregration of mass spectrometry (MS) proteomics data with next generation sequencing (NGS) by mapping identified peptides onto their putative genomic coordinates." ; sc:featureList edam:operation_3198 ; sc:name "PGx" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://pgx.fenyolab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3474 ; sc:citation ; sc:description "MATLAB script for Potential-based Hierarchical Agglomerative (PHA) clustering." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "Potential-based Hierarchical Agglomerative (PHA) clustering" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46134-fast-hierarchical-clustering-method-pha" ; biotools:primaryContact "Yonggang Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description """Software package as collection template and associated materials for SARS-CoV-2 metadata. Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.""" ; sc:featureList edam:operation_0335, edam:operation_2409, edam:operation_3096 ; sc:license "CC-BY-4.0" ; sc:name "PHA4GE SARS-CoV-2 Contextual Data Specification" ; sc:url "https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC10460485", "pubmed:37641717" ; sc:description "Web server for identifying and characterizing phage contigs in metagenomic data." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhaBOX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phage.ee.cityu.edu.hk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0769, edam:topic_3293, edam:topic_3316 ; sc:citation , "pmcid:PMC9178230", "pubmed:35639618" ; sc:description "Phylogeny-Aware Computing of Tolerance for Missense Mutations." ; sc:featureList edam:operation_3226, edam:operation_3461, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PHACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CompGenomeLab/PHACT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0218, edam:topic_2258, edam:topic_3336 ; sc:citation ; sc:description "semantically annotated corpus for pharmacovigilence (PV), consisting of 597 MEDLINE abstracts. Its fine-grained, multiple levels of annotation, added by domain-experts, make it a unique resource within the field, and aim to encourage the development/adaption of novel machine learning tools for extracting PV-related information from text." ; sc:featureList edam:operation_0306 ; sc:license "CC-BY-2.0" ; sc:name "PHAEDRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nactem.ac.uk/PHAEDRA/" ; biotools:primaryContact "Paul Thompson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0601, edam:topic_3173, edam:topic_3387 ; sc:citation , "pmcid:PMC10206091", "pubmed:37221245" ; sc:description "Epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3208, edam:operation_3216, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:name "PhaeoEpiView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://PhaeoEpiView.univ-nantes.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0623, edam:topic_0637, edam:topic_3324, edam:topic_3474 ; sc:citation , "pubmed:36464489" ; sc:description "Virus classification for viral genomic fragments using PhaGCN2." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhaGCN2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KennthShang/PhaGCN2.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_3520 ; sc:citation ; sc:description """Phage Commander is a software tool for rapid annotation of bacteriophage genomes using multiple programs. A graphical utility for querying various gene prediction tools for FASTA formatted DNA sequences. Phage Commander provides utilities to query various gene-encoding prediction tools and results in various formats.""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "Phage Commander" ; sc:url "https://github.com/mlazeroff/PhageCommander" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """Bacteriophage Life Cycle Recognition with Machine Learning and Natural Language Processing. PhageAI is an application that simultaneously represents a repository of knowledge of bacteriophages and a tool to analyse genomes with Artificial Intelligence support.""" ; sc:featureList edam:operation_0363, edam:operation_3461, edam:operation_3935 ; sc:name "PhageAI" ; sc:url "https://phage.ai/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Workflow" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3179, edam:topic_3382, edam:topic_3519 ; sc:citation , "pubmed:37450356" ; sc:description "An Open Source Digital Microfluidic Extension With Applications for Phage Discovery." ; sc:featureList edam:operation_0308, edam:operation_0337, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "PhageBox" ; sc:url "https://github.com/Dreycey/PhageBox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3303 ; sc:citation , "pubmed:35576688" ; sc:description "An R package to design phage cocktails from experimental phage-bacteria infection networks." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhageCocktail" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/PhageCocktail/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0654 ; sc:citation ; sc:description """It was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, It found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. The goal of this project is to provide an open-sourced, standardized and automated system to identify and classify prophages within prokaryotic genomes.""" ; sc:featureList edam:operation_2421, edam:operation_2429, edam:operation_2945 ; sc:name "PhageFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v2.1" ; sc:url "http://phage-finder.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0203, edam:topic_0736, edam:topic_0820 ; sc:citation , "pubmed:32096819" ; sc:description """Phage protein receptors have multiple interaction partners and high expressions. A knowledge resource to understand virus diversity. phageReceptor is a database of phage-host receptor interactions, which included 427 pairs of phage-host receptor interactions, 341 unique viral species/sub-species, and 69 bacterial species. Based on phageReceptor, we systematically analyzed the associations between phage-host receptor interactions, and characterized the phage protein receptors by structure, function, protein-protein interaction and expression. If you use this database, please cite the following manuscript: Phage protein receptors have multiple interaction partners and high expressions (see more details). PMID: doi: 10.11843/j.issn.0366-6964.2018.11.018 D01083026.""" ; sc:featureList edam:operation_2436 ; sc:name "phageReceptor" ; sc:url "http://www.computationalbiology.cn/phageReceptor/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0798, edam:topic_3299, edam:topic_3301 ; sc:citation , "pmcid:PMC9262239", "pubmed:35797343" ; sc:description "The Actinobacteriophage Database." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:name "phagesdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://phagesdb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3174, edam:topic_3324, edam:topic_3542, edam:topic_3957 ; sc:citation , "pmcid:PMC9901426", "pubmed:36755570" ; sc:description "A tool for phage tail module detection and annotation." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhageTailFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.microbiome-bigdata.com/PHISDetector/index/tools/PhageTailFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "PhageTB is a multilevel prediction method for predicting interactions between bacteriophages and pathogenic bacterial hosts." ; sc:featureList edam:operation_2945 ; sc:name "phagetb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/phagetb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3301 ; sc:citation ; sc:description "Determining Bacteriophage Termini and Packaging using NGS data." ; sc:featureList edam:operation_0415 ; sc:license "CC-BY-4.0" ; sc:name "PhageTerm" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/phageterm/" ; biotools:primaryContact "David Bikard", "Julian Garneau", "Marc Monot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "A framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields." ; sc:featureList edam:operation_2426 ; sc:name "Phaistos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.phaistos.org/" ; biotools:primaryContact "Wouter Boomsma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_0769 ; sc:citation , "pubmed:36161315" ; sc:description "Assort phage protein sequences into phamilies using MMseqs2" ; sc:featureList edam:operation_0291, edam:operation_0310, edam:operation_1812 ; sc:license "GPL-3.0" ; sc:name "PhaMMseqs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/chg60/PhaMMseqs.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description """PhANNs is a tool to classify any phage ORF as one of 10 structural protein class, or as "others". It uses an ensemble of Artificial Neural Networks. PhANNs predicts the structural class of a phage ORF by running an artificial neural network ensemble that we created against a fasta file of protein sequences. If you upload a multi-fasta file, we’ll provide you estimates of the structural classes of all the proteins, and we’ll let you download the sequences for each class as a fasta file.""" ; sc:featureList edam:operation_0267, edam:operation_0436, edam:operation_0480 ; sc:license "MIT" ; sc:name "PhANNs" ; sc:url "http://edwards.sdsu.edu/phanns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0637, edam:topic_0659, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:36938868" ; sc:description "PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes." ; sc:featureList edam:operation_0553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PHANTASM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dr-joe-wirth/phantasm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:description "It is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "phantasus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phantasus.html" ; biotools:primaryContact "Alexey Sergushichev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3056 ; sc:citation ; sc:description "Pareto front based statistical tool for detecting heterogeneity in gene sets and biological modules from time-course data." ; sc:featureList edam:operation_3224 ; sc:name "Phantom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/phantom/index.html" ; biotools:primaryContact "Jinyan Chan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3585 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3585 ; sc:name "Protein interaction data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179 ; sc:citation , , , "pmcid:PMC2597701", "pmcid:PMC3431496", "pmcid:PMC3931556", "pubmed:19029915", "pubmed:22955991", "pubmed:3931556" ; sc:description "This package computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays." ; sc:featureList edam:operation_3218, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "phantompeakqualtools" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.2" ; sc:url "https://code.google.com/archive/p/phantompeakqualtools/" ; biotools:primaryContact "Anshul Kundaje" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168 ; sc:citation ; sc:description "Pathway-based approach using HierArchical structure of collapsed RAre variants Of High-throughput sequencing data for Multiple phenotypes is a novel statistical approach for multivariate analysis of rare variants using pathway information. It is possible to investigate an association between multiple phenotypes and each pathway or entire pathways simultaneously, regarding the relatedness across entire pathways, using collapsed rare variants using gene information." ; sc:featureList edam:operation_2497 ; sc:name "PHARAOH-multi" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://statgen.snu.ac.kr/software/pharaoh-multi/" ; biotools:primaryContact "Sungyoung Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0769, edam:topic_2640, edam:topic_3336, edam:topic_3360 ; sc:citation , , "pmcid:PMC5753377", "pmcid:PMC8728279", "pubmed:30053271", "pubmed:34850112" ; sc:description "PharmacoDB allows scientists to search across publicly available datasets to find instances where a compound or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - compound pair from any of the studies included in the database" ; sc:featureList edam:operation_0224, edam:operation_3435, edam:operation_3446 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PharmacoDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://pharmacodb.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0208, edam:topic_0622 ; sc:citation , "pubmed:26656004" ; sc:description "Set of functions to perform large-scale analysis of pharmacogenomic data." ; sc:featureList edam:operation_2403 ; sc:license "Artistic-2.0" ; sc:name "PharmacoGx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PharmacoGx.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0202, edam:topic_0634, edam:topic_3336 ; sc:citation , "pmcid:PMC9687941", "pubmed:36358909" ; sc:description "The Pharmacorank Search Tool for the Retrieval of Prioritized Protein Drug Targets and Drug Repositioning Candidates According to Selected Diseases." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "Pharmacorank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://protein.som.geisinger.edu/Pharmacorank/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0154, edam:topic_0209, edam:topic_0602 ; sc:citation "pubmed:18424800" ; sc:description "PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design." ; sc:featureList edam:operation_0482, edam:operation_2409 ; sc:name "PharmaGist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/PharmaGist" ; biotools:primaryContact "PharmaGist Administrator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_3016 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2331 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3577 ; sc:citation ; sc:description "A tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report." ; sc:featureList edam:operation_0004 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "PharmCAT" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "https://pharmcat.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2275, edam:topic_3343 ; sc:citation , "pmcid:PMC6929024", "pubmed:31757043" ; sc:description "PharMD is a tool to retrieve pharmacophore models from MD trajectories of protein-ligand complexes, identification of redundant pharmacophores and virtual screening with multiple pharmacophore models using different scoring schemes." ; sc:featureList edam:operation_0244, edam:operation_0482, edam:operation_2422, edam:operation_2476 ; sc:license "BSD-3-Clause" ; sc:name "pharmd" ; sc:url "https://github.com/ci-lab-cz/pharmd" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071, edam:topic_3373, edam:topic_3374, edam:topic_3474 ; sc:citation , "pubmed:34339812" ; sc:description "A new expert system for drug-excipient compatibility evaluation." ; sc:featureList edam:operation_2421, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PharmDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pharmde.computpharm.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_0634, edam:topic_3071, edam:topic_3474 ; sc:citation , "pmcid:PMC9276653", "pubmed:35821017" ; sc:description "The heterogeneous pharmacological medical biochemical network PharMeBINet." ; sc:featureList edam:operation_1812, edam:operation_2429, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PharMeBINet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pharmebi.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2649 ; sc:name "PharmGKB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0208, edam:topic_0625, edam:topic_2815, edam:topic_3325 ; sc:citation , "pmcid:PMC3660037", "pubmed:22992668" ; sc:description "Database on the impact of human genetic variations on drug response. PharmGKB curates primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "PharmGKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pharmgkb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0749, edam:topic_3336, edam:topic_3517 ; sc:citation , "pmcid:PMC10767932", "pubmed:37831083" ; sc:description "Curated collection of all human genome-wide association studies." ; sc:featureList edam:operation_3223, edam:operation_3431, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PharmGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/pharmgwas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3336 ; sc:citation "pubmed:20430828" ; sc:description "Web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target." ; sc:featureList edam:operation_2489, edam:operation_2492 ; sc:name "PharmMapper" ; sc:url "http://59.78.96.61/pharmmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pmcid:PMC5793840", "pubmed:28472422" ; sc:description "Potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database." ; sc:featureList edam:operation_0478, edam:operation_2575, edam:operation_3501 ; sc:name "PharmMapper" ; sc:softwareHelp ; sc:softwareVersion "2017" ; sc:url "http://lilab.ecust.edu.cn/pharmmapper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_0634, edam:topic_2885, edam:topic_3293 ; sc:citation ; sc:description """Pharmosome: An Integrative and Collective Database for Explorations and Analysis of SNP Associated with Disease. Today’s single nucleotide polymorphism (SNP) databases are limited to a narrow set of SNPs, which has led to a lack of interactivity between different databases, limited tools to analyze and manipulate the already existing data and complexity in the graphical user interface.""" ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_0555, edam:operation_3661 ; sc:license "MIT" ; sc:name "Pharmosome" ; sc:url "https://github.com/peterhabib/Pharmosome_Web" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:35301752" ; sc:description "A machine-learning scoring function to identify the best protein-ligand complexes for structure-based pharmacophore screening with high enrichments." ; sc:featureList edam:operation_3501, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PharmRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Prasanth-Kumar87/PharmRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3318, edam:topic_3374, edam:topic_3474 ; sc:citation , "pubmed:33991595" ; sc:description "PharmSD is a novel AI-based computational platform for solid dispersion formulation design." ; sc:featureList edam:operation_4009 ; sc:name "PharmSD" ; sc:url "http://pharmsd.computpharm.org" ; biotools:primaryContact "Defang Ouyang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_0625, edam:topic_3168, edam:topic_3375 ; sc:citation , "pmcid:PMC8618518", "pubmed:34834582" ; sc:description "A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation." ; sc:featureList edam:operation_0331, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PharmVIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pharmvip.nbt.or.th" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0659, edam:topic_0769, edam:topic_3174 ; sc:citation , "pmcid:PMC9805569", "pubmed:36453861" ; sc:description "Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_0362, edam:operation_0464, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pharokka" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gbouras13/pharokka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0625, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:33156327" ; sc:description """Pharos is the web interface for data collected by the Illuminating the Druggable Genome initiative. Target, disease and ligand information are collected and displayed. You are using an outdated browser. Please upgrade your browser to improve your experience.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3436 ; sc:name "Pharos" ; sc:softwareHelp ; sc:url "https://pharos.nih.gov/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0919 ; sc:encodingFormat edam:format_3016 ; sc:name "Chromosome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3179, edam:topic_3518 ; sc:citation ; sc:description "A pig haplotype reference panel for genotype imputation." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3454, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "PHARP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://alphaindex.zju.edu.cn/PHARP/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Software for haplotype reconstruction, and recombination rate estimation from population data" ; sc:featureList edam:operation_0487, edam:operation_3454 ; sc:license "MIT" ; sc:name "PHASE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://stephenslab.uchicago.edu/software.html#phase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , , "pmcid:PMC2845346", "pubmed:20008575", "pubmed:25573918" ; sc:description "Haplotyping programs package: LinkPHASE,HiddenPHASE, DualPHASE and DAGPHASE. 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Phasepy is a Python based package for fluid phase equilibria and interfacial properties calculation from equation of state (EoS). Phasepy uses several tools (i.e., NumPy, SciPy, Pandas, Matplotlib) allowing use Phasepy under Jupyter Notebooks. Phasepy models phase equilibria with the traditional ϕ-γ and ϕ-ϕ approaches, where ϕ (fugacity coefficient) can be modeled as a perfect gas, virial gas or EoS fluid, whereas γ (activity coefficient) can be described by conventional models (NRTL, Wilson, Redlich-Kister expansion, and the group contribution modified-UNIFAC). Interfacial properties are based on the square gradient theory couple to ϕ-ϕ approach. The available EoSs are the cubic EoS family extended to mixtures through the quadratic, modified-Huron-Vidal, and Wong-Sandler mixing rules""" ; sc:featureList edam:operation_3454 ; sc:name "Phasepy" ; sc:url "https://github.com/gustavochm/phasepy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation ; sc:description "A program for phasing macromolecular crystal structures with maximum likelihood methods." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "Phaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "2.5" ; sc:url "http://www.phaser.cimr.cam.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:25246430" ; sc:description "Software to systemically characterize phasiRNAs (Phase siRNAs)/tasiRNAs and their regulatory cascades ‘miRNA/phasiRNA  -> PHAS gene -> phasiRNAs -> target genes’ in plants." ; sc:featureList edam:operation_0438, edam:operation_2238 ; sc:name "PhaseTank" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://phasetank.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Script", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33541212" ; sc:description "an integrated analyser for plant phased siRNAs." ; sc:featureList edam:operation_2008, edam:operation_3223, edam:operation_3454 ; sc:name "PhasiRNAnalyzer" ; sc:url "https://cbi.njau.edu.cn/PPSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_3168, edam:topic_3557 ; sc:citation "pubmed:21672955" ; sc:description "PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views." ; sc:featureList edam:operation_3208 ; sc:name "PHAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phast.wishartlab.com/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_3168, edam:topic_3557 ; sc:citation , "pmcid:PMC4987931", "pubmed:27141966" ; sc:description "PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids." ; sc:featureList edam:operation_3208 ; sc:license "Other" ; sc:name "PHASTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phaster.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC10320120", "pubmed:37194694" ; sc:description "Web server designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PHASTEST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phastest.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0749, edam:topic_3305 ; sc:citation ; sc:description "phastSim is a Python package for efficient simulation of sequence evolution for pandemic-scale datasets. Fast sequence evolution simulation for SARS-CoV-2 phylogenies and other genomic epidemiological datasets. phastSim is available either through PyPi or by cloning this repository directly:." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326 ; sc:license "GPL-3.0" ; sc:name "phastSim" ; sc:url "https://github.com/NicolaDM/phastSim" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0623, edam:topic_0637, edam:topic_3697 ; sc:citation , "pmcid:PMC10311294", "pubmed:37387136" ; sc:description "Phage virion protein classification based on chaos game representation and vision transformer." ; sc:featureList edam:operation_0337, edam:operation_3092, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhaVIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phage.ee.cityu.edu.hk/phavip" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:encodingFormat edam:format_2330 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "Support Vector Machines based Predictor of human Deleterious Single Nucleotide Polymorphisms." ; sc:featureList edam:operation_3225 ; sc:name "PhD-SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://snps.biofold.org/phd-snp/" ; biotools:primaryContact "Emidio Capriotti", "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3474 ; sc:citation , "pmcid:PMC5570245", "pubmed:28482034" ; sc:contributor ; sc:description "A binary classifier for predicting pathogenic variants in coding and non-coding regions." ; sc:featureList edam:operation_3227, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "PhD-SNPg" ; sc:softwareHelp ; sc:url "http://snps.biofold.org/phd-snpg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:24267009" ; sc:description "Webserver to predict Dicer cleavage sites in pre-miRNA. Dicer, an RNase III enzyme, plays vital role in RNA interference pathway, processes both pre-miRNAs (precursor microRNAs) and double-stranded (ds) RNAs to generate effector molecules. Thus it is very important to know true Dicer processing sites in the pre-miRNA molecules to understand the RNA interference pathway." ; sc:featureList edam:operation_2423 ; sc:name "PHDcleav" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/phdcleav/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0820, edam:topic_2814 ; sc:author "Burkhard Rost" ; sc:citation ; sc:contributor "Chris Sander" ; sc:description "Prediction of helical transmembrane regions." ; sc:featureList edam:operation_0269 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PHDhtm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL Heidelberg", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.42" ; sc:url "http://ppopen.informatik.tu-muenchen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071, edam:topic_3473 ; sc:citation , "pmcid:PMC9043280", "pubmed:35495148" ; sc:description "A Flexible and Scalable Personal Health Data Management Framework Based on Blockchain Technology." ; sc:featureList edam:operation_3436, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:name "PHDMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hvic.biosino.org/PHDMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3407 ; sc:citation , "pubmed:32976925" ; sc:description """Pheromone-Directed Seeker for metabolic pathways. PhDSeeker is a bio-inspired algorithm for synthesizing linear and branched metabolic pathways. Pheromone Directed Seeker (PhDSeeker) is a tool based on a bio-inspired algorithm for the automatic synthesis of linear and branched feasible metabolic pathways [1]. It allows relating several compounds simultaneously, ensuring the availability of the substrates for every reaction in the solution.""" ; sc:featureList edam:operation_2421, edam:operation_3660, edam:operation_3926, edam:operation_3929 ; sc:license "GPL-3.0" ; sc:name "PhDSeeker" ; sc:url "https://sinc.unl.edu.ar/web-demo/phds/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3063, edam:topic_3474, edam:topic_3577 ; sc:citation ; sc:description "Automated Disease Phenotyping based on Unsupervised Embeddings from Electronic Health Records." ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Phe2vec" ; sc:url "https://github.com/HPIMS/phe2vec" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:name "Processed microarray data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3365 ; sc:description "A package for drawing pretty heatmaps in R. The ordinary heatmap function in R has several drawbacks when it comes to producing publication quality heatmaps. It is hard to produce pictures with consistent text, cell and overall sizes and shapes. The function pheatmap tries to alleviate the problems by offering more fine grained control over heatmap dimensions and appearance." ; sc:featureList edam:operation_0531 ; sc:name "pheatmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-EE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cran.r-project.org/web/packages/pheatmap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3047, edam:topic_3053 ; sc:citation ; sc:description "Accurate prediction of human essential genes using only nucleotide composition and association information." ; sc:featureList edam:operation_2454 ; sc:name "Pheg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cefg.uestc.edu.cn/Pheg/" ; biotools:primaryContact "Feng-Biao Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3574 ; sc:citation "pubmed:21824970" ; sc:description "Realtime webtool for prediction, network-based analysis and visualization of phenotype-gene associations in the context of human diseases." ; sc:featureList edam:operation_0276, edam:operation_2423 ; sc:name "PheGenEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phegenex-umh.cs.umn.edu:8080/PheGenEx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:33245779" ; sc:description """PheLiGe is an interactive database of billions of human genotype-phenotype associations. Genome-wide association studies have provided a vast array of publicly available SNP × phenotype association results. However, they are often in disparate repositories and formats, making downstream analyses difficult and time consuming. PheLiGe (https: phelige.com) is a database that provides easy access to such results via a web interface. The underlying database currently stores >75 billion genotype-phenotype associations from 7347 genome-wide and 1.2 million region-wide (e.g. cis-eQTL) association scans. The web interface allows for investigation of regional genotype-phenotype associations across many phenotypes, giving insights into the biological function affected by the variant in question. Furthermore, PheLiGe can compare regional patterns of association between different traits. This analysis can ascertain whether a co-association is due to pleiotropy or linkage""" ; sc:featureList edam:operation_0283, edam:operation_2422, edam:operation_3196 ; sc:name "PheLiGe" ; sc:url "https://phelige.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3170, edam:topic_3277, edam:topic_3934 ; sc:citation , "pmcid:PMC7339867", "pubmed:31932777" ; sc:description "PhEMD is a package for relating a network of single-cell samples. By first modeling the cell-state landscape of a model system and then computing pairwise distances between samples using EMD, PhEMD constructs a low-dimensional embedding that uncovers intrinsic manifold structure." ; sc:featureList edam:operation_3432, edam:operation_3629, edam:operation_3659 ; sc:name "PhEMD" ; sc:url "https://github.com/wschen/phemd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602 ; sc:citation "pubmed:19420068" ; sc:description "Web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format, output is electric/dipole moments and interactive visualization as well as the full electrostatic characteristics." ; sc:featureList edam:operation_0335, edam:operation_0386, edam:operation_0400 ; sc:name "PHEMTO" ; sc:url "http://phemto.orgchm.bas.bg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0602, edam:topic_0625, edam:topic_0634 ; sc:citation , "pmcid:PMC8147460", "pubmed:34034817" ; sc:description "PhenCards is a web server for linking human phenotype information to biomedical knowledge." ; sc:featureList edam:operation_0224 ; sc:name "PhenCards" ; sc:url "https://phencards.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0634, edam:topic_2259, edam:topic_3407 ; sc:citation , "pmcid:PMC8442701", "pubmed:34541463" ; sc:description "standalone tool for identifying trends within sets of biological phenotypes using semantic similarity and the Unified Medical Language System metathesaurus." ; sc:featureList edam:operation_3432, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhenClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jenwilson521/PhenClust_Supplemental" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3325, edam:topic_3474 ; sc:citation , "pubmed:34788791" ; sc:description "PheneBank aims at automatic extraction and validation of a database of human phenotype-disease associations in the scientific literature." ; sc:featureList edam:operation_2422, edam:operation_3096, edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:license "MIT" ; sc:name "PheneBank" ; sc:url "http://www.phenebank.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "Infer the molecular mechanism driving your expression phenotype." ; sc:featureList edam:operation_0533 ; sc:name "PheNetic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/phenetic/#/index" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "Network-based analysis of eQTL data to prioritize driver mutations." ; sc:featureList edam:operation_0533 ; sc:license "GPL-2.0" ; sc:name "PheNetic eQTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Ghent University", "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC9224645", "pubmed:35743744" ; sc:description "A User-Friendly Genetic Variant Detection and Visualization Tool for Precision Medicine." ; sc:featureList edam:operation_3196, edam:operation_3208, edam:operation_3227, edam:operation_3283 ; sc:isAccessibleForFree true ; sc:name "PhenGenVar" ; sc:operatingSystem "Windows" ; sc:url "http://dblab.hallym.ac.kr/PhenGenVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_2269, edam:topic_3168 ; sc:citation ; sc:description "Pheniqs is a flexible generic barcode classifier for high-throughput next-gen sequencing that caters to a wide variety of experimental designs and has been designed for efficient data processing. It is used for accurate, high performance Bayesian decoding and confidence estimation for combinatorial barcode indexing." ; sc:featureList edam:operation_3185, edam:operation_3200, edam:operation_3933 ; sc:name "Pheniqs" ; sc:softwareHelp , , ; sc:url "http://biosails.github.io/pheniqs" ; biotools:primaryContact "Kristin C. Gunsalus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0081, edam:topic_1317, edam:topic_3473, edam:topic_3569 ; sc:citation , , , "pmcid:PMC6778852", "pubmed:12393927", "pubmed:31588918" ; sc:description "Software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods." ; sc:featureList edam:operation_2409, edam:operation_2480, edam:operation_3562, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:name "PHENIX" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1.13" ; sc:url "http://www.phenix-online.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3077, edam:topic_3382 ; sc:citation ; sc:description "PhenoSEED is a tool for phenotyping of seed samples on an individual seed basis. Originally designed for the BELT system, it includes functions for colour calibration and morphological, colour and patterning analysis." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3553 ; sc:name "phenoSEED" ; sc:url "https://gitlab.com/usask-speclab/phenoseed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3298 ; sc:citation , "pmcid:PMC5530315", "pubmed:28327910" ; sc:description """Open source software for phenotypic data collection. It consists on a server software and a mobile application. It can be easily implemented in collaborative research and development projects involving data collecting and forward analyses.""" ; sc:featureList edam:operation_2495 ; sc:name "Phenobook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://getphenobook.com/" ; biotools:primaryContact "Leonardo S. Vanzetti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3934 ; sc:citation ; sc:description "A discovery tool to assess complex phenotypes in high-dimension, single-cell datasets." ; sc:featureList edam:operation_3435, edam:operation_3695, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhenoComb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SciOmicsLab/PhenoComb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3170, edam:topic_3407, edam:topic_3518 ; sc:citation , "pmcid:PMC7520039", "pubmed:32428201" ; sc:description """Identification of population-level differentially expressed genes in one-phenotype data. PhenoComp is an algorithm to identify population-level differential genes in one-phenotype data. This algorithm is based on RankComp, an algorithm used to identify individual-level differentially expressed genes in each sample.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3435 ; sc:name "PhenoComp" ; sc:url "https://github.com/XJJ-student/PhenoComp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815, edam:topic_3500 ; sc:citation , "pmcid:PMC3649640", "pubmed:23660285" ; sc:description "Analyzing curated annotations to associate animal models with human diseases." ; sc:featureList edam:operation_2421 ; sc:name "PhenoDigm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.sanger.ac.uk/science/tools/phenodigm" ; biotools:primaryContact "Jules Jacobsen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2855 ; sc:encodingFormat edam:format_3033 ; sc:name "Distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_2229, edam:topic_2259, edam:topic_3336, edam:topic_3523 ; sc:citation , "pmcid:PMC4225524", "pubmed:24256072" ; sc:description "This tool is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters." ; sc:featureList edam:operation_0300, edam:operation_2238, edam:operation_2436, edam:operation_3432, edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "phenoDist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phenoDist.html" ; biotools:primaryContact "Xian Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3168 ; sc:citation ; sc:description "An R package and Web application for the examination of phenotypes linked to genes and gene sets." ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhenoExam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://snca.atica.um.es/PhenoExamWeb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3518 ; sc:citation "pubmed:20478033" ; sc:description "Perform gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. The tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps." ; sc:featureList edam:operation_2436, edam:operation_3695 ; sc:name "PhenoFam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/phenofam/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3382 ; sc:citation ; sc:description "Automated processing of webcam images for phenological classification." ; sc:featureList edam:operation_3443 ; sc:name "phenofun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://r-forge.r-project.org/projects/phenofun/" ; biotools:primaryContact "Annette Menzel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3574, edam:topic_3676 ; sc:citation , "pmcid:PMC7144978", "pubmed:32271766" ; sc:description """Gene to phenotype associations for rare genetic diseases. Visualisation of top gene-phenotype relations can be found at https://phenogenon.phenopolis.org/. Web site created using create-react-app. Phenogenon is a tool to predict associations between genes and phenotypes in large exome cohorts. Link to our publication: Phenogenon: Gene to phenotype associations for rare genetic diseases. The vcf file should include all the samples that would be tested in Phenogenon. In order to index the file, please ensure it is sorted by both chromosomes and locations.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:name "Phenogenon" ; sc:url "https://phenogenon.phenopolis.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3338 ; sc:citation "pubmed:20507906" ; sc:description "PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes." ; sc:featureList edam:operation_2429, edam:operation_2454, edam:operation_3223, edam:operation_3232, edam:operation_3280 ; sc:name "PhenoHM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phenome.cchmc.org" ; biotools:primaryContact "Anil Jegga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3316, edam:topic_3382, edam:topic_3810 ; sc:citation ; sc:description """an open-source GUI for plant image analysis. PhenoImage – Wheat and Rice Center for Heat Resilience. PhenoImage is an open-source GUI based cross-platform solution for high-throughput phenotyping (HTP) image processing with the aim to make image analysis accessible to users with either little or no programming skills. The open-source nature provides the possibility to extend its usability to meet user-specific requirements. The availability of multiple functions and filtering parameters provides flexibility to analyze images from a wide variety of plant species and platforms. PhenoImage can be run on a personal computer, as well as on high-performance computing clusters for processing large-scale phenotypic data.""" ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3443 ; sc:name "PhenoImage" ; sc:url "http://wrchr.org/phenolib/phenoimage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3574 ; sc:citation "pubmed:26192085" ; sc:description "Tool focusing on discovering genes based on user-specific disease/phenotype terms." ; sc:featureList edam:operation_3439 ; sc:name "Phenolyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phenolyzer.wglab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3298, edam:topic_3382 ; sc:citation "pubmed:22009677" ; sc:description "Phenomics of yeast Mutants (PhenoM): contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26 C) and restrictive temperature (32 C)." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_2436, edam:operation_2495, edam:operation_3232 ; sc:name "PhenoM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phenom.ccbr.utoronto.ca/" ; biotools:primaryContact "Ke Jin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:24336645" ; sc:description "Freeware that provides approaches for efficient exploration and management of phenotype data." ; sc:featureList edam:operation_2238, edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "PhenoMan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://code.google.com/p/phenoman/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3298, edam:topic_3325, edam:topic_3366 ; sc:citation , "pmcid:PMC5467641", "pubmed:26251998" ; sc:description "Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The repository identifies similar patients in the database based on semantic similarity between clinical features, automatically prioritized genes from whole-exome data, and candidate genes entered by the users." ; sc:featureList edam:operation_2422, edam:operation_3197, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "PhenomeCentral" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.16" ; sc:url "https://phenomecentral.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382 ; sc:citation ; sc:description "Phenomenal is an automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping." ; sc:featureList edam:operation_0282, edam:operation_3435, edam:operation_3799 ; sc:name "Phenomenal" ; sc:url "https://github.com/openalea/phenomenal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation , "pmcid:PMC4622021", "pubmed:26507285" ; sc:description "Database of phenotypes extracted from the scientific literature using text mining." ; sc:featureList edam:operation_2421 ; sc:name "PhenoMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phenominer.mml.cam.ac.uk/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3574, edam:topic_3577 ; sc:citation "pubmed:24110477" ; sc:description "Software that aims to help clinicians to identify the correct differential diagnosis in the field of human genetics." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "Phenomizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.charite.de/phenomizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0625, edam:topic_0769, edam:topic_3172 ; sc:citation , "pmcid:PMC10068743", "pubmed:36944259" ; sc:description "A toolkit for multiomics data integration for phenotypic space exploration. Phenonaut allows users to describe their data and apply a series of generic or specialised data-centric transforms and measures." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2423, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Phenonaut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CarragherLab/phenonaut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3277 ; sc:citation , "pmcid:PMC10191354", "pubmed:37196000" ; sc:description "Building and validating GA4GH phenopackets." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "phenopacket-tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/phenopackets/phenopacket-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "It infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "phenopath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phenopath.html" ; biotools:primaryContact "Kieran Campbell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "Visualization software for high dimensional data" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PhenoPlot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/49563-hsailem-phenoplot" ; biotools:primaryContact "Heba Sailem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815, edam:topic_3053, edam:topic_3474 ; sc:citation "pubmed:18300252" ; sc:description "Web-based tool designed to detect novel gene-disease associations in humans. It is based on known gene-disease associations, protein-protein interaction data, protein functional annotation at a molecular level and protein sequence data. Machine learning principles are used to integrate heterogeneous data sources. It can be used to prioritize genes based on their likelihood to be associated with a given disease or to prioritize diseases for a given query gene." ; sc:featureList edam:operation_2421, edam:operation_2492 ; sc:name "PhenoPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phenopred.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description "phenopype is a high throughput phenotyping pipeline for Python to support ecologists and evolutionary biologists in extracting high dimensional phenotypic data from digital images. phenopype integrates state-of-the-art computer vision functions (using opencv-python as the main backbone), the possibility for GUI-based interactions and a project management ecosystem to facilitate rapid data collection and reproducibility." ; sc:featureList edam:operation_3443, edam:operation_3937 ; sc:license "LGPL-3.0" ; sc:name "phenopype" ; sc:url "https://mluerig.github.io/phenopype/" ; biotools:primaryContact "Moritz D. Lürig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:21714868" ; sc:description "Tool to add phenotypes to simulated genotypes It reads the output of coalescent simulators and simulates a qualitative or quantitative phenotype according to user-defined parameters." ; sc:featureList edam:operation_3197 ; sc:name "phenosim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://evoplant.uni-hohenheim.de/downloads/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0610, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC7882932", "pubmed:33613986" ; sc:description """A Shiny application to visualize trait data in the phenotypic space of the global spectrum of plant form and function. PhenoSpace is a Shiny application – built using the Shiny R package – that helps users to manipulate and visualize data pertaining to the global spectrum of plant form and function.""" ; sc:featureList edam:operation_0337, edam:operation_2939, edam:operation_3196, edam:operation_3214, edam:operation_3891 ; sc:license "MIT" ; sc:name "PhenoSpace" ; sc:url "https://shiny.cefe.cnrs.fr/PhenoSpace/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:33471061" ; sc:description """A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology. PhenoTagger is a hybrid method that combines dictionary and deep learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. It is an ontology-driven method without requiring any manually labeled training data, as that is expensive and annotating a large-scale training dataset covering all classes of HPO concepts is highly challenging and unrealistic.""" ; sc:featureList edam:operation_2422, edam:operation_3092, edam:operation_3280, edam:operation_3778 ; sc:name "PhenoTagger" ; sc:url "https://github.com/ncbi-nlp/PhenoTagger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071 ; sc:author "Simon Jupp" ; sc:citation ; sc:description "Enter phenotypes descriptions and annotate these description with ontology terms using the entity/quality (EQ) pattern." ; sc:featureList edam:operation_0226 ; sc:name "Phenotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://wwwdev.ebi.ac.uk/fgpt/phenotator/" ; biotools:primaryContact "Simon Jupp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3518 ; sc:description "Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided." ; sc:featureList edam:operation_2424, edam:operation_2990, edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "phenoTest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phenoTest.html" ; biotools:primaryContact "Evarist Planet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3063, edam:topic_3473, edam:topic_3574 ; sc:citation "pubmed:23636887" ; sc:description "Open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders." ; sc:featureList edam:operation_0324, edam:operation_2497, edam:operation_3197, edam:operation_3672 ; sc:name "PhenoTips" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phenotips.org/" ; biotools:primaryContact "PhenoTips Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0780, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC9730636", "pubmed:36482291" ; sc:description "An automatic high-throughput phenotyping pipeline to track maize organs over time." ; sc:featureList edam:operation_0292, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PhenoTrack3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/openalea/phenotrack3d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3524 ; sc:citation ; sc:description "Flexible simulation of phenotypes under different models, including genetic variant and infinitesimal genetic effects (reflecting population structure) as well as non-genetic covariate effects, observational noise and additional correlation effects." ; sc:featureList edam:operation_2426 ; sc:name "PhenotypeSimulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/PhenotypeSimulator/index.html" ; biotools:primaryContact "Hannah Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6460638", "pubmed:30626929" ; sc:description """Rapid and accurate interpretation of clinical exomes using Phenoxome. Phenoxome is a web-based tool developed at the Children's Hospital of Philadelphia. It prioritizes candidate variants based upon the hypothesis that rare and deleterious variants in the genes known to be associated with the patient's phenotypes are more likely to be disease-causing in the clinical WES/WGS practices.""" ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:name "Phenoxome" ; sc:url "https://phenoxome.chop.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3668 ; sc:name "Disease name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:name "Phenotype name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1150 ; sc:name "Disease ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1622 ; sc:name "Disease report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3305, edam:topic_3325 ; sc:author "Giulia Babbi" ; sc:citation , "pmcid:PMC6631446", "pubmed:31307376" ; sc:description """A tool for characterizing biological functions underlying different phenotypes. a web server for associating phenotypes with molecular functional annotations. PhenPath includes a database and a tool:. '""" ; sc:featureList edam:operation_2422, edam:operation_3501, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PhenPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:url "http://phenpath.biocomp.unibo.it" ; biotools:primaryContact "Giulia Babbi", "Pier Luigi Martelli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3172, edam:topic_3308, edam:topic_3518 ; sc:citation ; sc:description "PHENotypes SIMulator" ; sc:featureList edam:operation_2415, edam:operation_2476, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "PHENSIM" ; sc:url "https://phensim.atlas.dmi.unict.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269 ; sc:citation , "pmcid:PMC4493137", "pubmed:26147094" ; sc:description "Package contains methods for statistical analysis of phenotypic data." ; sc:featureList edam:operation_2238 ; sc:license "Other" ; sc:name "PhenStat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PhenStat.html" ; biotools:primaryContact "Hamed Haselimashhadi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16845042" ; sc:description "This tool performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file." ; sc:featureList edam:operation_0245, edam:operation_0320, edam:operation_0400, edam:operation_2406, edam:operation_2416 ; sc:name "PHEPS" ; sc:url "http://pheps.orgchm.bas.bg/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3324, edam:topic_3837 ; sc:citation ; sc:description """Phage Host Exploration pipeline. This repository is the source code of bioinformatics pipeline, which creates files used in Pheri program. We strongly recommend NOT to install this software on your server, as it is not needed for Pheri program and files created by this pipeline are already included in Pheri installation. This repository is meant for people, which would like to go into the details of our work. This is repository of Phage Host ExploRatIon tool. The main purpose of this program is to predict phage hosts from sequence in FASTA format. Currently we are able to predict 8 host genera with very high accuracy (around 97%). These genera are Arthrobacter, Escherichia, Gordonia, Lactococcus, Mycobacterium, Pseudomonas, Staphylococcus, Streptococcus. PHERI uses preprocessed data stored in the folder files. The whole preprocessing pipeline can be found here. To install this tool please use our docker image.""" ; sc:featureList edam:operation_2454 ; sc:license "MIT" ; sc:name "PHERI" ; sc:url "https://github.com/andynet/pheri_preprocessing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3325, edam:topic_3337 ; sc:citation , "pmcid:PMC9620826", "pubmed:36083022" ; sc:description "A tool using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PheRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phers.hugheylab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0625, edam:topic_3077, edam:topic_3298 ; sc:citation , "pmcid:PMC5837456", "pubmed:29040602" ; sc:description "PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank." ; sc:featureList edam:operation_2403, edam:operation_3208 ; sc:name "PHESANT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/MRCIEU/PHESANT" ; biotools:primaryContact "Louise AC Millard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3298 ; sc:citation , "pmcid:PMC5837456", "pubmed:29040602" ; sc:description "PHESANT (PHEnome Scan ANalysis Tool) is a software package for performing comprehensive phenome scans in UK Biobank." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "PHESANT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MRCIEU/PHESANT" ; biotools:primaryContact "Louise A. C. Millard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623, edam:topic_0781, edam:topic_3293 ; sc:citation "pubmed:21081560" ; sc:description "Database that provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families." ; sc:featureList edam:operation_0224, edam:operation_0291, edam:operation_2422, edam:operation_3432 ; sc:name "PhEVER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pbil.univ-lyon1.fr/databases/phever/help.html" ; biotools:primaryContact "Leonor Palmeira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3324, edam:topic_3325, edam:topic_3335, edam:topic_3474 ; sc:citation , "pmcid:PMC9719543", "pubmed:36463386" ; sc:description "An artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases." ; sc:featureList edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "PHEVIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sites.gatech.edu/cssb/phevir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_3053, edam:topic_3337 ; sc:citation "pubmed:20335276" ; sc:description "Analyze many phenotypes compared to a single genetic variant (or other attribute). This method was originally described using electronic medical record (EMR) data from EMR-linked in the Vanderbilt DNA biobank, BioVU, but can also be applied to other richly phenotyped sets. ::DEVELOPER Biomedical Language Processing Lab." ; sc:featureList edam:operation_2497 ; sc:name "PheWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phewascatalog.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3298, edam:topic_3324, edam:topic_3337, edam:topic_3577 ; sc:citation , "pubmed:33051675" ; sc:description """PheWAS me is a web-app for interactive exploration of multimorbidity patterns in PheWAS. Electronic health records (EHRs) linked with a DNA biobank provide unprecedented opportunities for biomedical research in precision medicine. Should multiple-comparisons adjustment be done on P-Values of phewas results file?. Supplied are snps that have been preloaded.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196 ; sc:name "PheWAS-ME" ; sc:url "https://prod.tbilab.org/phewas_me/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3316, edam:topic_3334, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:32822005" ; sc:description """A Free Cloud-Computing Platform for Big-Data, Brain-Wide Imaging Association Studies. Neuroimaging based phenome-wide association study. Neuroimaging based phenome-wide association studies (PheWAS) is a big data discovery approach to systematically explore relationships between behavioral, environmental, or genetic factors of interest and a wide variety of neuroimaging markers (phenotypes) using a unified factor-to-phenotype strategy. A free cloud computing platform for implementing big-data neuroimaging association studies. The recent emergence of neuroimaging genomic databases of large healthy and diseased cohorts enables new approaches for scientific discovery, known as discovery science, to perform broad surveys examining true system-level gene-brain associations.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3283 ; sc:name "PheWAS" ; sc:url "http://phewas.loni.usc.edu/phewas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3298, edam:topic_3517 ; sc:citation ; sc:description "Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects." ; sc:featureList edam:operation_3197 ; sc:name "PheWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PheWAS/PheWAS" ; biotools:primaryContact "Leena Choi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0602, edam:topic_0625, edam:topic_2840 ; sc:citation , "pmcid:PMC7382647", "pubmed:32734156" ; sc:description """Phexpo a package for bidirectional enrichment analysis of phenotypes and chemicals. Phexpo is an R package for enrichment analysis of phenotypes (from the Human Phenotype Ontology(Köhler et al., 2019)) and chemicals.""" ; sc:featureList edam:operation_2422, edam:operation_3501 ; sc:name "phexpo" ; sc:url "https://github.com/GHLCLab/phexpo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2885, edam:topic_3168, edam:topic_3500 ; sc:citation , "pmcid:PMC10516101", "pubmed:37744223" ; sc:description "Assisted detection of point heteroplasmy in sanger sequencing chromatograms." ; sc:featureList edam:operation_3203, edam:operation_3215, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PHFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MSuarezMenendez/PHFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053 ; sc:citation , "pmcid:PMC5210566", "pubmed:27915230" ; sc:description "PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles." ; sc:featureList edam:operation_0224 ; sc:name "PHI-base" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phi-base.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3318, edam:topic_3382, edam:topic_3940 ; sc:citation , "pmcid:PMC7671433", "pubmed:33575580" ; sc:description """PHi-C is deciphering Hi-C data into polymer dynamics. PHi-C consists of Python3 codes for deciphering Hi-C data into polymer dynamics simulations. The input is a contact matrix data generated from a hic file through Juicer. PHi-C assumes that a genomic region of interest at an appropriate resolution can be modeled using a polymer network model including attractive and repulsive interactions between monomers. Instead of finding optimized 3D conformations, PHi-C's optimization procedure provides optimal interaction parameters of the polymer network model. We can then reconstruct an optimized contact matrix. Finally, we can carry out polymer dynamics simulations of the polymer network model equipped with the optimal interaction parameters.""" ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "PHi-C" ; sc:url "https://github.com/soyashinkai/PHi-C" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_0798, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:32311023" ; sc:description """Phigaro is a high-throughput prophage sequence annotation. Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2429 ; sc:license "MIT" ; sc:name "Phigaro" ; sc:url "https://github.com/bobeobibo/phigaro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "Philius predicts protein transmembrane topology and signal peptides." ; sc:featureList edam:operation_2479 ; sc:name "Philius" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://noble.gs.washington.edu/proj/philius/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_0219, edam:topic_0602, edam:topic_3324 ; sc:citation , "pmcid:PMC9248916", "pubmed:35776535" ; sc:description "A high-throughput database of macromolecular host-pathogen interactions on the Web." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "PHILM2Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://philm2web.live" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3299 ; sc:citation , "pmcid:PMC5328592", "pubmed:28198697" ; sc:description "Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). It specifically allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "philr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/philr.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3957 ; sc:citation , "pmcid:PMC10547927", "pubmed:37740324" ; sc:description "Software suite for PhIP-Seq data analysis." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "phippery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/matsengrp/phippery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3837, edam:topic_3957 ; sc:citation ; sc:description """Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships. A tool to predict prokaryotic hosts for phage (meta)genomic sequences. The tool uses information on sequence similarity between phage and bacteria genomes as well as sequence relatedness among bacteria. Phirbo estimates the phage-host relationship by comparing the content and order between phage and host ranked lists using Rank-Biased Overlap (RBO) measure. Briefly, RBO fosters comparison of ranked lists of different lengths with heavier weights for matching the higher-ranking items. RBO ranges between 0 and 1, where 0 means that the lists are disjoint (have no items in common) and 1 means that the lists are identical in content and order.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Phirbo" ; sc:url "https://github.com/aziele/phirbo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0204, edam:topic_0622, edam:topic_3168, edam:topic_3557 ; sc:citation "pubmed:15033869" ; sc:description "Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes." ; sc:featureList edam:operation_0438 ; sc:name "PHIRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biw.kuleuven.be/logt/PHIRE.htm" ; biotools:primaryContact "Rob Lavigne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3676 ; sc:citation ; sc:description """A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem. PhISCS-BnB is a fast tool for reconstructing the perfect tumor phylogeny using single-cell data via branch and bound.""" ; sc:featureList edam:operation_0324, edam:operation_3196, edam:operation_3227 ; sc:name "PhISCS-BnB" ; sc:url "https://github.com/algo-cancer/PhISCS-BnB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3299, edam:topic_3697, edam:topic_3941, edam:topic_3957 ; sc:citation ; sc:description """PHISDetector a tool to detect diverse in silico phage-host interaction signals for virome studies. Phage-host interactions are appealing systems to study bacterial adaptive evolution and are increasingly recognized as playing an important role in human health and diseases, which may contribute to novel therapeutic agents, such as phage therapy to combat multi-drug resistant infections. PHISDetector, a web tool to detect and systematically study diverse in silico phage-host interaction signals, including analyses for Sequence composition, CRISPR, Prophage, Genetic homology and protein-protein interactions. PHISDetector receives bacterial or virus genomic sequences in GenBank or FASTA format as input.""" ; sc:featureList edam:operation_0436, edam:operation_2421, edam:operation_2492, edam:operation_3461 ; sc:name "PHISDetector" ; sc:url "http://www.microbiome-bigdata.com/PHISDetector/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_2269, edam:topic_2275 ; sc:citation , "pmcid:PMC10311319", "pubmed:37387189" ; sc:description "Minimum message length inference of joint distributions of backbone and sidechain dihedral angles." ; sc:featureList edam:operation_0249, edam:operation_0384, edam:operation_0387, edam:operation_0479, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:name "PhiSiCal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lcb.infotech.monash.edu.au/phisical" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0623, edam:topic_0749 ; sc:citation "pubmed:19900969" ; sc:description "Database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. The database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (EMBL, UniProt, NCBI taxonomy database, NCBI Genome, ICTVdb, PubMed Central)." ; sc:featureList edam:operation_0438, edam:operation_3439 ; sc:name "phiSITE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phisite.org" ; biotools:primaryContact "phiSITE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC9520798", "pubmed:36171552" ; sc:description "A tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties." ; sc:featureList edam:operation_0417, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pHisPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xiaofengsong/pHisPred" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:34904625" ; sc:description "A tool to predict prokaryotic hosts for phage (meta)genomic sequences. PHIST links viruses to hosts based on the number of k-mers shared between their sequences." ; sc:featureList edam:operation_2421, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PHIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/refresh-bio/phist" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3300, edam:topic_3308, edam:topic_3500 ; sc:citation , "pmcid:PMC9048696", "pubmed:35238346" ; sc:description "Phitest for Analyzing the Homogeneity of Single-cell Populations." ; sc:featureList edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhitestR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Vivianstats/PhitestR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3421 ; sc:citation , "pubmed:33129577" ; sc:description """Updating the database of predicted three-dimensional structures of HLA with HLA-DR, HLA-DQ and HLA-DP molecules. An online database of predicted three-dimensional structures of HLA molecules. Predicted HLA three-dimensional structures database. pHLA3D was developed to improve the epitope analysis in the context of organ transplantation. This is a free database of 3D structures of HLA molecules. constructed by using homology modeling.""" ; sc:featureList edam:operation_0416, edam:operation_0477 ; sc:name "pHLA3D" ; sc:url "http://www.phla3d.com.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0654, edam:topic_3071 ; sc:citation "pubmed:21613134" ; sc:description "Program written in C++ that constructs datasets from NCBI data (GenBank). This uses the megaphylogeny method to construct extremely large datasets, but is convenient for small ones too." ; sc:featureList edam:operation_0310, edam:operation_2421 ; sc:name "PHLAWD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://phlawd.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_1929 ; sc:name "Text" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2085 ; sc:name "Structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1394 ; sc:name "Alignment score or penalty" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation , , "pmcid:PMC4489315", "pmcid:PMC5013910", "pubmed:25943547", "pubmed:27256311" ; sc:description "Search a protein sequence against a protein database using HMMER." ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_2421, edam:operation_3460 ; sc:name "PHMMER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.23.0" ; sc:url "https://www.ebi.ac.uk/metagenomics/sequence-search/search/phmmer" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:author "Erik Sonnhammer" ; sc:citation , ; sc:description "Predict transmembrane topology and signal peptides from the amino acid sequence of a protein." ; sc:featureList edam:operation_0269, edam:operation_0418 ; sc:name "Phobius (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "Stockholm Bioinformatics Center" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/pfa/phobius" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0736, edam:topic_1775, edam:topic_3542 ; sc:citation ; sc:description "Transmembrane topology and signal peptides prediction from the amino acid sequence of a protein." ; sc:featureList edam:operation_0267, edam:operation_1777 ; sc:name "Phobius API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/pfa/phobius_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654 ; sc:citation ; sc:description "Phobos is a tandem repeat search tool for complete genomes.PHOBOS can search for tandem repeats with a unit size of more than 5000 bp, which in the STAMP modules implies that primers can also be designed for minisatellites and tandem repeats with even longer units. Search settings and the output format of PHOBOS can be adjusted in a flexible manner, making it an ideal multipurpose tandem repeat search tool" ; sc:featureList edam:operation_2421 ; sc:name "Phobos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.3.12" ; sc:url "http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3293, edam:topic_3500 ; sc:citation "pubmed:19435885" ; sc:description "Identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds." ; sc:featureList edam:operation_0324, edam:operation_0325, edam:operation_0546, edam:operation_0557, edam:operation_3478 ; sc:name "PHOG" ; sc:url "http://phylofacts.berkeley.edu/orthologs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510 ; sc:citation "pubmed:25913879" ; sc:description "Predicting lysine phosphoglycerylation sites in proteins incorporating with position-specific propensity." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "Phogly-PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://app.aporc.org/Phogly-PseAAC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3534 ; sc:citation ; sc:description """Prediction of phosphoglycerylated lysine residues using structural properties of amino acids. The train and test datasets used for implementing PhoglyStruct are .mat files by the names 'train' and 'test' respectively (the three features namely tau, pc and ph are not present in train and test but in the .mat files 'original_train' and 'original_test' has all the features which can be viewed for reference). The codes in this repository are in two categories. One is based on commercial software (Matlab), while the other on non-commercial software (Octave).""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0417 ; sc:name "PhoglyStruct" ; sc:url "https://github.com/abelavit/PhoglyStruct" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3068, edam:topic_3071 ; sc:citation , "pubmed:33342295" ; sc:description """Markedness and implicational relationships in phonological development. Phon is a software program that supports the building of textual and phonological data corpora. While it was originally created to support the study of child language development, Phon can be used ... PhonBank is the child phonology component of the TalkBank system. TalkBank is a system for sharing and studying conversational interactions. PhonBank is supported by grant RO1-HD051698 from NIH-NICHHD to Brian MacWhinney and Yvan Rose. PHON is designed and built by Yvan Rose and Greg Hedlund. Currently available materials include:. Phon is a software program that supports the building of textual and phonological data corpora.""" ; sc:featureList edam:operation_0224, edam:operation_3432, edam:operation_3659 ; sc:name "PhonBank" ; sc:url "https://phonbank.talkbank.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0602, edam:topic_2229, edam:topic_3520 ; sc:citation , "pubmed:33682416" ; sc:description "PHONEMeS (PHOsphorylation NEtworks for Mass Spectrometry) is a method to model signalling networks based on untargeted phosphoproteomics mass spectrometry data and kinase/phosphatase-substrate interactions." ; sc:featureList edam:operation_0417, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "PHONEMeS" ; sc:url "https://github.com/saezlab/PHONEMeS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3520 ; sc:citation , "pmcid:PMC8583545", "pubmed:34778549" ; sc:description "PHONI (Practical Heuristic ON Incremental matching statistics computation) is a framework supports the currently memory-friendliest way to compute the matching statistics of a pattern on highly-repetitive texts, given that the input text is precomputed with the MONI index-" ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_3211 ; sc:license "MIT" ; sc:name "PHONI" ; sc:url "https://github.com/koeppl/phoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123 ; sc:citation "pubmed:19383128" ; sc:description "Web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial context of experimentally identified P-sites." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "Phos3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phos3d.mpimp-golm.mpg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0123, edam:topic_2814 ; sc:citation "pubmed:18710483" ; sc:description "System for estimating the site of phosphorylation in a phosphorylated peptide with ambiguous sites. It does this by generating ions from peptide sequences and calculating their masses, generating different ions and masses for water-loss, different cysteine modifications and different charge states." ; sc:featureList edam:operation_0417, edam:operation_2406 ; sc:name "PhosCalc" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/danmaclean/phoscalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0601, edam:topic_3510 ; sc:citation "pubmed:17680694" ; sc:description "PhoScan is a software of prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PhoScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.au.tsinghua.edu.cn/phoscan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0780 ; sc:citation ; sc:description "PHOSFER uses a novel machine-learning approach in order to predict phosphorylation sites in soybean proteins, and will be expanded to predict for other plants in the future." ; sc:featureList edam:operation_2479 ; sc:name "PHOSFER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://saphire.usask.ca/saphire/phosfer/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166 ; sc:citation ; sc:description "A web server for the identification of phosphate-binding sites on protein structures." ; sc:featureList edam:operation_3092 ; sc:name "Phosfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://phosfinder.bio.uniroma2.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0160, edam:topic_0601 ; sc:citation "pubmed:21081558" ; sc:description "The database manages posttranslational modification sites of various species ranging from bacteria to human. It contains phosphorylated, N-glycosylated or acetylated sites. All sites are obtained from high-resolution mass spectrometric data. The database is comprised of three main components: the database environment, the prediction platform and the toolkit section." ; sc:featureList edam:operation_0253, edam:operation_0417, edam:operation_3092, edam:operation_3644, edam:operation_3755 ; sc:name "PHOSIDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phosida.com" ; biotools:primaryContact "Matthias Mann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0601, edam:topic_3474 ; sc:citation , "pubmed:34320631" ; sc:description "An integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhosIDN" ; sc:url "https://github.com/ustchangyuanyang/PhosIDN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0623 ; sc:citation "pubmed:24574117" ; sc:description "Tool to predict novel phosphorylation networks based on the preference of certain kinase families to phosphorylate specific functional protein families (domains). It identifies the potentially phosphorylated proteins from a given set of proteins and predicts target kinases which in turn would phosphorylate these identified phosphoproteins based on their domain compositions." ; sc:featureList edam:operation_2479, edam:operation_3092 ; sc:name "PhosNetConstruct" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nii.ac.in/phosnetconstruct.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0780, edam:topic_3520 ; sc:citation "pubmed:17984086", "pubmed:19880383" ; sc:description "Contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner." ; sc:featureList edam:operation_0417, edam:operation_3092, edam:operation_3501 ; sc:name "PhosPhAt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phosphat.mpimp-golm.mpg.de/" ; biotools:primaryContact "Waltraud X. Schulze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3520 ; sc:citation , "pubmed:37584946" ; sc:description "Interactive web platform to analyze quantitative phosphoproteomics data." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Phospho-Analyst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://analyst-suites.org/apps/phospho-analyst/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0166 ; sc:citation ; sc:description "Database of three-dimensional structures of phosphorylation sites which stores information retrieved from the Phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites." ; sc:featureList edam:operation_2996 ; sc:name "Phospho3d" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:url "http://www.phospho3d.org/" ; biotools:primaryContact "Allegra Via", "Andreas Zanzoni" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2775 ; sc:name "Kinase name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:name "Sequence accession (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence motif (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence motif (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence motif (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0601 ; sc:citation , "pmcid:PMC3013696", "pubmed:21062810" ; sc:description "Experimentally verified phosphorylation sites in eukaryotic proteins." ; sc:featureList edam:operation_0224 ; sc:name "PhosphoELM database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phospho.elm.eu.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_3068, edam:topic_3520 ; sc:citation , "pubmed:33119075" ; sc:description """Interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets. Phosphomatics helps you make sense of your high-throughput phosphoproteomics data. Our aim is to help you connect the phosphorylation sties that you observe in your mass spectrometry experiments to known upstream kinases. This provides a greater understanding of the regulatory signaling networks operating in your systems. You will be automatically redirected to your results once they're ready. This may take a minute or two depending on the size of your input data and our server utilisation.""" ; sc:featureList edam:operation_0417, edam:operation_2422 ; sc:name "Phosphomatics" ; sc:url "https://phosphomatics.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269 ; sc:citation , "pubmed:28968644" ; sc:description "It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "phosphonormalizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phosphonormalizer.html" ; biotools:primaryContact "Sohrab Saraei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601 ; sc:citation "pubmed:25304781" ; sc:description "Method for predicting kinase substrates using cellular context information, and is currently able to make predictions for 59 human kinases." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PhosphoPICK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.scmb.uq.edu.au/phosphopick/phosphopick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0821, edam:topic_2815, edam:topic_3510 ; sc:citation ; sc:description "Novel bioinformatics approach to predict kinase-specific phosphorylation substrates and sites in the human proteome by combining informative protein sequence and functional features to build the prediction models using random forest (RF)." ; sc:featureList edam:operation_3092 ; sc:name "PhosphoPredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phosphopredict.erc.monash.edu/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0123, edam:topic_2815, edam:topic_3500, edam:topic_3510 ; sc:citation , "pmcid:PMC4539857", "pubmed:26283093" ; sc:description "Cross-species mapping of orthologous protein post-translational modifications." ; sc:featureList edam:operation_0417 ; sc:license "GPL-1.0" ; sc:name "PhosphOrtholog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phosphortholog.com/" ; biotools:primaryContact "Jean Yee Hwa Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3557 ; sc:citation "pubmed:22471441" ; sc:description "Novel bioinformatical tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN (Linding et al) and contains various statistical modules for futher analysis." ; sc:featureList edam:operation_2423 ; sc:name "PhosphoSiteAnalyzer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/phosphosite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601, edam:topic_2259, edam:topic_3070, edam:topic_3678 ; sc:citation "pubmed:22135298" ; sc:description "Online systems biology resource providing comprehensive info and tools to study protein post-translational modification in man and mouse." ; sc:featureList edam:operation_0417, edam:operation_3645, edam:operation_3755 ; sc:name "PhosphoSitePlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.phosphosite.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601 ; sc:citation "pubmed:24623121" ; sc:description "Web server for prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PhosphoSVM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sysbio.unl.edu/PhosphoSVM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC8787428", "pubmed:34882763" ; sc:description "An automated phosphoproteomic pipeline in R." ; sc:featureList edam:operation_2939, edam:operation_3223, edam:operation_3501, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PhosPiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TCB-yehong/PhosPiR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:37290543" ; sc:description "Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions." ; sc:featureList edam:operation_0417, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PhosPPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phosppi.sjtu.edu.cn/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2899 ; sc:name "Drug name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_0634, edam:topic_2229 ; sc:citation , "pmcid:PMC9394491", "pubmed:35994309" ; sc:description "Pathway analysis database of drug response based on phosphorylation activity measurements." ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_0533, edam:operation_3926, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Phosprof" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phosprof.medals.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_0749, edam:topic_3520 ; sc:citation ; sc:description """PhosR enables processing and functional analysis of phosphoproteomic data. PhosR is a package for the comprehensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomic data including filtering, imputation, normalisaton and batch correction, which enables integration of multiple phosphoproteomic datasets. Downstream analytical tools consists of site- and protein-centric pathway analysis to evaluate activities of kinases and signalling pathways, large-scale kinase-substrate annotation from dynamic phosphoproteomic profiling, and visualisation and construction of signalomes present in the phosphoproteomic data of interest.""" ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3557, edam:operation_3891, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "PhosR" ; sc:url "https://github.com/PYangLab/PhosR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_2885 ; sc:citation "pubmed:19995808" ; sc:description "A database of phosphorylation-related SNP (phosSNP) which are non-synonymous SNP (nsSNP) that affect the protein phosphorylation status. Using an in-house developed kinase-specific phosphorylation site predictor (GPS 2.0), we computationally detected that �_70% of the reported nsSNPs are potential phosSNPs." ; sc:featureList edam:operation_0331, edam:operation_0417, edam:operation_0484, edam:operation_3196, edam:operation_3197 ; sc:name "PhosSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phossnp.biocuckoo.org/" ; biotools:primaryContact "Jian Ren", "Yu Xue", "Zhaolei Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "A phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae." ; sc:featureList edam:operation_3092 ; sc:name "PhosTryp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://phostryp.bio.uniroma2.it" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3063, edam:topic_3474 ; sc:citation , "pmcid:PMC8929166", "pubmed:35310161" ; sc:description "Deep-learning based prediction of phospho-variants using sequence information." ; sc:featureList edam:operation_0253, edam:operation_0331, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhosVarDeep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lisalikegaga/PhosVarDeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0593, edam:topic_3277 ; sc:citation , "pmcid:PMC9237726", "pubmed:35608303" ; sc:description "An open-source library for cross-sample analysis of FTIR spectroscopy data." ; sc:featureList edam:operation_2939, edam:operation_3214, edam:operation_3799, edam:operation_3891, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Photizo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DendrouLab/Photizo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3068, edam:topic_3071 ; sc:citation , "pubmed:32757305" ; sc:description """Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues. calculational modules and databases of absorption and emission spectra for diverse compounds. PhotochemCAD™ is a program of calculational modules and accompanying database of spectra aimed at advancing the photosciences. A streamlined version of the same database of spectra can now be viewed on our new website. The user is directed to the following journal articles for full description of the program and database:.""" ; sc:featureList edam:operation_3435, edam:operation_3799, edam:operation_3860 ; sc:name "PhotochemCAD" ; sc:url "http://www.photochemcad.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3299, edam:topic_3474 ; sc:citation ; sc:description """A webserver for photosynthetic protein prediction from a genome neighborhood feature. Multi-label classifier for predicting photosynthetic protein via genome neighborhood feature. A Tool for Exploring Photosynthetic functions and evolution. PhotoModPlus is a genome neighborhood-based platform for exploring photosynthetic functions and evolution in photosynthetic prokaryotes. Currently, there are two main applications inside, PhotoModPlus GNN and PhotoModPlus Prediction. *User can access this site on a mobile phone, tablet, desktop computer or wide-screen.""" ; sc:featureList edam:operation_0477, edam:operation_1777, edam:operation_3092 ; sc:name "PhotoModPlus" ; sc:url "http://bicep.kmutt.ac.th/photomod" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3314, edam:topic_3382 ; sc:description "This program parametrize the point source solution to the photon diffusion in human tissues." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Photon diffusion in tissues simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/36249-photon-diffusion-in-tissues-simulator" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC8294542", "pubmed:34288935" ; sc:description "A high level Python API for designing and optimizing machine learning pipelines." ; sc:featureList edam:operation_0479, edam:operation_3435, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PHOTONAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.photon-ai.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """An Inter-disciplinary Platform for Visual Interpretation and Labeling of ICESat-2 Geolocated Photon Data. 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Gordon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2269, edam:topic_3168 ; sc:citation , , ; sc:description "The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. 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It is also a C++ and Python library that can be used to create new applications or to extend the current functionality." ; sc:featureList edam:operation_0567 ; sc:name "Phycas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hydrodictyon.eeb.uconn.edu/projects/phycas/index.php/Phycas_Home" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3170 ; sc:citation ; sc:description "PhycoMine is data warehouse system created to fostering the analysis of complex and integrated data from microalgae species in a single computational environment." ; sc:featureList edam:operation_0571, edam:operation_3223, edam:operation_3463, edam:operation_3501, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhycoMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phycomine.iq.usp.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3314 ; sc:citation , "pmcid:PMC8922167", "pubmed:35295748" ; sc:description "A tool for exploring covariates of pathogen spread." ; sc:featureList edam:operation_0558, edam:operation_2940, edam:operation_3478, edam:operation_3659, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PhyCovA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://evolcompvir-kuleuven.shinyapps.io/PhyCovA/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_1920 ; sc:name "Resource metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910, edam:format_3159 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:name "Phylogenetic tree image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_3159 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:author "Lukasz Kreft" ; sc:citation , "pubmed:28525531" ; sc:contributor "Michiel Van Bel" ; sc:description "Phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx." ; sc:featureList edam:operation_0558, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhyD3" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "VIB" ; sc:softwareHelp , ; sc:softwareVersion "1.1" ; sc:url "https://phyd3.bits.vib.be" ; biotools:primaryContact "Lukasz Kreft", "VIB BITS Core Facility" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:12824402", "pubmed:15215406" ; sc:description "Tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0533, edam:operation_3092 ; sc:name "Phydbac2" ; sc:url "http://igs-server.cnrs-mrs.fr/phydbac/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC7553321", "pubmed:33001973" ; sc:description """Design of follow-up single-cell sequencing experiments of tumors. PhyDOSE - Phylogenetic Design Of Single-cell sequencing Experiments. The input to PhyDOSE is a set of candidate trees, a frequency matrix obtained from bulk data, and a confidence level. 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The main functions of phydoser include:.""" ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3227 ; sc:name "PhyDOSE" ; sc:url "https://github.com/elkebir-group/phydoser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3293 ; sc:citation , "pmcid:PMC5134231", "pubmed:27905871" ; sc:description "Open source software package that performs rapid calculation of phylogenetic information content using the latest advances in phylogenetic informativeness based theory." ; sc:featureList edam:operation_0324, edam:operation_0567 ; sc:name "PhyInformR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://carolinafishes.github.io/software/phyinformR/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0157, edam:topic_0194, edam:topic_0602, edam:topic_0780 ; sc:citation ; sc:description """a UNIX shell toolkit for processing and analyzing phylogenomic data. Docs · Report Bug · Request Feature. PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data. Quick Start — phykit documentation. PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process multiple sequence alignments and phylogenies for broad applications. If you found PhyKIT useful, please cite PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. bioRxiv. doi: 10.1101/2020.10.27.358143. This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the online documentation.""" ; sc:featureList edam:operation_0324, edam:operation_3192, edam:operation_3659 ; sc:license "MIT" ; sc:name "PhyKIT" ; sc:url "https://jlsteenwyk.com/PhyKIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797 ; sc:author "Joseph MEX Lucas" ; sc:citation , , "pmcid:PMC4155083", "pmcid:PMC5495381", "pubmed:25103980", "pubmed:28671949" ; sc:description "PhylDiag computes synteny blocs between two genomes. 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Cai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080 ; sc:citation "pubmed:24148814" ; sc:description "Human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. 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It operates in two modes: first, the hierarchy of probes is defined interactively, second, the intensity data of a hybridized chip is loaded and analyzed according to the hierarchy. The program can export hierarchy trees to Newick-format and analyzed data to Excel. 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Users can browse the Featured Tree Collections or Upload Trees to your own workplace both registerially and anonymously." ; sc:featureList edam:operation_0326, edam:operation_0555, edam:operation_0558, edam:operation_0567, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:name "PhyloCloud" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phylocloud.cgmlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0602, edam:topic_0623, edam:topic_3293, edam:topic_3944 ; sc:citation , "pubmed:33416870" ; sc:description """PhyloCorrelate is inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling. Phylocorrelate is a phylogenetic profiling tool that detects pairs of gene/protein families with similar phylogenetic distributions. 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PhyloCorrelate uses the GTDB bacterial tree and gene occurrences from AnnoTree including entries from KEGG, PFAM, and TIGRFAM.""" ; sc:featureList edam:operation_0314, edam:operation_0323, edam:operation_0326, edam:operation_0533, edam:operation_2436 ; sc:name "PhyloCorrelate" ; sc:url "http://phylocorrelate.uwaterloo.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0621, edam:topic_3512 ; sc:citation ; sc:description "PhyloCSF++ is a fast and user-friendly implementation of PhyloCSF with annotation tools PhyloCSF can identify protein-coding regions in the genome based on multiple-sequence alignments. PhyloCSF++ is an implementation of the original methods PhyloCSF and PhyloCSF HMM. 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Input is a protein sequence up to 2000 a.a." ; sc:featureList edam:operation_1777, edam:operation_3767 ; sc:name "PhyloFacts FAT-CAT" ; sc:url "http://phylogenomics.berkeley.edu/phylofacts/fatcat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0194, edam:topic_0621, edam:topic_3293, edam:topic_3944 ; sc:citation , "pmcid:PMC8345874", "pubmed:34358228" ; sc:description "PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences." ; sc:featureList edam:operation_0544, edam:operation_0552, edam:operation_0553, edam:operation_3192, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PhyloFisher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TheBrownLab/PhyloFisher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , "pmcid:PMC7593591", "pubmed:33109753" ; sc:description """Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes. by Harald Gruber-Vodicka, Elmar A. Pruesse, and Brandon Seah. phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset. Manual. phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore the phylogenetic composition of an Illumina (meta)genomic dataset.""" ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3460, edam:operation_3472, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "phyloFlash" ; sc:url "https://github.com/HRGV/phyloFlash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0084, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description """Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs. 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You can install the components with one line as follows.""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0503 ; sc:name "PhyloFold" ; sc:url "https://github.com/heartsh/phylofold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3056, edam:topic_3299, edam:topic_3500 ; sc:citation ; sc:description "Phylogeographic data aggregation and repurposing." ; sc:featureList edam:operation_0492, edam:operation_3192, edam:operation_3431, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "phylogatR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "Beta test" ; sc:url "https://phylogatr.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0622, edam:topic_0654, edam:topic_3293 ; sc:citation ; sc:description "Phylogenetic analysis of DNA sequences or genomes by Fourier transform" ; sc:featureList edam:operation_0324, edam:operation_0492, edam:operation_2871 ; sc:isAccessibleForFree true ; sc:name "Phylogenetic analysis of DNA sequences or genomes by Fourier transform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/52072-phylogenetic-analysis-of-dna-sequences-or-genomes-by-fourier-transform" ; biotools:primaryContact "Changchuan Yin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3365 ; sc:description "Computerized tools (\"workflows\") to process large amounts of data from cross-disciplinary sources as well as tools for designing and running workflows." ; sc:featureList edam:operation_0323, edam:operation_0567, edam:operation_2238 ; sc:name "Phylogenetics_AT_JST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/PasqualeInfn/JST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_0625, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31588499" ; sc:description """Phylogenize is a web tool that allows users to link microbial genes to environments, accounting for phylogeny. More specifically, given community composition data, phylogenize links genes in microbial genomes to either microbial prevalence in, or specificity for, a given environment, while also taking into account an important potential confounder: the phylogenetic relationships between microbes.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3659 ; sc:name "phylogenize" ; sc:url "https://phylogenize.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0780, edam:topic_3382 ; sc:citation , "pmcid:PMC6602505", "pubmed:31114886" ; sc:description "Interactive web-based visualization and sharing of phylogenetic trees." ; sc:featureList edam:operation_0326, edam:operation_0558, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "phylogeny IO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://phylogeny.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3301, edam:topic_3697 ; sc:description "This package provides a convenient way to map microbiome-related information. It relies on the phyloseq package and provides methods for mappiin samples, drawing network diagrams, plotting phylogenetic trees and maps, and correlating physical distance with ecological distance." ; sc:featureList edam:operation_0337 ; sc:name "phylogeo" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://zachcp.github.io/phylogeo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0092, edam:topic_3293 ; sc:description "Java library for producing rich kmls containing phylogenetic data that can be rendered in google earth web browser. In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices." ; sc:featureList edam:operation_2429 ; sc:name "PhyloGeoRef" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kdiverson/phyloGeoRef" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:24749775" ; sc:description "Simulate the evolution of DNA sequences under a model of coalescence on a 2-dimensional grid in which each cell is treated as one population. Going backward in time, populations can exchange gene copies and/or host coalescence events between two or more gene copies, at each generation." ; sc:featureList edam:operation_2426 ; sc:name "PhyloGeoSim 1.0 beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ebe.ulb.ac.be/ebe/PhyloGeoSim.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0602, edam:topic_0622, edam:topic_0749, edam:topic_2259, edam:topic_3168, edam:topic_3169, edam:topic_3512 ; sc:citation ; sc:description "Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy." ; sc:featureList edam:operation_0258, edam:operation_0292, edam:operation_0346, edam:operation_0547 ; sc:name "Phylogibbs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phylogibbs.unibas.ch" ; biotools:primaryContact "Mikhail Pachkov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "PhyloHMM (phylogenetic hidden Markov model) is a website with data, software and supporting materials for conserved sequences in disordered regions" ; sc:featureList edam:operation_2479 ; sc:name "PhyloHMM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v2" ; sc:url "http://www.moseslab.csb.utoronto.ca/phylo_HMM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3050, edam:topic_3293 ; sc:citation "pubmed:24443378" ; sc:description "Web based application that places biodiversity information aggregated from many sources onto compact phylogenetic trees." ; sc:featureList edam:operation_0324, edam:operation_0567 ; sc:name "Phylojive" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phylojive.ala.org.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3572 ; sc:citation ; sc:description "Identify contaminant or untargeted organism sequences in genome assemblies." ; sc:featureList edam:operation_3218 ; sc:name "PhylOligo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/itsmeludo/Phyloligo/" ; biotools:primaryContact "Ludovic Mallet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0194, edam:topic_2269, edam:topic_3293, edam:topic_3299 ; sc:citation ; sc:description "Efficient assessment of phylogenomic model adequacy." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "PhyloMAd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/duchene/phylomad" ; biotools:primaryContact "David A. Duchêne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC9169257", "pubmed:35668363" ; sc:description "An R package for phylogeny-aware microbiome data analysis." ; sc:featureList edam:operation_0323, edam:operation_3658, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "phyloMDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liudoubletian/phyloMDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3361, edam:topic_3697 ; sc:citation , "pmcid:PMC10088256", "pubmed:37041566" ; sc:description "Phylogeny-based test of mediation effect in microbiome." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PhyloMed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KiRinHong/miMediation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0621, edam:topic_0634 ; sc:citation , , , , "pmcid:PMC2238872", "pmcid:PMC3013701", "pmcid:PMC3964985", "pmcid:PMC8728271", "pubmed:17962297", "pubmed:21075798", "pubmed:24275491", "pubmed:34718760" ; sc:description "PhylomeDB is a public database for complete catalogs of gene phylogenie. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing." ; sc:featureList edam:operation_0499, edam:operation_0544, edam:operation_2423, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PhylomeDB" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:softwareVersion "5.0" ; sc:url "http://phylomeDB.org" ; biotools:primaryContact "Toni Gabaldón" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_1423, edam:format_1910, edam:format_1912 ; sc:name "Phylogenetic data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0326 ; sc:license "GPL-3.0" ; sc:name "Phylommand" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mr-y/phylommand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0204, edam:topic_0654 ; sc:description "PhyloNet (Phylogenetic Regulatory Network) is a motif discovery program.  It represents a very new paradigm for motif discovery: based on sequences of several evolutionarily related genomes, PhyloNet predicts a near complete set of conserved motifs of the organism of interest,as well as gene clusters that share these motifs, without reliance of additional data such as gene regulation." ; sc:featureList edam:operation_0238 ; sc:name "PhyloNet" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v2b" ; sc:url "http://stormo.wustl.edu/PhyloNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_3168, edam:topic_3277 ; sc:citation , "pubmed:31790149" ; sc:description "This is the phylonium tool for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods." ; sc:featureList edam:operation_0325, edam:operation_0546, edam:operation_3211 ; sc:name "phylonium" ; sc:url "http://github.com/evolbioinf/phylonium" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_3293, edam:topic_3407 ; sc:citation "pubmed:19443453" ; sc:description "Allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related." ; sc:featureList edam:operation_0327, edam:operation_0544, edam:operation_3221, edam:operation_3625 ; sc:name "PhyloPars" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/phylopars/" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0203, edam:topic_3293 ; sc:citation "pubmed:16948844" ; sc:description "Webserver which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain evolutionary branches or even single species. The output can be saved in HTML, Excel or plain text format for further analysis. Output is linked to the FatiGO web interface creating easy access to functional information." ; sc:featureList edam:operation_0224, edam:operation_0324, edam:operation_0544, edam:operation_0553 ; sc:name "PhyloPat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cmbi.ru.nl/phylopat" ; biotools:primaryContact "T. Hulsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3293, edam:topic_3518 ; sc:citation , "pmcid:PMC4000467", "pubmed:24771669" ; sc:description "Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes." ; sc:featureList edam:operation_0308, edam:operation_0309 ; sc:name "PhylOPDb" ; sc:softwareHelp ; sc:url "http://g2im.u-clermont1.fr/phylopdb/help.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC9235490", "pubmed:35758792" ; sc:description "Boosting regulatory function prediction accuracy using evolutionary information." ; sc:featureList edam:operation_0445, edam:operation_2437, edam:operation_3192, edam:operation_3663, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PhyloPGM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BlanchetteLab/PhyloPGM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3174, edam:topic_3512, edam:topic_3697 ; sc:citation , "pmcid:PMC8098674", "pubmed:33986979" ; sc:description "PhyloPrimer is a taxon-specific oligonucleotide design platform. PhyloPrimer was born from a collaboration between the University of Bristol and ENOVEO, a company involved in bioremediation and microbial monitoring projects that looks into a wide variety of environmental samples with the aim of identifying specific genes and microorganisms." ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_3237 ; sc:license "GPL-3.0" ; sc:name "PhyloPrimer" ; sc:url "https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer" ; biotools:primaryContact "Gilda Varliero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_0621, edam:topic_3293 ; sc:citation "pubmed:21252074" ; sc:description "A web-based tool for the generation and visualization of phylogenetic profiles across Eukarya. It exploits 120 available eukaryotic genome sequences to allow users to visualize the evolutionary trajectories of defined subsets of model organism genes." ; sc:featureList edam:operation_0296, edam:operation_0314, edam:operation_0323, edam:operation_0533 ; sc:name "PhyloPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compsysbio.org/phylopro/" ; biotools:primaryContact "John Parkinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_3056, edam:topic_3293 ; sc:citation ; sc:description "Dynamic visualization and exploration of multi-layered phylogenetic profiles." ; sc:featureList edam:operation_0324, edam:operation_0567 ; sc:name "PhyloProfil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BIONF/phyloprofile" ; biotools:primaryContact "Ingo Ebersberger", "Ngoc-Vinh Tran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053, edam:topic_3293 ; sc:citation ; sc:description "Dynamic visualization and exploration of multi-layered phylogenetic profiles." ; sc:featureList edam:operation_0323, edam:operation_0324, edam:operation_0567 ; sc:license "MIT" ; sc:name "PhyloProfile" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BIONF/phyloprofile" ; biotools:primaryContact "Vinh Tran" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3056, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC4748697", "pubmed:26870609" ; sc:description "PhyloPythiaS+ allows the analysis of Gb-sized metagenomes with inexpensive hardware and recovery of species or genera-level bins with low error rates in a fully automated fashion." ; sc:featureList edam:operation_3197 ; sc:license "Other" ; sc:name "PhyloPythiaS+" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/algbioi/ppsp" ; biotools:primaryContact "Alice McHardy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3050, edam:topic_3293 ; sc:citation ; sc:description """R package for biogeographic regionalization and spatial conservation. An R package for biogeographic regionalization (the classification of geographical areas in terms of their biotas) and macroecology. With macroecological datasets of ever increasing size and complexity, phyloregion offers the possibility of handling and executing very large scale analysis of biogeographic regionalization. It also allows fast and memory efficient analysis of standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment. phyloregion can run on any operating system (Mac, Linux, Windows or even high performance computing cluster) with R 3.6.0 (or higher) installed.""" ; sc:featureList edam:operation_0324, edam:operation_3432, edam:operation_3435 ; sc:name "phyloregion" ; sc:url "https://github.com/darunabas/phyloregion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0160 ; sc:citation "pubmed:23621982" ; sc:description "Program for predicting consensus structures of aligned RNA sequences by incorporating phylogenetic-based covarying mutations." ; sc:featureList edam:operation_2441 ; sc:name "PhyloRNAalifold" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/PhyloRNAalifold/" ; biotools:primaryContact "Shaojie Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:17244358", "pubmed:20435683" ; sc:description "Web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445, edam:operation_0448, edam:operation_2575 ; sc:name "Phyloscan" ; sc:url "http://bayesweb.wadsworth.org/phyloscan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3301 ; sc:citation , "pmcid:PMC3632530", "pubmed:23630581" ; sc:description "Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data." ; sc:featureList edam:operation_0337, edam:operation_2945, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "phyloseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.19.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/phyloseq.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174 ; sc:citation ; sc:description "Suite of software tools to conduct phylogenetic analysis of genomes and metagenomes. Using a reference database of protein sequences, PhyloSift can scan new sequences against that data for homologs and identify phylogentic relationships of the new sequence compared to the database sequences." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "Phylosift" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://phylosift.wordpress.com/about-2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:21504561" ; sc:description "Extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R." ; sc:featureList edam:operation_0324, edam:operation_2426 ; sc:name "PhyloSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/goldman-srv/phylosim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0637, edam:topic_3299 ; sc:citation ; sc:description "Taxon selection, data retrieval and marker identification for phylogenomics ." ; sc:featureList edam:operation_0224 ; sc:name "phyloSkeleton" ; sc:softwareHelp ; sc:url "https://bitbucket.org/lionelguy/phyloskeleton/" ; biotools:primaryContact "Lionel Guy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:32067951" ; sc:description """Transcripts' Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family. A tool to model the evolution and structural impact of alternative splicing. PhyloSofS (Phylogenies of Splicing isoforms Structures) is a fully automated computational tool that infers plausible evolutionary scenarios explaining a set of transcripts observed in several species and models the three-dimensional structures of the produced protein isoforms.""" ; sc:featureList edam:operation_0264, edam:operation_0477, edam:operation_3478 ; sc:license "MIT" ; sc:name "PhyloSofS" ; sc:url "https://github.com/PhyloSofS-Team/PhyloSofS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3293, edam:topic_3944 ; sc:citation , "pmcid:PMC8733950", "pubmed:35068947" ; sc:description "A web-based tool to analyze paralogous clade divergence in phylogenetic trees." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Phylostat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://phylo.io" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:name "Phylogenetic tree image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_3293, edam:topic_3307 ; sc:citation , "pmcid:PMC10017117", "pubmed:36936370" ; sc:description "Graphical tool to investigate temporal signal of heterochronous sequences datasets." ; sc:featureList edam:operation_0323, edam:operation_0558, edam:operation_3659, edam:operation_3942 ; sc:isAccessibleForFree true ; sc:name "Phylostems" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pvbmt-apps.cirad.fr/apps/phylostems" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0621, edam:topic_0637, edam:topic_3050 ; sc:citation , "pmcid:PMC6892540", "pubmed:31800571" ; sc:description """This tool provides a simple way to produce distributions of trees with subsets of taxa. If larger subsets are required you can download full trees. The tool first trims to a subset, and then samples trees from a chosen pseudo-posterior distribution. Note that any further analyses should only be conducted with a large sample of trees. Select species from the list which follows the taxonomy. Then copy and paste or drag and drop them into the box to the right.""" ; sc:featureList edam:operation_3192, edam:operation_3431, edam:operation_3478, edam:operation_3557 ; sc:name "phylosubsets" ; sc:url "http://vertlife.org/phylosubsets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0654, edam:topic_3077 ; sc:citation , "pmcid:PMC6027284", "pubmed:29874797" ; sc:description "An automated pipeline for retrieving orthologous DNA sequences from GenBank in R." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "phylotaR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ropensci/phylotaR" ; biotools:primaryContact "Dominic J. Bennett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3518 ; sc:citation "pubmed:20581189" ; sc:description "Application for the visualization and analysis of PhyloChip microarrays. It is a popular 16S rRNA gene microarray for microbial surveys, and has been successfully used to study the microbial diversity of several interesting environments. However, its adoption has been limited by a lack of accessible analysis software. It fills this need and is the first desktop application providing end-to-end PhyloChip analysis." ; sc:featureList edam:operation_0571 ; sc:name "PhyloTrac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phylotrac.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3277, edam:topic_3293 ; sc:citation ; sc:description "PhyloTrack is a JavaScript–based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation." ; sc:featureList edam:operation_3208 ; sc:name "PhyloTrack" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/phylotrack/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation "pubmed:20802801" ; sc:description "Collection of programs for cophylogeny testing." ; sc:featureList edam:operation_0324 ; sc:name "phylotree" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://csurs.csr.uky.edu/phylotree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3301 ; sc:description "Identifies microbial operational taxonomic units (OTUs) from metagenomic data." ; sc:featureList edam:operation_3460 ; sc:name "PhylOTU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sharpton/PhylOTU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3673 ; sc:citation ; sc:description "In silico predictor of gene subtypes." ; sc:featureList edam:operation_2995 ; sc:name "Phylotyper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/superphy/insilico-subtyping" ; biotools:primaryContact "Matthew Whiteside" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0625, edam:topic_0749, edam:topic_3676 ; sc:citation ; sc:description "Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Phylovar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mae6/Phylovar.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0092 ; sc:citation , "pmcid:PMC3866560", "pubmed:24191071" ; sc:description "Web service that generates in-browser animations of biogeographic and phylogeographic histories from annotated phylogenetic input" ; sc:featureList edam:operation_0337 ; sc:name "Phylowood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mlandis.github.io/phylowood/" ; biotools:primaryContact "Michael Landis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0203, edam:topic_3175 ; sc:citation , "pmcid:PMC10655845", "pubmed:37879113" ; sc:description "R package for efficient identification of outlier sequences in phylogenomic datasets." ; sc:featureList edam:operation_0337, edam:operation_0556, edam:operation_3192, edam:operation_3478, edam:operation_3695, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PhylteR" ; sc:url "https://cloud.sylabs.io/library/theo.treecou/tool/phylter_singularity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0654 ; sc:citation "pubmed:26530724" ; sc:description "Software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes." ; sc:featureList edam:operation_0292, edam:operation_2423 ; sc:name "PHYLUCE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://phyluce.readthedocs.org/en/latest/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2924 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2924 ; sc:name "Protein sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3293 ; sc:author "Stephane Guindon" ; sc:citation , , , , , "pmcid:PMC1160113", "pubmed:15980534" ; sc:description "Phylogenetic estimation software using Maximum Likelihood" ; sc:featureList edam:operation_0547 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PhyML" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.atgc-montpellier.fr/phyml/" ; biotools:primaryContact "Stephane Guindon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3174 ; sc:citation "pubmed:19648916" ; sc:description "A classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs" ; sc:featureList edam:operation_0291, edam:operation_2451, edam:operation_3460 ; sc:name "Phymm" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "4.0" ; sc:url "https://ccb.jhu.edu/software/phymmbl/index.shtml" ; biotools:primaryContact "Steven L. Salzberg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation ; sc:description "A database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses." ; sc:featureList edam:operation_2928 ; sc:isAccessibleForFree true ; sc:name "Phymyco-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:url "http://phymycodb.genouest.org/" ; biotools:primaryContact "GenOuest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3293 ; sc:citation ; sc:description """An R package for phylogenetic species-distribution modelling in ecological communities. Model Based Phylogenetic Analysis. A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package ().""" ; sc:featureList edam:operation_0324, edam:operation_3927, edam:operation_3946 ; sc:license "GPL-3.0" ; sc:name "phyr" ; sc:url "https://github.com/daijiang/phyr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2275 ; sc:citation , , "pmcid:PMC5298202", "pubmed:19247286", "pubmed:25950237" ; sc:description "Major update to the original Phyre server. The new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. It uses the alignment of hidden Markov models via HHsearch1 to significantly improve accuracy of alignment and detection rate." ; sc:featureList edam:operation_0300, edam:operation_0477, edam:operation_3092 ; sc:name "Phyre" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0194, edam:topic_0621, edam:topic_0736, edam:topic_3299 ; sc:citation ; sc:description """PhyRepID is a comparative phylogenomics approach for large-scale quantification of protein repeat evolution. Protein repeats consisting of domains or motifs are involved in key biological processes such as neural development, host-pathogen interactions, and speciation. Expansion and contraction of these repeats can strongly impact protein function as was shown for KNL1 and PRDM9. However, these known cases could only be identified manually and were previously incorrectly reported as conserved in large-scale analyses, because signatures of repeat evolution are difficult to resolve automatically. We developed PhyRepID to compare protein domain repeat evolution and analysed 4939 groups of orthologous proteins (OGs) from 14 vertebrate species.""" ; sc:featureList edam:operation_0324, edam:operation_3092, edam:operation_3630 ; sc:name "PhyRepID" ; sc:url "https://github.com/ivanbelzen/PhyRepID/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3293 ; sc:citation "pubmed:15921519" ; sc:description "Program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences." ; sc:featureList edam:operation_3478 ; sc:name "Phyrex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rossnes.org/phyrex/" ; biotools:primaryContact "Roald Rossnes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pmcid:PMC3692127", "pubmed:23620286" ; sc:description "Biophysical identification of transcription factor binding sites." ; sc:featureList edam:operation_0438 ; sc:name "PhysBinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://bioit.dmbr.ugent.be/physbinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3293, edam:topic_3944 ; sc:citation ; sc:description """Physcraper is a python package for continual update of evolutionary estimates using the Open Tree of Life. The goal of physcraperex R package is to present tools for visualizing and analysing results from Physcraper, a python toolkit for updating existing phylogenetic knowledge with new molecular data. To render the BMC Bioinformatics template version.""" ; sc:featureList edam:operation_0544, edam:operation_0552, edam:operation_0567, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "Physcraper" ; sc:softwareHelp ; sc:url "https://github.com/McTavishLab/physcraper" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:author ; sc:citation , ; sc:description "A multi-algorithmic framework for phylogenetic inference" ; sc:featureList edam:operation_0547 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "physher" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.0.0" ; sc:url "https://github.com/4ment/physher" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3308 ; sc:citation ; sc:description "A sustainable integration of stochastic Boolean and agent-based modelling frameworks." ; sc:featureList edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PhysiBoSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/PhysiBoSS/PhysiBoSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3315, edam:topic_3318 ; sc:citation ; sc:description "This tool is intended to help detect (sometimes hard-to-spot) unphysical behavior of simulations, which may have statistically important influence on their results. It is part of a two-fold approach to increase the robustness of molecular simulations." ; sc:featureList edam:operation_2428, edam:operation_2476, edam:operation_3891 ; sc:name "physical validation" ; sc:url "https://physical-validation.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:description """PhysiCell-X is the distributed-shared parallel version of PhysiCell (http://physicell.org). PhysiCell is a open-source, multi-physics, multi-scale, agent-based simulator for biological systems. It provides both the stage (micro-environment) and actors (cells or agents) for simulation.""" ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PhysiCell-X" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.bsc.es/gsaxena/physicell_x" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123 ; sc:citation "pubmed:26339154" ; sc:description "UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools." ; sc:featureList edam:operation_2479 ; sc:name "PHYSICO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/physico2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3315, edam:topic_3316, edam:topic_3318 ; sc:citation , "pmcid:PMC10027115", "pubmed:36949818" ; sc:description "A generalized framework for model Calibration and Optimization Of modeLing projects." ; sc:featureList edam:operation_2426, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PhysiCOOL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/IGGoncalves/PhysiCOOL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3303 ; sc:author "Marek Matejak" ; sc:citation , "pubmed:26736546" ; sc:contributor "Marek Matejak" ; sc:description "Free open-source Modelica library designed for modeling human physiology. This library contains basic physical laws governing human physiology, usable for cardiovascular circulation, metabolic processes, nutrient distribution, thermoregulation, gases transport, electrolyte regulation, water distribution, hormonal regulation and pharmacological regulation." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Physiolibrary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "matfyz.cz" ; sc:softwareHelp ; sc:softwareVersion "2.3.1" ; sc:url "http://www.physiolibrary.org" ; biotools:primaryContact "Marek Mateják" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3307, edam:topic_3315, edam:topic_3375 ; sc:citation , "pmcid:PMC10027063", "pubmed:36950142" ; sc:description "A pharmacokinetics and pharmacodynamics module for PhysiCell." ; sc:featureList edam:operation_2426, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PhysiPKPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/drbergman/PhysiPKPD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0610, edam:topic_3293 ; sc:citation , "pmcid:PMC4868591", "pubmed:27190724" ; sc:description "PhySortR is an R package that can be used for the sorting of phylogenetic trees." ; sc:featureList edam:operation_0325 ; sc:license "GPL-3.0" ; sc:name "PhySortR" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.8" ; sc:url "https://cran.r-project.org/web/packages/PhySortR/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0634, edam:topic_3293 ; sc:citation , "pmcid:PMC4429496", "pubmed:25968323" ; sc:description "Phylogenetic tree visualisation and sample positioning for M. tuberculosis." ; sc:featureList edam:operation_0567 ; sc:name "PhyTB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/phylotrack/" ; biotools:primaryContact "Benavente ED", "Clark TG", "Coll F" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3305, edam:topic_3343, edam:topic_3390 ; sc:citation ; sc:description """Identification of foods containing compounds with specific pharmacological properties. Phytebyte is an extensible software framework used to train machine learning models to identify bioactive compounds found in food. The use case captured in 'run.py' is training models using known drug compounds that target a specific gene, and identifying plant compounds in FooDB that may behave similarly.""" ; sc:featureList edam:operation_0224, edam:operation_2489, edam:operation_2929 ; sc:license "AGPL-3.0" ; sc:name "PhyteByte" ; sc:url "https://github.com/seanharr11/phytebyte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3572 ; sc:citation , "pmcid:PMC9676013", "pubmed:36205601" ; sc:description "Quality Control for Phylogenetic Analyses." ; sc:featureList edam:operation_0324, edam:operation_3218, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Phytest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/phytest-devs/phytest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0780, edam:topic_3071, edam:topic_3293 ; sc:citation , "pmcid:PMC7841916", "pubmed:33509084" ; sc:description """Identification and characterization of the LRR repeats in plant LRR-RLKs. The predict-phytolrr program could identify LRRs effectively, especially for LRR motifs in plant LRR-RLKs. The program is based on the position specific scoring matrix (PSSM) algorithm and its training dataset are 4000 LRR motifs highly conserved sequences (HCSs) from LRR-RLKs of 17 land plant species.""" ; sc:featureList edam:operation_0239, edam:operation_0324, edam:operation_3092 ; sc:license "GPL-3.0" ; sc:name "Phyto-LRR" ; sc:url "https://phytolrr.com/findlrr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:name "Chemical formula" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_0780, edam:topic_2275, edam:topic_3810 ; sc:citation , "pubmed:35234849" ; sc:description "A platform for virtual screening and computer-aided drug designing." ; sc:featureList edam:operation_0479, edam:operation_2422, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "phytochemdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phytochemdb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3298, edam:topic_3316, edam:topic_3810 ; sc:citation , "pmcid:PMC10025408", "pubmed:36950362" ; sc:description "Scalable, modular phenomics data processing pipelines." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PhytoOracle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/phytooracle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0623, edam:topic_0780, edam:topic_0797 ; sc:citation "pubmed:22110026" ; sc:description "Comparative hub for plant genome and gene family data and analysis." ; sc:featureList edam:operation_0553, edam:operation_2495, edam:operation_3223, edam:operation_3672 ; sc:name "Phytozome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.phytozome.net/" ; biotools:primaryContact "David M. Goodstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3293, edam:topic_3524 ; sc:citation ; sc:description "Performs phylogenetics analyses on trees and sequences.." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "Phyx" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/FePhyFoFum/phyx" ; biotools:primaryContact "Stephen A. Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_3053, edam:topic_3336 ; sc:citation ; sc:description "Genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritize potential drug targets at the gene, pathway and network level. The long-term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies, this prioritisation system can generate evidence to support identification of the specific modulated genes that are responsible for the genetic association signal." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "Pi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Pi.html" ; biotools:primaryContact "Hai Fang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7521829", "pubmed:32995068" ; sc:description """A Deep Learning Approach to Extract Topological Persistence Images. NOTE: This page is under construction. Here we provide sample code to compute persistence images (PIs) using the proposed Image PI-Net model. We load weights from a pre-trained model trained on the CIFAR10 dataset.""" ; sc:featureList edam:operation_3443, edam:operation_3891, edam:operation_3927 ; sc:license "MIT" ; sc:name "PI-Net" ; sc:url "https://github.com/anirudhsom/PI-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:11093258", "pubmed:11455607", "pubmed:15937195", "pubmed:16080151", "pubmed:17284455", "pubmed:17526530" ; sc:description "PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein." ; sc:featureList edam:operation_0267, edam:operation_0384, edam:operation_0387, edam:operation_0474 ; sc:name "PI2PE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pipe.scs.fsu.edu/" ; biotools:primaryContact "Pi2PE Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3247, edam:format_3475, edam:format_3681, edam:format_3684, edam:format_3702, edam:format_3711, edam:format_3713 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2206, edam:format_3247, edam:format_3475, edam:format_3681, edam:format_3764, edam:format_3765 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:encodingFormat edam:format_2206, edam:format_3247, edam:format_3475, edam:format_3681, edam:format_3764, edam:format_3765 ; sc:name "Protein identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3120, edam:topic_3520 ; sc:author ; sc:citation , , "pubmed:25938255", "pubmed:30474983" ; sc:description "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PIA - Protein Inference Algorithms" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CUBiMed.RUB" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "https://github.com/medbioinf/pia" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3336, edam:topic_3517 ; sc:citation , "pubmed:37285660" ; sc:description "In silico discovery of shared and distinct drug targets for adult- and childhood-onset disease." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "PIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genetictargets.com/PIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation "pubmed:18163529" ; sc:description "Perform estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects." ; sc:featureList edam:operation_3439 ; sc:name "PIAGE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2259 ; sc:author "Ramon Aragüés" ; sc:citation , "pubmed:16510498" ; sc:description "Software framework that facilitates the work with protein interaction networks by 1) integrating data from multiple sources in a centralized database, 2) providing a library that handles all operations related with the network and 3) automating the analysis of protein-protein interactions networks." ; sc:featureList edam:operation_2497 ; sc:name "PIANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://sbi.imim.es/piana/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3053 ; sc:citation , "pmcid:PMC3632109", "pubmed:23444143" ; sc:description "Performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, this package contains functions for combining the results of multiple runs of gene set analyses." ; sc:featureList edam:operation_3224 ; sc:license "GPL-2.0" ; sc:name "piano" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.4" ; sc:url "http://bioconductor.org/packages/release/bioc/html/piano.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3295, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7080813", "pubmed:32226440" ; sc:description """A Web Server for Pseudouridine-Site (Ψ) Identification and Functional Annotation. Retrieve the results by the job ID. Ψ-WHISTLE is a prediction framework dedicated for transcriptome-wide Ψ RNA methylation site prediction using a machine learning approach.""" ; sc:featureList edam:operation_0417, edam:operation_0433, edam:operation_0463, edam:operation_2422 ; sc:name "PIANO" ; sc:url "http://piano.rnamd.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797, edam:topic_2885, edam:topic_3293 ; sc:citation "pubmed:22965131" ; sc:description "Tool for validating novel Single Nucleotide Variants (SNVs). It utilizes the details in the alignment files in order to identify the reproducible genotypes, hence distinguishing the true variants from artifacts. It can also be used to compare the nucleotide signals in different BAM files." ; sc:featureList edam:operation_0324, edam:operation_2478 ; sc:name "pibase" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ikmb.uni-kiel.de/pibase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0130, edam:topic_0602, edam:topic_3557 ; sc:citation "pubmed:17584791" ; sc:description "Server which recognizes various kinds of interactions, such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex." ; sc:featureList edam:operation_0248, edam:operation_0394, edam:operation_2492, edam:operation_2949, edam:operation_3083 ; sc:name "PIC" ; sc:url "http://crick.mbu.iisc.ernet.in/~PIC/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:name "ID list" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3174 ; sc:citation , "pmcid:PMC4603748", "pubmed:26451672" ; sc:contributor ; sc:description "Microbial phenotype prediction" ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-3.0" ; sc:name "PICA" ; sc:operatingSystem "Linux" ; sc:provider "AT-CUBE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/univieCUBE/PICA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation "pubmed:21653520" ; sc:description "Identifies short indel polymorphisms in population sequencing data." ; sc:featureList edam:operation_0452 ; sc:name "PiCall" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/vibansal/software/picall" ; biotools:primaryContact "Vikas Bansal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Assigns all the reads in a file to a single new read-group. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH)." ; sc:name "picard_AddOrReplaceReadGroups" ; sc:url "https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Add or Replace Read Groups in an input BAM or SAM file." ; sc:featureList edam:operation_0231 ; sc:name "picard_arrg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Generate Bam Index Stats for a provided BAM file." ; sc:featureList edam:operation_2238 ; sc:name "picard_bamindexstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Converts a BED file to a Picard Interval List. This tool provides easy conversion from BED to the Picard interval_list format which is required by many Picard processing tools. Note that the coordinate system of BED files is such that the first base or position in a sequence is numbered \"0\", while in interval_list files it is numbered \"1\"." ; sc:name "picard_bedtointervallist" ; sc:url "https://gatk.broadinstitute.org/hc/en-us/articles/360036883931-BedToIntervalList-Picard-" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Produces a summary of alignment metrics from a SAM or BAM file. This tool takes a SAM/BAM file input and produces metrics detailing the quality of the read alignments as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters. Note that these quality filters are specific to Illumina data; for additional information, please see the corresponding GATK Dictionary entry." ; sc:featureList edam:operation_3198, edam:operation_3695 ; sc:name "picard_collectalignmentsummarymetrics" ; sc:url "https://gatk.broadinstitute.org/hc/en-us/articles/360036883111-CollectAlignmentSummaryMetrics-Picard-" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3676 ; sc:description """Collects hybrid-selection (HS) metrics for a SAM or BAM file. This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection. Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments such as exome sequencing; for more information, please see the corresponding GATK Dictionary entry.""" ; sc:name "picard_collecthsmetrics" ; sc:url "https://gatk.broadinstitute.org/hc/en-us/articles/360036856051-CollectHsMetrics-Picard-" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932, edam:format_1933 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932, edam:format_1933 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Create an unaligned BAM file." ; sc:featureList edam:operation_0335 ; sc:name "picard_fastqtosam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is not the same as sorting as done by the SortSam tool, which sorts by either coordinate values or query name. The ordering in ReorderSam is based on exact name matching of contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are not included in the output." ; sc:featureList edam:operation_0231 ; sc:name "picard_reordersam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Replace Sam Header with the header from another sam file. The tool does not do any significant validation, so it's up to the user to make sure that the elements in the header are relevant and that the new header has all the required things." ; sc:featureList edam:operation_0292 ; sc:name "picard_replacesamheader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Create a FASTQ file." ; sc:featureList edam:operation_0335 ; sc:name "picard_samtofastq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.1" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:description "A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program." ; sc:featureList edam:operation_3197 ; sc:license "MIT" ; sc:name "Picard" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.17.x" ; sc:url "https://github.com/broadinstitute/picard" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Reports high-level measures of alignment based on a provided sam or bam file." ; sc:featureList edam:operation_3793 ; sc:name "picardasmetrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "This Galaxy tool uses Picard to report detailed metrics about reads that fall within windows of a certain GC bin on the reference genome." ; sc:featureList edam:operation_3793 ; 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sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3172, edam:topic_3301, edam:topic_3407 ; sc:citation ; sc:description """A Cellular Automaton for Spatial Organisation. picCASO is a MATLAB package to simulate the dynamics of spatial patterning of a microbial consortium on a 2-dimensional surface.""" ; sc:featureList edam:operation_2426 ; sc:name "picCASO" ; sc:url "https://github.com/RamanLab/picCASO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0821, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC10031857", "pubmed:36949401" ; 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sc:citation ; sc:description "An effective pipeline to extract ensemble-level cancer progression models from cross-sectional data." ; sc:featureList edam:operation_0323 ; sc:isAccessibleForFree true ; sc:name "PicNiC" ; sc:url "https://sites.google.com/site/troncopackage/picnic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3053 ; sc:citation "pubmed:21994225" ; sc:description "Software tool to detect pico-inplace-inversions between closely related species." ; sc:featureList edam:operation_2423 ; sc:name "PicoInversionMiner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://faculty.cs.niu.edu/~hou/PicoInversion.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; 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sc:name "PICR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/picr/" ; biotools:primaryContact "PRIDE support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes." ; sc:featureList edam:operation_0362, edam:operation_2495, edam:operation_3200, edam:operation_3478 ; sc:name "PICRUSt" ; sc:softwareHelp ; sc:url "http://picrust.github.io/picrust/" ; biotools:primaryContact "Curtis Huttenhower" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:featureList edam:operation_3658 ; sc:license "Artistic-2.0" ; sc:name "PICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PICS.html" ; biotools:primaryContact "Renan Sauteraud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:33624747" ; sc:description """Next-generation fine mapping via probabilistic identification of causal SNPs. LD-based PICS Probabilities for Index SNPs. 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Multiple protein, DNA and RNA sequences may be analyzed." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0499, edam:operation_2479 ; sc:name "PicXAA-Web" ; sc:url "http://gsp.tamu.edu/picxaa/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2344 ; sc:name "Pathway ID (NCI-Nature)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2984 ; sc:encodingFormat edam:format_2331 ; sc:name "Pathway or network report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Biomolecular interactions and cellular processes assembled into human signaling pathways." ; sc:featureList edam:operation_0224 ; sc:name "Pathway Interaction Database (PID)" ; sc:softwareHelp ; sc:url "http://pid.nci.nih.gov/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3071, edam:topic_3520 ; sc:citation , "pubmed:33912970" ; sc:description "PIDE (Particle Irradiation Data Ensemble) is a radiobiological database compiling more than 1100 pairs of in-vitro cell survival experiments after photon and ion irradiation." ; sc:featureList edam:operation_3503, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "PIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.gsi.de/bio-pide" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0199, edam:topic_0602, edam:topic_0749 ; sc:citation "pubmed:23703214" ; sc:description "PiDNA web server predicts the interaction between a protein and a single DNA sequence by applying an atomic level knowledge based scoring function on numerous in silico mutated complex structures." ; sc:featureList edam:operation_0331, edam:operation_0445, edam:operation_0477, edam:operation_2423, edam:operation_2575 ; sc:name "PiDNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dna.bime.ntu.edu.tw/pidna" ; biotools:primaryContact "Center for Systems Biology, National Taiwan University" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3489, edam:topic_3810 ; sc:citation , "pmcid:PMC7230844", "pubmed:32235513" ; sc:description """A User-Friendly Plant DNA Fingerprint Database Management System. The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data ||| HOMEPAGE MISSING!""" ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3894 ; sc:name "PIDS" ; sc:url "https://ssr.pids.online:8445/ssr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0602, edam:topic_3474, edam:topic_3557 ; sc:citation ; sc:description "PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques." ; sc:featureList edam:operation_2492, edam:operation_2949, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PIE the search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/CBBresearch/Wilbur/IRET/PIE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Visualizing cells from scRNA-seq data as pie charts. PieParty is a visualization tool allowing to represent every cell in single-cell sequencing plots (UMAP, tSNE, ect.) as a pie chart. Each slice in a pie chart represents the expression of a single gene. Custom gene lists and coloring can be applied.""" ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_3935 ; sc:name "PieParty" ; sc:url "https://github.com/harbourlab/PieParty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3053, edam:topic_3336, edam:topic_3342 ; sc:citation , "pmcid:PMC9252812", "pubmed:35610036" ; sc:description "Web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions." ; sc:featureList edam:operation_0282, edam:operation_3226, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PiER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.genetictargets.com/PiER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:23730833" ; sc:description "Excel encoded application (compatible with OpenOffice Calc) that includes various graphical and numerical outputs which allow NGS practitioners to assessing and comparing the precision in allele frequency estimation for both pool and diploid individual SNP data under various sampling, coverage and experimental error designs." ; sc:featureList edam:operation_0296, edam:operation_3221 ; sc:name "PIFs" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www1.montpellier.inra.fr/CBGP/software/PoolSeqUtils/" ; biotools:primaryContact "Mathieu Gautier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation , "pmcid:PMC5353782", "pubmed:28298217" ; sc:description "This package infers biological signatures from gene expression profiles using data from one platform, and evaluate them on a different one. It also identifies clusters of highly coexpressed genes using coexpression network analysis, summarizing the biological information of each module in an eigengene, learning a Bayesian network that models the probabilistic dependencies between modules, and building a decision tree based on the expression of eigengenes." ; sc:featureList edam:operation_3658 ; sc:license "GPL-2.0" ; sc:name "Pigengene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Pigengene.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3500, edam:topic_3810 ; sc:citation ; sc:description "A compendium of genetic regulatory effects across pig tissues." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3454, edam:operation_3463, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "PigGTEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://piggtex.farmgtex.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0199, edam:topic_0625, edam:topic_2830, edam:topic_3930 ; sc:citation , "pmcid:PMC10484671", "pubmed:37548401" ; sc:description "PIgLET is a suite of computational tools that improves genotype inference and downstream AIRR-seq data analysis. The package as two main tools. The first is Allele Clusters, this tool is designed to reduce the ambiguity within the IGHV alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes. The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "PIgLET" ; sc:softwareHelp ; sc:url "https://bitbucket.org/yaarilab/piglet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2628 ; sc:name "BioGRID interaction ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2302 ; sc:name "STRING ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3932 ; sc:encodingFormat edam:format_3475 ; sc:name "Q-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0203, edam:topic_2640 ; sc:citation , "pmcid:PMC8178832", "pubmed:34088263" ; sc:description "PIGNON is a protein-protein interaction (PPI)-guided functional enrichment analysis for quantitative proteomics. This algorithm measures the clustering of proteins with a shared Gene Ontology (GO) annotation within the provided PPI network weighted with quantitative proteomics data. The significance of this clustering measure is then estimated from a normal distribution approximated from a Monte Carlo Sampling Distribution. To correct for multiple hypothesis testing, we assess the false discovery rate at various thresholds against a null model." ; sc:featureList edam:operation_2436, edam:operation_2949, edam:operation_3223, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PIGNON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LavalleeAdamLab/PIGNON" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation , ; sc:description "Web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion." ; sc:featureList edam:operation_0474 ; sc:name "PIGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://circe.med.uniroma1.it/pigs/" ; biotools:primaryContact "Paolo Marcatili" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation "pmcid:PMC5570210", "pubmed:28472367" ; sc:description "PIGSPro is a web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion. Its final output is a complete three-dimensional model of the target antibody that can be downloaded or displayed on-line. The server is freely accessible to all." ; sc:featureList edam:operation_0477 ; sc:name "PIGSpro" ; sc:url "https://cassandra.med.uniroma1.it/pigspro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0176, edam:topic_0199 ; sc:citation , "pubmed:33400510" ; sc:description """A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface. The PIIMS Server (Protein Interface In silico Mutation Scanning) was developed successfully to predict hot spots from interface of protein-protein complex by calculating the binding free energy changes upon alanine mutation scanning. Additional, the mutation scanning strategy is introduced for understanding the impacts of hot spot mutations. Most biological processes involve multiple proteins interacting with each other. The protein-protein interactions (PPIs) are the basis for almost all biological processes. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. These residues are critical in understanding the principles of PPI.""" ; sc:featureList edam:operation_2476, edam:operation_2492, edam:operation_3891 ; sc:name "PIIMS" ; sc:url "http://chemyang.ccnu.edu.cn/ccb/server/PIIMS/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3172, edam:topic_3314 ; sc:citation ; sc:description "A Python-based Informatics Kit for Analysing Chemical Units." ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PIKAChU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BTheDragonMaster/pikachu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0108, edam:topic_0128, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8170782", "pubmed:34078261" ; sc:description "Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction." ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PIKE-R2P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JieZheng-ShanghaiTech/PIKE-R2P" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2885, edam:topic_3168, edam:topic_3678 ; sc:citation , , "pmcid:PMC3037855", "pubmed:21261974" ; sc:description "Fexible command-line toolkit for efficient handling, filtering, and comparison of genomic position (GP) files produced by next-generation sequencing experiments. PileLineGUI adds a graphical interface." ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_2409, edam:operation_3208, edam:operation_3227 ; sc:license "LGPL-2.1" ; sc:name "PileLine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://sing.ei.uvigo.es/pileline/index.php/Main_Page" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0798, edam:topic_2885 ; sc:citation ; sc:description "PILER is a tool for identification and classification of genomic repeats." ; sc:featureList edam:operation_0495, edam:operation_0496, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PILER" ; sc:softwareHelp ; sc:url "https://www.drive5.com/piler/" ; biotools:primaryContact "Robert C. Edgar" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , "pmcid:PMC1790904", "pubmed:17239253" ; sc:description "software for finding CRISPR repeats" ; sc:featureList edam:operation_0237 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pilercr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.drive5.com/pilercr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:citation , ; sc:description "Convert a .mpileup file into a SynTView .coverage file." ; sc:featureList edam:operation_0335 ; sc:name "pileup2cov" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.0.1" ; sc:url "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3015, edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Convert a pileup to VCF with filtering." ; sc:featureList edam:operation_3695 ; sc:name "pileup_to_vcf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.1" ; sc:url "https://toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3338, edam:topic_3473, edam:topic_3518 ; sc:citation "pubmed:21653547" ; sc:description "The Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover additional genes with similar expression patterns in large compendia of microarray data. By carefully defining the lists of relevant genes, the user controls the specificity of discoveries." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223 ; sc:name "PILGRM" ; sc:url "http://pilgrm.princeton.edu" ; biotools:primaryContact "Greene Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33026994" ; sc:description """A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. A general framework and library for visual piling/stacking. A JavaScript Library for Interactive Visual Piling.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3436, edam:operation_3802 ; sc:license "MIT" ; sc:name "piling" ; sc:url "https://piling.js.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC4237348", "pubmed:25409509" ; sc:description "Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies." ; sc:featureList edam:operation_0310, edam:operation_2945, edam:operation_3198 ; sc:name "pilon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v1.16" ; sc:url "http://www.broadinstitute.org/software/pilon/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3053, edam:topic_3474 ; sc:citation , "pubmed:36124788" ; sc:description "Pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers." ; sc:featureList edam:operation_2454, edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PiLSL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JieZheng-ShanghaiTech/PiLSL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3050, edam:topic_3168 ; sc:citation ; sc:description "PIMBA is a pipeline for metabarcoding analysis, which allows the use of customized databases, as well as other reference databases." ; sc:featureList edam:operation_3460, edam:operation_3797, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "PIMBA" ; sc:url "https://github.com/reinator/pimba" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0820, edam:topic_3444 ; sc:citation , "pubmed:35730989" ; sc:description "Voxel-wise intermodal coupling analysis of two or more modalities using local covariance decomposition." ; sc:featureList edam:operation_0269, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pIMCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hufengling/pIMCo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0605, edam:topic_3336, edam:topic_3373 ; sc:citation , "pubmed:33075523" ; sc:description """An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. “PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion”. Abstract:The accumulation of various types of drug informatics data and computational approaches for drug repositioning can accelerate pharmaceutical research and development.""" ; sc:featureList edam:operation_3432 ; sc:name "PIMD" ; sc:url "https://github.com/Sepstar/PIMD/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331, edam:format_3261, edam:format_3468, edam:format_3475, edam:format_3506, edam:format_3556 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0607 ; sc:author "Chris Morris (STFC)" ; sc:citation ; sc:description "Laboratory Information Management System (LIMS) to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes." ; sc:featureList edam:operation_2409 ; sc:name "PiMS LIMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "STFC" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.limswiki.org/index.php/PiMS" ; biotools:primaryContact "Chris Morris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC8627104", "pubmed:34837944" ; sc:description "Efficient iterative Hi-C scaffolder based on N-best neighbors." ; sc:featureList edam:operation_0479, edam:operation_0524, edam:operation_3216, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pin_hic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dfguan/pin_hic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_3489 ; sc:citation "pubmed:22067443" ; sc:description "Integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. Moreover, it provides a variety of built-in tools to filter and analyze the network for gaining insight into the network." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_3083, edam:operation_3439, edam:operation_3501 ; sc:name "PINA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://omics.bjcancer.org/pina/" ; biotools:primaryContact "Jianmin Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:22419782" ; sc:description "Protein-protein interaction(PPI) network alignment method aiming to map similar parts of PPI networks in terms of protein similarity (by both sequence and function) and the local network similarity. It incorporates not only sequence similarity and topological similarity of proteins in the equivalencing process but also uses the function similarity of protein pairs." ; sc:featureList edam:operation_3439 ; sc:name "PINALOG" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbg.bio.ic.ac.uk/~pinalog/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_3957 ; sc:citation ; sc:description "PINAWeb (Protein-Protein Interaction Networks Aligners) is a user-friendly web-based tool to obtain and compare the results produced by different aligners. PPINs can be uploaded either from the STRING database or from a user database, and for each of the following 5 aligners: AligNet, HubAlign, LGraal, Pinalog, and Spinal, PINAWeb outputs the alignments produced, as well as their associated topological and biological correctness scores. When more than one aligner is considered, it also reports a comparison of the obtained results. The source code of PINAWeb is freely available on GitHub to enable researchers to add other aligners, network databases or alignment score metrics." ; sc:featureList edam:operation_0295, edam:operation_0491, edam:operation_2492, edam:operation_3927 ; sc:name "PINAWeb" ; sc:url "https://bioinfo.uib.es/~recerca/PINAWeb" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0622, edam:topic_0654, edam:topic_0749, edam:topic_2640, edam:topic_3168 ; sc:citation "pubmed:26740525" ; sc:description "Method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies." ; sc:featureList edam:operation_2423, edam:operation_3680 ; sc:name "PINCAGE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://moma.ki.au.dk/prj/pincage/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0749, edam:topic_3336, edam:topic_3512 ; sc:citation , "pmcid:PMC7515706", "pubmed:32821942" ; sc:description "improved CRISPR/Cas9 screening by efficient cleavage at conserved residues." ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_3216 ; sc:name "PINCER" ; sc:url "https://github.com/veeneman/PINCER" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3325 ; sc:author "Kai Ye" ; sc:citation , "pmcid:PMC2781750", "pubmed:19561018" ; sc:description "A pattern growth approach to detect break points of large deletions and medium sized insertions from paired end short reads." ; sc:featureList edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Pindel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://gmt.genome.wustl.edu/packages/pindel/" ; biotools:primaryContact "Kai Ye", "Support Forum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Convert Pindel to VCF and index." ; sc:featureList edam:operation_0335 ; sc:name "pindel2vcf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.5a3" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/pindel2vcf/pindel2vcf/0.2.5a3" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:32463229" ; sc:description """An Automation Tool to Extract and Visualize Protein-Centric Functional Networks. PINE (Protein Interaction Network Extractor) is a tool for visualizing protein-protein interactions. PINE is provided in two forms: a command line version built in Python and a graphical user interface (GUI). Ontology and Pathway Term Status.""" ; sc:featureList edam:operation_0417, edam:operation_3755, edam:operation_3925 ; sc:license "Apache-2.0" ; sc:name "PINE" ; sc:url "https://github.com/csmc-vaneykjlab/pine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2885, edam:topic_3168, edam:topic_3895, edam:topic_3912 ; sc:citation , "pmcid:PMC7901017", "pubmed:33464043" ; sc:description """Prime Editing Guide RNA Design Automation Using PINE-CONE. CRISPR-based technologies are paramount in genome engineering and synthetic biology. Prime editing (PE) is a technology capable of installing genomic edits without double-stranded DNA breaks (DSBs) or donor DNA. Prime editing guide RNAs (pegRNAs) simultaneously encode both guide and edit template sequences. They are more design intensive than CRISPR single guide RNAs (sgRNAs). As such, application of PE technology is hindered by the limited throughput of manual pegRNA design. To that end, we designed a software tool, Prime Induced Nucleotide Engineering Creator of New Edits (PINE-CONE), that enables high-throughput automated design of pegRNAs and prime editing strategies. PINE-CONE translates edit coordinates and sequences into pegRNA designs, accessory guides, and oligonucleotides for facile cloning workflows""" ; sc:featureList edam:operation_0308, edam:operation_3096, edam:operation_3196 ; sc:name "PINE-CONE" ; sc:url "https://github.com/xiaowanglab/PINE-CONE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0634, edam:topic_3295, edam:topic_3325, edam:topic_3517 ; sc:citation , "pmcid:PMC6203199", "pubmed:30359302" ; sc:description """Phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants. PINES (Phenotype-Informed Noncoding Element Scoring). Functional characterization of the noncoding genome is essential for the biological understanding of gene regulation and disease.""" ; sc:featureList edam:operation_0362, edam:operation_3196, edam:operation_3226, edam:operation_3461 ; sc:name "PINES" ; sc:url "http://genetics.bwh.harvard.edu/pines/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_0821 ; sc:citation , "pmcid:PMC7319557", "pubmed:32469073" ; sc:description """a versatile web platform for downstream analysis and visualization of proteomics data. PiNET server is a server for mapping and annotaion of protein peptides.""" ; sc:featureList edam:operation_0417, edam:operation_2429, edam:operation_3755 ; sc:name "piNET" ; sc:url "http://www.pinet-server.org/pinet/peptideToProtein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_2275, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:33693581" ; sc:description "PInet is a point cloud patch-wise attention base Protein-Protein Interaction interface predictor." ; sc:featureList edam:operation_0416, edam:operation_0474, edam:operation_2492, edam:operation_3094, edam:operation_3436 ; sc:name "PInet" ; sc:url "https://github.com/FTD007/PInet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3168, edam:topic_3169, edam:topic_3656 ; sc:citation , "pmcid:PMC3290535", "pubmed:22393380" ; sc:contributor ; sc:description "Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach." ; sc:featureList edam:operation_3658 ; sc:license "Artistic-2.0" ; sc:name "PING" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PING.html" ; biotools:primaryContact "Renan Sauteraud" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1082 ; sc:name "Pathway or network identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2338 ; sc:name "Ontology identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation ; sc:description "Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories." ; sc:featureList edam:operation_3501 ; sc:name "PiNGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1.11" ; sc:url "http://www.psb.ugent.be/esb/PiNGO/Home.html" ; biotools:primaryContact "Steven Maere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0780, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC8188708", "pubmed:34107869" ; sc:description "A comprehensive information resource for Pin-II type protease inhibitors." ; sc:featureList edam:operation_0224, edam:operation_0471, edam:operation_1850 ; sc:isAccessibleForFree true ; sc:name "PINIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pinir.ncl.res.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:31935100" ; sc:description """A Python Library for Building Atomic Neural Networks of Molecules and Materials. PiNN: a Python library for building atomic neural networks. PiNN is a Python library built on top of TensorFlow for building atomic neural network potentials. The PiNN library also provides elemental layers and abstractions to implement various atomic neural networks.""" ; sc:featureList edam:operation_0337, edam:operation_0394, edam:operation_3927 ; sc:license "BSD-3-Clause" ; sc:name "PiNN" ; sc:url "https://github.com/Teoroo-CMC/PiNN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_2533, edam:topic_3053, edam:topic_3474 ; sc:citation "pubmed:24436305" ; sc:description "Machine-learning predictor to ascertain which newly observed INDELs are likely to be pathogenic." ; sc:featureList edam:operation_2423 ; sc:name "PinPor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://watson.compbio.iupui.edu/pinpor/" ; biotools:primaryContact "Xinjun Zhang", "Yunlong Liu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3115 ; sc:encodingFormat edam:format_3033 ; sc:name "Microarray metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Processed microarray data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0203, edam:topic_2640, edam:topic_3053, edam:topic_3366, edam:topic_3518 ; sc:citation ; sc:description "Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens." ; sc:featureList edam:operation_3223, edam:operation_3233 ; sc:license "BSD-4-Clause" ; sc:name "pint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pint.html" ; biotools:primaryContact "Olli-Pekka Huovilainen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2259 ; sc:citation "pubmed:20538652" ; sc:description "Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted." ; sc:featureList edam:operation_0226, edam:operation_2422, edam:operation_2497, edam:operation_3562, edam:operation_3672 ; sc:name "PINT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://csb2.ym.edu.tw/pint/" ; biotools:primaryContact "PINT Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_2815 ; sc:citation "pubmed:21602267" ; sc:description "Web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. It is available for 5 species (human, mouse, rat, worm and yeast)." ; sc:featureList edam:operation_0314, edam:operation_2464, edam:operation_3083, edam:operation_3223 ; sc:name "PINTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.esat.kuleuven.be/pinta/" ; biotools:primaryContact "Yves Moreau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:description "Program for detecting and analysing 16S rRNA chimeras and other anomalies. Pintail is a tool for identifying anomalies, including chimeras, within 16S rDNA sequences. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene." ; sc:featureList edam:operation_0224 ; sc:name "Pintail" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.1" ; sc:url "http://www.softpedia.com/get/Science-CAD/Pintail.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC8796362", "pubmed:34849583" ; sc:description "Penalized Integrative Matrix Factorization method for Multi-omics data." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PIntMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mpierrejean/pintmf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "A pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence." ; sc:featureList edam:operation_0264, edam:operation_0433 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "PIntron" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-BICOCCA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://pintron.algolab.eu/" ; biotools:primaryContact "Paola Bonizzoni", "Raffaella Rizzi", "Yuri Pirola" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:12595245" ; sc:description "Find reoccuring three-dimensional patterns of amino acids. These amino-acids are close in space but not necessarily close or co-linear in sequence, for example the serine-protease catalytic triad. Unlike other tools, PINTS does not aim to find proteins adopting a similar fold." ; sc:featureList edam:operation_0474 ; sc:name "PINTS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.russelllab.org/cgi-bin/tools/pints.pl" ; biotools:primaryContact "Rob Russell", "Yvonne Lara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2259 ; sc:citation "pubmed:24885165" ; sc:description "Open source, native web application that facilitates the visualization of protein interactions" ; sc:featureList edam:operation_3083 ; sc:name "PINV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosual.cbio.uct.ac.za/pinv.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_3475, edam:format_3752 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3168, edam:topic_3512, edam:topic_3577 ; sc:citation ; sc:description "An open-source software to help in designing NGS panels" ; sc:featureList edam:operation_3227, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PIO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://vincentalcazer.shinyapps.io/Panel_informativity_optimizer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC8256826", "pubmed:34235432" ; sc:description "A pipeline for processing SNP data featured as linkage disequilibrium bin mapping, genotype imputing and marker synthesizing." ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3196, edam:operation_3557, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PIP-SNP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/noble-research-institute/PIP_SNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation "pubmed:24931978" ; sc:description "Tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework." ; sc:featureList edam:operation_2479, edam:operation_3637 ; sc:name "Pipasic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/pipasic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_3168, edam:topic_3510 ; sc:citation "pubmed:10908355", "pubmed:11108697", "pubmed:11470834", "pubmed:12235383", "pubmed:12801878", "pubmed:12824430", "pubmed:14982955" ; sc:description "Takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_2409, edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PipeAlign2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lbgi.fr/pipealign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description "PipeComp is a general framework for the evaluation of computational pipelines, reveals performant single-cell RNA-seq preprocessing tools." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "pipeComp" ; sc:url "https://github.com/plger/pipeComp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3577, edam:topic_3676 ; sc:citation , "pubmed:35751816" ; sc:description "Somatic Variant Calling Workflow for Ion Torrent Sequencing Data." ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PipeIT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ckynlab/PipeIT2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3673 ; sc:description "Analysis and workflow development of Next Generation Sequencing and gene expression." ; sc:featureList edam:operation_0292, edam:operation_2403, edam:operation_2495, edam:operation_3198, edam:operation_3227 ; sc:name "Pipeline Pilot" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://accelrys.com/products/pipeline-pilot/component-collections.html" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0607, edam:topic_3071 ; sc:citation ; sc:description "Simple and flexible graphic pipeline construction and maintenance tool." ; sc:featureList edam:operation_0335 ; sc:name "PipelineDog" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.npmjs.com/package/pipelinedog" ; biotools:primaryContact "Jinchuan Xing", "Yazhou Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3524 ; sc:citation , "pubmed:24890372" ; sc:description "Software to evaluate the performance of bioinformatics pipelines for next‐generation resequencing." ; sc:featureList edam:operation_3760 ; sc:name "Pipeliner" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/brunonevado/Pipeliner" ; biotools:primaryContact "B. Nevado" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3299, edam:topic_3474 ; sc:citation ; sc:description """PipeMaster is inferring population divergence and demographic history with approximate Bayesian computation and supervised machine-learning in R. PipeMaster is an R-package to build demographic models and simulate data under the coalescent. Current implementation can simulate sanger-type and NexGen data for single species or complex of species; single-locus data for hierarchical demographic models of comparative phylogeography; and species trees with one horizontal connection.""" ; sc:featureList edam:operation_2426, edam:operation_3658, edam:operation_3659 ; sc:name "PipeMaster" ; sc:url "http://www.github.com/gehara/PipeMaster" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0154, edam:topic_0203, edam:topic_3474 ; sc:citation ; sc:description "PIPENN stands for 'Protein Interface Prediction from sequence with an Ensemble of Neural Nets'. 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sc:featureList edam:operation_0463 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PIPmiR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3379 ; sc:citation , "pubmed:34385069" ; sc:description "A web tool to improve patient selection for oncology early phase clinical trials." ; sc:featureList edam:operation_2428, edam:operation_3359, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PIPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pipo.vhio.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154 ; sc:description "PIPprofileR is a tool to easily generate and explore Profiles of Percent Identical Positions from a fasta file (nucloetide or peptide sequences)." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PIPprofileR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/IFB-ElixirFr/PIPprofileR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775, edam:topic_2275 ; sc:citation "pubmed:10591098" ; sc:description "Compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins." ; sc:featureList edam:operation_0531, edam:operation_2949 ; sc:name "PIPSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pipsa.h-its.org/pipsa/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_1929 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3245 ; sc:name "Spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2032 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "A workflow and open-source software tool with a graphical user interface (GUI), that enables completely automated post-translational modification (PTM) identification and quantification exclusively from data-independent acquisition (DIA)." ; sc:featureList edam:operation_2238, edam:operation_3092, edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PIQED" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jgmeyerucsd/PIQEDia" ; biotools:primaryContact "jessegmeyer@gmail.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3489 ; sc:citation , , , "pmcid:PMC4086067", "pmcid:PMC5325209", "pubmed:24861615", "pubmed:28234898" ; sc:description "Proteomics Identifications & Quantitations Data Management & Integration Service (PIQMIe) is a web server for semi-quantitative proteomics data management and analysis." ; sc:featureList edam:operation_2409, edam:operation_3630, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PIQMIe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://www.research-software.nl/software/piqmie" ; biotools:primaryContact , "Roland Kanaar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0114, edam:topic_0621, edam:topic_0749, edam:topic_3169 ; sc:author "Russell Neches" ; sc:citation ; sc:description """A efficient peak finder for high coverage ChIP-seq experiments, written in Python. 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Up to 10 protein sequences may be submitted." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2479, edam:operation_2575, edam:operation_3092 ; sc:name "PiRaNhA" ; sc:url "http://www.bioinformatics.sussex.ac.uk/PIRANHA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_3170 ; sc:citation "pubmed:23024010" ; sc:description "Peak-caller for CLIP- and RIP-Seq high-throughput protein-RNA interaction data. It accepts input in BED or BAM format and identifies regions of significant enrichment for reads. It can also optionally incorporate additional external covariates into the peak-calling process, and identify sites of differential binding occupancy between cell types, conditions or development stages." ; sc:featureList edam:operation_2436 ; sc:name "Piranha" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/piranha/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3295, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8728152", "pubmed:34871445" ; sc:description "piRBase is a manually curated resource of piRNAs, which focused on piRNA function analyses as well as piRNA annotation." ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "piRBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bigdata.ibp.ac.cn/piRBase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:33330918" ; sc:description """Systematic evaluation of the effects of genetic variants on PIWI-interacting RNA expression across 33 cancer types. the database of various piRNA associated data to support piRNA functional study. piRBase is a manually curated resource of piRNAs, which focused on piRNA function analyses as well as piRNA annotation.""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3232 ; sc:name "piRNA-eQTL" ; sc:url "http://www.regulatoryrna.org/database/piRNA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3071, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "piRNAdb it's a piwi-interacting RNA sequences storage and search system, providing some others relevant information like alignments, clusters, datasets and targets of these piRNAs." ; sc:featureList edam:operation_0291, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "piRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pirnadb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3474 ; sc:citation "pubmed:26677964" ; sc:description "SVM classifier based on a combination of Miwi CLIP-Seq derived features and position derived features to predict potential targets of piRNAs on mRNAs." ; sc:featureList edam:operation_2423 ; sc:name "pirnaPre" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.regulatoryrna.org/software/piRNA/piRNA_target_mRNA/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0203, edam:topic_0659, edam:topic_0798, edam:topic_3512 ; sc:citation , "pmcid:PMC7327968", "pubmed:32655289" ; sc:description """Computational Identification of piRNAs Using Features Based on RNA Sequence, Structure, Thermodynamic and Physicochemical Properties. piRNAPred is an algorithm for the computational identification of piRNAs using features based on RNA sequence, structure, thermodynamic and physicochemical properties.""" ; sc:featureList edam:operation_0278, edam:operation_2495, edam:operation_3936 ; sc:name "piRNAPred" ; sc:url "https://github.com/IshaMonga/piRNAPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0634, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC8786328", "pubmed:34965192" ; sc:description "An updated resource for searching through the piRNAome of multiple species." ; sc:featureList edam:operation_0313, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "piRNAQuest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2" ; sc:url "http://dibresources.jcbose.ac.in/zhumur/pirnaquest2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168, edam:topic_3293 ; sc:citation ; sc:description "Pirouette is an R package that assesses the inference error made by Bayesian phylogenetics for a given macroevolutionary diversification model. pirouette makes use of BEAST2, but its philosophy applies to any Bayesian phylogenetic inference tool." ; sc:featureList edam:operation_0326, edam:operation_0327, edam:operation_3478 ; sc:name "pirouette" ; sc:url "https://github.com/richelbilderbeek/pirouette_example_30/blob/master/README.md" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3322, edam:topic_3360, edam:topic_3577 ; sc:citation ; sc:description "piRPheno is a manually curated database platform that provides experimentally supported associations between piRNAs and disease phenotypes. piRNAs have been experimentally validated as a novel class of biomarkers and potential drug targets for disease diagnosis, therapy and prognosis. The discovery of relationships between piRNAs and disease phenotypes has become increasingly important. piRPheno provides experimentally validated associations between piRNAs and disease phenotypes through manual curation on publications. piRPheno provides user-friendly web interfaces and RESTful application programming interfaces for users to browse, search, prioritize, analyze and access data freely." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3435 ; sc:name "piRPheno" ; sc:url "http://www.biomedical-web.com/pirpheno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pubmed:22508794" ; sc:description """pIRS is a program for simulating paired-end reads from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform.""" ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "pirs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/galaxy001/pirs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_2330 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Identify C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. Allows C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable." ; sc:featureList edam:operation_0253, edam:operation_0337 ; sc:name "pirScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cosbi4.ee.ncku.edu.tw/pirScan/" ; biotools:primaryContact "Heng-Chi Lee", "Wei-Sheng Wu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1136 ; sc:name "PIRSF ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623 ; sc:citation ; sc:description "Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains." ; sc:featureList edam:operation_0224 ; sc:name "PIRSF whole-protein classification database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0092, edam:topic_0602, edam:topic_2828 ; sc:citation ; sc:description "An interactice webserver for macromolecular assemblies from X-ray crystallography data." ; sc:featureList edam:operation_0570, edam:operation_2421, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:name "PISA" ; sc:operatingSystem "Linux", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0593, edam:topic_0769, edam:topic_0820, edam:topic_3444 ; sc:citation , "pmcid:PMC7203746", "pubmed:31930377" ; sc:description """PISA-SPARKY is an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. A python tool for simulating and fitting PISA wheels to oriented solid-state NMR data. The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research computing. The pisa.py script is hosted on NMRFAM servers and can be used remotely from the PISA-SPARKY GUI plugin available with NMRFAM-SPARKY as of Dec 2019. This page is still under construction and will include more usage information over time. The mobile element that conveys methicillin resistance to staph includes a gene that encodes for Cch. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/nmrfam-sparky (PINE.NMRFAM.WISC.EDU/download_packages.html), bio.tools/rnmr (NMRFAM.WISC.EDU), bio.tools/pacsy (NMRFAM.WISC.EDU), bio.tools/ponderosa-cs (NMRFAM.WISC.EDU)""" ; sc:featureList edam:operation_0249, edam:operation_0337, edam:operation_3938 ; sc:name "PISA-SPARKY" ; sc:url "https://sbgrid.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3070, edam:topic_3344, edam:topic_3365, edam:topic_3366, edam:topic_3572, edam:topic_3678 ; sc:author , ; sc:citation , , "pmcid:PMC9649664", "pubmed:36357404" ; sc:contributor , , , ; sc:description """pISA-tree is a data management solution developed to contribute to the reproducibility of research and analyses. Hierarchical set of batch files is used to create standardized nested directory tree and associated files for research projects. It is in accordance with the ISA-tab framework (Investigation/Study/Assay) and fulfills minimal requirements of FAIR paradigm. The tree structure can be generated on the fly, actively during project development and growth. pISA-tree can support small to moderate projects and is a step towards the FAIR data guiding principles. In addition, two related R packages were developed: pisar -- R support for pISA-tree and seekr -- R interface with the SEEK API. The latter connects the project folders with the externally maintained and developed open source web platform FAIRDOMHub for sharing scientific research assets.""" ; sc:featureList edam:operation_2409, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pISA-tree" ; sc:operatingSystem "Windows" ; sc:provider , "National Institute of Biology, Department of Biotechnology and Systems Biology" ; sc:softwareHelp ; sc:softwareVersion "2.0", "2.0.1", "2.01", "2.02", "3.03", "3.04" ; sc:url "https://github.com/NIB-SI/pISA-tree" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_0736, edam:topic_3168 ; sc:citation "pubmed:15980589" ; sc:description "Allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity." ; sc:featureList edam:operation_2479 ; sc:name "PISCES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dunbrack.fccc.edu/pisces/" ; biotools:primaryContact "Qifang Xu", "Roland Dunbrack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621 ; sc:citation , "pmcid:PMC7970533", "pubmed:33746558" ; sc:description "PiSCES (Pi(scine) stream community estimation system) predicts a fish assemblage for any stream in the conterminous United States by referencing HUC-based distributional information for over 1,000 native and non-native species obtained from NatureServe, the USGS and the Peterson Field Guide to Freshwater Fishes of North America." ; sc:featureList edam:operation_0224, edam:operation_3659, edam:operation_3799 ; sc:name "PiSCES" ; sc:url "https://qed.epacdx.net/pisces/" ; biotools:primaryContact "Mike Cyterski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3055, edam:topic_3170, edam:topic_3316 ; sc:citation ; sc:description """A package for rapid quantitation and quality control of large scale mRNA-seq datasets. PISCES: a package for quantitation and QC of large scale mRNA-seq datasets. PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon. PISCES: pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries.""" ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3223, edam:operation_3436, edam:operation_3800 ; sc:license "Apache-2.0" ; sc:name "PISCES" ; sc:url "https://github.com/Novartis/pisces" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2814 ; sc:citation ; sc:description "Suggestions of the most likely biological unit for a given X-ray crystal structure of a protein based on the crystal symmetry operators and a method of scoring each trial protein-protein interface." ; sc:featureList edam:operation_2475 ; sc:name "PITA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/pita/" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_2830, edam:topic_3473, edam:topic_3474, edam:topic_3930 ; sc:citation , "pubmed:36346590" ; sc:description "A Webtool to Predict Immunogenicity for Humanized and Fully Human Therapeutic Antibodies." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:name "PITHA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sysbio.unl.edu/PITHA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:20838465" ; sc:description "Java software to find minimal sets of precursors of target compounds in a metabolic network." ; sc:featureList edam:operation_3439 ; sc:name "PITUFO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sites.google.com/site/pitufosoftware" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3520 ; sc:citation "pubmed:23709496" ; sc:description "Open source tool that performs peptide identification from tandem mass spectrograms using the six-frame translation of the complete genome. Differently from peptidomics methods that also allow a search against the complete genome, it does not limit analysis of the genome to a small set of sequences that match a list of de novo reconstructions. Instead, it performs an exhaustive scan of the translation of the six reading frames of the complete genome." ; sc:featureList edam:operation_2479, edam:operation_3631 ; sc:name "PIUS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://dtai.cs.kuleuven.be/ml/systems/pius/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0621 ; sc:citation ; sc:description "Protein Interactions VisualizatiOn Tool is a Java-based tool, for visualizing protein-protein interactions. It is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for easily connecting remote proteins to the displayed map. It is currently configured to work with proteins from four different species, and present functional annotations, designations of homologs from the four species, and links to information pages." ; sc:featureList edam:operation_2479 ; sc:name "PIVOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://acgt.cs.tau.ac.il/pivot/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0199, edam:topic_0634, edam:topic_3120 ; sc:citation ; sc:description """Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome. Prioritizing Variants of Uncertain Significance with Spatial Genomic Patterns. PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in 3D proteome. PIVOTAL is a computational tool for prioritizing variants of uncertain significance (VUS), utilizing the spatial distribution of known disease mutations, evolutionary conservation and co-evolution on three-dimensional protein structures. To get started, search for your variants, protein or disease of interest.""" ; sc:featureList edam:operation_0477, edam:operation_2421, edam:operation_3226, edam:operation_3461 ; sc:name "PIVOTAL" ; sc:url "http://pivotal.yulab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3517 ; sc:citation ; sc:description "The penalized inverse-variance weighted (pIVW) estimator is a Mendelian randomization method for estimating the causal effect of an exposure variable on an outcome of interest based on summary-level GWAS data. The pIVW estimator accounts for weak instruments and horizontal pleiotropy simultaneously." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "pIVW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/siqixu/mr.pivw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association." ; sc:featureList edam:operation_3214 ; sc:name "PIXiE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/PNNL-Comp-Mass-Spec/PIXiE" ; biotools:primaryContact "Erin Baker", "Thomas Metz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2269, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description """Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (AKA monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always). Unbiased estimation of nucleotide diversity within and between populations.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3659, edam:operation_3907 ; sc:license "MIT" ; sc:name "pixy" ; sc:softwareHelp ; sc:url "https://anaconda.org/conda-forge/pixy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3512 ; sc:description "Fast fusion detection using kallisto" ; sc:featureList edam:operation_0415 ; sc:name "Pizzly" ; sc:url "https://github.com/pmelsted/pizzly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation ; sc:description "Partial and Joint Decomposiiton (PJD) is a R package for visualizing biologically structured gene expression matrix environment based on low rank models. Currently, it provides user 4 different styles of decomposition: (1) Separately, (2) Concatenately, (3) Jointly, (4) Statistically." ; sc:featureList edam:operation_2939, edam:operation_3659, edam:operation_3891, edam:operation_3960 ; sc:name "PJD" ; sc:url "https://github.com/CHuanSite/PJD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3375, edam:topic_3407 ; sc:citation , "pmcid:PMC6989246", "pubmed:32055585" ; sc:description """R package to convert the pharmacokinetic parameters. The Parameter Converter of the Pharmacokinetic Models. Pharmacokinetics is the study of drug absorption, distribution, metabolism, and excretion.""" ; sc:featureList edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "PKconverter" ; sc:url "https://ek-lee.shinyapps.io/PKconverter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0199, edam:topic_2814 ; sc:citation "pubmed:11340657", "pubmed:16845054" ; sc:description "This tool takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change." ; sc:featureList edam:operation_0250, edam:operation_0331, edam:operation_0400 ; sc:name "pKD" ; sc:url "http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained." ; sc:featureList edam:operation_0337, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "pkgDepTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html" ; biotools:primaryContact "Seth Falcon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3303, edam:topic_3379 ; sc:citation , "pubmed:36169229" ; sc:description "Electronic common technical document submission with analysis using R." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pkglite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://merck.github.io/pkglite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:35801905" ; sc:description "A tool for analyzing dependency heaviness of R packages." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pkgndep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=pkgndep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651, edam:format_3653 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3366, edam:topic_3520 ; sc:description "Merges individual Q-TOF .pkl files into a single file for database searching." ; sc:featureList edam:operation_0335, edam:operation_3436 ; sc:name "PklFileMerger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uib.no/en/rg/probe/66698/pklfilemerger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0736, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:17526524", "pubmed:22693223" ; sc:description "pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB. pKNOT-v2 has been updated with a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or PDB IDs and return knot analysis." ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_2406, edam:operation_2415 ; sc:name "pKNOT-v2" ; sc:url "http://pknot.life.nctu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099 ; sc:citation "pubmed:9925784" ; sc:description "Experimental code demonstrating a dynamic programming algorithm for RNA pseudoknot prediction." ; sc:featureList edam:operation_2441 ; sc:name "PKNOTS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://eddylab.org/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3512, edam:topic_3542 ; sc:citation "pubmed:15294028", "pubmed:17478505" ; sc:description "Server for single sequence RNA secondary structure prediction including pseudoknots, source code, binary executable, and web service available." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "pknotsRG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_0154, edam:topic_3071, edam:topic_3489 ; sc:citation , "pubmed:34260689" ; sc:description "A Protein Data Bank extension database of pKa and pI theoretical values" ; sc:featureList edam:operation_0400, edam:operation_0403, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pKPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypka.org/pKPDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2269, edam:topic_3300, edam:topic_3375 ; sc:citation , "pmcid:PMC7790364", "pubmed:33426260" ; sc:description "pksensi is an R package that implements the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic toxicokinetic model with multivariate outputs. An R package to apply global sensitivity analysis in physiologically based kinetic modeling." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "pksensi" ; sc:softwareHelp ; sc:url "https://nanhung.rbind.io/pksensi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0601, edam:topic_0749 ; sc:citation , "pubmed:34661630" ; sc:description "A novel method for predicting kinase of specific phosphorylation sites based on maximum weighted bipartite matching algorithm and phosphorylation sequence enrichment analysis." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PKSPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/guoxinyunncu/PKSPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0160 ; sc:citation , "pubmed:32427287" ; sc:description "A profile link based search method for protein remote homology detection." ; sc:featureList edam:operation_0289, edam:operation_0296, edam:operation_2421 ; sc:name "PL-search" ; sc:url "http://bliulab.net/PL-search/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3365, edam:topic_3517 ; sc:citation "pubmed:24642062" ; sc:description "Piecewise-constant and Low-rank Approximation for Multi-sample aCGH Data Analysis." ; sc:featureList edam:operation_3233 ; sc:name "PLA" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ust.hk/Software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3336 ; sc:citation , "pubmed:36054653" ; sc:description "A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations." ; sc:featureList edam:operation_0337, edam:operation_0482, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PLA-MoRe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/QingyuLiaib/PLA-MoRe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3510 ; sc:citation "pubmed:24825614" ; sc:description "Search protein sequences to identify candidate prion subsequences using a hidden-Markov model (HMM) algorithm." ; sc:featureList edam:operation_2479 ; sc:name "PLAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plaac.wi.mit.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1176 ; sc:name "GO concept ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3320, edam:topic_3810 ; sc:citation , "pmcid:PMC10134664", "pubmed:37106367" ; sc:description "Comprehensive database of plant alternative splicing events in response to stress." ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PlaASDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zzdlab.com/PlaASDB/ASDB/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "PlabiPD currently hosts data functional annotation of plant genomes using the MapMan Annotation, it also offers a webservice \"Mercator\" to automatically annotate and classify plant FASTA sequence in bulk submission. Also to visualize Plant expression data on metabolic maps." ; sc:featureList edam:operation_2421 ; sc:name "PlabiPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "fzj" ; sc:softwareHelp ; sc:url "https://plabipd.de" ; biotools:primaryContact "Björn Usadel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33137644" ; sc:description """A tool to characterize gene sets using placenta cell-specific gene enrichment analysis. Single-cell RNA-Sequencing (scRNA-Seq) has improved our understanding of individual cell types in the human placenta. However, placental scRNA-Seq data is not readily accessible when trying to understand how expression patterns in model systems correspond to those from first trimester human placenta. Therefore, we developed PlacentaCellEnrich, a tool that takes a gene set as input, and then reports if the input set is enriched for genes with placenta cell-specific expression patterns, based on human placenta scRNA-Seq data. The PlacentaCellEnrich tool is freely available at https: placentacellenrich.gdcb.iastate.edu for non-profit academic use under the MIT license.""" ; sc:featureList edam:operation_2436 ; sc:license "MIT" ; sc:name "PlacentaCellEnrich" ; sc:url "https://placentacellenrich.gdcb.iastate.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:26510693" ; sc:description "Platform for distributed proteomics software." ; sc:featureList edam:operation_2409 ; sc:name "Pladipus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "0.4.1" ; sc:url "https://github.com/compomics/pladipus" ; biotools:primaryContact "Lennart Martens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780 ; sc:citation , "pmcid:PMC7438957", "pubmed:32556150" ; sc:description "PlaMoM is a comprehensive database compiles plant mobile macromolecules" ; sc:name "PlaMoM" ; sc:url "http://119.81.164.251/plamom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_0621, edam:topic_3053 ; sc:citation "pubmed:19520768" ; sc:description "A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_2422, edam:operation_3280 ; sc:name "PLAN2L" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zope.bioinfo.cnio.es/plan2l" ; biotools:primaryContact "M. Krallinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0611, edam:topic_3067, edam:topic_3500 ; sc:citation , "pmcid:PMC8353266", "pubmed:34318308" ; sc:description "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3352, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "PLANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ebi.ac.uk/ols/ontologies/plana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_2885, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:19906711" ; sc:description "Contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. Probes matching the transcript-coding regions in the correct orientation have been determined. For each such probe alignment region, the mRNA and EST sequences that contain the probe sequence have also been determined. In the textual part of the database interface, data on the sequences that cover the probe alignment region and SNPs that are located inside it is summarized." ; sc:featureList edam:operation_0309, edam:operation_0484, edam:operation_3198, edam:operation_3208 ; sc:name "PLANdbAffy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://affymetrix2.bioinf.fbb.msu.ru" ; biotools:primaryContact "Jim Kent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3172, edam:topic_3174, edam:topic_3301, edam:topic_3941 ; sc:citation , "pubmed:32735679" ; sc:description """Planet Microbe is a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. Data packages are "data containers" that conform to the Frictionless Data standard: http://frictionlessdata.io/specs/data-package/. The Planet Microbe cyberinfrastructure system for marine microbiology brings together canonical marine datasets (such as HOT, TARA, OSD) into a unified platform, which leverages ontology terms to annotate, standardize and make the datasets metadata findable, accessible, interoperable and reusable (FAIR).""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3436 ; sc:license "MIT" ; sc:name "Planet Microbe" ; sc:softwareHelp ; sc:url "https://www.planetmicrobe.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0621, edam:topic_0625, edam:topic_3315 ; sc:citation , "pubmed:31950976" ; sc:description "PlanGexQ is a user-friendly interactive tool for the curation and annotation of planarian morphologies and gene expression patterns in a centralized database. PlanGexQ allows any user to define reference morphologies using mathematical graphs and a drag-and-drop interface. Gene expression pattern images can be uploaded to the program and then registered into the reference morphologies. Annotations with terms from the planarian anatomy ontology are autommatically created by analyzing the gene expression patterns and their textual descriptions. PlanGexQ represents a complete methodology for centralizing with formal and annotated descriptions the morphologies and gene expression patterns of planarian worms." ; sc:featureList edam:operation_0224, edam:operation_3435, edam:operation_3559 ; sc:name "PlanGexQ" ; sc:url "https://lobolab.umbc.edu/plangexq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_0780, edam:topic_3071 ; sc:citation , "pmcid:PMC6997939", "pubmed:32016319" ; sc:description """a curated sequence reference dataset for plant ITS DNA metabarcoding. The ITS, ITS1 and ITS2 reference dataset for subkingdom Viridiplantae.""" ; sc:featureList edam:operation_0291, edam:operation_0477, edam:operation_2422, edam:operation_3192, edam:operation_3200 ; sc:license "CC-BY-4.0" ; sc:name "PLANiTS" ; sc:url "https://github.com/apallavicini/PLANiTS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3308, edam:topic_3500 ; sc:citation ; sc:description "Homology-based predicted interactome for multiple planarian transcriptomes." ; sc:featureList edam:operation_2492 ; sc:name "PlanNET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://compgen.bio.ub.edu/PlanNET" ; biotools:primaryContact "J F Abril" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0654, edam:topic_3053 ; sc:citation , "pubmed:34019636" ; sc:description "pLannotate is web server for automatically annotating engineered plasmids. pLannotate re-annotates engineered plasmids and shows you where the fragments are." ; sc:featureList edam:operation_0362, edam:operation_0578, edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "pLannotate" ; sc:url "http://plannotate.barricklab.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3474 ; sc:citation , "pubmed:32232439" ; sc:description """Plant 3D is a plant phenotyping toolkit for 3D point clouds. Plant 3D (P3D) automatically extracts common phenotyping features of interest from high-resolution 3D scans of plant architectures. P3D is open-source and is bundled with a stand-alone Windows application. P3D is written in C++ using OpenGL, QT, TensorFlow, and the point cloud library (PCL). P3D can visualize and process data imported as a 3D point cloud (pcd or txt formats) or a mesh (obj format).""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3196 ; sc:license "MIT" ; sc:name "Plant 3D" ; sc:url "https://github.com/iziamtso/P3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_0821, edam:topic_2275, edam:topic_3071 ; sc:citation , "pmcid:PMC8094579", "pubmed:33997360" ; sc:description "Plant cytochrome P450 database and web-based tools for structural construction and ligand docking. It is a reliable template-based structure prediction method (PCPCM), and predicted the structures of 180 plant P450s with known functions. In addition, we developed a method for docking plant P450s with ligands (PCPLD). Both PCPCM and PCPLD were available for users on the webserver." ; sc:featureList edam:operation_0477, edam:operation_3899, edam:operation_3938 ; sc:name "Plant Cytochrome P450 Database" ; sc:url "http://p450.biodesign.ac.cn/" ; biotools:primaryContact "Huifeng Jiang", "Jian Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3344, edam:topic_3474 ; sc:description "A Matlab code to classify the type of disease using SVM. A Matlab code is written to classify the type of disease affected leaf. Here I have considered two different types of diseases, i.e 'Anthranose' & 'Blackspot'. Segmentation of the disease affected area was performed by K means clustering. Over 13 different statistical and texture based features are extracted." ; sc:featureList edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Plant Disease Classification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50624-plant-disease-classification" ; biotools:primaryContact "Manu BN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0780, edam:topic_3344 ; sc:description "The basic aim of this project is to detect the plant leaf diseases . This is helpful to a farmer to get solution of disease and proper plantation they can achieve" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "plant disease detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/62609-plant-disease-detection" ; biotools:primaryContact "jagabandhu mallik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_0749, edam:topic_0780, edam:topic_3474 ; sc:citation , "pmcid:PMC7274489", "pubmed:32528639" ; sc:description """Plant-mSubP is a computational framework for the prediction of single- and multi-target protein subcellular localization using integrated machine-learning approaches. The subcellular localization of proteins is very important for characterizing its function in a cell. Accurate prediction of the subcellular locations in computational paradigm has been an active area of interest. Most of the work has been focused on single localization prediction. Only few studies have discussed the multi-target localization, but have not achieved good accuracy so far; in plant sciences, very limited work has been done. Here we report the development of a novel tool Plant-mSubP, which is based on integrated machine learning approaches to efficiently predict the subcellular localizations in plant proteomes. The proposed approach predicts with high accuracy 11 single localizations and three dual locations of plant cell""" ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_2489 ; sc:name "Plant-mSubP" ; sc:url "http://bioinfo.usu.edu/Plant-mSubP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0623, edam:topic_0780, edam:topic_3300 ; sc:citation , "pmcid:PMC7874474", "pubmed:33568053" ; sc:description "Orthology and synteny analysis of receptor-like kinases \"RLK\" and receptor-like proteins \"RLP\" in legumes." ; sc:featureList edam:operation_3216, edam:operation_3432, edam:operation_3663 ; sc:license "MIT" ; sc:name "plant-rlk-rlp" ; sc:url "https://github.com/drestmont/plant_rlk_rlp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC9300056", "pubmed:35875835" ; sc:description "A repository and pathway browser for genes involved in signaling networks linked to the endoplasmic reticulum." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "Plant ER UPRome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://uprome.tamu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation ; sc:description "Plant PhysioSpace is a robust tool to compare stress response across plant species." ; sc:featureList edam:operation_2436, edam:operation_3799, edam:operation_3891, edam:operation_3935 ; sc:name "Plant PhysioSpace" ; sc:url "http://physiospace.shinyapps.io/plant/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0780 ; sc:author "Alison Horne", "Thomas Van Parys" ; sc:citation , "pubmed:31004550" ; sc:description "The Plant PTM Viewer is an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species." ; sc:featureList edam:operation_0417, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Plant PTM Viewer" ; sc:provider "Patrick Willems" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.psb.ugent.be/PlantPTMViewer" ; biotools:primaryContact "Patrick Willems" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC9369029", "pubmed:35955817" ; sc:description "A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression." ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "Plant_SNP_TATA_Z-tester" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.sysbio.ru/Plant_SNP_TATAdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071, edam:topic_3391 ; sc:author ; sc:citation , ; sc:description "The Plant Co-expression Annotation Resource, or plantannot in short, is a system developed to find proteins that have no annotation or function assigned (PUFs, or Proteins of Unknown Function) and could be related to molecular mechanisms regarding abiotic stresses in plants. The systems aggregates orthology, coexpression networks and genomic data to filter the genomes of 53 plants (downloaded from Phytozome and NCBI) and select candidate proteins in that regard." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "plantannot" ; sc:softwareVersion "0.0.1", "2.0" ; sc:url "https://www.machado.cnptia.embrapa.br/plantannot2" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3308 ; sc:citation , , "pmcid:PMC148162", "pmcid:PMC99092", "pubmed:11752327", "pubmed:9847207" ; sc:description "Database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences." ; sc:featureList edam:operation_0438 ; sc:name "PlantCARE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:url "http://bioinformatics.psb.ugent.be/webtools/plantcare/html/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382, edam:topic_3383 ; sc:citation , "pmcid:PMC5713628", "pubmed:29209576" ; sc:description "Plant image analysis using OpenCV." ; sc:featureList edam:operation_3443 ; sc:name "PlantCV v2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/danforthcenter/plantcv-v2-paper" ; biotools:primaryContact "Malia A. Gehan", "Noah Fahlgren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3168, edam:topic_3295, edam:topic_3375, edam:topic_3940 ; sc:citation , "pubmed:34037796" ; sc:description "PlantDeepSEA is a webserver based on deep learning models of chromatin accessibility for multiple plant species. It can predict the impact of genomic variants on chromatin accessibility in multiple tissues. Therefore, it can be used to prioritize genomic variants and discover high-impact cis-regulatory sites within a sequence." ; sc:featureList edam:operation_0331, edam:operation_0438, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PlantDeepSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://plantdeepsea.ncpgr.cn/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0780 ; sc:citation , "pubmed:37646937" ; sc:description "PlanTEnrichment is a tool that permits enrichment analysis of transposable elements associated with a given gene list. It takes, for example, a group of differentially expressed plant genes under a particular biological condition as input and returns the list of transposable elements associated with those genes, along with their calculated enrichment scores and statistical significances." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "PlanTEnrichment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tools.ibg.deu.edu.tr/plantenrichment/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pubmed:36271793" ; sc:description "A platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples." ; sc:featureList edam:operation_0264, edam:operation_2436, edam:operation_3223, edam:operation_3431, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "PlantExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biotec.njau.edu.cn/plantExp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0623, edam:topic_0632, edam:topic_0780 ; sc:citation "pubmed:23632162" ; sc:description "PlantGSEA is a tool for gene set enrichment analysis in plants." ; sc:featureList edam:operation_2436, edam:operation_2495, edam:operation_3224, edam:operation_3501 ; sc:name "PlantGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://structuralbiology.cau.edu.cn/PlantGSEA" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:36409390" ; sc:description """Plant Intron Splicing Efficiency Database. Search gene intron ratio levels from plants public RNA-Seq libraries""" ; sc:featureList edam:operation_0224, edam:operation_2499, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "plantintron" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plantintron.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_0780, edam:topic_3673 ; sc:citation , "pmcid:PMC10184434", "pubmed:37197714" ; sc:description "A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index." ; sc:featureList edam:operation_0525, edam:operation_3211, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "PlantLAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinformatics.um6p.ma/PlantLAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0780, edam:topic_1775, edam:topic_3510 ; sc:citation "pubmed:23729470" ; sc:description "Web server for predicting plant protein subcellular localization by substantiality motif." ; sc:featureList edam:operation_1777, edam:operation_2489, edam:operation_3092 ; sc:name "PlantLoc" ; sc:url "http://cal.tongji.edu.cn/PlantLoc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3071, edam:topic_3175, edam:topic_3810 ; sc:citation , "pmcid:PMC10025401", "pubmed:36950350" ; sc:description "An interactive database for 195 plant species LTR-retrotransposons." ; sc:featureList edam:operation_0450, edam:operation_3192, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "PlantLTRdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinformatics.um6p.ma/PlantLTRdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation "pubmed:22080512" ; sc:description "An NSF-funded multi-institutional project developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes." ; sc:featureList edam:operation_3214, edam:operation_3557, edam:operation_3660, edam:operation_3672 ; sc:name "PlantMetabolomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://plantmetabolomics.vrac.iastate.edu/ver2/" ; biotools:primaryContact "Julie A. Dickerson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_0780, edam:topic_3297 ; sc:citation , "pmcid:PMC9076895", "pubmed:35523906" ; sc:description "A database for the molecular weight and isoelectric points of the plant proteomes." ; sc:featureList edam:operation_0338, edam:operation_0398, edam:operation_0403, edam:operation_0417, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "PlantMWpIDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plantmwpidb.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_0780, edam:topic_3300 ; sc:citation "pubmed:22058132" ; sc:description "Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. Plant Natural Antisense Transcripts DataBase is a platform for annotating and discovering NATs by integrating various data sources." ; sc:featureList edam:operation_0438, edam:operation_1781, edam:operation_2409, edam:operation_2436 ; sc:name "PlantNATsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/pnatdb/" ; biotools:primaryContact "Dijun Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0780, edam:topic_3170 ; sc:citation ; sc:description "PlantNexus is an interactive web tool for gene co-expression exploration and visualization for barley and sorghum." ; sc:featureList edam:operation_0314, edam:operation_2943, edam:operation_3925 ; sc:name "PlantNexus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plantnexus.ohio.edu/" ; biotools:primaryContact "Michael A. Held" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3053 ; sc:citation "pubmed:26476450" ; sc:description "Database-assisted system for recognizing combinatorial cis-regulatory elements with distance constraint in plant co-expressed genes." ; sc:featureList edam:operation_2478 ; sc:name "PlantPAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plantpan2.itps.ncku.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0219, edam:topic_0780, edam:topic_3068 ; sc:citation , "pmcid:PMC7010657", "pubmed:32042035" ; sc:description "PlantPepDB is a manually curated database of plant peptides having different functions and therapeutic activities. It contains 3848 peptide entries collected from 11 databases and 835 published research articles. Each entry provides comprehensive information about a peptide that includes its sequence, functional information, source, physicochemical properties, tertiary structure, etc. These peptides have been collected and complied from published databases and research articles. On the basis of their activities, we classified the peptides in 9 categories. Detailed information of these categories and sub-categories can be found on statistics page." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3767 ; sc:name "PlantPepDB" ; sc:url "http://www.nipgr.ac.in/PlantPepDB/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:35842742" ; sc:description "A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "PlantPhoneDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jasonxu.shinyapps.io/PlantPhoneDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0601, edam:topic_0780 ; sc:citation "pubmed:21703007" ; sc:description "Web tool for predicting potential phosphorylation sites in plant proteins." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PlantPhos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/PlantPhos/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0780 ; sc:citation "pubmed:11752333", "pubmed:21418024" ; sc:description "It is a web querying system for a database collecting plant protease inhibitors data. Protease inhibitors in plants are naturally occurring proteins that inhibit the function of endogenous and exogenous proteases. PlantPIs contains information extracted principally from MEROPS database, filtered, annotated and compared with data stored in other protein and gene public databases, using both automated techniques and domain expert evaluations." ; sc:featureList edam:operation_0224 ; sc:name "PlantPIs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plantpis.ba.itb.cnr.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_0780, edam:topic_3050, edam:topic_3489 ; sc:citation ; sc:description "plantR is an R package and workflow for managing species records from biological collections. The package plantR provides tools for downloading, processing, cleaning, validating, summarizing and exporting records of plant species occurrences from biological collections. Please read the Introduction and Tutorial of the package for more details." ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3096 ; sc:license "GPL-3.0" ; sc:name "plantR" ; sc:url "https://github.com/LimaRAF/plantR" ; biotools:primaryContact "Renato A. F. de Lima" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0780, edam:topic_3168, edam:topic_3299, edam:topic_3810 ; sc:citation ; sc:description "Plant Repeat Database (Plantre) provides re-annotated repeat sequences of plant using a uniform pipeline. The current version of plantrep contains 206.04Gb of 396,041,410 repeats from 459 species that were divided into 15 clades based on their phylogeny: algae, bryophyte, lycophytes, fern, gymnosperms, ANA (early angiosperms), magnolids, monocots, base eudicots, super rosids, fabids, malvid, super asterids, lamiids, and campanulids." ; sc:featureList edam:operation_0237, edam:operation_0362, edam:operation_3965 ; sc:name "PlantRep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.plantrep.cn/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3678 ; sc:citation ; sc:description "PlantRGS is a web server for identification of most suitable candidate reference gene(s) for quantitative gene expression studies in plants. PlantRGS identifies the most suitable reference genes with minimum expression variance across the selected experimental conditions based on microarray data." ; sc:featureList edam:operation_2495 ; sc:name "PlantRGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.nipgr.res.in/PlantRGS/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:encodingFormat edam:format_2330 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Structured and interconnected genome and gene data for 12 major plant species ranging from model organisms like Arabidopsis to important crops, like wheat. Additionally it provides a platform for integrative and comparative plant genome research for which specialized online tools such as Crows Nest, a comparative map viewer or an RNAseqExpression Browser." ; sc:featureList edam:operation_2421 ; sc:name "PlantsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "hmgu" ; sc:softwareHelp ; sc:url "http://pgsb.helmholtz-muenchen.de/plant/index.jsp" ; biotools:primaryContact "Heidrun Gundlach", "Klaus Mayer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0780, edam:topic_3383, edam:topic_3385, edam:topic_3474 ; sc:citation ; sc:description """Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution. PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.""" ; sc:featureList edam:operation_3552, edam:operation_3799, edam:operation_3927 ; sc:license "MIT" ; sc:name "PlantSeg" ; sc:url "https://github.com/hci-unihd/plant-seg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3308 ; sc:citation , "pmcid:PMC4225725", "pubmed:24219505" ; sc:description "An online plant transcription factor and transcriptional regulator categorization and analysis tool." ; sc:featureList edam:operation_0438 ; sc:name "PlantTFcat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plantgrn.noble.org/PlantTFcat/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0623, edam:topic_0749, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC2808933", "pubmed:19858103" ; sc:description "Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST." ; sc:featureList edam:operation_0224, edam:operation_0438, edam:operation_0445, edam:operation_1781, edam:operation_3439 ; sc:name "PlantTFDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plntfdb.bio.uni-potsdam.de/v1.0/" ; biotools:primaryContact "PlnTFDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0623, edam:topic_0769, edam:topic_0780, edam:topic_3308 ; sc:citation , "pmcid:PMC9928214", "pubmed:36798801" ; sc:description "Tools for comparative gene family analysis in plant genomics." ; sc:featureList edam:operation_0524, edam:operation_0548, edam:operation_0553, edam:operation_2421, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PlantTribes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://bioconda.github.io/search.html?q=PlantTribes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0780, edam:topic_2275, edam:topic_3810 ; sc:citation , "pmcid:PMC7006421", "pubmed:32028878" ; sc:description "PlaPPISite is a comprehensive database presenting fine-grained protein-protein interaction (PPI) site annotations. It covers both experimentally verified and predicted PPIs for 13 plants including Chlamydomonas reinhardtii, Arabidopsis thaliana, Ricinus communis, Glycine max, Oryza sativa, Solanum lycopersicum, Solanum tuberosum, Vitis vinifera, Zea mays, Brachypodium distachyon, Selaginella moellendorffii, Populus trichocarpa and Medicago truncatula." ; sc:featureList edam:operation_0477, edam:operation_2489, edam:operation_2492, edam:operation_3094, edam:operation_3925 ; sc:name "PlaPPISite" ; sc:url "http://zzdlab.com/plappisite/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2229, edam:topic_3170, edam:topic_3335, edam:topic_3407 ; sc:citation , "pmcid:PMC9393487", "pubmed:36003902" ; sc:description "A comprehensive web portal for cardiovascular single-cell genomics." ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PlaqView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.plaqview.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3673 ; sc:citation , "pmcid:PMC10311310", "pubmed:37387134" ; sc:description "Flow-based MILP algorithm for plasmid contigs binning." ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_3359, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PlasBin-flow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cchauve/PlasBin-flow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "PlasFlow" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/smaegol/PlasFlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0798 ; sc:citation ; sc:description """PlasForest is a homology-based random forest classifier for plasmid detection in genomic datasets. A random forest classifier of contigs to identify contigs of plasmid origin in contig and scaffold genomes.""" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "PlasForest" ; sc:url "https://github.com/leaemiliepradier/PlasForest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC7214025", "pubmed:32091572" ; sc:description "PlasGUN is a gene prediction in plasmid metagenomic short reads using deep learning." ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_2454 ; sc:license "GPL-3.0" ; sc:name "PlasGUN" ; sc:url "https://github.com/zhenchengfang/PlasGUN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3382, edam:topic_3511 ; sc:citation "pubmed:15215471" ; sc:description "Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.), allows users to define custom features to display, contains a library of commonly used plasmids, and, generates nice looking images in a variety of output formats." ; sc:featureList edam:operation_0575, edam:operation_0578, edam:operation_2429 ; sc:name "PlasMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/PlasMapper/index.html" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_0654, edam:topic_0798, edam:topic_3474 ; sc:citation , "pmcid:PMC10269668", "pubmed:37191574" ; sc:description "Accurate and sensitive bacterial plasmid prediction tool based on machine learning of shared k-mers and genomic features." ; sc:featureList edam:operation_0525, edam:operation_0578, edam:operation_3431, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Plasmer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://anaconda.org/iskoldt/plasmer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3474, edam:topic_3895 ; sc:citation ; sc:description """Alignment-based Lab-of-Origin Prediction of Synthetic Plasmids. A pan-genome based lab-of-origin prediction of engineered DNA.""" ; sc:featureList edam:operation_3431 ; sc:name "PlasmidHawk" ; sc:url "https://gitlab.com/treangenlab/plasmidhawk.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3299, edam:topic_3305, edam:topic_3474, edam:topic_3500 ; sc:citation ; sc:description "Prediction of plasmid hosts using random forest." ; sc:featureList edam:operation_0310, edam:operation_0452, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "PlasmidHostFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cge.cbs.dtu.dk/services/PlasmidHostFinder/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_3603 ; sc:name "Sequence image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2331, edam:format_3475 ; sc:name "Nucleic acid report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3301 ; sc:author ; sc:description "PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification." ; 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sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation , , ; sc:description "Genome assembler for plasmids." ; sc:featureList edam:operation_0525 ; sc:name "plasmidspades" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.9.0" ; sc:url "http://cab.spbu.ru/software/spades/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2830 ; sc:citation ; sc:description "Single Cell RNA-sequencing reveals cellular heterogeneity, stage transition and antigenic variation during stress adaptation in synchronized Plasmodium falciparum." ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3501 ; sc:name "plasmo_sync" ; sc:url "http://bit.ly/plasmo_sync" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium." ; sc:featureList edam:operation_0224 ; sc:name "Plasmodium genome resources (PlasmoDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plasmodb.org/plasmo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3324 ; sc:citation "pubmed:21122144" ; sc:description "Automatically identify red blood cells and red blood cells infected with Plasmodium in a set of images. The software identifies cells using a circlular Hough transform, then looks for stained spots within cells as evidence of infection. Identified cells that are misshapen (debris on the slide) or have too much stain (white blood cells) are discarded." ; sc:featureList edam:operation_3443 ; sc:name "Plasmodium Autocount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.vicbioinformatics.com/software.autocount.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3673 ; sc:citation ; sc:description "Population-level genome-wide STR typing in Plasmodium species reveals higher resolution population structure and genetic diversity relative to SNP typing. PlasmoSTR contains population and genome-wide information about genetic variation and other characteristics of short tandem repeats (STRs) in Plasmodium falciparum and Plasmodium vivax." ; sc:featureList edam:operation_0484, edam:operation_2939, edam:operation_3196, edam:operation_3659, edam:operation_3891 ; sc:name "PlasmoSTR" ; sc:url "https://shiny.wehi.edu.au/han.ji/PlasmoSTR/" ; biotools:primaryContact "Melanie Bahlo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0798, edam:topic_3174 ; sc:citation , "pmcid:PMC10326302", "pubmed:37369026" ; sc:description "Automated bacterial plasmid assembly tool." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "plassembler" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/gbouras13/plassembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23956306" ; sc:description "Software for the reconstruction of gene networks which applied a Lasso method from a Bayesian perspective." ; sc:featureList edam:operation_3439 ; sc:name "pLasso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nba.uth.tmc.edu/homepage/liu/pLasso/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Parallel Local Alignment Search Tool for Database Comparison." ; sc:featureList edam:operation_0495 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.0" ; sc:name "Plast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.irisa.fr/symbiose/projects/plast/" ; biotools:primaryContact "Dominique Lavenier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3168 ; sc:citation "pubmed:20522510" ; sc:description "PLAST-ncRNA is an online tool for aligning distantly similar non-coding RNA sequences to a genome using the Probalign program. Useful for detection of potential homologous ncRNA sequences in large genomes." ; sc:featureList edam:operation_0314, edam:operation_2478, edam:operation_3182 ; sc:name "PLAST-ncRNA" ; sc:url "http://plastrna.njit.edu" ; biotools:primaryContact "Satish Chikkagoudar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3174, edam:topic_3293, edam:topic_3301, edam:topic_3941 ; sc:citation , "pubmed:35266524" ; sc:description "A database of microorganisms and proteins linked to plastic biodegradation." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "PlasticDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://plasticdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC5120557", "pubmed:27875984" ; sc:description "Nucleotide-resolution analysis of next-generation sequencing and genomics data." ; sc:featureList edam:operation_2403 ; sc:name "Plastid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://plastid.readthedocs.io/en/latest/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_0780, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC10209082", "pubmed:37225726" ; sc:description "Prediction of protein subplastid localization and origin with PlastoGram." ; sc:featureList edam:operation_0477, edam:operation_2489, edam:operation_3891, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "PlastoGram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biogenies.info/PlastoGram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3474 ; sc:citation , "pmcid:PMC7725325", "pubmed:33074084" ; sc:description """PlasTrans: Identify the conjugative and mobilizable plasmid fragments in plasmidome using sequence signatures. PlasTrans is designed to distinguish the transmissible plasmid-derived sequences from the non-transmissible plasmid-derived sequences in the plasmid metageomic data. It take a "fasta" file that contains the plasmid sequences as input and outputs a tabular file with transferability annotation for each sequence.""" ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "PlasTrans" ; sc:url "https://github.com/zhenchengfang/PlasTrans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3511 ; sc:citation "pubmed:18566288" ; sc:description "Python scripts for the analyses and visualization of probe level Affymetrix exon array data." ; sc:featureList edam:operation_2495 ; sc:name "PLATA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sandberg.cmb.ki.se/plata/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC7433917", "pubmed:32658266" ; sc:description """PLATform for Assembling NUcleotide Sequences. This is an accurate de novo assembler for bacterial genomes using an iterative error-removal process. Platanus_B is a de novo assembler for isolated bacterial genomes. The features of this tool are as follows: (1) It requires at least one Illuimina paired-end library. This library is useful for large-scale and/or high-resolution analysis. (2) It also can accept Oxford-Nanopore and/or PacBio long reads ("iterate" command). (3) Implementing the iteration of sequence-extensions, gap-closing and error-removals, it can archive assemblies with contiguity and accuracy for many cases. (4) As an utility function, it can combine multiple assemblies through the "combine" command.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Platanus_B" ; sc:url "http://platanus.bio.titech.ac.jp/platanus-b/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3033 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2330, edam:format_3033, edam:format_3547 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3033, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0108, edam:topic_2229, edam:topic_3382, edam:topic_3572 ; sc:citation ; sc:description "Provides basic S4 data structures and routines for analyzing plate based flow cytometry data." ; sc:featureList edam:operation_3695, edam:operation_3741 ; sc:license "Artistic-2.0" ; sc:name "plateCore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/plateCore.html" ; biotools:primaryContact "Errol Strain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0632, edam:topic_0749, edam:topic_0769 ; sc:citation , "pmcid:PMC8162687", "pubmed:34048502" ; sc:description "PlateEditor is a free web application to work with multi-well plates. PlateEditor is a web-based application for the management of multi-well plate layouts and associated data. PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data aggregation. PlateEditor is fully client-side: no data are ever transferred to the server, ensuring complete security and privacy of your research data." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PlateEditor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://plateeditor.sourceforge.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3306, edam:topic_3520 ; sc:citation , "pmcid:PMC9123465", "pubmed:35607664" ; sc:description "A software-controllable plate-scale perfusion system for culture of adherent cells." ; sc:featureList edam:operation_3431, edam:operation_3968 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PlateFlo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://plateflo.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Analysis of Platelet Aggregate Morphology Using 2-D Autocorrelation" ; sc:featureList edam:operation_3436, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Analysis of Platelet Aggregate Morphology Using 2-D Autocorrelation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28555-analysis-of-platelet-aggregate-morphology-using-2-d-autocorrelation" ; biotools:primaryContact "Thomas Colace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3516 ; sc:citation "pubmed:22125222" ; sc:description "Software package to fit a Bayesian Gaussian mixture model (GMM) on the SNP array signal intensity data, and infer individual’s allele-specific copy number genotypes at genome-wide SNP loci in a SNP array." ; sc:featureList edam:operation_3196 ; sc:name "PlatinumCNV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://kumasakanatsuhiko.jp/projects/platinumcnv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3516, edam:topic_3517 ; sc:citation "pubmed:19908384" ; sc:description "System for the analysis of genome-wide association data that will incorporate several analytical approaches as filters to allow a scientist to choose whatever analytical methods they wish to apply. It was designed to aid in retrieving, evaluating, formatting, and analyzing genotypic and clinical data from the latest large-scale genotyping studies. It also implements a battery of quality control procedures to assess the data." ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3218 ; sc:name "PLATO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ritchielab.psu.edu/software/plato-download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2640, edam:topic_3520, edam:topic_3676 ; sc:citation , "pmcid:PMC7772914", "pubmed:33375939" ; sc:description """Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy. PLATO is a semi-supervised learning approach for somatic variant calling and peptide identification which can be used in personalized cancer immunotherapy. The current version provides peptide identification from MS/MS data. It uses AutoML service on Azure for modeling part. ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/plato""" ; sc:featureList edam:operation_3227, edam:operation_3631, edam:operation_3767, edam:operation_3891, edam:operation_3935 ; sc:name "PLATO" ; sc:url "http://github.com/esherafat/PLATO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071 ; sc:citation ; sc:description "General-use embeddable JavaScript widget used for browsing and searching ontologies. It is generically configurable for use with any ontology served by the Ontology Lookup Service (OLS). It’s features include the ability to visualise matching ontology terms in their rightful place in the tree, and to expand and collapse nodes as desired." ; sc:featureList edam:operation_3559 ; sc:name "PLATO Plugin for Autocomplete on Ontologies" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareVersion "1" ; sc:url "http://wwwdev.ebi.ac.uk/fgpt/PLATOdemo/" ; biotools:primaryContact "Simon Jupp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2275, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC9103655", "pubmed:35563636" ; sc:description "A Predictive Drug Discovery Web Platform for Efficient Target Fishing and Bioactivity Profiling of Small Molecules." ; sc:featureList edam:operation_0224, edam:operation_2489, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "PLATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://plato.uniba.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC7319588", "pubmed:32421769" ; sc:description "PlaToLoCo is the first web meta-server for visualization and annotation of low complexity regions in proteins." ; sc:featureList edam:operation_0495, edam:operation_2421, edam:operation_3192, edam:operation_3904 ; sc:name "PlaToLoCo" ; sc:url "http://platoloco.aei.polsl.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "A tool designed for efficient and accurate variant-detection in high-throughput sequencing data using local realignment of reads and local assembly. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb." ; sc:featureList edam:operation_0292, edam:operation_0487, edam:operation_3197 ; sc:license "Not licensed" ; sc:name "platypus" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.well.ox.ac.uk/platypus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """Platypus is an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes. R package for the analysis of single-cell immune repertoires. 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Micrococcal nuclease digestion followed by deep sequencing (MNase-seq) is the most used method to investigate nucleosome organization on a genome-wide scale. We present plot2DO, a flexible tool for evaluating the quality of MNase-seq and MNase-ChIP-seq data, and for visualizing the distribution of nucleosomes near the functional regions of the genome. Apart from MNase-seq data analysis, plot2DO was also used to investigate DNA fragments obtained in other types of experiments, such as ChIP-seq, ATAC-seq, and chemical cleavage mapping. 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Mena-Chalco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3168, edam:topic_3382 ; sc:citation ; sc:description "plotgardener is a genomic data visualization package for R. Using grid graphics, plotgardener empowers users to programmatically and flexibly generate multi-panel figures. plotgardener accomplishes these goals by utilizing 1) a coordinate-based plotting system, and 2) edge-to-edge containerized data visualization. The coordinate-based plotting system grants users precise control over the size, position, and arrangement of plots. Its edge-to-edge plotting functions preserve the mapping between user-specified containers and the represented data. This allows users to stack plots with confidence that vertically aligned data will correspond to the same regions." ; sc:featureList edam:operation_0306, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "plotgardener" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PhanstielLab/plotgardener" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2306 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , ; sc:description "Get the coverage of a genome." ; sc:featureList edam:operation_0256 ; sc:name "plotgenomecoverage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , "pmcid:PMC3267995", "pubmed:22189471" ; sc:description "plotIBD is a perl script to assist with plotting sampled inheritance vectors in pedigrees" ; sc:featureList edam:operation_0337 ; sc:name "plotIBD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20111108" ; sc:url "http://faculty.washington.edu/wijsman/software.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description "PlotMI is a program for visualization of pairwise interactions in a set of input sequences by computing the pairwise mutual information between positional k-mer distributions." ; sc:featureList edam:operation_0337, edam:operation_3472, edam:operation_3695 ; sc:license "MIT" ; sc:name "plotMI" ; sc:url "https://github.com/hartonen/plotMI" ; biotools:primaryContact "Jussi Taipale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3474 ; sc:citation , "pmcid:PMC10546746", "pubmed:37789265" ; sc:description "Python package for visualizing sequence data using ggplot2." ; sc:featureList edam:operation_0292, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "plotnineSeqSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://caotianze.github.io/plotnineseqsuite/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Plot potential open reading frames in a nucleotide sequence." ; sc:featureList edam:operation_0436 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "plotorf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/plotorf.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3374 ; sc:description "PLOTPHYTREE(TREE) renders a phylogenetic tree object into a MATLAB figure as a phylogram." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:name "plotphytree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/14636-plotphytree" ; biotools:primaryContact "Bingley L" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation "pubmed:16845104" ; sc:description "Tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output." ; sc:featureList edam:operation_0237 ; sc:name "PlotRep" ; sc:url "http://repeats.abc.hu/cgi-bin/plotrep.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2885 ; sc:citation , "pubmed:35426899" ; sc:description "Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies." ; sc:featureList edam:operation_0525, edam:operation_0570, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "plotsr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/schneebergerlab/plotsr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3678 ; sc:citation ; sc:description "PlotXpress is a shiny app that simplifies the analysis and plotting of data from a dual luciferase experiment in 96-well format." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "plotXpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huygens.science.uva.nl/PlotXpress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3365 ; sc:citation ; sc:description "This package performs tests for paired high-throughput data." ; sc:featureList edam:operation_3224 ; sc:license "GPL-2.0" ; sc:name "PLPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PLPE.html" ; biotools:primaryContact "Soo-heang Eo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654 ; sc:citation ; sc:description "The present package implements a flexible framework for modeling the relationship between DNA copy number and gene expression data using Piecewise Linear Regression Splines." ; sc:featureList edam:operation_2495, edam:operation_3233 ; sc:license "GPL-2.0" ; sc:name "plrs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/plrs.html" ; biotools:primaryContact "Gwenael G.R. Leday to" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC7073013", "pubmed:32190163" ; sc:description """The Prospective Lynch Syndrome Database reports enable evidence-based personal precision health care. The aims of the Prospective Lynch Syndrome Database (PLSD) are to provide empirical prospectively observed data on the incidences of cancer in different organs, survival following cancer and the effects of interventions in carriers of pathogenic variants of the mismatch repair genes (path_MMR) categorized by age, gene and gender. Although PLSD is assumption-free, as with any study the ascertainment procedures used to identify the study cohort will introduce selection biases which have to be declared and considered in detail in order to provide robust and valid results.""" ; sc:featureList edam:operation_3435, edam:operation_3503 ; sc:name "PLSD" ; sc:url "http://www.PLSD.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3301, edam:topic_3315 ; sc:citation , "pmcid:PMC10025448", "pubmed:36653900" ; sc:description "A multivariate and non-parametric batch effect correction framework based on Projection to Latent Structures Discriminant Analysis for microbiome data." ; sc:featureList edam:operation_2939, edam:operation_3659, edam:operation_3891, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:name "PLSDA-batch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EvaYiwenWang/PLSDAbatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3277, edam:topic_3697 ; sc:citation , "pmcid:PMC8728149", "pubmed:34850116" ; sc:description "Advancing a comprehensive database of bacterial plasmids." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PLSDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ccb.uni-saarland.de/plsdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:35438150" ; sc:description "A blood platelets-based gene expression database for disease investigation." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0571 ; sc:isAccessibleForFree true ; sc:name "PltDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pltdb-hust.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0780, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC9126412", "pubmed:35605006" ; sc:description "Plant transfer RNA database." ; sc:featureList edam:operation_0464, edam:operation_2421, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "PltRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.nipgr.ac.in/PtRNAdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3301 ; sc:citation ; sc:description "Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis." ; sc:featureList edam:operation_2409 ; sc:name "PluMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://biorg.cis.fiu.edu/pluma/" ; biotools:primaryContact "Trevor Cickovski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation , ; sc:description "PLUMED is a plugin that works with a large number of molecular dynamics codes (Codes interfaced with PLUMED ). It can be used to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods. PLUMED can also work as a Command Line Tools to perform analysis on trajectories saved in most of the existing formats." ; sc:featureList edam:operation_0250, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:name "Plumed" ; sc:softwareHelp ; sc:softwareVersion "2.4.1" ; sc:url "https://plumed.github.io/doc-v2.4/user-doc/html/index.html" ; biotools:primaryContact "Carlo Camilloni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3474 ; sc:citation "pubmed:21752249" ; sc:description "Computer program to reconstruct and evaluate majority rule supertrees: MR(-), MR(+) and MR(+)g. It searches tree space by NNI (nearest-neighbor interchange) and TDR (taxa-deletion-reinsertion). Only fully resolved input and supertrees are considered, multifurcating trees may be returned as the strict consensus of equally best scoring trees." ; sc:featureList edam:operation_0323 ; sc:name "PluMiST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cibiv.at/software/plumist/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229 ; sc:citation , "pmcid:PMC5549834", "pubmed:28712847" ; sc:contributor ; sc:description "A robust and rapid image processing software which allows the automatic evaluation of pluripotency in large low-magnification images." ; sc:featureList edam:operation_3443 ; sc:license "Other" ; sc:name "Pluri-IQ" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.cnbc.pt/equipment/microscopyUnit.asp#divImageAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2229, edam:topic_3510 ; sc:citation , "pubmed:27966493" ; sc:description "Predicting proteins responsible for pluripotency for mouse as well as human but here we construct this server using data of the mouse." ; sc:featureList edam:operation_1777 ; sc:name "PluriPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bicresources.jcbose.ac.in/ssaha4/pluripred/" ; biotools:primaryContact "Sudipto Saha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web service" ; sc:applicationSubCategory edam:topic_0091 ; sc:description "Pluto empowers scientific teams to manage and analyze all of their data from sequencing/omics experiments (e.g. RNA-seq, CUT&RUN) plus low-throughput (e.g. ELISA, imaging, cell counts, etc) quantitative assays. We're proud to offer a modern, discovery-focused, single source of truth platform that feels like Graphpad Prism + Google Sheets + bioinformatics analysis and visualization that can be done in your browser, with no coding required." ; sc:isAccessibleForFree false ; sc:name "Pluto Bio" ; sc:url "https://pluto.bio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_3752 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:encodingFormat edam:format_2331, edam:format_3752 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:encodingFormat edam:format_2331 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3050, edam:topic_3489 ; sc:citation ; sc:description """PlutoF is an online data management platform and computing service provider for biology and related disciplines. Registered users can enter and manage a wide range of data, e.g., taxon occurrences, metabarcoding data, taxon classifications, traits, and lab data. It features an annotation module where third-party annotations (on material source, geolocation and habitat, taxonomic identifications, interacting taxa, etc.) can be added to any collection specimen, living culture or DNA sequence record. It also features an analysis module by providing digital services for molecular sequence identification and species discovery from eDNA samples.""" ; sc:featureList edam:operation_2403, edam:operation_3431, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:name "PlutoF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://plutof.ut.ee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2269 ; sc:citation , "pmcid:PMC2358895", "pubmed:18366694" ; sc:description "Probe level Locally moderated Weighted median-t and Locally Moderated Weighted-t." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "plw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/plw.html" ; biotools:primaryContact "Magnus Astrand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased." ; sc:featureList edam:operation_3465 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "plyranges" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "http://bioconductor.org/packages/release/bioc/html/plyranges.html" ; biotools:primaryContact "Stuart Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_3390, edam:topic_3697 ; sc:citation ; sc:description """A framework for detecting and quantifying relationship alterations in microbial community. Profile Monitoring for Microbial Community Alteration. PM2RA is a method that uses Hoteling’s T2 statistics to project multiple-dimensional microbial community to 1-dimensional space, to quantify the relationship alteration regarding two or more microbes between different conditions. *The average computation time of PM2RA for a dataset contains 100 features is 30 minutes (running on a Linux with 8 processors).""" ; sc:featureList edam:operation_3200, edam:operation_3435, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "PM2RA" ; sc:url "http://www.pm2ra-xingyinliulab.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168 ; sc:description "PM4NGS is designed to generate a standard organizational structure for Next Generation Sequencing (NGS) data analysis. It includes a directory structure for the project, several Jupyter notebooks for data management and CWL workflows for pipeline execution." ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "PM4NGS" ; sc:softwareHelp ; sc:softwareVersion "0.0.6" ; sc:url "https://pm4ngs.readthedocs.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_3518 ; sc:citation , "pmcid:PMC5828362", "pubmed:29482592" ; sc:description "Protein Microarray Analyser, a user-friendly tool for data processing and normalization." ; sc:featureList edam:operation_2495 ; sc:name "PMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/protein-microarray-analyser/" ; biotools:primaryContact "Jessica Da Gama Duarte" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Curated proteolytic events and pathways from the literature." ; sc:featureList edam:operation_0224 ; sc:name "PMAP-CutDB proteolytic event database" ; sc:softwareHelp ; sc:url "http://www.proteolysis.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_0153, edam:topic_2269, edam:topic_3172, edam:topic_3308, edam:topic_3520 ; sc:citation , "pubmed:36622218" ; sc:description "A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes. This R package provides functionality for quality control processing, statistical analysis and visualization of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level; isobaric labeled or unlabeled), lipidomic, and metabolomic data." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2428, edam:operation_2939, edam:operation_2945, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "pmartR" ; sc:url "https://github.com/pmartR/pmartR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3304, edam:topic_3382 ; sc:citation ; sc:description "pMAT (Photometry Modular Analysis Tool) is An Open-Source, Modular Software Suite for the Analysis of Fiber Photometry Calcium Imaging." ; sc:featureList edam:operation_3096, edam:operation_3435, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "pMAT" ; sc:url "https://github.com/djamesbarker/pMAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0199 ; sc:citation "pubmed:14980022" ; sc:description "Implementation of PMB in Pseq-gen and Data file to use with Ziheng Yang’s PAML for protein sequence analysis." ; sc:featureList edam:operation_0250, edam:operation_2403, edam:operation_2479 ; sc:name "PMB matrix" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.uhnresearch.ca/labs/tillier/software.htm#4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2640, edam:topic_3173, edam:topic_3299 ; sc:citation , "pubmed:34647978" ; sc:description "Efficient inference of expressive models of cancer evolution with high prognostic power." ; sc:featureList edam:operation_0547, edam:operation_2426, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PMCE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BIMIB-DISCo/PMCE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814 ; sc:citation ; sc:description "A tool collects three dimensional protein models obtained by structure prediction methods." ; sc:featureList edam:operation_3431 ; sc:name "PMDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:url "https://bioinformatics.cineca.it/PMDB/" ; biotools:primaryContact "Tiziana Castrignanò" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0780, edam:topic_3168, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description """The gene structure and super-hypervariability of the complete Penaeus monodon Dscam gene. PmDscam is a tool for sequence alignment of hypervariable shrimp Dscam (Down syndrome cell adhesion molecule). Using NGS and Sanger sequencing, a 260-kbp Dscam genome draft from Black tiger shrimp (Penaeus monodon) was completed. Based on our analysis, hypervariability of PmDscam occurs both on the extracellular region and the cytoplasmic tail. From one PmDscam genome locus and through alternative splicing, there are 54,756 potential combinations involving extracellular regions, plus 512 potential combinations of cytoplasmic tails. Therefore, PmDscam has super-hypervariability all derived from one PmDscam genome locus.""" ; sc:featureList edam:operation_0264, edam:operation_0446, edam:operation_0524, edam:operation_2421 ; sc:name "PmDscam" ; sc:url "http://pmdscam.dbbs.ncku.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:21576754" ; sc:description "Algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment." ; sc:featureList edam:operation_0502 ; sc:name "PMFastR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/PMFastR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_2275, edam:topic_3382, edam:topic_3500 ; sc:citation "pubmed:17478496" ; sc:description "Tool to generate protein pictures, animations, and movies." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_0570, edam:operation_2514 ; sc:name "PMG" ; sc:url "http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3360, edam:topic_3697 ; sc:citation , "pubmed:36007229" ; sc:description "Compositional alternative to phylogenetic grouping of microbiome data." ; sc:featureList edam:operation_0323, edam:operation_3436, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PMGs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/asliboyraz/PMGs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0780, edam:topic_3172 ; sc:citation , "pmcid:PMC10767808", "pubmed:37819039" ; sc:description "The Plant Metabolome Hub (PMhub), available at https: pmhub.org.cn, is a valuable resource designed to provide scientists with comprehensive information on plant metabolites. It offers extensive details about their reference spectra, genetic foundations, chemical reactions, metabolic pathways and biological functions. The PMhub contains chemical data for 188 837 plant metabolites gathered from various sources, with 1 467 041 standard in-silico high-resolution tandem mass-spectrometry (HRMS MS) spectra corresponding to these metabolites. Beyond its extensive literature-derived data, PMhub also boasts a sizable collection of experimental metabolites; it contains 144 366 detected features in 10 typical plant species, with 16 423 successfully annotated by using standard in-silico HRMS MS data, this collection is further supplemented with thousands of features gathered from reference metabolites" ; sc:featureList edam:operation_0224, edam:operation_3660, edam:operation_3803, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "PMhub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pmhub.org.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2229, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:33554247" ; sc:description """Prediction and collection of protein-metabolite interactions. PMIDB provides both interactions and non-interactions between protein and metabolite, which not only reduces the experimental cost for biological experimenters, but also facilitates the construction of more accurate algorithms for researchers using machine learning. PMIDB provides a user-friendly interface for browsing the biological function of the metabolites/proteins of interest, experimental technology for identifying PMIs, PMIs in different species, which provides important support for further understanding of cellular processes. Interactions between proteins and small molecule metabolites play a vital role in regulating protein functions and controlling various cellular processes.""" ; sc:featureList edam:operation_2492, edam:operation_3092, edam:operation_3891 ; sc:name "PMI-DB" ; sc:url "http://easybioai.com/PMIDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3314, edam:topic_3489 ; sc:citation , "pubmed:33031632" ; sc:description """Evaluating retrieval qualities of Google Scholar and PubMed. Augment your PubMed literature search from the command-line by linking data downloaded from NIH's Open Citation Collection (NIH-OCC), which includes scientific influence, translation, and citation counts, with PubMed IDs (PMIDs), rather than clicking and clicking and clicking on Google Scholar Cited by N links. 1) Get citation counts, given PMIDs. Command-line users can immediately augment their PubMed search results using the pmidcite scripts and library, which download citation data from the National Institutes of Health Open Citation Collection (NIH-OCC) database using NIH's "iCite" Application Programming Interface (API). We have found PubMed plus NIH-OCC citation data combined using pmidcite is a "Better" experience than using Google Scholar if your research is in the health sciences and you are amenable to consider working from the command line. 2) Sort citation counts, given PMIDs.""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3802 ; sc:license "LGPL-3.0" ; sc:name "pmidcite" ; sc:url "https://github.com/dvklopfenstein/pmidcite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3408, edam:topic_3577, edam:topic_3673 ; sc:citation ; sc:description """New pmIG database to better understand IG repertoire and selection processes in disease and vaccination. pmIG: Populations matched germline alleles. Database: Population matched germline alleles. Trans-Omics for Precision Medicine (TOPMed) Program.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3227, edam:operation_3894 ; sc:name "pmIG" ; sc:url "https://github.com/InduKhatri/pmIG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_2885 ; sc:citation "pubmed:20719744" ; sc:description "It includes the miRNAs of two model plants, Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Four major functional modules, \"SNPs\", \"Pri-miRNAs\", \"MiR—Tar\", and \"Self-reg\", are provided." ; sc:featureList edam:operation_0308, edam:operation_0463, edam:operation_0484, edam:operation_2409, edam:operation_2428 ; sc:name "PmiRKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bis.zju.edu.cn/pmirkb/" ; biotools:primaryContact "Dijun Chen", "Lingfeng Gou", "Ming Chen", "Yijun Meng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0659, edam:topic_0749, edam:topic_3068 ; sc:citation , "pubmed:35567946" ; sc:description "A positive miRNA-target regulations database." ; sc:featureList edam:operation_0306, edam:operation_0463, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "PmiRtarbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lwb-lab.cn/PmiRtarbase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC8756190", "pubmed:34677586" ; sc:description "Penn Machine Learning Benchmarks (PMLB) is a large collection of curated benchmark datasets for evaluating and comparing supervised machine learning algorithms." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PMLB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EpistasisLab/pmlb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:8801187" ; sc:description "Estimate the gene flow parameter q for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either single or multi locus, haploid or diploid, genotype data. Suitable molecular data types minimally include allozymes, microsatellites, and RFLPs." ; sc:featureList edam:operation_2423 ; sc:name "PMLE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.rannala.org/docs/pmle20.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_0780, edam:topic_3474 ; sc:citation , "pubmed:32087005" ; sc:description """PmliPred is a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction. We have proposed a new method for fulfilling plant miRNA-lncRNA interaction prediction (PmliPred). The deep learning model and shallow machine learning model are trained using raw sequences and manually extracted features respectively. Then they are hybridized based on fuzzy decision for prediction. PmliPred shows a better performance and generalization ability comparing with the existing methods. Several new miRNA-lncRNA interactions in Solanum lycopersicum are successfully identified using quantitative RT-PCR from the candidates predicted by PmliPred, which further verifies its effectiveness.""" ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "PmliPred" ; sc:url "http://bis.zju.edu.cn/PmliPred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3324, edam:topic_3523 ; sc:citation ; sc:description "The Parallel Mixed Model approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "pmm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pmm.html" ; biotools:primaryContact "Anna Drewek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0637, edam:topic_3388, edam:topic_3423, edam:topic_3577 ; sc:citation , "pubmed:32987570" ; sc:description """A knowledge representation model towards precision medicine. The Precision Medicine Ontology (PMO) has been developed as a standardized ontology for human precision medicine with consistent, reusable and sustainable descriptions of human disease terms, genomic molecular, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Institute of Medical Information, Chinese Academy of Medical Sciences. The Precision Medicine Ontology focuses on the development of a high level patients-centric ontology for the academic research, thus, it systematically integrates biomedicine vocabularies from GO, NCBI Gene, DrugBank, HPO, MeSH, SNOMED CT, etc.""" ; sc:featureList edam:operation_0362, edam:operation_0558, edam:operation_3778 ; sc:name "PMO" ; sc:url "http://www.phoc.org.cn/pmo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3302, edam:topic_3382, edam:topic_3500 ; sc:description "Detection of Animal Faecal Parasites Using an ioLight Portable Microscope" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Margaret Duff PMP Project 2017" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/64346-margaret-duff-pmp-project-2017" ; biotools:primaryContact "Margaret Duff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3071, edam:topic_3303 ; sc:citation ; sc:description """pmparser enables one to easily create and maintain a relational database of data from PubMed/MEDLINE. pmparser can download the publicly available XML files, parse them, incorporate PubMed’s regular updates, and combine the data with the NIH Open Citation Collection. PMDB, our implementation of the database, is available to download on Zenodo. For a detailed description of pmparser and PMDB, check out the preprint. The tar file contains a compressed dump of PMDB, which was created in PostgreSQL 12 using the pmparser R package.""" ; sc:featureList edam:operation_0224, edam:operation_1812 ; sc:license "GPL-2.0" ; sc:name "pmparser" ; sc:url "https://pmparser.hugheylab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3518 ; sc:citation "pubmed:19808935" ; sc:description "The database integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. Includes model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_0463, edam:operation_3431, edam:operation_3432 ; sc:name "Plant MicroRNA Database (PMRD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.cau.edu.cn/PMRD" ; biotools:primaryContact "Su Zhen Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:17597879" ; sc:description "Tool that utilizes Position Weight Matrices to search for putative Transcription Factor Binding Sites. PMSearch takes Position Frequency Matrices (PFMs) and DNA sequences to initiate a prediction task. The user may upload motifs/matrices (Position Frequency Matrices, PFM or Position Weight Matrices, PWM) or retrieve PFMs from our local dataset as input." ; sc:featureList edam:operation_0438 ; sc:name "PMSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mcube.nju.edu.cn/jwang/lab/soft/PMS/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_3056, edam:topic_3930 ; sc:citation ; sc:description """population matched (PM) germline allelic variants of T-cell receptor (TR) loci. Web site created using create-react-app. The germline alleles for TR and IG (Variable, Diversity, Joining and Constant) genes are organized from approximately 2500 individuals from 26 different ethnicities representing five major super populations. For more information on how we obtained our results please refer to the documentation section.""" ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_2421, edam:operation_3227 ; sc:name "pmTR" ; sc:url "https://pmtrig.lumc.nl/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3681 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A library for proteomics QC report based on the MultiQC framework. Specifically, pmultiqc generates a QC report for the quantms pipeline." ; sc:featureList edam:operation_2428 ; sc:name "pmultiqc" ; sc:url "https://github.com/bigbio/pmultiqc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , "pmcid:PMC5793831", "pubmed:15879453", "pubmed:28453649" ; sc:description "Web portal for the annotation of pathological protein variants." ; sc:featureList edam:operation_3225, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PMut" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2017" ; sc:url "http://mmb.irbbarcelona.org/PMut" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation ; sc:description """Learning Interpretable Single-Cell Representations with Pathway Modules. pmVAE leverages biological prior information in the form of pathway gene sets to construct interpretable representations of single-cell data. It uses pathway module sub networks to construct a latent space factorized by pathway gene sets. Each pathway has a corresponding module which behaves as a mini VAE acting only on the participating genes. These modules produce latent representations that can be direcrly interpreted within the context of a specific pathway. To account for overlapping pathway gene sets (due to e.g. signaling hierarchies) we have a custom training procedure to encourage module independence.""" ; sc:featureList edam:operation_0533, edam:operation_3926, edam:operation_3929 ; sc:license "MIT" ; sc:name "pmVAE" ; sc:url "https://github.com/ratschlab/pmvae" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "Generate hybrid structures/topologies for amino acid mutations" ; sc:featureList edam:operation_0331, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:name "PMX" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pmx.mpibpc.mpg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0654 ; sc:citation , "pubmed:33300028" ; sc:description """proto-Nucleic Acid Builder (pNAB) The proto-Nucleic Acid Builder is a program for modeling the 3D strucutres of DNA, RNA, and nucleic acid analogs. Nucleic acids with alternative backbones or nucleobases can be constructed by the program by supplying the 3D structure of isolated backbones or nucleobases. The program can perform a helical parameter search and backbone conformation search and find reasonable nucleic acid structures. Geometric and energetic criteria are used to evaluate candidate structures. The program is written in C++ and Python, and has a graphical user interface. The program is available for the Linux, MacOS, and Windows platforms.""" ; sc:featureList edam:operation_0455, edam:operation_0475, edam:operation_0479, edam:operation_2518, edam:operation_3095 ; sc:license "GPL-2.0" ; sc:name "proto-Nucleic Acid Builder" ; sc:url "https://github.com/GT-NucleicAcids/pnab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0199, edam:topic_0621, edam:topic_0780, edam:topic_3500 ; sc:citation , "pmcid:PMC7923538", "pubmed:33653259" ; sc:description "PnB Designer is a web application to design prime and base editor guide RNAs for animals and plants." ; sc:featureList edam:operation_3096, edam:operation_3196, edam:operation_3204 ; sc:name "PnB Designer" ; sc:url "http://fgcz-shiny.uzh.ch/PnBDesigner/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0976 ; sc:name "Identifier (by type of data)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3175 ; sc:citation , "pubmed:34551435" ; sc:description "A universal platform for annotating and analyzing non-classically secreted proteins of Gram-positive bacteria" ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "PncsHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pncshub.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0659, edam:topic_0780, edam:topic_3047, edam:topic_3512 ; sc:citation , "pmcid:PMC7078067", "pubmed:32185394" ; sc:description "PncStress is a manually curated archive of experimentally validated stress-responsive ncRNAs in plant. The database contains that have been experimentally verified response to different kind of abiotic or biotic stress." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3925 ; sc:name "PncStress" ; sc:url "http://bis.zju.edu.cn/pncstress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "PnetCDF: A Parallel I/O Library for NetCDF File Access" ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "PnetCDF" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "https://parallel-netcdf.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0196, edam:topic_2885, edam:topic_3305, edam:topic_3673 ; sc:citation , "pmcid:PMC9837567", "pubmed:36748701" ; sc:description "A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3196, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PneumoKITy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CarmenSheppard/PneumoKITy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0203, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC9315718", "pubmed:35890455" ; sc:description "An R Package for Rapid Candidate Gene Selection through Pooled Next-Generation Sequencing." ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3196, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PNGSeqR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/smilejeen/PNGseqR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0108, edam:topic_0128, edam:topic_0154, edam:topic_0203 ; sc:citation ; sc:description """An in silico approach to identification, categorization and prediction of nucleic acid binding proteins. PNIDB-the database of protein-nucleic acid interactions. PNIDB is database of protein-nucleic acid binding interactions identified by protein structure on the Protein Data Bank(PDB), as well as a collection of functional classified nucleic binding proteins based on ligand type and mmCIF keywords, each entry in PNIDB contains a comprehensive list of following annotations:. As the chief actors within the cells, protein’s interaction with nucleic acid involves many vital activities that are extremely important in the cellular process, such as transcription, translation, and DNA repair,therefore, the study on nucleic acid-protein binding activities can help to uncover the network or even the mechanism of related cellular process.""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0389, edam:operation_0420, edam:operation_0478 ; sc:name "PNIDB" ; sc:url "http://server.malab.cn/PNIDB/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:19943959" ; sc:description "Quickly find nodes closest to a queried vertex in any protein network available from BioGRID or specified by the user." ; sc:featureList edam:operation_2464 ; sc:name "PNNS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gaussian.bu.edu/pnns.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:name "Taxon" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:name "Taxonomic classification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2732 ; sc:name "Family name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1870 ; sc:name "Genus name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2912 ; sc:name "Strain accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Taxonomic classification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3301 ; sc:citation ; sc:description "Compilation of all names of Bacteria and Archaea which have been validly published according to the Bacteriological Code since 1. Jan. 1980, and nomenclatural changes which have been validly published since." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Prokaryotic Nomenclature up-to-date (PNU)" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "bacdive" ; sc:softwareHelp ; sc:url "http://bacdive.dsmz.de/api/pnu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3379, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9754976", "pubmed:36531584" ; sc:description "Primary Open-Angle Glaucoma Diagnosis from Optic Disc Photographs Using a Siamese Network." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "POAGNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bionlplab/poagnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0203, edam:topic_0749 ; sc:citation "pubmed:15215385", "pubmed:16845065" ; sc:description "POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists." ; sc:featureList edam:operation_0335, edam:operation_0438 ; sc:name "POBO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ekhidna.biocenter.helsinki.fi/poxo/pobo/" ; biotools:primaryContact "POBO Webmaster" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1476 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0209, edam:topic_3382, edam:topic_3534 ; sc:citation , "pmcid:PMC10148677", "pubmed:37086438" ; sc:description "Tool for the refinement of protein-ligand binding site shape from alpha spheres." ; sc:featureList edam:operation_2575, edam:operation_3216, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pocket Concavity" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/genki-kudo/Pocket-to-Concavity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:21910474" ; sc:description "Combined geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures." ; sc:featureList edam:operation_0477 ; sc:name "PocketAnalyzerPCA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/papca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:22618878" ; sc:description "PocketAnnotate performs binding site level annotation of query proteins." ; sc:featureList edam:operation_0224, edam:operation_0445, edam:operation_2575 ; sc:name "PocketAnnotate" ; sc:url "http://proline.biochem.iisc.ernet.in/pocketannotate/" ; biotools:primaryContact "Nagasuma Chandra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:17949996" ; sc:description "Algorithm for finding binding site (pockets) in protein structures." ; sc:featureList edam:operation_2479, edam:operation_2575 ; sc:name "PocketDepth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proline.physics.iisc.ernet.in/pocketdepth/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:22080553" ; sc:description "To assist in understanding the flexible protein-ligand interactions, we constructed this tool, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. 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Bassen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0208 ; sc:description "Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies." ; sc:featureList edam:operation_0224, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "pogos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pogos.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203 ; sc:citation "pubmed:19407353" ; sc:description "Visualization tool for the PointCloud and Virtual Embryo data sets. 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To use the macro, download 'Poji.ijm' and install it in Fiji or ImageJ. You may optionally download and install the 'Split and Save Channels.ijm' file to correctly set up the files before using Poji. Also deposited are several premade Excel-tables for faster analysis of the output of Poji and two different image sets as test data for the use of Poji. For general use of macro, please refer to 'Userguide.pdf'.""" ; sc:featureList edam:operation_3359, edam:operation_3431 ; sc:name "Poji" ; sc:url "https://github.com/roherzog/Poji" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0634, edam:topic_3120, edam:topic_3676 ; sc:citation ; sc:description "Pokemon is a structure based variance component test for studying rare variants" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "POKEMON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bushlab-genomics/POKEMON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0769, edam:topic_3474 ; sc:citation , "pubmed:33715003" ; sc:description "Poky is a software suite for multidimensional NMR and 3D structure calculation of biomolecules. The Poky suite is a superset and enhanced version of popular software packages supported by new integrated programs. It provides automated and visualized platforms for various essential tasks such as resonance assignments, structure calculation, dynamics studies, and more. It is not only a significant advance in the research platform but also a new software platform for convenient technology development. In the technology development platform, its new extensible and scalable features by scripting and batching will enable users to freely use the offered automated analysis templates and build their own library sets to keep up with the rapid pace of technology." ; sc:featureList edam:operation_0320, edam:operation_0337, edam:operation_3891 ; sc:name "Poky" ; sc:url "https://poky.clas.ucdenver.edu" ; biotools:primaryContact "Woonghee Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3299, edam:topic_3794 ; sc:citation , "pmcid:PMC8728242", "pubmed:34747466" ; sc:description "A resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs." ; sc:featureList edam:operation_0314, edam:operation_0443, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "Pol3Base" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rna.sysu.edu.cn/pol3base/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation "pmcid:PMC523650", "pubmed:8165140" ; sc:description "Identification of Polymerase III-transcribed elements in genomic sequences." ; sc:featureList edam:operation_0415 ; sc:name "Pol3scan" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-PARMA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/Percud/Pol3scan.git" ; biotools:primaryContact "Prof. Riccardo Percudani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3360 ; sc:citation ; sc:description """a Technique to Discover Single-cell Biomarker Using 2D Visual Information. In this work, we design the Polar Gini Curve (PGC) technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data. Theoretically, a Polar Gini Curve characterizes the shape and ‘evenness’ of cell-point distribution of cell-point set. To quantify whether a gene could be a marker in a cell cluster, we can combine two Polar Gini Curves: one drawn upon the cell-points expressing the gene, and the other drawn upon all cell-points in the cluster. We hypothesize that the closers these two curves are, the more likely the gene would be cluster markers. We demonstrate the framework in several simulation case-studies. Applying our framework in analyzing neonatal mouse heart single-cell data, the detected biomarkers may characterize novel subtypes of cardiac muscle cells""" ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_3802 ; sc:name "Polar Gini Curve" ; sc:url "https://figshare.com/projects/Polar_Gini_Curve/76749" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:33989151" ; sc:description "PolarMask is a tool for single shot instance segmentation with polar representation." ; sc:license "Apache-2.0" ; sc:name "PolarMask" ; sc:url "http://github.com/xieenze/PolarMask" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC9235478", "pubmed:35758773" ; sc:description "PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PolarMorphism" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UMCUGenetics/PolarMorphism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0601, edam:topic_0621, edam:topic_0820, edam:topic_2229 ; sc:citation , "pubmed:33186585" ; sc:description "A Database of Transmembrane and Secreted Proteins showing Apical-Basal Polarity." ; sc:featureList edam:operation_0417, edam:operation_2241, edam:operation_3802 ; sc:name "PolarProtDb" ; sc:url "http://polarprotdb.enzim.hu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0736, edam:topic_0820, edam:topic_2229, edam:topic_3375 ; sc:citation , "pmcid:PMC8384406", "pubmed:34185052" ; sc:description "Predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning." ; sc:featureList edam:operation_0238, edam:operation_0269, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PolarProtPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polarprotpred.ttk.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3053, edam:topic_3292 ; sc:citation "pubmed:21993301" ; sc:description "Polbase is a repository of biochemical, genetic, and structural information about DNA Polymerases." ; sc:featureList edam:operation_0282, edam:operation_0321, edam:operation_0477, edam:operation_2442 ; sc:name "Polbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polbase.neb.com/" ; biotools:primaryContact "Polbase Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """RNA-Seq analysis using approximate likelihood. Polee is an alternative methodology for the analysis of RNA-Seq data. A lot of RNA-Seq analyses do not consider the full likelihood, but instead take a two-step approach of first estimating transcript or gene expression then treating those estimates as observations in subsequent analysis. This is more efficient than a full probabilistic model encompassing all the reads in the experiment, but does not fully account for uncertainty. To overcome this shortcoming Polee makes a compact and efficient approximation of the likelihood function, and substitutes it in place of the real thing. The end result is more accurate analysis of RNA-Seq (e.g., differential expression) while remaining tractable on inexpensive computers.""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "Polee" ; sc:url "https://github.com/dcjones/polee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0769, edam:topic_2229 ; sc:citation , "pubmed:36792366" ; sc:description "A Nextflow workflow for polishing PacBio CLR genome assemblies" ; sc:featureList edam:operation_0310, edam:operation_3195 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "polishCLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/isugifNF/polishCLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3452 ; sc:citation , "pubmed:32221611" ; sc:description """Structural Studies by Electron Tomography and Image Processing. Image enhancement in FIB-SEM (Focused Ion Beam Scanning Electron Microscopy).""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552 ; sc:license "GPL-3.0" ; sc:name "PolishEM" ; sc:url "http://www.cnb.csic.es/%7ejjfernandez/polishem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3382, edam:topic_3474, edam:topic_3810, edam:topic_3934 ; sc:citation , "pmcid:PMC9653958", "pubmed:36362251" ; sc:description "An Open-Source Pollen Viability Status Recognition System Based on Deep Learning Neural Networks." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PollenDetect" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/Tanzhihao1998/Identification-of-pollen-activity/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3408 ; sc:citation , "pubmed:29742399" ; sc:description "An open-source software tool to study blood flow and cell-level biological activity during vessel morphogenesis." ; sc:featureList edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "PolNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mobernabeu/polnet" ; biotools:primaryContact "Miguel O. Bernabeu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621 ; sc:citation , "pubmed:32697830" ; sc:description """Polynomial Lasso Bagging for signed gene regulatory network inference from expression data. POLYNOMIAL LASSO BAGGING ALGORITHM FOR SIGNED GENE REGULATORY NETWORK INFERENCE. Code : The Python file PoLoBag.py can be run in Python 3.x (for Python 2.x just change the part for writing output to file at the end). Here degree d = 2 in the algorithm. Before running change the infilename parameter as per your static gene expression filename. The output will be a sorted edge list. The first column denotes regulator, the second column denotes target gene and the third column is a signed edge weight. The weights are normalized to have a maximum absolute value of 1. Edges with non-zero weights are sorted in the output list based on the absolute value of these weights.""" ; sc:featureList edam:operation_3435, edam:operation_3463, edam:operation_3659, edam:operation_3766, edam:operation_3802 ; sc:license "GPL-2.0" ; sc:name "PoLoBag" ; sc:url "https://github.com/gourabghoshroy/PoLoBag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3055 ; sc:citation "pubmed:16685720" ; sc:description "Program for polygenic analysis and power analysis of human quantitative traits. It is convenient to use this to analyze multiple models / traits in large pedigrees." ; sc:featureList edam:operation_2495 ; sc:name "POLY" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://csg.sph.umich.edu/chen/public/software/poly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0160, edam:topic_3407, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7671507", "pubmed:33151940" ; sc:description "A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species." ; sc:featureList edam:operation_0303, edam:operation_0428, edam:operation_2404 ; sc:name "Poly(A)-DG" ; sc:url "https://github.com/Szym29/PolyADG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7337927", "pubmed:32463457" ; sc:description """PolyA-miner is an accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization. More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR).""" ; sc:featureList edam:operation_2428, edam:operation_2436, edam:operation_3450 ; sc:name "PolyA-miner" ; sc:url "http://www.liuzlab.org/PolyA-miner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3511 ; sc:citation "pubmed:10231571" ; sc:description "Program for detection of human polyadenylation signals. To avoid training on possibly flawed data, the development of the program began with a de novo characterization of human mRNA 3′ processing signals. This information was used in training two quadratic discriminant functions that the program uses to evaluate potential polyA signals." ; sc:featureList edam:operation_0428 ; sc:name "polyadq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cb.utdallas.edu/tools/polyadq/polyadq_form.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3511 ; sc:citation "pubmed:23813000" ; sc:description "Predict the 12 main variants of human poly(A) motifs, i.e., AATAAA, ATTAAA, AAAAAG, AAGAAA, TATAAA, AATACA, AGTAAA, ACTAAA, GATAAA, CATAAA, AATATA, and AATAGA." ; sc:featureList edam:operation_0428 ; sc:name "PolyAMotif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sfb.kaust.edu.sa/Pages/Software.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3169 ; sc:citation "pubmed:24608116" ; sc:description "R package for ranking ChIP-seq peaks with shape information. polyaPeak uses a Bayesian hierarchical model to incorporate the peak shapes in the ranking. The shapes are described by a mixture of multivariate Polya distributions. Real data analyses show that polyaPeak outperforms several popular peak calling software including MACS, CisGenome and PICS." ; sc:featureList edam:operation_3222 ; sc:name "PolyaPeak" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web1.sph.emory.edu/users/hwu30/software/polyaPeak.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation "pubmed:19795571" ; sc:description "PolyApred is a support vector machine (SVM) based method for the prediction of polyadenylation signal (PAS) in human DNA sequence." ; sc:featureList edam:operation_2945 ; sc:name "polyapred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/polyapred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:35769001" ; sc:description "A user-friendly R package for measuring poly(A) tail length from NGS-based short-read and PacBio-based long-read sequencing data." ; sc:featureList edam:operation_0314, edam:operation_0428, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PolyAtailor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BMILAB/PolyAtailor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:10581034" ; sc:description "UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use." ; sc:featureList edam:operation_0484, edam:operation_0526, edam:operation_3197, edam:operation_3228 ; sc:name "PolyBayes" ; sc:url "http://clavius.bc.edu/~marth/PolyBayes/pages/main.html" ; biotools:primaryContact "Gabor Marth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:33586368" ; sc:description """An enhanced genomic variant classifier using extreme gradient boosting. PolyBoost is a post-analysis tool for the batch processing output of PolyPhen-2 that replaces the naive Bayes classifier with an extreme gradient boosting XGBoost classifier.""" ; sc:featureList edam:operation_3225, edam:operation_3359 ; sc:license "BSD-3-Clause" ; sc:name "PolyBoost" ; sc:url "https://github.com/djparente/polyboost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description """It is a pipeline to reconcile cluster solutions from multiple clustering algorithms. It allows the user to apply multiple clustering algorithms to a dataset, then performs multiple reconciliations to understand the relationships between the solutions.""" ; sc:featureList edam:operation_3432 ; sc:license "MIT" ; sc:name "polyClustR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/syspremed/polyClustR" ; biotools:primaryContact "Kate Eason" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0862 ; sc:name "Dotplot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw dotplots for all-against-all comparison of a sequence set." ; sc:featureList edam:operation_0490 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "polydot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/polydot.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0862 ; sc:name "Dotplot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Draw dotplots for all-against-all comparison of a sequence set." ; sc:featureList edam:operation_0490 ; sc:name "polydot (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/seqstats/emboss_polydot" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Displays all-against-all dotplots of a set of sequences." ; sc:featureList edam:operation_2403 ; sc:name "polydot WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/polydot.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "This package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression." ; sc:featureList edam:operation_3566 ; sc:license "Artistic-2.0" ; sc:name "polyester" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/polyester.html" ; biotools:primaryContact "Jack Fu", "Jeff Leek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0607, edam:topic_2269 ; sc:citation ; sc:description "Add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "Polyfit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Polyfit.html" ; biotools:primaryContact "Conrad Burden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0602, edam:topic_0736 ; sc:citation , "pmcid:PMC7714222", "pubmed:33270805" ; sc:description """An interactive visual simulator for distance-based protein folding. PolyFold is an interactive visual simulator for distance-based protein folding. The goal of PolyFold is to give both researchers and non-experts an intuitive and easy-to-use visual interface which elucidates the process of distance-based protein folding. PolyFold embeds powerful stochastic optimization algorithms with on-demand customizations and interactive manipulations in real-time to fold a protein molecule through the satisfaction of spatial constraints derived from a protein's inter-residue distance matrix.""" ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_0474, edam:operation_2415, edam:operation_2949 ; sc:license "GPL-3.0" ; sc:name "PolyFold" ; sc:url "https://github.com/Bhattacharya-Lab/PolyFold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0610, edam:topic_0625, edam:topic_3056 ; sc:citation , "pubmed:32648364" ; sc:description """A generalized framework for AMOVA with multiple hierarchies and ploidies. This software uses the genotypic frequencies under double-reduction to estimate the allele frequencies from allelic phenotypes for polyploids. The software performs a variety of population genetic analyses including genetic diversity analysis, phenotypic or genotypic distribution, linkage disequilibrium and genetic differentiation tests, genetic distance, principal coordinate and hierarchical clustering analyses, individual inbreeding coefficient, individual heterozygosity index and pairwise relatedness estimations, population assignment, parentage analysis, AMOVA and Bayesian clustering.""" ; sc:featureList edam:operation_0283, edam:operation_3196, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "polygene" ; sc:url "https://github.com/huangkang1987/polygene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_0781, edam:topic_2830 ; sc:citation "pubmed:18552348" ; sc:description "The datasets list genes, environmental risk factors and autoantibodies in a number of polygenic diseases and provide KEGG pathway analysis etched out by susceptibility genes. Host/pathogen interactions are also characterised for herpes simplex, helicobacter pylori and the HIV-1/AIDS virus." ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_2497, edam:operation_3461, edam:operation_3501 ; sc:name "PolygenicPathways" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.polygenicpathways.co.uk" ; biotools:primaryContact "C.J. Carter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "polyHap is a program for phasing polyploids and copy number regions. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences." ; sc:featureList edam:operation_3454 ; sc:name "polyHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "http://www.imperial.ac.uk/people/l.coin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3518 ; sc:citation , "pmcid:PMC9590153", "pubmed:36274121" ; sc:description "Haplotyping in polyploids based on bi-allelic marker dosage data." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PolyHaplotyper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/PolyHaplotyper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3053 ; sc:citation ; sc:description "Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents." ; sc:featureList edam:operation_0282 ; sc:name "polymapR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/polymapR/index.html" ; biotools:primaryContact "Peter Bourke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885 ; sc:citation , ; sc:description "An automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat. PolyMarker generates a multiple alignment between the target SNP sequence and the IWGSC chromosome survey sequences (IWGSC, 2014 ) for each of the three wheat genomes. It then generates a mask with informative positions which are highlighted with respect to the target genome." ; sc:featureList edam:operation_2419 ; sc:license "Not licensed" ; sc:name "PolyMarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polymarker.tgac.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_0659, edam:topic_2885 ; sc:citation "pubmed:22080514" ; sc:description "Polymorphism in microRNA Target Site (PolymiRTS) is a database of naturally occurring DNA variations in predicted and experimentally identified microRNA (miRNA) target sites. PolymiRTS aims to identify SNPs that might affect miRNA targeting in humans and mice." ; sc:featureList edam:operation_0282, edam:operation_0463, edam:operation_0484, edam:operation_3197, edam:operation_3232 ; sc:name "PolymiRTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.uthsc.edu/miRSNP/" ; biotools:primaryContact "Dr. Yan Cui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0749, edam:topic_3512, edam:topic_3517 ; sc:citation , "pmcid:PMC8860573", "pubmed:35061909" ; sc:description "Exploring functional relations among common human genetic variants." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "Polympact" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bcglab.cibio.unitn.it/polympact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Features Polynote is a different kind of notebook. It supports mixing multiple languages in one notebook, and sharing data between them seamlessly. It encourages reproducible notebooks with its immutable data model. (Learn more) Here are some of its unique features:""" ; sc:featureList edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "Polynote" ; sc:softwareVersion "0.5.0" ; sc:url "https://polynote.org/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0160, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC8633103", "pubmed:34849879" ; sc:description "A package for haplotype reconstruction in connected polyploid F1 populations." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_2944, edam:operation_3196, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PolyOrigin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/chaozhi/PolyOrigin.jl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:20354512" ; sc:description "Tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations." ; sc:featureList edam:operation_0331 ; sc:name "POLYPHEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetics.bwh.harvard.edu/pph2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_1775, edam:topic_3325, edam:topic_3473 ; sc:citation , , "pmcid:PMC2855889", "pmcid:PMC4480630", "pubmed:20354512", "pubmed:23315928" ; sc:description "Polymorphism Phenotyping (PolyPhen) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein." ; sc:featureList edam:operation_0477, edam:operation_1777, edam:operation_2422, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PolyPhen-2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetics.bwh.harvard.edu/pph2/" ; biotools:primaryContact "Ivan Adzhubey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0625, edam:topic_0749, edam:topic_3168 ; sc:citation "pubmed:9207020" ; sc:description "UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3185, edam:operation_3196 ; sc:name "PolyPhred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://droog.gs.washington.edu/polyphred/" ; biotools:primaryContact "Brent Ewing", "Phil Green" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "polyploid-genotyping" ; sc:softwareHelp ; sc:url "https://github.com/pblischak/polyploid-genotyping" ; biotools:primaryContact "Paul D Blischak" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0157, edam:topic_0196 ; sc:citation , "pmcid:PMC8812927", "pubmed:35073327" ; sc:description "Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3195, edam:operation_3198 ; sc:name "Polypolish" ; sc:softwareHelp ; sc:url "https://github.com/rrwick/Polypolish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_0634, edam:topic_0736, edam:topic_2815 ; sc:citation "pubmed:21059684" ; sc:description "Collection of sequences of all human proteins containing runs of seven or more glutamine residues and their annotated sequences with domain information. It can be interrogated such that the sequence context of polyglutamine repeats in disease and non-disease associated proteins can be investigated." ; sc:featureList edam:operation_0237, edam:operation_0246, edam:operation_0303, edam:operation_3431, edam:operation_3436 ; sc:name "PolyQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pxgrid.med.monash.edu.au/polyq" ; biotools:primaryContact "Ashley M. Buckle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3071, edam:topic_3305, edam:topic_3512 ; sc:citation , "pmcid:PMC10440501", "pubmed:37599593" ; sc:description """Integrated database on polyglutamine diseases. Information on the 9 known different diseases that result from increased number of CAG triplets.""" ; sc:featureList edam:operation_2421, edam:operation_3204 ; sc:license "CC-BY-4.0" ; sc:name "PolyQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://polyq.pt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0654 ; sc:citation , "pmcid:PMC8570814", "pubmed:34358315" ; sc:description "Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3232, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "polyqtlR" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://cran.r-project.org/package=polyqtlR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3452 ; sc:description "Toolbox for polyenergetic quantitative (polyquant) X-ray CT reconstruction with demos: including metal artifact and scatter correction." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Polyquant CT reconstruction toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71706-polyquant-ct-reconstruction-toolbox" ; biotools:primaryContact "Jonathan Mason" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3407 ; sc:citation , "pubmed:34329395" ; sc:description "Efficient random sampling in convex polytopes relies on a 'rounding' preprocessing step, in which the polytope is rescaled so that the width is as uniform as possible across different dimensions." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PolyRound" ; sc:url "https://gitlab.com/csb.ethz/PolyRound" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3324500", "pubmed:22509333" ; sc:description """A comprehensive database of microbial polysaccharide antigens and their antibodies. PolysacDB database has been developed to facilitate easy retrieval of information pertaining to microbial surface polysaccharides.""" ; sc:featureList edam:operation_2945 ; sc:name "polysacdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/polysacdb/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0602, edam:topic_0634, edam:topic_3172 ; sc:citation "pubmed:18487273" ; sc:description "PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences." ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0331, edam:operation_2422 ; sc:name "PolySearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/polysearch" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_2840, edam:topic_3053, edam:topic_3068 ; sc:citation , "pmcid:PMC4489268", "pubmed:25925572" ; sc:description "Significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more." ; sc:featureList edam:operation_3625 ; sc:name "PolySearch2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polysearch.cs.ualberta.ca/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3314 ; sc:citation , "pubmed:37022310" ; sc:description "General coarse-grained molecular dynamics polymerization scheme." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PolySMart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HMakkiMD/PolySMart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3293 ; sc:citation , "pmcid:PMC5576982", "pubmed:28186960" ; sc:description "Polyunphased is an extension to polytomous phenotypes of the Unphased package and is a flexible software tool for genetic association analysis in nuclear families." ; sc:featureList edam:operation_3194 ; sc:license "GPL-3.0" ; sc:name "Polyunphased" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/abureau/polyUnphased" ; biotools:primaryContact "Alexandre Bureau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2814 ; sc:citation "pubmed:15073023" ; sc:description "Protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs." ; sc:featureList edam:operation_0570, edam:operation_2464, edam:operation_2479 ; sc:name "POLYVIEW-2D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polyview.cchmc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0176, edam:topic_0736, edam:topic_3500 ; sc:citation "pubmed:15073023", "pubmed:20504857" ; sc:description "Integrate high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains are also integrated into the visualization." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0478, edam:operation_2429, edam:operation_2476 ; sc:name "POLYVIEW-MM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://polyview.cchmc.org/conform.html" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_3172, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC8279420", "pubmed:34197462" ; sc:description "POMAShiny is an user-friendly web-based workflow for metabolomics and proteomics data analysis." ; sc:featureList edam:operation_2939, edam:operation_3557, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "POMAShiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://142.93.143.140:3838/POMAShiny/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2305, edam:format_3003, edam:format_3007 ; sc:name "Nucleic acid features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3070, edam:topic_3168 ; sc:citation , , "pmcid:PMC9209812", "pubmed:32353878", "pubmed:35100366" ; sc:description "Comprehensive online database for fission yeast. PomBase provides comprehensive manual literature curation, annotation of genomic sequence and features, genome-wide data sets, and supports sophisticated user-defined queries." ; sc:featureList edam:operation_0224, edam:operation_0346, edam:operation_0362, edam:operation_2422, edam:operation_2944, edam:operation_3778 ; sc:name "PomBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://www.pombase.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2305, edam:format_2306, edam:format_3003, edam:format_3007 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:author "Ensembl team" ; sc:citation ; sc:description "Map your data to the current assembly." ; sc:featureList edam:operation_2944 ; sc:name "PomBase assembly converter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Tools/AssemblyConverter?db=core" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2572, edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "Ensembl Genomes team" ; sc:citation ; sc:description "Get a subset of data from a BAM | VCF." ; sc:featureList edam:operation_2121 ; sc:name "PomBase data slicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://genomebrowser.pombase.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1352 ; sc:name "Regular expression" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Kim Rutherford" ; sc:citation ; sc:description "Search PomBase protein set for a given motif." ; sc:featureList edam:operation_0239 ; sc:name "PomBase Motif search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "Sanger Institute" ; sc:softwareHelp , ; sc:softwareVersion "2" ; sc:url "https://www.pombase.org/motif_search" ; biotools:primaryContact "PomBase" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3499 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885 ; sc:author "Ensembl team" ; sc:citation ; sc:description "Upload a set of SNPs in our standard format and export a file containing consequence types." ; sc:featureList edam:operation_3225 ; sc:name "PomBase VEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://genomebrowser.pombase.org/tools.html" ; biotools:primaryContact "Ensembl Genomes webteam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:description "Implementation of a novel method specifically designed for quantifying exon-level gene expression in RNA-Seq." ; sc:featureList edam:operation_2495 ; sc:name "POME" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.stat.purdue.edu/~yuzhu/pome.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0621, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description """2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells. Pomegranate is a nuclear and whole-cell detection, reconstruction, and 3D segmentation tool for static images of fission yeast. See the Documentation folder for all user guides, tutorials and documentation. Included here are a quick start guide to get Pomegranate installed via the Hauf Lab update site, as well as the accompanying Pomegranate User Guide. The Pomegranate User Guide will contain a link to a repository containing samples images and outputs.""" ; sc:featureList edam:operation_3443, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "Pomegranate" ; sc:url "https://github.com/erodb/Pomegranate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_3518, edam:topic_3678 ; sc:citation "pubmed:19435879" ; sc:description "Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of information such as PubMed references, Gene Ontology terms, GO terms, etc." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:name "Pomelo II" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pomelo2.bioinfo.cnio.es" ; biotools:primaryContact "Ramon Diaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3391 ; sc:citation ; sc:description "POMO (Plotting Omics-associations for Multiple Organisms) is a web application to integrate and visualize genomic feature relationships and annotations across a broad range of organisms – human, mouse, nematode, fly, yeast, zebra fish, e. coli, arabidopsis, rice and tomato." ; sc:featureList edam:operation_0337 ; sc:name "POMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20140613" ; sc:url "http://pomo.cs.tut.fi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7898817", "pubmed:33560568" ; sc:description """Novel disease-associated variants, common sequence variants, and results from newborn screening. The Pompe disease GAA variant database represents an effort to collect all known variants in the GAA gene and is maintained and provide by the Pompe center, Erasmus MC.""" ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3196, edam:operation_3225 ; sc:name "Pompe" ; sc:url "http://www.pompevariantdatabase.nl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3174, edam:topic_3293, edam:topic_3697 ; sc:citation , "pmcid:PMC9665866", "pubmed:36179077" ; sc:description "Integrating phylogenetic and functional data in microbiome studies." ; sc:featureList edam:operation_0323, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "POMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gavinmdouglas/POMS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A method to predict changes in disorder regions contained in protein caused by amino acid substitutions." ; sc:featureList edam:operation_2423 ; sc:name "PON-Diso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://structure.bmc.lu.se/PON-Diso/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Predicts the pathogenicity of amino acid substitutions." ; sc:featureList edam:operation_3461 ; sc:name "PON-P2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://structure.bmc.lu.se/PON-P2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3371 ; sc:citation , "pubmed:27153720" ; sc:description "Prediction of effects of amino acid substitutions on protein solubility." ; sc:featureList edam:operation_0409 ; sc:name "PON-Sol" ; sc:softwareHelp ; sc:url "http://structure.bmc.lu.se/PON-Sol" ; biotools:primaryContact "Mauno Vihinen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:25190042" ; sc:description "Software package for automated protein 3D structure determination." ; sc:featureList edam:operation_0474, edam:operation_0570 ; sc:name "PONDEROSA-CS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ponderosa.nmrfam.wisc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:27283948" ; sc:description "Freely available software package for post-processing output from clustering inference using population genetic data" ; sc:featureList edam:operation_2497, edam:operation_3083 ; sc:name "pong" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://brown.edu/Research/Ramachandran_Lab/projects/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3510, edam:topic_3512 ; sc:citation "pubmed:14668245", "pubmed:16844984" ; sc:description "PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP." ; sc:featureList edam:operation_0252, edam:operation_0418 ; sc:name "PONGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pongo.biocomp.unibo.it/" ; biotools:primaryContact "Piero Fariselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3474 ; sc:citation "pubmed:23311589" ; sc:description "Estimate allele frequencies and detect selective sweeps, using NGS data from a sample of pooled individuals from the same population." ; sc:featureList edam:operation_3197 ; sc:name "Pool-hmm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=56&Itemid=63" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3056 ; sc:citation ; sc:description "Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3435, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "poolfstat" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/poolfstat/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:21264334" ; sc:description "Computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. In future version, haplotype unknown analysis will be supported." ; sc:featureList edam:operation_0487, edam:operation_3658 ; sc:name "PoolHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Gregor-Mendel-Institute/poolhap" ; biotools:primaryContact "Quan Long" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:21264334" ; sc:description "Computer program that infers haplotype (or epitype in case of DNA methylation sequencing) from a pool. In its current release, only pathogen sequencing application is implemented. In pathogen studies utilizing next generation sequencing, investigators ofte n collect samples naturally as pools of multiple strains, e.g., when the samples are taken from patients’ blood. To analyze these types of within-host polymorphisms, one would ideally like to determine the haplotypes in the sample." ; sc:featureList edam:operation_0487 ; sc:name "PoolHap2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/poolhap2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0781, edam:topic_3168 ; sc:citation "pubmed:25359889" ; sc:description "Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling." ; sc:featureList edam:operation_2403, edam:operation_3197 ; sc:name "Pooling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://alan.cs.gsu.edu/NGS/?q=content/pooling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:23730833" ; sc:description "Program implementing a Markov Chain Monte Carlo algorithm to sample the posterior distribution of the different parameters underlying the Bayesian hierarchical model. It is primarily aimed at estimating in Pool-Seq experiment the effective diploid size of pools/replicates (e.g. identified by molecular barcodes) from SNP allele count data. Note that each pool (or replicate) are assumed to originate from the same population." ; sc:featureList edam:operation_0296 ; sc:name "poolne_estim" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www1.montpellier.inra.fr/CBGP/software/PoolSeqUtils/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:34982676" ; sc:description "Exploring the Potential of Pooling for Salient Object Detection." ; sc:featureList edam:operation_0479, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PoolNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/backseason/PoolNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0625, edam:topic_2885 ; sc:citation , "pubmed:31804671" ; sc:description "PopSTR - A Population based microsatellite genotype enables clinical and population-scale genotyping of microsatellites." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "popSTR2" ; sc:url "https://github.com/DecodeGenetics/popSTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053 ; sc:description "Computer package to estimate historical demographic parameters of closely related species/populations (e.g. population size, migration rate, mutation rate, recombination rate, splitting events) within a Isolation with migration model. The software performs coalescent simulation in the framework of approximate Bayesian computation. It can also be used to perform Bayesian model choice to discriminate between different demographic scenarios." ; sc:featureList edam:operation_3359 ; sc:name "popABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://code.google.com/p/popabc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3056, edam:topic_3796 ; sc:citation ; sc:description "A population genetic genome browser for grain amaranths and their wild relatives." ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3208, edam:operation_3227 ; sc:license "CC0-1.0" ; sc:name "PopAmaranth" ; sc:url "http://amaranthgdb.org/popamaranth.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation , "pmcid:PMC9728135", "pubmed:36507898" ; sc:description "Patch Order Prediction and Appearance Recovery for Self-supervised Medical Image Analysis." ; sc:featureList edam:operation_0479, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "POPAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://GitHub.com/JLiangLab/POPAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3305, edam:topic_3315, edam:topic_3324 ; sc:citation , "pmcid:PMC8478209", "pubmed:34473700" ; sc:description "PopART-IBM an individual-based model for simulating HIV epidemic in high-prevalence settings, as used in the HPTN 071 (PopART) trial." ; sc:featureList edam:operation_2426, edam:operation_3799, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PopART-IBM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BDI-pathogens/POPART-IBM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3056 ; sc:citation "pubmed:24027417" ; sc:description "Comprehensive set of computational tools for evolutionary analysis of whole-genome alignments consisting of multiple individuals, from multiple populations or species." ; sc:featureList edam:operation_0323, edam:operation_2238, edam:operation_2495 ; sc:name "POPBAM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://popbam.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3053, edam:topic_3056, edam:topic_3365 ; sc:citation "pubmed:21564908" ; sc:description "Newly-developed population genetic data analysis program. It calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures." ; sc:featureList edam:operation_2403, edam:operation_3478 ; sc:name "POPDIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genetics.agrsci.dk/~bernt/popgen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3421, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC7438201", "pubmed:32874057" ; sc:description """Risk prediction platform for pancreatic fistula after pancreatoduodenectomy using artificial intelligence. Risk Prediction Platform for Postoperative Pancreatic Fistula (POPF).""" ; sc:featureList edam:operation_3557 ; sc:name "POPF" ; sc:url "http://popfrisk.smchbp.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3056 ; sc:citation "pubmed:26002882" ; sc:description "Web-based browser that can conveniently show the results of population analysis." ; sc:featureList edam:operation_0484, edam:operation_3658 ; sc:name "PopGeV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.soyomics.com/popgev/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:citation , "pmcid:PMC8668730", "pubmed:34938457" ; sc:description "An R package to assess the sustainability of harvesting regimes of bird populations." ; 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sc:citation , "pmcid:PMC8728255", "pubmed:34664660" ; sc:description "An interactive application for the functional characterization and prioritization of adaptive genomic variants in humans." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PopHumanVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pophumanvar.uab.cat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "POPI is a SVM-based prediction server using informative physicochemical properties for predicting immunogenicity of binding peptides of MHC class I and II." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "POPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; 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sc:license "GPL-2.0" ; sc:name "PopIns2" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/kehrlab/PopIns2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0804 ; sc:citation "pubmed:22085524" ; sc:description "Support vector machine and weighted degree string kernel to predict immunogenicity of HLA-A2 binding peptides." ; sc:featureList edam:operation_1777, edam:operation_2479 ; sc:name "POPISK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://140.113.239.45/POPISK/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3652 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; 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SNPMuSiC predicts whether protein variants are deleterious or benign due to stability issues, thus providing a molecular-level interpretation of disease phenotype.""" ; sc:featureList edam:operation_0250, edam:operation_0331, edam:operation_2430 ; sc:name "MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC" ; sc:url "http://dezyme.com/" ; biotools:primaryContact "Dezyme Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:21253599" ; sc:description "Toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals." ; sc:featureList edam:operation_3197 ; sc:name "PoPoolation" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/popoolation/" ; biotools:primaryContact "Robert Kofler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3056 ; sc:citation ; sc:description "PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. 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By clustering these distances into ‘within-strain’ and ‘between-strain’ distances a network of within-strain comparisons can be constructed." ; sc:featureList edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PopPUNK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/johnlees/PopPUNK" ; biotools:primaryContact "John Lees" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166 ; sc:citation "pubmed:12087181", "pubmed:12824328" ; sc:description "Algorithm to calculate accessible surfaces areas at atomic and residue level." ; sc:featureList edam:operation_0384, edam:operation_0387, edam:operation_1816, edam:operation_2950 ; sc:name "POPS" ; sc:url "http://mathbio.nimr.mrc.ac.uk/wiki/POPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0128 ; sc:citation "pubmed:16108084" ; sc:description "Computational tool for modeling and predicting protease specificity. It provides a novel method for building computational models of protease specificity, which while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user." ; sc:featureList edam:operation_1777, edam:operation_2479 ; sc:name "PoPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pops.csse.monash.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0602 ; sc:citation "pubmed:15980485" ; sc:description "POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed." ; sc:featureList edam:operation_0234, edam:operation_0384, edam:operation_0387, edam:operation_1816 ; sc:name "POPSCOMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://mathbio.crick.ac.uk/wiki/POPSCOMP" ; biotools:primaryContact "Franca Fraternali", "Jens Kleinjung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:35662457" ; sc:description "A R Package for Pre-processing and Quality Control Analysis of Single Cell RNA-seq Data." ; sc:featureList edam:operation_2428, edam:operation_3223, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "popsicleR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bicciatolab/popsicleR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293 ; sc:citation "pubmed:24603277" ; sc:description "Program for making population trees from allele frequency data." ; sc:featureList edam:operation_2238, edam:operation_2403 ; sc:name "POPTREE" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.kms.ac.jp/~genomelb/takezaki/poptree2/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3385 ; sc:citation , "pmcid:PMC4795740", "pubmed:26987120" ; sc:description "PopulationProfiler is a software tool that reduces per-cell measurements to population statistics. 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sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "A Code for Deterministic and Systematic Analyses of Porosities." ; sc:license "Apache-2.0" ; sc:name "porE" ; sc:url "https://github.com/kaitrepte/porE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:description "Calculates the pore size distribution of 2D porous media images by watershed segmentation algorithm" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Pore size distribution of 2D porous media images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50623-pore-size-distribution-of-2d-porous-media-images" ; biotools:primaryContact "Arash Rabbani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622 ; sc:citation , "pmcid:PMC9869717", "pubmed:36698762" ; sc:description "Porechop_ABI (ab initio) is an extension of Porechop whose purpose is to process adapter sequences in ONT reads." ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3237, edam:operation_3472, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Porechop_ABI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.5.0" ; sc:url "https://github.com/bonsai-team/Porechop_ABI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0820 ; sc:citation ; sc:description "An automated tool for the visualization of sequence and conservation of pore-lining residues in transmembrane protein structures." ; sc:featureList edam:operation_0564, edam:operation_2241 ; sc:name "PoreLogo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/software/PoreLogo/" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25143291" ; sc:description "Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis." ; sc:featureList edam:operation_2478 ; sc:name "Poretools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/arq5x/poretools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0820, edam:topic_2814 ; sc:citation ; sc:description "A fully automated method designed to detect and characterise transmembrane protein channels from their 3D structure." ; sc:featureList edam:operation_0270 ; sc:name "PoreWalker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/software/PoreWalker/" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0621, edam:topic_0659, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34226915" ; sc:description "An approach for accurate prediction of RNA pseudouridine sites." ; sc:featureList edam:operation_0443, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "Porpoise" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://web.unimelb-bioinfortools.cloud.edu.au/Porpoise/" . a sc:SoftwareApplication ; 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Our approach preprocesses the search space and builds an enhanced suffix array which is stored on file. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows to efficiently compute a matrix similarity threshold for a PSSM, given an E-value or a P-value." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "PoSSuMsearch" ; sc:operatingSystem "Linux" ; sc:provider "BiBiServ", "Bielefeld university", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bibiserv.cebitec.uni-bielefeld.de/possumsearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Michael Beckstette", "Robert Homann" ; sc:citation ; sc:description "Significant speedup of database searches with HMMs by search space reduction with PSSM family models." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:name "PoSSuMsearch2" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://bibiserv.cebitec.uni-bielefeld.de/possumsearch2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:description "Perform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor." ; sc:featureList edam:operation_3664 ; sc:license "GPL-2.0" ; sc:name "POST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/POST.html" ; biotools:primaryContact "Xueyuan Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3360, edam:topic_3697 ; sc:citation , "pmcid:PMC9171974", "pubmed:35668471" ; sc:description "Phylogeny-guided microbiome OTU-specific association test (POST)." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "POSTm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=POSTm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3475 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide mass fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation "pubmed:19253288" ; sc:description "Post-translational modification software." ; sc:featureList edam:operation_0417, edam:operation_2929, edam:operation_3441, edam:operation_3628, edam:operation_3645, edam:operation_3646, edam:operation_3695, edam:operation_3755 ; sc:name "POSTMan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uib.no/en/rg/probe/65847/postman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3474 ; sc:citation ; sc:description """Post-prediction inference. Many modern problems leverage machine learning methods to predict outcomes based on observable covariates. In the subsequent statistical modeling, e.g. to understand population trends in outcomes, often involves treating predicted outcomes as interchangeable with observed outcomes. 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Watson-Haigh", "Radoslaw Suchecki" ; sc:description "Web-based tool for integrating genetic map location with gene expression data and inferred functional annotation in wheat." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "POTAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Adelaide" ; sc:softwareHelp ; sc:url "https://github.com/CroBiA/potage" ; biotools:primaryContact "Nathan S. Watson-Haigh", "Radoslaw Suchecki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0203, edam:topic_0780 ; sc:citation ; sc:description "Visualisation tool for speeding up gene discovery in wheat." ; sc:featureList edam:operation_0571 ; sc:license "CC-BY-4.0" ; sc:name "POTAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crobiad.agwine.adelaide.edu.au/potage/" ; biotools:primaryContact "Rad Suchecki" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:25450216" ; sc:description "Post-Translational Modifications Mass Spectrometry Calculator is a free web application that simplifies mass spectrometry calculations for post-translationally modified (PTM) proteins. The application is able to calculate: a) the kind, the number and the combinations of possible PTMs for a peptide or protein sequence and the corresponding mass, b) the charge of a peptide, protein or protein fragment in their modified or unmodified state, c) the protein fragments produced upon proteolytic cleavage of PTM modified proteins and their masses. A particular focus is on PTM-modified histones. A histone variant browser is included in the web application. It could be useful in analysis of mass-spec data for epigenetically modified histones and other proteins." ; sc:featureList edam:operation_3645 ; sc:name "POTAMOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v2.0" ; sc:url "https://potamos.med.uoi.gr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0736, edam:topic_0769, edam:topic_3318 ; sc:citation ; sc:description "An automated pipeline for batch analysis of optical tweezers data." ; sc:featureList edam:operation_0279, edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "POTATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/REMI-HIRI/POTATO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3569 ; sc:citation "pubmed:23361985" ; sc:description "MATLAB toolbox for mechanistic mathematical modeling. It allows reaction network or ordinary differential equation (ODE) based modeling." ; sc:featureList edam:operation_2426 ; sc:name "PottersWheel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.potterswheel.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0637 ; sc:citation ; sc:description "Pout2Prot converts Percolator output files to protein group and subgroup files using Occam's razor or anti-Occam's razor. These output files can directly be used in Prophane for further downstream taxonomic and functional analysis" ; sc:featureList edam:operation_3460, edam:operation_3637, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Pout2Prot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pout2prot.ugent.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3056, edam:topic_3301, edam:topic_3517 ; sc:citation ; sc:description "A next-generation homoplasy counting method for genome-wide association studies." ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_0488, edam:operation_3196, edam:operation_3227, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "POUTINE" ; sc:url "https://github.com/Peter-Two-Point-O/POUTINE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0157, edam:topic_0769, edam:topic_3293 ; sc:citation "pubmed:15980533" ; sc:description "The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences." ; sc:featureList edam:operation_0258, edam:operation_0492, edam:operation_0499, edam:operation_0550 ; sc:name "POWER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://power.nhri.org.tw/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3304, edam:topic_3379 ; sc:citation , "pubmed:32673043" ; sc:description "Optimising sample size and precision in experimental psychology and human neuroscience." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:name "power contours" ; sc:url "https://shiny.york.ac.uk/powercontours/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3295, edam:topic_3305, edam:topic_3674 ; sc:citation ; sc:description """This tool is for maximizing power and sensitivity to identify between-group differences in DNA methylation. Scripts for POWEREDBiSeq, a tool which estimates power in bisulfite sequencing (BS) studies. To use POWEREDBiSeq, you must first download the script POWEREDBiSeqFunctions.R In R, set the working directory to the folder that contains it and run source("POWEREDBiSeqFunctions.R").""" ; sc:featureList edam:operation_3186, edam:operation_3230, edam:operation_3695, edam:operation_3919 ; sc:name "POWEREDBiSeq" ; sc:url "https://github.com/ds420/POWEREDBiSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3517 ; sc:citation ; sc:description """An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. Power and sample size calculation for eQTL analysis based on ANOVA or simple linear regression. It can also calculate power/sample size for testing the association of a SNP to a continuous type phenotype.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3659, edam:operation_3791 ; sc:license "GPL-2.0" ; sc:name "powerEQTL" ; sc:url "https://bwhbioinfo.shinyapps.io/powerEQTL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3169, edam:topic_3170 ; sc:description "Estimate and predict power among groups and multiple sample sizes with simulated data, the simulations are operated based on distribution parameters estimated from the provided input dataset." ; sc:featureList edam:operation_2424, edam:operation_3741 ; sc:license "Artistic-2.0" ; sc:name "PowerExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PowerExplorer.html" ; biotools:primaryContact "Xu Qiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_1317 ; sc:author ; sc:citation , ; sc:contributor "European FP7 e-Infrastructure grant, WeNMR, grant no. 261572", "European H2020 e-Infrastructure grant, BioExcel, grant no. 675728", "European H2020 e-Infrastructure grant, EGI-Engage, grant no. 654142", "European H2020 e-Infrastructure grant, INDICO-DataCloud, grant no. 653549", "European H2020 e-Infrastructure grant, West-Life VRE, grant no. 675858", "Netherlands Organization for Scientific Research (NWO) , TOP-PUNT grant no. 718.015.001", "Netherlands Organization for Scientific Research (NWO), ECHO grant no.711.011.009", "Netherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442" ; sc:description "Automatically fit high-resolution atomic structures into cryo-EM densities. Perform a full-exhaustive 6-dimensional cross-correlation search between the atomic structure and the density." ; sc:featureList edam:operation_2406 ; sc:funder "European FP7 e-Infrastructure grant, WeNMR, grant no. 261572", "European H2020 e-Infrastructure grant, BioExcel, grant no. 675728", "European H2020 e-Infrastructure grant, BioExcel, grant no. 823830", "European H2020 e-Infrastructure grant, EGI-Engage, grant no. 654142", "European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536", "European H2020 e-Infrastructure grant, INDICO-DataCloud, grant no. 653549", "European H2020 e-Infrastructure grant, West-Life VRE, grant no. 675858", "Netherlands Organization for Scientific Research (NWO) , TOP-PUNT grant no. 718.015.001", "Netherlands Organization for Scientific Research (NWO), ECHO grant no.711.011.009", "Netherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442" ; sc:license "Apache-2.0" ; sc:name "PowerFit web portal" ; sc:operatingSystem "Linux", "Mac" ; sc:provider , "Utrecht University", "http://uu.nl" ; sc:softwareHelp , , , , ; sc:softwareVersion "2.0" ; sc:url "http://milou.science.uu.nl/services/POWERFIT" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:18200600" ; sc:description "Code for approximate power calculations for identification of gene x gene and gene x environment interactions in genomewide association studies using a two-stage analysis." ; sc:featureList edam:operation_2423 ; sc:name "powerGWASinteraction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kooperberg.fhcrc.org/soft.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation "pubmed:17283440" ; sc:description "SAS Macro for power calculations for genetic association tests exploiting gene-environment interaction." ; sc:featureList edam:operation_2423 ; sc:name "PowerGxE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hsph.harvard.edu/peter-kraft/software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063 ; sc:citation ; sc:description "This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "powerTCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/powerTCR.html" ; biotools:primaryContact "Hillary Koch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3342, edam:topic_3360, edam:topic_3416 ; sc:citation ; sc:description "A web based user-friendly tool for future translational study design." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "PowerTools" ; sc:url "https://joelarkman.shinyapps.io/PowerTools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:32186690" ; sc:description """an R package for power assessment in microbiome case-control studies. power assessment in microbiome case-control studies. Power analysis is essential to decide the sample size of metagenomic sequencing experiments in a case-control study for identifying differentially abundant microbes. However, the complexity of microbiome data characteristics such as excessive zeros, over-dispersion, compositional effect, intrinsically microbial correlations and variable sequencing depths makes the power analysis particularly challenging as the analytical form is usually unavailable. Here, we develop a simulation-based strategy and R package powmic to estimate the empirical statistical power while considering the complexity of data characteristics.""" ; sc:name "powmic" ; sc:url "https://github.com/lichen-lab/powmic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518, edam:topic_3934 ; sc:citation , "pubmed:32614380" ; sc:description """Simulation, power evaluation and sample size recommendation for single-cell RNA-seq. POWSC: A computational tool for power evaluation and sample size estimation in scRNA-seq. POWSC is a R package designed for scRNA-seq with a wild range of usage. It can play three roles: parameter estimator, data simulator, and power assessor. As the parameter estimator, POWSC accurately captures the characterized parameters (Fig.B) for any specific cell type from a given real expression data (Fig.A). As the data simulator, POWSC generates sythetic data (Fig.C) based on a rigorous simulation mechanism incluidng zero expression values. As the power assessor, POWSC performs comprehensive power analysis and reports the stratified targeted powers (Fig.D) for two forms of DE genes. A schemetic overview of the aglorithm is shown in (Fig.E). All the copyrights are explaned by Kenong Su kenong.su@emory.edu and Dr. Wu's lab http://www.haowulab.org.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3454 ; sc:name "POWSC" ; sc:url "https://github.com/suke18/POWSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation "pubmed:15215385", "pubmed:15980504", "pubmed:15987504", "pubmed:16845065" ; sc:description "POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes." ; sc:featureList edam:operation_3463, edam:operation_3766 ; sc:name "POXO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfo.biocenter.helsinki.fi/poxo" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation "pubmed:25172924" ; sc:description "Server which helps you in predicting the binding affinity of protein-protein complex of your interest." ; sc:featureList edam:operation_2464, edam:operation_2479 ; sc:name "PPA-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iitm.ac.in/bioinfo/PPA_Pred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:name "Chemical formula" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3373, edam:topic_3379 ; sc:citation , "pubmed:36301791" ; sc:description "Personalized Propagation Auto-Encoder Model For Predicting Drug-Target Interactions." ; sc:featureList edam:operation_2489, edam:operation_2492, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "PPAEDTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://120.77.11.78/PPAEDTI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0659, edam:topic_3168, edam:topic_3474 ; sc:citation , , "pmcid:PMC7285591", "pubmed:32517696" ; sc:description """PPAI is a web server for predicting protein-aptamer interactions. The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is very important and feasible to construct an accurate computational model to predict protein-aptamer interactions, which is benefit for understanding mechanisms of protein-aptamer interactions and improving aptamer-based therapies. PPAI is a novel web-server to predict aptamers and protein-aptamer interactions with sequence features of proteins/aptamers and machine learning framework which integrated Adaboost and Random Forest. PPAI not only provides more accurate prediction functions, but also provides the protein aptamer information to the user for query.""" ; sc:featureList edam:operation_0224, edam:operation_0253, edam:operation_2492, edam:operation_3092 ; sc:name "PPAI" ; sc:url "http://39.96.85.9/PPAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623, edam:topic_2269, edam:topic_2275 ; sc:citation , "pmcid:PMC8191105", "pubmed:34112081" ; sc:description "PPalign aligns Potts models and corresponding sequences / alignments" ; sc:featureList edam:operation_0300, edam:operation_0303, edam:operation_0477, edam:operation_0491, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "PPalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www-dyliss.irisa.fr/ppalign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2258, edam:topic_3343 ; sc:citation ; sc:description "web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data." ; sc:featureList edam:operation_0482 ; sc:name "PPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gdbtools.unibe.ch:8080/PPB/" ; biotools:primaryContact "Jean-Louis Reymond" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2640 ; sc:citation , "pmcid:PMC10182850", "pubmed:37140547" ; sc:description "ProteinPaint BAM track for read alignment visualization and variant genotyping." ; sc:featureList edam:operation_0337, edam:operation_0495, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "ppBAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://proteinpaint.stjude.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602 ; sc:citation "pubmed:9789102" ; sc:description "Versatile dotmatrix program for the Apple Macintosh, optimized for the PowerPC." ; sc:featureList edam:operation_2451, edam:operation_2479 ; sc:name "PPCMatrix" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://www.bionut.ki.se/groups/tbu/software/#PPCMatrix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0749, edam:topic_3512 ; sc:citation , "pubmed:33539888" ; sc:description "PPD-Prokaryotic Promoter Database: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters." ; sc:featureList edam:operation_0440, edam:operation_2421 ; sc:name "PPD" ; sc:url "http://lin-group.cn/database/ppd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2840, edam:topic_3810 ; sc:citation , "pubmed:34061455" ; sc:description "The PPDB is a comprehensive relational database of pesticide chemical identity, physicochemical, human health and ecotoxicological data." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree false ; sc:license "Not licensed" ; sc:name "PPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sitem.herts.ac.uk/aeru/ppdb/en/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC7394329", "pubmed:30717654" ; sc:description "This server is made in order to provide an easy webserver to calculate FNAT, L-RMSD and I-RMSD values of docked and original poses of protein-peptide complexes." ; sc:featureList edam:operation_2945 ; sc:name "ppdbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/ppdbench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0593, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC6977024", "pubmed:31984271" ; sc:description """A Server for Predicting Long-Distance Energetic Couplings and Mutation-Induced Stability Changes in Proteins via Perturbations. Extracting Energetic Couplings and Destabilization Thermodynamics via Perturbations. pPerturb provides a rapid and experimentally consistent measure of the extent to which a particular residue is coupled to its neighbors till a distance of nearly 12-15 Å, considering both the first- and second-shell of interactions. The server can be used as a first step to explore the strength of the interaction network around a particular residue. A functional form of the percolation within the interaction network will also be provided to the user.""" ; sc:featureList edam:operation_0269, edam:operation_0331, edam:operation_2476, edam:operation_3094, edam:operation_3799 ; sc:name "pPerturb" ; sc:url "http://pbl.biotech.iitm.ac.in/pPerturb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "PPFINDER is a Perl-based procedure for finding processed pseudogenes in genome annotations (GTF format). PPFINDER identifies pseudogenes using two different methods, and creates a GTF file with pseudogene coordinates that can be used for masking the genome sequence. In gene prediction mode, PPFINDER will mask out the genomic sequence and rerun gene prediction. Rounds of pseudogene masking and gene prediction are iterated until convergence." ; sc:featureList edam:operation_2423, edam:operation_2454 ; sc:name "PPFINDER" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0" ; sc:url "http://mblab.wustl.edu/software.html#ppfinderLink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation , ; sc:description "Predicts the consensus secondary structure of RNA alignments." ; sc:featureList edam:operation_0278 ; sc:name "PPfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "3.1.1" ; sc:url "http://www.daimi.au.dk/~compbio/pfold/downloads.html#release" ; biotools:primaryContact "Zsuzsanna Sukosd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2814, edam:topic_3500 ; sc:citation "pubmed:15980481" ; sc:description "Tool for making pictures (and animations) of protein structures from PDB files." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_0570 ; sc:name "PPG" ; sc:url "http://bioserv.rpbs.univ-paris-diderot.fr/services/PPG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3452 ; sc:citation , "pmcid:PMC10292016", "pubmed:37378045" ; sc:description "MATLAB toolbox for extracting PPG fiducial points." ; sc:featureList edam:operation_0337, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PPGFeat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/132688-ppgfeat?s_tid=prof_contriblnk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3335 ; sc:citation , "pmcid:PMC7668389", "pubmed:33224967" ; sc:description """An Innovative Toolbox for Synthesizing Regular and Irregular Photoplethysmography Waveforms. Photoplethysmography (PPG) is increasingly used in digital health, exceptionally in smartwatches. The PPG signal contains valuable information about heart activity, and there is lots of research interest in its means and analysis for cardiovascular diseases. Unfortunately, to our knowledge, there is no arrhythmic PPG dataset publicly available-this paper attempt to provide a toolbox that can generate synthesized arrhythmic PPG signals. The model of a single PPG pulse in this toolbox utilizes two combined Gaussian functions. This toolbox supports synthesizing PPG waveform with regular heartbeats and three irregular heartbeats: compensation, interpolation, and reset""" ; sc:name "PPGSynth" ; sc:url "https://github.com/Elgendi/PPG-Synthesis/tree/master/code" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation ; sc:description "HyPPI classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. Permanent protein-protein complexes are only stable in their complexed state and the subunits would denature upon complex dissociation. Transient protein-protein complexes are stable in the complexed form as well as in the monomeric depending of the necessary function of the complex. Crystal artifacts have no biological function and are artifically formed during crystallization process. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface (ΔGHydrophobic) and the quotient of interface area ratios (IF-quotient). The IF-quotient takes the symmetry of the protein-protein interface into account." ; sc:featureList edam:operation_2406, edam:operation_2492 ; sc:name "HyPPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Hamburg - Center for Bioinformatics" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de/#ppi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_3474 ; sc:citation , "pubmed:35654412" ; sc:description "A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity." ; sc:featureList edam:operation_0337, edam:operation_2464, edam:operation_2492, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "PPI-Affinity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://protdcal.zmb.uni-due.de/PPIAffinity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0634, edam:topic_3520, edam:topic_3957 ; sc:citation , "pmcid:PMC8281810", "pubmed:34277709" ; sc:description "An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data." ; sc:featureList edam:operation_2464, edam:operation_2476, edam:operation_2492, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "PPI-MASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://minicad.appsbio.utalca.cl/ppi-mass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0160, edam:topic_0166, edam:topic_2830 ; sc:citation , "pubmed:36448715" ; sc:description "A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method." ; sc:featureList edam:operation_0239, edam:operation_0479, edam:operation_2421, edam:operation_2492, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PPI-Miner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bailab.siais.shanghaitech.edu.cn/services/ppi-miner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154 ; sc:citation ; sc:description "The PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences." ; sc:featureList edam:operation_2479 ; sc:name "PPI-PS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://faculty.uaeu.ac.ae/nzaki/PPI_PS.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0176, edam:topic_2275, edam:topic_2814 ; sc:citation , "pubmed:32621223" ; sc:description """Template-Based Modeling of Protein Complexes Using the PPI3D Web Server. Search, Analyse and Model Protein Interactions in 3D. Welcome to PPI3D − a web server for searching, analyzing and modeling protein interactions in the context of 3D structures.""" ; sc:featureList edam:operation_0477, edam:operation_2492, edam:operation_2575, edam:operation_3432, edam:operation_3899 ; sc:name "PPI3D" ; sc:url "http://bioinformatics.lt/ppi3d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108 ; sc:citation "pubmed:17239823" ; sc:description "Program for evaluation and design for high-level expression of foreign genes in pPIC9 vector." ; sc:featureList edam:operation_2423 ; sc:name "pPIC9" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.biosun.org.cn/ppic9/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0622, edam:topic_2259 ; sc:citation ; sc:description "Detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that." ; sc:featureList edam:operation_2949 ; sc:license "GPL-3.0" ; sc:name "PPICompare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/ppicompare/" ; biotools:primaryContact "Volkhard HelmsEmail author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0736, edam:topic_3318, edam:topic_3957 ; sc:citation ; sc:description "PPIDomainMiner is a tool for inferring domain-domain interactions from multiple sources of protein-protein interactions using tripartite graph modeling and vector similarity." ; sc:featureList edam:operation_3436, edam:operation_3767, edam:operation_3802 ; sc:name "PPIDomainMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ppidm.loria.fr/" ; biotools:primaryContact "Devignes Marie-Dominique" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3464, edam:format_3603 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3464, edam:format_3603 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128 ; sc:citation , "pubmed:30565464" ; sc:description "A web-based platform for building protein-protein interaction networks, performing clustering analyses according to protein abundances, and functional enrichment analyses." ; sc:featureList edam:operation_0276 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PPIExp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.fgvis.com/expressvis/PPIExp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0160, edam:topic_3474 ; sc:citation , "pmcid:PMC7158050", "pubmed:32293241" ; sc:description """a graph mining based detection of conserved structural arrangements in protein-protein interfaces. This document describes how run ppiGReMLIN. ppiGReMLIN is a scalable graph based strategy which models. protein-protein interfaces as graphs. Background: Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identification of drug targets.""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3899 ; sc:name "ppiGReMLIN" ; sc:url "https://ppigremlin.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3474, edam:topic_3542 ; sc:citation , "pmcid:PMC7029904", "pubmed:32218953" ; sc:description """Prediction of polyproline II secondary structure propensity in proteins. Please read the guide for details on how to tuse PPIIPred. Predicts polyproline II secondary structure from primary amino acid sequence using a bidirectional recurrent neural network. This can generate an alignment for an existing UNIPROT sequence and then run it through PPIIPred, instead of entering your own sequence (enter UNIPROT ID here).""" ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_2488 ; sc:name "PPIIPRED" ; sc:url "http://bioware.ucd.ie/PPIIPRED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , "pmcid:PMC4734591", "pubmed:26620522" ; sc:description "Protein-Protein Interaction database for Maize." ; sc:featureList edam:operation_2421 ; sc:name "PPIM" ; sc:softwareVersion "1.1" ; sc:url "http://comp-sysbio.org/ppim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2269 ; sc:citation ; sc:description "A network based statistical learning method to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. It identifies such proteins often involved in the same or similar biological functions." ; sc:featureList edam:operation_2436 ; sc:license "Artistic-2.0" ; sc:name "PPInfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PPInfer.html" ; biotools:primaryContact "Dongmin Jung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0128, edam:topic_0749, edam:topic_0769 ; sc:citation , "pmcid:PMC10290227", "pubmed:37359724" ; sc:description "Semantic integrative system for protein-protein interaction and application for host-pathogen datasets." ; sc:featureList edam:operation_0224, edam:operation_2492, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PPIntegrator" ; sc:url "https://github.com/YasCoMa/ppintegrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0202, edam:topic_2830, edam:topic_3047 ; sc:citation , "pubmed:31603323" ; sc:description "Exhaustive Repertoire of Druggable Cavities at Protein-Protein Interfaces of Known Three-Dimensional Structure." ; sc:featureList edam:operation_0478, edam:operation_2950, edam:operation_3351 ; sc:name "PPI" ; sc:url "http://drugdesign.unistra.fr/ppiome" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1930 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:30540478" ; sc:description "An automated software for identification of bioactive endogenous peptides" ; sc:featureList edam:operation_3631, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PPIP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Shawn-Xu/PPIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Predicting protein-protein interactions by combining heterogeneous features." ; sc:featureList edam:operation_2492 ; sc:name "ppiPre" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/src/contrib/Archive/ppiPre/" ; biotools:primaryContact "Lin Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0623, edam:topic_0736, edam:topic_3557 ; sc:citation "pubmed:19417070" ; sc:description "PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species." ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_0477, edam:operation_2464, edam:operation_3767 ; sc:name "PPISearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gemdock.life.nctu.edu.tw/ppisearch/" ; biotools:primaryContact "Dr. Jinn-Moon Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "Tools for the analysis of protein interaction data." ; sc:featureList edam:operation_2949 ; sc:license "Artistic-2.0" ; sc:name "ppiStats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ppiStats.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640 ; sc:citation "pubmed:23686313" ; sc:description "Novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome." ; sc:featureList edam:operation_3439 ; sc:name "PPISURV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioprofiling.de/GEO/PPISURV/ppisurv.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3320 ; sc:citation "pubmed:26508756" ; sc:description "Exploit expression data at the transcript-level and reveal alterations in protein connectivity caused by alternative splicing." ; sc:featureList edam:operation_3439 ; sc:name "PPIXpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ppixpress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_2275, edam:topic_3335, edam:topic_3474 ; sc:citation , "pubmed:31912313" ; sc:description """A Bioinformatics Tool for Predicting Peptide Ligands of Potassium Channels Based on Primary Structure Information. Potassium channels play a key role in regulating the flow of ions through the plasma membrane, orchestrating many cellular processes including cell volume regulation, hormone secretion and electrical impulse formation. Ligand peptides of potassium channels are molecules used in basic and applied research and are now considered promising alternatives in the treatment of many diseases, such as cardiovascular diseases and cancer. Currently, there are various bioinformatics tools focused on the prediction of peptides with different activities. However, none of the current tools can predict ligand peptides of potassium channels. In this work, we developed a tool called PPLK+C; this is the first tool that can predict peptide ligands of potassium channels""" ; sc:featureList edam:operation_0252, edam:operation_0418, edam:operation_0478 ; sc:name "PPLK+C" ; sc:url "https://github.com/bio-coding/PPLKC-" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description """Reproducible and Extensible Open-Source Software for Plant Phenological Phase Duration Prediction and Mapping. PPMaP is a software for plant phonological phase prediction and mapping. This work was implemented by the International Maize and Wheat Improvement Center (CIMMYT) as part of TAMASA (Taking Maize Agronomy to Scale) project in collaboration with IITA and IPNI.""" ; sc:featureList edam:operation_2429, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "PPMaP" ; sc:url "https://github.com/Atoundem/PPMaP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0632, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC8556342", "pubmed:34716373" ; sc:description "An interactive hub for pathways-based markers in plant genomes." ; sc:featureList edam:operation_0533, edam:operation_3282, edam:operation_3926 ; sc:isAccessibleForFree true ; sc:name "PPMdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ppmdb.easyomics.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2538 ; sc:name "Mutation identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3474 ; sc:citation , "pmcid:PMC10064562", "pubmed:37004080" ; sc:description "Allelic phenotype prediction of phenylketonuria based on the machine learning method." ; sc:featureList edam:operation_2422, edam:operation_2437, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "PPML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinfogenetics.info/PPML/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081 ; sc:description "Tool for finding common substructures of the two proteins." ; sc:featureList edam:operation_2487 ; sc:name "PPMs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/guofeics/ppms-online-document" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3293 ; sc:citation , "pmcid:PMC9927313", "pubmed:36602356" ; sc:description "Identifying functional association networks by phylogenetic profiling of prokaryotic genomes." ; sc:featureList edam:operation_0324, edam:operation_2437, edam:operation_3463, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PPNet" ; sc:url "https://github.com/liyangjie/PPNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3315, edam:topic_3379 ; sc:citation ; sc:description "Conditional power, predictive power and probability of success in clinical trials with continuous, binary and time-to-event endpoints." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PPoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ppos.herokuapp.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2749 ; sc:encodingFormat edam:format_2330 ; sc:name "Genome identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_2330, edam:format_2333 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pmcid:PMC2687945", "pubmed:19478005" ; sc:description "Promoter prediction program evaluation." ; sc:featureList edam:operation_0440 ; sc:name "PPPbenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/pppbenchmark" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:17932917" ; sc:description "Web-server for predicting RNA-binding residues of a protein." ; sc:featureList edam:operation_2479, edam:operation_2492 ; sc:name "Pprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/pprint/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0203, edam:topic_3474 ; sc:citation , "pubmed:36516298" ; sc:description "Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile." ; sc:featureList edam:operation_0314, edam:operation_0321, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pprint2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/pprint2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pmcid:PMC449700", "pubmed:15212693", "pubmed:17962309" ; sc:description "PPS (PTMs Peptide Scanner) is a novel software to reveal known or highly potential PTM sites in eukaryotic proteins." ; sc:featureList edam:operation_2479 ; sc:name "PPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://pps.biocuckoo.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3411 ; sc:citation , "pmcid:PMC8729005", "pubmed:34986802" ; sc:description "R package to perform PPS analysis on graphical models" ; sc:featureList edam:operation_1812, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nathan-gill/pps" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2085 ; sc:name "Structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Prediction of protein stability changes." ; sc:featureList edam:operation_2423 ; sc:name "PPSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://structure.bmc.lu.se/PPSC/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:name "Protein identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:description "Prokaryotic protein phosphatases." ; sc:featureList edam:operation_0224 ; sc:name "Prokaryotic protein phosphatase database (PptaseDB)" ; sc:url "http://vigen.biochem.vt.edu/p3d/p3d.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3068 ; sc:citation "pubmed:24440484" ; sc:description "Web tool of novel text-mining method for efficiently retrieving and extracting protein phosphorylation information from literature." ; sc:featureList edam:operation_0417 ; sc:name "PPTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ustc.edu.cn/pptm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3300, edam:topic_3474 ; sc:citation , "pubmed:32348463" ; sc:description """a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning. Codes of A novel therapeutic peptide prediction method using physicochemical property encoding and feature representation learning. This work is based on Anaconda3(py3.6), and therefore, we recommend using Anaconda for running these codes. The enviroment where PPTPP was built was exported as the file named PPTPPenvironment.yaml in the Zip file, please make sure you have the same environment to make everything works. Make sure JAVA, C++ complier have been properly installed on your machine to avoid the disappointment of getting errors. Your javac need to support the version 6, therefore, we recommend to use JDK 11 rather than 13.""" ; sc:featureList edam:operation_3631 ; sc:license "Apache-2.0" ; sc:name "PPTPP" ; sc:url "https://github.com/YPZ858/PPTPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659 ; sc:citation "pubmed:26076723" ; sc:description "Online tool to predict pseudouridine sites recognized by pseudouridine synthase in RNA." ; sc:featureList edam:operation_0415 ; sc:name "PPUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lyh.pkmu.cn/ppus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation ; sc:description "ppx provides a simple, programmatic means to access proteomics data that are publicly available in ProteomeXchange partner repositories." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ppx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wfondrie/ppx" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Matlab code and test data for protein quantification by peptide quality control." ; sc:featureList edam:operation_3218 ; sc:name "PQPQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://forshed.se/jenny/index.php?n=Research.SoftwareAmpCode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , "pubmed:31830256" ; sc:description "The main functionality of the this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). 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A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature.""" ; sc:featureList edam:operation_0308, edam:operation_3237, edam:operation_3431 ; sc:name "PR2" ; sc:url "https://app.pr2-primers.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_0659, edam:topic_3068, edam:topic_3168 ; sc:citation , "pubmed:34251760" ; sc:description "A database of eukaryotic rRNA primers and primer sets for metabarcoding studies compiled from the literature." ; sc:featureList edam:operation_0308, edam:operation_0346, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "pr2-primers" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://app.pr2-primers.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation "pubmed:25947299" ; sc:description "Find an optimal minimal distance global alignment of two amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences." ; sc:featureList edam:operation_0292, edam:operation_0496, edam:operation_2479 ; sc:name "PR2ALIGN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pr2align.rit.albany.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3305, edam:topic_3315, edam:topic_3324 ; sc:citation , "pmcid:PMC7749387", "pubmed:33367130" ; sc:description """An adaptive, interacting, cluster-based model for predicting the transmission dynamics of COVID-19. PRediction and Assesment of CoRona Infections and Transmission in India.""" ; sc:featureList edam:operation_2426 ; sc:name "PRACRITI" ; sc:url "http://pracriti.iitd.ac.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC9344836", "pubmed:35748708" ; sc:description "Platform for storing and using pangenomes for imputation." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3198, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Practical Haplotype Graph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/Home" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0611, edam:topic_2229, edam:topic_3382, edam:topic_3385 ; sc:citation ; sc:description "Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy)." ; sc:featureList edam:operation_2495, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "prada" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/prada.html" ; biotools:primaryContact "Florian Hahne" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3365 ; sc:citation "pubmed:24695405" ; sc:description "Flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification." ; sc:featureList edam:operation_2423 ; sc:name "PRADA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/PRADA:Overview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0736, edam:topic_3542 ; sc:citation "pubmed:10404624", "pubmed:12144176", "pubmed:12369910", "pubmed:14642759", "pubmed:15699183", "pubmed:15980472", "pubmed:15980473" ; sc:description "Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0346, edam:operation_0492 ; sc:name "PRALINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibivu.cs.vu.nl/programs/pralinewww/" ; biotools:primaryContact "Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:citation , "pubmed:31368486" ; sc:description "Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit | Next-generation PRALINE sequence alignment program | PRALINE 2, a reimplementation of the PSI-PRALINE multiple sequence alignment program | Progressive multiple sequence alignment" ; sc:featureList edam:operation_0300, edam:operation_0491, edam:operation_0492 ; sc:license "GPL-2.0" ; sc:name "PRALINE-2-A" ; sc:url "https://github.com/ibivu/PRALINE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0128, edam:topic_0749, edam:topic_3120 ; sc:citation , "pmcid:PMC9825767", "pubmed:36592044" ; sc:description "PRALINE - Protein and Rna humAn singLe-nucleotIde-variaNts in condEnsates - a database to interrogate proteins and RNAs contained in human condensates such as stress-granules (SGs), processing bodies (PBs), droplets, amyloids and many more." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2441, edam:operation_2492, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "PRALINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://alvinlee.bio.uniroma1.it/praline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3063, edam:topic_3305, edam:topic_3314 ; sc:citation ; sc:description "PrAna (Prescription Analysis) is an R package to calculate and visualize England NHS primary care prescribing data. 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This tool helps to understand the general practice level and postcode level variation of an API." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:license "MIT" ; sc:name "PrAna" ; sc:url "http://pranaviz.bath.ac.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3293 ; sc:citation , "pmcid:PMC7750968", "pubmed:32609371" ; sc:description """ML species tree estimation from the ranked gene trees under coalescence. can be used to compute the probabilities of ranked or unranked phylogenetic gene tree topologies given a species tree under the coalescent process. A ranked tree depicts not only the topological relationship among gene lineages, as an unranked tree does, but also the sequence in which the lineages coalesce. PRANC can also output "democratic vote" (most frequent) ranked or unranked topologies. PRANC can estimate the maximum likelihood species tree with branch lengths from the sample of ranked or unranked gene tree topologies. Greedy consensus tree can be used as a starting tree. Also, trees selected by the minimization of ancient coalescence (MAC) criterion can be used as starting trees.""" ; sc:featureList edam:operation_0547, edam:operation_0555, edam:operation_3947 ; sc:license "MIT" ; sc:name "PRANC" ; sc:url "http://github.com/anastasiiakim/PRANC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Probabilistic multiple alignment program for DNA, codon and amino-acid sequences." ; sc:featureList edam:operation_0492, edam:operation_2451 ; sc:name "PRANK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wasabiapp.org/software/prank/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "A probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences." ; sc:featureList edam:operation_0492, edam:operation_2451 ; sc:name "PRANK API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/msa/prank_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0769, edam:topic_3474 ; sc:citation , "pmcid:PMC6964052", "pubmed:31941435" ; sc:description """Pan Resistome analysis pipeline. PRAP is a platform independent Python3 tool used to analyze pan-resistome characteristics for multiple genomes. It accepts various format of sequence files as input files. The identification of antibiotic resistance genes is mainly based on the Comprehensive Antibiotic Resistance Database (CARD) and ResFinder database.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3196, edam:operation_3482 ; sc:license "GPL-3.0" ; sc:name "PRAP" ; sc:url "https://github.com/syyrjx-hyc/PRAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0749, edam:topic_3053, edam:topic_3170 ; sc:citation ; sc:description "Post-transcriptional regulation analysis pipeline for Iso-Seq." ; sc:featureList edam:operation_0438, edam:operation_2499 ; sc:name "PRAPI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bioinfor.org/bioinfor/tool/PRAPI/" ; biotools:primaryContact "Lianfeng Gu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:27112573" ; sc:description "Web server predicting structure property of a protein sequence without using any template information." ; sc:featureList edam:operation_0474 ; sc:name "PRaptorX Property" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://raptorx2.uchicago.edu/StructurePropertyPred/predict/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3542 ; sc:citation , "pubmed:36000562" ; sc:description "A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions." ; sc:featureList edam:operation_0319, edam:operation_0337, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PRAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.protein-science.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128 ; sc:citation "pubmed:23276706" ; sc:description "Integrated web server analyze protein interaction types. It accommodates three types of protein interactions, i.e., associations: two proteins i) physically contact with each other, ii) co-work for a pheotypic effect and iii) participate in the same pathway." ; sc:featureList edam:operation_2464 ; sc:name "PRASA" ; sc:softwareHelp ; sc:url "http://prasa.csbb.ntu.edu.tw/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2762 ; sc:name "Sequence signature report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:author "Inge Jonassen" ; sc:citation , ; sc:description "Discover patterns in unaligned protein sequences." ; sc:featureList edam:operation_0238 ; sc:name "Pratt (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Bergen" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/pfa/pratt" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3174, edam:topic_3175, edam:topic_3673, edam:topic_3796 ; sc:citation , "pmcid:PMC9825322", "pubmed:36579850" ; sc:description "Compact pan-genomic features for whole-genome population genomics." ; sc:featureList edam:operation_0524, edam:operation_3196, edam:operation_3209, edam:operation_3216, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PRAWNS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KiranJavkar/PRAWNS.git). a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:26671809" ; sc:description "Platform for prediction of RNA binding proteins using sequence information." ; sc:featureList edam:operation_2479, edam:operation_2492 ; sc:name "PRBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbi.seu.edu.cn/PRBP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_3474, edam:topic_3510 ; sc:citation "pubmed:21268114" ; sc:description "Identify RNA-binding residues from protein sequences which combines a hybrid feature with the enriched random forest (ERF) algorithm." ; sc:featureList edam:operation_2479, edam:operation_2492 ; sc:name "PRBR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbi.seu.edu.cn/PRBR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0607, edam:topic_2269, edam:topic_3473, edam:topic_3572 ; sc:citation , "pmcid:PMC5408773", "pubmed:27591081" ; sc:description "The package provides a testing workbench for evaluating precision-recall curves under various conditions in R." ; sc:featureList edam:operation_2238, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "prcbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ii.uib.no" ; sc:softwareHelp , ; sc:softwareVersion "0.5.2" ; sc:url "https://cran.r-project.org/package=prcbench" ; biotools:primaryContact "Takaya Saito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:author "Chong Wu", "Wei Pan" ; sc:citation "pmcid:PMC6818515", "pubmed:31662706" ; sc:description """A New Algorithm and Theory for Penalized Regression-based Clustering. Clustering is unsupervised and exploratory in nature. Yet, it can be performed through penalized regression with grouping pursuit, as demonstrated in Pan et al. (2013). In this paper, we develop a more efficient algorithm for scalable computation and a new theory of clustering consistency for the method. This algorithm, called DC-ADMM, combines difference of convex (DC) programming with the alternating direction method of multipliers (ADMM). This algorithm is shown to be more computationally efficient than the quadratic penalty based algorithm of Pan et al. (2013) because of the former's closed-form updating formulas. Numerically, we compare the DC-ADMM algorithm with the quadratic penalty algorithm to demonstrate its utility and scalability.""" ; sc:featureList edam:operation_3432, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "prclust" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/prclust/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3538 ; sc:citation "pubmed:17567614" ; sc:description "PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0470, edam:operation_3092 ; sc:name "PrDOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prdos.hgc.jp/cgi-bin/top.cgi" ; biotools:primaryContact "PrDOS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3474, edam:topic_3912 ; sc:citation , "pmcid:PMC9597991", "pubmed:36284264" ; sc:description "A machine learning framework for identifying anti-CRISPR proteins." ; sc:featureList edam:operation_0267, edam:operation_2575, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PreAcrs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Lyn-666/anti_CRISPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC7929366", "pubmed:33497434" ; sc:description "PreAntiCoV is a tool for identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies." ; sc:featureList edam:operation_0236, edam:operation_0250 ; sc:license "MIT" ; sc:name "PreAntiCoV" ; sc:url "https://github.com/poncey/PreAntiCoV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:14871866", "pubmed:16844993" ; sc:description "Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_2464 ; sc:name "PreBI" ; sc:url "http://pre-s.protein.osaka-u.ac.jp/prebi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_0623, edam:topic_3474 ; sc:citation , "pmcid:PMC8685504", "pubmed:34938773" ; sc:description "An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions." ; sc:featureList edam:operation_2489, edam:operation_3936, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PreBINDS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://binds.lifematics.work/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC4429080", "pubmed:25966034" ; sc:description "This package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output." ; sc:featureList edam:operation_0335, edam:operation_2424 ; sc:license "Artistic-2.0" ; sc:name "prebs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/prebs.html" ; biotools:primaryContact "Karolis Uziela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC10371765", "pubmed:37501705" ; sc:description "An ensemble learning algorithm for predicting cancer and non-cancer cells from single-cell transcriptomes." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PreCanCell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WangX-Lab/PreCanCell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:16135709" ; sc:description "Predict regulatory cis-acting elements through DNA sequences. This tool aimed at advanced mining of specific biological data: sequence data of DNA sequences that lie upstream of regions with known coding function." ; sc:featureList edam:operation_0438 ; sc:name "Precise" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.wageningenur.nl/en/show/PRECISE-Prediction-of-REgulatory-CISacting-Elements.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC6612899", "pubmed:31510654" ; sc:description "> NAME (PRECISE) SIMILAR TO (PUB. DIFFERENT) bio.tools/precise (Precise) | > CORRECT NAME OF TOOL COULD ALSO BE 'IMPLEMENTATION:PRECISE' | a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors | Example of usage of PRECISE is available at this address: https://github.com/NKI-CCB/PRECISE_figures Examples correspond to scripts used for creating figures" ; sc:featureList edam:operation_2436, edam:operation_3891 ; sc:license "MIT" ; sc:name "PRECISE" ; sc:url "https://github.com/NKI-CCB/PRECISE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654 ; sc:citation "pubmed:24829457" ; sc:description "Web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries." ; sc:featureList edam:operation_0308 ; sc:name "PrecisePrimer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://absynth.issb.genopole.fr/Bioinformatics/tools/PrecisePrimer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0749, edam:topic_3169, edam:topic_3474, edam:topic_3940 ; sc:citation ; sc:description """A machine learning framework for precise 3D domain boundary prediction at base-level resolution. preciseTAD: A machine learning framework for precise TAD boundary prediction. preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution.""" ; sc:featureList edam:operation_0303, edam:operation_0362, edam:operation_0445 ; sc:license "MIT" ; sc:name "preciseTAD" ; sc:url "https://bioconductor.org/packages/preciseTAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "Calculate and plot P/R and ROC curves for binary classification tasks." ; sc:isAccessibleForFree true ; sc:name "Precision-Recall and ROC Curves Generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/21528-precision-recall-and-roc-curves" ; biotools:primaryContact "Stefan Schroedl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3577, edam:topic_3922 ; sc:citation , "pubmed:33787868" ; sc:description "PrecisionProDB (Precision protein database) is a tool improving the proteomics performance for precision medicine. PrecisionProDB is a Python package for proteogenomics, which can generate a customized protein database for peptide search in mass spectrometry." ; sc:featureList edam:operation_3227, edam:operation_3436, edam:operation_3646, edam:operation_3767 ; sc:license "GPL-3.0" ; sc:name "PrecisionProDB" ; sc:softwareHelp ; sc:url "https://github.com/ATPs/PrecisionProDB" ; biotools:primaryContact "Jinchuan Xing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3314, edam:topic_3375, edam:topic_3379 ; sc:citation , "pubmed:24969748" ; sc:description "Classes for fundamental PKPD modeling in drug discovery (no support for a NLME modeling)." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "Preclinical PKPD modeling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43521-preclinical-pkpd-modeling" ; biotools:primaryContact "Peter Gennemark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2885, edam:topic_3407, edam:topic_3420 ; sc:citation , "pmcid:PMC7893021", "pubmed:33602974" ; sc:description """Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PrecocityDB Database and enrichment analysis of genes associated with precocious puberty The SQL file of database is stored as ZIP file precocity.zip The source code files must be kept in the home folder of Apache web server and the MySQL database connection information is stored in connect.php. Database and enrichment analysis of genes associated with precocious puberty. Precocious puberty is an important endocrine disorder affecting children. PrecocityDB is the first manually curated online database on genes, SNPs, pathways, and ontologies associated with precocious puberty.""" ; sc:featureList edam:operation_3501, edam:operation_3559, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "PrecocityDB" ; sc:url "http://www.precocity.bicnirrh.res.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3298 ; sc:author "Luciano Fernandez" ; sc:citation ; sc:contributor "Anders Blomberg", "Jonas Warringer", "Martin Zackrisson", "Olga Kourtchenko" ; sc:description "Tool developed to automate visualization, analysis and exploration of complex and highly resolved microbial growth data, as well as standardized extraction of the fitness components it contains. It is hope that this tool will promote simplicity, transparency and standardization in microbial growth phenomics, and provide a portal with the standalone software and online tools so that other microbiology labs can easily upload, assess and visualize their growth data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "PRECOG" ; sc:operatingSystem "Windows" ; sc:provider "Department of Marine Sciences", "gu.se" ; sc:softwareHelp ; sc:softwareVersion "1.0.0.16" ; sc:url "http://precog.lundberg.gu.se/" ; biotools:primaryContact "Luciano Fernandez" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_0820, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC9252787", "pubmed:35639758" ; sc:description "Exploring GPCR signaling mechanisms with deep protein representations." ; sc:featureList edam:operation_0269, edam:operation_2939, edam:operation_2995, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PRECOGx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://precogx.bioinfolab.sns.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0607, edam:topic_2269, edam:topic_3473 ; sc:citation ; sc:description "Integrated platform that enables robust performance evaluations of binary classifiers in R. Specifically, it offers accurate calculations of ROC (Receiver Operator Characteristics) and precision-recall curves." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Precrec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ii.uib.no" ; sc:softwareHelp , ; sc:softwareVersion "0.5.2" ; sc:url "https://cran.r-project.org/package=precrec" ; biotools:primaryContact "Takaya Saito" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623, edam:topic_3168, edam:topic_3300 ; sc:citation "pubmed:15215415" ; sc:description "PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles." ; sc:featureList edam:operation_0224, edam:operation_0269, edam:operation_0270 ; sc:name "PRED-GPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/" ; biotools:primaryContact "PRED-GPCR Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0820 ; sc:citation "pubmed:19367716" ; sc:description "PRED-SIGNAL is a tool that takes a Gram-positive bacteria protein sequence as input and predicts the probability of it being a lipoprotein signal peptides" ; sc:featureList edam:operation_0418, edam:operation_2423 ; sc:name "PRED-LIPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.compgen.org/tools/PRED-LIPO" ; biotools:primaryContact "Pantelis Bagos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation "pubmed:18988691" ; sc:description "PRED-SIGNAL is a tool that takes a protein sequence as input and predicts the signal peptides of archaea" ; sc:featureList edam:operation_0418, edam:operation_0422, edam:operation_2423 ; sc:name "PRED-SIGNAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.compgen.org/tools/PRED-SIGNAL" ; biotools:primaryContact "Pantelis Bagos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2258, edam:topic_2840, edam:topic_3474 ; sc:citation , "pubmed:32673477" ; sc:description """A Web Portal for Accurate Prediction of Human Skin Sensitizers. The Pred-Skin application is based on externally predictive QSAR models of skin sensitization. The models were built using the most extensive database containing human, in vivo (LLNA), in chemico (DPRA), and in vitro (KeratinoSens and H-CLAT) data, addressing all the key steps of the skin sensitization adverse outcome pathway (AOP). So far, PredSkin is the only tool available for predicting skin sensitization based on human data!.""" ; sc:featureList edam:operation_0252, edam:operation_0337, edam:operation_3928 ; sc:name "Pred-Skin" ; sc:url "http://predskin.labmol.com.br/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation "pubmed:20847219" ; sc:description "PRED-TAT is a tool that takes a protein sequence as input and discriminating Sec from Tat signal peptides and predicting their cleavage sites." ; sc:featureList edam:operation_0269, edam:operation_0270, edam:operation_0418, edam:operation_0422 ; sc:name "PRED-TAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.compgen.org/tools/PRED-TAT" ; biotools:primaryContact "Pantelis Bagos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_0820, edam:topic_2269, edam:topic_3510 ; sc:citation "pubmed:15070403", "pubmed:15215419" ; sc:description "PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0270, edam:operation_2489 ; sc:name "PRED-TMBB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.biol.uoa.gr/PRED-TMBB/" ; biotools:primaryContact "P.G. Bagos" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1964 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820 ; sc:citation , "pubmed:15070403", "pubmed:15215419", "pubmed:27587687" ; sc:description "Improved topology prediction and detection of beta-barrel outer membrane proteins" ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0270, edam:operation_2423 ; sc:name "PRED-TMBB2" ; sc:softwareVersion "1.1" ; sc:url "http://www.compgen.org/tools/PRED-TMBB2" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3033 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1288 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Genome map" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Sequence composition plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_2640, edam:topic_3055 ; sc:citation ; sc:description "Package for the position related analysis of quantitative functional genomics data." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "PREDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PREDA.html" ; biotools:primaryContact "Francesco Ferrari" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3336, edam:topic_3373, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC9951537", "pubmed:36829107" ; sc:description "A computational framework for prediction of acute oral toxicity based on multiple random forest models." ; sc:featureList edam:operation_0451, edam:operation_0452, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PredAOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://predaot.netlify.app/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:34608613" ; sc:description "PredAPP is a web server providing users an effective identification of antiparasitic peptides (APPs) ." ; sc:featureList edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PredAPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://predapp.xialab.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0199 ; sc:citation ; sc:description "An R package for network-based mutation impact prediction." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "predatoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://berkgurdamar.github.io/predatoR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2640, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:32591774" ; sc:description """prediction of driver frameshift indels in human cancer. The discrimination of driver from passenger mutations has been a hot topic in the field of cancer biology. Although recent advances have improved the identification of driver mutations in cancer genomic research, there is no computational method specific for the cancer frameshift indels (insertions or and deletions) yet. In addition, existing pathogenic frameshift indel predictors may suffer from plenty of missing values because of different choices of transcripts during the variant annotation processes. In this study, we proposed a computational model, called PredCID (Predictor for Cancer driver frameshift InDels), for accurately predicting cancer driver frameshift indels. Gene, DNA, transcript and protein level features are combined together and selected for classification with eXtreme Gradient Boosting classifier""" ; sc:featureList edam:operation_0331, edam:operation_0372, edam:operation_3227 ; sc:name "PredCID" ; sc:url "http://bioinfo.ahu.edu.cn:8080/PredCID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3053, edam:topic_3300, edam:topic_3474, edam:topic_3810 ; sc:author ; sc:citation , "pmcid:PMC8074503", "pubmed:33902670" ; sc:description "PredCRG is a computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel." ; sc:featureList edam:operation_0267, edam:operation_2454 ; sc:license "GPL-2.0" ; sc:name "PredCRG" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/PredCRG/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pubmed:20955172" ; sc:description "The web server PredCSF was developed by using modified one-versus-rest SVMs. The SVMs’input features are composed of physicochemical properties, evolutionary information, second structure and amino acid composition. Each SVM classifier’s output is the probability assigned to a superfamily." ; sc:featureList edam:operation_2479 ; sc:name "PredCSF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/PredCSF/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:24202542" ; sc:description "PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PREDDIMER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://model.nmr.ru/preddimer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0749, edam:topic_2269 ; sc:citation "pubmed:17451648" ; sc:description "Tool designed for biologists, its main function is to search for the cis-elements (nucleotides) that regulate the genes for a bacteria specie, assuming that one usually consider that a cis sequence regulates a gene if it is oriented in the same direction and if it is localized in a user-specified interval regarding to the beginning of the gene." ; sc:featureList edam:operation_0415 ; sc:name "Predector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.montefiore.ulg.ac.be/~hiard/PreDetector/PreDetector.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_0634, edam:topic_0749 ; sc:citation ; sc:description "Predector is an automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant-pathogens." ; sc:featureList edam:operation_2489, edam:operation_3092, edam:operation_3436, edam:operation_3461 ; sc:license "Apache-2.0" ; sc:name "Predector" ; sc:url "https://github.com/ccdmb/predector" ; biotools:primaryContact "James K. Hane" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_1775, edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:37401369" ; sc:description "Large-scale predicting protein functions through heterogeneous feature fusion." ; sc:featureList edam:operation_0474, edam:operation_2492, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "PredGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://predgo.denglab.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_3542 ; sc:citation ; sc:description "Prediction system for GPI-anchored proteins." ; sc:featureList edam:operation_3351 ; sc:isAccessibleForFree true ; sc:name "PredGPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/predgpi" ; biotools:primaryContact , "Andrea Pierleoni", "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3068, edam:topic_3168, edam:topic_3324 ; sc:citation , "pubmed:33027504" ; sc:description """an integrated web server platform for the detection and visualization of host-pathogen interactions using sequence-based methods. PredHPI an integrated web server platform for the prediction and visualization of host-pathogen interactions. The International Molecular Exchange Consortium (IMEX) had the initiative to cluster the largest public interaction data providers. From those we have selected five (HPIDB, MINT, DIP, BioGRID and IntAct) as we think are the most comprehensive. Moreover, four other resources outside IMEX were included, VirHostNet, STRING, VIH-1 NCBI and PHISTO. VirHostNet is one of the most complete resources for Vir-Host interactions. STRING is the largest repository of protein-protein interaction, in the service only the experimental interaction of STRING were included. Dataset used in the benchmark of the PredHPI manuscript were finally included.""" ; sc:featureList edam:operation_0303, edam:operation_2492, edam:operation_3461, edam:operation_3925 ; sc:name "PredHPI" ; sc:url "http://bioinfo.usu.edu/PredHPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0130, edam:topic_0602 ; sc:citation , "pmcid:PMC4086081", "pubmed:24852252" ; sc:description "Computational method that can effectively identify hot spots on protein-protein interaction interfaces by using optimally structural neighborhood properties." ; sc:featureList edam:operation_0272, edam:operation_2464, edam:operation_2492 ; sc:name "PredHS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.predhs.org" ; biotools:primaryContact "Lei Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3510 ; sc:citation "pubmed:25534958" ; sc:description "Web service which is constructed to predict the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machine." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PredHydroxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ncu.edu.cn/PredHydroxy.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0199, edam:topic_3474 ; sc:citation , "pubmed:34126874" ; sc:description "Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures." ; sc:featureList edam:operation_0474, edam:operation_2492, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PANDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pandaaffinity.pythonanywhere.com/welcome/default/index#" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0749, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation ; sc:description """PredicTF is a tool to predict bacterial transcription factors in complex microbial communities. Transcription Factors (TFs) are proteins controlling the rate of genetic information, regulating cellular gene expression.""" ; sc:featureList edam:operation_0310, edam:operation_0445, edam:operation_3192, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "PredicTF" ; sc:url "https://github.com/mdsufz/PredicTF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "This software aims at reconstructing haplotypes from next-generation sequencing data." ; sc:featureList edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PredictHaplo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.1.3" ; sc:url "https://github.com/cbg-ethz/PredictHaplo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9744141", "pubmed:36518292" ; sc:description "A predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2." ; sc:featureList edam:operation_3431, edam:operation_3659, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PredictION" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://genomicdashboard.herokuapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2259 ; sc:citation , , "pmcid:PMC3245161", "pubmed:22096235" ; sc:description "Set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases." ; sc:featureList edam:operation_3439 ; sc:license "Artistic-2.0" ; sc:name "predictionet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/predictionet.html" ; biotools:primaryContact , "Catharina Olsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_0625 ; sc:citation "pubmed:22096235" ; sc:description "The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model." ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3439 ; sc:name "PredictiveNetworks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://compbio.dfci.harvard.edu/predictivenetworks//" ; biotools:primaryContact "Benjamin Haibe-Kains" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2062 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3510 ; sc:author "Murat Cokol" ; sc:citation , "pmcid:PMC1083765", "pubmed:11258480" ; sc:contributor "Burkhard Rost", "Rajesh Nair" ; sc:description "Prediction and analysis of nuclear localization signals." ; sc:featureList edam:operation_2489, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PredictNLS" ; sc:operatingSystem "Linux" ; sc:provider "Columbia University", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.18" ; sc:url "https://www.rostlab.org/owiki/index.php/PredictNLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_3068, edam:topic_3314, edam:topic_3474 ; sc:citation , "pubmed:31584270" ; sc:description """Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models. Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical biology space to support the development of large-scale quantitative structure-activity relationship (QSAR) models. We propose a new deep learning consensus architecture (DLCA) that combines consensus and multitask deep learning approaches together to generate large-scale QSAR models.""" ; sc:featureList edam:operation_3436, edam:operation_3659, edam:operation_3799 ; sc:name "predictor" ; sc:url "https://predictor.ncats.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0622, edam:topic_2259, edam:topic_3308 ; sc:citation "pubmed:24532840" ; sc:description "Bayesian network model that integrates genomic, transcriptomic and proteomic data to predict protein abundance. Specifically, by using expression, sequence and interaction data, we effectively link transcriptional information with post-transcriptional and protein translational data." ; sc:featureList edam:operation_2423 ; sc:name "PredictPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.scmb.uq.edu.au:8080/proteinabundance/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0160, edam:topic_0166, edam:topic_0736 ; sc:citation "pubmed:12824312", "pubmed:12824314", "pubmed:15215403" ; sc:description "PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0468, edam:operation_0474 ; sc:name "PredictProtein" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ppopen.rostlab.org" ; biotools:primaryContact "PredictProtein Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929, edam:format_1957 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2330, edam:format_2331, edam:format_2332, edam:format_3464 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081, edam:topic_0089, edam:topic_0092, edam:topic_1775, edam:topic_3473, edam:topic_3474 ; sc:author "Guy Yachdav", "Laszlo Kajan" ; sc:citation , , , ; sc:contributor "Alexander von Humboldt foundation through the German Ministry for Research and Education", "Edda Kloppmann", "Laszlo Kajan" ; sc:description "Prediction of various aspects of protein structure and function. A user may submit a query to the server without registration." ; sc:featureList edam:operation_0236, edam:operation_0238, edam:operation_0245, edam:operation_0250, edam:operation_0267, edam:operation_0269, edam:operation_0272, edam:operation_0292, edam:operation_0296, edam:operation_0305, edam:operation_0306, edam:operation_0331, edam:operation_0346, edam:operation_0361, edam:operation_0418, edam:operation_0531, edam:operation_0564, edam:operation_1777, edam:operation_2241, edam:operation_2422, edam:operation_2464, edam:operation_2479, edam:operation_2485, edam:operation_2489, edam:operation_2574, edam:operation_2575, edam:operation_3092, edam:operation_3225, edam:operation_3460, edam:operation_3559 ; sc:funder "Alexander von Humboldt foundation through the German Ministry for Research and Education" ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PredictProtein Open" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "RostLab", "Technische Universität München" ; sc:softwareHelp , ; sc:softwareVersion "1.1.07" ; sc:url "http://ppopen.informatik.tu-muenchen.de/" ; biotools:primaryContact "PredictProtein Help Desk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15215402" ; sc:description "Tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. The tool reports back with predicted binding sites and downstream co-regulated genes." ; sc:featureList edam:operation_0435, edam:operation_0438, edam:operation_0445, edam:operation_0492, edam:operation_2575 ; sc:name "PredictRegulon" ; sc:url "http://www.cdfd.org.in/predictregulon/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330, edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2885, edam:topic_3053, edam:topic_3063, edam:topic_3325 ; sc:author , , "Antonin Pavelka", "Ondrej Salanda" ; sc:citation ; sc:contributor , , , "Brno University of Technology", "Eric D. Wieben", "European Regional Development Fund", "European Social Fund", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic" ; sc:description "A consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database." ; sc:featureList edam:operation_0331 ; sc:funder "Brno University of Technology", "European Regional Development Fund", "European Social Fund", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "PredictSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic", "Mayo Clinic, Rochester, New York, United States of America" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://loschmidt.chemi.muni.cz/predictsnp1" ; biotools:primaryContact "PredictSNP team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2275, edam:topic_2640 ; sc:description "PredictSNP Onco is the web tool for fully automated and fast analysis of the effect of mutations on stability and function in known cancer targets applying in silico methods of molecular modelling and bioinformatics." ; sc:isAccessibleForFree true ; sc:name "PredictSNP-ONCO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://loschmidt.chemi.muni.cz/predictsnp-onco/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3019 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3508 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2533, edam:topic_3063, edam:topic_3325 ; sc:author , , , "Antonin Pavelka" ; sc:citation ; sc:contributor , , , "Brno University of Technology", "Eric D. Wieben", "European Regional Development Fund", "European Social Fund", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic" ; sc:description "A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases." ; sc:featureList edam:operation_3225, edam:operation_3672 ; sc:funder "Brno University of Technology", "European Regional Development Fund", "European Social Fund", "Grant Agency of the Czech Republic", "Ministry of Education of the Czech Republic" ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "PredictSNP2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://loschmidt.chemi.muni.cz/predictsnp2" ; biotools:primaryContact "PredictSNP team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_1775 ; sc:citation "pubmed:18477637", "pubmed:18501020" ; sc:description "The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation" ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_3092 ; sc:name "Predikin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://predikin.biosci.uq.edu.au" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:37040252" ; sc:description "Predicting pathogenic inframe indels in humans through graph convolution neural network with graph sampling technique." ; sc:featureList edam:operation_3436, edam:operation_3461, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "PredinID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://predinid.bio.aielab.cc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0140, edam:topic_0154, edam:topic_3510, edam:topic_3512 ; sc:citation "pubmed:15215414" ; sc:description "Takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets." ; sc:featureList edam:operation_0331, edam:operation_0418 ; sc:name "PrediSi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.predisi.de/" ; biotools:primaryContact "Karsten Hiller" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1208 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_1317, edam:topic_2814 ; sc:citation , "pmcid:PMC3087350", "pubmed:20025768" ; sc:description "PreDisorder server is a valuable and accurate tool for protein structure prediction, protein determination and protein engineering." ; sc:featureList edam:operation_0474 ; sc:name "PreDisorder" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.1" ; sc:url "http://casp.rnet.missouri.edu/predisorder.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0593, edam:topic_0601, edam:topic_3444 ; sc:citation "pubmed:16845087" ; sc:description "PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions." ; sc:featureList edam:operation_0249, edam:operation_1844, edam:operation_2479 ; sc:name "PREDITOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601 ; sc:citation , "pubmed:34546927" ; sc:description "Predicting Multiple Lysine PTM Sites with Optimal Feature Representation and Data Imbalance Minimization." ; sc:featureList edam:operation_0417, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:name "predML-Site" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://103.99.176.239/predML-Site" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1712 ; sc:name "Chemical structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:34515778" ; sc:description "A random Forest model for predicting metabolic stability of drug candidates in human liver microsomes." ; sc:featureList edam:operation_0451, edam:operation_0452, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "PredMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://predms.netlify.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3400, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:32786686" ; sc:description "Prediction of Neuropeptides from Sequence Information Using Ensemble Classifier and Hybrid Features." ; sc:featureList edam:operation_0253, edam:operation_3092, edam:operation_3659 ; sc:name "PredNeuroP" ; sc:url "https://github.com/xialab-ahu/PredNeuroP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160, edam:topic_0601, edam:topic_3474 ; sc:citation , "pmcid:PMC7962192", "pubmed:33800121" ; sc:description "PredNTS (Prediction of Nitrotyrosine Sites Online Server) is an predictor of nitrotyrosine sites by integrating multiple sequence features." ; sc:featureList edam:operation_0253, edam:operation_0417, edam:operation_2422 ; sc:name "PredNTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://kurata14.bio.kyutech.ac.jp/PredNTS/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_2229 ; sc:citation , "pmcid:PMC8016359", "pubmed:33793659" ; sc:description "predPhogly-Site is a tool for predicting phosphoglycerylation sites by incorporating probabilistic sequence-coupling information into PseAAC and addressing data imbalance." ; sc:featureList edam:operation_0417, edam:operation_2422, edam:operation_3431, edam:operation_3435, edam:operation_3755 ; sc:license "MIT" ; sc:name "predPhogly-Site" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://103.99.176.239/predPhogly-Site" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0218, edam:topic_0769, edam:topic_3957 ; sc:citation , "pmcid:PMC9581021", "pubmed:36303787" ; sc:description "Large-Scale Protein Interactions Prediction by Multiple Evidence Analysis Associated With an In-Silico Curation Strategy." ; sc:featureList edam:operation_0306, edam:operation_2489, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PredPrIn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YasCoMa/predprin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3373, edam:topic_3374, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC10362732", "pubmed:37484492" ; sc:description """Attention-based graph neural network for predicting stability of compounds in human plasma. PredPS predicts plasma stability for a given compound as stable (≥ 85% remaining at 3 h) or unstable (< 85% remaining at 3 h) in human plasma.""" ; sc:featureList edam:operation_3927, edam:operation_3935, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PredPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://predps.netlify.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128 ; sc:citation ; sc:description "Computational method for Protein-RNA binding site prediction." ; sc:featureList edam:operation_0248 ; sc:license "Other" ; sc:name "PredRBR" ; sc:operatingSystem "Linux" ; sc:url "http://denglab.org/PredRBR/" ; biotools:primaryContact "Lei Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0749, edam:topic_3510 ; sc:citation , "pmcid:PMC4343075", "pubmed:25725063" ; sc:description "Database of Dna REgulatory Motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0438 ; sc:name "PreDREM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://server.cs.ucf.edu/predrem/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1964 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation , ; sc:description "Two independent algorithms, which predict the transmembrane regions of integral membrane proteins. The underlying model is a SVM classifier trained on sequence data of transmembrane proteins with known structures. Given a protein sequence as input, the algorithms predict the probable transmembrane regions based on amino acid adjacency frequency and position specific preference of amino acids in the transmembrane regions." ; sc:featureList edam:operation_0474 ; sc:name "PredTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-SI-hackathon" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://transpred.ki.si" ; biotools:primaryContact "Marjana Novič" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0166 ; sc:citation "pubmed:20534496", "pubmed:21609948" ; sc:description "PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors." ; sc:featureList edam:operation_0224, edam:operation_0267, edam:operation_0474, edam:operation_2464 ; sc:name "PredUs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0123 ; sc:citation "pubmed:22689641" ; sc:description "Predict local protein structures and protein flexibility from its sequence. Results can be visualized at the amino acid level through a table and graphics." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "PredyFlexy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/" ; biotools:primaryContact "Jean-Christophe Gelly" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1352 ; sc:name "Regular expression" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Regular expression search of protein sequence(s)." ; sc:featureList edam:operation_0338, edam:operation_3092 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "preg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/preg.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0593, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC7495898", "pubmed:32938375" ; sc:description """Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. Prediction of Protein-DNA Binding Energy Hot Spots. PreHots, a computational method that can effectively identify hot spots on protein-DNA binding interfaces using an ensemble approach.""" ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0420, edam:operation_3900 ; sc:name "PreHots" ; sc:url "https://dmb.tongji.edu.cn/tools/PreHots/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation "pubmed:16682423" ; sc:description "Predict the local structure of a protein in terms of backbone dihedral angle domains, identify sequence regions that form early during folding, and locate structural weaknesses, defined as regions whose sequence is not optimal with respect to the tertiary fold." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "Prelude Fugue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://babylone.ulb.ac.be/Prelude_and_Fugue/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0634, edam:topic_2640, edam:topic_3325, edam:topic_3423, edam:topic_3577 ; sc:citation , "pmcid:PMC6324052", "pubmed:30407536" ; sc:description """An integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. One important aspect of precision medicine aims to deliver the right medicine to the right patient at the right dose at the right time based on the unique 'omics' features of each individual patient, thus maximizing drug efficacy and minimizing adverse drug reactions. However, fragmentation and heterogeneity of available data makes it challenging to readily obtain first-hand information regarding some particular diseases, drugs, genes and variants of interest. Therefore, we developed the Precision Medicine Knowledgebase (PreMedKB) by seamlessly integrating the four fundamental components of precision medicine: diseases, genes, variants and drugs""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3920 ; sc:name "PreMedKB" ; sc:url "http://www.fudan-pgx.org/premedkb/index.html#/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:25178460" ; sc:description "Computational approach that harnesses the implicit information associated with library fragment profiles to infer nucleotide-resolution methylation values in addition to read counts data." ; sc:featureList edam:operation_0415 ; sc:name "PrEMeR-CG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserv.mps.ohio-state.edu/premer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3174, edam:topic_3325 ; sc:citation , "pmcid:PMC5310051", "pubmed:28196472" ; sc:description "Facilitates the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PreMeta" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dlin.web.unc.edu/software/premeta/" ; biotools:primaryContact "Zheng-Zheng Tang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2275, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:32616370" ; sc:description """An in silico phase I and II drug metabolism prediction platform. PreMetabo – Just another BMDRC Sites site. CYP 2C9, 2C19, 2D6, 3A4 Inhibitor / Non-inhibitor, CYP 2D6, 3A4 Substrate / Non-substrate. CYP 3A4, 1A2, 2C9, 2D6 Site of Metabolism (SOM) prediction.""" ; sc:featureList edam:operation_0478, edam:operation_3454, edam:operation_3896, edam:operation_3929 ; sc:name "PreMetabo" ; sc:url "https://premetabo.bmdrc.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3172211", "pubmed:21931639" ; sc:description "PreMieR is a web-server specially trained for the identification of mannose interacting residues (MIRs)." ; sc:featureList edam:operation_2945 ; sc:name "premier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/premier/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3934 ; sc:citation ; sc:description "A Framework to Estimate Intraclonal Heterogeneity and Subpopulation Changes from Perturbational Bulk Gene Expression Profiles." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Premnas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jhhung/Premnas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_2275 ; sc:citation ; sc:description "PremPLI predicts the effects of single mutations on protein-ligand interactions by calculating the binding affinity changes quantitatively. It can be used for guiding the design of ligand-binding proteins, identifying and understanding disease driver mutations, and finding potential resistance mutations for different drugs. The 3D structure of a protein-ligand complex is required for performing the prediction." ; sc:featureList edam:operation_0331, edam:operation_0478, edam:operation_3897, edam:operation_4009 ; sc:license "MIT" ; sc:name "PremPLI" ; sc:url "https://lilab.jysw.suda.edu.cn/research/PremPLI/" ; biotools:primaryContact "Minghui Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0130, edam:topic_0199, edam:topic_0203 ; sc:citation ; sc:description """Predicting the Effects of Single Mutations on Protein-RNA Interactions. PremPRI - Predicting the Effects of Mutations on. PremPRI predicts the effects of single muta-tions occurring in RNA binding proteins on the protein-RNA interactions by calculating the binding affinity changes quantitatively. It can be used for finding functionally importantvariants, understanding the molecular mechanisms, and designing new protein-RNA interaction inhibitors. The 3D structure of a protein-RNA complex is required forperforming the prediction.""" ; sc:featureList edam:operation_2492, edam:operation_3901, edam:operation_3902 ; sc:name "PremPRI" ; sc:url "http://lilab.jysw.suda.edu.cn/research/PremPRI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0736 ; sc:citation ; sc:description "PremPS evaluates the effects of single muta-tions on protein stability by calculating thechanges in unfolding Gibbs free energy. It canbe applied to a large number of tasks, in-cluding finding functionally important variants,understanding their molecular mechanismsand protein design. 3D structure of a proteinis required for this method." ; sc:featureList edam:operation_0331, edam:operation_0408, edam:operation_3461 ; sc:name "PremPS" ; sc:url "https://lilab.jysw.suda.edu.cn/research/PremPS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0621, edam:topic_3293, edam:topic_3407 ; sc:citation "pubmed:22096236" ; sc:description "The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved." ; sc:featureList edam:operation_0435, edam:operation_0579, edam:operation_2422, edam:operation_2454 ; sc:name "PreOpDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biocomputo2.ibt.unam.mx/OperonPredictor/" ; biotools:primaryContact "Blanca Taboada", "Enrique Merino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "It is a standalone full-interactive graphical suite for the pre-processing of gene expression data that aims at identify and remove sources of systematic and random variation in the measured data, other than differential expression. It integrates a variety of analytical tools that in some cases can be applied in any context. Other techniques require some specific conditions." ; sc:featureList edam:operation_2409, edam:operation_2495 ; sc:name "PreP" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "7" ; sc:url "http://chirimoyo.ac.uma.es/prep/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0780 ; sc:citation "pubmed:15826309", "pubmed:19433507" ; sc:description "The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included." ; sc:featureList edam:operation_2454, edam:operation_2489, edam:operation_3092, edam:operation_3096 ; sc:name "PREP Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prep.unl.edu/" ; biotools:primaryContact "Jeff Mower" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation , ; sc:description "Prepares Annotation file: clusterizes, filters exon and sorts annotations." ; sc:featureList edam:operation_3432, edam:operation_3695, edam:operation_3802 ; sc:name "prepareannotation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3343 ; sc:citation , "pmcid:PMC10019447", "pubmed:36776141" ; sc:description "A structure- and chemical similarity-informed database of predicted protein compound interactions." ; sc:featureList edam:operation_0477, edam:operation_2421, edam:operation_2492, edam:operation_2575, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "PrePCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://honiglab.c2b2.columbia.edu/prepci.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "Prephappy is a tool to help prepare input files for the haplotype reconstruction program HAPPY." ; sc:featureList edam:operation_0487 ; sc:name "Prephappy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130226" ; sc:url "http://valdarlab.unc.edu/prephappy.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621 ; sc:citation ; sc:description "Database of predicted and experimentally determined protein-protein interactions (PPI) for yeast and human. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information." ; sc:featureList edam:operation_2479 ; sc:name "PrePPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bhapp.c2b2.columbia.edu/PrePPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3474, edam:topic_3557 ; sc:citation "pubmed:26415726" ; sc:description "Computational method to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs." ; sc:featureList edam:operation_2464 ; sc:name "PrePPItar" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://doc.aporc.org/wiki/PrePPItar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3572 ; sc:citation ; sc:description "A library of core preprocessing routines." ; sc:featureList edam:operation_2409 ; sc:license "GPL-2.0" ; sc:name "preprocessCore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/preprocessCore.html" ; biotools:primaryContact "Benjamin Milo Bolstad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0203, edam:topic_2640, edam:topic_3360 ; sc:citation ; sc:description """A Patient Representation with Pairwise Relative Expression of Proteins on Biological Networks. Alterations in protein and gene expression levels are often used as features to predictive models such as clinical outcome prediction.""" ; sc:featureList edam:operation_0477, edam:operation_2495, edam:operation_3092, edam:operation_3436 ; sc:license "MIT" ; sc:name "PRER" ; sc:url "https://github.com/hikuru/PRER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:35722704" ; sc:description "A webserver for decoding the functional perturbations of RNA editing sites." ; sc:featureList edam:operation_0278, edam:operation_0314, edam:operation_0463, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "PRES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/PRES/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:35916740" ; sc:description "Predictor of Sensitization hazard for chemical substances released from Medical Devices." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "PreS MD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://presmd.mml.unc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_3170 ; sc:citation ; sc:description """incremental decision trees for prediction of Adenosine to Inosine RNA editing sites. This repository contains datasets for the paper titled "Incremental Decision Trees for Prediction of Adenosine to Inosine RNA Editing Sites". All Features.csv - Benchmark Dataset After Feature Extraction. Enter the query RNA sequences here Predict Clear. Selected Features.csv - Benchmark Dataset After Feature Selection. Insert RNA string of any length.""" ; sc:featureList edam:operation_2441, edam:operation_3096, edam:operation_3936 ; sc:license "CC0-1.0" ; sc:name "PRESa2i" ; sc:url "http://brl.uiu.ac.bd/presa2i/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2333 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3071, edam:topic_3170 ; sc:citation , ; sc:description "Generate design/target file and archive for SARTools inputs." ; sc:featureList edam:operation_3429 ; sc:name "presartools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/PF2-pasteur-fr/SARTools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3170, edam:topic_3318, edam:topic_3474 ; sc:citation , "pmcid:PMC8163769", "pubmed:34050150" ; sc:description "PRESCIENT (Potential eneRgy undeRlying Single-Cell gradIENTs) is a tool for simulating cellular differentiation trajectories with arbitrary cell state intializations. PRESCIENT frames differentiation as a diffusion process given by a stochastic ODE with a drift parameter given by a generative neural network. PRESCIENT models can simulate cellular differentiation trajectories for out-of-sample (i.e. not seen during training) cells, enabling robust fate prediction and perturbational analysis. Here, we package PRESCIENT as a command-line tool and PyPI package." ; sc:featureList edam:operation_0337, edam:operation_3891, edam:operation_3907 ; sc:license "MIT" ; sc:name "PRESCIENT" ; sc:softwareHelp ; sc:url "https://github.com/gifford-lab/prescient" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0821, edam:topic_3125 ; sc:citation , "pubmed:34037777" ; sc:description "Preselector is a tool for optimize your cloning – a resource for identifying restriction enzymes for preselection reactions." ; sc:featureList edam:operation_0365, edam:operation_0431, edam:operation_2422, edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "Preselector" ; sc:url "http://Preselector.uni-jena.de" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25107873" ; sc:description "This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples." ; sc:featureList edam:operation_2423 ; sc:name "preseq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://smithlabresearch.org/software/preseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3125, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """A server for identification of bacterial small-RNA sequences and their targets with probable binding region. Predicting small RNAs and their Targets. Here, we present a webserver, PresRAT which aims to identify novel sRNA and its target genes. PresRAT aims to predict potential bacterial sRNA and the potential target of that sRNA against a bacterial genome containing mRNA sequences. With an added advantage PresRAT can build and perform molecular dynamics simulation on 3D models these sRNA and sRNA-mRNA bound duplex regions. Bacterial small-RNAs (sRNA) are RNAs of varied length (40 to 500 nucleotide long) mostly encoded in the intergenic regions of bacterial chromosomes. Most sRNAs act as regulatory elements by base pairing with the 5' untranslated region of mRNA transcripts.These sRNAs play important roles in gene regulation by modifying the stability and expression of the target transcript.""" ; sc:featureList edam:operation_0441, edam:operation_0443, edam:operation_2439, edam:operation_2476 ; sc:name "PresRAT" ; sc:url "http://www.hpppi.iicb.res.in/presrat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "P.R.E.S.S. (Protein Residue-Level Structural Statistics) is an R-package developed to allow researchers to get access to and manipulate on a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles." ; sc:featureList edam:operation_2479 ; sc:name "P.R.E.S.S." ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://orion.math.iastate.edu/press/presspage/P.R.E.S.S..html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0804, edam:topic_3168 ; sc:citation "pubmed:24618469" ; sc:description "Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires." ; sc:featureList edam:operation_2478 ; sc:name "pRESTO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://presto.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3179, edam:topic_3520 ; sc:citation , "pubmed:36319392" ; sc:description "Measurement and control of a superconducting quantum processor with a fully integrated radio-frequency system on a chip." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Presto" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/intermod-pro/presto-measure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "Pretext is an OpenGL-powered pretext contact map viewer." ; 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Interactive Prevalence Tables From Multi-Gene Panel Testing. This website describes basic, aggregated and deidentified clinical and genotype data from patients referred for hereditary cancer multigene panel testing to Ambry Genetics from March 2012 through December 2016. Data were compiled, normalized, and visualized in collaboration from researchers at the Mayo Clinic. The collaborations between Mayo Clinic And Ambry Genetics should not be seen as an endorsement of any company or product. Please Enter Your Information to Continue. Select which updates you would like to receive""" ; sc:featureList edam:operation_3196, edam:operation_3202, edam:operation_3436 ; sc:name "Prevalence tool" ; sc:url "https://www.ambrygen.com/prevalence-tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3068, edam:topic_3293, edam:topic_3517 ; sc:citation ; sc:description """Data pre-processing for more informative bacterial GWAS. Manuscript in support of prewas software. R package to perform data pre-processing for more informative bacterial GWAS. The prewas R package allows users to create a binary SNP matrix from a whole genome alignment. The SNP matrix includes the following features: (1) multiple line representation of multiallelic sites, (2) multiple line represention for SNPs present in overlapping genes, and (3) choice over the reference allele. Additionally, users can collapse SNPs into genes so the output is a binary gene matrix. Output from the prewas package should be used as the input to bacterial GWAS tools such as hogwash. The package is currently under development by the Snitkin Lab - please check for a vignette/tutorial in January 2020""" ; sc:featureList edam:operation_3182, edam:operation_3227, edam:operation_3745 ; sc:name "prewas" ; sc:url "https://github.com/Snitkin-Lab-Umich/prewas_manuscript_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621, edam:topic_0623, edam:topic_3534 ; sc:citation "pubmed:21036863" ; sc:description "Database of peroxiredoxin (Prx or PRDX) protein sequences unambiguously classified into one of six distinct subfamilies. 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Gadberry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation ; sc:description "Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R | This package was developed for two purposes: (1) to generate data-driven transcript annotations based on nascent transcript sequencing data, and (2) to annotate de novo identified transcriptional units (e.g., genes and enhancers) based on existing annotations such as those from (1). The code for this package was employed in analyses underlying our manuscript in preparation: Transcriptional mechanisms and gene regulatory networks underlying early adipogenesis (this note will be updated upon publication) | primaryTranscriptAnnotation-vignette.pdf | See the vignette and user manual:" ; sc:featureList edam:operation_0441, edam:operation_2495, edam:operation_3644 ; sc:name "primaryTranscriptAnnotation" ; sc:url "https://github.com/WarrenDavidAnderson/genomicsRpackage/tree/master/primaryTranscriptAnnotation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293 ; sc:citation "pubmed:26130236" ; sc:description "Library and accompanying tools for phylogenetics. 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GeneRegulation, Genetics, ImmunoOncology, Preprocessing, RNASeq, Sequencing, Software, Transcription.""" ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3792 ; sc:license "GPL-2.0" ; sc:name "primirTSS" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/primirTSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082 ; sc:citation , "pmcid:PMC5113968", "pubmed:27855192" ; sc:description "An Interactive Homology Modeling Pipeline" ; sc:featureList edam:operation_0477 ; sc:name "PRIMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://primo.rubi.ru.ac.za/" ; biotools:primaryContact "Özlem Tastan Bishop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC7488447", "pubmed:32912334" ; sc:description """integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits. 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PRIMoRDiA ( PRIMoRDiA Macromolecular Reactivity Descriptors Access ) is a shared memory parallel software written in C++ for post electronic structure calculations, that efficiently reads output files from most used quantum mechanics packages, storing molecular information and processing it to generate several descriptors to evaluate the global and local reactivity of molecular systems. 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The input of the program is the PDB (Protein Data Bank) file of the structure." ; sc:featureList edam:operation_0477, edam:operation_0570 ; sc:name "PrinCCes" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://scholar.semmelweis.hu/czirjakgabor/s/princces/#t1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0128 ; sc:citation "pubmed:22689640" ; sc:description "Web server which analyzes the structural features and physicochemical properties of the protein-RNA interface." ; sc:featureList edam:operation_2479, edam:operation_2949 ; sc:name "PRince" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html" ; biotools:primaryContact "Dr.Ranjit Prasad Bahadur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_3520, edam:topic_3957 ; sc:citation , "pubmed:33471077" ; sc:description """an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE. PrInCE is a computational approach to infer protein-protein interaction networks from co-elution proteomics data, also called co-migration, co-fractionation, or protein correlation profiling.""" ; sc:featureList edam:operation_2492, edam:operation_3094, edam:operation_3767 ; sc:license "MIT" ; sc:name "PrInCE" ; sc:url "https://www.bioconductor.org/packages/devel/bioc/html/PrInCE.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3175, edam:topic_3295, edam:topic_3303, edam:topic_3674 ; sc:citation , "pmcid:PMC8442460", "pubmed:34521442" ; sc:description "Princess is a fast and scalable framework to detect and report haplotype resolved Single Nucleotide Variants (SNV) and Structural Variations (SVs) at scale. It can leverage your cluster environment to speed up the detection which starts with one or many fasta or fastq files." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3228, edam:operation_3454, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PRINCESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MeHelmy/princess" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_2814 ; sc:citation "pubmed:24174311" ; sc:description "Automated refinement method that intends to refine an input protein structure by addressing both sampling and selection." ; sc:featureList edam:operation_2415, edam:operation_2479 ; sc:name "Princeton_TIGRESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://atlas.princeton.edu/refinement/" ; biotools:primaryContact "Christodoulos A. Floudas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174, edam:topic_3308 ; sc:citation "pubmed:21278185" ; sc:description "PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions." ; sc:featureList edam:operation_3187, edam:operation_3192, edam:operation_3219 ; sc:license "GPL-3.0" ; sc:name "PRINSEQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://edwards.sdsu.edu/prinseq" ; biotools:primaryContact "PRINSEQ Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1137 ; sc:name "PRINTS code" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1355 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein signature" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0623 ; sc:citation ; sc:description "A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family." ; sc:featureList edam:operation_0224 ; sc:name "PRINTS protein motif fingerprint database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/" ; biotools:primaryContact "Professor T.K.Attwood" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1365 ; sc:name "Fingerprint" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Extract data from PRINTS database for use by pscan." ; sc:featureList edam:operation_1812 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "printsextract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/printsextract.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3577 ; sc:citation , "pmcid:PMC7173875", "pubmed:32315351" ; sc:description """A tool for rare disease gene prioritization using MEDLINE. Phenotype-driven rare disease gene prioritization relies on high quality curated resources containing disease, gene and phenotype annotations. However, the effectiveness of gene prioritization tools is constrained by the incomplete coverage of rare disease, phenotype and gene annotations in such curated resources. METHODS:We extracted rare disease correlation pairs involving diseases, phenotypes and genes from MEDLINE abstracts and used the information propagation algorithm GCAS to build an association network. We built a tool called PRIORI-T for rare disease gene prioritization that uses this network for phenotype-driven rare disease gene prioritization. The quality of disease-gene associations in PRIORI-T was compared with resources such as DisGeNET and Open Targets in the context of rare diseases""" ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_3226 ; sc:name "PRIORI-T" ; sc:url "https://web.rniapps.net/priori-t/PRIORI-T.tar.gz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269 ; sc:citation , "pmcid:PMC9841403", "pubmed:36592035" ; sc:description "A utility for improving phylodynamic analyses in BEAST." ; sc:featureList edam:operation_2409, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PrioriTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jsigao/prioritree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654 ; sc:citation ; sc:description "PRIORITY is a tool for de novo motif discovery in the context of transcription factor (TF) binding sites. It implements a new approach to motif discovery in which informative priors over sequence positions are used to guide the search." ; sc:featureList edam:operation_0238, edam:operation_2421 ; sc:name "PRIORITY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.0" ; sc:url "http://www.cs.duke.edu/~amink/software/priority/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3574, edam:topic_3930 ; sc:citation , "pmcid:PMC8728240", "pubmed:34751399" ; sc:description "A Comprehensive Resource for Genetic Targets in Immune-Mediated Disease" ; sc:featureList edam:operation_2421, edam:operation_3672, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Priority index" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pi.well.ox.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091 ; sc:description "Priorr is a prioritization program of disease-linked genetic variants devoloped within the Genetics&Genomics Department of La Fundacion Jimenez Diaz University Hospital. Priorr is conceived to analyse the output of the FJD-pipeline of SNVs or CNVs. This software program offers a number of useful functionalities for variant analysis such as: filtering by a virtual panel of genes. manual control of different population frequencies or pathogenicity predictors or filtering out variants that have been already found by another protocol." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "PriorR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TBLabFJD/PriorR" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2343 ; sc:name "Pathway ID (KEGG)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_3620 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC9947447", "pubmed:36823571" ; sc:description "PriPath: identifying affected pathways from differential gene expression via grouping, scoring and modeling with an embedded machine learning approach." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PriPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/malikyousef/PriPath.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0632 ; sc:citation "pubmed:18221808" ; sc:description "Interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3′ end of the primers – a property that is crucial for sequence selectivity / specificity." ; sc:featureList edam:operation_0308 ; sc:name "PRISE" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://alglab1.cs.ucr.edu/OFRG/PRISE.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3168, edam:topic_3511, edam:topic_3519, edam:topic_3944 ; sc:citation ; sc:description """Efficient De Novo Primer Discovery. Tool for assisting the search of primer sequences for metabarcoding experiments. Given a taxonomic identifier, a reference database, and a genetic target region, PriSeT identifies conserved sections suitable for PCR primers such that taxonomic coverage and separation are optimal.""" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3200 ; sc:license "GPL-3.0" ; sc:name "PriSeT" ; sc:url "https://github.com/mariehoffmann/PriSeT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081 ; sc:citation "pubmed:10526354" ; sc:description "PrISM (Protein Informatics System for Modeling) is an integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling." ; sc:featureList edam:operation_2479, edam:operation_2480 ; sc:name "PrISM" ; sc:operatingSystem "Linux" ; sc:url "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PrISM" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2275 ; sc:citation "pubmed:24829450" ; sc:description "Fast and accurate prediction of protein-protein interactions (PPIs)." ; sc:featureList edam:operation_3439 ; sc:name "PRISM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cosbi.ku.edu.tr/prism/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0781, edam:topic_3168 ; sc:citation "pubmed:21068001" ; sc:description "Set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity." ; sc:featureList edam:operation_0308 ; sc:name "PriSM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/prism" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3421, edam:topic_3673 ; sc:citation , "pubmed:33720334" ; sc:description "PRISM (Poisson RNA-profile Identification in Scaled Mixtures) is statistical framework that allows simultaneous extraction of a tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples, by exploiting single-cell reference data. This facilitates a separate analysis of cancer cell and the microenvironment phenotypes and of the tumor composition." ; sc:featureList edam:operation_0314, edam:operation_3731 ; sc:license "BSD-2-Clause" ; sc:name "PRISM" ; sc:url "https://bitbucket.org/anthakki/prism" ; biotools:primaryContact "Antti Häkkinen", "Sampsa Hautaniemi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3172, edam:topic_3174, edam:topic_3407 ; sc:citation , "pmcid:PMC7699628", "pubmed:33247171" ; sc:description """Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences. Novel antibiotics are urgently needed to address the looming global crisis of antibiotic resistance. Historically, the primary source of clinically used antibiotics has been microbial secondary metabolism. Microbial genome sequencing has revealed a plethora of uncharacterized natural antibiotics that remain to be discovered. However, the isolation of these molecules is hindered by the challenge of linking sequence information to the chemical structures of the encoded molecules""" ; sc:featureList edam:operation_0267, edam:operation_3216, edam:operation_3482 ; sc:name "PRISM" ; sc:url "http://prism.adapsyn.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2258, edam:topic_3172 ; sc:citation , "pmcid:PMC5570231", "pubmed:28460067" ; sc:description "PRediction Informatics for Secondary Metabolomes. Prediction of genetically encoded natural product structures based on microbial genomes. It takes a microbial genome sequence as input, identifies biosynthetic gene clusters, and generates combinatorial libraries of structure predictions." ; sc:featureList edam:operation_0436, edam:operation_3216, edam:operation_3803 ; sc:name "PRISM 3" ; sc:softwareHelp ; sc:url "http://magarveylab.ca/prism/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3370, edam:topic_3382 ; sc:citation , "pmcid:PMC5656717", "pubmed:29104852" ; sc:description "CPU/GPU software for fast simulation of Scanning Transmission Electron Microscopy (STEM) experiments." ; sc:featureList edam:operation_2426, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "Prismatic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prism-em.com/" ; biotools:primaryContact "Alan Pryor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9979837", "pubmed:36874981" ; sc:description "Gene annotation prediction from stratified gene-gene co-expression matrices." ; sc:featureList edam:operation_2437, edam:operation_2454, edam:operation_2492, edam:operation_3463, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PrismEXP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://maayanlab.cloud/prismexp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0128, edam:topic_3794 ; sc:citation , "pmcid:PMC10320048", "pubmed:37140045" ; sc:description "Predicting protein-RNA interaction using in vivo RNA structural information." ; sc:featureList edam:operation_0278, edam:operation_2441, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PrismNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://prismnetweb.zhanglab.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:33710953" ; sc:description "Privacy-Net is an adversarial approach for identity-obfuscated segmentation of medical images." ; sc:featureList edam:operation_3443 ; sc:name "Privacy-Net" ; sc:url "https://github.com/bachkimn/Privacy-Net-An-Adversarial-Approach-forIdentity-Obfuscated-Segmentation-of-MedicalImages" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3033, edam:format_3475 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "This tool offers a novel approach to narrow down long lists of candidates by prioritizing them based on how well they meet the research goal. It organizes and analyzes complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element." ; sc:featureList edam:operation_3226 ; sc:license "Artistic-2.0" ; sc:name "Prize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Prize.html" ; biotools:primaryContact "Daryanaz Dargahi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3575, edam:topic_3678 ; sc:citation , "pubmed:34550162" ; sc:description "Estimation of prevalence ratios using logistic models and confidence intervals with delta and bootstrap methods." ; sc:featureList edam:operation_3432, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "prLogistic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=prLogistic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0160, edam:topic_0166 ; sc:citation , "pubmed:32750855" ; sc:description """An Algorithm for Protein Motif Discovery. Motifs are the evolutionarily conserved patterns which are reported to serve the crucial structural and functional role. Identification of motif patterns in a set of protein sequences has been a prime concern for researchers in computational biology. The discovery of such a protein motif using existing algorithms is purely based on the parameters derived from sequence composition and length. However, the discovery of variable length motif remains a challenging task, as it is not possible to determine the length of a motif in advance. In current work, a k-mer based motif discovery approach called Pr[m], is proposed for the detection of the statistically significant un-gapped motif patterns, with or without wildcard characters. In order to analyze the performance of the proposed approach, a comparative study was performed with MEME and GLAM2, which are two widely used non-discriminative methods for motif discovery""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0245 ; sc:name "Prm" ; sc:url "https://bioserver.iiita.ac.in/Pr[m]/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0634, edam:topic_0749, edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC10768107", "pubmed:37831097" ; sc:description "Integrated database for plant RNA modifications. It contains 20 plant species and provides an intuitive interface to display the information. PRMD provides visualization and functional analysis tools, such as RMlevelDiff, RMplantVar, RNAmodNet and Blast to perform different analyses, and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (IGV) to visually display the analysis and statistical results." ; sc:featureList edam:operation_0417, edam:operation_0443, edam:operation_2441, edam:operation_3222 ; sc:name "PRMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.sc.cn/PRMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32542382" ; sc:description """A Repository of Predicted RNA Modifications in Plants. Epitranscriptomics is an emerging field that studies the function of RNA base modifications in post-transcriptional regulation of gene expressions. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. PRMdb is a plant RNA modification database, which is based on analysis of thousands of RNA-seq datasets, small RNA-seq and degradome-seq datasets from various plant species using the tool HAMR (High-throughput Analysis of Modified Ribonucleotides) (Kuksa et al., 2017; Ryvkin et al., 2013). The raw sequencing data used to create PRMdb are downloaded from NCBI SRA/GEO, Plant MPSS db or sRNA db at Danforth Center. Plant genomes and annotations were derived from JGI phytozyme or Ensembl Plants. Full List of Datasets Used to Create PRMdb. The sequencing data used to create PRMdb are derived from NCBI, Plant MPSS db or sRNA data at Danforth Center.""" ; sc:featureList edam:operation_0337, edam:operation_0464, edam:operation_2422, edam:operation_3192, edam:operation_3431 ; sc:name "PRMdb" ; sc:softwareHelp ; sc:url "http://www.biosequencing.cn/PRMdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474 ; sc:citation ; sc:description "Protein arginine methylation prediction tool." ; sc:featureList edam:operation_0417 ; sc:name "PRmePRed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.icgeb.res.in/PRmePRed/" ; biotools:primaryContact "Dinesh Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_2640, edam:topic_3295, edam:topic_3934 ; sc:citation , "pmcid:PMC9400327", "pubmed:36002797" ; sc:description "Deconvolution of tumor composition using partially available DNA methylation data." ; sc:featureList edam:operation_0417, edam:operation_3204, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PRMeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hedingqin/PRMeth" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9499272", "pubmed:36094961" ; sc:description "PrMFTP is a web application used to identify multi-functionalities of therapeutic Peptides." ; sc:featureList edam:operation_3631, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PrMFTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.ahu.edu.cn/PrMFTP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3304, edam:topic_3444 ; sc:citation , "pmcid:PMC4367516", "pubmed:25844159" ; sc:description "Preprints of the R-fMRI Network. A community funded preprint hosting service. Provides free-submission and free hosting of manuscripts for resting state functional magnetic resonance imaging (R-fMRI) and neuroscience related studies." ; sc:featureList edam:operation_3431 ; sc:name "PRN" ; sc:url "http://rfmri.org/PRN" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3511 ; sc:citation "pubmed:26748145" ; sc:description "Predict the dentify the N6-methyladenosine (m6A)." ; sc:featureList edam:operation_0415 ; sc:name "pRNAm-PC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/pRNAm-PC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0621, edam:topic_0623, edam:topic_3120 ; sc:citation "pubmed:20935045" ; sc:description "It provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific." ; sc:featureList edam:operation_0321, edam:operation_0474, edam:operation_3225, edam:operation_3559 ; sc:name "The Protein Ontology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pir.georgetown.edu/pro" ; biotools:primaryContact "Protein Information Resource" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3534 ; sc:description "Tool for predicting the binding sites for the given proteins." ; sc:featureList edam:operation_2575 ; sc:name "Pro-BS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/guofeics/pro-bs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0099, edam:topic_0654 ; sc:citation "pubmed:22230796" ; sc:description "Multiple aligner specifically designed for homologous promoter regions." ; sc:featureList edam:operation_0492 ; sc:name "Pro-Coffee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.crg.cat/apps/tcoffee/do:procoffee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2830, edam:topic_3384, edam:topic_3452 ; sc:citation , "pubmed:35661662" ; sc:description "Development and validation of a nomogram for predicting the likelihood of metastasis in prostate cancer patients undergoing Ga-68 PSMA PET/CT due to biochemical recurrence." ; sc:featureList edam:operation_0252, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "pro-gram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pro-gram.nzm.co" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0769, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC9733281", "pubmed:36494629" ; sc:description "A robust pipeline for the pre-processing of single channel protein microarray data." ; sc:featureList edam:operation_2479, edam:operation_2495, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "Pro-MAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://metaomics.uct.ac.za/shinyapps/Pro-MAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_2814 ; sc:citation "pubmed:21998155" ; sc:description "Predict the protein stability free energy difference (ΔG), arising from a single-site amino acid substitution compared to the wild-type, denoted as ΔΔG." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "Pro-Maya" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bental.tau.ac.il/ProMaya/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_1775 ; sc:description "Application for data/function analysis, plotting, and curve fitting. It is used by scientists and engineers to analyze their measurements and the mathematical models they use to describe them." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:name "pro Fit" ; sc:operatingSystem "Mac" ; sc:softwareHelp , ; sc:softwareVersion "6.2.16" ; sc:url "http://www.quansoft.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Predictor of Antibody-Antigen interactions based on the Random Forest Algorithm. User submitted sequences are automatically aligned and annotated according to their source organism and germline families." ; sc:featureList edam:operation_0474, edam:operation_2492 ; sc:name "proABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.biocomputing.it/proABC" ; biotools:primaryContact "Pier Paolo Olimpieri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830, edam:topic_3474 ; sc:citation ; sc:description """PRediction Of AntiBody Contacts v2 and its application to information-driven docking. To use ProABC-2, you just need to provide the sequences of the heavy and light chains. Your request is expected to take a few seconds before you receive the results.""" ; sc:featureList edam:operation_0272, edam:operation_0321, edam:operation_0478 ; sc:name "proABC-2" ; sc:url "https://bianca.science.uu.nl/proabc2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "Use Prob2plinkbig to convert large MACH probability files to PLINK dosage files." ; sc:featureList edam:operation_0335 ; sc:name "Prob2plinkbig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ctglab.nl/software/prob2plinkbig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2269, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:33381834" ; sc:description "Probabilistic graphlets capture biological function in probabilistic molecular networks." ; sc:featureList edam:operation_3435, edam:operation_3501, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "probabilistic graphlets" ; sc:url "https://github.com/Serdobe/Probabilistic_Graphlets" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_1929, edam:format_2306 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0114, edam:topic_0121, edam:topic_0622, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file." ; sc:featureList edam:operation_0335, edam:operation_3631 ; sc:license "Artistic-2.0" ; sc:name "proBAMr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/proBAMr.html" ; biotools:primaryContact "Xiaojing Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "This tool facilitates batch effects analysis and correction in high-throughput experiments. It was developed primarily for mass-spectrometry based proteomics (DIA/SWATH). The package contains functions for diagnostics (proteome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts." ; sc:featureList edam:operation_3435, edam:operation_3744 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "proBatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/symbioticMe/proBatch" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3308, edam:topic_3974 ; sc:citation , "pmcid:PMC8994916", "pubmed:35397520" ; sc:description "Joint modeling of epigenome and transcriptome effects in 3D genome." ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PROBC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.github.com/seferlab/probc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences." ; sc:featureList edam:operation_0492, edam:operation_2451 ; sc:name "ProbCons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://probcons.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Tool for progressive protein multiple sequence alignment based on probabilistic consistency." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:name "Probcons WS (jabaws)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.compbio.dundee.ac.uk/jabaws/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_2275, edam:topic_3277 ; sc:citation "pubmed:21576226" ; sc:description "PRUNE is a web server for the selection of a subset of protein-protein docking poses generated during sampling search using an interface area based edge-scoring function. PROBE is a web server for refining, scoring and ranking of the resulting protein-protein docking poses using a regression model." ; sc:featureList edam:operation_0478, edam:operation_0482, edam:operation_3659 ; sc:name "Protein Binding Evaluation (PROBE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pallab.serc.iisc.ernet.in/probe" ; biotools:primaryContact "Contact Form", "Pralay Mitra" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_3468 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2830 ; sc:author "James Robinson" ; sc:citation ; sc:contributor "James Robinson" ; sc:description "Search tool for generating probe and primer hit tables." ; sc:featureList edam:operation_0239 ; sc:name "Probe and Primer Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/ipd/imgt/hla/probe.html" ; biotools:primaryContact "James Robinson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654 ; sc:citation , "pubmed:11724738" ; sc:description "Probe Select is the probes program to select oligos for DNA microarray." ; sc:featureList edam:operation_2495 ; sc:name "Probe Select" ; sc:operatingSystem "Linux" ; sc:url "http://stormo.wustl.edu/resources.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3168 ; sc:citation ; sc:description "ProbeAlign is a program for annotating ncRNA structures by incorporating high-throughput sequencing based structure probing information." ; sc:featureList edam:operation_2421 ; sc:name "ProbeAlign" ; sc:operatingSystem "Linux" ; sc:softwareVersion "0.3" ; sc:url "http://genome.ucf.edu/ProbeAlign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3077, edam:topic_3300, edam:topic_3304 ; sc:citation , "pmcid:PMC8887962", "pubmed:35242020" ; sc:description "A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments." ; sc:featureList edam:operation_0335, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ProbeInterface" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gin.g-node.org/spikeinterface/probeinterface_library" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3168, edam:topic_3518 ; sc:citation "pubmed:15215432" ; sc:description "Using current releases of genomic sequence data, this tool allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and the tool reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit." ; sc:featureList edam:operation_0309 ; sc:name "ProbeLynx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pathogenomics.ca/probelynx" ; biotools:primaryContact "ProbeLynx team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:19351619" ; sc:description "A program that matches a large set of oligonucleotide sequences against a genome database using gapped alignments." ; sc:featureList edam:operation_0346, edam:operation_0492, edam:operation_2429 ; sc:name "ProbeMatch" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.cs.wisc.edu/%7Ejignesh/probematch/" ; biotools:primaryContact "Support (Please put \"ProbeMatch Help\" in the Subject line of your email.)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "ProbePlus is an analytical tool for analyzing Affymetrix GeneChip® Gene Expression Array data at probe level. It is able to extract CEL file; integrate Perfect Match (PM) and Mis-match (MM) for a probe pair; generate gene expression index (GEI) from the integrated probe intensities of multiple probe pairs in a probe set; and analyze data directly from probe level data without necessity of generating a GEI for a probe set." ; sc:featureList edam:operation_2495 ; sc:name "ProbePlus" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "http://qge.fhcrc.org/probeplus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_0654, edam:topic_3557 ; sc:citation "pubmed:16740623" ; sc:description "Oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals." ; sc:featureList edam:operation_0308 ; sc:name "PROBER" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://prober.cshl.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3308 ; sc:citation , "pmcid:PMC5758053", "pubmed:28501650" ; sc:description "PROBer is a program to quantify chemical modification profiles for a general set of sequencing-based ‘toeprinting’ assays, which aim at probing RNA structures (DMS/SHAPE-seq), detecting RNA modifications (Pseudo-seq), and investigating RNA-protein interactions (iCLIP)." ; sc:featureList edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "PROBer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.3.1" ; sc:url "http://pachterlab.github.io/PROBer/" ; biotools:primaryContact "Lior Pachter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_3169, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC7750938", "pubmed:32573679" ; sc:description """a recommender system to infer binding profiles for nucleic acid-binding proteins. the interaction between proteins and nucleic acids plays a crucial role in gene regulation and cell function. Determining the binding preferences of nucleic acid-binding proteins (NBPs), namely RNA-binding proteins (RBPs) and transcription factors (TFs), is the key to decipher the protein-nucleic acids interaction code. Today, available NBP binding data from in vivo or in vitro experiments are still limited, which leaves a large portion of NBPs uncovered. Unfortunately, existing computational methods that model the NBP binding preferences are mostly protein specific: they need the experimental data for a specific protein in interest, and thus only focus on experimentally characterized NBPs""" ; sc:featureList edam:operation_2492, edam:operation_2495, edam:operation_3767 ; sc:name "ProbeRating" ; sc:url "https://github.com/syang11/ProbeRating" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0632, edam:topic_3308 ; sc:citation ; sc:description "ProbeSpec is a utility for mapping the specificity of all candidate probes for a given sequence (e.g. transcript) against a background containing a large set of sequences (e.g. a transcriptome). Probe specificity is determined by the subsequence in the background that is most similar to its target, the specificity being set as the number of mismatches between the probe and the closest non-specific background sequence." ; sc:featureList edam:operation_0308, edam:operation_2429 ; sc:name "ProbeSpec" ; sc:operatingSystem "Windows" ; sc:url "http://www.cs.technion.ac.il/labs/cbl/probespec/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269 ; sc:citation , ; sc:description """It is a novel sensitive method for the detection of user-defined compositional bias in biological sequences. It automatically searches a user-supplied protein sequence for segments that contain unusually dense clusters of user-specified amino acid types and computes analytical estimates of the statistical significance of each cluster.""" ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "ProBias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lcg.rit.albany.edu/bias/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3068, edam:topic_3379, edam:topic_3398, edam:topic_3697 ; sc:citation , "pmcid:PMC9290863", "pubmed:35849028" ; sc:description "A database and semantic analysis engine for literature, clinical trials and patents related to probiotics." ; sc:featureList edam:operation_2421, edam:operation_3695, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "ProBioQuest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://kwanlab.bio.cuhk.edu.hk/PBQ/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_3125, edam:topic_3534 ; sc:citation "pubmed:20504855", "pubmed:22600737" ; sc:description "Web server which detects protein binding sites based on local structural alignments. Algorithms have been parallelized to allow for faster computing against the PDB. Pre-calculated protein similarity profiles for over 29,000 non-redundant proteins are also available." ; sc:featureList edam:operation_0509, edam:operation_2575, edam:operation_3092, edam:operation_3222 ; sc:name "ProBiS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://probis.cmm.ki.si" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510, edam:topic_3534 ; sc:citation , "pubmed:26509288" ; sc:description "Connected the ProBiS and CHARMMing web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation." ; sc:featureList edam:operation_2492 ; sc:name "ProBiS-CHARMMing" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://probis.nih.gov/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2275, edam:topic_3047, edam:topic_3534 ; sc:citation , "pubmed:35289616" ; sc:description "A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison." ; sc:featureList edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ProBiS-Dock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://insilab.org/probisdock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_3336, edam:topic_3534 ; sc:citation , "pubmed:34319727" ; sc:description "A Web Server and Interactive Web Repository of Small Ligand-Protein Binding Sites for Drug Design." ; sc:featureList edam:operation_0509, edam:operation_2421, edam:operation_2575, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "ProBiS-Dock Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://probis-dock-database.insilab.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1008 ; sc:name "Polypeptide chain ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:name "Protein name (UniProt)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_3336, edam:topic_3534 ; sc:citation , "pubmed:36269348" ; sc:description "ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites." ; sc:featureList edam:operation_0224, edam:operation_0474, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "ProBiS-Fold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://probis-fold.insilab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation , "pmcid:PMC4086080", "pubmed:24861616" ; sc:description "ProBiS is a web server for predicting ligands by similarity in binding sites." ; sc:featureList edam:operation_0445, edam:operation_0478, edam:operation_0482, edam:operation_2575, edam:operation_3092 ; sc:name "ProBiS-ligands" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://probis.cmm.ki.si/ligands" ; biotools:primaryContact "ProBiS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0820, edam:topic_2275 ; sc:citation "pubmed:25126110" ; sc:description "Webserver that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC, POPE or artificial)." ; sc:featureList edam:operation_2492 ; sc:name "ProBLM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.clemson.edu/sapp/problm_webserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172 ; sc:author "Ricardo R. Silva" ; sc:citation ; sc:description "ProbMetab is an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics" ; sc:featureList edam:operation_3633, edam:operation_3926, edam:operation_3928, edam:operation_3929 ; sc:license "GPL-2.0" ; sc:name "ProbMetab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://labpib.fmrp.usp.br/methods/probmetab/" ; biotools:primaryContact "Ricardo Z. N. Vêncio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:name "Compound name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3063, edam:topic_3500 ; sc:citation , "pmcid:PMC9375527", "pubmed:35962763" ; sc:description "A database for drug-resistant probiotic bacteria." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "ProbResist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://probresist.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation "pubmed:24376038" ; sc:description "Produce features found to be related to both the secondary and tertiary structures of the RNAs." ; sc:featureList edam:operation_2441 ; sc:name "ProbRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hkbic.cuhk.edu.hk/software/probrna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_2275, edam:topic_3542 ; sc:citation , "pubmed:33381815" ; sc:description """PROBselect is an accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection. PROBselect suggests a predictor that is likely to provide the best prediction of protein-binding residues the for the input proteins. PROBselect uses predictions generated by SCRIBER and estimated AUC of SSWRF and CRFPPI to make the recommendation.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_2492, edam:operation_3899, edam:operation_3904 ; sc:name "PROBselect" ; sc:url "http://bioinformatics.csu.edu.cn/PROBselect/home/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "PROC QTL is a user defined SAS (Statistical analysis system) procedure for mapping quantitative trait loci (QTL)." ; sc:featureList edam:operation_2238, edam:operation_2429 ; sc:name "PROC QTL" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://statgen.ucr.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0152, edam:topic_3068, edam:topic_3071 ; sc:citation , "pubmed:32119071" ; sc:description """protein-carbohydrate complex binding affinity database. ProCaff Version 1.0 has been Launched. ProCaff, a database on binding affinity of protein-carbohydrate complexes, ProCaff, which contains 3122 entries on dissociation constant (Kd), Gibbs free energy change (ΔG), experimental conditions, sequence, structure and literature information. Additional features include the options to search, display, visualization, download and upload the data.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3092 ; sc:name "ProCaff" ; sc:url "http://web.iitm.ac.in/bioinfo2/procaff/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_2640, edam:topic_3068, edam:topic_3360 ; sc:citation ; sc:description "A database of manually curated biomarkers for Prostate Cancer." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ProCanBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/procanbio/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3479 ; sc:name "Gene order" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3272 ; sc:encodingFormat edam:format_1910 ; sc:name "Species tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3479 ; sc:name "Gene order" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method. The method runs from a phylogeny tree (without branch lengths needed) with a marked ancestor and a block file. This homology-based method is based on iteratively detecting and assembling ancestral adjacencies, while allowing some micro-rearrangements of synteny blocks at the extremities of the progressively assembled CARs." ; sc:featureList edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "CECILL-B" ; sc:name "ProCARs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "26042016" ; sc:url "http://bioinfo.lifl.fr/procars/procars.php" ; biotools:primaryContact "PERRIN Amandine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_3474 ; sc:citation , "pubmed:34382131" ; sc:description "Provides tools for exploratory process data analysis. Process data refers to the data describing participants' problem-solving processes in computer-based assessments. It is often recorded in computer log files. This package provides functions to read, process, and write process data. It also implements two feature extraction methods to compress the information stored in process data into standard numerical vectors. This package also provides recurrent neural network based models that relate response processes with other binary or scale variables of interest. The functions that involve training and evaluating neural networks are wrappers of functions in 'keras'." ; sc:featureList edam:operation_3359, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProcData" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://CRAN.R-project.org/package=ProcData" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3360 ; sc:citation "pubmed:23930024" ; sc:description "Web-based application used to conduct probabilistic reverse dosimetry calculations. The tool is used for estimating a distribution of exposure concentrations likely to have produced biomarker concentrations measured in a population. Here we define biomarkers as the chemical or its metabolites that can be measured in human tissues or fluids." ; sc:featureList edam:operation_2238 ; sc:name "PROcEED" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://www.epa.gov/chemical-research/probabilistic-reverse-dosimetry-estimating-exposure-distribution-proceed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3292, edam:topic_3520 ; sc:citation ; sc:description "A package for processing protein mass spectrometry data." ; sc:featureList edam:operation_3214 ; sc:license "Artistic-2.0" ; sc:name "PROcess" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PROcess.html" ; biotools:primaryContact "Xiaochun Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:description "This program 1) converts fluorescent images to black and white, 2) removes insignificant objects, and 3) removes glare. The program is optimized for minicell image analysis." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Process Cell Images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/44119-process-cell-images" ; biotools:primaryContact "UVa iGem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_2814 ; sc:citation "pubmed:9008363" ; sc:description "Check the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR." ; sc:featureList edam:operation_2406 ; sc:name "PROCHECK" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3068, edam:topic_3169, edam:topic_3179 ; sc:citation , "pmcid:PMC8728212", "pubmed:34791440" ; sc:description "A PROkaryotic Chromatin ImmunoPrecipitation DataBase" ; sc:featureList edam:operation_0445, edam:operation_3222, edam:operation_3900 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "proChIPdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prochipdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:10980157", "pubmed:14751983", "pubmed:15072687", "pubmed:17963510" ; sc:description "Multi-layer protein comparison meta-server that computes structure similarities using various information theory measures. It integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. Based on a diverse set of similarity measures computes a consensus similarity profile for the entire protein set. All results can be clustered, visualised, analysed." ; sc:featureList edam:operation_2483, edam:operation_2487, edam:operation_2488, edam:operation_2997 ; sc:name "ProCKSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.procksi.net/" ; biotools:primaryContact "ProCKSI Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:description "PROCLASS allows to predict the class of protein from its amino acid sequence. It predict weather protein belong to class Alpha or Beta or Alpha+Beta or Alpha/Beta." ; sc:featureList edam:operation_2479, edam:operation_2990, edam:operation_2996 ; sc:name "PROCLASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webs.iiitd.edu.in/raghava/proclass/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0821, edam:topic_3474, edam:topic_3534 ; sc:citation , "pmcid:PMC7393547", "pubmed:32413515" ; sc:description """Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. in silico identification of protease substrate cleavage sites. a conditional random field approach that combines sequence and structural information. Procleave is developed to improve the performance of protease substrate cleavage site prediction by incorporating the real 3D structural features of substrates. significantly improves the prediction of protease substrate cleavage sites. We have mapped the substrates deposited in MEROPS onto the structural database PDB and obtained a subset of protein substrates with experimentally solved 3D structures.""" ; sc:featureList edam:operation_0394, edam:operation_0417, edam:operation_0418, edam:operation_0422, edam:operation_3431 ; sc:name "Procleave" ; sc:url "http://procleave.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3474 ; sc:citation , "pubmed:34145882" ; sc:description "A Machine-Learning Tool to Support (Re-)coding of Free-Texts of Occupations and Industries." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Procode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pro-code.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_1317 ; sc:citation , "pmcid:PMC3098589", "pubmed:21311038" ; sc:description "The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps." ; sc:featureList edam:operation_0474 ; sc:license "GPL-2.0" ; sc:name "procoil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/procoil.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3475, edam:format_3621, edam:format_3702, edam:format_3758, edam:format_3788 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3247, edam:format_3248, edam:format_3684 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121 ; sc:author , "PD Dr. Martin Eisenacher" ; sc:citation , "pubmed:26182917" ; sc:description "Conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ProCon (Proteomics Conversion Tool)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.654" ; sc:url "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.en#ProCon" ; biotools:primaryContact "PD Dr. Martin Eisenacher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3508 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Protein co-expression network construction using peptide level data, with statisical analysis. 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It can be used to accurately identify the burial depth status of amino acid residues in a protein." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "Prodepth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/Prodepth/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3175 ; sc:citation , "pubmed:33459758" ; sc:description "Reference Position Dependent Alignment. 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The ProdMX employs a compressed sparse matrix algorithm to reduce computational resources and time used to perform the matrix manipulation during functional domain analysis.""" ; sc:featureList edam:operation_0224, edam:operation_0247, edam:operation_1777 ; sc:license "MIT" ; sc:name "ProdMX" ; sc:url "https://github.com/visanuwan/prodmx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0622, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:15980440" ; sc:description "Repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information." ; sc:featureList edam:operation_0224, edam:operation_0246, edam:operation_0303, edam:operation_0320, edam:operation_2406 ; sc:name "PRODOC" ; sc:url "http://hodgkin.mbu.iisc.ernet.in/~prodoc/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1142 ; sc:name "ProDom accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1142 ; sc:name "ProDom accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1142 ; sc:name "ProDom accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1142 ; sc:name "ProDom accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1142 ; sc:name "ProDom accession number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2331 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0736 ; sc:citation ; sc:description "A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database." ; sc:featureList edam:operation_0224 ; sc:name "ProDom protein domain database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodom.prabi.fr/prodom/current/html/home.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3071 ; sc:description "A set of webservices allowing to browse ProDom-CG267 evolutionary scenarios." ; sc:featureList edam:operation_2422 ; sc:name "ProdomCG_evoscen" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.health2api.com/?p=10236" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3071, edam:topic_3293 ; sc:citation ; sc:description "Set of webservices allowing to browse ProDom-CG267 phylogenetic tree." ; sc:featureList edam:operation_2422 ; sc:name "ProdomCG_tree" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.health2api.com/?p=10237" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:18440972" ; sc:description "A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and shared regulators are detected. Common metabolic pathways are then viewed on KEGG maps." ; sc:featureList edam:operation_0533, edam:operation_1781, edam:operation_3439, edam:operation_3463, edam:operation_3660 ; sc:name "ProdoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.prodonet.tu-bs.de" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0114, edam:topic_0204, edam:topic_0621, edam:topic_0749 ; sc:citation , "pmcid:PMC8728284", "pubmed:34850133" ; sc:description "The most comprehensive database for gene regulation and gene expression in prokaryotes." ; sc:featureList edam:operation_0435, edam:operation_0445, edam:operation_0579, edam:operation_1781, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "PRODORIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.prodoric.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2814 ; sc:citation , , "pmcid:PMC3102222", "pubmed:21471012", "pubmed:33822884" ; sc:description "ProDy is a free and open-source Python package for protein structural dynamics analysis." ; sc:featureList edam:operation_2406 ; sc:license "MIT" ; sc:name "ProDy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0", "2.0" ; sc:url "http://prody.csb.pitt.edu/" ; biotools:primaryContact , , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0654 ; sc:citation "pubmed:11827492" ; sc:description "A profile-profile comparison program that compares PSI-BLAST profiles." ; sc:featureList edam:operation_0300 ; sc:name "prof_sim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://biozon.org/ftp/software/prof_sim/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0218, edam:topic_0821, edam:topic_1775, edam:topic_3474 ; sc:citation , "pubmed:36736370" ; sc:description "ProFAB-open protein functional annotation benchmark." ; sc:featureList edam:operation_1777, edam:operation_3092, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ProFAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://profab.kansil.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_2814 ; sc:author "Burkhard Rost" ; sc:citation ; sc:contributor "Chris Sander" ; sc:description "Solvent accessibility predictor." ; sc:featureList edam:operation_0384 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PROFacc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL Heidelberg", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.42" ; sc:url "http://ppopen.informatik.tu-muenchen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0091 ; sc:citation , "pmcid:PMC10401835", "pubmed:37545885" ; sc:description "Web-based protein fragment and structure analysis workstation." ; sc:featureList edam:operation_0403, edam:operation_0477, edam:operation_0570, edam:operation_2415, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "PROFASA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://profasa.ucc.ie/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3318, edam:topic_3372 ; sc:citation , "pmcid:PMC7693306", "pubmed:33142807" ; sc:description """Optimized Planning and Evaluation of Dental Implant Fatigue Testing. Software for fitting fatigue data.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "ProFatigue" ; sc:url "https://meteo.unican.es/temp/castie/Profatigue.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3500 ; sc:citation "pubmed:18460543" ; sc:description "Web based tool for the interpretation of genes that were identified to be functionally linked. 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New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_1777, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "PROFEAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi" ; biotools:primaryContact "Dr. Tao Lin", "Zhang Peng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0601, edam:topic_3293, edam:topic_3510 ; sc:citation , "pmcid:PMC10023195", "pubmed:36936371" ; sc:description "Python based program creating highly customizable 2D maps showing elements of interests (domains, repeats, PTM sites,...) called feature as defined in Uniprot." ; sc:featureList edam:operation_0239, edam:operation_0417, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProFeatMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://profeatmap.pythonanywhere.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC9842958", "pubmed:36698978" ; sc:description "A parallelized protein feature extraction suite for machine learning." ; sc:featureList edam:operation_0302, edam:operation_2492, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ProFeatX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo.usu.edu/profeatx/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_3170, edam:topic_3336 ; sc:citation ; sc:description "Profile filtering of expression data." ; sc:featureList edam:operation_2495 ; sc:name "ProFED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://ebi056.uni-muenster.de:3838/profed/" ; biotools:primaryContact "Jenny Potratz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3393 ; sc:citation , "pubmed:34666203" ; sc:description "Profeel is an open-source dosimetry data visualization software (MATLAB®), which can be used for 1D, 2D and 3D data comparison, data processing and analytics." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Profeel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TPakar/Profeel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3474 ; sc:citation "pubmed:26130574" ; sc:description "Protein Feature Engineering Toolkit for Machine Learning." ; sc:featureList edam:operation_2479 ; sc:name "ProFET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ddofer/ProFET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC10251600", "pubmed:37296454" ; sc:description "AI-based platform for small molecules liability profiling." ; sc:featureList edam:operation_3891, edam:operation_3935, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "ProfhEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://profhex.exscalate.eu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0820 ; sc:author "Burkhard Rost" ; sc:citation ; sc:contributor "Chris Sander" ; sc:description "Prediction of helical transmembrane regions." ; sc:featureList edam:operation_0269 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PROFhtm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL Heidelberg", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.42" ; sc:url "http://ppopen.informatik.tu-muenchen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation ; sc:description "Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the package that implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) and generates the peak table." ; sc:featureList edam:operation_3222 ; sc:license "CECILL-2.1" ; sc:name "proFIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.10" ; sc:url "http://bioconductor.org/packages/release/bioc/html/proFIA.html" ; biotools:primaryContact "Alexis Delabriere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Regularization and score distributions for position count matrices." ; sc:featureList edam:operation_0239 ; sc:license "MIT" ; sc:name "profileScoreDist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/profileScoreDist.html" ; biotools:primaryContact "Paal O. Westermark" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2062 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128 ; sc:author "Yanay Ofran" ; sc:citation , "pubmed:17237081" ; sc:contributor "Burkhard Rost", "Grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH)" ; sc:description "Prediction of protein-protein interaction sites identified from sequence." ; sc:featureList edam:operation_2464 ; sc:funder "Grants RO1-GM63029-01 and R01-GM64633-01 from the National Institutes of Health (NIH)" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PROFisis" ; sc:operatingSystem "Linux" ; sc:provider "Columbia University", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.11" ; sc:url "https://rostlab.org/owiki/index.php/PROFisis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1354 ; sc:name "Sequence profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0869 ; sc:name "Sequence-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Scan one or more sequences with a simple frequency matrix." ; sc:featureList edam:operation_0300 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "profit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/profit.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_2814, edam:topic_3474, edam:topic_3510 ; sc:citation , "pubmed:34542606" ; sc:description "A Protein Tertiary Structure Fitness Function for Quantifying the Accuracies of Model Structures." ; sc:featureList edam:operation_0295, edam:operation_0321, edam:operation_0477, edam:operation_2442, edam:operation_2487 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ProFitFun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/KYZ-LSB/ProTerS-FitFun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2275, edam:topic_3293, edam:topic_3336 ; sc:citation ; sc:description """A Comprehensive Web Server for Structure-based Kinase Selectivity Profiling. Kinase profiling is an efficient strategy for kinase inhibitor discovery, polypharmacological drug discovery and drug repositioning. A variety of methods have been established for kinase profiling, of which the combined mode of experimental and computational approaches is attractive, particularly in the early drug discovery. With the increasing number of kinase-inhibitor complex structures, structure-based kinase profiling is of great interest. To fully exploit the potential of structure-based kinase profiling in drug discovery and drug repositioning, we developed a versatile web server, termed ProfKin, for structure-based kinase profiling for small molecules of interest, which is established based on an in-house comprehensive structural database (KinLigDB) of manually curated kinase-ligand complex structures and associated information.""" ; sc:featureList edam:operation_0224, edam:operation_0478, edam:operation_0567 ; sc:name "ProfKin" ; sc:url "http://www.lilab-ecust.cn/profkin/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "A tool for searching a protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map." ; sc:featureList edam:operation_2929, edam:operation_3631, edam:operation_3643, edam:operation_3646, edam:operation_3647, edam:operation_3649, edam:operation_3767 ; sc:name "ProFound" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prowl.rockefeller.edu/prowl-cgi/profound.exe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_2259 ; sc:citation "pubmed:25657331" ; sc:description "This tool uses an accelerated version of the original profile kernel to train SVM based protein-protein interaction (PPI) prediction models and to predict new PPIs from sequence alone." ; sc:featureList edam:operation_2464, edam:operation_2492 ; sc:name "Profppikernel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rostlab.org/owiki/index.php/Profppikernel" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317 ; sc:author "Burkhard Rost" ; sc:citation "pubmed:12647405" ; sc:description "Neural network based prediction method of 3 state protein secondary structure states (helix, loop, turns) at over 78% accuracy from protein sequence." ; sc:featureList edam:operation_0267 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PROFsec" ; sc:operatingSystem "Linux" ; sc:provider "Columbia University", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.0.42" ; sc:url "http://www.predictprotein.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_1920 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0820 ; sc:author "Henry Bigelow" ; sc:citation , "pmcid:PMC1538807", "pubmed:16844988" ; sc:contributor "Burkhard Rost", "grant R01-LM07329-01 from the National Library of Medicine" ; sc:description "Per-residue prediction of bacterial transmembrane beta barrels." ; sc:featureList edam:operation_0268, edam:operation_0269 ; sc:funder "grant R01-LM07329-01 from the National Library of Medicine" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PROFtmb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Columbia University", "Irvine Cancer Center", "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1.1.12" ; sc:url "http://ppopen.informatik.tu-muenchen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3444 ; sc:citation , "pubmed:32771617" ; sc:description """Modelling subject variability in the spatial and temporal characteristics of functional modes. Recent work has highlighted the scale and ubiquity of subject variability in observations from functional MRI data (fMRI). Furthermore, it is highly likely that errors in the estimation of either the spatial presentation of, or the coupling between, functional regions can confound cross-subject analyses, making accurate and unbiased representations of functional data essential for interpreting any downstream analyses. Here, we extend the framework of probabilistic functional modes (PFMs) (Harrison et al., 2015) to capture cross-subject variability not only in the mode spatial maps, but also in the functional coupling between modes and in mode amplitudes""" ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "PROFUMO" ; sc:url "http://git.fmrib.ox.ac.uk/samh/profumo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1775, edam:topic_2814 ; sc:author "Roman Laskowski", "Thornton Group" ; sc:citation ; sc:contributor "James Watson" ; sc:description "Protein function prediction." ; sc:featureList edam:operation_1777 ; sc:name "ProFunc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/profunc" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0203, edam:topic_0625, edam:topic_3172, edam:topic_3295 ; sc:citation , "pmcid:PMC6326795", "pubmed:30239796" ; sc:description """A framework for the prioritization of candidate causal genes at molecular quantitative trait loci. ProGeM (Prioritisation of candidate causal Genes at Molecular QTLs) is a pipeline for the prioritisation of candidate causal genes - or mediating genes - for molecular quantitative trait loci (QTL) in an automatable fashion. knitr::opts_chunk$set(echo = FALSE).""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3226, edam:operation_3232, edam:operation_3799 ; sc:name "ProGeM" ; sc:url "https://github.com/ds763/ProGeM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3604 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0622, edam:topic_2533, edam:topic_2640, edam:topic_3175 ; sc:citation ; sc:description "The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 113322 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1600 articles and represents 420 and 542 different cancer types, according to the International classification of Diseases in Oncology (ICD-O) and NCIt \"neoplasm\" classification, respectively. Additionally, the website attempts to identify and present all publications (currently 3962 articles), referring to cancer genome profiling experiments." ; sc:featureList edam:operation_0305, edam:operation_0337, edam:operation_0362, edam:operation_3194, edam:operation_3233, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "Progenetix" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp , ; sc:url "http://progenetix.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622, edam:topic_0637, edam:topic_3174 ; sc:citation , "pmcid:PMC5210662", "pubmed:28053165", "pubmed:31647096" ; sc:description "proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. taxonomic clades, representatives of each species or habitat-specific organisms." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "proGenomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "HD-HuB" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://progenomes.embl.de/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_1775, edam:topic_2259 ; sc:citation , "pmcid:PMC5750219", "pubmed:29295995" ; sc:contributor ; sc:description "This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication \"Perturbation-response genes reveal signaling footprints in cancer gene expression\"." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "progeny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/progeny.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3068, edam:topic_3678 ; sc:citation "pubmed:22039152" ; sc:description "A manually curated, comprehensive repository of experimentally characterized bacterial and archaeal glycoproteins, generated from an exhaustive literature search." ; sc:featureList edam:operation_0305, edam:operation_0321, edam:operation_0477, edam:operation_2422, edam:operation_3501 ; sc:name "ProGlycProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.proglycprot.org/" ; biotools:primaryContact "Dr. Alka Rao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC3245024", "pubmed:22039152" ; sc:description "ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized eubacterial and archaeal glycoproteins, generated from an exhaustive literature search." ; sc:featureList edam:operation_2945 ; sc:name "proglycprot (Prokaryotic Glycoproteins)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/proglycprot/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_0154, edam:topic_0623, edam:topic_3168 ; sc:citation "pubmed:19494185" ; sc:description "Facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. It is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences." ; sc:featureList edam:operation_0224, edam:operation_2429, edam:operation_2871 ; sc:name "ProGMap" ; sc:url "http://www.bioinformatics.nl/progmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3518 ; sc:citation "pubmed:19393097" ; sc:description "Database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between gene expression and prognosis." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3463 ; sc:name "PrognoScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.prognoscan.org/" ; biotools:primaryContact "Hideaki Mizuno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3173, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC8561914", "pubmed:34727887" ; sc:description "Pathway/gene set-based tumour volume prediction using multiple kernel learning." ; sc:featureList edam:operation_0314, edam:operation_3659, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PrognosiT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/begumbektas/prognosit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3697 ; sc:citation , "pmcid:PMC7972227", "pubmed:33731016" ; sc:description "ProgPerm is a tool for progressive permutation for a dynamic representation of the robustness of microbiome discoveries. The proposed method progressively permutes the grouping factor labels of microbiome and performs multiple differential abundance tests in each scenario. We compare the signal strength of top hits from the original data with their performance in permutations, and will observe an apparent decreasing trend if these top hits are true positives identified from the data. The method can evaluate the overall association between microbiome and the grouping factor, rank the robustness of the discovered microbes, and list the discoveries, their effect sizes, and individual abundances." ; sc:featureList edam:operation_0490, edam:operation_3435, edam:operation_3936 ; sc:license "MIT" ; sc:name "ProgPerm" ; sc:url "https://biostatistics.mdanderson.org/shinyapps/ProgPerm" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "ProHits is an open source software package designed to help scientists store, search and analyze mass spectrometry data, in particular for protein-protein interaction experiments." ; sc:featureList edam:operation_2421 ; sc:name "ProHits" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.1" ; sc:url "http://prohitsms.com/Prohits_download/list.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0905 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein interaction raw data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_3047 ; sc:citation ; sc:description "A suite of web-based tools for visualizing and analyzing protein interaction data." ; sc:featureList edam:operation_2949, edam:operation_3083, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:name "ProHits-viz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prohits-viz.lunenfeld.ca/" ; biotools:primaryContact "James D R Knight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3300, edam:topic_3400, edam:topic_3474 ; sc:citation , "pubmed:32964284" ; sc:description """improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations. Prediction of Pro-inflammatory Peptides. SINGLE PREDICTIONMore detailed prediction on one peptide. Input your peptide sequence here. The sequence should be in FASTA format. Example. Please be patient after submitting and do not close this page.""" ; sc:featureList edam:operation_0418, edam:operation_3631 ; sc:name "ProIn-Fuse" ; sc:url "http://kurata14.bio.kyutech.ac.jp/ProIn-Fuse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pmcid:PMC10057851", "pubmed:36930671" ; sc:description "An interpretable protein inference tool leveraging on biological networks." ; sc:featureList edam:operation_3649, edam:operation_3741, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "ProInfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PennHui2016/ProInfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510 ; sc:citation "pubmed:27301453" ; sc:description "Webserver for the prediction of proinflammatory antigenicity of peptides and proteins." ; sc:featureList edam:operation_0346, edam:operation_2479, edam:operation_3092 ; sc:name "ProInflam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metabiosys.iiserb.ac.in/proinflam/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077 ; sc:author "Sarah Djebali" ; sc:description "project is a program that projects genomic features onto their sequences. Please contact Sarah Djebali (sarah dot djebali at crg dot es for any question)." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "project" ; sc:operatingSystem "Linux" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://big.crg.cat/services/project" ; biotools:primaryContact "Sarah Djebali" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description "An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering | An R package for creating projection matrices from gene weights extracted from high dimensional genomic analysis | Application of projectR for spatial analysis | The most up-to-date version of projectR can be installed directly from the Github Repository:" ; sc:featureList edam:operation_3891 ; sc:license "GPL-2.0" ; sc:name "projectR" ; sc:softwareHelp ; sc:url "https://github.com/genesofeve/projectR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:15980536" ; sc:description "Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps." ; sc:featureList edam:operation_0310, edam:operation_0523, edam:operation_0525, edam:operation_2429 ; sc:name "Projector 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bamics2.cmbi.ru.nl/websoftware/projector2/projector2_start.php" ; biotools:primaryContact "Sacha A.F.T. van Hijum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1932 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3297 ; sc:author "Alexander Raknes" ; sc:citation ; sc:description "Galaxy workflow for the analysis of differential expressed genes between two prokaryote transcriptome datasets." ; sc:featureList edam:operation_2945 ; sc:name "Prokaryote RNA sequence analysis workflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NO" ; sc:softwareVersion "1.0" ; sc:url "https://galaxy-uit.bioinfo.no/u/ehj000/p/prokaryote-rnaseq-dataset" ; biotools:primaryContact "Alexander Raknes", "Erik Hjerde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3301, edam:topic_3305, edam:topic_3673, edam:topic_3796 ; sc:citation , "pmcid:PMC8142932", "pubmed:34055480" ; sc:description "An automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses." ; sc:featureList edam:operation_3192, edam:operation_3359, edam:operation_3644, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProkEvo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/npavlovikj/ProkEvo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0781 ; sc:author "Torsten Seemann" ; sc:citation , "pubmed:24642063" ; sc:description "Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files." ; sc:featureList edam:operation_0362, edam:operation_0436, edam:operation_2454 ; sc:name "Prokka" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Melbourne, Australia", "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/tseemann/prokka" ; biotools:primaryContact "Torsten Seemann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC9344657", "pubmed:35915508" ; sc:description "Differential richness inference for 16S rRNA marker gene surveys." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Prokounter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mskb01/prokounter" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC10320063", "pubmed:37140037" ; sc:description "In-depth characterization and visualization of bacterial genomes." ; sc:featureList edam:operation_0525, edam:operation_2429, edam:operation_3180, edam:operation_3184, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Proksee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://proksee.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """ProkSeq for complete analysis of RNA-seq data from prokaryotes. ProkSeq is an automated RNA-seq data analysis package for Prokaryotic, where users can perform all the necessary steps of RNA-seq data analysis from quality control to pathway enrichment analysis. It has a wide variety of options for differential expression, normalized expression, visualization, and quality control, and publication-quality figures. It is also less time consuming as the user does not need to observe and control the analysis process. The user needs to specify the descriptions of the samples and define the parameter file accordingly. ProkSeq also automatically do the quality filtering of the bad reads and run the analysis on good quality reads. conda install -c snandids prokseq.""" ; sc:featureList edam:operation_0335, edam:operation_3192, edam:operation_3223, edam:operation_3680 ; sc:license "ISC" ; sc:name "ProkSeq" ; sc:url "https://anaconda.org/snandiDS/prokseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0601, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16845116" ; sc:description "Investigate protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only." ; sc:featureList edam:operation_0250, edam:operation_0320, edam:operation_0417, edam:operation_2406, edam:operation_2487 ; sc:name "ProKware" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ProKware.mbc.nctu.edu.tw/" ; biotools:primaryContact "ProKware Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:author "Dr. Michael Kohl" ; sc:citation ; sc:description """It includes adresses the problem of protein list comparison, which can be challenging due to different or changing database accession numbers. In addition to a simple accession based comparison, ProLiC permits a more reliable comparison of an arbitrary number of protein lists by considering measured sequence and/or peptide information.""" ; sc:featureList edam:operation_2997 ; sc:isAccessibleForFree true ; sc:name "ProLiC (Protein List Comparator)" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1" ; sc:url "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.de#ProLiC" ; biotools:primaryContact "PD Dr. Martin Eisenacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0176, edam:topic_2275, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC8466659", "pubmed:34563256" ; sc:description "ProLIF (Protein-Ligand Interaction Fingerprints) is a tool designed to generate interaction fingerprints for complexes made of ligands, protein, DNA or RNA molecules extracted from molecular dynamics trajectories, docking simulations and experimental structures." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_2929, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ProLIF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/chemosim-lab/ProLIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128 ; sc:description "One-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level." ; sc:featureList edam:operation_2422 ; sc:name "PROLIFIC" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.pharmaceutical-bioinformatics.de/prolific/184/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Set of programs dedicated to perform proteomics data computations and render the obtained results in user-friendly GUIs. It focuses on: result validation (using custom filters and target decoy analysis), merge/comparison of datasets and label-free quantification (spectral count and LC-MS analyses)." ; sc:featureList edam:operation_3203, edam:operation_3214, edam:operation_3436, edam:operation_3634, edam:operation_3649, edam:operation_3694, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.1" ; sc:name "Proline" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://proline.profiproteomics.fr/" ; biotools:primaryContact "Christophe Bruley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0176, edam:topic_0769, edam:topic_0820, edam:topic_3382 ; sc:citation , "pubmed:34038536" ; sc:description """ProLint is a user-friendly framework for the automated analysis and interactive visualization of Protein-Lipid interactions. The time requirement to analyze and interpret data generated through Molecular Dynamics (MD) simulations usually exceeds the time to set up and perform the simulations. Add to this the continuing trend of increased system sizes, simulated for longer time scales and the need for a much larger set of proteins, it becomes clear how analysis and visualization of lipid-protein interactions can become a significant bottleneck. ProLint aimes to bridge this widening gap between data generation and gaining insight on biologically-relevant interactions between. prolintpy is a lightweight python library that is used by the ProLint webserver on the backend to analyze Protein-Lipid interactions.. Use this tool if you want to customize analysis and visualization of lipid-protein interactions and want to scale-up your workflow beyond the capabilities of the ProLint webserver.""" ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "ProLint" ; sc:url "http://www.prolint.ca" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC4866734", "pubmed:27175778" ; sc:description "Pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation." ; sc:featureList edam:operation_0247 ; sc:license "GPL-2.0" ; sc:name "pRoloc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pRoloc.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "ProLoc-GO is an efficient sequence-based method by mining informative Gene Ontology terms for predicting protein subcellular localization." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "ProLoc-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://140.113.239.45/prolocgo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "This package comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and Shiny." ; sc:featureList edam:operation_0247 ; sc:license "GPL-2.0" ; sc:name "pRolocGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pRolocGUI.html" ; biotools:primaryContact "Laurent Gatto", "Lisa M Breckels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3379, edam:topic_3393 ; sc:citation , "pmcid:PMC9903472", "pubmed:36750951" ; sc:description "A novel model for predicting prolonged stay of patients with type-2 diabetes mellitus." ; sc:featureList edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "prolonged LOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cytjt007.shinyapps.io/prolonged_los/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2259, edam:topic_3070, edam:topic_3172, edam:topic_3511 ; sc:citation "pubmed:23417801" ; sc:description "Algorithm which represents the successful integration of a genome scale transcriptional regulatory network with a biochemically detailed metabolic network, bridging two important classes of systems biology models that have rarely been combined quantitatively." ; sc:featureList edam:operation_3439 ; sc:name "PROM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://price.systemsbiology.org/research/prom/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0821, edam:topic_3382, edam:topic_3518 ; sc:citation , "pmcid:PMC7041094", "pubmed:32093608" ; sc:description """semiquantitative densitometric measurement of protein microarrays. pip install -U git+https://github.com/theia-dev/proMAD.git#egg=proMAD. There could be missing functionality and undocumented behavior. If you have feedback to improve the service please send your idea to info@promad.dev. You can also install the latest version directly from GitHub.""" ; sc:featureList edam:operation_3192, edam:operation_3443, edam:operation_3799 ; sc:license "MIT" ; sc:name "proMAD" ; sc:url "https://promad.dev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081, edam:topic_0082, edam:topic_3542 ; sc:citation "pubmed:17267437", "pubmed:17452345", "pubmed:18503087" ; sc:description "PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints." ; sc:featureList edam:operation_0267, edam:operation_0492, edam:operation_2488 ; sc:name "PROMALS3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/promals3d" ; biotools:primaryContact "PROMALS3D Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15050833", "pubmed:17488838" ; sc:description "ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations." ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3092, edam:operation_3222 ; sc:name "ProMateus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioportal.weizmann.ac.il/promate/" ; biotools:primaryContact "Asaf Carmi", "Dana Reichmann", "Jaimie Prilusky", "Mati Cohen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_1317, edam:topic_2275 ; sc:citation ; sc:description "A server for estimating the effect of mutations on protein thermal stability." ; sc:featureList edam:operation_0331, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "ProMaya" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareVersion "1" ; sc:url "http://bental.tau.ac.il/ProMaya/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2571 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3603 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3603 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0780, edam:topic_3520 ; sc:citation ; sc:description "A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data." ; sc:featureList edam:operation_0224, edam:operation_3631, edam:operation_3694, edam:operation_3767, edam:operation_3801 ; sc:name "ProMEX protein mass spectral library" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://promex.pph.univie.ac.at/promex/" ; biotools:primaryContact "Dr. V. Egelhofer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0621, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:9088706" ; sc:description "Computer program to recognize vertebrate RNA polymerase II promoters." ; sc:featureList edam:operation_0440 ; sc:name "PromFD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://stormo.wustl.edu/src/PromFD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0622, edam:topic_0749, edam:topic_0798 ; sc:citation , "pmcid:PMC8989519", "pubmed:35323968" ; sc:description "proMGE is a resource for the retrieval of 6 Mobile Genetic Element (MGE) categories in 76K genomes (totalling to 2.4 million prokaryotic MGEs) and classification of new ones in user provided protein sequences from genomes and genomic fragments." ; sc:featureList edam:operation_3208, edam:operation_3482, edam:operation_3501 ; sc:license "Not licensed" ; sc:name "proMGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://promge.embl.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:12824362" ; sc:description "Predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445 ; sc:name "PromH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promoter" ; biotools:primaryContact "Victor V. Solovyev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0621 ; sc:citation ; sc:description """Shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. This is the project page for ProminTools: a collection of bioinformatic tools for the analysis of protein seqeunces thought to be involved in biomineralization.""" ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_3904 ; sc:license "GPL-3.0" ; sc:name "ProminTools" ; sc:url "https://github.com/skeffington/Promin-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3375 ; sc:citation "pubmed:21071407" ; sc:description "PROMISCUOUS is a database of drugs, including withdrawn or experimental drugs, annotated with drug-protein and protein-protein relationships compiled from public resources via text and data mining including manual curation. Measures of structural similarity for drugs as well as known side-effects can be easily connected to protein-protein interactions to establish and analyse networks responsible for multi-pharmacology." ; sc:featureList edam:operation_0276, edam:operation_0306, edam:operation_2464, edam:operation_3439 ; sc:name "PROMISCUOUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/promiscuous" ; biotools:primaryContact "Joachim von Eichborn", "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables." ; sc:featureList edam:operation_0253 ; sc:license "GPL-2.0" ; sc:name "PROMISE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PROMISE.html" ; biotools:primaryContact "Stan Pounds", "Xueyuan Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Agentless technology to quickly and remotely inspect yan organisations endpoint environment to discover, analyze, and remediate any abnormalities that then in turn lead to failed audits and uncorrect business intelligence." ; sc:featureList edam:operation_3760 ; sc:name "Promisec Endpoint Manager" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.promisec.com/products/#pem" ; biotools:primaryContact "promisec contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0780, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC8453180", "pubmed:34589187" ; sc:description "A novel web-based tool to facilitate analysis and visualization of the molecular interaction networks from co-fractionation mass spectrometry (CF-MS) experiments." ; sc:featureList edam:operation_0337, edam:operation_3629, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PROMISed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://myshiny.mpimp-golm.mpg.de/PDP1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123 ; sc:citation "pubmed:26357091" ; sc:description "Method for predicting protein function using Multiple Kernels." ; sc:featureList edam:operation_1777, edam:operation_2479 ; sc:name "ProMK" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/guoxian85/home/promk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0128, edam:topic_0202, edam:topic_2229, edam:topic_3068 ; sc:citation ; sc:description "ProMoCell (Protein interaction-based functional Modules of the Cell of an organism) is a network-based zoning approach that can determine the functional modules of a cell of an organism and can potentially be utilized for parallel whole-cell simulation. ProMoCell is a single-click web service and it is very simple, user-friendly and easy to use. Presumably, no other web services like ProMoCell exists till date." ; sc:featureList edam:operation_0533, edam:operation_2492, edam:operation_3432 ; sc:name "ProMoCell" ; sc:url "https://cosmos.iitkgp.ac.in/ProMoCell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0769, edam:topic_1317, edam:topic_2269, edam:topic_2275 ; sc:citation , "pmcid:PMC7872268", "pubmed:33507980" ; sc:description """ProMod3 is a versatile homology modelling toolbox. ProMod3 is a modelling engine based on the OpenStructure [biasini2013] computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms.""" ; sc:featureList edam:operation_0292, edam:operation_0321, edam:operation_0477, edam:operation_2421 ; sc:name "ProMod3" ; sc:url "https://openstructure.org/promod3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0128, edam:topic_0202, edam:topic_2229, edam:topic_3068 ; sc:citation ; sc:description "ProModb (Protein interaction-based functional Module database) is a repository that documents computationally generated whole-cell protein-protein interaction network-based functional modules of an organism." ; sc:featureList edam:operation_0533, edam:operation_2492, edam:operation_3432 ; sc:name "ProModb" ; sc:url "https://cosmos.iitkgp.ac.in/ProModb/index.php" ; biotools:primaryContact "Barnali Das" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3518, edam:topic_3520 ; sc:citation , "pmcid:PMC10010602", "pubmed:36922981" ; sc:description "A comprehensive R package for label-free proteomics data analysis and predictive modeling." ; sc:featureList edam:operation_0477, edam:operation_3557, edam:operation_3634, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "promor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://caranathunge.github.io/promor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0203, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:12824364", "pubmed:15215378" ; sc:description "Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site." ; sc:featureList edam:operation_0440, edam:operation_2429, edam:operation_2871, edam:operation_3186 ; sc:name "PromoSer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biowulf.bu.edu/zlab/PromoSer/" ; biotools:primaryContact "PromoSer Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0176, edam:topic_0601, edam:topic_3382, edam:topic_3520 ; sc:citation "pubmed:15215467" ; sc:description "ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images." ; sc:featureList edam:operation_0398, edam:operation_0403, edam:operation_0417, edam:operation_3645 ; sc:name "ProMoST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.mcw.edu/promost.html" ; biotools:primaryContact "PrpMoST Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0749, edam:topic_3168, edam:topic_3301, edam:topic_3474 ; sc:citation , "pmcid:PMC8597233", "pubmed:34789306" ; sc:description "Machine-learning-based general bacterial promoter prediction tool." ; sc:featureList edam:operation_0440, edam:operation_3359, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Promotech" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioinformaticsLabAtMUN/PromoTech" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , "pubmed:10366655" ; sc:description "Prediction of transcription start sites of vertebrate Pol II promoters in DNA sequences." ; sc:featureList edam:operation_0445 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Promoter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/Promoter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749, edam:topic_0780, edam:topic_3473 ; sc:citation "pubmed:23766287" ; sc:description "PromoterCAD is a web server for designing synthetic promoters in plants with altered transcriptional regulation. PromoterCAD uses published high-throughput expression and motif data from Arabidopsis thaliana to guide DNA design." ; sc:featureList edam:operation_0239, edam:operation_0314, edam:operation_2454, edam:operation_2495 ; sc:name "PromoterCAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://promotercad.org/" ; biotools:primaryContact "PromoterCAD Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0749 ; sc:citation "pubmed:15980503" ; sc:description "Takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool." ; sc:featureList edam:operation_0440 ; sc:name "PromoterPlot" ; sc:url "http://promoterplot.fmi.ch/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749 ; sc:author "Ewan Birney" ; sc:citation , ; sc:description "Compare two DNA sequences allowing for inversions and translocations, ideal for promoters." ; sc:featureList edam:operation_0491, edam:operation_0495 ; sc:name "PromoterWise (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/psa/promoterwise/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:19593472" ; sc:description "Tool to identify promoter regions in genomic DNA sequence, based on difference in stability between neighboring regions." ; sc:featureList edam:operation_0440 ; sc:name "PromPredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nucleix.mbu.iisc.ernet.in/prompredict/prompredict.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description "PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison algorithms and a full-featured easy to use graphical user interface (GUI) application with an integrated help-system." ; sc:featureList edam:operation_2422, edam:operation_2424, edam:operation_2429, edam:operation_2479, edam:operation_2945 ; sc:name "PROMPT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.7" ; sc:url "http://www.geneinfo.eu/prompt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0121, edam:topic_3070, edam:topic_3344 ; sc:citation ; sc:description "PRotein cOnformational Motion PredicTion toolbox." ; sc:featureList edam:operation_0244 ; sc:isAccessibleForFree true ; sc:name "PROMPT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/49054-prompt" ; biotools:primaryContact "Gaik Tamazian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3170, edam:topic_3360, edam:topic_3520 ; sc:citation , "pmcid:PMC8165452", "pubmed:33887487" ; sc:description "ProMS (Protein Marker Selection) is a python package designed to tackle a novel problem of multiview feature selection: given multiple views of same set of samples, select important features from one view of interest (target view) by integrating information from other views. It was initially developed to select protein biomarkers using proteomics data with the help of additional omics views (e.g. RNAseq)." ; sc:featureList edam:operation_3891, edam:operation_3936, edam:operation_3960 ; sc:license "MIT" ; sc:name "ProMS" ; sc:url "https://github.com/bzhanglab/proms" ; biotools:primaryContact "Bing Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3053 ; sc:citation , "pmcid:PMC3658923", "pubmed:23497159" ; sc:description "Perl-based application to discover de novo motifs underlying co-regulated genes in maize, Arabidopsis or rice." ; sc:featureList edam:operation_0238 ; sc:name "Promzea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.promzea.org" ; biotools:primaryContact "Christophe Liseron-Monfils", "Manish Raizada" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0128, edam:topic_0199, edam:topic_3511 ; sc:citation , "pmcid:PMC8728258", "pubmed:34606614" ; sc:description "Database for binding affinities of protein-nucleic acid complexes and their mutants." ; sc:featureList edam:operation_0478, edam:operation_2421, edam:operation_3802, edam:operation_3900, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ProNAB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/pronab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_3922 ; sc:citation ; sc:description """A web-based portal to interactively explore clear cell renal cell carcinoma proteogenomics networks. an interactive WebGL visualizer of 3D Networks. NCI supported Clinical Proteomic Tumor Analysis Consortium (CPTAC), is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome (proteins) and genome (DNA and RNA) analysis technologies to different cancer types. CPTAC is composed of expertise in proteomics, genomics, cancer biology, oncology, and clinical chemistry, while creating open community resources that are widely used by the cancer community. This page provides visualization of the networks estimated based on proteogenomic data from CPTAC-CCRCC discovery project. For more information, visit the CPTAC-CCRCC data portal. Co-expression network was constructed based on phospho-peptide data of 103 Clear Cell Renal Cell Carcinoma (ccRCC) samples.""" ; sc:featureList edam:operation_0224, edam:operation_3463, edam:operation_3925 ; sc:name "ProNetView-ccRCC" ; sc:url "http://ccrcc.cptac-network-view.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_2275 ; sc:citation "pubmed:23217202" ; sc:description "Convenient tool for generating atomic-style nano shapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the atoms in the shapes are assigned according to the user’s preferences allowing various scenarios of modeling." ; sc:featureList edam:operation_0477 ; sc:name "ProNOI" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://compbio.clemson.edu/pronoi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "Frameshift-correction for long-read (meta)genomics." ; sc:featureList edam:operation_0265, edam:operation_0310, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "proovframe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/thackl/proovframe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25015988" ; sc:description "Hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high performance computing cluster." ; sc:featureList edam:operation_3195 ; sc:name "proovread" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bioinfo.biozentrum.uni-wuerzburg.de/groups/genomics/research/development_of_bioinformatical_tools/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2330, edam:format_3467 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , "pubmed:14985543" ; sc:description "Neural network prediction of arginine and lysine propeptide cleavage sites in eukaryotic protein sequences." ; sc:featureList edam:operation_0422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ProP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/ProP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3174, edam:topic_3341, edam:topic_3697 ; sc:citation ; sc:description """Deciphering active prophages from metagenomes. PropagAtE (Prophage Activity Estimator) uses genomic coordinates of integrated prophage sequences and short sequencing reads to estimate if a given prophage was in the lysogenic (dormant) or lytic (active) stage of infection.""" ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3216 ; sc:name "PropagAtE" ; sc:url "https://github.com/AnantharamanLab/PropagAtE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0637, edam:topic_3174, edam:topic_3407 ; sc:citation , "pubmed:36169225" ; sc:description "A comprehensive database for profiling prokaryotic pan-genome dynamics." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "ProPan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/propan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123 ; sc:citation "pubmed:22368391" ; sc:description "Calculate the basic property of peptides/proteins. The properties include the Isoelectric point (pI), Mass weight (MW) and Hydrophobicity (Hy). Additionally, amino acid composition of all peptides/proteins in the list was also calculated." ; sc:featureList edam:operation_0250, edam:operation_2479 ; sc:name "ProPAS" ; sc:operatingSystem "Windows" ; sc:softwareHelp , , ; sc:url "http://bioinfo.hupo.org.cn/tools/ProPAS/propas.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0593, edam:topic_2275 ; sc:citation , "pmcid:PMC7776311", "pubmed:33388027" ; sc:description """a database for protein-peptide identification based on a hybrid clustering algorithm. PROPEDIA is a database of peptide-protein complexes clusterized in three methodologies: (i) peptide sequences; (ii) structure interface; and (iii) binding sites. PROPEDIA main goal is to give new insights into peptide design of biotechnological interests.""" ; sc:featureList edam:operation_0418, edam:operation_0478, edam:operation_3432, edam:operation_3646, edam:operation_4009 ; sc:name "Propedia" ; sc:url "https://bioinfo.dcc.ufmg.br/propedia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36005887" ; sc:description "Testing for differences in cell type proportions in single cell data." ; sc:featureList edam:operation_0314, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "propeller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phipsonlab.github.io/propeller-paper-analysis/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC4287952", "pubmed:25273110" ; sc:description "This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data." ; sc:featureList edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "PROPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PROPER.html" ; biotools:primaryContact "Hao Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3168, edam:topic_3293 ; sc:citation , "pmcid:PMC7847139", "pubmed:33516169" ; sc:description "PROP is a web application to perform phylogenetic analysis considering the effect of gaps." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:license "MIT" ; sc:name "PROP" ; sc:url "https://www.rs.tus.ac.jp/bioinformatics/prop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_0654, edam:topic_3518 ; sc:citation , "pmcid:PMC9805568", "pubmed:36377787" ; sc:description "Achieving improved accuracy for imputation of ancient DNA." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3454, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "prophaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/scicompuu/prophaser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3298 ; sc:citation ; sc:description "Profiling of phenotypic characteristics in yeast." ; sc:featureList edam:operation_0224 ; sc:name "PROPHECY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://prophecy.lundberg.gu.se/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1354 ; sc:name "Sequence profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Scan one or more sequences with a Gribskov or Henikoff profile." ; sc:featureList edam:operation_0300 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "prophet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/prophet.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0622, edam:topic_0659 ; sc:citation , "pmcid:PMC6774505", "pubmed:31577829" ; sc:description "ProphET is a stand-alone prophage sequence prediction tool with self-updating reference database." ; sc:featureList edam:operation_0464, edam:operation_2421, edam:operation_3216, edam:operation_3431 ; sc:name "ProphET" ; sc:url "https://github.com/jaumlrc/ProphET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3053 ; sc:citation ; sc:description "Heterogeneous network prioritization tools." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "ProphTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cnluzon/prophtools" ; biotools:primaryContact "Carmen Navarro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:22095919" ; sc:description "Novel toolkit for identifying pockets, cavities and channels of protein structures." ; sc:featureList edam:operation_0245 ; sc:name "PROPORES" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://gepard.bioinformatik.uni-saarland.de/software/propores/propores-page" ; biotools:primaryContact "Po-Hsien Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0820 ; sc:citation , "pubmed:33844545" ; sc:description "ProPores2 is a web service and stand-alone tool for identifying, manipulating, and visualizing pores in protein structures. ProPores2 is a C++ command line tool for analysing pores (and cavities) in proteins. It provides three components that can be run together or individually." ; sc:featureList edam:operation_0384, edam:operation_0387, edam:operation_0570 ; sc:license "GPL-3.0" ; sc:name "ProPores2" ; sc:url "https://service.bioinformatik.uni-saarland.de/propores" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3174, edam:topic_3308 ; sc:citation "pubmed:22102570" ; sc:description "A database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0362, edam:operation_2495, edam:operation_3432 ; sc:name "ProPortal" ; sc:url "http://proportal.mit.edu/" ; biotools:primaryContact "ProPortal Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Identifying Proportionally Abundant Features Using Compositional Data Analysis." ; sc:featureList edam:operation_0253, edam:operation_3222 ; sc:license "GPL-2.0" ; sc:name "propr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.5.1" ; sc:url "https://cran.r-project.org/web/packages/propr/index.html" ; biotools:primaryContact "Thomas Quinn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:11751237" ; sc:description "This server allows users to predict MHC class II binders." ; sc:featureList edam:operation_0252, edam:operation_0445, edam:operation_2575, edam:operation_3222 ; sc:name "Propred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/propred/" ; biotools:primaryContact "Dr. G. P. S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:12761064" ; sc:description "Online service for identifying the MHC Class-I binding regions in antigens. It implements matrices for 47 MHC Class-I alleles, proteasomal and immunoproteasomal models. The main aim of this server is to help users in identifying the promiscuous regions." ; sc:featureList edam:operation_0252, edam:operation_0422, edam:operation_2479, edam:operation_2575 ; sc:name "ProPred1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/propred1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:20887258" ; sc:description "Proprint web-server predicts physical or functional interactions between protein molecules." ; sc:featureList edam:operation_2945 ; sc:name "proprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/proprint/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2269 ; sc:citation , "pmcid:PMC5860179", "pubmed:29048458" ; sc:description "This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways." ; sc:featureList edam:operation_2990 ; sc:license "GPL-2.0" ; sc:name "PROPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PROPS.html" ; biotools:primaryContact "Lichy Han" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1775 ; sc:citation ; sc:description "PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated." ; sc:featureList edam:operation_0236, edam:operation_0239, edam:operation_0292, edam:operation_0405 ; sc:name "PROPSEARCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://abcis.cbs.cnrs.fr/propsearch/" ; biotools:primaryContact "Uwe Hobohm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "A protein model quality predictor." ; sc:featureList edam:operation_0321 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ProQ" ; sc:operatingSystem "Linux" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://proq.bioinfo.se/ProQ/ProQ.html" ; biotools:primaryContact "Bjorn Wallner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_3474 ; sc:citation "pubmed:26733453" ; sc:description "Neural network based predictor that based on a number of structural features predicts the quality of a protein model. It is optimized to find correct models in contrast to other methods which are optimized to find native structures." ; sc:featureList edam:operation_0250, edam:operation_2479 ; sc:name "ProQ2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ifm.liu.se/ProQ2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_3168 ; sc:citation , "pmcid:PMC7057213", "pubmed:32133992" ; sc:description """Estimating local protein model quality. ProQ3/ProQ3D: Improved model quality assessment.""" ; sc:featureList edam:operation_0267, edam:operation_0477, edam:operation_3455 ; sc:name "ProQ3D" ; sc:url "http://proq3.bioinfo.se/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:17037911" ; sc:description "Differential proteomics analysis using for various stable isotope labeling schemes." ; sc:featureList edam:operation_2238, edam:operation_3203, edam:operation_3215, edam:operation_3441, edam:operation_3635, edam:operation_3638, edam:operation_3640, edam:operation_3694, edam:operation_3705, edam:operation_3715 ; sc:name "ProRata" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/archive/p/prorata/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130 ; sc:citation ; sc:description "PRORATE is a novel approach to predict protein folding rates for two-state and multi-state protein folding kinetics, which combines a variety of structural topology and complex network properties that are calculated from protein three-dimensional structures." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PRORATE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/folding/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_2885 ; sc:citation "pubmed:22102581" ; sc:description "An integrated curated repository and analysis platform or research on biological characteristics of amino acid tandem repeats." ; sc:featureList edam:operation_0237, edam:operation_0379, edam:operation_0380, edam:operation_2479 ; sc:name "ProRepeat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prorepeat.bioinformatics.nl:443/dev/f?p=131:1:3958512077619968" ; biotools:primaryContact "Jack A. M. Leunissen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description "Predicting effects of mutations on protein stability using graph neural networks." ; sc:featureList edam:operation_0331, edam:operation_2476, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ProS-GNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shuyu-wang/ProS-GNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_1317, edam:topic_2814 ; sc:citation "pubmed:17517781", "pubmed:8108378" ; sc:description "ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling." ; sc:featureList edam:operation_0303, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2406 ; sc:name "ProSA-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://prosa.services.came.sbg.ac.at/prosa.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0130, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:35246677" ; sc:description "ProSAP (Protein Stability Analysis Pod) is standalone and user-friendly software with graphical user interface (GUI). ProSAP provides an integrated analysis workflow for thermal shift assay, which includes five modules: data preprocessing, data visualization, TPP analysis, NPARC analysis and iTSA analysis. With the assistance of the user-friendly interface, researchers can easily compare several statistical strategies, analyze the results and draw the conclusion from the proteomics quantitative table obtained by Proteome Discoverer or MaxQuant. Users would also benefit from a comprehensive overview of the performance of different algorithms, and apply appropriate algorithms to their dataset easily." ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProSAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hcji/ProSAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_0654, edam:topic_2814 ; sc:citation "pubmed:27284084" ; sc:description "Tool to explore the relation between sequence and structural properties." ; sc:featureList edam:operation_2479 ; sc:name "ProSAT+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prosat.h-its.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0102, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:15593408", "pubmed:16845114" ; sc:description "Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures" ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2429 ; sc:name "ProSAT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://projects.villa-bosch.de/dbase/ps2/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0625, edam:topic_2640, edam:topic_3520 ; sc:citation ; sc:description "Single-sample proteome enrichment enables missing protein recovery and phenotype association." ; sc:featureList edam:operation_3463, edam:operation_3501, edam:operation_3557, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PROSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bwbio/PROSE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3053, edam:topic_3056 ; sc:citation ; sc:description "PROcessor of SEQuences is a program for sequence editing and population genetics analysis. It is quite a convenient tool for sequence handling and preliminary molecular evolution analysis. However, it is recommended to check the results of the analyses by the other software since the program is under development and not all the parts of the program are thoroughly tested and completely reliable" ; sc:featureList edam:operation_0231, edam:operation_0310, edam:operation_2945, edam:operation_3096 ; sc:name "ProSeq" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "3.5" ; sc:url "http://dps.plants.ox.ac.uk/sequencing/proseq.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0130, edam:topic_0621, edam:topic_0623, edam:topic_0736 ; sc:citation , "pubmed:36828269" ; sc:description "ProSequence Assisted Protein - DataBase, ProSeqAProDB is a comprehensive, non-redundant and manually curated dataset of proteins which are translated in a pre-pro-form." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:name "ProSeqAProDb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proseqaprodb.mkulab.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0081, edam:topic_0199 ; sc:citation , "pubmed:34788797" ; sc:description "An interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications." ; sc:featureList edam:operation_0259, edam:operation_0492, edam:operation_0564 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ProSeqViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biocomputingup.github.io/ProSeqViewer-documentation/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0593, edam:topic_2814, edam:topic_2828 ; sc:citation "pubmed:20460469" ; sc:description "Comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling." ; sc:featureList edam:operation_0249, edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2406 ; sc:name "PROSESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.prosess.ca" ; biotools:primaryContact "Cam MacDonell", "Contact Form", "David Wishart", "Guohui Lin", "Jianjun (Ben) Zhou", "Joseph Cruz", "Mark Berjanskii", "Paul Lu", "Paul Stothard", "Peter Tang", "Yongjie (Jack) Liang", "You Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0202, edam:topic_2275, edam:topic_3336 ; sc:citation , "pmcid:PMC7592117", "pubmed:32976709" ; sc:description """Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. Installation requirements for PRosettaC:. PRosettaC is a computational protocol for the prediction of PROTAC-induced ternary complexes. It was benchmarked against ten available ternary complex crystal structures, and was able to predict six of them to atomic accuracy in one of the top three clusters. The protocol receives as input, two protein structures (protein target and E3 ligase), including their appropriate ligands (binders), as well as the PROTAC chemical structure in a SMILES representation, and outputs predicted models for the ternary complex. to /etc/pbs.conf (on all cluster nodes). Another option is to write this line to a file, e.g. env.txt, and then set the enrionment parameter SCHEDULER_PARAMS=/Path_to_env.txt before starting PRosettaC (see below "Additional parameters").""" ; sc:featureList edam:operation_2476, edam:operation_2844, edam:operation_3899, edam:operation_3938 ; sc:license "MIT" ; sc:name "PRosettaC" ; sc:url "https://prosettac.weizmann.ac.il/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1353 ; sc:name "Sequence motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Process the PROSITE motif database for use by patmatmotifs." ; sc:featureList edam:operation_1812 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "prosextract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/prosextract.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "An R package for variable selection with second-generation p-values." ; sc:featureList edam:operation_3658, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProSGPV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/ProSGPV/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_2332 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1963 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2332 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Sequence image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation "pubmed:25828799", "pubmed:28150248" ; sc:description "Free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations." ; sc:featureList edam:operation_0417, edam:operation_0564, edam:operation_2429, edam:operation_2479, edam:operation_3645, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "ProSight Lite" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://prosightlite.northwestern.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2062 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2062 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3653 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation "pubmed:14632120" ; sc:description "Web portal for PTM search in top-down experiments." ; sc:featureList edam:operation_0335, edam:operation_0564, edam:operation_3643, edam:operation_3644, edam:operation_3645, edam:operation_3646, edam:operation_3647, edam:operation_3648, edam:operation_3755, edam:operation_3767 ; sc:name "ProSight PTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prosightptm.northwestern.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0844 ; sc:encodingFormat edam:format_2331 ; sc:name "Molecular mass" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:description "Generate exact masses for CID/ECD fragments with PTMs." ; sc:featureList edam:operation_0398, edam:operation_0417 ; sc:name "ProSight PTM Ion Predictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://prosightptm.northwestern.edu/ionpredictor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0623, edam:topic_1775 ; sc:citation , "pmcid:PMC3531220", "pubmed:23161676" ; sc:description "Consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them." ; sc:featureList edam:operation_0253, edam:operation_0296, edam:operation_0361, edam:operation_2414 ; sc:name "PROSITE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://prosite.expasy.org" ; biotools:primaryContact "PROSITE helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:author "PROSITE" ; sc:citation , ; sc:description "Scan a protein against PROSITE or HAMAP patterns and profiles." ; sc:featureList edam:operation_0239, edam:operation_3092 ; sc:name "PROSITE Scan (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/pfa/ps_scan/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0622, edam:topic_3474 ; sc:citation , "pubmed:36988160" ; sc:description "Machine learning-based method for the identification of small ORFs in prokaryotic genomes." ; sc:featureList edam:operation_0415, edam:operation_0436, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "ProsmORF-pred" ; sc:url "http://www.nii.ac.in/prosmorfpred.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:19420061" ; sc:description "ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections between SSEs, coordinates of SSE start and ends, etc and then retrieves all structures from a database that contain this pattern." ; sc:featureList edam:operation_0245, edam:operation_0319, edam:operation_0360, edam:operation_2487, edam:operation_2488 ; sc:name "ProSMoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/ProSMoS/" ; biotools:primaryContact "Shuoyong Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """Accurate Variant Calling from Single Cell DNA Sequencing Data. ProSolo: bulk backing vocals for single cell solos. ProSolo is a variant caller for multiple displacement amplified DNA sequencing data from diploid single cells. It relies on a pair of samples, where one is from an MDA single cell and the other from a bulk sample of the same cell population, sequenced with any next-generation sequencing technology.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3557, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ProSolo" ; sc:url "https://github.com/prosolo/prosolo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation ; sc:description "Promoter prediction program based on unsupervised clustering of physical properties of DNA." ; sc:featureList edam:operation_0440 ; sc:name "ProSOM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/ProSOM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3071 ; sc:citation "pubmed:17072907" ; sc:description "Software of using Ciphergen outcome files to reduce the count of peaks to a biological more interesting subset." ; sc:featureList edam:operation_2479, edam:operation_3695 ; sc:name "ProSpect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" ; biotools:primaryContact "Yudi Pawitan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_0769, edam:topic_2814 ; sc:citation "pubmed:15215441" ; sc:description "An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0474 ; sc:name "PROSPECT-PSPP" ; sc:url "http://csbl.bmb.uga.edu/protein_pipeline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602, edam:topic_3407, edam:topic_3473, edam:topic_3474 ; sc:citation , "pubmed:32501138" ; sc:description """A web server for predicting protein histidine phosphorylation sites. Background: Phosphorylation of histidine residues plays crucial roles in signaling pathways and cell metabolism in prokaryotes such as bacteria. While evidence has emerged that protein histidine phosphorylation also occurs in more complex organisms, its role in mammalian cells has remained largely uncharted. Thus, it is highly desirable to develop computational tools that are able to identify histidine phosphorylation sites. Result: Here, we introduce PROSPECT that enables fast and accurate prediction of proteome-wide histidine phosphorylation substrates and sites. Our tool is based on a hybrid method that integrates the outputs of two convolutional neural network (CNN)-based classifiers and a random forest-based classifier""" ; sc:featureList edam:operation_0417 ; sc:name "PROSPECT" ; sc:url "http://PROSPECT.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3512 ; sc:citation "pubmed:15766383" ; sc:description "This tool can be used to enrich lists of genes found at a suspected disease locus. Given a list of genes, it will return a ranked list ordered by the likelihood of involvement in disease." ; sc:featureList edam:operation_2454, edam:operation_3224, edam:operation_3501, edam:operation_3672 ; sc:name "Prospectr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genetics.med.ed.ac.uk/prospectr/" ; biotools:primaryContact "IGMM Admin Hub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3534 ; sc:citation , "pubmed:37874948" ; sc:description "Platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction." ; sc:featureList edam:operation_0417, edam:operation_0418, edam:operation_0422 ; sc:isAccessibleForFree true ; sc:name "ProsperousPlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://prosperousplus.unimelb-biotools.cloud.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3120, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:12702210" ; sc:description "Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants." ; sc:featureList edam:operation_0232, edam:operation_0526, edam:operation_0527, edam:operation_2499 ; sc:name "ProSplicer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prosplicer.mbc.nctu.edu.tw/" ; biotools:primaryContact "ProSplicer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC7856244", "pubmed:33385701" ; sc:description "A deep learning framework for registration of MRI and histopathology images of the prostate." ; sc:featureList edam:operation_3443, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "ProsRegNet" ; sc:url "https://github.com/pimed//ProsRegNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0203, edam:topic_3120, edam:topic_3168 ; sc:citation , "pubmed:33367682" ; sc:description """a new server for the design of stable and highly expressed protein variants. PROSS: the Protein Repair One-Stop Shop. Why read this if you can simply download the files, right?. Well, I've seen too many dumb errors with processing PROSS results and gene ordering that could have been prevented by reading this page. Even the easiest experiment with PROSS designs will take you x1,000 longer than reading this. So...""" ; sc:featureList edam:operation_0294, edam:operation_0321, edam:operation_0337 ; sc:name "PROSS" ; sc:url "https://pross.weizmann.ac.il" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199 ; sc:citation , "pubmed:35973091" ; sc:description "AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations." ; sc:featureList edam:operation_0331 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PROST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://prost.erc.monash.edu/seq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_0121, edam:topic_0621, edam:topic_2275 ; sc:citation , "pmcid:PMC9992864", "pubmed:36827259" ; sc:description "Improved global protein homolog detection with major gains in function identification. PRotein Ortholog Search Tool is a new homolog detection tool that utilizes ESM-1b language model and iDCT quantization method. PROST is fast and accurate compared to traditional tools." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0477, edam:operation_2421, edam:operation_3501, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PROST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mesihk.github.io/prost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:27976474" ; sc:description "This package provides a GUI interface for DAPAR." ; sc:featureList edam:operation_3223 ; sc:license "Artistic-2.0" ; sc:name "Prostar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Prostar.html" ; biotools:primaryContact "Samuel Wieczorek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:20430700" ; sc:description "Web server to find the similar structural repeats in a three-dimensional protein structure." ; sc:featureList edam:operation_2406 ; sc:name "ProSTRIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cluster.physics.iisc.ernet.in/prostrip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0749 ; sc:citation , "pubmed:35020788" ; sc:description "PROmoting SYNthetic hARmony is a read merger that will take information from the reference into account when deciding whether to merge a read pair." ; sc:featureList edam:operation_0232, edam:operation_2422, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "ProSynAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Benjamin-Crysup/prosynar" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_2350 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0128, edam:topic_0130, edam:topic_3306, edam:topic_3373, edam:topic_3534 ; sc:description "The identification of critical amino acids for redesigning the structurally characterized protein-protein interfaces paves the way for developing protein-based therapeutics to dealing with diverse range of diseases. To find such amino acids positions, the residues across the protein interaction surfaces are either randomly or strategically mutated. Scanning mutations in this manner is experimentally costly. Therefore, computational methods have been developed to estimate the impact of an interfacial mutation on protein-protein interactions. In this work, we present the PROT-ON tool that scans all possible interfacial mutations by using EvoEF1 (active in both on the web server and stand-alone versions) or FoldX (active only in the stand-alone version) with the aim of finding the most mutable positions." ; sc:featureList edam:operation_2949 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PROT-ON" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://proton.tools.ibg.edu.tr:8001" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108 ; sc:citation , "pubmed:23986565" ; sc:description "The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments." ; sc:featureList edam:operation_3741 ; sc:license "GPL-2.0" ; sc:name "prot2D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/prot2D.html" ; biotools:primaryContact "Sebastien Artigaud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0622, edam:topic_0736, edam:topic_3676 ; sc:citation , "pmcid:PMC7157182", "pubmed:32293014" ; sc:description """Prot2HG is a database of protein domains mapped to the human genome. Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3226, edam:operation_3227 ; sc:name "Prot2HG" ; sc:url "http://www.prot2hg.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3382 ; sc:citation , "pmcid:PMC9512884", "pubmed:36008698" ; sc:description "A Deep Learning Model for Rapid, Photorealistic Macromolecular Visualization." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Prot2Prot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://durrantlab.com/prot2prot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3293, edam:topic_3407 ; sc:citation , "pmcid:PMC6394115", "pubmed:30649284" ; sc:description "Simulation based framework to estimate the evolutionary traceability of protein." ; sc:featureList edam:operation_3216, edam:operation_3501, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "protTrace" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , ; sc:url "https://github.com/BIONF/protTrace" ; biotools:primaryContact "Ingo Ebersberger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_2330 ; sc:name "Chemical formula" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:encodingFormat edam:format_3508, edam:format_3620, edam:format_3752 ; sc:name "Protein isoelectric point" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2970 ; sc:encodingFormat edam:format_3508, edam:format_3620, edam:format_3752 ; sc:name "Protein hydropathy data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1522 ; sc:encodingFormat edam:format_3467, edam:format_3579, edam:format_3591, edam:format_3603, edam:format_3752 ; sc:name "Protein sequence hydropathy plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_3508, edam:format_3620, edam:format_3752 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1520 ; sc:encodingFormat edam:format_3508, edam:format_3620, edam:format_3752 ; sc:name "Peptide hydrophobic moment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2979 ; sc:encodingFormat edam:format_3508, edam:format_3620, edam:format_3752 ; sc:name "Peptide property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520, edam:topic_3524 ; sc:description "Online calculation (simulation) of many physicochemical parameters of peptides/proteins." ; sc:featureList edam:operation_0250, edam:operation_0407, edam:operation_2426, edam:operation_2574 ; sc:license "Other" ; sc:name "Prot pi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.protpi.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3047, edam:topic_3068, edam:topic_3379 ; sc:citation , "pubmed:33010159" ; sc:description """PROTAC-DB is the first web-accessible database dedicated to proteolysis-targeting chimeras (PROTACs). Users can search compounds through target, chemical structure, compound name, and ID. The chemical structures, biological activities, and physiochemical properties of these compounds were manually extracted from the literature or calculated by some programs. We will constantly add new data and improve the usability of the interface. The latest version of PROTAC-DB was released on 2020-09-09. an online database of PROTACs. Example: EGFR AR ARV-771 dBET1 13. PROTACs Warheads E3 ligands Linkers.""" ; sc:featureList edam:operation_2421, edam:operation_3454, edam:operation_3938 ; sc:name "PROTAC-DB" ; sc:url "http://cadd.zju.edu.cn/protacdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation "pubmed:26515826" ; sc:description "Vvector graphics library for displaying various biological sequence related data on web pages." ; sc:featureList edam:operation_0564, edam:operation_2479 ; sc:name "Protael" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteins.burnham.org:8080/Protael/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Smart Tag and Add-In solution for Microsoft Office applications and allows querying the ProThesaurus Web Service from within an Office application while typing your documents." ; sc:featureList edam:operation_3096 ; sc:name "ProTag" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://services.bio.ifi.lmu.de:1046/prothesaurus/#Documentation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078 ; sc:description "Protein Biological Unit Database is a new database of asymmetric units and biological units (BU) from PDB and PQS, and uses SCOP and PSIBLAST to provide ASU and BU for all entries with proteins in particular superfamilies or families." ; sc:featureList edam:operation_2421 ; sc:name "ProtBuD" ; sc:operatingSystem "Windows" ; sc:url "http://dunbrack.fccc.edu/ProtBuD/ProtBuD.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2758 ; sc:name "Pfam clan ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:name "Protein name (UniProt)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_2814, edam:topic_2828 ; sc:citation , "pmcid:PMC9825537", "pubmed:36300618" ; sc:description "The Protein Common Assembly Database (ProtCAD) – A comprehensive structural resource of protein complexes." ; sc:featureList edam:operation_0310, edam:operation_2475, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "ProtCAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://dunbrack2.fccc.edu/protcad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0602, edam:topic_1317 ; sc:citation "pubmed:22110041" ; sc:description "A network of protein-chemical structure interactions. Progress in structure determination methods means that the set of experimentally determined 3D structures of proteins in complex with small molecules is growing exponentially. ProtChemSI exploits and extends this useful set of structures by both collecting and annotating the existing data as well as providing models of potential complexes inferred by protein or chemical structure similarity." ; sc:featureList edam:operation_0360, edam:operation_0474, edam:operation_0477, edam:operation_0478, edam:operation_3767 ; sc:name "ProtChemSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pcidb.russelllab.org/" ; biotools:primaryContact "Olga Kalinina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0602, edam:topic_0736 ; sc:citation "pubmed:21036862" ; sc:description "ProtCid is a database of similar protein-protein interfaces in crystal structures of homologous proteins. Its main goal is to identify and cluster homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins." ; sc:featureList edam:operation_0247, edam:operation_0303, edam:operation_0477, edam:operation_2475, edam:operation_3432 ; sc:name "ProtCID" ; sc:softwareHelp ; sc:url "http://dunbrack2.fccc.edu/protcid" ; biotools:primaryContact "ProtCID Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2814, edam:topic_3511 ; sc:citation , "pmcid:PMC4432771", "pubmed:25982853" ; sc:description "A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins." ; sc:featureList edam:operation_2403, edam:operation_2406 ; sc:name "ProtDCal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.sce.carleton.ca/ProtDCal/" ; biotools:primaryContact "Yasser B. Ruiz Blanco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:19572216" ; sc:description "Open-source software able to automatically mutate any residue positions and find the best amino acids in an arbitrary protein structure without requiring pairwise approximations. It is based on CHARMM and it searches automatically for mutations optimizing a protein folding free energy." ; sc:featureList edam:operation_0474 ; sc:name "ProtDes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jaramillolab.issb.genopole.fr/display/sbsite/Download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3512 ; sc:citation "pubmed:19517987" ; sc:description "Software devoted to protein-coding sequences identification. The input is a set of DNA sequences that need not to be aligned. The method takes advantage of the specific substitution pattern of coding sequences together with the consistency of reading frames." ; sc:featureList edam:operation_2454 ; sc:name "protea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.lifl.fr/protea/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:7577841" ; sc:description "Generate interactive graphical representations that highlight uncertainty in atomic coordinate, in three ways: traditional spheres, ellipsoids, and rigid-body volumes." ; sc:featureList edam:operation_0570, edam:operation_2406 ; sc:name "PROTEAND" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://simtk.org/home/proteand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:33661641" ; sc:description "A Tool for Protease Selection in Bottom-Up Proteomics" ; sc:featureList edam:operation_3643, edam:operation_3645, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "ProteaseGuru" ; sc:url "https://github.com/smith-chem-wisc/ProteaseGuru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0203, edam:topic_0602, edam:topic_0749 ; sc:citation "pubmed:19483101" ; sc:description "Identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction." ; sc:featureList edam:operation_0248, edam:operation_0272, edam:operation_0438, edam:operation_0445, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ProteDNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://serv.csbb.ntu.edu.tw/ProteDNA/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3071 ; sc:citation "pubmed:24771560" ; sc:description "Free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats." ; sc:featureList edam:operation_3559 ; sc:name "Protege 5.0" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protege.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_2830, edam:topic_3324 ; sc:citation "pubmed:20959289" ; sc:description "Protegen is a web-based database and analysis system that curates, stores and analyzes protective antigens. Protegen includes basic antigen information and experimental evidence curated from peer-reviewed articles. It also includes detailed gene/protein information (e.g. DNA and protein sequences, and COG classification). Different antigen features, such as protein weight and pI, and subcellular localizations of bacterial proteins are precomputed." ; sc:featureList edam:operation_0252, edam:operation_0560, edam:operation_2479 ; sc:name "Protegen" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.violinet.org/protegen" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3318 ; sc:description "MATLAB based functions these would be utilized to observe the effect of the allergen of the protein" ; sc:isAccessibleForFree true ; sc:name "Protein Analyzing Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/72322-protein-analyzing-tools" ; biotools:primaryContact "Asadur Rahman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3070, edam:topic_3318, edam:topic_3382 ; sc:description "Protein Array Tool is a MATLAB tool for the converting an image of an R&D Systems Proteome Profiler Array into a list of relative protein levels." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Protein Array Tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/35128-protein-array-tool" ; biotools:primaryContact "Danny Allen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0736 ; sc:citation , "pubmed:31424530" ; sc:description "A CNN for performing semantic segmantation of multi-domain protein structures. Multi-Scale Structural Analysis of Proteins by Deep Semantic Segmentation." ; sc:featureList edam:operation_0303, edam:operation_0474 ; sc:name "Protein Domain Segmentor" ; sc:softwareHelp ; sc:url "https://github.com/egurapha/prot_domain_segmentor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:description "Protein Cavity Search is a software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice." ; sc:featureList edam:operation_2421, edam:operation_2479 ; sc:name "Protein Cavity Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.21" ; sc:url "http://sourceforge.net/projects/cavity-search/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1048 ; sc:encodingFormat edam:format_2330 ; sc:name "Database ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "An interactive resource of non-covalent contacts from over 100,000 publicly available crystal structures in the Protein Data Bank" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "Protein Contacts Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mrc-lmb.cam.ac.uk/pca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified. The program requires two input files: the first should contain the protein names and protein sequences while the second should contain the peptide sequences and optionally also contain the protein name associated with each peptide sequence." ; sc:featureList edam:operation_2479 ; sc:name "Protein Coverage Summarizer" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.3.5053" ; sc:url "http://omics.pnl.gov/software/protein-coverage-summarizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0821 ; sc:citation , "pmcid:PMC1924966", "pubmed:16841926" ; sc:description "The Protein Digestion Simulator can be used to read a text file containing protein or peptide sequences (FASTA format or delimited text) then output the data to a tab-delimited file. It can optionally digest the input sequences using trypsin, partial trypsin rules, or various other enzymes. The digested peptides will also have predicted normalized elution time (NET) values computed for them." ; sc:featureList edam:operation_2479 ; sc:name "Protein Digestion Simulator" ; sc:operatingSystem "Windows" ; sc:softwareVersion "2.2.5679" ; sc:url "http://omics.pnl.gov/software/protein-digestion-simulator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1238 ; sc:encodingFormat edam:format_3475 ; sc:name "Proteolytic digest" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0137, edam:topic_3520 ; sc:description "Calculates theoretical enzymatic peptides and AMTs." ; sc:featureList edam:operation_0422 ; sc:license "Apache-2.0" ; sc:name "Protein Digestion Simulator Basic" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://omics.pnl.gov/software/protein-digestion-simulator" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0845 ; sc:encodingFormat edam:format_3983 ; sc:name "Molecular charge" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1545 ; sc:name "Protein dipole moment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1467 ; sc:encodingFormat edam:format_3982 ; sc:name "Protein chain" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:description "An Internet server calculates the net charge, dipole moment and mean radius of any 3D protein structure or its constituent peptide chains, and displays the dipole vector superimposed on a ribbon backbone of the protein." ; sc:featureList edam:operation_0320, edam:operation_0386 ; sc:name "Protein Dipole Moments Server" ; sc:softwareVersion "1.0" ; sc:url "https://dipole.weizmann.ac.il" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "List is a list or Protein Disorder Predictors" ; sc:featureList edam:operation_0436 ; sc:name "Protein Disorder Predictors" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.disprot.org/predictors.php" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_0130, edam:topic_0199, edam:topic_0736 ; sc:citation "pubmed:22645321" ; sc:description "The Protein Frustratometer is an energy landscape theory inspired algorithm that aims at quantifying the degree of local frustration manifested in protein molecules. By analyzing protein frustration one can gain insight into protein biological function and how mutations alter this function." ; sc:featureList edam:operation_0303, edam:operation_0331, edam:operation_0474, edam:operation_0477, edam:operation_2415 ; sc:name "Protein Frustratometer" ; sc:url "http://lfp.qb.fcen.uba.ar/embnet/charge.php?app=Frustratometer&chains=NO" ; biotools:primaryContact "Dr. Adrián G. Turjanski", "Dr. Ignacio E. Sánchez", "Msc. Leandro G. Radusky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3510 ; sc:author "Lukasz Kreft" ; sc:citation , "pubmed:31392322" ; sc:description """We have compiled a new database regarding protein quality control in E. coli. It is very exhaustive and integrates all experimental studies on chaperone interactions with protein solubility, abundance, folding, rna translation, protein structure, etc. We are using it as a tool to discover new relations and regulatory motif in the data, but we would also like to share it with the community as an online database with a very simple functionality: once the user specifies a set of E. coli proteins, the site returns all the features in which that set of protein differs from the background.""" ; sc:isAccessibleForFree true ; sc:name "Protein Homeostasis Database" ; sc:provider "Reshmi Ramakrishnan" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://phdb.switchlab.org/#/home" ; biotools:primaryContact "Joost Schymkowitz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1317, edam:topic_3382 ; sc:citation , "pubmed:31930403" ; sc:description """Online molecular viewer platform with high quality rendering capabilities. Easy to use and able to generate publication quality molecular illustrations. This website requires javascript and CORS enabled to work properly. Some browser addons may disable this settings. Please enable them in your browser and refresh the page.""" ; sc:featureList edam:operation_0337 ; sc:name "Protein Imager" ; sc:url "https://3dproteinimaging.com/protein-imager" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121, edam:topic_0736, edam:topic_2275 ; sc:citation , "pmcid:PMC3889916", "pubmed:23624946" ; sc:contributor "SIB Swiss Institute of Bioinformatics" ; sc:description """Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. PMP has reached its end of life and no longer provides data.""" ; sc:featureList edam:operation_0224, edam:operation_2414, edam:operation_3431 ; sc:name "Protein Model Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.proteinmodelportal.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0623, edam:topic_3500 ; sc:citation "pubmed:20007151" ; sc:description "Web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. It allows users to generate and manage collections of naming rules, optionally building upon the growing body of rules generated at the J. Craig Venter Institute (JCVI). Users can check their protein names against a selected collection, generating both statistics and corrected names." ; sc:featureList edam:operation_0477, edam:operation_2409, edam:operation_3431 ; sc:name "Protein Naming Utility" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.jcvi.org/pn-utility" ; biotools:primaryContact "J. Goll" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:16301202", "pubmed:16845113", "pubmed:21075745" ; sc:description "Approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0390, edam:operation_2416, edam:operation_2488 ; sc:name "Protein Peeling 3 D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dsimb.inserm.fr/dsimb_tools/peeling3/" ; biotools:primaryContact "Jean-Christophe Gelly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0160 ; sc:citation , , "pmcid:PMC332411", "pubmed:2172928", "pubmed:9475985" ; sc:description "Protein sequence alignment viewed as sequence logos. The total height of the sequence information part is computed as the relative entropy between the observed fractions of a given symbol and the respective a priori probabilities." ; sc:featureList edam:operation_0564 ; sc:license "Other" ; sc:name "Protein Sequence Logos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rth.dk/resources/plogo/" ; biotools:primaryContact "RTH Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "The Protein Sequence Motif Extractor reads a fasta file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence. Results are stored in a new file containing the regions of the protein that contain the specified motif. The default output format is a new fasta file named _Motifs.fasta, but you can alternatively use /T to specify that a tab-delimited text file be created." ; sc:featureList edam:operation_2479 ; sc:name "Protein Sequence Motif Extractor" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.0.4752" ; sc:url "http://omics.pnl.gov/software/protein-sequence-motif-extractor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:31038685" ; sc:description "Machine learning based regression predictive models for engineering protein solubility." ; sc:featureList edam:operation_0267, edam:operation_0409, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "protein solubility" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/xiaomizhou616/protein_solubility" ; biotools:primaryContact "Kang Zhou", "Xiaonan Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone." ; sc:featureList edam:operation_2414 ; sc:name "Protein Spotlight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.expasy.org/spotlight/" ; biotools:primaryContact "Spothlight Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_1929 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:17990506" ; sc:description "ProteinART is a web tool that uses combinatorial optimization for protein inference from tandem mass spectrometry peptide identifications. It uses a set of confidently identified peptides, peptide detectability, and a protein database to provide the most likely set of identified proteins." ; sc:featureList edam:operation_3767 ; sc:name "ProteinART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://darwin.informatics.indiana.edu/applications/ProteinInference/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2772 ; sc:name "HPA antibody id" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0203, edam:topic_0621, edam:topic_0623, edam:topic_1317, edam:topic_2640, edam:topic_2815 ; sc:citation ; sc:description "Database with millions of high-resolution images. Expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images." ; sc:featureList edam:operation_0224, edam:operation_0337 ; sc:name "The Human Protein Atlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://www.proteinatlas.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0601, edam:topic_0602, edam:topic_3306 ; sc:citation ; sc:description "ProteinBERT is a protein language model pretrained on ~106M proteins from UniRef90. The pretrained model can be fine-tuned on any protein-related task in a matter of minutes. ProteinBERT achieves state-of-the-art performance on a wide range of benchmarks. ProteinBERT is built on TenforFlow/Keras." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0479 ; sc:name "ProteinBERT" ; sc:url "https://github.com/nadavbra/protein_bert" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0632, edam:topic_0736, edam:topic_3542 ; sc:citation "pubmed:19395596" ; sc:description "Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers." ; sc:featureList edam:operation_0267, edam:operation_0308, edam:operation_0470, edam:operation_2488 ; sc:name "The Protein Crystallisation Construct Designer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://xtal.nki.nl/ccd" ; biotools:primaryContact "A. Murachelli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3070, edam:topic_3318, edam:topic_3344 ; sc:description "Visualization of protein contact map" ; sc:featureList edam:operation_0337, edam:operation_0392, edam:operation_2429 ; sc:isAccessibleForFree true ; sc:name "ProteinContactMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47157-proteincontactmap-zip" ; biotools:primaryContact "Guangdi Li" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3520 ; sc:author "Martin Raus" ; sc:contributor "Marek Šebela" ; sc:description "Protein mass spectroscopy cleavage prediction." ; sc:featureList edam:operation_2403, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "ProteinCutter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Palacky University Olomouc, Czech Republic" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://software.cr-hana.upol.cz/proteincutter/" ; biotools:primaryContact "Martin Raus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:15215453", "pubmed:20538653" ; sc:description "ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time." ; sc:featureList edam:operation_0295, edam:operation_0360, edam:operation_0510, edam:operation_2487 ; sc:name "ProteinDBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteindbs.rnet.missouri.edu/" ; biotools:primaryContact "shyuc@missouri.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121 ; sc:citation "pubmed:20013361" ; sc:description "Computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking." ; sc:featureList edam:operation_3767 ; sc:name "ProteinDecision" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://digbio.missouri.edu/ProteinDecision/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2828, edam:topic_3306, edam:topic_3534 ; sc:citation , "pubmed:31750992" ; sc:description "Structural and biochemical analysis of Bacillus anthracis prephenate dehydrogenase reveals an unusual mode of inhibition by tyrosine via the ACT domain." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3453, edam:operation_3454 ; sc:name "proteindiffraction" ; sc:url "http://proteindiffraction.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2007 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3508 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3508 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3538 ; sc:citation , "pmcid:PMC7778965", "pubmed:33305318" ; sc:description "The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles including intrinsically disordered proteins" ; sc:featureList edam:operation_0224, edam:operation_2406 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Protein Ensemble Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "4" ; sc:url "https://proteinensemble.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_3299 ; sc:citation , "pubmed:34450622" ; sc:description "Estimation of Recombination and Substitution rates in alignments of protein sequences by approximate Bayesian computation." ; sc:featureList edam:operation_0492, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ProteinEvolverABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/miguelarenas/proteinevolverabc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0623, edam:topic_0749, edam:topic_3474 ; sc:citation ; sc:description "ProteInfer is an approach for predicting the functional properties of protein sequences using deep neural networks." ; sc:featureList edam:operation_1777, edam:operation_3767, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ProteInfer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/google-research/proteinfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775 ; sc:citation "pubmed:22962465" ; sc:description "Software of two domain-based protein function prediction methods that encode domain recurrence and order information." ; sc:featureList edam:operation_1777, edam:operation_2479 ; sc:name "ProteinFuncPred" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sfb.kaust.edu.sa/Pages/Software.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0128, edam:topic_0160, edam:topic_3520, edam:topic_3534 ; sc:description "Several on-line tools, including OLMAT for peptide mass fingerprinting." ; sc:featureList edam:operation_2929 ; sc:name "ProteinGuru" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.proteinguru.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3293 ; sc:citation , "pmcid:PMC3386163", "pubmed:22761559" ; sc:description "Identifies enrichment for proteins of different phylogenetic ages in protein sets of interest. Over thirty eukaryotic species are currently supported and other protein attributes can be uploaded to combine with the protein age analysis." ; sc:featureList edam:operation_0324, edam:operation_3501, edam:operation_3745 ; sc:license "GPL-1.0" ; sc:name "ProteinHistorian" ; sc:softwareHelp ; sc:url "http://lighthouse.ucsf.edu/ProteinHistorian/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "ProteinInfer is a softwarr for combinatorial perspective of the protein inference problem" ; sc:featureList edam:operation_3767 ; sc:name "ProteinInfer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ust.hk/proteininfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121 ; sc:citation "pubmed:23385215" ; sc:description "The new inference algorithm which explores an ensemble learning strategy to address the sparsity parameter selection problem in Lasso model." ; sc:featureList edam:operation_2479, edam:operation_3767 ; sc:name "ProteinLasso" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/proteinlasso/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_2269, edam:topic_3336 ; sc:citation , "pubmed:33978752" ; sc:description "ProteinLens is a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules. ProteinLens constructs a fully atomistic, energy-weighted graph representation of a biomolecular structure and explores the long-range communication or connectivity between any specific sites in the system. Example of usage are identify potential allosteric sites, explore allosteric pathways, and identify residues that play a key role in signalling and/or cooperativity." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2476, edam:operation_3659, edam:operation_4009 ; sc:license "CC-BY-NC-4.0" ; sc:name "ProteinLens" ; sc:softwareHelp , , ; sc:url "https://www.proteinlens.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3518, edam:topic_3520 ; sc:citation , "pmcid:PMC7557219", "pubmed:33073088" ; sc:description """A User-Friendly Tool for Normalization and Analysis of TMT and Label-Free Protein Quantification. As input, proteiNorm expects tab-separated peptide (optional) and protein data (not on logarithmic scale) as produced by software such as MaxQuant 9, where each row represents a peptide or protein and the column names of the measured intensities (samples) beginning with “Reporter intensity corrected” followed by an integer and an optional label (e.g. “Reporter intensity corrected 5 TMT2”) for TMT experiments.""" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3557, edam:operation_3634, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "proteiNorm" ; sc:url "https://sbyrum.shinyapps.io/proteiNorm/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0797 ; sc:citation , , , "pmcid:PMC3114741", "pubmed:21526987" ; sc:description "Proteinortho is a tool to detect orthologous genes within different species" ; sc:featureList edam:operation_0291, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Proteinortho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "6.3.1" ; sc:url "https://gitlab.com/paulklemm_PHD/proteinortho" ; biotools:primaryContact "Marcus Lechner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078 ; sc:description "Significance assessment for distance measures of time-course protein profiles" ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "proteinProfiles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/proteinProfiles.html" ; biotools:primaryContact "Julian Gehring" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3474, edam:topic_3957 ; sc:citation ; sc:description "A webserver for predicting protein-protein interactions." ; sc:featureList edam:operation_2421, edam:operation_2464, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "ProteinPrompt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://proteinformatics.org/ProteinPrompt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3468, edam:format_3747 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:14632076" ; sc:description "Validation of protein identifications by MS/MS and database searches." ; sc:featureList edam:operation_3644, edam:operation_3648, edam:operation_3664, edam:operation_3695, edam:operation_3767 ; sc:name "ProteinProphet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/ProteinProphet.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3489, edam:topic_3520 ; sc:citation ; sc:description "A suite of protein identification tools." ; sc:featureList edam:operation_2929, edam:operation_3647 ; sc:name "ProteinProspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prospector.ucsf.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305, edam:format_2332, edam:format_3464 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305, edam:format_2332, edam:format_3464 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "The Proteins REST API provides access to key biological data from UniProt and data from Large Scale Studies (LSS) mapped to UniProt. The services provide sequence feature annotations from UniProtKB, variation data from UniProtKB and mapped from LSS (1000 Genomes, ExAC and COSMIC), proteomics data mapped from LSS (PeptideAtlas, MaxQB and EPD), antigen sequences mapped from Human Protein Atlas (HPA), proteomes and taxonomy search and retrieval, and reference genome coordinate mappings." ; sc:featureList edam:operation_2422 ; sc:name "Proteins API" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/proteins/api" ; biotools:primaryContact "Andrew Nightingale", "Maria Martin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0102, edam:topic_2275 ; sc:citation ; sc:description "It is a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates." ; sc:featureList edam:operation_0337, edam:operation_2429 ; sc:name "ProteinShader beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.4" ; sc:url "http://proteinshader.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0154, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:32971019" ; sc:description """Fast and Flexible Protein Design Using Deep Graph Neural Networks. Generate protein sequences matching a predetermined geometry¶.""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0474, edam:operation_2476 ; sc:name "ProteinSolver" ; sc:url "http://design.proteinsolver.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3683 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Analysis of mass spectrometry proteomics quality control metrics." ; sc:featureList edam:operation_2479 ; sc:license "Apache-2.0" ; sc:name "Proteinspector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bitbucket.org/proteinspector/qc_analysis/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1208 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2992 ; sc:encodingFormat edam:format_3508, edam:format_3603, edam:format_3604 ; sc:name "Protein structure image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein property" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3534 ; sc:citation , ; sc:description "It supports various commonly required tasks of structure-based molecular modeling. It provides functionalities for structure quality assessment , hydrogen placement, the search for alternative conformations, the generation of 2D-interaction diagrams, protein-protein interface classification as well as automatic pocket detection and druggablity assessment." ; sc:featureList edam:operation_0321, edam:operation_0339, edam:operation_0570, edam:operation_2406, edam:operation_2575, edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "ProteinsPlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0123, edam:topic_2814, edam:topic_3474 ; sc:citation , "pubmed:34019657" ; sc:description "ProteinTools is a toolkit to analyze protein structures. ProteinTools is a web server committed to ease the analysis of protein structures in a single interface." ; sc:featureList edam:operation_0393, edam:operation_0394, edam:operation_1839, edam:operation_2406, edam:operation_2429 ; sc:name "ProteinTools" ; sc:url "https://proteintools.uni-bayreuth.de" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_3752 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3070, edam:topic_3542 ; sc:citation , "pubmed:36448315" ; sc:description "Convolutional ProteinUnetLM competitive with LSTM-based protein secondary structure predictors." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ProteinUnetLM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://biolib.com/SUT/ProteinUnetLM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "ProteinVolume (PV) is a Java program that calculates the components of the solvent-excluded (geometric) volume of a protein: van der Waals and void volume." ; sc:featureList edam:operation_2479 ; sc:name "ProteinVolume" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://gmlab.bio.rpi.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2814 ; sc:citation , "pmcid:PMC7147804", "pubmed:32231351" ; sc:description """Web-based molecular visualization in virtual reality. ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.""" ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:license "BSD-3-Clause" ; sc:name "ProteinVR" ; sc:url "http://durrantlab.com/protein-vr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071, edam:topic_3520 ; sc:citation ; sc:description "A multi-user platform for analysis and management of proteomics data." ; sc:featureList edam:operation_2945 ; sc:name "Proteios Software Environment" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.19.0" ; sc:url "http://www.proteios.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:16845015" ; sc:description "The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0474, edam:operation_0477, edam:operation_2575 ; sc:name "Protemot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protemot.csbb.ntu.edu.tw/" ; biotools:primaryContact "Protemot Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0621 ; sc:citation "pubmed:26116928" ; sc:description "Analyze and visualize synteny at the protein level between two organisms." ; sc:featureList edam:operation_0573, edam:operation_2429, edam:operation_2479 ; sc:name "Proteny" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/thiesgehrmann/proteny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121 ; sc:citation ; sc:description """Peptides that were identified, in collaboration, by Spanish National Cancer Research Centre (CNIO) and Centro Nacional de Investigaciones Cardiovasculares (CNIC). We interrogate peptides from eight large-scale human proteomics experiments and databases, irrespective of tissue or cell type, for the vast majority of the protein-coding genes in these experiments. The peptide has to be included in at least 2 experiments.""" ; sc:featureList edam:operation_2423 ; sc:name "PROTEO: Peptide evidence for the human genome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CNIC", "CNIO", "cnio.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://proteo.bioinfo.cnio.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0219, edam:topic_0622 ; sc:citation , "pubmed:25297486" ; sc:description "Open source proteogenomics annotation software supporting PSI standards." ; sc:featureList edam:operation_3672 ; sc:name "ProteoAnnotator" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.proteoannotator.org/" ; biotools:primaryContact "Andrew Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:33165572" ; sc:description """integrating bottom-up with top-down proteomics data for improved proteoform assessment. Here we present a high-performance software for proteome analysis that combines different mass spectrometric approaches, such as, top-down for intact protein analyses and both bottom-up and middle-down, for proteolytic fragment characterization. ProteoCombiner capitalizes on the data arising from different experiments and proteomics search engines and presents the results in a user-friendly manner.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3755 ; sc:name "ProteoCombiner" ; sc:url "https://proteocombiner.pasteur.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3391 ; sc:citation ; sc:description "An R-based open-source software termed ProteoDisco that allows for flexible incorporation of genomic variants, fusion-genes and (aberrant) transcriptomic variants from standardized formats into protein variant sequences. ProteoDisco allows for a flexible step-by-step workflow allowing for in-depth customization to suit a myriad of research approaches in the field of proteogenomics, on all organisms for which a reference genome and transcript annotations are available." ; sc:name "ProteoDisco" ; sc:url "https://github.com/ErasmusMC-CCBC/ProteoDisco/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:35657588" ; sc:description "Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite." ; sc:featureList edam:operation_0417, edam:operation_3645, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Proteoform Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smith-chem-wisc.github.io/ProteoformSuite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071, edam:topic_3520 ; sc:citation ; sc:description "ProteoformClassifier is a tool that classifies proteoform identifications and validates that proteoform results are transparent about ambiguity." ; sc:featureList edam:operation_3627, edam:operation_3755, edam:operation_3767 ; sc:license "MIT" ; sc:name "ProteoformClassifier" ; sc:softwareHelp , ; sc:url "https://github.com/smith-chem-wisc/ProteoformClassifier" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_3621 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3120, edam:topic_3308 ; sc:author , , "Elvis Ndah" ; sc:citation , , "pmcid:PMC4357689", "pubmed:25510491", "pubmed:31040227" ; sc:contributor , "Alexander Koch", "Sandra Steyaert" ; sc:description "Proteogenomic pipeline integrating ribosome profiling (RIBO-seq) data in the search for new proteoforms in proteomic validation data. The pipeline does a genome-wide construction of candidate translation products based on ribosome occupancy." ; sc:featureList edam:operation_0362, edam:operation_2284, edam:operation_2423, edam:operation_3182, edam:operation_3198, edam:operation_3225, edam:operation_3563, edam:operation_3661, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PROTEOFORMER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0", "2.0" ; sc:url "https://github.com/Biobix/proteoformer" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3474, edam:topic_3576 ; sc:citation , "pmcid:PMC9237736", "pubmed:35639661" ; sc:description "Conditional generative modeling for de novo protein design with hierarchical functions." ; sc:featureList edam:operation_0477, edam:operation_3359, edam:operation_3557, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ProteoGAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/timkucera/proteogan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:21325302" ; sc:description "Platform for creating MS/MS data analysis workflows using scripts." ; sc:featureList edam:operation_3214 ; sc:name "Proteomatic" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/specht/proteomatic" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1528 ; sc:name "Protein isoelectric point" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_3520 ; sc:citation , "pmcid:PMC5210655", "pubmed:27789699" ; sc:description "The database of pre-computed isoelectric points for proteomes from different model organisms (5029 species). Goals of the database include making statistical comparisons of the various prediction methods (18 algorithms implemented) as well as facilitating biological investigation of protein isoelectric point space." ; sc:featureList edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Proteome-pI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://isoelectricpointdb.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0123, edam:topic_1775, edam:topic_2275 ; sc:citation "pubmed:15215412" ; sc:description "High-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. The tool uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers." ; sc:featureList edam:operation_1777, edam:operation_2479, edam:operation_2489 ; sc:name "Proteome Analyst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.cs.ualberta.ca/~bioinfo/PA/" ; biotools:primaryContact "Proteome Analyst Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1238 ; sc:encodingFormat edam:format_2330 ; sc:name "Proteolytic digest" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0123, edam:topic_0137, edam:topic_3520 ; sc:citation "pubmed:22324799" ; sc:description "R classes for prediction of proteome coverage based on iterative digestion by MED-FASP or similar." ; sc:featureList edam:operation_0422 ; sc:name "ProteomeDigestSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jgmeyerucsd/ProteomeDigestSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0219, edam:topic_2269, edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33416829" ; sc:description """ProteomeExpert: A Docker image based web-server for exploring, modeling, visualizing, and mining large-scale proteomic data sets. The application is based on the Shiny package and can be run locally or on a server.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3799 ; sc:name "ProteomeExpert" ; sc:url "https://proteomic.shinyapps.io/peserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_0121, edam:topic_3344 ; sc:citation ; sc:description "A project that's aim is to translate the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. It offers a repository of synthesized peptides and different tools for analyzing them." ; sc:featureList edam:operation_2414, edam:operation_2422, edam:operation_3436, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:name "ProteomeTools" ; sc:url "http://www.proteometools.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , , , "pmcid:PMC9825490", "pubmed:36370099" ; sc:description "This consortium has been set up to provide a globally coordinated submission of mass spectrometry proteomics data to the main existing proteomics repositories, and to encourage optimal data dissemination." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2479, edam:operation_3214, edam:operation_3431 ; sc:name "ProteomeXchange" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.proteomexchange.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description """We provide a proteomics software toolbox (i.e., offering pre-installed, pre-configured and tested own tools and free third-party software) on our hardware infrastructure. The toolbox can be used on our high-performance hardware infrastructure via high-bandwidth internet connection or at your site (via virtualization).""" ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "Proteomics toolbox" ; sc:provider "BioInfra.Prot" ; sc:softwareVersion "1" ; sc:url "http://www.ruhr-uni-bochum.de/mpc/medical_bioinformatics/bioinfraprot/index.html.en" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3071 ; sc:citation ; sc:description "These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard BioConductor data structures." ; sc:featureList edam:operation_0335 ; sc:license "Artistic-2.0" ; sc:name "ProteomicsAnnotationHubData" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ProteomicsAnnotationHubData.html" ; biotools:primaryContact "Laurent Gatto" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603, edam:format_3604 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3308, edam:topic_3520 ; sc:citation "pubmed:24870543" ; sc:description "Explorable, interactive human proteome database, including MS/MS data." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2930, edam:operation_2949, edam:operation_3694, edam:operation_3741 ; sc:name "ProteomicsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.proteomicsdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9903315", "pubmed:36693629" ; sc:description "Online platform for community-curated datasets and tutorials for machine learning in proteomics." ; sc:featureList edam:operation_3633, edam:operation_3643, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ProteomicsML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.proteomicsml.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "An Extendable Quality Control Pipeline Server for High-Throughput Proteomics implemented in Python. Drag'n drop RAW files into automated pipelines. Explore the results in an interactive dashboard." ; sc:featureList edam:operation_0337, edam:operation_3630, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ProteomicsQC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/LewisResearchGroup/ProteomicsQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_0769, edam:topic_3518 ; sc:citation ; sc:description """Efficient network-based functional analysis portal for proteomics data. Differential expression pathway and network analysis tool. Deselect a sample to exclude it. Set maximum number allowed missing values for each condition.""" ; sc:featureList edam:operation_2939, edam:operation_3891, edam:operation_3928 ; sc:name "ProteoMill" ; sc:url "https://proteomill.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_2259 ; sc:citation "pubmed:23924514" ; sc:description "Web server that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks." ; sc:featureList edam:operation_2403, edam:operation_2497 ; sc:name "ProteoMirExpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jjwanglab.org/proteomirexpress/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_1317, edam:topic_3068, edam:topic_3307, edam:topic_3571 ; sc:citation ; sc:description "Interactive encyclopedia of proteins, RNA, DNA and other molecules with 3D structures." ; sc:featureList edam:operation_0570, edam:operation_2421, edam:operation_3096, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:name "Proteopedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:url "http://www.proteopedia.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "This package creates a HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data." ; sc:featureList edam:operation_0321 ; sc:license "GPL-2.0" ; sc:name "proteoQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/proteoQC.html" ; biotools:primaryContact "Bo Wen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:16083278" ; sc:description "Blind spectral search of tandem mass spectra of peptides." ; sc:featureList edam:operation_3644 ; sc:name "ProteoSAFe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/ProteoSAFe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:28520987" ; sc:description """Protein differential expression analysis designed with the end-proteomics user in mind. It aims to fully automate the process of statistically evaluating differential expression in mass spectrometry-based bottom-up (shotgun) quantitative proteomics data by requiring minimal user interaction time and generating publication-quality data plots.""" ; sc:featureList edam:operation_3635 ; sc:name "Proteosign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.med.uoc.gr/ProteoSign/" ; biotools:primaryContact "IOANNIS ILIOPOULOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description """a software tool to biologically annotate and quantify modification-specific, peptide-centric proteomics datasets. ProteoSushi transforms peptide-centric, PTM-enriched peptide data into condensed and annotated PTM site output that is easy to understand and analyze.""" ; sc:featureList edam:operation_0417, edam:operation_1812, edam:operation_2422, edam:operation_3755, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ProteoSushi" ; sc:url "http://github.com/HeldLab/ProteoSushi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_3520 ; sc:citation , "pmcid:PMC7423749", "pubmed:32347222" ; sc:description """a tool for the analysis and interactive visualization of phosphoproteomics data. Interactive tool for Phosphoproteomics.""" ; sc:featureList edam:operation_0337, edam:operation_3741, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "ProteoViz" ; sc:url "https://github.com/ByrumLab/ProteoViz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis." ; sc:featureList edam:operation_2406, edam:operation_2479 ; sc:name "ProteoWizard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteowizard.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0140, edam:topic_0157, edam:topic_1775, edam:topic_3534 ; sc:citation "pubmed:15980469" ; sc:description "An archive of functional signatures in protein termini." ; sc:featureList edam:operation_1777, edam:operation_1778, edam:operation_2414, edam:operation_2479 ; sc:name "ProTeus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.proteus.cs.huji.ac.il/index.php" ; biotools:primaryContact "Michal Linial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199 ; sc:citation , "pmcid:PMC7330979", "pubmed:32611389" ; sc:description """An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures. Protein engineering using Proteus. Proteus is a Webtool, database, and method to propose mutations for proteins used in industrial applications. Proteus uses the hypothesis of mutation transference of residue pairs in contact detected in PDB to suggest mutations for a target protein.""" ; sc:featureList edam:operation_0331, edam:operation_0394, edam:operation_2950, edam:operation_3227 ; sc:name "Proteus" ; sc:url "http://proteus.dcc.ufmg.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_2275, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:18483082" ; sc:description "PROTEUS2 is a web server for comprehensive protein structure prediction and structure-based annotation. 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The program also simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding." ; sc:featureList edam:operation_2406 ; sc:name "ProtEvol" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://ub.cbm.uam.es/software/Prot_Evol.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0769 ; sc:citation , "pmcid:PMC7340977", "pubmed:32670509" ; sc:description """A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics. ProTExA is a web-tool that provides a post-processing workflow for the analysis of protein and gene expression datasets. Using network-based bioinformatics approaches, ProTExA facilitates differential expression analysis and co-expression network analysis as well as pathway and post-pathway analysis. Specifically, for a given set of protein-gene expression data across samples, ProTExA: (1) performs statistical analysis and filtering to highlight the differentially expressed proteins-genes, (2) performs enrichment analysis to identify top-scored pathways, (3) generates pathway-to-pathway and pathway-to-gene networks (4) generates protein and gene co-expression networks using a variety of methodologies, and (5) applies clustering methodologies to identify sub-networks of co-expressed proteins-genes""" ; sc:featureList edam:operation_2436, edam:operation_3463, edam:operation_3741, edam:operation_3766, edam:operation_3928 ; sc:name "ProTExA" ; sc:url "http://bioinformatics.cing.ac.cy/protexa/#step-1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:description "A modified version of ProtExcluder for building conda package" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "protexcluder" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/NBISweden/ProtExcluder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:32892224" ; sc:description """protein fold recognition by combining Directed Fusion Graph and PageRank algorithm. a: ProtFold-DFG is based on the DeepSVM-fold(CCM), DeepSVM-fold(PSFM), MotifCNN-fold(CCM), MotifCNN-fold(PSFM) and LTR, uses transitive closure and KL-divergence to construct the Directed Fusion Graph and gets the final ranking result through PageRank algorithm.""" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0474, edam:operation_2415 ; sc:name "ProtFold-DFG" ; sc:url "http://bliulab.net/ProtFold-DFG/download" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , "pubmed:12079362" ; sc:description "Prediction of cellular role, enzyme class and Gene Ontology category." ; sc:featureList edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ProtFun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.2" ; sc:url "http://cbs.dtu.dk/services/ProtFun/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3179, edam:topic_3324, edam:topic_3518 ; 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biotools:primaryContact "Laurent Gatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0218, edam:topic_3474, edam:topic_3542 ; sc:citation , "pmcid:PMC9329459", "pubmed:35896542" ; sc:description "A deep unsupervised language model for protein design." ; sc:featureList edam:operation_0267, edam:operation_0408, edam:operation_0477, edam:operation_2488, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ProtGPT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huggingface.co/nferruz/ProtGPT2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0130, edam:topic_0199, edam:topic_3068 ; sc:citation , "pubmed:33196841" ; sc:description "ProThermDB, thermodynamic Database for Proteins and Mutants (ProThermDB) contains more than 32,000 data of several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change, and heat capacity change along with experimental methods and conditions, sequence, structure, and literature information. Besides, the current version of the database includes ~0.12 million thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for the visualization of mutations at sequence and structure levels. 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It aims to present a simple and consistent command-line interface across otherwise disparate third party tools." ; sc:featureList edam:operation_2409, edam:operation_3630, edam:operation_3631 ; sc:license "MIT" ; sc:name "protk" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/iracooke/protk" ; biotools:primaryContact "Ira Cook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3299 ; sc:citation ; sc:description """A Python package for the analysis and design of chimeric proteins. Welcome to ProtLego! An Open-source Python Library for Chimera Design and Analysis — ProtLego 1.0.0 documentation. Fuzzle is a database of evolutionary related protein fragments. Search for related Entries in the Database: Submit Examples: 1pky, c.23, Flavodoxin Sequence (2HNA).""" ; sc:featureList edam:operation_0450, edam:operation_2421, edam:operation_3918 ; sc:name "Protlego" ; sc:url "https://hoecker-lab.github.io/protlego/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:23449253" ; sc:description "Fast and robust software tool for analyzing large shotgun proteomics mass spectrometry data sets." ; sc:featureList edam:operation_2406 ; sc:name "ProtMAX" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.univie.ac.at/mosys/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0593, edam:topic_0749 ; sc:citation , "pubmed:35775902" ; sc:description "Protein-bound Nucleic Acid filters and fragment libraries (protNAff) is a tool to create filters that select structures of Protein - Nucleic acids complexes from the PDB and to build libraries of protein-bound RNA fragments." ; sc:featureList edam:operation_1812, edam:operation_2518, edam:operation_3695, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "protNAff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://colab.research.google.com/github/isaureCdB/ProtNAff/blob/master/filtering-clustering.ipynb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0623 ; sc:citation , "pmcid:PMC4408594", "pubmed:25911153" ; sc:description "Database and resource of protein families in Arthropod genomes." ; sc:featureList edam:operation_3646 ; sc:name "ProtoBug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.protobug.cs.huji.ac.il/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3892 ; sc:citation , "pubmed:32092258" ; sc:description """Robust Automation of Binding Free Energy Calculations. 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ProtoCaller uses a variety of tools to automate the free energy calculation process, such as: Biopython, BioSimSpace, CHARMM-GUI, (optionally) Modeller, Open Babel, ParmEd, PDB2PQR, pdbfixer, RDKit.""" ; sc:featureList edam:operation_2476, edam:operation_3893 ; sc:license "GPL-3.0" ; sc:name "ProtoCaller" ; sc:softwareHelp ; sc:url "https://github.com/protocaller/protocaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_3524 ; sc:citation "pubmed:25150250" ; sc:description "Virtual laboratory environment that promote reproducibility of biological experiments and reuse of experimental data." ; sc:featureList edam:operation_2426 ; sc:name "ProtocolNavigator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protocolnavigator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_0602, edam:topic_0749, edam:topic_3520 ; sc:citation "pubmed:18724940" ; sc:description "Recently developed technique to map in vivo substrates of proteolytic events. It uses 1D SDS-PAGE and mass spectrometry to globally identify shifts in gel-migration and corresponding changes in the topography of proteolytic fragments." ; sc:featureList edam:operation_0303, edam:operation_0366, edam:operation_2429, edam:operation_2929 ; sc:name "PROTOMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.scripps.edu/chemphys/cravatt/protomap/" ; biotools:primaryContact "Benjamin F. Cravatt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:encodingFormat edam:format_2068 ; sc:name "Sequence motif (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2071 ; sc:encodingFormat edam:format_2068 ; sc:name "Sequence motif (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_2554 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Motif search and discovery in protein sequences." ; sc:featureList edam:operation_0238, edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.0" ; sc:name "Protomata" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://tools.genouest.org/tools/protomata/" ; biotools:primaryContact "GenOuest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_1978 ; sc:name "Protein family report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation ; sc:description "Automatic hierarchical classification of protein sequences." ; sc:featureList edam:operation_0224 ; sc:name "ProtoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.protonet.cs.huji.ac.il/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602 ; sc:citation , ; sc:description "Fully automated hydrogen prediction tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. It investigates hydrogen bonds, metal interactions and repulsive atom contacts for all possible states and calculates an optimal hydrogen bonding network within these degrees of freedom." ; sc:featureList edam:operation_0394, edam:operation_2949 ; sc:name "Protoss" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Hamburg - Center for Bioinformatics" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de/#protoss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0659, edam:topic_0780, edam:topic_3324 ; sc:citation , "pmcid:PMC8607299", "pubmed:34791104" ; sc:description "A web-based application for molecular identification of Prototheca species." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3460, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Prototheca-ID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://prototheca-id.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_3336, edam:topic_3379 ; sc:citation , "pmcid:PMC4086068", "pubmed:24838562" ; sc:description "ProTox is a web server for the in silico prediction of oral toxicities of small molecules in rodents." ; sc:featureList edam:operation_0474, edam:operation_2428, edam:operation_2489, edam:operation_3092 ; sc:name "ProTox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tox.charite.de/tox" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_1775, edam:topic_3307 ; sc:citation "pubmed:10027275" ; sc:description "Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY)." ; sc:featureList edam:operation_0236, edam:operation_0398, edam:operation_0399, edam:operation_0405, edam:operation_0406, edam:operation_2479, edam:operation_3767 ; sc:name "ProtParam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/protparam" ; biotools:primaryContact "ProtParam Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0622, edam:topic_0625, edam:topic_3293 ; sc:citation , "pmcid:PMC4489284", "pubmed:25956654" ; sc:description "Identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling." ; sc:featureList edam:operation_0314 ; sc:name "ProtPhylo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.protphylo.org/" ; biotools:primaryContact "Dr. Fabiana Perocchi", "Dr. Yiming Cheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0130, edam:topic_0199, edam:topic_0736, edam:topic_3297 ; sc:citation , "pmcid:PMC9133766", "pubmed:35664235" ; sc:description "The web server that readily proposes protein stabilizing mutations with high PPV." ; sc:featureList edam:operation_0331, edam:operation_3659, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:name "Protposer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webapps.bifi.es/the-protposer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_0154 ; sc:description "Software for calculating the widely used structural and physicochemical features of proteins and peptides from amino acid sequence." ; sc:featureList edam:operation_2479 ; sc:name "protpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://code.google.com/p/protpy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3510 ; sc:citation "pubmed:25619996" ; sc:description "Comprehensive R package for generating various numerical representation schemes of proteins and peptides from amino acid sequence." ; sc:featureList edam:operation_2479 ; sc:name "protr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/protr/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3173, edam:topic_3676, edam:topic_3922 ; sc:citation ; sc:description """An Interactive Multi-Omics Data Browser for Proteogenomic Studies. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) initiative has generated extensive multi-omics data resources of deep proteogenomic profiles for multiple cancer types. To enable the broader community of biological and medical researchers to intuitively query, explore, and download data and analysis results from various CPTAC projects, we built a prototype user-friendly web application called “ProTrack” with the CPTAC clear cell renal cell carcinoma (ccRCC) data set ( http: ccrcc.cptac-data-view.org ). Here we describe the salient features of this application which provides a dynamic, comprehensive, and granular visualization of the rich proteogenomic data. Statement of Significance The CPTAC initiative ( https: proteomics.cancer.gov ) has generated multi-omics data for multiple cancer types to understand the proteogenomic aberrations of these malignancies""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3200 ; sc:name "ProTrack" ; sc:url "http://ccrcc.cptac-data-view.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0623, edam:topic_1775 ; sc:citation , "pubmed:34460380" ; sc:description "Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank." ; sc:featureList edam:operation_0474, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ProtRe-CN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/ProtRe-CN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2275, edam:topic_3572 ; sc:citation "pubmed:26478257" ; sc:description "Meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model." ; sc:featureList edam:operation_2406, edam:operation_2480 ; sc:name "ProTSAV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_1775 ; sc:description "Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature." ; sc:featureList edam:operation_0236, edam:operation_0405 ; sc:name "ProtScale" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/protscale/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2275, edam:topic_3697 ; sc:citation , ; sc:description """Proteome Mining of Sortase A Dependent Proteins (SDPs) in Lactic Acid Bacteria and Docking Analysis of SDPs Interaction with Sortase A. NIGEBProtScreen Reporting System.""" ; sc:featureList edam:operation_0239, edam:operation_3891, edam:operation_3899 ; sc:name "ProtScreen" ; sc:url "http://nigebprotscreen.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_0736 ; sc:citation , "pubmed:32401507" ; sc:description """Estimating the Effect of Single-Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein. Estimating Change in Protein Thermodynamic Stability owing to Single Point Mutation. Developed for protein structures, ProTSPoM uses a combination of Random Forest Regressors (RFR) and Gradient Boosted Regressors (GBR) along with residue properties, fold level attributes, environmental compatibility, and evolutionary information to predict the change in Gibbs free energy originating out of single point missense mutations. ProTSPoM outperforms all existing state-of-the-art methods in both the Pearson correlation coefficient and root-mean-squared-error parameters for the S2648, S350, S1925 and p53 databases (even if we do not include evolutionary information). ProTSPoM execuatable ProTSPoM benchmark data.""" ; sc:featureList edam:operation_0303, edam:operation_0331, edam:operation_0394, edam:operation_0474 ; sc:name "ProTSPoM" ; sc:url "http://cosmos.iitkgp.ac.in/ProTSPoM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Protsweep can be used for analysis and possible identification of newly obtained protein sequences." ; sc:featureList edam:operation_2479, edam:operation_2502 ; sc:name "ProtSweep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.welcome#protsweep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2547, edam:format_3747, edam:format_3752 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2547, edam:format_3747, edam:format_3752 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929, edam:format_2330, edam:format_2547, edam:format_3747, edam:format_3752 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1709 ; sc:encodingFormat edam:format_3508, edam:format_3603, edam:format_3604 ; sc:name "Protein secondary structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0736, edam:topic_2814, edam:topic_3534, edam:topic_3542 ; sc:citation "pubmed:24162465" ; sc:description "Interactive protein feature visualization and integration with experimental proteomic data." ; sc:featureList edam:operation_0472, edam:operation_2241, edam:operation_2486, edam:operation_3092, edam:operation_3636 ; sc:name "Protter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wlab.ethz.ch/protter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0084, edam:topic_0154, edam:topic_3293, edam:topic_3678 ; sc:citation , "pmcid:PMC5215816", "pubmed:15647292", "pubmed:21335321" ; sc:description "ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment." ; sc:featureList edam:operation_0292, edam:operation_0331, edam:operation_0477, edam:operation_0550, edam:operation_2479 ; sc:name "ProtTest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://darwin.uvigo.es/software/prottest_server.html?" ; biotools:primaryContact "D. Posada", "F. Abascal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC9710675", "pubmed:36699412" ; sc:description "R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "protti" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://jpquast.github.io/protti/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2229, edam:topic_3306, edam:topic_3542 ; sc:citation , "pubmed:34232869" ; sc:description "ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using various Transformers Models." ; sc:featureList edam:operation_0267, edam:operation_2489, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "ProtTrans" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/agemagician/ProtTrans" ; biotools:primaryContact "Ahmed Elnaggar", "Christian Dallago", "Michael Heinzinger", "Yu Wang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_3016 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_3016 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2187 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3779 ; sc:encodingFormat edam:format_2187 ; sc:name "Annotated text" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_1317, edam:topic_2533, edam:topic_3510, edam:topic_3574 ; sc:author ; sc:description "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API." ; sc:featureList edam:operation_2520, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "ProtVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp ; sc:url "https://www.ebi.ac.uk/ProtVar/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520, edam:topic_3922 ; sc:citation ; sc:description "A versatile tool for in silico protease evaluation and selection in a proteomic and proteogenomic context." ; sc:featureList edam:operation_3644, edam:operation_3645, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ProtView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SSPuliasis/ProtView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2269, edam:topic_3520 ; sc:citation ; sc:description """Comparing Label-Free Shotgun Proteomics Datasets Using Accumulated Peptide Probabilities. Comparing multiple label-free shotgun proteomics datasets requires various data processing and formatting steps, including peptide-spectrum matching, protein inference, and quantification. Finally, the compilation of results files into a format that allows for downstream analyses. ProtyQuant performs protein inference and quantification calculations and combines the results of individual datasets into plain text tables. These are lightweight, human-readable, and easy to import into databases or statistical software. ProtyQuant reads validated pepXML from proteomic workflows such as the Trans-Proteomic Pipeline (TPP), which makes it compatible with many commercial and free search engines. For protein inference and quantification, a modified version of the PIPQ program (He et al. 2016) was integrated. In contrast to simple spectral-counting, PIPQ sums up peptide probabilities""" ; sc:featureList edam:operation_3631, edam:operation_3634, edam:operation_3767 ; sc:name "ProtyQuant" ; sc:url "https://bitbucket.org/lababi/protyquant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3120 ; sc:citation ; sc:description "A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein." ; sc:featureList edam:operation_0361, edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "PROVEAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://provean.jcvi.org/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769 ; sc:citation , "pmcid:PMC7723325", "pubmed:32638008" ; sc:description "ProVision is a data analysis dashboard written in the R-shiny framework. This dashboard is designed to analyse label free and TMT proteomics data downstream from maxQuant." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3634 ; sc:license "GPL-3.0" ; sc:name "ProVision" ; sc:url "https://provision.shinyapps.io/provision/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation "pubmed:18428719" ; sc:description "Software tools and integrated databases to facilitate analyzing the output from protein mass spectrometry experiments." ; sc:featureList edam:operation_2929, edam:operation_3214, edam:operation_3627, edam:operation_3631, edam:operation_3767 ; sc:name "PROWL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prowl.rockefeller.edu/" ; biotools:primaryContact "Brian T. Chait" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0196 ; sc:citation ; sc:description "Prowler is a trimming algorithm for Oxford Nanopore sequence data." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3218 ; sc:license "MIT" ; sc:name "Prowler" ; sc:url "https://github.com/ProwlerForNanopore/ProwlerTrimmer" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3315, edam:topic_3474 ; sc:citation "pmcid:PMC6812563", "pubmed:31649491" ; sc:description """Proximal Distance Algorithms. Code for the numerical experiments from manuscripts for the proximal distance algorithm. 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You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1)." ; sc:featureList edam:operation_3192 ; sc:name "PRUNETREE" ; sc:operatingSystem "Windows" ; sc:softwareVersion "5.0" ; sc:url "http://lajeunesse.myweb.usf.edu/publications.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0634, edam:topic_3360, edam:topic_3422 ; sc:citation , "pmcid:PMC7952700", "pubmed:33707596" ; sc:description "Tool for prioritization of disease candidates from proteomics data using a combination of shortest-path and random walk algorithms." ; sc:featureList edam:operation_0306, edam:operation_3928 ; sc:name "PRYNT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Boizard/PRYNT" ; biotools:primaryContact "Julie Klein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:16844981" ; sc:description "(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. 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The final three dimensional structure is built using the modeling package MODELLER." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "(PS)2 - v3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://ps2v3.life.nctu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3336, edam:topic_3375, edam:topic_3379 ; sc:citation , , "pmcid:PMC7275349", "pubmed:32503412" ; sc:description """a multimodal workflow for identification and prioritization of drugs based on pathway signatures. PS4DR (Pathway Signatures for Drug Repositioning). This package comprises a modular workflow designed to identify drug repositioning candidates using multi-omics data sets. A schematic figure of the workflow is presented below. The R scripts necessary to run the MSDRP pipeline are located in the R directory.""" ; sc:featureList edam:operation_2436, edam:operation_3928, edam:operation_3938 ; sc:license "Apache-2.0" ; sc:name "PS4DR" ; sc:url "https://github.com/ps4dr/ps4dr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3360 ; sc:citation , "pubmed:31821408" ; sc:description """a software package for flexible identification of phenotype-specific subpathways in cancer progression. Flexible Identification of Phenotype-Specific Subpathways. A network-based systems biology tool for flexible identification of phenotype-specific subpathways in the cancer gene expression data with multiple categories (such as multiple subtype or developmental stages of cancer)""" ; sc:featureList edam:operation_0571, edam:operation_2943, edam:operation_3083 ; sc:license "GPL-2.0" ; sc:name "psSubpathway" ; sc:url "https://cran.r-project.org/web/packages/psSubpathway/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation "pubmed:15130850" ; sc:description "ps_scan (ScanProsite tool) is a perl program used to scan one or several patterns, rules and/or profiles from PROSITE against one or several protein sequnces in Swiss-Prot or FASTA format. It requires two compiled external programs from the PFTOOLS package : “pfscan” used to scan a sequence against a profile library and “psa2msa” which is necessary for the “-o msa” output format only." ; sc:featureList edam:operation_2479 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ps_scan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prosite.expasy.org/scanprosite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3321 ; sc:citation "pubmed:18352819" ; sc:description "Novel SNP selection procedure for whole genome association studies with two-stage designs." ; sc:featureList edam:operation_3197, edam:operation_3695 ; sc:name "PS_SNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://engr.case.edu/li_jing/PS_SNP.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_2269, edam:topic_3315, edam:topic_3542 ; sc:citation "pubmed:8111135", "pubmed:8453370" ; sc:description "Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present." ; sc:featureList edam:operation_0267, edam:operation_0468, edam:operation_0470, edam:operation_2416, edam:operation_2488 ; sc:name "PSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bmerc-www.bu.edu/psa/request.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640 ; sc:description "MATLAB script for detecting PSA failure after radiation treatment for prostate cancer" ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "PSA failure detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/35733-detecting-psa-failure-after-radiation-treatment-for-prostate-cancer" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:22674656" ; sc:description "Pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation." ; sc:featureList edam:operation_3218 ; sc:name "Psafe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Genomic_Protein_Sequence_Analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172 ; sc:citation ; sc:description "Open source software that is designed for the curation and analysis of metabolic models. It supports model version tracking, model annotation, data integration, data parsing and formatting, consistency checking, automatic gap filling, and model simulations." ; sc:featureList edam:operation_3660 ; sc:name "PSAMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://zhanglab.github.io/psamm/" ; biotools:primaryContact "Ying Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3512, edam:topic_3572 ; sc:citation "pubmed:24222208" ; sc:description "Software to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study." ; sc:featureList edam:operation_0447, edam:operation_0492 ; sc:name "PSAR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioen-compbio.bioen.illinois.edu/psar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins. This is a comprehensive on-line Internet tool that allows the rapid visualization of an analysis, by output in GIF format. It assists the user in analyzing and presenting the primary structure of proteins and mutiple alignment of protein sequences" ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_2945 ; sc:name "PSAweb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/psa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "PSAweb is a web server, developed to analyze the amino acid sequence and multiple sequence alignment of proteins." ; sc:featureList edam:operation_2945 ; sc:name "PSAweb: Analysis of Protein Sequence and Multiple Alignment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/psa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_2640 ; sc:citation ; sc:description "Network-Based Matching of Patients and Targeted Therapies for Precision Oncology* | The extensive acquisition of high-throughput molecular profiling data across model systems (human tumors and cancer cell lines) and drug sensitivity data, makes precision oncology possible allowing clinicians to match the right drug to the right patient. Current supervised models for drug sensitivity prediction, often use cell lines as exemplars of patient tumors and for model training. However, these models are limited in their ability to accurately predict drug sensitivity of individual cancer patients to a large set of drugs, given the paucity of patient drug sensitivity data used for testing and high variability across different drugs. To address these challenges, we developed a multilayer network-based approach to impute individual patients’ responses to a large set of drugs" ; sc:featureList edam:operation_3557 ; sc:name "psb-app" ; sc:url "https://qingzliu.shinyapps.io/psb-app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC7137786", "pubmed:32296690" ; sc:description """A Machine Learning-Based Computational Identifier for Predicting Polystyrene Binding Peptides. PSBP-SVM: A Machine Learning-BasedComputational Identifier for. Predicting Polystyrene Binding Peptides.""" ; sc:featureList edam:operation_0252, edam:operation_3936, edam:operation_3937 ; sc:name "PSBP-SVM" ; sc:url "http://server.malab.cn/PSBP-SVM/index.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0623, edam:topic_1775, edam:topic_3534 ; sc:citation "pubmed:22669905" ; sc:description "Database of proteins classified by their functional surfaces." ; sc:featureList edam:operation_0384, edam:operation_0387, edam:operation_1816, edam:operation_3666 ; sc:name "PSC" ; sc:url "http://pocket.uchicago.edu/psc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_2275, edam:topic_3172, edam:topic_3375 ; sc:citation , "pmcid:PMC7924326", "pubmed:33672700" ; sc:description "A structured and searchable 3D-Database for Plant Secondary Compounds." ; sc:featureList edam:operation_0245, edam:operation_3431, edam:operation_3899, edam:operation_3938 ; sc:name "PSC-db" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pscdb.appsbio.utalca.cl" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0869 ; sc:name "Sequence-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Scan protein sequence(s) with fingerprints from the PRINTS database." ; sc:featureList edam:operation_0338, edam:operation_2421, edam:operation_3092 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/pscan.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3169, edam:topic_3179 ; sc:citation ; sc:description "PscanChIP is a web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria." ; sc:featureList edam:operation_3501 ; sc:name "Pscan-ChIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.beaconlab.it/pscan_chip_dev/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0153, edam:topic_0634, edam:topic_0736, edam:topic_3512 ; sc:citation , "pmcid:PMC7448521", "pubmed:32847609" ; sc:description """Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. code to reproduce simulation studies presented in the PSCAN paper. PSCAN Protein-structure-guided scan methods for gene-level association test and signal region detection. Tang ZZ, Sliwoski GR, Chen G, Jin B, Bush WS, Li B, and Capra JA (2020). PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection. Genome Biology. PSCAN package has the main PSCAN function that implements protein-structure-guided scan (PSCAN) methods for detecting gene-level associations and signal variants.""" ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3227, edam:operation_3432 ; sc:license "MIT" ; sc:name "PSCAN" ; sc:url "https://github.com/tangzheng1/PSCAN2020" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2755 ; sc:encodingFormat edam:format_2330 ; sc:name "Transcription factor name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , ; sc:description "Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria." ; sc:featureList edam:operation_0238 ; sc:license "GPL-3.0" ; sc:name "PscanChIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.beaconlab.it/pscan_chip_dev" ; biotools:primaryContact "Federico Zambelli", "Giulio Pavesi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0140, edam:topic_2229, edam:topic_3383 ; sc:citation , "pubmed:36413068" ; sc:description "Bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method." ; sc:featureList edam:operation_0418, edam:operation_2489, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PScL-2LSAESM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/csbio-njust-edu/PScL-2LSAESM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0625, edam:topic_3520 ; sc:citation , "pmcid:PMC10172113", "pubmed:37012480" ; sc:description "pSCoPE ensures duty-cycle time for analyzing prioritized peptides across all single cells (thus increasing data consistency) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth." ; sc:featureList edam:operation_3630, edam:operation_3643, edam:operation_3767, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pSCoPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://scp.slavovlab.net/pSCoPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation , "pmcid:PMC8195342", "pubmed:34122478" ; sc:description "A Comprehensive Multi-Omics Association Database of Secondary Growth in Response to Stress in Populus trichocarpa." ; sc:featureList edam:operation_2421, edam:operation_3223, edam:operation_3431, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PSDX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://forestry.fafu.edu.cn/db/SDX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0099, edam:topic_0622, edam:topic_0654 ; sc:citation , "pmcid:PMC5355101", "pubmed:28076851" ; sc:description "A python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods." ; sc:featureList edam:operation_2403 ; sc:name "Pse-Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.hitsz.edu.cn/Pse-Analysis/" ; biotools:primaryContact "Bin Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0099, edam:topic_0654 ; sc:citation , "pmcid:PMC4489303", "pubmed:25958395" ; sc:description "Web server for generating various modes of pseudo components of DNA, RNA, and protein sequences." ; sc:featureList edam:operation_2403 ; sc:name "Pse-in-One" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.hitsz.edu.cn/Pse-in-One/" ; biotools:primaryContact "Bin Liu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3572, edam:topic_3577 ; sc:citation ; sc:description "Deconvolution of gene expression data by Population-Specific Expression Analysis." ; sc:featureList edam:operation_2495, edam:operation_3658, edam:operation_3659 ; sc:license "Artistic-2.0" ; sc:name "PSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PSEA.html" ; biotools:primaryContact "Alexandre Kuhn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_3168 ; sc:citation ; sc:description "A phenotypic similarity ensemble approach for prioritizes candidate genes to aid mendelian disease diagnosis." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phoenix.bgi.com/psea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_3473, edam:topic_3510 ; sc:citation "pubmed:17976365" ; sc:description "Algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms. The design of this tool incorporated the sequence order information to improve the conventional amino acid compositions. The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PseAAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/PseAAC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC2358896", "pubmed:18416838" ; sc:description "This is a web-server for predicting proteins secreted by Malarial Parasite P.falciparum into infected-erythrocyte." ; sc:featureList edam:operation_2945 ; sc:name "pseapred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pseapred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Prediction of Plasmodium Secretory and Infected Erythrocyte Associated Proteins." ; sc:featureList edam:operation_2945 ; sc:name "pseapred2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/pseapred2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0654 ; sc:citation "pubmed:24732113" ; sc:description "Represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides." ; sc:featureList edam:operation_2478 ; sc:name "PseKNC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/pseknc/default.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC9892456", "pubmed:36741328" ; sc:description "A new stacked ensemble-learning method for identifying RNA pseudouridine sites." ; sc:featureList edam:operation_0415, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PseU-ST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jluzhangxinrubio/PseU-ST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC8637112", "pubmed:34868261" ; sc:description "RNA Pseudouridine Site Identification with Deep Learning Algorithm." ; sc:featureList edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PseUdeep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dan111262/PseUdeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3954 ; sc:description "Simulate pseudo B-mode ultrasonic images with customized tissue echogenicity maps" ; sc:featureList edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Pseudo B-Mode Ultrasound Image Simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/34199-pseudo-b-mode-ultrasound-image-simulator" ; biotools:primaryContact "Debdoot Sheet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31474000" ; sc:description "A Regression-Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets | Regression-Based Simulation Applications for Correction and Normalization of Complex Metabolomics and Proteomics Datasets | Wang, Shisheng, and Hao Yang. \"pseudoQC: A Regression‐Based Simulation Software for Correction and Normalization of Complex Metabolomics and Proteomics Datasets.\" Proteomics (2019): 1900264. (DOI: 10.1002/pmic.201900264)" ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3799 ; sc:license "MIT" ; sc:name "pseudoQC" ; sc:url "https://www.omicsolution.org/wukong/pseudoQC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0621, edam:topic_2885, edam:topic_3673 ; sc:citation , "pubmed:33319644" ; sc:description """A genomic visualization and exploration resource for the Drosophila pseudoobscura subgroup. Searchable genome sequences of Drosophila pseudoobscura subgroup species.""" ; sc:featureList edam:operation_2421, edam:operation_3208, edam:operation_3227 ; sc:name "PseudoBase" ; sc:url "http://pseudobase.biology.duke.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2314 ; sc:name "GI number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2744 ; sc:name "Locus ID (PseudoCAP)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC3013766", "pubmed:20929876" ; sc:contributor ; sc:description "Pseudomonas genome database." ; sc:featureList edam:operation_0224 ; sc:name "PseudoCAP pseudomonas genome database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.pseudomonas.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0203, edam:topic_0621, edam:topic_3512 ; sc:citation , "pmcid:PMC7319564", "pubmed:32449938" ; sc:description "an integrated online platform for gene inactivation inference." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3663 ; sc:name "PseudoChecker" ; sc:softwareHelp ; sc:url "http://pseudochecker.ciimar.up.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "PseudoDomain is used to identify processed pseudogenes of mammalian genomes. Unlike most existing tools, it is based on profile HMM-based homology search. It searches genomic sequences against protein domain database.Therefore, when protein annotations of the genome is not available, it still can accurately identify processed pseudogenes." ; sc:featureList edam:operation_2421 ; sc:name "PseudoDomain" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20130916" ; sc:url "http://sourceforge.net/projects/pseudodomain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0780, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC9144304", "pubmed:35629939" ; sc:description "Normalizing and Correcting Variable and Complex LC-MS Metabolomic Data with the R Package pseudoDrift." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "pseudoDrift" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jrod55/pseudoDrift" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0610, edam:topic_0621, edam:topic_0622 ; sc:citation ; sc:description "Pseudofinder is a bioinformatics tool that detects pseudogene candidates from annotated genbank files of bacterial and archaeal genomes." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pseudofinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/filip-husnik/pseudofinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:34244782" ; sc:description """Cell pseudotime reconstruction based on genetic algorithm The package pseudoga can be used to perform pseudotime analysis on single cell gene expression data. Given a homogeneous population of cells, the cells can be ordered to form a trajectory. Given a heterogeneous population and cell cluster ids, the packages can be used to find a tree structure based on pseudotime ordering of cells.""" ; sc:featureList edam:operation_0314, edam:operation_2939, edam:operation_3680, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PseudoGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/indranillab/pseudoga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_2815, edam:topic_3053 ; sc:citation , "pmcid:PMC3567485", "pubmed:23396300" ; sc:description "Innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes." ; sc:featureList edam:operation_0272 ; sc:name "pseudoMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pseudomap.mbc.nctu.edu.tw/php/index.php" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0622, edam:topic_0634 ; sc:citation "pubmed:10984027", "pubmed:10984043", "pubmed:15608211", "pubmed:18978025", "pubmed:20929876" ; sc:description "It integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. The genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs, including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3209, edam:operation_3431, edam:operation_3482 ; sc:name "Pseudomonas Genome Database" ; sc:operatingSystem "Linux" ; sc:url "http://www.pseudomonas.com" ; biotools:primaryContact "Pseudomonas aeruginosa Community Annotation Project (PseudoCAP)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0622, edam:topic_0634 ; sc:citation "pubmed:10984043", "pubmed:15608211", "pubmed:20929876" ; sc:description "This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3431, edam:operation_3482 ; sc:name "Pseudomonas Genome Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pseudomonas.com/" ; biotools:primaryContact "Pseudomonas Genome DB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC8082818", "pubmed:33926517" ; sc:description "A robust DE test method that accounts for the uncertainty in pseudotime inference" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3891 ; sc:license "MIT" ; sc:name "PseudotimeDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SONGDONGYUAN1994/PseudotimeDE" ; biotools:primaryContact "Jingyi Jessica Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0114 ; sc:citation "pubmed:12169562", "pubmed:12824341", "pubmed:16845039", "pubmed:19369500" ; sc:description "PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_0570, edam:operation_2439, edam:operation_2441 ; sc:name "PSEUDOVIEWER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pseudoviewer.inha.ac.kr/" ; biotools:primaryContact "PseudoViewer3 Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "PSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.crg.cat/apps/tcoffee/do:tmcoffee" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2854 ; sc:name "Position-specific scoring matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "Iterative protein sequence similarity search based on BLAST: search with a custom, position-specific, scoring matrix which can help find distant evolutionary relationships." ; sc:featureList edam:operation_0346 ; sc:name "PSI-BLAST (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "NCBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/psiblast" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Position Specific Iterative BLAST (PSI-BLAST) refers to a feature of NCBI BLAST 2.0 in which a position-specific scoring matrix (PSSM) profile is constructed from set of BLAST alignments." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "PSI-BLAST API (EBI)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/psiblast_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158, edam:format_3243 ; sc:name "Protein interaction data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "IntAct team" ; sc:citation ; sc:description "Validate files in PSI-MI XML 2.5 and PSI-PAR format, and generate a table with error messages." ; sc:featureList edam:operation_0336 ; sc:name "PSI-MI Validator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/intact/validator/start.xhtml" ; biotools:primaryContact "Marine Dumousseau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3125, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7285933", "pubmed:32565674" ; sc:description """Predicting Mouse Pseudouridine Sites From Sequence and Genome-Derived Features. Pseudouridine (Ψ) is the first discovered and the most abundant RNA modification that has been widely study in the past decades. Experimental-validated mouse Ψ Sites. High-accuracy predictor for mouse Ψ site identification.""" ; sc:featureList edam:operation_0224, edam:operation_0253, edam:operation_0417, edam:operation_0433 ; sc:name "PSI-MOUSE" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/psimouse" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2854 ; sc:name "Position-specific scoring matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Bill Pearson" ; sc:citation , ; sc:description "Iterative protein sequence similarity search based on Smith & Waterman algorithm with PSI-BLAST profile construction : find distantly related protein sequences." ; sc:featureList edam:operation_0346 ; sc:name "PSI-Search (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "University of Virginia" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/psisearch" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Bill Pearson" ; sc:citation , ; sc:description "PSI-Search 2 combines the sensitivity of the Smith-Waterman search algorithm (SSEARCH) with the PSI-BLAST profile construction strategy to find distantly related protein sequences." ; sc:featureList edam:operation_0346 ; sc:name "PSI-Search 2 (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sss/psisearch2" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "This tool uses SSEARCH to perform a rigorous Smith & Waterman search of a protein database." ; sc:featureList edam:operation_2451 ; sc:name "PSI-Search API (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/sss/psisearch_rest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description """Open-Source Software for High-Throughput Quantum Chemistry. OpenFermion is an open source library (licensed under Apache 2) for compiling and analyzing quantum algorithms which simulate fermionic systems. This plugin library allows the electronic structure package Psi4 (licensed under GNU Lesser General Public License version 3) to interface with OpenFermion. Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties. We routinely perform computations with >2500 basis functions on multi-core machines.""" ; sc:featureList edam:operation_3893 ; sc:license "LGPL-3.0" ; sc:name "Psi4" ; sc:url "https://github.com/psi4/psi4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3320, edam:topic_3379 ; sc:author "Nuno Daniel Saraiva Agostinho" ; sc:citation ; sc:contributor "Nuno Luís Barbosa Morais" ; sc:description "Interactive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. 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Prototype work for a unified API for writing PSIMS standardized XML documents, currently just mzML and MzIdentML.""" ; sc:featureList edam:operation_0336, edam:operation_2409, edam:operation_2949 ; sc:license "Apache-2.0" ; sc:name "psims" ; sc:url "https://github.com/mobiusklein/psims" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_0621, edam:topic_3304, edam:topic_3957 ; sc:citation ; sc:description "The Postsynaptic Interaction Database is a comprehensive resource of the human postsynaptic (PS) binary protein-protein interactions. 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Search the database using a protein id." ; sc:featureList edam:operation_2422 ; sc:name "PSIQUIC (DIP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://dip.doe-mbi.ucla.edu/dip/Main.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3047, edam:topic_3332 ; sc:citation , "pubmed:32394459" ; sc:description """A Psi4 plugin for efficient simulations of X-ray absorption spectra based on the transition-potential and Δ-Kohn-Sham method. For details, please refer to our paper in the Journal of Computational Chemistry and the documentation (still in progress). Parts of the program were inspired by the psi4numpy package. To install and use PSIXAS, you will need Psi4 already installed on your computer. You can then checkout the repository:.""" ; sc:featureList edam:operation_3432, edam:operation_3860 ; sc:license "GPL-3.0" ; sc:name "PSIXAS" ; sc:url "https://github.com/Masterluke87/psixas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140, edam:topic_2229, edam:topic_3474 ; sc:citation ; sc:description "PSL-Recommender is a python package for prediction of proteins subcellular locations. PSL-Recommender uses logistic matrix factorization to build a recommender system for protein subcellular localization problem. This package is based on previous implementation of logistic matrix factorization by Logistic matrix factorization for implicit feedback data and Neighborhood regularized logistic matrix factorization for drug-target interaction prediction." ; sc:featureList edam:operation_0303, edam:operation_0418, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PSL-Recommender" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RJamali/PSL-Recommender" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3489 ; sc:description "PSLID provides open-access, structured, well-annotated databases of fluorescence microscope images depicting subcellular location proteins." ; sc:featureList edam:operation_3443 ; sc:name "PSLID" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "5.0" ; sc:url "http://murphylab.web.cmu.edu/services/PSLID/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0140, edam:topic_2229 ; sc:citation "pubmed:15699023" ; sc:description "Method for subcellular localization proteins belongs to prokaryotic genomes." ; sc:featureList edam:operation_2479, edam:operation_2489 ; sc:name "PSLpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/pslpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:36508242" ; sc:description "A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results." ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "psm_utils" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/compomics/psm_utils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation "pubmed:26275897" ; sc:description "Open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed." ; sc:featureList edam:operation_0295 ; sc:name "PSMAlign" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://homepage.cs.latrobe.edu.au/ypchen/psmalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194 ; sc:citation ; sc:description "Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer population history from whole genome sequence data." ; sc:featureList edam:operation_0324 ; sc:license "MIT" ; sc:name "PSMC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/lh3/psmc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:16792813" ; sc:description "R package to infer population structure using genomic markers." ; sc:featureList edam:operation_2478 ; sc:name "PSMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhaocenter.org/software/#Population_Genetics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3318, edam:topic_3382 ; sc:citation ; sc:description "Analyzing engineered point spread functions using phasor-based single-molecule localization microscopy." ; sc:featureList edam:operation_3435, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "pSMLM" ; sc:url "https://github.com/HohlbeinLab/SMALL-LABS-pSMLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2815 ; sc:citation , "pubmed:36086543" ; sc:description "A Package for Retrospective Cohort Matching in Python." ; sc:featureList edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PsmPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/psmpy/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_3512 ; sc:citation , "pubmed:35817303" ; sc:description "Predicting snoRNA-disease association using matrix completion technique" ; sc:featureList edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PSnoD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/linDing-groups/PSnoD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0769, edam:topic_2275, edam:topic_2885 ; sc:citation , "pmcid:PMC8886843", "pubmed:35227289" ; sc:description "A database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow." ; sc:featureList edam:operation_0331, edam:operation_3431, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "PSnpBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://psnpbind.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC6925685", "pubmed:31886228" ; sc:description """A Consensus Method for Optimizing Multiple Classifier Results for Predicting the Subcellular Localization of Bacterial Proteins. Several computational approaches for predicting subcellular localization have been developed and proposed. These approaches provide diverse performance because of their different combinations of protein features, training datasets, training strategies, and computational machine learning algorithms. In some cases, these tools may yield inconsistent and conflicting prediction results. It is important to consider such conflicting or contradictory predictions from multiple prediction programs during protein annotation, especially in the case of a multiclass classification problem such as subcellular localization""" ; sc:featureList edam:operation_0270, edam:operation_0418, edam:operation_2489 ; sc:name "PSO-LocBact" ; sc:url "http://ncrna-pred.com/psolocbact.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3293 ; sc:description "The PSODA project provides an open-source phylogenetic search tool that reads the same data file format as PAUP*" ; sc:featureList edam:operation_2421 ; sc:name "PSODA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.96" ; sc:url "http://dna.cs.byu.edu/psoda/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3300, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:34889887" ; sc:description "A Feature Fusion Predictor for RNA Pseudouridine Sites with Particle Swarm Optimizer Based Feature Selection and Ensemble Learning Approach." ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "PsoEL-PseU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.xwanglab.com/PsoEL-PseU/Server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602 ; sc:citation ; sc:description "PSOPIA (Prediction Server Of Protein-protein InterActions) is an AODE for predicting protein-protein interactions using three seqeucne based features; (I) sequence similarities to a known interacting protein pair, (II) statistical propensities of domain pairs observed in interacting proteins and (III) a sum of edge weights along the shortest path between homologous proteins in a PPI network." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PSOPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130501" ; sc:url "http://mizuguchilab.org/PSOPIA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0780 ; sc:citation ; sc:description "It is a high-precision localization prediction method for bacterial proteins. It has remained the most precise bacterial protein subcellular localization (SCL) predictor.  PSORTb version improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PSORTb" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "3.0.3" ; sc:url "http://www.psort.org/psortb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0820 ; sc:citation "pubmed:15608169", "pubmed:21071402" ; sc:description "PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset)." ; sc:featureList edam:operation_1777, edam:operation_2423, edam:operation_2489, edam:operation_3092 ; sc:name "PSORTdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://db.psort.org" ; biotools:primaryContact "PSORTdb Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0820, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC7214030", "pubmed:32108861" ; sc:description """PSORTm is a modified version of PSORTb 3.0.2 for protein subcellular localization prediction (SCL), and PSORTdb-based cell envelope classification, that can predict protein SCL from metagenomic sequences. PSORT.org provides links to the PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction.""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0310, edam:operation_0418, edam:operation_2489 ; sc:license "GPL-3.0" ; sc:name "PSORTm" ; sc:url "https://www.psort.org/psortm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC9505940", "pubmed:36142614" ; sc:description "Predicting Protein Stability Changes upon Point Mutations with a Gaussian Network Model." ; sc:featureList edam:operation_0331, edam:operation_2950, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PSP-GNM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sambitmishra0628/PSP-GNM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3244 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:33661636" ; sc:description "A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R." ; sc:featureList edam:operation_0337, edam:operation_3646, edam:operation_3755 ; sc:name "PSpecteR" ; sc:url "https://github.com/EMSL-Computing/PSpecteR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """GNU PSPP is a program for statistical analysis of sampled data. It is a free as in freedom replacement for the proprietary program SPSS, and appears very similar to it with a few exceptions. The most important of these exceptions are, that there are no “time bombs”; your copy of PSPP will not “expire” or deliberately stop working in the future. Neither are there any artificial limits on the number of cases or variables which you can use. There are no additional packages to purchase in order to get “advanced” functions; all functionality that PSPP currently supports is in the core package.""" ; sc:featureList edam:operation_2238, edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "PSPP" ; sc:softwareHelp ; sc:softwareVersion "1.6.2" ; sc:url "https://www.gnu.org/software/pspp/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:name "Quality control report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_0780, edam:topic_3500, edam:topic_3517 ; sc:citation , "pmcid:PMC10074814", "pubmed:37020193" ; sc:description "Integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data." ; sc:featureList edam:operation_2939, edam:operation_3197, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PSReliP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/solelena/PSReliP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:20691398" ; sc:description "Identify putative sRNA regions through the information retrieved from the sRNA of interest." ; sc:featureList edam:operation_0415 ; sc:name "PsRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioserver1.physics.iisc.ernet.in/psrna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_0780 ; sc:citation "pubmed:21622958" ; sc:description "psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analysis of next generation data, and outputs a comprehensive list of small RNA-target pairs." ; sc:featureList edam:operation_2430, edam:operation_2945 ; sc:name "psRNATarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://plantgrn.noble.org/psRNATarget/." ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation "pubmed:22693224" ; sc:description "psRobot is a web-based tool for plant small RNA meta-analysis. psRobot computes stem-loop small RNA prediction, which aligns user uploaded sequences to the selected genome, extracts their predicted precursors, and predicts whether the precursors can fold into stem-loop shaped secondary structure. psRobot also computes small RNA target prediction, which predict the possible targets of user provided small RNA sequences from the selected transcript library." ; sc:featureList edam:operation_0278, edam:operation_0438, edam:operation_0463, edam:operation_2489 ; sc:name "psRobot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://omicslab.genetics.ac.cn/psRobot/" ; biotools:primaryContact "psRobot Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2275, edam:topic_3047, edam:topic_3512 ; sc:citation , "pmcid:PMC8979021", "pubmed:35386297" ; sc:description "A Web Server for Predicting the Regulation of miRNAs Expression by Small Molecules." ; sc:featureList edam:operation_0463, edam:operation_0478, edam:operation_3792, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "PSRR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rnadrug.shinyapps.io/PSRR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0602, edam:topic_0625 ; sc:citation "pubmed:22982105" ; sc:description "Method for detecting gene pathways associated with a multivariate quantitative trait or phenotype." ; sc:featureList edam:operation_3439 ; sc:name "PsRRR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.imperial.ac.uk/~gmontana/psrrr.htm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:36481763" ; sc:description "A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:name "PSRTTCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/PSRTTCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0130, edam:topic_2814 ; sc:citation "pubmed:23957210" ; sc:description "Protein structural statistics program for Unix-like environments." ; sc:featureList edam:operation_0492, edam:operation_2479, edam:operation_2480 ; sc:name "PSS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://thomasgaillard.fr/pss/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0736, edam:topic_0820 ; sc:citation ; sc:description "An enabling QTY server for designing water-soluble α-helical transmembrane proteins | Although the QTY/NTY code-based design is relative straightforward, the design job is still time-consuming if only a manual manner is available, especially for library design, which will be impractical without computing power. Here a web-based PSS sever was developed for facilitating the protein design based on the QTY/NTY code. This server is expected to be used widely by scientists who are endeavoring in the research about alpha-helical proteins | QTY/NTY Design for Protein Solubilizing | Membrane proteins play vital roles in all living systems" ; sc:featureList edam:operation_0269, edam:operation_2241, edam:operation_2485 ; sc:name "PSS" ; sc:url "http://pss.sjtu.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2814 ; sc:citation , , ; sc:description "Allows searching a database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query." ; sc:featureList edam:operation_2406, edam:operation_2479 ; sc:name "PSS-SQL" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://zti.polsl.pl/dmrozek/science/pss-sql.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0610, edam:topic_0621, edam:topic_3293 ; sc:citation , "pmcid:PMC8888259", "pubmed:35261742" ; sc:description "A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cjpardodelahoz/pss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0781, edam:topic_3293, edam:topic_3324 ; sc:citation ; sc:description "Pathogen Sequence Signature Analysis. Computational analysis of nucleotides sequences of different microorganisms. It uses phylogenetic analysis to identify the Serotype/Clade and Genotype of selected microorganisms. Analyses may be performed on very large data sets. 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Yesylevskyy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:23154528" ; sc:description "Software for case-control genetic association studies in human gene mapping. The software is based on single-SNP p-values resulting from an association test, for example, the chi-square test comparing genotype or allele frequencies in cases and controls." ; sc:featureList edam:operation_2478 ; sc:name "PTest" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.jurgott.org/linkage/PTest.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:19906706" ; sc:description """Protein Topology Graph Library is a database on protein secondary structure topologies, including search facilities, the visualization as intuitive topology diagrams as well as in the 3D structure, and additional information. Secondary structure-based protein topologies are represented uniquely as undirected labeled graphs in four different ways allowing for exploration under different aspects.""" ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0570, edam:operation_2486, edam:operation_2488 ; sc:name "PTGL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ptgl.uni-frankfurt.de/" ; biotools:primaryContact "Ina Koch", "Tim Schaefer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation , "pmcid:PMC4086064", "pubmed:24875471" ; sc:description "Web server for unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2495, edam:operation_3439, edam:operation_3463 ; sc:name "PTHGRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.byanbioinfo.org/pthgrn" ; biotools:primaryContact "Bin Yan", "Daogang Guan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0601, edam:topic_0769 ; sc:citation , "pubmed:33964156" ; sc:description "ptm is an R package for the study of methionine sulfoxidation and other post-translational modifications. ptm is an R package containing utilities for the analysis of post-translational modifications (PTMs) in proteins, with particular emphasis on the sulfoxidation of methionine residues." ; sc:featureList edam:operation_0417, edam:operation_3645, edam:operation_3647 ; sc:license "GPL-2.0" ; sc:name "ptm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://metositeptm.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0621, edam:topic_3474 ; sc:citation "pubmed:21258065" ; sc:description "Software that can be applied to the output of blind PTM (Post-translational Modification) search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We showed that our technique outperforms two standard clustering algorithms on a simulated dataset." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PTMClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genes.toronto.edu/PTMClust/" ; biotools:primaryContact "Prof. Brendan Frey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. It currently contains 316,546 modified sites from 69 different PTM types which are also propagated through ortholgs between 19 different eukaryotic species. A total of 1.6 million sites and 17 million functional associations more than 100,000 proteins can currently be explored." ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-3.0" ; sc:name "PTMCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ptmcode.embl.de/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0176, edam:topic_0593, edam:topic_0601, edam:topic_2229 ; sc:citation , "pubmed:34643234" ; sc:description "Predict the impact of post-translation modification on protein dynamics based on molecular dynamic simulation" ; sc:featureList edam:operation_0244, edam:operation_0417, edam:operation_2476, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "PTMdyna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ccbportal.com/PTMdyna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0601, edam:topic_0634, edam:topic_3334, edam:topic_3336 ; sc:citation , "pmcid:PMC9848059", "pubmed:36548389" ; sc:description "PTMint Database of Experimentally Verified PTM Regulation on Protein-Protein Interaction." ; sc:featureList edam:operation_0417, edam:operation_0477, edam:operation_0478, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PTMint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ptmint.sjtu.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0601 ; sc:citation "pubmed:24291233" ; sc:description "Tool for predicting post-transcriptional modification sites based on protein sequence." ; sc:featureList edam:operation_0417, edam:operation_2479 ; sc:name "PTMPred" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://doc.aporc.org/wiki/PTMPred" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pmcid:PMC4506239", "pubmed:25631240" ; sc:description "Tool to model the confidence with which mass modifications are correctly localized for each peptide. PTMProphet considers all of the possible configurations for localization, and applies a statistical model to predict which modification sites are most probable based on the spectrum evidence." ; sc:featureList edam:operation_3755 ; sc:name "PTMProphet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5.0" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0601, edam:topic_0634, edam:topic_2640, edam:topic_3517 ; sc:citation , "pmcid:PMC7683509", "pubmed:33240890" ; sc:description """A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification. PTMsnp! Identifying mutations that. Protein post-translational modifications (PTMs) is one of the most important regulation mechanisms in mammalian cells, which orchestrates the proper function of almost all cellular proteins. Genetic mutations, can significantly alter the status of PTMs, leading to serious pathological changes in body systems. Therefore, annotation of genetic mutations based on the effects on PTM may be important for providing potential guidance in the development of new therapeutic strategies and drugs for patients. PTMsnp is specifically designed to characterize such genetic mutations, and can be further used to find key proteins that potentially drive disease progression.""" ; sc:featureList edam:operation_0417, edam:operation_3196, edam:operation_3227, edam:operation_3645 ; sc:name "PTMsnp" ; sc:url "http://ptmsnp.renlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3520 ; sc:citation , "pubmed:24215026" ; sc:description "A program developed for identification of Post-Translational Modification in MS/MS data and it is embedded to the X!Tandem project." ; sc:featureList edam:operation_0417 ; sc:name "PTMTreeSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pongor.itk.ppke.hu/ptmtreesearch/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3295, edam:topic_3520 ; sc:citation , "pmcid:PMC8157737", "pubmed:34039258" ; sc:description "PTMViz is a tool for analyzing and visualizing histone post translational modification data. PTMViz is a histone post tranliastional modification analysis tool built within the shiny graphical user interface of the R programming language. Within PTMViz the user can create figures and scrutinize thier data using one of two functions: Protein) The protein function lets the user view thier data in an interactive volcano plot and heatmap as well as a provided data table of its differential analysis results, and PTM) The PTM function will return an interactive data table, barachart figures, and a differential analysis of the provided histone ptm data." ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_3645, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "PTMViz" ; sc:url "https://github.com/ByrumLab/PTMViz" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3407 ; sc:citation , "pmcid:PMC8986922", "pubmed:35462956" ; sc:description "Plant transfer RNA-derived non-coding RNAs (tncRNAs) database." ; sc:featureList edam:operation_0464, edam:operation_2421, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "PtncRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nipgr.ac.in/PtncRNAdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:34279571" ; sc:description "PTNet is a graph-based learning model which simulates the miRNAs (microRNAs) that regulate gene expression post-transcriptionally in silico." ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PTNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/CompbioLabUCF/PTNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Parallelised versions of various tools." ; sc:name "ptools" ; sc:url "https://bioweb.pasteur.fr/packages/pack@ptools@0.99d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0203, edam:topic_0601 ; sc:citation "pubmed:24758252" ; sc:description "Tool for the study of the combinatorial nature of post-transcriptional trans-factors. It allows the identification of clusters of trans-factors (RBPs and miRNAs) from interaction maps and it performs the biological characterization of identified clusters giving information about the overlap among the target genes, the GO enrichments and similarity among GO terms." ; sc:featureList edam:operation_0417, edam:operation_2495 ; sc:name "PTRcombiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://disi.unitn.it/~passerini/software/PTRcombiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "PTRStalker is a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "PTRStalker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioalgo.iit.cnr.it/index.php?pg=ptrs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:description "Small collection of programs concerned with parallel sequencing of multiple samples on the 454 platform. untag supports Parallel Tagged Sequencing by sorting sequences according to their tags and by removing those tags when producing output files (in FASTA or SFF format) for downstream processing with standard 454 or other assembly software." ; sc:featureList edam:operation_0310 ; sc:name "PTS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "https://bioinf.eva.mpg.de/pts/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_3752 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0781, edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation , "pmcid:PMC8443750", "pubmed:34526611" ; sc:description "High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome." ; sc:featureList edam:operation_0310, edam:operation_3198, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PTV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.pasteur.fr/vlegrand/ptv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056 ; sc:citation , "pmcid:PMC7496249", "pubmed:32061017" ; sc:description """Easy-to-use software for the analysis of genetic data of diploids and polyploids. Genodive version 3.0 is a user-friendly program for the analysis of population genetic data.""" ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3557, edam:operation_3891 ; sc:name "genodive" ; sc:url "http://www.patrickmeirmans.com/software/Home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2815, edam:topic_3053 ; sc:citation "pmcid:PMC7153108", "pubmed:32308839" ; sc:description """A Web Tool for Developing Pedigree Diagrams Using the Standardized Human Pedigree Nomenclature Integrated with Biomedical Vocabularies. The integration of genetic information in current clinical routine has raised a need for tools to exploit family genetic knowledge. On the clinical side, an application for managing and visualizing pedigree diagrams could provide genetics specialists with an integrated environment with potential positive impact on their current practice.""" ; sc:name "genoDraw" ; sc:url "https://genodraw.com/authentication/login" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0622, edam:topic_0625, edam:topic_0780 ; sc:citation , "pmcid:PMC7146957", "pubmed:32272889" ; sc:description """A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL based on overlapping ratios, OC (Overlap coefficient) or JC (Jaccard coefficient). The resulting clusters can be further analyzed and separated into sub-clusters using a second script, GOMCL-sub. This tool helps researchers to reduce time spent on manual curation of large lists of GO terms and minimize biases introduced by shared GO terms in data interpretation.""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3432 ; sc:name "GOMCL" ; sc:url "http://www.lsugenomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0623, edam:topic_0821, edam:topic_2275 ; sc:citation , "pmcid:PMC7296393", "pubmed:32542364" ; sc:description """an integrated resource for glycosyltransferase sequences and annotations. Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB""" ; sc:featureList edam:operation_0361, edam:operation_0478, edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "GTDB" ; sc:url "https://www.biosino.org/gtdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_3071, edam:topic_3314 ; sc:citation , "pubmed:33063413" ; sc:description "A free web platform to comprehensively analyze constitutive property and herbicide-likeness to estimate chemical bioavailability." ; sc:featureList edam:operation_3795, edam:operation_3799, edam:operation_3802 ; sc:name "HerbiPAD" ; sc:url "http://agroda.gzu.edu.cn:9999/ccb/database/HerbiPAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3315 ; sc:citation , "pmcid:PMC7355272", "pubmed:32657375" ; sc:description """A mathematically optimal algorithm for sketching biological data. Hopper: Diverse sampling for biological datasets. Hopper implements the greedy k-centers algorithm, iteratively generating a farthest-first traversal of the input data. The resulting subset realizes a 2-approximation to the optimal Hausdorff distance between the subset and the full dataset. See the full pre-print here: https://www.biorxiv.org/content/10.1101/835033v1. Hopper: A Mathematically Optimal Sketching Algorithm for Biological Data. Hopper is a mathematically motivated sketching algorithm for single-cell data, which preserves transcriptional diversity using a farthest-first traversal on the data. The algorithm will be presented at ISMB 2020, will appear in an upcoming issue of Bioinformatics, and is available as a pre-print on bioRxiv.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3935 ; sc:name "Hopper" ; sc:url "http://hopper.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3315, edam:topic_3372 ; sc:citation , "pmcid:PMC7323896", "pubmed:32422648" ; sc:description """Program for comprehensive HARDY-WEINBERG equilibrium testing. HW_TEST, a software developed for Microsoft Windows that can be managed without any difficulties by users with a minimum of programming skills and statistical/mathematical background, is a program that tests the null hypothesis of Hardy-Weinberg proportions using genotype data from autosomal genetic markers with two to twelve alleles.""" ; sc:featureList edam:operation_2238, edam:operation_3196 ; sc:name "HW_TEST" ; sc:url "https://github.com/Lemes-RenanB/HardyWeinbergTesting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3399, edam:topic_3474 ; sc:citation , "pubmed:32324561" ; sc:description """An Application to the Prediction of Pro-/Anti- Longevity Genes. Understanding the ageing process is a very challenging problem for biologists. To help in this task, there has been a growing use of classification methods (from machine learning) to learn models that predict whether a gene influences the process of ageing or promotes longevity. One type of predictive feature often used for learning such classification models is Protein-Protein Interaction (PPI) features. One important property of PPI features is their uncertainty, i.e., a given feature (PPI annotation) is often associated with a confidence score, which is usually ignored by conventional classification methods. Hence, we propose the Lazy Feature Selection for Uncertain Features (LFSUF) method, which is tailored for coping with the uncertainty in PPI confidence scores""" ; sc:featureList edam:operation_2454, edam:operation_2492, edam:operation_3936 ; sc:name "LFSUF" ; sc:url "http://github.com/pablonsilva/FSforUncertainFeatureSpaces" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3517 ; sc:citation , "pmcid:PMC7750933", "pubmed:32696040" ; sc:description """An R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics. Subtracting Summary Statistics of One or more Cohorts from Meta-GWAS Results.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "MetaSubtract" ; sc:url "https://cran.r-project.org/web/packages/MetaSubtract" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2640, edam:topic_3068, edam:topic_3338, edam:topic_3518 ; sc:citation , "pmcid:PMC7687678", "pubmed:33238004" ; sc:description """A database of organ-specific metastasis induced by human cancer cell lines in mouse models. The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metastases. In order to shed light on this behaviour, several studies were performed by the injection of human cancer cell lines into immunocompromised mouse models.""" ; sc:featureList edam:operation_0224, edam:operation_3778 ; sc:name "MetaTropismDB" ; sc:url "http://www.introni.it/Metastasis/metastasis.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_2640, edam:topic_3295, edam:topic_3474 ; sc:citation , "pmcid:PMC7076991", "pubmed:32183722" ; sc:description """An automated and modular deep learning approach for DNA methylation analysis. MethylNet is a command line tool and python library that provides classes to handle deep learning tasks for methylation data. It is built off of pythonic MethylationArray data types introduced in (https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess), and uses PyTorch to explore/make predictions on the methylation data.""" ; sc:featureList edam:operation_0417, edam:operation_2436, edam:operation_3196, edam:operation_3204 ; sc:license "MIT" ; sc:name "MethylNet" ; sc:url "https://github.com/Christensen-Lab-Dartmouth/MethylNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7706182", "pubmed:33258967" ; sc:description """a manually curated database for pathogenic non-coding variants and benign controls. 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The idea is also called the Dynamic Elastic Net, as proposed in the paper "Learning (from) the errors of a systems biology model" (Engelhardt, Froelich, Kschischo 2016) . To use the experimental SBML import function, the 'rsbml' package is required. 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We describe 10 straightforward writing tips-and a web tool, PubReCheck-guiding authors to help address the most common cases that remain difficult for text-mining tools. We anticipate these guides will help authors' work be found more readily and used more widely, ultimately increasing the impact of their work and the overall benefit to both authors and readers.""" ; sc:featureList edam:operation_0306, edam:operation_0362, edam:operation_0558 ; sc:name "PubReCheck" ; sc:url "http://www.ncbi.nlm.nih.gov/research/pubrecheck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068 ; sc:citation ; sc:description "Framework which runs on a user defined schedule allowing you to download latest PubMed abstracts, run them through your favorite text mining tool and then uploads the results to public FTP" ; sc:featureList edam:operation_0306 ; sc:license "MIT" ; sc:name "PubRunner" ; sc:softwareHelp ; sc:url "http://www.pubrunner.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623, edam:topic_2275 ; sc:citation , "pmcid:PMC4086066", "pubmed:24957597" ; sc:description "PubServer collects homologous sequences from NR database and retrieves and filters associated publications." ; sc:featureList edam:operation_0224, edam:operation_0477, edam:operation_2422, edam:operation_3092, edam:operation_3695 ; sc:name "PubServer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pubserver.burnham.org/" ; biotools:primaryContact "Adam Godzik", "Lukasz Jaroszewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0218, edam:topic_0219, edam:topic_3473 ; sc:citation "pubmed:23703206" ; sc:description "Web server for text based mining to assist biocuration." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3280, edam:operation_3778 ; sc:name "PubTator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/" ; biotools:primaryContact "Zhiyong Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0602, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:20525783" ; sc:description "PUDGE is a protein structure prediction server. Modeling is divided into 5 stages: template selection, alignment, model building, model refinement and model evaluation." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0322, edam:operation_0474, edam:operation_0477 ; sc:name "PUDGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174, edam:topic_3673 ; sc:citation ; sc:description "An Efficient and Accurate Aligner Based on the Pufferfish Index." ; sc:featureList edam:operation_0292, edam:operation_0524, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:name "PuffAligner" ; sc:url "https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2258 ; sc:description "Interface to PubChem." ; sc:featureList edam:operation_2422 ; sc:name "PUG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pullseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcthomas/pullseq" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3300, edam:topic_3306, edam:topic_3512 ; sc:citation , "pubmed:36754843" ; sc:description "A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation." ; sc:featureList edam:operation_0479, edam:operation_3216, edam:operation_3454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PULPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pulps.zbiolab.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_3320, edam:topic_3474, edam:topic_3520 ; sc:citation "pubmed:26146086" ; sc:description "Semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation, which uses 48 features spanning various categories." ; sc:featureList edam:operation_1777, edam:operation_2479, edam:operation_2499 ; sc:name "PULSE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.kimlab.org/software/pulse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0781, edam:topic_3572 ; sc:citation ; sc:description "Tool to analyse protein sequence coverage of phage display libraries." ; sc:featureList edam:operation_2479 ; sc:name "PuLSE" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/stevenshave/PuLSE" ; biotools:primaryContact "Manfred Auer", "Steven Shave" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749, edam:topic_3379, edam:topic_3444, edam:topic_3520 ; sc:citation , "pubmed:33961312" ; sc:description "Pulseq-CEST is a tool to ensure multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard." ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "Pulseq-CEST" ; sc:url "https://pulseq-cest.github.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_3170 ; sc:citation ; sc:description "Flexible interface and readily accommodates numerous different experimental designs." ; sc:featureList edam:operation_3563 ; sc:license "GPL-3.0" ; sc:name "pulseR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dieterich-lab/pulseR" ; biotools:primaryContact "A. Uvarovskii", "C. Dieterich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7353919", "pubmed:32714656" ; sc:description """RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data. Description: This package, based on 4sU-seq data and RNA-seq data, analyzes the transcription, processing and degradation rates of genes. pulseTD can not only recognize the transcriptional dynamic rate of the measurement time points, but also obtain continuous changes in transcriptional dynamics. More importantly, it is able to predict the trend of mRNA transcription and expression changes in the future. In terms of performance, pulseTD has better robustness and accuracy than other methods. Maintainer: The package maintainer xindd_2014@163.com. Title: Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data.""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3715 ; sc:name "pulseTD" ; sc:url "https://github.com/bioWzz/pulseTD_0.2.0" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1638 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547, edam:format_3752 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3320 ; sc:citation , "pmcid:PMC3626802", "pubmed:23379655" ; sc:description "This package calculates gene expression from Affymetrix 3' arrays and provides methods to process exon arrays, producing gene and isoform expression for alternative splicing study. It also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions." ; sc:featureList edam:operation_2495, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "puma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/puma.html" ; biotools:primaryContact "Xuejun Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0781, edam:topic_3174 ; sc:citation ; sc:description "Papillomavirus genome annotation tool | PuMA is now available to access through iMicrobe" ; sc:featureList edam:operation_0362 ; sc:license "GPL-3.0" ; sc:name "PuMA" ; sc:url "https://www.imicrobe.us/#/apps/puma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC7281100", "pubmed:32375258" ; sc:description """Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics Using Probabilistic Modeling. To interpret measurements, we present an inference based approach, termed Probabilistic modeling for Untargeted Metabolomics Analysis (PUMA). Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample.""" ; sc:featureList edam:operation_2238, edam:operation_3501, edam:operation_3927, edam:operation_3928 ; sc:name "PUMA" ; sc:url "https://github.com/HassounLab/PUMA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_2330 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3452, edam:topic_3517 ; sc:citation , "pmcid:PMC8419981", "pubmed:34488838" ; sc:description "Fine-tuning polygenic risk score models using GWAS summary statistics" ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PUMAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/qlu-lab/PUMAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3047, edam:topic_3382 ; sc:citation , "pmcid:PMC7343294", "pubmed:32502904" ; sc:description """A tool for automated detection, tracking, and analysis of multiple types of fluorescently labeled biomolecules. Recent advances in imaging technology and fluorescent probes have made it possible to gain information about the dynamics of subcellular processes at unprecedented spatiotemporal scales. Unfortunately, a lack of automated tools to efficiently process the resulting imaging data encoding fine details of the biological processes remains a major bottleneck in utilizing the full potential of these powerful experimental techniques. Here we present a computational tool, called PunctaSpecks, that can characterize fluorescence signals arising from a wide range of biological molecules under normal and pathological conditions""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:name "PunctaSpecks" ; sc:url "http://faculty.cas.usf.edu/gullah/Software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC9580871", "pubmed:36304323" ; sc:description "An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells." ; sc:featureList edam:operation_0335, edam:operation_3443, edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Punctatools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/stjude/punctatools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:15215388", "pubmed:16845085" ; sc:description "Program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images." ; sc:featureList edam:operation_0308, edam:operation_0331, edam:operation_0484, edam:operation_0487, edam:operation_3196 ; sc:name "PupaSuite" ; sc:url "http://pupasuite.bioinfo.cipf.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:15980522" ; sc:description "Interactive web-based SNP analysis tool that allows for the selection of relevant SNPs within a gene, based on different characteristics of the SNP itself, such as validation status, type, frequency/population data and putative functional properties (pathological SNPs, SNPs disrupting potential transcription factor binding sites, intron/exon boundaries;.)." ; sc:featureList edam:operation_0331, edam:operation_0445, edam:operation_0484, edam:operation_3196 ; sc:name "PupasView" ; sc:url "http://pupasuite.bioinfo.cipf.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3360, edam:topic_3382 ; sc:citation , "pmcid:PMC8249868", "pubmed:34220432" ; sc:description "Flexible Open-Source Platform for High-Resolution Pupillometry in Vision Research. PupilEXT can record eye images using a stereo camera system or a single camera to measure the pupil diameter in real-time. Additionally, it is possible to analyse externally-recorded images without connected cameras through the PupilEXT interface." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PupilEXT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/openPupil/Open-PupilEXT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0769 ; sc:citation , "pubmed:34874538" ; sc:description "An open-source tool for processing pupillometry data." ; sc:featureList edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PuPl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/kinleyid/pupl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation "pubmed:23749958" ; sc:description "MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data." ; sc:featureList edam:operation_2423 ; sc:name "PurBayes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/package=PurBayes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070 ; sc:citation "pubmed:18546494" ; sc:description "This tool is a PubMed article recommendation system based on content-based filtering, based on preferred articles." ; sc:featureList edam:operation_3280, edam:operation_3432, edam:operation_3695 ; sc:name "PURE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bic.kyoto-u.ac.jp/pathway/PURE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC5157099", "pubmed:27999612" ; sc:description "This package estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). It is designed for targeted short read sequencing data, integrating well with standard somatic variant detection pipelines and supporting for tumor samples without matching normal samples." ; sc:featureList edam:operation_2995, edam:operation_3233 ; sc:license "Artistic-2.0" ; sc:name "PureCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.3" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PureCN.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3798 ; sc:license "MIT" ; sc:name "purge_dups" ; sc:url "https://github.com/dfguan/purge_dups" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199 ; sc:citation ; sc:description "Purge Haplotigs is a pipeline to help with curating heterozygous diploid genome assemblies." ; sc:featureList edam:operation_0487, edam:operation_0523, edam:operation_0524, edam:operation_0525 ; sc:license "MIT" ; sc:name "Purge Haplotigs" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://bitbucket.org/mroachawri/purge_haplotigs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3056, edam:topic_3299 ; sc:citation , "pubmed:34406359" ; sc:description "Estimation of inbreeding-purging genetic parameters in pedigreed populations." ; sc:featureList edam:operation_3196, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "purgeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/elcortegano/purgeR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2764 ; sc:name "Protein name (UniProt)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0218, edam:topic_3336 ; sc:citation , "pmcid:PMC10069378", "pubmed:37010519" ; sc:description "Database of purification conditions for proteins." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:name "PurificationDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://purificationdatabase.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:23427994" ; sc:description "Reliable method to detect automatically structural domains as protein units. This server provides number of domains and domain boundary for a chain with continues-domains." ; sc:featureList edam:operation_2406, edam:operation_2479 ; sc:name "Putracer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf.modares.ac.ir/software/PUTracer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:25573917" ; sc:description "Tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data." ; sc:featureList edam:operation_2499 ; sc:name "PVAAS" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://pvaas.sourceforge.net/" ; biotools:primaryContact "Liguo Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "The package contains a function for filtering genes by the Proportion of Variation ACcounted for by the first principal component." ; sc:featureList edam:operation_3675, edam:operation_3695 ; sc:license "GPL-2.0" ; sc:name "pvac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pvac.html" ; biotools:primaryContact "Jun Lu", "Pierre R. Bushel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0199, edam:topic_0804, edam:topic_2640 ; sc:citation , "pmcid:PMC7056579", "pubmed:31907209" ; sc:description """A Computational Toolkit to Identify and Visualize Cancer Neoantigens. pVACtools is a cancer immunotherapy suite consisting of the following tools:. A browser-based user interface that assists users in launching, managing, reviewing, and visualizing the results of pVACtools processes. pVACviz relies on the pVACapi and a client application. The source code for the client application can be found here.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0560, edam:operation_3631, edam:operation_3802 ; sc:name "pVACtools" ; sc:url "http://www.pvactools.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_1637, edam:format_1638, edam:format_1639 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3547 ; sc:name "Processed microarray data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "This package contains the function to assess the batch sourcs by fitting all \"sources\" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix." ; sc:featureList edam:operation_0571 ; sc:license "GPL-2.0" ; sc:name "pvca" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pvca.html" ; biotools:primaryContact "Jianying LI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_2814, edam:topic_3520 ; sc:citation "pubmed:19717460" ; sc:description "Software tool for the analysis and visualization of high resolution LC-MS/MS Data" ; sc:featureList edam:operation_3435, edam:operation_3628, edam:operation_3629, edam:operation_3630, edam:operation_3631, edam:operation_3632, edam:operation_3634, edam:operation_3637, edam:operation_3638, edam:operation_3646, edam:operation_3649, edam:operation_3705, edam:operation_3715 ; sc:name "PVIEW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.princeton.edu/pview/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080 ; sc:citation ; sc:description "This tool adapts the Gviz package for protein sequences and data." ; sc:featureList edam:operation_0361, edam:operation_0564 ; sc:license "Artistic-2.0" ; sc:name "Pviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Pviz.html" ; biotools:primaryContact "Renan Sauteraud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510 ; sc:citation "pubmed:25147360" ; sc:description "Visualization library for displaying protein sequence features in a web browser" ; sc:featureList edam:operation_0564, edam:operation_2479 ; sc:name "pviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research-pub.gene.com/pviz/examples/" ; biotools:primaryContact "Alexandre Masselot", "Kiran Mukhyala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:33360984" ; sc:description """Pixel-wise Voting Network for 6DoF Object Pose Estimation. We add a jupyter notebook visualization.ipynb for the keypoint detection pipeline of PVNet, aiming to make it easier for readers to understand our paper.""" ; sc:featureList edam:operation_3659 ; sc:license "Apache-2.0" ; sc:name "PVNet" ; sc:url "https://github.com/zju3dv/pvnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_2814 ; sc:citation , "pmcid:PMC7296392", "pubmed:32542363" ; sc:description """A computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. Five Species of malarial parasite (Plasmodium) are know to affect Humans, i.e., P. falciparum, P. ovale, P. malariae, P. vivax and P. knowlesi. P01 is one the strain of P. vivax which has been collected and annotated, which is directly connected to a patient in Papua Indonesia (PvP01), isolates from China (PvC01) and Thailand (PvT01), and have an improved version of genome over P. vixax Sal-1, Also reported as closely related to P. falciparum.""" ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0409, edam:operation_0474, edam:operation_3938 ; sc:name "PvP01" ; sc:url "http://www.scfbio-iitd.res.in/PvP01" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3306, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC7072630", "pubmed:32028709" ; sc:description """Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method. In this work, we developed a novel PVP predictor named PVPred-SCM which is an efficient and interpretable method for predicting and analyzing PVPs.""" ; sc:featureList edam:operation_0321, edam:operation_0480, edam:operation_3092 ; sc:name "PVPred-SCM" ; sc:url "http://camt.pythonanywhere.com/PVPred-SCM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_0623, edam:topic_3510 ; sc:citation "pubmed:18442995" ; sc:description "Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments." ; sc:featureList edam:operation_0292, edam:operation_0416, edam:operation_0448, edam:operation_0492, edam:operation_2479 ; sc:name "PVS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imed.med.ucm.es/PVS/" ; biotools:primaryContact "PVS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3295, edam:topic_3337, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC7386203", "pubmed:32665031" ; sc:description "Proteome-Wide Association Study (PWAS) is a protein-centric, gene-based method for conducting genetic association studies." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3436, edam:operation_3557 ; sc:name "PWAS" ; sc:url "https://github.com/nadavbra/pwas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3511 ; sc:citation ; sc:description "A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform \"de novo\" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools." ; sc:featureList edam:operation_0239, edam:operation_0240, edam:operation_0415 ; sc:license "GPL-2.0" ; sc:name "PWMEnrich" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/PWMEnrich.html" ; biotools:primaryContact "Robert Stojnic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3308 ; sc:citation ; sc:description "Fast tool for scanning entire genomes with a position-specific weight matrix." ; sc:featureList edam:operation_0438 ; sc:name "PWMScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccg.vital-it.ch/pwmscan/" ; biotools:primaryContact "Giovanna Ambrosini", "Philipp Bucher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "This tool performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and proteins. A separate downstream analysis of proteomic data including pathway identification and enrichment analysis, TF identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream TF and regulators." ; sc:featureList edam:operation_2497, edam:operation_3194 ; sc:license "GPL-2.0" ; sc:name "pwOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/pwOmics.html" ; biotools:primaryContact "Astrid Wachter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3518 ; sc:citation , "pubmed:31035919" ; sc:description "Computationally efficient tool to estimate power in EWAS as a function of sample and effect size for two-group comparisons of DNAm." ; sc:featureList edam:operation_0430, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "pwrEWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://biostats-shinyr.kumc.edu/pwrEWAS/" ; biotools:primaryContact "Stefan Graw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation "pmcid:PMC7059686", "pubmed:32148360" ; sc:description "Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data." ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3799 ; sc:name "PWST" ; sc:url "https://ulbbf.shinyapps.io/pwst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pubmed:31944957" ; sc:description """Learning Pixel-wise Warping Maps for Video Stabilization. As the videos captured by hand-held cameras are often perturbed by high-frequency jitters, stabilization of these videos is an essential task. Many video stabilization methods have been proposed to stabilize shaky videos. However, most methods estimate one global homography or several homographies based on fixed meshes to warp the shaky frames into their stabilized views. Due to the existence of parallax, such single or a few homographies can not well handle the depth variation. In contrast to these traditional methods, we propose a novel video stabilization network, called PWStableNet, which comes up pixel-wise warping maps, i.e., potentially different warping for different pixels, and stabilizes each pixel to its stabilized view. To our best knowledge, this is the first deep learning based pixel-wise video stabilization""" ; sc:featureList edam:operation_2429 ; sc:name "PWStableNet" ; sc:url "https://github.com/mindazhao/PWStableNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_2814, edam:topic_2828 ; sc:citation ; sc:description "A program for displaying and examining Protein Crystallographic X-ray diffraction images." ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_2238, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:name "PXImage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ccp4.ac.uk/jwc/Xhtml/PXImage/PXImage.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2814, edam:topic_2828, edam:topic_3524 ; sc:citation ; sc:description "A program for carrying out simulations of Protein Crystallographic diffraction images and analysing the unique data coverage for one or more crystal settings and series of diffraction images. It is itended primarly as a teaching tool." ; sc:featureList edam:operation_0477, edam:operation_0570, edam:operation_3445 ; sc:isAccessibleForFree true ; sc:name "PXSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ccp4.ac.uk/jwc/Xhtml/PXSim/PXSim.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC10114106" ; sc:description "R package of tools for conducting exposure-wide analysis and deriving polyexposure risk scores." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "PXStools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yixuanh/PXStools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0769 ; sc:citation , "pubmed:35621307" ; sc:description "Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD." ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "py-MCMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GOMC-WSU/py-MCMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC6766978", "pubmed:31491860" ; sc:description "A New Free and Open Source Software for Displacement and Strain Measurements in the Field of Experimental Mechanics | py2DIC is a free and open source software for 2D DIC developed at the Geodesy and Geomatics Division, University of Rome \"La Sapienza\" | pydic is a free suite of python tools for local digital image correlation analysis" ; sc:featureList edam:operation_3443, edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "py2DIC" ; sc:url "http://github.com/Geod-Geom/py2DIC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3175, edam:topic_3474, edam:topic_3676 ; sc:citation ; sc:description """subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing. Comprehensive cancer signatures with reusable modules written in python, integrating SNV, SV and MSI profiles in signatures decomposed using non-negative matrix factorisation, and produce production ready pdf reports. A python package for deciphering cancer signatures. Install the dependencies, then download and install pyCancerSig""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "pyCancerSig" ; sc:url "https://github.com/jessada/pyCancerSig" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3981 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2275 ; sc:author , ; sc:citation , "pubmed:31808797" ; sc:description "pyDockEneRes is a web server for computational characterisation of protein-protein interactions." ; sc:featureList edam:operation_0250, edam:operation_0482, edam:operation_3899 ; sc:name "pyDockEneRes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Barcelona Supercomputing Center" ; sc:softwareHelp , ; sc:url "https://life.bsc.es/pid/pydockeneres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation ; sc:description """pyGAPS is a Python-Based Framework for Adsorption Isotherm Processing and Material Characterisation. Material characterisation through adsorption is a widely-used laboratory technique. The isotherms obtained through volumetric or gravimetric experiments impart insight through their features but can also be analysed to determine material characteristics such as specific surface area, pore size distribution, surface energetics, or used for predicting mixture adsorption. The pyGAPS (python General Adsorption Processing Suite) framework was developed to address the need for high-throughput processing of such adsorption data, independent of the origin, while also being capable of presenting individual results in a user-friendly manner.""" ; sc:name "pyGAPS" ; sc:url "https://github.com/pauliacomi/pyGAPS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "pyOpenMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/OpenMS/pyopenms-extra/blob/master/docs/source/index.rst" ; biotools:primaryContact "Hannes L. Rost" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2269 ; sc:citation ; sc:description "pyPESTO is a widely applicable and highly customizable Python package for parameter estimation." ; sc:featureList edam:operation_2426, edam:operation_3658, edam:operation_3799 ; sc:name "pyPESTO" ; sc:softwareHelp ; sc:url "https://github.com/ICB-DCM/pyPESTO/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2572, edam:format_3006 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation ; sc:description "Peak Identifier for Nascent Transcript Starts" ; 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A python modelling framework built on top of CNS. Support for both trRosetta distance predictions and CASP format contact predictions, both binary and distance based. pyconsFold require a working installation of CNS. This needs to be done manually due to license.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0303, edam:operation_0474, edam:operation_3899 ; sc:license "GPL-3.0" ; sc:name "pyconsFold" ; sc:url "https://github.com/johnlamb/pyconsfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_3306, edam:topic_3524 ; sc:citation ; sc:description "GUI-based tool for rapid, versatile and customizable analysis of non-covalent interactions in molecular dynamics (MD) trajectories." ; sc:featureList edam:operation_2949 ; sc:name "PyContact" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://pycontact.github.io/" ; biotools:primaryContact "Maximilian Scheurer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3361 ; sc:citation ; sc:description "Open source, Python based, hardware and software for controlling behavioural neuroscience experiments." ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:name "pyControl" ; sc:softwareHelp ; sc:url "https://github.com/pyControl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3382 ; sc:citation , "pmcid:PMC7788933", "pubmed:33413088" ; sc:description "This tool is a lightweight and multiscale network for biomedical image segmentation." ; sc:featureList edam:operation_3443 ; sc:name "PyConvU-Net" ; sc:url "https://github.com/StevenAZy/PyConvU-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:description "PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data." ; sc:featureList edam:operation_2238, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "pycoQC" ; sc:softwareVersion "2.5.2" ; sc:url "https://a-slide.github.io/pycoQC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3524 ; sc:citation ; sc:description "Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration." ; sc:featureList edam:operation_3763 ; sc:name "PyCoTools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/CiaranWelsh/pycotools" ; biotools:primaryContact "Ciaran Welsh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0621, edam:topic_3385, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC7444595", "pubmed:32776920" ; sc:description """Reliable estimation of membrane curvature for cryo-electron tomography. This Python-based software was developed mainly to analyse curvature of membranes in 3D originating from high-resolution, noisy cryo-electron tomograms. Additionally, the software was also applied to other volumetric data with segmented structures or directly surface data, e.g. brain or organs from MRI and cells from confocal light microscopy. Accepted image data formats are: MRC, EM, VTI, NII. Accepted surface data formats are: VTP, VTK, STL, PLY. Moreover, the software can be used to calculate distances between two adjacent membranes and thicknesses of a membrane organelle. Furthermore, the software enables to calculate density distribution of particles mapped on a membrane, e.g. membrane-bound ribosomes. This package contains Python scripts applying the PyCurv package and combining different functions into the workflows described above, the main are:.""" ; sc:featureList edam:operation_0337, edam:operation_0461, edam:operation_3216, edam:operation_3435 ; sc:license "LGPL-3.0" ; sc:name "PyCurv" ; sc:url "https://github.com/kalemaria/pycurv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099, edam:topic_0623, edam:topic_0749, edam:topic_3170 ; sc:citation ; sc:description """a comprehensive software for Direct Coupling Analysis of RNA and Protein Sequences. Direct coupling analysis software for protein and RNA sequences. pydca is Python implementation of direct coupling analysis (DCA) of residue coevolution for protein and RNA sequence families using the mean-field and pseudolikelihood maximization algorithms. Given multiple sequence alignment (MSA) files in FASTA format, pydca computes the coevolutionary scores of pairs of sites in the alignment. In addition, when an optional file containing a reference sequence is supplied, scores corresponding to pairs of sites of this reference sequence are computed by mapping the reference sequence to the MSA. The software provides command line utilities or it can be used as a library""" ; sc:featureList edam:operation_0272, edam:operation_2422, edam:operation_3192 ; sc:license "MIT" ; sc:name "pydca" ; sc:url "https://github.com/KIT-MBS/pydca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3444 ; sc:citation ; sc:description "A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Tensor and Diffusional Kurtosis Imaging." ; sc:featureList edam:operation_3443, edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "PyDesigner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/m-ama/PyDesigner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3344 ; sc:author ; sc:citation , ; sc:description "Pydfc is an open-source Python toolbox designed to facilitate the implementation of multi-analysis dynamic Functional Connectivity (dFC) assessment using MRI data from the human brain." ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "pydfc" ; sc:softwareVersion "v1.0.1" ; sc:url "https://github.com/neurodatascience/dFC" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC9551626", "pubmed:36215263" ; sc:description "pyDHM is an open-source Python library aimed at Digital Holographic Microscopy (DHM) applications. The pyDHM is a user-friendly library written in the robust programming language of Python that provides a set of numerical processing algorithms for reconstructing amplitude and phase images for a broad range of optical DHM configurations. The pyDHM implements phase-shifting approaches for in-line and slightly off-axis systems and enables phase compensation for telecentric and non-telecentric systems. In addition, pyDHM includes three propagation algorithms for numerical focusing complex amplitude distributions in DHM and digital holography (DH) setups. 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Jens Kortus is our overall theoretical guide and head of decisions, whereas Susi Lehtola has recently joined the team and provides new perspectives.""" ; sc:license "Apache-2.0" ; sc:name "pyflosic" ; sc:url "https://github.com/pyflosic/pyflosic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3510 ; sc:citation , "pmcid:PMC5985001", "pubmed:29414697" ; sc:description "A Python framework for graphing, analysis, and simulation of the biophysical properties of proteins." ; sc:featureList edam:operation_2415 ; sc:license "MIT" ; sc:name "PyFolding" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/quantumjot/PyFolding" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0199, edam:topic_3047, edam:topic_3372 ; sc:citation ; sc:description "pyFoldX: python bindings for FoldX." ; sc:featureList edam:operation_0477, edam:operation_3893, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "pyFoldX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/leandroradusky/pyFoldX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3297, edam:topic_3315 ; sc:citation ; sc:description """Python Framework for Object Oriented Modelling of Bioprocesses. 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In contrast to 'full-blown' software suites, pyFOOMB can be used by scientists with little programming skills in the easy-access language Python. pyFOOMB comes with a MIT license, and anyone interested in using, understanding, or contributing to pyFOOMB is happily invited to do so.""" ; sc:featureList edam:operation_3659, edam:operation_3799, edam:operation_3927 ; sc:license "MIT" ; sc:name "pyFOOMB" ; sc:url "http://github.com/MicroPhen/pyFOOMB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3370, edam:topic_3382 ; sc:citation ; sc:description "A Python based FRAP analysis tool box." ; sc:featureList edam:operation_3443 ; sc:name "PyFRAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/alexblaessle/PyFRAP" ; biotools:primaryContact "Alexander Bläßle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_3314, edam:topic_3315 ; sc:citation , "pubmed:31962460" ; sc:description """Computational nanoplasmonics in the quasistatic limit for biosensing applications. PyGBe—pronounced pigbē—is a Python library that applies the boundary integral method for biomolecular electrostatics and nanoparticle plasmonics. PyGBe achieves both algorithmic and hardware acceleration. The solution algorithm uses a Barnes-Hut treecode to accelerate each iteration of a GMRES solver to O(N logN), for N unknowns. It exploits NVIDIA GPU hardware on the most computationally intensive parts of the code using CUDA kernels in the treecode, interfacing with PyCUDA. Some parts of the code are written in C++, wrapped using SWIG.""" ; sc:featureList edam:operation_2426, edam:operation_3431 ; sc:license "BSD-3-Clause" ; sc:name "PyGBe" ; sc:url "http://pygbe.github.io/pygbe/docs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3500, edam:topic_3679 ; sc:citation , "pmcid:PMC10320995", "pubmed:37403146" ; sc:description "Python tool to generate pseudorandom series for human and non-human animal behavioural experiments. It includes both a graphical user interface (GUI) as well as a simple Python API." ; sc:featureList edam:operation_0230 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyGellermann" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YannickJadoul/PyGellermann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3474 ; sc:citation , "pmcid:PMC9900208", "pubmed:36721325" ; sc:description "A Python package for gene discovery using network-based machine learning." ; sc:featureList edam:operation_2454, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PyGenePlexus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/krishnanlab/PyGenePlexus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3474, edam:topic_3524 ; sc:citation , "pmcid:PMC8100330", "pubmed:33967731" ; sc:description "PyGeNN is a Python library for GPU-enhanced neural networks. PyGeNN is a Python package which exposes all of GeNN's functionality to Python with minimal overhead. This provides an alternative, arguably more user-friendly, way of using GeNN and allows modelers to use GeNN within the growing Python-based machine learning and computational neuroscience ecosystems." ; sc:featureList edam:operation_2426, edam:operation_3927 ; sc:name "PyGeNN" ; sc:url "https://github.com/BrainsOnBoard/pygenn_paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:32745185" ; sc:description """reproducible plots for multivariate genomic data sets. Standalone program and library to plot beautiful genome browser tracks. pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.""" ; sc:featureList edam:operation_0335, edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "pyGenomeTracks" ; sc:softwareHelp ; sc:url "https://github.com/deeptools/pyGenomeTracks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0769 ; sc:citation , "pmcid:PMC10246576", "pubmed:37228014" ; sc:description "Manipulating genomic intervals and data files in Python." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pygenomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/gtamazian/pygenomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2640, edam:topic_3170, edam:topic_3372 ; sc:citation , "pmcid:PMC7579948", "pubmed:33092528" ; sc:description """PyGNA is a framework for statistical network analysis of high-throughput experiments. It can be used both as a standalone command line application or it can be used as API to develop custom analyses. A simple Snakemake workflow to perform network analyses using the Python Geneset Network Analysis (PyGNA) package.""" ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3927 ; sc:license "MIT" ; sc:name "PyGNA" ; sc:url "http://github.com/stracquadaniolab/pygna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814, edam:topic_3047 ; sc:citation ; sc:description "API for docking based virtual screening workflow generation." ; sc:featureList edam:operation_0478 ; sc:name "PyGOLD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.ccb.tu-dortmund.de/ag-koch/pygold/" ; biotools:primaryContact "Oliver Koch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0602, edam:topic_3307, edam:topic_3336, edam:topic_3344 ; sc:citation ; sc:description "pyGOMoDo is a Python library to perform homology modeling and docking specifically designed for human GPCRs. pyGOMoDo is a python wrap-up of the updated functionalities of GOMoDo web-service (https://gomodo.grs.kfa-juelich.de). It was designed for convenient use with Jupyter notebooks." ; sc:name "pyGOMoDo" ; sc:url "https://github.com/rribeiro-sci/pygomodo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0202, edam:topic_3336 ; sc:citation , "pubmed:37489036" ; sc:description "Package for the generation of input files for molecular dynamic simulation with GROMACS." ; sc:featureList edam:operation_0244, edam:operation_2409, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pyGROMODS" ; sc:url "https://doi.org/10.5281/zenodo.7912747" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0605, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC7207050", "pubmed:32160033" ; sc:description """Python Application for Computing Graph Traversal Edit Distance. Graph Traversal Edit Distance (GTED) is a measure of distance (or dissimilarity) between two graphs introduced. This measure is based on the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals of the two graphs. GTED was motivated by and provides the first mathematical formalism for sequence coassembly and de novo variation detection in bioinformatics. Many problems in applied machine learning deal with graphs (also called networks), including social networks, security, web data mining, protein function prediction, and genome informatics. The kernel paradigm beautifully decouples the learning algorithm from the underlying geometric space, which renders graph kernels important for the aforementioned applications. In this article, we introduce a tool, PyGTED to compute GTED""" ; sc:featureList edam:operation_0337, edam:operation_0524, edam:operation_3096 ; sc:name "PyGTED" ; sc:url "https://github.com/Ali-E/GTED" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1245 ; sc:encodingFormat edam:format_3996 ; sc:name "Sequence cluster (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation ; sc:description "pyHCA and hcatk (HCA toolkit) are a python library and executable for the Hydrophobic Cluster Analysis of protein sequences. pyHCA implements various class and function for handling sequences and analyses them hcatk provides off the hands set of program to perform hydrophobic cluster analyses." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "CECILL-C" ; sc:name "pyHCA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/T-B-F/pyHCA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0176, edam:topic_2830, edam:topic_3520 ; sc:citation ; sc:description """Derivation and visualization of protection factors from Hydrogen-Deuterium Exchange Mass Spectrometry at near residue resolution. Abstract Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) is a powerful technique to monitor the intrinsic and conformational dynamics of proteins. Most HDX-MS experiments compare protein states (e.g. apoprotein vs liganded) and provide detailed information on differential dynamics between them obtained from multiple overlapping peptides. However, differential dynamics are difficult to compare across protein derivatives, oligomeric assemblies, homologues and samples treated under different buffer and protease conditions. A main reason is that peptide-based D-uptake differences do not inform on absolute intrinsic dynamics at the level of single aminoacyl residues""" ; sc:featureList edam:operation_0310, edam:operation_0404, edam:operation_2476 ; sc:license "MIT" ; sc:name "PyHDX" ; sc:url "https://github.com/Jhsmit/PyHDX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0202, edam:topic_3382 ; sc:citation , "pubmed:34529294" ; sc:description "A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data." ; sc:featureList edam:operation_0310, edam:operation_3447, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PyHI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xuewuzhang-UTSW/PyHI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "PyHIST is a Histological Image Segmentation Tool: a lightweight semi-automatic pipeline to extract tiles with foreground content from SVS histopathology whole image slides (with experimental support for other formats). It is intended to be an easy-to-use tool to preprocess histological image data for usage in machine learning tasks. The PyHIST pipeline involves three main steps: 1) produce a mask for the input WSI that differentiates the tissue from the background, 2) create a grid of tiles on top of the mask, evaluate each tile to see if it meets the minimum content threshold to be considered as foreground and 3) extract the selected tiles from the input WSI at the requested resolution." ; sc:featureList edam:operation_2422, edam:operation_3443, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyHIST" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/manuel-munoz-aguirre/PyHIST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_2885, edam:topic_3053 ; sc:citation , "pmcid:PMC5292802", "pubmed:28166716" ; sc:description "This implements several methods for HLA association analysis, to fill the gap. PyHLA is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data." ; sc:featureList edam:operation_0252 ; sc:license "GPL-2.0" ; sc:name "PyHLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/felixfan/PyHLA" ; biotools:primaryContact "Yanhui Fan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0623 ; sc:citation , "pmcid:PMC10159651", "pubmed:37074928" ; sc:description "Python library binding to HMMER for efficient sequence analysis." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyHMMER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://anaconda.org/bioconda/pyhmmer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author "J. Gonzalez-Vallinas" ; sc:citation , , , ; sc:description "Suite of tools for the analysis of high-throughput sequencing data. It can be used to analyzed CLIP-seq and ChIP-seq data, as well as to calculate the differential enrichment of CLIP-seq, ChIP-seq and other types of datasets between two conditions, with or without replicates. It also includes a number of useful tools for the transformation and manipulation of genomic-based datasets." ; sc:featureList edam:operation_2238, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Pyicoteo" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "2.0.7" ; sc:url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo" ; biotools:primaryContact "Eduardo Eyras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3168, edam:topic_3474, edam:topic_3934 ; sc:citation , "pmcid:PMC10166583", "pubmed:37097893" ; sc:description "pyInfinityFlow is a Python package that enables imputation of hundreds of features from Flow Cytometry using XGBoost regression1. It is an adaptation of the original implementation in R2 with the goal of optimizing the workflow for large datasets by increasing the speed and memory efficiency of the analysis pipeline." ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pyInfinityFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KyleFerchen/pyInfinityFlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_2814 ; sc:citation ; sc:description """PyInteraph2 and PyInKnife2 to analyze networks in protein structural ensembles. PyInKnife2 is a set of Python scripts to run an updated version of the PyInKnife pipeline [ for Protein Structure Network (PSN) analysis using PyInteraph2.""" ; sc:featureList edam:operation_0244, edam:operation_0276, edam:operation_1839, edam:operation_3436, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "PyInKnife2" ; sc:url "https://github.com/ELELAB/PyInKnife2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0602 ; sc:citation , "pubmed:31778155" ; sc:description """Longitudinal Omics Analysis and Trend Identification. This repository contains PyIOmica, a Python package that provides bioinformatics utilities for analyzing (dynamic) omics datasets. PyIOmica extends MathIOmica usage to Python and implements new visualizations and computational tools for graph analyses. The documentation is available at Read the Docs: https://pyiomica.readthedocs.io/en/latest/. Welcome to PyIOmica’s documentation! — pyiomica 1.1.2 documentation. Free document hosting provided by Read the Docs""" ; sc:featureList edam:operation_3083, edam:operation_3501, edam:operation_3559 ; sc:license "MIT" ; sc:name "pyiomica" ; sc:softwareHelp ; sc:url "https://pypi.python.org/pypi/pyiomica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2830, edam:topic_3168, edam:topic_3930 ; sc:citation , "pmcid:PMC7364545", "pubmed:32677886" ; sc:description """PyIR is a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. PyIR is a minimally-dependent high-speed wrapper for the IgBLAST immunoglobulin and T-cell analyzer. This is achieved through chunking the input data set and running IgBLAST single-core in parallel to better utilize modern multi-core and hyperthreaded processors.""" ; sc:featureList edam:operation_1812, edam:operation_3359, edam:operation_3695 ; sc:name "PyIR" ; sc:url "http://github.com/crowelab/PyIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:34390579" ; sc:description "PyJAMAS is a Python-based platform for the analysis of microscopy images. PyJAMAS can be used for image processing, object detection—using both machine learning and traditional approaches—, and quantitation of cellular dynamics." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PyJAMAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/rfg_lab/pyjamas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_2229, edam:topic_3293, edam:topic_3500, edam:topic_3945 ; sc:citation , "pmcid:PMC10237437", "pubmed:37267256" ; sc:description "Enabling representation of the whole animal kingdom in information space." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "PyKleeBarcode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WandrilleD/pyKleeBarcode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3372, edam:topic_3384, edam:topic_3444, edam:topic_3520 ; sc:citation , "pmcid:PMC6980400", "pubmed:31978052" ; sc:description """An image analysis workflow for open and reproducible research on femoral knee cartilage. Transparent research in musculoskeletal imaging is fundamental to reliably investigate diseases such as knee osteoarthritis (OA), a chronic disease impairing femoral knee cartilage. To study cartilage degeneration, researchers have developed algorithms to segment femoral knee cartilage from magnetic resonance (MR) images and to measure cartilage morphology and relaxometry. The majority of these algorithms are not publicly available or require advanced programming skills to be compiled and run. However, to accelerate discoveries and findings, it is crucial to have open and reproducible workflows. We present pyKNEEr, a framework for open and reproducible research on femoral knee cartilage from MR images. pyKNEEr is written in python, uses Jupyter notebook as a user interface, and is available on GitHub with a GNU GPLv3 license""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "pyKNEEr" ; sc:url "https://sbonaretti.github.io/pyKNEEr/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3315, edam:topic_3520 ; sc:citation , "pubmed:33904714" ; sc:description "PyKrev is a Python library for the analysis of complex mixture FT-MS data. PyKrev is a comprehensive suite of tools for analysis and visualization of FT-MS data after formula assignment has been performed. These comprise formula manipulation and calculation of chemical properties, intersection analysis between multiple lists of formulas, calculation of chemical diversity, assignment of compound classes to formulas, multivariate analysis, and a variety of visualization tools producing van Krevelen diagrams, class histograms, PCA score, and loading plots, biplots, scree plots, and UpSet plots. The library is showcased through analysis of hot water green tea extracts and Scotch whisky FT-ion cyclotron resonance-MS data sets. PyKrev addresses the lack of a single, cohesive toolset for researchers to perform FT-MS analysis in the Python programming environment encompassing the most recent data analysis techniques used in the field." ; sc:featureList edam:operation_1812, edam:operation_2939, edam:operation_2943, edam:operation_3891 ; sc:license "MIT" ; sc:name "PyKrev" ; sc:url "https://github.com/Kzra/pykrev" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1476, edam:format_3877 ; sc:name "Structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2878 ; sc:encodingFormat edam:format_1476, edam:format_2330 ; sc:name "Protein structural motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Script" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0166, edam:topic_0769, edam:topic_1317, edam:topic_3315, edam:topic_3332, edam:topic_3474 ; sc:author ; sc:citation , "pmcid:PMC8685811", "pubmed:34930115" ; sc:description "Python-C Parallel KVFinder (pyKVFinder) is an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. Besides conventional cavity properties such as volume and area, which are stored as Python dictionaries, pyKVFinder computes cavity depth and hydropathy. Similar to cavity points, these spatial and physicochemical properties are stored as Python ndarrays and can be visualized using Python molecular visualization widgets. In general, pyKVFinder is designed for efficient scripting routines built on easy-to-handle data structures, such as Python dictionaries and NumPy N-dimensional arrays (ndarrays), and can be building blocks for data science and drug design applications." ; sc:featureList edam:operation_0250, edam:operation_2483, edam:operation_2575, edam:operation_3351 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pyKVFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider ; sc:softwareHelp ; sc:url "https://github.com/LBC-LNBio/pyKVFinder" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0202, edam:topic_2258, edam:topic_3047, edam:topic_3474 ; sc:citation , "pmcid:PMC10385924", "pubmed:37507792" ; sc:description """Python LAMMPS 3D molecular descriptors package. A Python-based post-processing routines for calculating 3D molecular descriptors from molecular dynamics (MD) simulations. PyL3dMD is compatible with the popular simulation package LAMMPS and enables users to compute more than 2000 3D molecular descriptors from atomic trajectories generated by MD simulations.""" ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3890, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyL3dMD" ; sc:url "https://github.com/panwarp/PyL3dMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3516, edam:topic_3517 ; sc:citation ; sc:description """Local Ancestry Prediction with PyLAE. 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These methods generate lists of single fluorophore positions that capture nanoscale structural details of subcellular organisation, but to develop biological insight, we must post-process and visualize this data in a meaningful way. A large number of algorithms have been developed for localization post-processing, transforming point data into representations which approximate traditional microscopy images, and performing specific quantitative analysis directly on points. 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Therefore, pymia is highly flexible, allows for fast prototyping, and reduces the burden of implementing data handling and evaluation. Founded, actively developed and maintained, by Fabian Balsiger and Alain Jungo.""" ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "pymia" ; sc:softwareHelp ; sc:url "https://github.com/rundherum/pymia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:36773591" ; sc:description "A deep learning toolkit for annotation-efficient medical image segmentation." ; sc:featureList edam:operation_3096, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PyMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HiLab-git/PyMIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3892 ; sc:citation , "pubmed:36378163" ; sc:description "An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method." ; sc:featureList edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PyMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ChenGiuseppe/PyMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2275 ; sc:citation "pubmed:22536966" ; sc:description "A simple and intuitive interface between the popular molecular graphics system PyMOL and several other tools (i.e., BLAST, ClustalW, Muscle, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modelling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. 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sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pymzML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.1" ; sc:url "http://pymzml.github.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC7522368", "pubmed:33041750" ; sc:description """Pyneal is an open source software package to support real-time functional magnetic resonance imaging (fMRI). 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Pyntacle relies on multi-core/process programming paradigms to speedup the execution of complex analysis routines." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Pyntacle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://pyntacle.css-mendel.it/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0176, edam:topic_2229, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC7595628", "pubmed:33075044" ; sc:description """Computational tool for modelling of multi-cell flows in complex geometries. A user ready, well documented software package PyOIF contains an implementation of a robust validated computational model for cell flow modelling. The software is capable of simulating processes involving biological cells immersed in a fluid. The examples of such processes are flows in microfluidic channels with numerous applications such as cell sorting, rare cell isolation or flow fractionation. Besides the typical usage of such computational model in the design process of microfluidic devices, PyOIF has been used in the computer-aided discovery involving mechanical properties of cell membranes. With this software, single cell, many cell, as well as dense cell suspensions can be simulated. Many cell simulations include cell-cell interactions and analyse their effect on the cells""" ; sc:featureList edam:operation_2476, edam:operation_3436, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "PyOIF" ; sc:url "https://github.com/icimrak/espresso/releases/tag/pyoif-v2.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3382 ; sc:citation , "pmcid:PMC7388197", "pubmed:32766455" ; sc:description """A Python toolkit for uploading images and metadata to OMERO. Code snipets for updating whole properties of whole ISA tree, for example permissions settings. When building a distribution for release through BioConda, the Python setuptools are used. Library of artifacts for integration with Seek4Science using Seek's REST API. Example data, notebooks and scripts for demonstrating features of OMEROConnect and pyOmeroUpload.""" ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3431 ; sc:license "MIT" ; sc:name "PyOmeroUpload" ; sc:url "https://github.com/SynthSys/pyOmeroUpload" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2640, edam:topic_3053 ; sc:citation , "pmcid:PMC10085746", "pubmed:37037472" ; sc:description "Python package for plotting OncoPrints." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "PyOncoPrint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pnucolab/pyoncoprint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3053 ; sc:citation , "pmcid:PMC5079480", "pubmed:27402905" ; sc:description "A Python package for gene regulatory network reconstruction." ; sc:featureList edam:operation_3439 ; sc:name "PyPanda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/davidvi/pypanda" ; biotools:primaryContact "David G.P. van IJzendoorn", "Marieke L. Kuijjer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:26369703" ; sc:description "Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB) using its XML-based API." ; sc:featureList edam:operation_2406 ; sc:name "PyPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/williamgilpin/pypdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0659, edam:topic_3512, edam:topic_3922 ; sc:citation ; sc:description "pypgatk is a Python library part of the ProteoGenomics Analysis Toolkit. It provides different bioinformatics tools for proteogenomics data analysis" ; sc:featureList edam:operation_3227, edam:operation_3649, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "pypgatk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bigbio/py-pgatk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3385, edam:topic_3452 ; sc:citation , "pmcid:PMC8284402", "pubmed:34212892" ; sc:description "pyPhase is an open-source Python package for phase retrieval from phase contrast images in the Fresnel regime." ; sc:featureList edam:operation_2422, edam:operation_3443, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.1" ; sc:name "PyPhase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.in2p3.fr/mlanger/pyPhase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """A python toolbox for assessing microbial growth and cell viability in high-throughput colony screens. A python toolbox for phenotype analysis of arrayed microbial colonies written by Stephan Kamrad (stephan.kamrad at crick.ac.uk).""" ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3799 ; sc:license "MIT" ; sc:name "pyphe" ; sc:url "http://www.github.com/Bahler-Lab/pyphe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3384, edam:topic_3517 ; sc:citation , "pubmed:34981404" ; sc:description "A Phenome-Disease Association Tool for Electronic Medical Record Analysis." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pyPheWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pyphewas.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3361, edam:topic_3418 ; sc:citation , "pmcid:PMC10070037", "pubmed:37021295" ; sc:description "Visualization tool for exploratory analysis of phenome-disease associations." ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pyPheWAS Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MASILab/pyPheWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3303, edam:topic_3375 ; sc:citation , "pubmed:32857502" ; sc:description """A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism""" ; sc:featureList edam:operation_0244, edam:operation_0400, edam:operation_3435 ; sc:license "LGPL-3.0" ; sc:name "PypKa" ; sc:url "https://github.com/mms-fcul/PypKa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0128, edam:topic_2275 ; sc:citation ; sc:description "Program/script written in Python to analyze protein-ligand interaction from the molecular docking result." ; sc:featureList edam:operation_0478 ; sc:name "PyPLIF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.1" ; sc:url "https://code.google.com/p/pyplif/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0780, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:32687350" ; sc:description """Welcome to PyPLIF-HIPPOS's project page. PyPLIF-HIPPOS is an upgraded version of PyPLIF (Python-based Protein-Ligand Interaction Fingerprinting), a tool for molecular docking post-analysis. It will translate the 3D coordinates of both ligand(s) (generated from docking simulation) and protein into a series of interaction bitstring (also known as Interaction Fingerprint) (see image below). HIPPOS (/ˌhipoʊz/) is a recursive acronym of HIPPOS Is PyPLIF On Steroids. From this point forward, PyPLIF-HIPPOS is simplified to HIPPOS. module to read and process the molecule files from the molecular. The current version only support the Sybil mol2 format, but it is planned.""" ; sc:featureList edam:operation_2929, edam:operation_3899, edam:operation_3938 ; sc:license "GPL-3.0" ; sc:name "PyPLIF HIPPO" ; sc:url "https://github.com/radifar/PyPLIF-HIPPOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0769, edam:topic_3382 ; sc:citation ; sc:description "PyPlr is a versatile, integrated system of hardware and software to support a broad spectrum of research applications concerning the human pupillary light reflex (PLR). PyPlr is a custom Python library for integrating a research-grade video-based eye-tracker system with a light source and streamlining stimulus design, optimisation and delivery, device synchronisation, and extraction, cleaning, and analysis of pupil data." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyPlr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/pyplr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3068, edam:topic_3419 ; sc:citation , "pmcid:PMC8409663", "pubmed:34469455" ; sc:description "PyPlutchik is a module for visualizing the emotional fingerprint of corpora and text annotated with the Plutchik's model of emotions." ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "PyPlutchik" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/alfonsosemeraro/pyplutchik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3386, edam:topic_3500 ; sc:citation ; sc:description """A tool to automatically quantify Point-Of-Care Tests from images. Lateral flow Point-Of-Care Tests (POCTs) are a valuable tool for rapidly detecting pathogens and the associated immune response in humans and animals. In the context of the SARS-CoV-2 pandemic, they offer rapid on-site diagnostics and can relieve centralized laboratory testing sites, thus freeing resources that can be focused on especially vulnerable groups. However, visual interpretation of the POCT test lines is subjective, error prone and only qualitative. Here we present pyPOCQuant, an open-source tool implemented in Python 3 that can robustly and reproducibly analyze POCTs from digital images and return an unbiased and quantitative measurement of the POCT test lines""" ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:name "pyPOCQuant" ; sc:url "https://gitlab.com/csb.ethz/pypocquant/-/tree/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0769, edam:topic_3047 ; sc:citation , "pubmed:33819017" ; sc:description "pyPolyBuilder is tool for automated preparation of molecular topologies and initial configurations for molecular dynamics simulations of arbitrary supramolecules." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_2476 ; sc:license "MIT" ; sc:name "pyPolyBuilder" ; sc:url "https://github.com/mssm-labmmol/pypolybuilder" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0130, edam:topic_0154 ; sc:citation , "pmcid:PMC8323899", "pubmed:34329304" ; sc:description "Python Protein Graph Analyser. Allow the creation and analysis of protein residue network (PRN) models from various input data. Works as a plugin for PyMOL." ; sc:featureList edam:operation_0248, edam:operation_0276, edam:operation_2949, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pyProGA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gitlab.com/Vlado_S/pyproga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_2275 ; sc:citation , "pubmed:35065401" ; sc:description "An easy to use GUI for comparative protein modeling." ; sc:featureList edam:operation_0477, edam:operation_2476, edam:operation_4008, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "PyProtModel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/msisakht/pyprotmodel.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3293 ; sc:citation "pubmed:24603985" ; sc:description "Pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets." ; sc:featureList edam:operation_0310 ; sc:name "PyRAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dereneaton.com/software/pyrad/" ; biotools:primaryContact "Deren Eaton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3299, edam:topic_3384 ; sc:citation , "pubmed:36738608" ; sc:description "A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "PyRaDiSe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ubern-mia/pyradise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC8688400", "pubmed:34950679" ; sc:description "Intra-layer Pyramid-Scale Feature Aggregation Network for Retinal Vessel Segmentation." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Pyramid-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JerRuy/Pyramid-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3300, edam:topic_3304, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC9125180", "pubmed:35615283" ; sc:description "An Open-Source Python Library for Animal Behavior Analysis." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyRAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pyratlib/pyrat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:37257630" ; sc:description "Multi-view ensemble clustering for cancer subtype discovery." ; sc:featureList edam:operation_2422, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Pyrea" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/mdbloice/Pyrea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3071 ; sc:citation ; sc:description "PyRice is an API to access some Rice public databases at the same time with consistent output. PyRice design is modular and implements a smart query system which fits the computing resources to optimize the query speed." ; sc:featureList edam:operation_0224, edam:operation_3907 ; sc:license "MIT" ; sc:name "PyRice" ; sc:softwareHelp ; sc:url "https://github.com/SouthGreenPlatform/PyRice" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:34270903" ; sc:description "PyRMD is a Ligand-Based Virtual Screening tool written in Python powered by machine learning." ; sc:featureList edam:operation_3359, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "PyRMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cosconatilab/PyRMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3572 ; sc:citation ; sc:description "Intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads." ; sc:featureList edam:operation_3695 ; sc:name "PyroCleaner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/pyrocleaner/index.php/Main_Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description "PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment." ; sc:featureList edam:operation_3198 ; sc:name "PyroMap" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://hivdb.stanford.edu/pages/resources.html" ; biotools:primaryContact "HIV db support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:19668203" ; sc:description "Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis." ; sc:featureList edam:operation_3218 ; sc:name "PyroNoise" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://userweb.eng.gla.ac.uk/christopher.quince/Software/PyroNoise.html" ; biotools:primaryContact "Chris Quince" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3372 ; sc:citation ; sc:description "Interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting." ; sc:featureList edam:operation_2479 ; sc:name "PyRosetta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.012" ; sc:url "http://www.pyrosetta.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0632, edam:topic_0654 ; sc:citation "pubmed:23124743" ; sc:description "Program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads." ; sc:featureList edam:operation_0369 ; sc:name "PyroTrimmer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pyrotrimmer.kopri.re.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3316, edam:topic_3512 ; sc:citation ; sc:description """a python package for RNA-Seq workflows. pyrpipe: python rna-seq pipeliner. Example to identify orphan transcripts in maize by pyrpipe. A python package for RNA-Seq workflows — pyrpipe 0.0.1 documentation. pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop bioinformatic or any other computational pipelines in pure python. pyrpipe provides an easy-to-use framework for importing any UNIX command in python. pyrpipe comes with specialized classes and functions to easily code RNA-Seq processing workflows. pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs in an object oriented manner. pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data.""" ; sc:featureList edam:operation_3192, edam:operation_3680, edam:operation_3800 ; sc:license "MIT" ; sc:name "pyrpipe" ; sc:url "http://pyrpipe.rtfd.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3316, edam:topic_3500 ; sc:citation , "pubmed:34729801" ; sc:description "A python package for selective sweep detection and co-evolutionary gene cluster identification." ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pyRSD-CoEv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/QianZiTang/pyRSD-CoEv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3336 ; sc:citation "pubmed:29167582" ; sc:description "Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets." ; sc:featureList edam:operation_2430, edam:operation_2945, edam:operation_3431 ; sc:name "PyRx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.9.2" ; sc:url "http://pyrx.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation ; sc:description "A Python module for reading and manipulating SAM/BAM/VCF/BCF files." ; sc:featureList edam:operation_2121, edam:operation_2409 ; sc:license "MIT" ; sc:name "pysam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pysam-developers/pysam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3168 ; sc:description "A Python utility for calculating statistics against genome position based on sequence alignments from a SAM, BAM or CRAM file." ; sc:featureList edam:operation_2238 ; sc:license "Not licensed" ; sc:name "pysamstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/alimanfoo/pysamstats" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3241 ; sc:encodingFormat edam:format_2585 ; sc:name "Kinetic model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259 ; sc:author , "Johann M Rohwer" ; sc:citation , "pubmed:15454409" ; sc:contributor "J.-H.S.H Hofmeyr" ; sc:description """The Python Simulator for Cellular Systems (PySCeS) is a A flexible, user friendly tool for the analysis of cellular systems. Computer modelling has become an integral tool in the analysis and understanding of the reaction networks that underlie cellular processes. PySCeS, first released in 2003, is an extremely flexible, user-extendible, open source, software actively used and developed by a community of researchers and developers.""" ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "PySCeS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.8" ; sc:url "https://pysces.github.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3524 ; sc:citation ; sc:description "Collection of metabolic pathway analysis tools." ; sc:featureList edam:operation_2497 ; sc:license "BSD-3-Clause" ; sc:name "PySCeSToolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PySCeS/PyscesToolbox" ; biotools:primaryContact "Johann M Rohwer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3314, edam:topic_3372, edam:topic_3474 ; sc:citation , "pubmed:32668948" ; sc:description "PySCF is an open-source collection of electronic structure modules powered by Python. The package aims to provide a simple, lightweight, and efficient platform for quantum chemistry calculations and methodology development." ; sc:name "PySCF" ; sc:url "http://www.PySCF.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """A tool for reconstructing and analyzing gene regulatory network from single-cell RNA-Seq data. Dashboard is available now for creating your own GRNs. Cell specific GRNs and network analysis results can be saved as a pickle object and upload onto PySCNet-Dashboard. It provides parameter settings and allows for parameter adjustment and GRNs customization.""" ; sc:featureList edam:operation_0313, edam:operation_2437, edam:operation_3463 ; sc:license "MIT" ; sc:name "PySCNet" ; sc:url "https://github.com/MingBit/PySCNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0166, edam:topic_0199, edam:topic_3336 ; sc:citation , "pmcid:PMC10640396", "pubmed:38023327" ; sc:description "pyScoMotif is a Python package that enables the rapid search of similar 3D structural motifs across large sets of proteins. Concretely, given a reference set of residues in a PDB file, it will find other protein structures with the same set of residues that are in a similar geometrical arrangement." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0245, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "pyScoMotif" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/3BioCompBio/pyScoMotif" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:32302889" ; sc:description """An ease of use tool for analysis of scratch assays. Image acquisition has greatly benefited from the automation of microscopes and has been followed by an increasing amount and complexity of data acquired. Here, we present the PyScratch, a new tool for processing spatial and temporal information from scratch assays. PyScratch is an open-source software implemented in Python that analyses the migration area in an automated fashion. METHODS:The software was developed in Python. Wound healing assays were used to validate its performance. The images were acquired using Cytation 5™ during 60 h. Data were analyzed using One-Way ANOVA. RESULTS:PyScratch performed a robust analysis of confluent cells, showing that high plating density affects cell migration. Additionally, PyScratch was approximately six times faster than a semi-automated analysis""" ; sc:featureList edam:operation_3446, edam:operation_3799 ; sc:name "PyScratch" ; sc:url "https://pypi.org/project/pyscratch/#files" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3068, edam:topic_3517 ; sc:citation ; sc:description "Comprehensive tool for microbial pangenome-wide association studies." ; sc:featureList edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "pyseer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mgalardini/pyseer" ; biotools:primaryContact "John A. Lees", "Marco Galardini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3168, edam:topic_3314, edam:topic_3382 ; sc:citation ; sc:description "An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PySeq2500" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nygctech/PySeq2500" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0154, edam:topic_3314, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32011127" ; sc:description """A PyMOL Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles. In PyMOL window, go to Plugin -> Plugin manager -> Install new plugin, choose Pyshifts.py file in your local Pyshifts folder, and click OK on the next step. You will then see a pop-up message Plugin "PyShiftsPlugin" has been installed.""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3802 ; sc:name "PyShifts" ; sc:url "https://github.com/atfrank/PyShifts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation ; sc:description "PySHS package is a python open source software which simulates the Second Harmonic Scattering (SHS) of different kind of colloidal nano-object." ; sc:featureList edam:operation_2476, edam:operation_2940 ; sc:name "PySHS" ; sc:url "https://pypi.org/project/pyshs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593 ; sc:citation ; sc:description """Pre-operational Sentinel-3 Snow and Ice (SICE) Products. Python scripts behind the SICE toolchain for albedo retrieval. sice_f.py reads the SICE-generated S3 geotiff files, converts them into ascii files, compiles and runs sice.f, reads the text outputs and save them into geotiff again.""" ; sc:featureList edam:operation_2422 ; sc:name "pySICE" ; sc:url "https://github.com/GEUS-SICE/pySICE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3332 ; sc:citation ; sc:description "Pysimm is a python package designed to facilitate structure generation, simulation, and modification of molecular systems. Pysimm provides a collection of simulation tools and smooth integration with highly optimized third party software." ; sc:featureList edam:operation_2476 ; sc:license "MIT" ; sc:name "pysimm" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v0.1" ; sc:url "https://pysimm.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0769, edam:topic_2258, edam:topic_3343 ; sc:citation , "pubmed:33709154" ; sc:description "PySmash is a Python package and individual executable program for representative substructure generation and application. PySmash is a user-friendly and integrated tool which offers convenience and advantage for the automatic structural alerts derivation and application is presented." ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_3938 ; sc:license "MIT" ; sc:name "PySmash" ; sc:softwareHelp ; sc:url "https://github.com/kotori-y/pySmash" ; biotools:primaryContact , , "Shao Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0593, edam:topic_3318 ; sc:citation , "pubmed:32687710" ; sc:description """Software for Nonadiabatic Quantum Molecular Dynamics. The ab initio multiple spawning (AIMS) method enables nonadiabatic quantum molecular dynamics simulations in an arbitrary number of dimensions, with potential energy surfaces provided by electronic structure calculations performed on-the-fly. However, the intricacy of the AIMS algorithm complicates software development, deployment on modern shared computer resources, and postsimulation data analysis. PySpawn is a nonadiabatic molecular dynamics software package that addresses these issues. The program is designed to be easily interfaced with electronic structure software, and an interface to the TeraChem software package is described here. PySpawn introduces a task-based reorganization of the AIMS algorithm, allowing fine-grained restart capability and setting the stage for efficient parallelization in a future release""" ; sc:featureList edam:operation_0244, edam:operation_0387, edam:operation_2476 ; sc:name "PySpawn" ; sc:url "https://github.com/blevine37/pySpawn17" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC6505635", "pubmed:31114675" ; sc:description "Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive." ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "pysradb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/saketkc/pysradb" ; biotools:primaryContact "Saket Choudhary" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0196, edam:topic_3168, edam:topic_3474 ; sc:citation , "pubmed:33733362" ; sc:description "pysster (Sequence-Structure classifier) is a Python package for training and interpretation of convolutional neural networks on biological sequence data. Sequences are classified by learning sequence (and optionally structure) motifs and the package offers sensible default parameters, a hyper-parameter optimization procedure and options to visualize learned motifs." ; sc:featureList edam:operation_0267, edam:operation_3096, edam:operation_3925 ; sc:license "MIT" ; sc:name "pysster" ; sc:url "https://github.com/budach/pysster" ; biotools:primaryContact "Jiecong Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , "pubmed:34875008" ; sc:description "Python library for attractor identification and control in Boolean networks." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pystablemotifs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jcrozum/pystablemotifs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3047, edam:topic_3385 ; sc:citation ; sc:description "PySTACHIO (Python Single-molecule TrAcking stoiCHiometry Intensity and simulatiOn) is flexible, extensible, beginner-friendly and optimized program for analysis of single-molecule microscopy." ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_3799 ; sc:name "PySTACHIO" ; sc:url "https://github.com/ejh516/pystachio-smt" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3314, edam:topic_3474, edam:topic_3892 ; sc:citation ; sc:description "PySurf: A Framework for Database Accelerated Quantum Chemistry." ; sc:featureList edam:operation_0387, edam:operation_2476, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "PySurf" ; sc:url "http://github.com/mfsjmenger/pysurf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_3322, edam:topic_3452 ; sc:citation ; sc:description "Subtype and Stage Inference, or SuStaIn, is an algorithm for discovery of data-driven groups or \"subtypes\" in chronic disorders. This repository is the Python implementation of SuStaIn, with the option to describe the subtype progression patterns using either the event-based model, the piecewise linear z-score model or the scored events model." ; sc:featureList edam:operation_0547, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "pySuStaIn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ucl-pond/pySuStaIn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0821, edam:topic_3336, edam:topic_3375 ; sc:citation ; sc:description "Python library for work with genome scale metabolic models. This library contains functions to work with Genome Scale Metabolic Models with the goal of finding drug targets against cancer." ; sc:featureList edam:operation_2495, edam:operation_3439 ; sc:name "pyTARG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SergioBordel/pyTARG" ; biotools:primaryContact "Vytautas Raskevicius" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3244, edam:format_3651, edam:format_3654 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:23292976" ; sc:description "Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more." ; sc:featureList edam:operation_3767 ; sc:license "Apache-2.0" ; sc:name "Pyteomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.4.2" ; sc:url "http://packages.python.org/pyteomics/" ; biotools:primaryContact "Issue tracker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3318, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """A tool for Traction Force and Monolayer Stress Microscopy. pyTFM is a python package that allows you to analyze force generation and stresses in cells, cell colonies and confluent cell layers growing on a 2 dimensional surface. This package implements the procedures of Traction Force Microscopy and Monolayer Stress Microscopy. In addition to the standard measures for stress and force generation, it also includes the line tension, a measure for the force transfer exclusively across cell-cell boundaries. pyTFM includes an addon for the image annotation tool clickpoints allowing you to quickly analyze and vizualize large datasets.""" ; sc:featureList edam:operation_3435, edam:operation_3553 ; sc:license "GPL-3.0" ; sc:name "pyTFM" ; sc:url "https://pytfm.readthedocs.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0621, edam:topic_2275 ; sc:citation , "pubmed:36539938" ; sc:description "Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies." ; sc:featureList edam:operation_2476, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyThinFilm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/ATB-UQ/PyThinFilm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3318, edam:topic_3372, edam:topic_3382 ; sc:citation ; sc:description """Microscope is a Python package for the control of automated microscopes. It is easy to use and especially well suited for complex microscopes with hard timing requirements. It is aimed at those that are building their own microscopes or want programmatic control for microscope experiments.""" ; sc:featureList edam:operation_3436, edam:operation_3454, edam:operation_3552 ; sc:license "GPL-3.0" ; sc:name "Python-Microscope" ; sc:url "https://micronoxford.com/python-microscope-cockpit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3474 ; sc:description "PyTorch is an optimized tensor library for deep learning using GPUs and CPUs." ; sc:license "BSD-3-Clause" ; sc:name "PyTorch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pytorch.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3068, edam:topic_3974 ; sc:citation , "pmcid:PMC8977015", "pubmed:35366804" ; sc:description "A Python tool for calculating penetrance tables of high-order epistasis models." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "PyToxo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bglezseoane/pytoxo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC7725757", "pubmed:32500364" ; sc:description """An end-to-end analysis toolkit for eye tracking. This is a toolkit to analyse and visualize eye tracking data. It provides the following functionality:. After extraction of features, PyTrack can perform tests such as the student T-Test, Welch T-Test, ANOVA, RMANOVA, n-way ANOVA and Mixed ANOVA. The between and within group factors can be specified. This involves extraction of parameters or meta-data related to blinks, fixations, saccades, microsaccades and pupil diameter. The features extracted are as follows:.""" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "PyTrack" ; sc:url "https://pytrack-ntu.rtfd.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3047, edam:topic_3314 ; sc:citation , "pmcid:PMC8362049", "pubmed:34197646" ; sc:description "PyUNIxMD is an object-oriented Python program for molecular dynamics simulations involving multiple electronic states. It is mainly for studying the nonadiabatic dynamics of excited molecules." ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyUNIxMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/skmin-lab/unixmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3382 ; sc:citation , "pmcid:PMC9044207", "pubmed:35494872" ; sc:description "A Python framework for remote photoplethysmography." ; sc:featureList edam:operation_3695, edam:operation_3891, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pyVHR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://phuselab.github.io/pyVHR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0781, edam:topic_3376 ; sc:citation , "pmcid:PMC5219722", "pubmed:28061810" ; sc:description "Design gene knockouts in complex viruses with overlapping genes automatically." ; sc:featureList edam:operation_3095 ; sc:license "MIT" ; sc:name "Pyviko" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/louiejtaylor/pyViKO" ; biotools:primaryContact "Louis J. Taylor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3277, edam:topic_3382 ; sc:citation , "pubmed:33314210" ; sc:description """Visualization and Analysis of path sampling trajectories. Rare event methods applied to molecular simulations are growing in popularity, accessible and customizable software solutions have thus been developed and released. One of the most recent is PyRETIS, an open Python library for performing path sampling simulations. Here, we introduce PyVisA, a postprocessing package for path sampling simulations, which includes visualization and analysis tools for interpreting path sampling outputs. PyVisA integrates PyRETIS functionalities and aims to facilitate the determination of: (a) the correlation of the order parameter with other descriptors; (b) the presence of latent variables; and (c) intermediate meta-stable states. To illustrate some of the main PyVisA features, we investigate the proton transfer reaction in a protonated water trimer simulated via a simple polarizable model (Stillinger-David)""" ; sc:featureList edam:operation_0244, edam:operation_0387, edam:operation_3890 ; sc:name "PyVisA" ; sc:url "https://pyvisa.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0121, edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC9910386", "pubmed:36745440" ; sc:description "A Python Package for Visual Field Analysis." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyVisualFields" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mohaEs/PyVisualField" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293, edam:topic_3474 ; sc:citation "pubmed:26397960" ; sc:description "Open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution." ; sc:featureList edam:operation_3562 ; sc:name "Pyvolve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/sjspielman/pyvolve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:24990608" ; sc:description "PyMOL plugin to find conserved water molecules in X-ray protein structure." ; sc:featureList edam:operation_2423 ; sc:name "PyWATER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hiteshpatel379/PyWATER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0625, edam:topic_3170 ; sc:citation , "pmcid:PMC10359619", "pubmed:37399090" ; sc:description "Python package for weighted gene co-expression network analysis." ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyWGCNA" ; sc:url "http://pypi.org/project/PyWGCNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3382 ; sc:citation , "pubmed:37540469" ; sc:description "pyWitness is a python package to manipulate, process, model, fit eyewitness recognition memory data, and create simulations. It is written in python, but by employing reticulate, you can use it with R too." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "pyWitness" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lmickes.github.io/pyWitness/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2828, edam:topic_3452 ; sc:citation , "pubmed:32153299" ; sc:description """an open-source package for 2D X-ray near-edge spectroscopy analysis. PyXAS is a python library for fast 2D/3D XANES analysis with graphic user interface (GUI) provided.""" ; sc:featureList edam:operation_0337, edam:operation_3214, edam:operation_3443 ; sc:name "PyXAS" ; sc:url "https://github.com/gmysage/pyxas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3382, edam:topic_3520, edam:topic_3542 ; sc:citation , , "pmcid:PMC7380677", "pubmed:32557917" ; sc:description """A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system. PyXlinkViewer is a cross-platform plugin for the widely-used PyMOL molecular graphics system designed to enable rapid visualisation of protein crosslinking-mass spectrometry (XL-MS) data.""" ; sc:featureList edam:operation_0320, edam:operation_0337, edam:operation_0477 ; sc:license "GPL-3.0" ; sc:name "PyXlinkViewer" ; sc:url "https://github.com/BobSchiffrin/PyXlinkViewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3304, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9161555", "pubmed:35663407" ; sc:description "An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "PyZebrascope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KawashimaLab/PyZebraScope_public" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:34240105" ; sc:description "An ultra-fast amino acid sequence similarity search server against public metagenomes." ; sc:featureList edam:operation_0310, edam:operation_0346, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:name "PZLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pzlast.riken.jp/meta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33332269" ; sc:description "Hyperspectral Image Super-Resolution via Deep Progressive Zero-Centric Residual Learning." ; sc:featureList edam:operation_3435 ; sc:license "MIT" ; sc:name "PZRes-Net" ; sc:url "https://github.com/zbzhzhy/PZRes-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3176 ; sc:citation ; sc:description "Saturation-based ChIP-seq and ChIP-nexus caller. Q works with the irreproducible discovery rate (IDR) procedure. Q can be run with or without data from a control experiment." ; sc:featureList edam:operation_3215 ; sc:license "BSD-3-Clause" ; sc:name "Q" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://charite.github.io/Q/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_3512, edam:topic_3519 ; sc:citation , "pmcid:PMC5097360", "pubmed:27814676" ; sc:description "Q-nexus is a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control." ; sc:featureList edam:operation_2403 ; sc:license "Other" ; sc:name "Q-nexus" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v1.3.0" ; sc:url "http://charite.github.io/Q/" ; biotools:primaryContact "Peter Hansen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3170, edam:topic_3360, edam:topic_3473 ; sc:citation , "pmcid:PMC8627836", "pubmed:34819397" ; sc:description "Smart Software for Assisting Oncology and Cancer Research." ; sc:featureList edam:operation_0224, edam:operation_2940, edam:operation_2943, edam:operation_3503 ; sc:isAccessibleForFree true ; sc:name "Q-omics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://qomics.sookmyung.ac.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC10272742", "pubmed:37332588" ; sc:description "Quantitative vascular analysis tool." ; sc:featureList edam:operation_3359, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Q-VAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bramcal/Q-VAT.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071, edam:topic_3473 ; sc:citation , "pubmed:33588537" ; sc:description "High-throughput design of Peierls and charge density wave phases in Q1D organometallic materials." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3454 ; sc:name "Q1D" ; sc:url "https://moldis.tifrh.res.in/data/rmq1d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3168, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description """Optimizing taxonomic classification of marker gene amplicon sequences. QIIME 2 plugin supporting taxonomic classification. This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org""" ; sc:featureList edam:operation_3225, edam:operation_3435, edam:operation_3460 ; sc:license "BSD-3-Clause" ; sc:name "q2-feature-classifier" ; sc:url "https://github.com/qiime2/q2-feature-classifier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC9665871", "pubmed:36130056" ; sc:description "Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "q2-fondue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/bokulich-lab/q2-fondue" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC6759219", "pubmed:31552137" ; sc:description "machine-learning tools for microbiome classification and regression | QIIME 2 plugin for machine learning prediction of sample data | Microbiome studies often aim to predict outcomes or differentiate samples based on their microbial compositions, tasks that can be efficiently performed by supervised learning methods. The q2-sample-classifier plugin makes these methods more accessible, reproducible, and interpretable to a broad audience of microbiologists, clinicians, and others who wish to utilize supervised learning methods for predicting sample characteristics based on microbiome composition or other \"omics\" data" ; sc:featureList edam:operation_3659 ; sc:license "BSD-3-Clause" ; sc:name "q2-sample-classifier" ; sc:url "https://github.com/qiime2/q2-sample-classifier" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_2182 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_2182 ; sc:name "Nucleic acid sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697 ; sc:author "Adam Rivers", "Kyle Weber" ; sc:description "q2_ITSxpress: a Qiime2 plugin for ITSxpress, software to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files" ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "q2_ITSxpress" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "v1.6.0" ; sc:url "https://github.com/USDA-ARS-GBRU/q2_itsxpress" ; biotools:primaryContact "Adam Rivers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:22125256" ; sc:description "MATLAB library that uses constrained fuzzy logic models based on prior knowledge networks to address two questions about a biological system: 1) What perturbation results in a specified downstream effect? and 2) In what environments do those perturbations produce that effect?" ; sc:featureList edam:operation_3439 ; sc:name "Q2LM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/saezrodriguez/cno/matlab/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:30525668" ; sc:description "A software tool that rapidly checks the signal from all heavy labeled peptides and flags those that fail quality control metrics in targeted proteomics experiments." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Q4SRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/PNNL-Comp-Mass-Spec/Q4SRM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3855 ; sc:citation , "pmcid:PMC6287880", "pubmed:30532242" ; sc:description "The quantum tensor contraction handler." ; sc:featureList edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "qTorch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/aspuru-guzik-group/qtorch" ; biotools:primaryContact "N. Sawaya", "S. Fried" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:23700309" ; sc:description "QA-RecombineIt is a web server for quality assessment and recombination of 3D protein models." ; sc:featureList edam:operation_0321, edam:operation_0322, edam:operation_0477, edam:operation_0481, edam:operation_3455 ; sc:name "QA-RecombineIt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iimcb.genesilico.pl/qarecombineit/" ; biotools:primaryContact "Marcin Pawlowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC7339533" ; sc:description """QSAR-derived Affinity Fingerprints (part 2): modeling performance for cytotoxicity prediction. To generate the results in our paper run run_QAFFP.py as indicated in the file launch_all.sh. All the data sets used in the publications are in the folder: sdf_files.""" ; sc:featureList edam:operation_2489, edam:operation_3216, edam:operation_3659 ; sc:name "QAFFP" ; sc:url "https://github.com/isidroc/QAFFP_regression" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:33051648" ; sc:description """Aligning nanopore reads accurately using current-level modeling. QAlign is a tool to apply quantization for nanopore long reads.""" ; sc:featureList edam:operation_0292, edam:operation_3198, edam:operation_3216, edam:operation_3227 ; sc:license "MIT" ; sc:name "QAlign" ; sc:url "https://github.com/joshidhaivat/QAlign.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3384 ; sc:citation ; sc:description "QALMA (Quality Assurance for Linac with MATLAB), a MALAB toolkit which aims to simplify the quantitative analysis of quality assurance for medical linear accelerator." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "QALMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "V1" ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX-D-17-00089" ; biotools:primaryContact "Georgios Kalantzis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_0781, edam:topic_3168, edam:topic_3324 ; sc:citation , "pmcid:PMC7227348", "pubmed:32414327" ; sc:description """An integrated software for virus community sequencing data analysis. QAP (Quasispecies Analysis Package) is an integrated software to analyze viral quasispecies (QS) high through-put sequencing data, including next generation sequencing (NGS) and third generation sequencing (TGS) data.""" ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "QAP" ; sc:url "https://github.com/mingjiewang/qap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0199, edam:topic_3170, edam:topic_3321 ; sc:citation ; sc:description "RNA-seq Quantification of Alternative Polyadenylation." ; sc:featureList edam:operation_0428 ; sc:license "GPL-3.0" ; sc:name "QAPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/morrislab/qapa" ; biotools:primaryContact "Benjamin J. Blencowe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3520 ; sc:citation "pubmed:23729472" ; sc:description "The QARIP (Quantitative Analysis of Regulated Intramembrane Proteolysis) web-server aids in the quantitative and qualitative analysis of proteomics-based regulated intramembrane proteolysis (RIP) data." ; sc:featureList edam:operation_0270, edam:operation_2436, edam:operation_2929, edam:operation_3630 ; sc:name "QARIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webclu.bio.wzw.tum.de/qarip/" ; biotools:primaryContact "D. Frishman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Quality Assessment of Protein Structure" ; sc:featureList edam:operation_2945 ; sc:name "qaspro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/qaspro/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:description "Quantitative Analysis and Visualization of PET Images (QAV-PET) is an open-source software implemented in the popular MATLAB coding environment that allows easy, intuitive, and efficient visualization and quantification of multi-modal medical images." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "QAV-PET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/45923-brentfoster-qav-pet" ; biotools:primaryContact "Brent Foster" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3987 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:description """Qiime2 artifacts are structured compressed archives containing a dataset (e.g., FASTQ reads, representative sequences in FASTA format, a phylogenetic tree in Newick format, etc.) and an exhaustive set of metadata (including the command that generated it, information on the execution environment, citations on the used software, and all the metadata of the artifacts used to produce it). While artifacts can improve the shareability and reproducibility of Qiime workflows, they are less easily integrated with general bioinformatics pipelines, and even accessing metadata in the artifacts requires the full Qiime2 installation (not to mention that every release of Qiime2 will produce incompatible artifacts). Qiime Artifact Extractor (qxa) allows to easily interface with Qiime2 artifacts from the command line, without needing the full Qiime2 environment installed.""" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Qiime Artifact eXtractor (qax)" ; sc:softwareHelp ; sc:softwareVersion "0.3", "0.5", "0.9" ; sc:url "https://github.com/telatin/qax" ; biotools:primaryContact "Andrea Telatin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0798, edam:topic_3169, edam:topic_3173, edam:topic_3517 ; sc:citation ; sc:description """a novel genome browser visualization for point processes. Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as CADD scores and GWAS eQTL hits, and may have broad utility to the genomics community""" ; sc:featureList edam:operation_3208, edam:operation_3227, edam:operation_3435 ; sc:name "qBED" ; sc:url "http://epigenomegateway.wustl.edu/browser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3383, edam:topic_3572 ; sc:citation ; sc:description "Quality of biological images, reconstructed using localization microscopy data." ; sc:featureList edam:operation_3443 ; sc:name "qbioimages" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/blazi13/qbioimages/blob/master/storm_simulation_movie.py" ; biotools:primaryContact "Błażej Ruszczycki", "Tytus Bernas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24508279" ; sc:description "Package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences." ; sc:featureList edam:operation_3218 ; sc:name "QC-Chain" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://computationalbioenergy.org/qc-chain.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0821, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description """qc3C - reference-free quality control for Hi-C DNA sequencing libraries. The primary aim of qc3C is to infer the proportion of "signal" within a Hi-C sequencing library and thereby provide a means of quality control. A big advantange of qc3C is that this can be done without access to a reference sequence, which until now has been a significant stopping point for projects not involving model organisms.""" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3218, edam:operation_3472 ; sc:license "AGPL-3.0" ; sc:name "qc3C" ; sc:url "https://github.com/cerebis/qc3C" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2316 ; sc:name "Cell line name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1187 ; sc:name "PubMed ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "QC Genomics is a public resource providing a central access to the largest collection of genomic data. It allows scientists to browse, visualize, compare, and analyze thousands of publicly available genomic data sets." ; sc:featureList edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "qcGenomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ngs-qc.org/qcgenomics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3512 ; sc:description "Tool to calculate relative mRNA Gene Expression." ; sc:featureList edam:operation_0308 ; sc:name "qcalculator" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.gene-quantification.de/download.html#qcalculator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples." ; sc:featureList edam:operation_0484, edam:operation_3197 ; sc:name "QCALL" ; sc:url "http://www.sanger.ac.uk/" ; biotools:primaryContact "Richard Durbin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "Integrates diverse clustering algorithms and an interactive heatmap display interface. It directly imports raw experimental data in a matrix format and displays these data in a heatmap." ; sc:featureList edam:operation_3432 ; sc:name "QCanvas" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://compbio.sookmyung.ac.kr/~qcanvas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3517, edam:topic_3572 ; sc:citation ; sc:description "Tools for (automated and manual) quality control of the results of Epigenome-Wide Association Studies." ; sc:featureList edam:operation_2428 ; sc:name "QCEWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/QCEWAS/" ; biotools:primaryContact "Ilja Nolte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3517, edam:topic_3572 ; sc:citation "pubmed:24395754" ; sc:description "R package that automates the quality control of genome-wide association result files." ; sc:featureList edam:operation_3218 ; sc:name "QCGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/QCGWAS/" ; biotools:primaryContact "Peter J. van der Most" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3316, edam:topic_3520 ; sc:citation , , "pubmed:29324744", "pubmed:33724836" ; sc:description "An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories." ; sc:featureList edam:operation_0337, edam:operation_2428 ; sc:name "QCloud2" ; sc:softwareHelp , , , , ; sc:url "https://qcloud2.crg.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:citation ; sc:description "NGS reads clustering" ; sc:featureList edam:operation_0291, edam:operation_0310 ; sc:license "Other" ; sc:name "QCluster" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.dei.unipd.it/~ciompin/main/qcluster.html" ; biotools:primaryContact "Matteo Comin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3033 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3508 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092, edam:topic_0121, edam:topic_0622, edam:topic_3053, edam:topic_3393, edam:topic_3520, edam:topic_3572 ; sc:citation ; sc:description "The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats." ; sc:featureList edam:operation_2409, edam:operation_2428, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "qcmetrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/qcmetrics.html" ; biotools:primaryContact "Laurent Gatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_2229, edam:topic_3520 ; sc:citation , "pubmed:36154077" ; sc:description "The Quantitative Cell Proteomic Atlas is a comprehensive panel of targeted proteomic assays to profile activation of biochemical pathways in cancer cells." ; sc:featureList edam:operation_0314, edam:operation_0417, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "QCPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://qcpa.mskcc.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_3360, edam:topic_3520 ; sc:citation , "pubmed:30942071" ; sc:description """A Web Tool for the Automated Assessment of Protein Expression and Data Quality of Labeled Mass Spectrometry Experiments. QCQuan is for "separating the wheat from the chaff", i.e. quickly assessing whether or not your experiment(s) produced useful information. The differential expression analysis is based on simple statistical procedures, but any protein found to be differential using QCQuan should also be found differential by other, more complex methods.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:name "QCQuan" ; sc:url "http://qcquan.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814 ; sc:citation ; sc:description "New method to evaluate the quality of structure predictions, especially for template free structure prediction. It captures both global and local structural features, with emphasis on global topology." ; sc:featureList edam:operation_0271, edam:operation_0474, edam:operation_2423, edam:operation_2428, edam:operation_2479 ; sc:name "QCS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/QCS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2269, edam:topic_3393 ; sc:citation , "pubmed:33346821" ; sc:description "Issues Of Z-factor and an approach to avoid them for quality control in high-throughput screening studies." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "qcSSMDhomo" ; sc:url "https://github.com/Karena6688/qcSSMDhomo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:description "Basic quality control of gwas datasets. Compute per-sample and per-SNP summary statistics for a cohort, and use these to filter out samples and SNPs (either by removing them from the files or by writing exclusion lists). It can also be used to perform various subsetting and merging operations, and to manipulate sample information in preparation for association testing." ; sc:featureList edam:operation_3218 ; sc:license "MIT" ; sc:name "QCTOOL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v2" ; sc:url "http://www.well.ox.ac.uk/~gav/qctool/#overview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3070 ; sc:citation "pubmed:18351912" ; sc:description "Detect communities at a much finer scale or with a higher accuracy than other existing algorithms." ; sc:featureList edam:operation_3083, edam:operation_3432 ; sc:name "Qcut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cs.utsa.edu/~jruan/Software.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_2330 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Query-driven module discovery in microarray data." ; sc:featureList edam:operation_2495 ; sc:name "QDB (Query Driven Biclustering)" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "2.4.1" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Dhollander_2007/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC8100226", "pubmed:33967730" ; sc:description "QDECR is an R package to perform vertex-wise analyses on cortical surface maps. It is an attempt to enrich vertex-wise analyses with features commonly found in R, such as easy design matrix creation, using multiply imputed datasets, handling complex formulas, etc. Users familiar with R will immediately notice that the package works similar to most other statistical models in R." ; sc:featureList edam:operation_3557, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "QDECR" ; sc:url "https://www.qdecr.com" ; biotools:primaryContact "Sander Lamballais" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:citation ; sc:description """distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks. Protein model quality estimation, in many ways, informs protein structure prediction. Despite their tight coupling, existing model quality estimation methods do not leverage inter-residue distance information or the latest technological breakthrough in deep learning that has recently revolutionized protein structure prediction. Results We present a new distance-based single-model quality estimation method called QDeep by harnessing the power of stacked deep residual neural networks (ResNets). Our method first employs stacked deep ResNets to perform residue-level ensemble error classifications at multiple predefined error thresholds and then combines the predictions from the individual error classifiers for estimating the quality of a protein structural model""" ; sc:featureList edam:operation_0321, edam:operation_0475, edam:operation_0477 ; sc:name "QDeep" ; sc:url "https://github.com/Bhattacharya-Lab/QDeep" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102 ; sc:citation , "pubmed:34473228" ; sc:description "QDistance is a global and local model quality estimation algorithm using predicted inter-residue distance by trRosetta. It supports inputs of both single model and multiple models." ; sc:featureList edam:operation_0474, edam:operation_3092, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "QDistance" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://yanglab.nankai.edu.cn/QDistance" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC4248318", "pubmed:25236618" ; sc:description "Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "QDNAseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QDNAseq.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0654, edam:topic_3169, edam:topic_3300 ; sc:citation , "pmcid:PMC7641308", "pubmed:32544226" ; sc:description """a method to quantitatively assess RNA-DNA hybrid formation genome-wide. R-loops are dynamic, co-transcriptional nucleic acid structures that facilitate physiological processes but can also cause DNA damage in certain contexts. Perturbations of transcription or R-loop resolution are expected to change their genomic distribution. Next-generation sequencing approaches to map RNA-DNA hybrids, a component of R-loops, have so far not allowed quantitative comparisons between such conditions. Here, we describe quantitative differential DNA-RNA immunoprecipitation (qDRIP), a method combining synthetic RNA-DNA-hybrid internal standards with high-resolution, strand-specific sequencing. We show that qDRIP avoids biases inherent to read-count normalization by accurately profiling signal in regions unaffected by transcription inhibition in human cells, and by facilitating accurate differential peak calling between conditions""" ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3799 ; sc:name "qDRIP" ; sc:url "https://github.com/cimprichlab/crossley_et_al_2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0654, edam:topic_3306, edam:topic_3315 ; sc:citation ; sc:description "Q-FADD (Quantitation of Fluorescence Accumulation after DNA Damage) method, which enhances the analytical power of the widely used laser microirradiation technique." ; sc:featureList edam:operation_0477, edam:operation_2476, edam:operation_3799 ; sc:license "MIT" ; sc:name "qFADDpy" ; sc:url "https://qfadd.colorado.edu/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:description "A part of PLINK as a somewhat ad-hoc procedure to perform family-based tests of association with quantitative phenotypes." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "QFAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cog-genomics.org/plink/1.9/fam_assoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_0121, edam:topic_3520 ; sc:description "QFeatures is a Bioconductor package that provides infrastructure to management and process quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manage quantitative data across different assay levels (such as precursors, peptide spectrum matches, peptides and proteins or protein groups) in a coherent and tractable format." ; sc:license "Artistic-2.0" ; sc:name "qfeatures" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/release/bioc/html/QFeatures.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0611, edam:topic_2828, edam:topic_3336 ; sc:citation ; sc:description """Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. qFit is a collection of programs for modeling multi-conformer protein structures. Electron density maps obtained from high-resolution X-ray diffraction data are a spatial and temporal average of all conformations within the crystal. qFit evaluates an extremely large number of combinations of sidechain conformers, backbone fragments and small-molecule ligands to locally explain the electron density.""" ; sc:featureList edam:operation_0321, edam:operation_0479, edam:operation_0480, edam:operation_0481 ; sc:license "MIT" ; sc:name "qFit 3" ; sc:url "https://github.com/ExcitedStates/qfit-3.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0780, edam:topic_3293 ; sc:citation , "pmcid:PMC10260390", "pubmed:37285316" ; sc:description "Quartet Fiduccia-Mattheyses revisited for larger phylogenetic studies." ; sc:featureList edam:operation_0544, edam:operation_0548, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "QFM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sharmin-mim/qfm_java" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Comparative analyses of QTL (Quantitative Trait Locus) mapping data sets." ; sc:featureList edam:operation_0282, edam:operation_2429 ; sc:name "QGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.3.10" ; sc:url "http://www.qgene.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0602, edam:topic_2269, edam:topic_3055 ; sc:citation , "pubmed:31883004" ; sc:description """an R package for large-scale quantitative genetic analyses. Statistical tools for Quantitative Genetic Analyses. An R package for Quantitative Genetic and Genomic analyses. Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses. Rohde et al. (2019) . The qgg package was developed based on the hypothesis that certain regions on the genome, so-called genomic features, may be enriched for causal variants affecting the trait. Several genomic feature classes can be formed based on previous studies and different sources of information such as genes, chromosomes or biological pathways""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "qgg" ; sc:url "http://psoerensen.github.io/qgg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123 ; sc:citation "pubmed:15215360" ; sc:description "Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins." ; sc:featureList edam:operation_0321, edam:operation_0393, edam:operation_0405, edam:operation_3432 ; sc:name "Qgrid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://qgrid.readthedocs.io/en/latest/" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0749, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:22576365" ; sc:description "QGRS-H Predictor is a webserver that maps and analyzes phylogenetically conserved putative Quadruplex forming ??G??-Rich Sequences (QGRS) in the mRNAs, ncRNAs and other nucleotide sequences. QGRS-H Predictor generates information on composition and distribution of putative homologous G-quadruplexes in semi-globally aligned nucleotide sequences based on published algorithms." ; sc:featureList edam:operation_0415, edam:operation_0429, edam:operation_0438, edam:operation_2429 ; sc:name "QGRS-H Predictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://quadruplex.ramapo.edu/qgrs/app/start" ; biotools:primaryContact "Dr. Paramjeet Bagga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_0160, edam:topic_3168, edam:topic_3320 ; sc:citation "pubmed:16845096" ; sc:description "Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene." ; sc:featureList edam:operation_0232, edam:operation_0239, edam:operation_0429 ; sc:name "QGRS Mapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ramapo.edu/QGRS/index.php" ; biotools:primaryContact "Lawrence D'Antonio", "Manuel Viotti", "Oleg Kikin", "Paramjeet Bagga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3055, edam:topic_3512, edam:topic_3517 ; sc:citation ; sc:description """Quantitative Genetic Scoring, or how to put a number on an arbitrary genetic region. QGS: Quantitative Genetic Scoring. QGS is a computer program to create genetic variables from SNP data. For every individual, it calculates the genetic distance to a reference population. QGS works with both VCF or PLINK format data.""" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3799, edam:operation_3891, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "QGS" ; sc:url "https://github.com/machine2learn/QGS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:name "Workflow metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_1957 ; sc:name "Raw image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:name "Experimental measurement" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382 ; sc:description """Qiber3D is an open-source software package for the morphometric quantification of networks from 3D image stacks. Qiber3D combines the required tools for a complete analytical workflow, from the raw image to final measured values.""" ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Qiber3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.7" ; sc:url "https://github.com/theia-dev/Qiber3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3360, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7070161", "pubmed:32206688" ; sc:description "a web-based tool for utilizing, sharing, and building image-processing pipelines." ; sc:featureList edam:operation_3443, edam:operation_3799, edam:operation_3937 ; sc:name "QIFP" ; sc:url "https://qifp.stanford.edu/qifp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "Open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. The pipeline is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations." ; sc:featureList edam:operation_2945 ; sc:name "QIIME" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://qiime.org/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Suite" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation ; sc:description "QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3218, edam:operation_3460, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "QIIME 2" ; sc:softwareHelp , , ; sc:softwareVersion "2.0" ; sc:url "https://qiime2.org" ; biotools:primaryContact "Greg Caporaso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:description "QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3218, edam:operation_3460, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "qiime_add_on" ; sc:url "http://qiime.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:description "QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3218, edam:operation_3460, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "qiime_core" ; sc:url "http://qiime.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_3172, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC9344843", "pubmed:35731214" ; sc:description "Identifying interactions in omics data for clinical biomarker discovery using symbolic regression." ; sc:featureList edam:operation_3557, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "QLattice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/abzu-ai/QLattice-clinical-omics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3293 ; sc:citation , ; sc:description """Fast and accurate method to estimate empirical models of protein evolution. Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow. In this paper, we propose QMaker, a new ML method to estimate a general time-reversible Q matrix from a large protein dataset consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites""" ; sc:featureList edam:operation_0324, edam:operation_0477, edam:operation_0492 ; sc:name "QMaker" ; sc:url "http://www.iqtree.org/#download" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0769, edam:topic_3314, edam:topic_3315, edam:topic_3316 ; sc:citation , "pubmed:32384844" ; sc:description """Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion quantum Monte Carlo. Effective core potentials (pseudopotentials) in formats suitable for QMCPACK and many quantum chemical and electronic structure codes are available at https://pseudopotentiallibrary.org.""" ; sc:featureList edam:operation_3907 ; sc:name "QMCPACK" ; sc:url "https://qmcpack.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2815, edam:topic_3277, edam:topic_3337, edam:topic_3518 ; sc:citation "pubmed:19439685" ; sc:description "QMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used." ; sc:featureList edam:operation_0321, edam:operation_0331, edam:operation_0477, edam:operation_3459 ; sc:name "QMEAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://swissmodel.expasy.org/qmean" ; biotools:primaryContact "Gabriel Studer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_3500 ; sc:citation , "pubmed:32045715" ; sc:description """A new approach for quantifying mitochondrial genome rearrangement. qMGR is an algorithm used to study the rearrangement of mitochondrial genomes. Using it, we can calculate rearrangement frequency of a single gene or rearrangement score of a single genome in a certain population. 1. Input a benchmark arrangement. please choose... Typical vertebrate arrangement Typical invertebrate arrangement. 2. Input one or more mitogenome arrangements in a taxon.""" ; sc:featureList edam:operation_3799 ; sc:license "LGPL-3.0" ; sc:name "qMGR" ; sc:url "http://qmgr.hnnu.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description "This is the Qmin - Mineral Chemistry Virtual Assistant. The models herein presented perform mineral classification, missing value imputation by multivariate regression and mineral formula prediction by several Random Forest classification and regression nested models." ; sc:featureList edam:operation_3431, edam:operation_3454, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Qmin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apps.cprm.gov.br/qmin/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071, edam:topic_3344 ; sc:citation "pubmed:26819474" ; sc:description "Quick and easy way to check the status of biomedical research on Galaxy and review your history." ; sc:featureList edam:operation_2409 ; sc:name "QMLGalaxyPortal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Tarostar/QMLGalaxyPortal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3306 ; sc:citation ; sc:description "NAMD QM/MM interface extends existing NAMD features to the quantum mechanical level, presenting features that are not yet available in any QM/MM implementation." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Hybrid QM-MM NAMD" ; sc:softwareHelp ; sc:url "http://www.ks.uiuc.edu/Research/qmmm/" ; biotools:primaryContact "Marcelo C R Melo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0092, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:11552684" ; sc:description "Program for visualizing protein structures on Windows-based computers." ; sc:featureList edam:operation_0570, edam:operation_2406 ; sc:name "QMol" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0654 ; sc:citation , "pmcid:PMC4489302", "pubmed:25883153" ; sc:description "Model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences." ; sc:featureList edam:operation_0278, edam:operation_2481 ; sc:name "QmRLFS-finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder" ; biotools:primaryContact "Piroon Jenjaroenpun", "Thidathip Wongsurawat", "Vladimir Kuznetsov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3517, edam:topic_3572 ; sc:citation , "pmcid:PMC3340416", "pubmed:22262732" ; sc:description "A powerful test that directly incorporates sequencing qualities in association tests with multiple rare variants. It allows for the adjustment of additional covariates and is robust towards the inclusion of noncausal variants and variants having effects with different magnitudes and directions. Furthermore, it can coherently account for missing genotypes and conjoin in a principled way individuals or variants sequenced at varying coverage depths." ; sc:featureList edam:operation_2238 ; sc:license "Not licensed" ; sc:name "qMSAT" ; sc:operatingSystem "Linux" ; sc:url "http://qmsat.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3053 ; sc:citation ; sc:description "Simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. It can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions." ; sc:featureList edam:operation_3196 ; sc:name "QMSIM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10" ; sc:url "http://www.aps.uoguelph.ca/~msargol/qmsim/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0154 ; sc:citation , "pmcid:PMC9798252", "pubmed:36519304" ; sc:description "Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_3901, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "qNABpredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biomine.cs.vcu.edu/servers/qNABpredict/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:17119010" ; sc:description "Software package written in Java for generating phylogenetic networks from quartet data." ; sc:featureList edam:operation_3439 ; sc:name "QNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/qnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3172, edam:topic_3474 ; sc:citation "pubmed:23231464" ; sc:description "Python implementation of a method for searching large metagenomic dataset to identify qnr fluoroquinolone antibiotic resistance genes." ; sc:featureList edam:operation_0338 ; sc:name "qnr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.math.chalmers.se/qnr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Aligner for three or more sequences. Used for phylogenetic analysis and identification of conserved motifs." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_0492 ; sc:name "QOMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://www.cise.ufl.edu/~tamer/other_files/msa.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:18689821" ; sc:description "Alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms." ; sc:featureList edam:operation_0292 ; sc:name "Qpalma" ; sc:softwareHelp ; sc:url "http://www.fml.mpg.de/raetsch/projects/qpalma" ; biotools:primaryContact "Gunnar Rätsch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3519 ; sc:citation ; sc:description "The package contains functions to perform normalization of high-throughput qPCR data. 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It contains notes on how and where each data was processed.""" ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3443 ; sc:name "QSIPrep" ; sc:url "https://pennlinc.github.io/qsiprep_paper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3316, edam:topic_3384 ; sc:citation ; sc:description "QSMxT is a complete and end-to-end QSM processing and analysis framework that excels at automatically reconstructing and processing QSM for large groups of participants." ; sc:featureList edam:operation_3431, edam:operation_3454, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "QSMxT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/QSMxT/QSMxT" ; biotools:primaryContact "Ashley Wilton Stewart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3934 ; sc:citation , "pmcid:PMC7755412", "pubmed:32663244" ; sc:description """quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets. Non-parametric dimensionality reduction techniques, such as t-distributed stochastic neighbor embedding (t-SNE), are the most frequently used methods in the exploratory analysis of single-cell datasets. Current implementations scale poorly to massive datasets and often require downsampling or interpolative approximations, which can leave less-frequent populations undiscovered and much information unexploited.

Results< h4>We implemented a fast t-SNE package, qSNE, which uses a quasi-Newton optimizer, allowing quadratic convergence rate and automatic perplexity (level of detail) optimizer""" ; sc:featureList edam:operation_3935 ; sc:name "qSNE" ; sc:url "https://bitbucket.org/anthakki/qsne/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3383 ; sc:citation ; sc:description "Software package for quantitative analysis of single molecule localization microscopy data in live and fixed cells." ; sc:featureList edam:operation_3443 ; sc:license "CC-BY-4.0" ; sc:name "qSR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/cisselab/qSR" ; biotools:primaryContact "I. I. Cissé" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:19239711" ; sc:description "Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality." ; sc:featureList edam:operation_0310 ; sc:name "QSRA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mocklerlab.org/tools/2" ; biotools:primaryContact "Mockler Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2259, edam:topic_2640, edam:topic_2815, edam:topic_3300 ; sc:citation ; sc:description "Analyze lineage- and mutation-specific cell surface transcriptome marker from patient cancer samples. It is a fast and efficient tool to find novel tumor-specific cell surface markers for advanced cancer therapies." ; sc:featureList edam:operation_3197 ; sc:name "QSurface" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.sookmyung.ac.kr/~qsurface/" ; biotools:primaryContact "Sukjoon YoonEmail author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3306 ; sc:citation , "pubmed:31532987" ; sc:description "Quality Threshold Clustering of Molecular Dynamics | Clustering Molecular Dynamics trajectories is a common analysis that allows grouping together similar conformations. Several algorithms have been designed and optimized to perform this routine task and among them, Quality Threshold (QT) stands as a very attractive option. QT guarantees that in retrieved clusters, no pair of frames will have a similarity value greater than a specified threshold and hence a set of strongly correlated frames is obtained for each cluster. For more information about QT, please refer to Heyer et. al. work (Heyer, L. J.; Kruglyak, S.; Yooseph, S. Exploring Expression Data: Identification and Analysis of Coexpressed Genes. 1999, No. 213, 1106–1115. Genome Research) | Python Implementation of Quality Threshold Clustering for Molecular Dynamics | A python implementation of Heyer, 1999's Quality Threshold clustering algorithm specialized for molecular dynamics trajectories" ; sc:featureList edam:operation_2476, edam:operation_3432, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "Quality Threshold Clustering Molecular Dynamics" ; sc:url "https://github.com/rglez/QT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3303, edam:topic_3376 ; sc:citation , "pmcid:PMC310826", "pubmed:10568750" ; sc:description "Some simple MATLAB files that perform QT clustering" ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "QT Clustering using Euclidean Distance, Jackknife Correlation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/26432-qt-clustering-using-euclidean-distance-jackknife-correlation" ; biotools:primaryContact "Misha Koshelev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0218, edam:topic_3474 ; sc:citation ; sc:description "Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data." ; sc:featureList edam:operation_0553, edam:operation_3557, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "QT-GILD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pythonLoader/QT-GILD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation , ; sc:description "> CORRECT NAME OF TOOL COULD ALSO BE 'local dependence' | quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data | A new local covariance matrix estimation for the classification of gene expression profiles in RNA-Seq data | This package provides an R function to classify RNA-Seq gene expression profiles" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3800 ; sc:license "MIT" ; sc:name "qtQDA" ; sc:url "https://github.com/goknurginer/qtQDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "It provides a one-stop interface for family based tests of linkage disequilibrium. The general models are supported, and can be used to analyse quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested." ; sc:featureList edam:operation_0488 ; sc:license "BSD-3-Clause" ; sc:name "QTDT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csg.sph.umich.edu/abecasis/qtdt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:34406385" ; sc:description "qTeller is a comparative RNA-seq expression platform to compare expression across multiple data sources in a user-provided gene list or genomic interval, or to visually compare expression between two genes." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_2495, edam:operation_3216, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "qTeller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://qteller.maizegdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:18720898" ; sc:description "QTL linkage analysis program. It calculates a wide variety of QTL linkage statistics for nuclear families. Score statistics are emphasized, as are statistics appropriate for ascertained (nonpopulation) samples such as concordant and discordant sibling pairs. Currently, only sib-pair and sibship data are supported, but we plan to extend the capability to arbitrary pedigrees soon." ; sc:featureList edam:operation_0283 ; sc:name "QTL-ALL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://watson.hgen.pitt.edu/register/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC6643884", "pubmed:31092608" ; sc:description "Testing Pleiotropy vs. Separate QTL in Multiparental Populations." ; sc:featureList edam:operation_0282, edam:operation_2238, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "qtl2pleio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fboehm/qtl2pleio" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL." ; sc:featureList edam:operation_2421, edam:operation_2429 ; sc:name "QTLBIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.7" ; sc:url "http://pages.stat.wisc.edu/~yandell/qtl/software/qtlbim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC7687904", "pubmed:33235230" ; sc:description """comprehensive QTL annotation of GWAS results. This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs).""" ; sc:featureList edam:operation_0282, edam:operation_3226, edam:operation_3232, edam:operation_3661, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Qtlizer" ; sc:url "https://bioconductor.org/packages/release/bioc/html/Qtlizer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_3053 ; sc:citation ; sc:description "Mapping Quantitative Trait Loci (QTLs) with Additive Effects, Epistatic Effects and QTL Environment Interactions." ; sc:featureList edam:operation_2429 ; sc:name "QTLMapper" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6" ; sc:url "http://ibi.zju.edu.cn/software/qtlmapper/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation , , , "pubmed:17459962" ; sc:description "QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines." ; sc:featureList edam:operation_2429 ; sc:name "QTLNETWORK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://ibi.zju.edu.cn/software/qtlnetwork/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_3056 ; sc:citation ; sc:description "Tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps." ; sc:featureList edam:operation_3232 ; sc:license "CC-BY-NC-4.0" ; sc:name "QTLtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://qtltools.github.io/qtltools/" ; biotools:primaryContact "Halit Ongen", "Olivier Delaneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3300 ; sc:citation , "pmcid:PMC9339332", "pubmed:35703938" ; sc:description "An interactive webtool for genetic analysis in the Collaborative Cross and Diversity Outbred mouse populations." ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_3196, edam:operation_3232 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QTLViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://qtlviewer.jax.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "It is a command-line tool to retrieve and semantically annotate results obtained from QTL mapping experiments. It takes full-text articles from the Europe PMC repository as input and outputs the extracted QTLs into a relational database (SQLite) and text file (CSV)." ; sc:featureList edam:operation_0226, edam:operation_3232 ; sc:license "Apache-2.0" ; sc:name "QTL TableMiner++(QTM)" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/candygene/QTM" ; biotools:primaryContact "Richard Finkers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3365, edam:topic_3518 ; sc:citation "pubmed:18773231" ; sc:description "Computer software which packaged with modules for microarray data analysis, diallele design analysis and mixed model analysis." ; sc:featureList edam:operation_2238, edam:operation_2495 ; sc:name "QTModel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibi.zju.edu.cn/software/qtmodel/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3071, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:25368506" ; sc:description "Integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies." ; sc:featureList edam:operation_3218 ; sc:name "QuaCRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserv.mps.ohio-state.edu/QuaCRS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:16845097" ; sc:description "QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences." ; sc:featureList edam:operation_0237, edam:operation_0429, edam:operation_2233, edam:operation_2403 ; sc:name "QuadFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xiuchengquek/QuadFinder" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "Software package for calling single-nucleotide variants in four sequenced genomes: normal-tumor pairs coupled with parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting." ; sc:featureList edam:operation_0484, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-4-Clause" ; sc:name "QuadGT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iro.umontreal.ca/%7Ecsuros/quadgt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_0749, edam:topic_2640 ; sc:citation , "pmcid:PMC7092414", "pubmed:32293263" ; sc:description """a method for detecting cancer driver genes with low mutation frequency. Cancer is caused by genetic mutations, but not all somatic mutations in human DNA drive the emergence or growth of cancers. While many frequently-mutated cancer driver genes have already been identified and are being utilized for diagnostic, prognostic, or therapeutic purposes, identifying driver genes that harbor mutations occurring with low frequency in human cancers is an ongoing endeavor. Typically, mutations that do not confer growth advantage to tumors - passenger mutations - dominate the mutation landscape of tumor cell genome, making identification of low-frequency driver mutations a challenge. The leading approach for discovering new putative driver genes involves analyzing patterns of mutations in large cohorts of patients and using statistical methods to discriminate driver from passenger mutations""" ; sc:featureList edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "QuaDMutNetEx" ; sc:url "https://github.com/bokhariy/QuaDMutNetEx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0634, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36124670" ; sc:description "The RNA G-quadruplex and RG4-binding proteins database." ; sc:featureList edam:operation_2436, edam:operation_3208, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "QUADRatlas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rg4db.cibio.unitn.it" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0203, edam:topic_0654, edam:topic_3512 ; sc:citation "pubmed:17901879", "pubmed:19330720" ; sc:description "A website to serve the quadruplex community. Contains conference information, forums, database and parsers." ; sc:featureList edam:operation_0314, edam:operation_0429, edam:operation_0483, edam:operation_2442 ; sc:name "Quadruplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.quadruplex.org" ; biotools:primaryContact "Danzhou Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:21114842" ; sc:description "A program for detecting and correcting errors in next generation sequencing reads." ; sc:featureList edam:operation_0231, edam:operation_2425, edam:operation_3195, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:name "Quake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbcb.umd.edu/software/quake" ; biotools:primaryContact "David R. Kelley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3033 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_2640, edam:topic_3572 ; sc:citation ; sc:description "Provides quality control and quality assessment tools for gated flow cytometry data." ; sc:featureList edam:operation_2428 ; sc:license "Artistic-2.0" ; sc:name "QUALIFIER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QUALIFIER.html" ; biotools:primaryContact "Mike Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:22914218" ; sc:description "Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data." ; sc:featureList edam:operation_3218 ; sc:name "QualiMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://qualimap.bioinfo.cipf.es/" ; biotools:primaryContact "QualiMap Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3315, edam:topic_3519 ; sc:citation "pubmed:9171217" ; sc:description "Variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR." ; sc:featureList edam:operation_3664 ; sc:name "QUALITY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://indra.mullins.microbiol.washington.edu/quality/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:21501521" ; sc:description "Apply quality filter over NGS data. You can see quality distribution graphs and one graph for each base." ; sc:featureList edam:operation_0564, edam:operation_3218 ; sc:name "Quality Assessment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/qualevaluato/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_3572 ; sc:description "Quality score based filtering of nucleotides." ; sc:featureList edam:operation_3218 ; sc:name "qualityFilter" ; sc:url "https://github.com/galaxyproject/tools-devteam/tree/4066016ffafd7918ba9826db4f3c6fb41315e942/tools/quality_filter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0602, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:23632165" ; sc:description "QualitySNPng is a web tool for the detection and interactive visualization of single nucleotide polymorphisms. It does not require a sequenced reference genome." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3202 ; sc:name "QualitySNPng" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.nl/QualitySNPng" ; biotools:primaryContact "QualitySNPng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3365 ; sc:citation , ; sc:description "Convert a file in FASTA/Qual format to FastQ format." ; sc:featureList edam:operation_0335 ; sc:name "qualtofastq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_2229, edam:topic_3474, edam:topic_3520 ; sc:citation , , "pmcid:PMC7319958", "pmcid:PMC8041382", "pubmed:32591519", "pubmed:33661646" ; sc:description """Focus on the spectra that matter by clustering of quantification data in shotgun proteomics. Quandenser: QUANtification by Distillation for ENhanced Signals with Error Regulation. Quandenser condenses quantification data from label-free mass spectrometry experiments. An installer for all major platforms (Windows, OS X, Ubuntu, etc.) can be found on the Release page. Furthermore, Java >=1.6 has to be installed.""" ; sc:featureList edam:operation_3431, edam:operation_3432, edam:operation_3631, edam:operation_3634, edam:operation_3635, edam:operation_3767 ; sc:license "Apache-2.0" ; sc:name "Quandenser+Triqler" ; sc:url "https://github.com/statisticalbiotechnology/quandenser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3468 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3652 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3468 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3652 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3603 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3468 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:17584939" ; sc:description "MATLAB program for protein quantitation by iTRAQ." ; sc:featureList edam:operation_3441, edam:operation_3630, edam:operation_3635, edam:operation_3639 ; sc:name "Quant" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/protms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_3572 ; sc:citation ; sc:description "Protein multiple sequence alignment benchmarking through secondary structure prediction." ; sc:featureList edam:operation_0447 ; sc:name "QuanTest" ; sc:operatingSystem "Linux" ; sc:url "http://www.bioinf.ucd.ie/download/QuanTest.tgz" ; biotools:primaryContact "Quan Le" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_1964 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_1964 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0091, edam:topic_0203, edam:topic_3519 ; sc:author "Miha Svalina" ; sc:citation , "pmcid:PMC5445471", "pubmed:28545393" ; sc:contributor , , , "Maruša Pompe-Novak" ; sc:description "Web-based tool for the quantification of qPCR data using standard curve approach and QC-based decision support system in a high-throughput setting. It deals with all the issues of qPCR related calculations from data consistency, pipetting errors, standard curve parameters, individual sample efficiencies/inhibition, range of quantification and normalization to one or several reference genes. In this way it enables robust quality controlled quantification of nucleic acids." ; sc:featureList edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "quantGenius" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-SI-hackathon", "National Institute of Biology, Department of Biotechnology and Systems Biology" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://quantgenius.nib.si/" ; biotools:primaryContact , , "Miha Svalina" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3071, edam:topic_3315 ; sc:citation "pubmed:25992957" ; sc:description "Software package for automating egg counting in Drosophila genetics research." ; sc:featureList edam:operation_3443 ; sc:name "QuantiFly" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dwaithe/quantifly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3315, edam:topic_3382 ; sc:citation ; sc:description """new tool-kit for measuring planar polarized protein distributions and cell properties in developing tissues. QuantifyPolarity, is a free software, capable of quantifying planar polarity and cell shape automatically in epithelia using comprehensive mathematical formulas. QuantifyPolarity provides image visualization, cell polarity and shape quantification services to students, scientists and other professional establishments around the world.""" ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3799, edam:operation_3891 ; sc:name "QuantifyPolarity" ; sc:url "https://github.com/QuantifyPolarity/QuantifyPolarity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3360, edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC10033788", "pubmed:36947346" ; sc:description "Comprehensive and integrated physician-centered cloud platform for radiomics and machine learning research." ; sc:featureList edam:operation_0303, edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "QuantImage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://medgift.github.io/quantimage-v2-info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3510 ; sc:citation , "pmcid:PMC5512976", "pubmed:28716000" ; sc:description "Provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids." ; sc:featureList edam:operation_2479 ; sc:license "MIT" ; sc:name "quantiprot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://git.e-science.pl/wdyrka/quantiprot" ; biotools:primaryContact "Witold Dyrka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:17341461" ; sc:description "Analytical tool for the analysis of copy number variation using whole genome SNP genotyping data. In its first implementation it was developed for data arising from Illumina® platforms." ; sc:featureList edam:operation_0262 ; sc:name "QuantiSNP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/quantisnp/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8154128", "pubmed:34056383" ; sc:description "Quantitative Toxicity Prediction via Meta Ensembling of Multitask Deep Learning Models." ; sc:featureList edam:operation_3436, edam:operation_3799, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "QuantitativeTox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Abdulk084/QuantitativeTox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3305 ; sc:citation "pubmed:11782049" ; sc:description "Program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative trait include independent individuals and case parent designs." ; sc:featureList edam:operation_2238 ; sc:name "QUANTO" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://biostats.usc.edu/Quanto.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:33091296" ; sc:description """A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC Workflow. Contribute to tachengxmu/QuantPipe development by creating an account on GitHub.""" ; sc:featureList edam:operation_3636, edam:operation_3767, edam:operation_3801 ; sc:name "QuantPipe" ; sc:url "https://github.com/tachengxmu/QuantPipe/releases" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "Statistical analysis of time-resolved and non-time-resolved Microspot Immunoassays." ; sc:featureList edam:operation_2238 ; sc:name "QuantProReloaded" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://code.google.com/p/quantproreloaded/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pmcid:PMC4495646", "pubmed:26040460" ; sc:description "A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "quantro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/quantro.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data." ; sc:featureList edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "quantsmooth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/quantsmooth.html" ; biotools:primaryContact "Jan Oosting" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_2885, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC6986090", "pubmed:31992201" ; sc:description """a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. QuantTB is a SNP based method to identify and quantify individual strains present in Tuberculosis whole genome sequencing datasets. These instructions will guide you through the process of using QuantTB, so that you can deploy it on your own local system. Tested to work for Mac OSX and Ubuntu.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3482 ; sc:license "GPL-3.0" ; sc:name "QuantTB" ; sc:url "https://github.com/AbeelLab/quanttb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3298, edam:topic_3500 ; sc:citation , "pmcid:PMC3885606", "pubmed:24416295" ; sc:description "Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays." ; sc:featureList edam:operation_0314, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "QuantWorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.quantworm.org/" ; biotools:primaryContact "Weiwei Zhong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3383, edam:topic_3384, edam:topic_3512 ; sc:citation , "pmcid:PMC10000431", "pubmed:36899840" ; sc:description "The Quanty-cFOS.ijm is an ImageJ/Fiji tool developed to count specifically Fos/c-fos labelled cells in fixed brain slices or more generally to count cell markers in 2D fluorescent images or on Maximum Intensity Projections (MIP) in an unbiased manner." ; sc:featureList edam:operation_0314, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Quanty-cFOS" ; sc:url "https://github.com/cberri/Quanty-cFOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0082, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:22972754" ; sc:description "Computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only." ; sc:featureList edam:operation_0474 ; sc:name "QUARK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/QUARK/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3382 ; sc:citation , "pubmed:33690813" ; sc:description "QuArray is an application for tissue array whole slide image export and signal analysis. The application is for the export and analysis of Tissue Array (TA) histology whole slide images (WSI)." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:license "MIT" ; sc:name "QuArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/c-arthurs/QuArray" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0209, edam:topic_0602, edam:topic_3343 ; sc:citation , "pmcid:PMC7320630", "pubmed:32221612" ; sc:description """Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. Data on protein-drug and protein-chemical interactions are rapidly accumulating in databases such as DrugBank and STITCH.""" ; sc:featureList edam:operation_0224, edam:operation_0533, edam:operation_3502 ; sc:name "QuartataWeb" ; sc:url "http://quartata.csb.pitt.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC8122155", "pubmed:34025946" ; sc:description "QUARTERplus (QUality Assessment for pRotein inTrinsic disordEr pRedictions.) webserver provides accurate intrinsic disorder predictions using a novel meta-model that are accompanied by interpretable quality assessment (QA) scores. QA scores quantify the quality of the associated disorder predictions for each amino acid in the input sequence." ; sc:featureList edam:operation_0470, edam:operation_0474, edam:operation_3904 ; sc:name "QUARTERplus" ; sc:url "http://biomine.cs.vcu.edu/servers/QUARTERplus/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0780, edam:topic_3169 ; sc:citation , "pmcid:PMC10407605", "pubmed:37560017" ; sc:description "quarTeT is a collection of tools for tolerome-to-tolerome (T2T) genome assembly and basic analysis in automatic workflow." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "quarTeT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.atcgn.com:8080/quarTeT/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2814 ; sc:citation ; sc:description "Identifies clustering of somatic mutations in proteins over the entire quaternary structure." ; sc:featureList edam:operation_0415 ; sc:license "GPL-2.0" ; sc:name "QuartPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QuartPAC.html" ; biotools:primaryContact "Gregory Ryslik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2269, edam:topic_3053, edam:topic_3168, edam:topic_3170, edam:topic_3516 ; sc:citation "pubmed:25480375" ; sc:description "R package, that implements a statistical method for: i) genotyping from next-generation sequencing reads, and ii) conducting inference on allelic imbalance at heterozygous sites." ; sc:featureList edam:operation_3196 ; sc:name "QuASAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/piquelab/QuASAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC8041170", "pubmed:33844699" ; sc:description "QuASeR is a quantum accelerated de novo DNA sequence reconstruction. It is a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms." ; sc:featureList edam:operation_0524, edam:operation_3644 ; sc:license "AGPL-3.0" ; sc:name "QuASeR" ; sc:url "https://github.com/QE-Lab/QuASeR" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0166 ; sc:citation "pubmed:15980465" ; sc:description "QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs)." ; sc:featureList edam:operation_0238, edam:operation_0253 ; sc:name "QuasiMotiFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://quasimotifinder.tau.ac.il/" ; biotools:primaryContact "Server Administrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0781, edam:topic_3053, edam:topic_3168, edam:topic_3474 ; sc:citation "pubmed:23383997" ; sc:description "Software of Inference of Quasispecies subjected to Recombination. We present a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. We offer an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies." ; sc:featureList edam:operation_2423 ; sc:name "QuasiRecomb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cbg-ethz/QuasiRecomb" ; biotools:primaryContact "Armin Töpfer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3382 ; sc:citation , "pubmed:35532087" ; sc:description "Profiling Viral Quasispecies via Self-tuning Spectral Clustering with PacBio Long Sequencing Reads." ; sc:featureList edam:operation_3198, edam:operation_3432, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "QuasiSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zenodo.org/badge/latestdoi/340494542" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0781, edam:topic_3168 ; sc:citation ; sc:description "A Collection of Tools for Viral Quasispecies Analysis | Abstract Summary quasitools is a collection of newly-developed, open-source tools for analyzing viral quasispcies data. The application suite includes tools with the ability to create consensus sequences, call nucleotide, codon, and amino acid variants, calculate the complexity of a quasispecies, and measure the genetic distance between two similar quasispecies. These tools may be run independently or in user-created workflows. Availability The quasitools suite is a freely available application licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https: phac-nml.github.io quasitools Contact gary.vandomselaar@canada.ca" ; sc:featureList edam:operation_3185, edam:operation_3192, edam:operation_3196 ; sc:license "Apache-2.0" ; sc:name "quasitools" ; sc:url "https://phac-nml.github.io/quasitools/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_1957, edam:format_2572, edam:format_2573 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3327 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_3327 ; sc:name "Sequence alignment (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3053, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC2919714", "pubmed:20371516" ; sc:description "This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest." ; sc:featureList edam:operation_2238, edam:operation_3198, edam:operation_3219 ; sc:license "GPL-2.0" ; sc:name "QuasR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QuasR.html" ; biotools:primaryContact "Michael Stadler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_2269, edam:topic_3510 ; sc:citation "pubmed:26355503" ; sc:description "A linear programming based approach to find significance residue positions as well as quantifying their significance in MHC II DR molecules." ; sc:featureList edam:operation_3092 ; sc:name "QUASSI" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/quassi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:23422339" ; sc:description """QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.""" ; sc:featureList edam:operation_0337, edam:operation_3180 ; sc:license "GPL-2.0" ; sc:name "QUAST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://quast.sourceforge.net/quast" ; biotools:primaryContact "QUAST Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2814 ; sc:citation "pubmed:20148364" ; sc:description "Predict the quaternary structural attribute of a protein according to its sequence information alone." ; sc:featureList edam:operation_2479, edam:operation_3350 ; sc:name "Quat-2L" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jci-bioinfo.cn/Quat-2L" ; biotools:primaryContact "Xuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC3531103", "pubmed:23203871" ; sc:description "R package that performs causal reasoning on biological networks, including publicly available networks such as String-db. It is a free alternative to commercial products such as Quiagen and Inginuity pathway analysis. For a given a set of differentially expressed genes, it computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic, Ternary Dot product Scoring Statistic and Fisher's exact test." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "QuaternaryProd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QuaternaryProd.html" ; biotools:primaryContact "Carl Tony Fakhry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0121, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC7190164", "pubmed:32348325" ; sc:description """Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding. Prediction of protein quaternary structural attributes through hybrid feature encoding method by using machine learning approach. Choose the subunit if the input sequence is not compelet sequence but a single chain of protein oligomer.""" ; sc:featureList edam:operation_0474, edam:operation_3092, edam:operation_3350 ; sc:name "QUATgo" ; sc:url "http://predictor.nchu.edu.tw/QUATgo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:28172469" ; sc:description "The core function of this R package is to provide the implementation of the well-cited and well-reviewed algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data; (ii) visualization of identified biclusters; (iii) bicluster-based co-expression network elucidation and visualization; (iv) downloading of bioclusters and network." ; sc:featureList edam:operation_0313 ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "QUBIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/QUBIC.html" ; biotools:primaryContact "Yu Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3332 ; sc:citation , "pmcid:PMC5462671", "pubmed:29086120" ; sc:description "Calculation of 2D molecular descriptors based on the bilinear, quadratic and linear algebraic forms. Compute these kinds of indices, applying matrix transformations (simple-stochastic, double-stochastic and mutual probability), cut-offs, local calculations and aggregation operators." ; sc:featureList edam:operation_2480 ; sc:name "QuBiLs-MAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tomocomd.com/qubils-mas" ; biotools:primaryContact "José R. Valdés-Martiní" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2269 ; sc:citation , "pubmed:32058625" ; sc:description """Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra. QuBiLs-MIDAS software is for the calculation of 3D molecular descriptors based on the two-linear (bilinear), three-lineal and four-linear (multi-linear or. QuBiLs-MIDAS software is for the calculation of 3D molecular descriptors based on the two-linear (bilinear), three-lineal and four-linear (multi-linear or N-linear) algebraic forms.""" ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3659 ; sc:name "QuBiLS-MIDAS" ; sc:url "http://tomocomd.com/qubils-midas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_3053, edam:topic_3500 ; sc:citation , "pmcid:PMC9235488", "pubmed:35758818" ; sc:description "Quartet-based co-estimation of species trees and gene trees." ; sc:featureList edam:operation_0544, edam:operation_0547, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "QuCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/maryamrabiee/quco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3318, edam:topic_3520 ; sc:description "QUDeX-MS is a tool for hydrogen/deuterium exchange calculation for mass spectra with isotopic fine structure" ; sc:featureList edam:operation_3215, edam:operation_3631, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "QUDeX-MS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/45715-qudex-ms" ; biotools:primaryContact "Joseph Salisbury" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3383 ; sc:citation ; sc:description "Qudi is a general, modular, multi-operating system suite written in Python 3 for controlling laboratory experiments." ; sc:featureList edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "Qudi" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6" ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX-D-16-00092" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593 ; sc:citation ; sc:description "QUantitative Evaluation of Experimental Nmr restraints is a new software for quantifying the information contained in the experimental NMR restraints. The method is based on a description of the structure in distance space and concepts derived from information theory. It allows for an objective description of the amount of available experimental information, which is shown to be related to the positional uncertainty of the NMR ensemble." ; sc:featureList edam:operation_2479 ; sc:name "QUEEN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.cmbi.ru.nl/software/queen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0080 ; sc:citation "pubmed:17825976" ; sc:description "Retrieval program with a graphical user interface for ACNUC databases . It can query any ACNUC database, e.g., for nucleotide of protein sequences." ; sc:featureList edam:operation_2421 ; sc:name "QUERY_WIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pbil.univ-lyon1.fr/software/query_win.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "A web-based platform to manage and retrieve data from human exome sequencing projects." ; sc:featureList edam:operation_3226 ; sc:name "QueryOr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genomes.cribi.unipd.it/cgi-bin/queryor/login.pl" ; biotools:primaryContact "Claudio Forcato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation "pubmed:19160518" ; sc:description "Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-seq or ChIPseq)." ; sc:featureList edam:operation_0415 ; sc:license "GPL-2.0" ; sc:name "QuEST" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mendel.stanford.edu/sidowlab/downloads/quest/" ; biotools:primaryContact "Arend Sidow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0654, edam:topic_0749, edam:topic_3293 ; sc:citation "pubmed:26284082" ; sc:description "Suite of tools to classify and compare TAL (Transcription Activator-Like) effectors functionally and phylogenetically." ; sc:featureList edam:operation_0325 ; sc:name "QueTAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3068 ; sc:citation ; sc:description "Speed up editing of sequence alignments. It allows the simultaneous editing of many nucleotide or amino acid sequences using mouse functions and shortcuts, as well as automatic overlapping of sequence fragments, searching and sorting of sequences, and multiple alignment using ClustalX." ; sc:featureList edam:operation_0492, edam:operation_3096 ; sc:name "QuickAlign" ; sc:operatingSystem "Mac" ; sc:softwareVersion "1.03" ; sc:url "http://bioinfweb.info/Software/QuickAlign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC10412403", "pubmed:37498562" ; sc:description "Parallelized BAM file access API for high-throughput sequence analysis informatics." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "quickBAM" ; sc:softwareHelp ; sc:url "https://gitlab.com/yiq/quickbam/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3382 ; sc:citation , "pmcid:PMC8577749", "pubmed:34752463" ; sc:description "A toolkit and ImageJ PlugIn to quickly transform microscope images into scientific figures" ; sc:featureList edam:operation_0292, edam:operation_3096, edam:operation_3359, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "QuickFigures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/grishkam/QuickFigures" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "A fast browser for Gene Ontology terms and annotations." ; sc:featureList edam:operation_0224, edam:operation_3559 ; sc:name "QuickGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/QuickGO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "A tool for fast canonical neighbor-joining tree construction but use RapidNJ instead." ; sc:featureList edam:operation_3478 ; sc:name "QuickJoin" ; sc:operatingSystem "Linux" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0.10" ; sc:url "http://www.daimi.au.dk/~mailund/quick-join.html" ; biotools:primaryContact "Thomas Mailund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3316, edam:topic_3570 ; sc:citation , "pmcid:PMC8518384", "pubmed:34062051" ; sc:description "quickLD (qLD) is a tool to calculate Linkage disequilibrium (the non-random association between alleles at different loci), with highly efficient CPU and GPU kernels that utilize dense linear algebra (DLA) operations." ; sc:featureList edam:operation_0488, edam:operation_3192, edam:operation_3196, edam:operation_3436, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "quickLD" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/pephco/quickLD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3382 ; sc:description "QuickLook plugin for displaying PDB files and provides two visualisation options. plugin can use pymol to quickly render thumbnail images, while the heart of the plugin lies with the integration of a HTML-5 PDB viewer, Jolecule." ; sc:featureList edam:operation_0337 ; sc:name "QuickLookPDB" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://benporebski.github.io/CrystallographyQLPlugins/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC6169397", "pubmed:30018084" ; sc:description "Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3196, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "quickmerge" ; sc:url "https://github.com/mahulchak/quickmerge" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3170 ; sc:citation ; sc:description "Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner." ; sc:featureList edam:operation_0337, edam:operation_0531, edam:operation_2935, edam:operation_2938, edam:operation_2939, edam:operation_2943, edam:operation_3196, edam:operation_3463, edam:operation_3501, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "Quickomics" ; sc:url "http://quickomics.bxgenomics.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3382 ; sc:citation , "pmcid:PMC9175388", "pubmed:35672681" ; sc:description "QuickPed is an interactive web application for drawing and analysing pedigrees. A created pedigree may be saved as an image or as a text file in ped format. You may also obtain various information about the pedigree, including relatedness coefficients and verbal descriptions of relationships." ; sc:featureList edam:operation_0337, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QuickPed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://magnusdv.shinyapps.io/quickped" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3070, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC8642913", "pubmed:34863116" ; sc:description "Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis." ; sc:featureList edam:operation_0337, edam:operation_3446, edam:operation_3458 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "quickPIV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Marc-3d/quickPIV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0623 ; sc:citation "pubmed:24586435" ; sc:description "Fast multiple sequence alignment algorithm designed for graphics processors." ; sc:featureList edam:operation_0492 ; sc:name "QuickProbs" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=quickprobs&subpage=about" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_2815, edam:topic_2885 ; sc:citation "pubmed:17517769" ; sc:description "Resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module." ; sc:featureList edam:operation_3196 ; sc:name "QuickSNP" ; sc:url "http://bioinformoodics.jhmi.edu/quickSNP.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0654, edam:topic_3301 ; sc:citation "pubmed:23786768" ; sc:description "Quadratic, iterative, K-mer based reconstruction technique that utilizes sparsity promoting ideas from the field of compressed sensing to reconstruct the composition of a bacterial community (when the input data is 454-like pyrosequencing data)." ; sc:featureList edam:operation_0323 ; sc:name "Quikr" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/quikr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation , "pmcid:PMC4919057", "pubmed:27336171" ; sc:description "Tool for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC." ; sc:featureList edam:operation_0226, edam:operation_3083 ; sc:name "QuIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:url "https://quin.jax.org/" ; biotools:primaryContact "DUYGU UCAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3473, edam:topic_3520 ; sc:citation , "pubmed:33681984" ; sc:description "QUIN-XL will then proceed to read the SIM-XL files and extract quantification values for your cross-links. This step can take a while depending on how many .raw files you have to analyse and their sizes." ; sc:featureList edam:operation_2476, edam:operation_3767, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "QUIN-XL" ; sc:url "http://patternlabforproteomics.org/quinxl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0219 ; sc:citation ; sc:description """an R package to query, download and wrangle PGS Catalog data. The goal of quincunx is to provide programmatic access to the Polygenic Score (PGS) Catalog, an open resource for polygenic scores and associated metadata describing their development and respective assessment.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3695 ; sc:license "MIT" ; sc:name "quincunx" ; sc:url "https://github.com/maialab/quincunx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation "pubmed:22904078" ; sc:description "Aggressive compression of FASTQ and SAM/BAM files." ; sc:featureList edam:operation_0335 ; sc:license "BSD-3-Clause" ; sc:name "Quip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://homes.cs.washington.edu/%7Edcjones/quip/" ; biotools:primaryContact "Daniel C. Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0154, edam:topic_0749, edam:topic_3295, edam:topic_3674 ; sc:citation "pubmed:18487274" ; sc:description "Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, visualization and quantification of the bisulfite sequence data is rapid. 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Hence, QUOD facilitates the identification of candidate dispensable genes which often underlie lineage-specific adaptation to varying environmental conditions." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "QUOD" ; sc:softwareHelp ; sc:url "https://github.com/ksielemann/QUOD" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3489 ; sc:description "Complete end-to-end solution for literature search and document management in the life science fields." ; sc:featureList edam:operation_0305, edam:operation_2421 ; sc:name "QUOSA" ; sc:softwareVersion "1.3" ; sc:url "http://www.elsevier.com/solutions/quosa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_2640, edam:topic_3382 ; sc:citation , "pubmed:32569415" ; sc:description """Autonomous Tool for Measuring Intracellular Dynamics using Temporal Variance. Trafficking of intracellular cargo is essential to cellular function and can be defective in pathological states including cancer and neurodegeneration. Tools to quantify intracellular traffic are thus necessary for understanding this fundamental cellular process, studying disease mechanisms, and testing the effects of therapeutic pharmaceuticals. IQuoVadoPro that autonomously quantifies the movement of fluorescently tagged intracellular cargo. QuoVadoPro infers the extent of intracellular motility based on the variance of pixel illumination in a series of time-lapse images. The algorithm is an unconventional approach to the automatic measurement of intracellular traffic and is suitable for quantifying movements of intracellular cargo under diverse experimental paradigms.""" ; sc:featureList edam:operation_3799 ; sc:name "QuoVadoPro" ; sc:url "https://github.com/ThomasSchwarzLab/QuoVadoPro/blob/master/instructions_ReadMeFirst.docx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3398, edam:topic_3474 ; sc:citation ; sc:description """a open-source web application for the organisation of large scale biological treasure hunts. This repository contain the source code of the web application. The web application is developped in R and uses the Shiny package. The app can be installed on a Shiny server and used to play the QuoVidi game. QuoVidi (previously known as BioGO) is an interface to manage large (and small) scale treasure hunt. It was intially designed to organise a biological treasure hunt, but can be adapted to any situations.""" ; sc:featureList edam:operation_3283, edam:operation_3802 ; sc:license "Apache-2.0" ; sc:name "QuoVidi" ; sc:url "http://www.quovidi.xyz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0634, edam:topic_3384, edam:topic_3385 ; sc:citation ; sc:description "Aims to help improve the speed, objectivity and reproducibility of digital pathology analysis and biomarker interpretation by offering an open, powerful, flexible, extensible software platform for whole slide image analysis." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "QuPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.2" ; sc:url "https://qupath.github.io/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3245 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , ; sc:description "Web application to support the analysis and integration of even complex mass spectrometry-based proteomics experiments. It guides through the process of protein identification, quantification and statistical evaluation of multivariate experimental setups featuring data visualization and normalization methods, significance tests, PCA and cluster analysis. 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It accounts for inter-gene correlations using the variance inflation factor technique, quantifying the deviation from a null hypothesis with a P value and a probability density function." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "qusage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/qusage.html" ; biotools:primaryContact "Christopher Bolen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant." ; sc:featureList edam:operation_2424 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.0" ; sc:name "qvalue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/qvalue.html" ; biotools:primaryContact "Andrew J. Bass", "John D. Storey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:36581214" ; sc:description "Automated hemodynamic assessment for cranial 4D flow MRI." ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "QVT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/uwmri/QVT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:26026138" ; sc:description "Lossy compression algorithm for storing quality values associated with DNA sequencing." ; sc:featureList edam:operation_3218 ; sc:name "QVZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mikelhernaez/qvz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0176, edam:topic_3306 ; sc:citation ; sc:description "Gateway for Easy Simulation with VMD and NAMD." ; sc:featureList edam:operation_2476 ; sc:name "QwikMD" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://www.ks.uiuc.edu/Research/qwikmd/" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3315, edam:topic_3365 ; sc:citation ; sc:description "Free software environment for statistical computing and graphics." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.r-project.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_3308 ; sc:citation , "pmcid:PMC7544209", "pubmed:32976561" ; sc:description """a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions. A web server and R package for plotting RNA secondary structures, trans RNA-RNA, RNA-DNA and DNA-DNA interactions and genomic interactions. R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation information.""" ; sc:featureList edam:operation_0468, edam:operation_0502, edam:operation_0570, edam:operation_2441, edam:operation_3469 ; sc:name "R-chie" ; sc:url "http://www.e-rna.org/rchie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2269 ; sc:citation "pubmed:21233166" ; sc:description "Software to remote access to R/Bioconductor on EBI’s 64-bit Linux Cluster. Start the workbench by downloading the package for your operating system or via Java Web Start, and you will get access to an instance of R running on one of EBI’s powerful machines. You can install additional packages, upload your own data, work with graphics and collaborate with colleagues, all as if you are running R locally, but unlimited by your machine’s memory, processor or data storage capacity." ; sc:featureList edam:operation_2409 ; sc:name "R-Cloud Workbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/Tools/rcloud/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:18420654", "pubmed:18483080" ; sc:description "The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures." ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_0502, edam:operation_0503 ; sc:name "R-Coffee" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tcoffee.crg.cat/apps/tcoffee/do:rcoffee" ; biotools:primaryContact "Cedric Notredame" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC8702036", "pubmed:34946828" ; sc:description "A Deep Learning Network to Predict Off-Target Activities with Mismatch, Insertion and Deletion in CRISPR-Cas9 System." ; sc:featureList edam:operation_0415, edam:operation_2575, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "R-CRISPR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://codeocean.com/capsule/9553651/tree/v1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335 ; sc:citation , "pmcid:PMC7924703", "pubmed:33816879" ; sc:description "R-DECO is an open-source Matlab based graphical user interface for the detection and correction of R-peaks." ; sc:featureList edam:operation_3215, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "R-DECO" ; sc:url "https://gitlab.esat.kuleuven.be/biomed-public/r-deco" ; biotools:primaryContact "Jonathan Moeyersons" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3518 ; sc:description "R implementation of GADA (Genetic Alteration Detector Algorithm) - used to detect CNVs from aCGH and intensity array SNP data" ; sc:featureList edam:operation_0484, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "R-GADA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/isglobal-brge/R-GADA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3574 ; sc:citation "pubmed:19883371" ; sc:description "R code for testing genetic conflicts (GC) that increase disease risk in human pregnancy with penalized mixture logistic regression." ; sc:featureList edam:operation_2238, edam:operation_2495 ; sc:name "R-GC-test" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.stt.msu.edu/~cui/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC9303298", "pubmed:35758606" ; sc:description "Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions." ; sc:featureList edam:operation_0441, edam:operation_2429, edam:operation_3196, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "R-loop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bishop-Laboratory/RLoop-QC-Meta-Analysis-Miller-2022" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_2640, edam:topic_3300, edam:topic_3334 ; sc:citation , "pmcid:PMC8728142", "pubmed:34792163" ; sc:description "A knowledgebase for genome-wide R-loop formation and regulation." ; sc:featureList edam:operation_0306, edam:operation_3208, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:name "R-loopBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rloopbase.nju.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:35324441" ; sc:description "A Green, Accurate, and Unsupervised Point Cloud Registration Method." ; sc:featureList edam:operation_2939, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "R-PointHop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pranavkdm/R-PointHop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3055 ; sc:citation , "pubmed:12724300" ; sc:description "Software for mapping quantitative trait loci in experimental crosses." ; sc:featureList edam:operation_2429 ; sc:license "GPL-3.0" ; sc:name "R-QTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rqtl.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0099, edam:topic_3170 ; sc:citation "pubmed:22287631" ; sc:description "User-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. It accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values." ; sc:featureList edam:operation_3680 ; sc:name "R-SAP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://mcdonaldlab.biology.gatech.edu/r-sap/" ; biotools:primaryContact "Vinay Mittal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0154, edam:topic_3047, edam:topic_3297 ; sc:citation , "pubmed:36495921" ; sc:description "A Database of Binding Affinities for RNA-small Molecule Interactions." ; sc:featureList edam:operation_0337, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "R-SIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://web.iitm.ac.in/bioinfo2/R_SIM/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269 ; sc:description "A software to calculate imputation quality estimate from dosage data." ; sc:featureList edam:operation_3557 ; sc:name "r2_hat" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.09" ; sc:url "https://yunliweb.its.unc.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3518 ; sc:citation , ; sc:description "The R2 platform is an online genomics analysis tool which can analyze a large collection of public data, but also allows shielded analysis of your own microarray dataset. freely accessible and intended to be used by biologists, even those with little or no bioinformatics training." ; sc:featureList edam:operation_2945 ; sc:name "R2 platform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://r2.amc.nl" ; biotools:primaryContact "Dr. Jan Koster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3370, edam:topic_3407, edam:topic_3520 ; sc:citation ; sc:description "Provides functions for aligning 2D gas chromatography mass spectrometry derived metabolite peaks obtained from primary processing and generates an alignment table that allows for a comparison of common peaks across samples and metabolite identification." ; sc:featureList edam:operation_3214 ; sc:license "MIT" ; sc:name "R2DGC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/R2DGC/index.html" ; biotools:primaryContact "Emily Gordon", "Ryne Ramaker", "Sara Cooper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description """computational framework for template-based RNA secondary structure visualisation across non-coding RNA types. The R2DT software (RNA 2D Templates) automatically generates RNA secondary structure in standard layouts using templates from the following sources:. This is an embeddable component that you can include into your website to visualise RNA secondary structures. Visualise RNA secondary structure in standard orientations. Visualise RNA secondary structure using standard layouts. Visualise RNA secondary structure in standard orientations using RNA 2D Templates (R2DT).""" ; sc:featureList edam:operation_0278, edam:operation_0477, edam:operation_0502, edam:operation_0570, edam:operation_3469 ; sc:license "Apache-2.0" ; sc:name "R2DT" ; sc:url "https://rnacentral.org/r2dt" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:name "RNA secondary structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:author "Anton Petrov" ; sc:citation , ; sc:description "Visualise RNA secondary structure in standard orientations using RNA 2D Templates (R2DT)." ; sc:featureList edam:operation_0278, edam:operation_0570 ; sc:name "R2DT (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/Tools/rna/r2dt/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3372 ; sc:citation , "pubmed:35729090" ; sc:description "Calibration of Numerical Groundwater Flow Models with Bayesian Optimization in R." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "r2ogs5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.opengeosys.org/ogs5/r2ogs5" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3168 ; sc:description "Package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. 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Input is an RNA 3D structure in PDB format, output includes a graphical display showing structural superposition." ; sc:featureList edam:operation_0360, edam:operation_0483, edam:operation_0570, edam:operation_2441 ; sc:name "R3D-BLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.cs.nthu.edu.tw/R3D-BLAST/" ; biotools:primaryContact "Chin Lung Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "Search tool for similar RNA 3D substructures." ; sc:featureList edam:operation_0278 ; sc:name "R3D-BLAST2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://140.114.85.168/R3D-BLAST2/" ; biotools:primaryContact "Chin Lung Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0166 ; sc:citation "pubmed:23716643" ; sc:description "The R3D Align is a web server for global nucleotide to nucleotide alignments of RNA 3D structures." ; sc:featureList edam:operation_0295, edam:operation_0502, edam:operation_0510 ; sc:name "R3D Align" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.bgsu.edu/r3dalign/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , "pubmed:21349869" ; sc:description "Comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided." ; sc:featureList edam:operation_2403, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "R453Plus1Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/R453Plus1Toolbox.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation , "pmcid:PMC3384350", "pubmed:22434875" ; sc:description "A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each." ; sc:featureList edam:operation_0564, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "R4RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/R4RNA.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author , "Luca Alessandri" ; sc:description "rCASC, Cluster Analysis of Single Cells, is part of the reproducible-bioinformatics.org project and provides single cell analysis functionalities within the reproducible rules described by Sandve et al. [PLoS Comp Biol. 2013]. rCASC is designed to provide a complete workflow for cell-subpopulation discovery." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rCASC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.0.1" ; sc:url "https://github.com/kendomaniac/rCASC" ; biotools:primaryContact "Raffaele A Calogero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3500 ; sc:citation , "pubmed:31799690" ; sc:description """Kernel-based method for estimating isotopic niche size and overlap. The isotopic niche of consumers represents biologically relevant information on resource and habitat use. Several tools have been developed to quantify niche size and overlap. Nonetheless, methods adapted by spatial ecologists to quantify animal home ranges can be modified for use in stable isotope ecology when data are not normally distributed in bivariate space. We offer a tool that draws on existing spatial metrics, such as Minimum Convex Polygon (MCP) and Standard Ellipse Area (SEA), and add novel metrics using Kernel Utilization Density (KUD) estimators to measure isotopic niche size and overlap. We present examples using empirical and simulated data to demonstrate the performance of the package Kernel Isotopic Niches in R (rKIN) under various scenarios.""" ; sc:featureList edam:operation_3435, edam:operation_3642 ; sc:name "rKIN" ; sc:url "https://github.com/salbeke/rKIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:31382415" ; sc:description "Ion Filtering R Package for Untargeted Analysis of Metabolomic LDI-MS Images." ; sc:featureList edam:operation_1812, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rMSIKeyIon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LlucSF/rMSIKeyIon" ; biotools:primaryContact "Esteban del Castillo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description """An open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization. Automated annotation of matrix-related signals in MSI. rMSIcleanup is an open-source R package to annotate matrix-related signals in MSI data. The algorithm takes into account the chemical formula and the spatial distribution to determine which ions are matrix-related. The algorithm incorporates an overlapping peak detection feature to prevent misclassification of overlapped or isobaric ions. Additionally, the package generates a visual report to transparently justify each annotation""" ; sc:featureList edam:operation_2939, edam:operation_3215, edam:operation_3553, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "rMSIcleanup" ; sc:url "https://github.com/gbaquer/rMSIcleanup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3277 ; sc:citation , "pmcid:PMC6341041", "pubmed:30686929" ; sc:description "R package to interface with the Mycology Collections Portal." ; sc:featureList edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rMyCoPortal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FranzKrah/rMyCoPortal" ; biotools:primaryContact "Franz-Sebastian Krah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3360 ; sc:citation , "pmcid:PMC6715143", "pubmed:31467462" ; sc:description "Calculating Power for the General Linear Multivariate Model With One or More Gaussian Covariates | An R package implementing power and sample size methods for the general linear multivariate model | The rPowerlib package for R (>3.0.0) calculates power for the general linear multivariate model with or without Gaussian covariates | This package is based on the SAS/IML product POWERLIB (http://www.jstatsoft.org/v30/i05) developed by Keith E. Muller and colleagues. At present, the rPowerlib package DOES NOT include the full functionality of POWERLIB. For features such as power confidence intervals and more statistical tests, please try POWERLIB (http://github.com/samplesizeshop/powerlib) or GLIMMPSE (https://glimmpse.samplesizeshop.org). Please visit http://SampleSizeShop.org for more information about calculating power and sample size" ; sc:license "GPL-3.0" ; sc:name "rPowerlib" ; sc:url "http://github.com/SampleSizeShop/rPowerlib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC6592976", "pubmed:31037477" ; sc:description "Regularized reference electrode standardization technique." ; sc:featureList edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rREST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ShiangHu/Unified-EEG-reference-rREST" ; biotools:primaryContact "Dezhong Yao", "Pedro A. Valdés Sosa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0593, edam:topic_0749, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC6816579", "pubmed:31618265" ; sc:description """Computational design and interpretation of single-RNA translation experiments. RNA Sequence to NAscent Protein simulator. Python 2.7 or 3.5+ Version of the Single Molecule Translation Simulator (MatLab) by Dr. Luis Aguilera. rSNAPsim - RNA Sequence to NAscent Protein Simulation. Translated by Will Raymond - 2018/2019""" ; sc:featureList edam:operation_0244, edam:operation_0284, edam:operation_2476 ; sc:license "MIT" ; sc:name "rSNAPsim" ; sc:url "https://github.com/MunskyGroup/rSNAPsim.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6529933", "pubmed:31156694" ; sc:description "Machine learning based R package for prediction of bacterial transcription units." ; sc:featureList edam:operation_0435, edam:operation_0438, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rSeqTU-A" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://s18692001.github.io/rSeqTU/" ; biotools:primaryContact "Sheng-Yong, Niu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269 ; sc:author "Andrew Tikhonov", "Misha Kapushesky" ; sc:citation ; sc:contributor "Karim Chime" ; sc:description "Workbench for remote access to R/Bioconductor on EBI's cluster." ; sc:featureList edam:operation_2238 ; sc:name "R Cloud Workbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/rcloud/" ; biotools:primaryContact "Andrew Tikhonov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3512 ; sc:citation ; sc:description "Set of R functions for filtering, normalization, Bayesian hierarchical modelling and MCMC procedures in cDNA microarray analysis." ; sc:featureList edam:operation_2495, edam:operation_3695 ; sc:name "R functions for cDNA array analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tsenglab.biostat.pitt.edu/software.htm#cDNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2815, edam:topic_3407 ; sc:citation "pubmed:20519200" ; sc:description "R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome." ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_2497, edam:operation_3223, edam:operation_3660 ; sc:name "R spider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mips.helmholtz-muenchen.de/proj/rspider" ; biotools:primaryContact "R Spider Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:description "Assembler for raw de novo genome assembly of long uncorrected reads." ; sc:featureList edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Ra" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/lbcb-sci/ra" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0625, edam:topic_0634, edam:topic_3295 ; sc:citation , "pmcid:PMC7170216", "pubmed:32311035" ; sc:description """building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms.""" ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_3927 ; sc:name "RA-map" ; sc:url "http://ramap.elixir-luxembourg.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_2814, edam:topic_3306, edam:topic_3510 ; sc:citation , "pmcid:PMC9252778", "pubmed:35639512" ; sc:description "A webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets." ; sc:featureList edam:operation_0302, edam:operation_0564, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "RaacFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfor.imu.edu.cn/raacfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0130, edam:topic_0154, edam:topic_0157, edam:topic_0736 ; sc:citation , "pubmed:32524143" ; sc:description """a new sequence logo generator by using reduced amino acid clusters. Sequence logos give a fast and concise display in visualizing consensus sequence.""" ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_3432 ; sc:name "RaacLogo" ; sc:url "http://bioinfor.imu.edu.cn/raaclogo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2815, edam:topic_3444 ; sc:citation , "pubmed:36565485" ; sc:description "A brain tumor segmentation network using parallel processing of multiple spatial frames." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RAAGR2-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Rehman1995/RAAGR2-Net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3654 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:17068186" ; sc:description "Algorithm for interpreting O-16/O-18 differential proteomics data." ; sc:featureList edam:operation_3215, edam:operation_3630, edam:operation_3632, edam:operation_3634, edam:operation_3635, edam:operation_3659, edam:operation_3664, edam:operation_3705 ; sc:name "RAAMS" ; sc:url "http://informatics.mayo.edu/svn/trunk/mprc/raams/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Rabbit-In-a-Hat comes with WhiteRabbit and is designed to read and display a WhiteRabbit scan document. WhiteRabbit generates information about the source data while Rabbit-In-a-Hat uses that information and through a graphical user interface to allow a user to connect source data to tables and columns within the CDM. Rabbit-In-a-Hat generates documentation for the ETL process it does not generate code to create an ETL" ; sc:license "Apache-2.0" ; sc:name "Rabbit in a Hat" ; sc:softwareVersion "CDM version (v4, v5 or v6)" ; sc:url "http://ohdsi.github.io/WhiteRabbit/RabbitInAHat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3168 ; sc:citation , "pubmed:36327193" ; sc:description "Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RabbitFX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/RabbitBio/RabbitFX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622 ; sc:citation , "pubmed:32845281" ; sc:description """Accelerating hash-based genome analysis on modern multi-core architectures. RabbitMash is an efficient highly optimized implementation of Mash which can take full advantage of modern hardware including multi-threading, vectorization, and fast I/O.""" ; sc:featureList edam:operation_0310, edam:operation_3432 ; sc:name "RabbitMash" ; sc:url "https://github.com/ZekunYin/RabbitMash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3303 ; sc:citation , "pubmed:32790850" ; sc:description """High-speed scalable quality control for sequencing data. A tool designed to provide high-speed scalable quality control for sequencing data which can take full advantage of modern hardware. It includes a variety of function modules and supports different sequencing technologies (Illumina, Oxford Nanopore, PacBio). RabbitQC achieves speedups between one and two orders-of-magnitude compared to other state-of-the-art tools.""" ; sc:featureList edam:operation_3192, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "RabbitQC" ; sc:url "https://github.com/ZekunYin/RabbitQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation , "pubmed:37330158" ; sc:description "More efficient and versatile quality control for sequencing data." ; sc:featureList edam:operation_3218, edam:operation_3501, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RabbitQCPlus" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/RabbitBio/RabbitQCPlus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_3673 ; sc:citation , "pmcid:PMC10190105", "pubmed:37198663" ; sc:description "Enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches." ; sc:featureList edam:operation_0525, edam:operation_3211, edam:operation_3432, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "RabbitTClust" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/RabbitBio/RabbitTClust" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3365 ; sc:citation , "pubmed:35333310" ; sc:description "A highly optimized and practical toolkit for the detection of viruses and microorganisms in sequencing data. It can handle large-scale datasets such as bacterial reference genomes on commonly used servers with limited compute resources." ; sc:featureList edam:operation_1812, edam:operation_3359, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RabbitV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RabbitBio/RabbitV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_2885, edam:topic_3173, edam:topic_3360 ; sc:citation , "pubmed:36243962" ; sc:description "Rheumatoid Arthritis Bioinformatics/Big data Center (RABC) is the first big data resource platform that provides data storage, processing, and analysis for RA research. It not only solves the current problems in the use of RA data, but also brings more well-categorized and uniformly processed data, and multiple data analysis results. The practical and user-friendly platform provides researchers to explore biomarkers relevant to the pathogenesis, diagnosis, and treatment of RA." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "RABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.onethird-lab.com/RABC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_2640 ; sc:citation "pubmed:26056275" ; sc:description "Very efficient feature selection algorithm. It was applied to find tumor associated regulators in diverse cancer types." ; sc:featureList edam:operation_3439 ; sc:name "RABIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rabit.dfci.harvard.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3474 ; sc:citation ; sc:description "Random Boolean Network Creation, Simulation, and Prediction Toolbox (RaBooNet) allows for creation, simulation, and prediction of random Boolean networks." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "RaBooNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/60779-random-boolean-network-creation-simulation-and-prediction-toolbox-raboonet" ; biotools:primaryContact "Dana Ferranti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3387 ; sc:citation ; sc:description "Library which solves the individual bioenergetic balance for different aquaculture sea fish and shellfish. It also allows for spatialized model runs and population simulations." ; sc:featureList edam:operation_2423 ; sc:name "RAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/RAC/index.html" ; biotools:primaryContact "Baldan Damiano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Reference-Assisted Chromosome Assembly (RACA)" ; sc:featureList edam:operation_0310 ; sc:name "RACA" ; sc:url "http://bioen-compbio.bioen.illinois.edu/RACA/" ; biotools:primaryContact "Jaebum Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3365, edam:topic_3518 ; sc:citation "pubmed:15980552" ; sc:description "Collection of web tools designed to assist with the analysis of DNA microarray data and results." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232, edam:operation_3463 ; sc:name "RACE" ; sc:url "http://race.unil.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_3053, edam:topic_3307, edam:topic_3569 ; sc:citation , "pmcid:PMC6006707", "pubmed:29914482" ; sc:description "Computational tool for modeling gene regulatory circuits using randomization." ; sc:featureList edam:operation_2426 ; sc:license "Apache-2.0" ; sc:name "RACIPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/simonhb1990/RACIPE-1.0" ; biotools:primaryContact "Bin Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation , ; sc:description "Prediction of RNA joint secondary structures under the general type of interaction including kissing hairpins. Predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.  It can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities." ; sc:featureList edam:operation_0271, edam:operation_2423 ; sc:name "RactIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://rtips.dna.bio.keio.ac.jp/ractip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3293, edam:topic_3308 ; sc:citation , "pmcid:PMC7355293", "pubmed:32657393" ; sc:description """Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Robust and Accurate Deconvolution (RAD). RAD is a toolkit that unmixes bulk tumor samples. Given a non-negative bulk RNA expression matrix B \\in R_+^{m x n}, where each row i is a gene, each column j is a tumor sample, our goal is to infer an expression profile matrix C \\in R_+^{m x k}, where each column l is a cell community, and a fraction matrix F \\in R_+^{k x n}, such that:.""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3891 ; sc:license "MIT" ; sc:name "RAD" ; sc:url "https://github.com/CMUSchwartzLab/RAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3674 ; sc:citation , "pubmed:33532827" ; sc:description "RAD (Region Associated DEG : Identify Region Associated Differentially Expressed Genes) is a web application to identify region associated differentially expressed genes." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3658 ; sc:name "RAD" ; sc:url "https://labw.org/rad" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "Andreas Heger" ; sc:citation ; sc:description "Identify gapped approximate repeats and complex repeat architectures involving many different types of repeats." ; sc:featureList edam:operation_0237 ; sc:name "RADAR (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/pfa/radar" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7391703", "pubmed:32727537" ; sc:description """annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. RADAR can be run on the command line by following the instructions on the Docs page or through the web here. Running RADAR through the website will print the results after several moments. You can try running RADAR through the web form with a sample file with one variant. Alternatively, you may also input a list of variants into the form as text. If variants are provided in both file and text formats, the variant file will be scored and the text field will be ignored. Directory containing files, one for each chromosome.""" ; sc:featureList edam:operation_3222, edam:operation_3226, edam:operation_3227, edam:operation_3902 ; sc:name "RADAR" ; sc:url "http://radar.gersteinlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2640, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , , "pmcid:PMC6927177", "pubmed:31870409" ; sc:description "Differential analysis of MeRIP-seq data with a random effect model." ; sc:featureList edam:operation_0244, edam:operation_0308, edam:operation_2495, edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "RADAR" ; sc:softwareHelp ; sc:url "https://github.com/scottzijiezhang/RADAR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0218, edam:topic_0602, edam:topic_0634, edam:topic_3518 ; sc:citation , "pubmed:32338561" ; sc:description "a knowledgebase focusing on radiation-associated genes." ; sc:featureList edam:operation_0306, edam:operation_2495, edam:operation_3223 ; sc:name "RadAtlas" ; sc:url "http://biokb.ncpsb.org/radatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3306, edam:topic_3421, edam:topic_3444, edam:topic_3452 ; sc:citation ; sc:description "MATLAB programming tools for radiomics analysis." ; sc:featureList edam:operation_3659, edam:operation_3907, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RADIOMICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51948-radiomics" ; biotools:primaryContact "Martin Vallières" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3384 ; sc:description "RadiomicsEnabler allows to extract, de-identify, visualize, curate and export medical images from PACS or EDS." ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "RadiomicsEnabler" ; sc:softwareVersion "01" ; sc:url "https://medexprim.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3056, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:27312412" ; sc:description "Perl pipeline which makes the processing of RAD-seq data easier and allows rapid and automated exploration of parameters/data for phylogenetic inference." ; sc:featureList edam:operation_2478 ; sc:name "RADIS" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www1.montpellier.inra.fr/CBGP/software/RADIS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC8944106", "pubmed:35331160" ; sc:description "Determining the applicability of the RSNA radiology lexicon (RadLex) in high-grade glioma MRI reporting." ; sc:featureList edam:operation_2422, edam:operation_3436, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RadLex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.radlex.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3452 ; sc:description "Radon backprojection algorithm (simple, not filtered)" ; sc:featureList edam:operation_0249, edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Radon BackProjection Algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/52577-radon-backprojection-algorithm" ; biotools:primaryContact "Enio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_2885 ; sc:citation ; sc:description """a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data. Complete workflow to perform analyses and generate figures from the RADSex paper (https://www.biorxiv.org/content/10.1101/2020.04.22.054866v1). The radsex software is part of RADSex, a computational workflow for the analysis of sex-determination using RAD-Sequencing data. This workflow contains the software radsex and the R package sgtr; a Snakemake implementation of the workflow is available here. This workflow implements all the analyses presented in the RADSex paper and generates figures for each analyses as well as most figures included in the paper. Data is defined in data/info.tsv; reads are downloaded from the NCBI SRA repository and genomes are downloaded from provided links. All parameters are defined in config.yaml.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3216, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "RADSex" ; sc:softwareHelp ; sc:url "https://github.com/SexGenomicsToolkit/radsex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3063, edam:topic_3384, edam:topic_3474 ; sc:citation , "pmcid:PMC9484781", "pubmed:36128510" ; sc:description "RadText is a high-performance Python Radiology Text Analysis System." ; sc:featureList edam:operation_0306, edam:operation_1812, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RadText" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/bionlplab/radtext" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description "Software for processing RAD (Restriction site Associated DNA)Sequencing data. The software is a pipeline for transforming Illumina reads into candidate genetic markers." ; sc:featureList edam:operation_0527 ; sc:name "RADtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.2.4" ; sc:url "https://www.wiki.ed.ac.uk/display/RADSequencing/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053, edam:topic_3168, edam:topic_3516 ; sc:citation , ; sc:description "User-defined perl procedure for performing de novo RAD genotyping in mapping populations. It can deal with both single-end and paired-end RAD sequencing data." ; sc:featureList edam:operation_2429, edam:operation_3196 ; sc:name "RADtyping" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "http://www2.ouc.edu.cn/mollusk/detailen.asp?id=727" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3168, edam:topic_3174, edam:topic_3474, edam:topic_3576 ; sc:citation ; sc:description """A superior method for virus-host prediction. Random Forest Assignment of Hosts. One fundamental question when trying to describe viruses of Bacteria and Archaea is: Which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), which outperformed other methods for virus-host prediction. Our rationale was that the machine could learn the associations between genes and hosts much more efficiently than a human, while also using the information contained in the hypothetical proteins. 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RainbowSTORM is an open-source, user-friendly ImageJ/Fiji plug-in for end-to-end spectroscopic analysis and visualization of sSMLM data. RainbowSTORM provides a variety of spectroscopic processing and post-processing methods that allow users to calibrate, preview, and quantitatively analyze emission spectra acquired using a wide range of sSMLM systems and fluorescent molecules. ImageJ, with "Batteries Included". ImageJ is an open source image processing program designed for scientific multidimensional images. 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RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "rampart" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/TGAC/RAMPART" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0202, edam:topic_0820, edam:topic_3047, edam:topic_3344 ; sc:citation ; sc:description "a web application and database for the exploration and prediction of receptor activity modifying protein interactions" ; sc:name "RampDB" ; sc:url "https://rampdb.biology.gatech.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2058 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_2078 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3518 ; sc:author "Oleksii Nikolaienko" ; sc:citation , "pmcid:PMC8696093", "pubmed:34383893" ; sc:description """an R package for detection of rare aberrantly methylated regions. ramr is an R package for detection of low-frequency aberrant methylation events in large datasets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), and to generate sets of all possible regions to be used as reference sets for enrichment analysis.""" ; sc:featureList edam:operation_3204, edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ramr" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/ramr/" ; biotools:primaryContact "Oleksii Nikolaienko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3295, edam:topic_3517 ; sc:citation ; sc:description "A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "RaMWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ramwas.html" ; biotools:primaryContact "Andrey A Shabalin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6305237", "pubmed:30613396" ; sc:description "R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations." ; sc:featureList edam:operation_3359, edam:operation_3501, edam:operation_3797 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ranacapa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gauravsk/ranacapa" ; biotools:primaryContact "Gaurav Kandlikar", "Madeline Cowen", "Mahendra Mariadassou", "Martinez Arbizu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_0780, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC7310859", "pubmed:32469863" ; sc:description """A fast and accurate method for polyploid haplotype reconstruction. Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. We have designed Ranbow, a new tool for haplotype reconstruction of polyploid genome from short read sequencing data. Ranbow integrates all types of small variants in bi- and multi-allelic sites to reconstruct haplotypes. To evaluate Ranbow and currently available competing methods on real data, we have created and released a real gold standard dataset from sweet potato sequencing data""" ; sc:featureList edam:operation_0292, edam:operation_0487, edam:operation_3196, edam:operation_3227 ; sc:name "Ranbow" ; sc:url "https://www.molgen.mpg.de/ranbow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "randcorr is a MATLAB function that implements the algorithm by Pourahmadi and Wang for generating a random p x p correlation matrix." ; sc:isAccessibleForFree true ; sc:name "randcorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/68810-randcorr" ; biotools:primaryContact "Statovic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3382 ; sc:citation , "pmcid:PMC9169273", "pubmed:35668480" ; sc:description "An easy-to-use utility to generate a big variety of chemical structure depictions (random depiction styles and image augmentations) based on RDKit, CDK, Indigo and PIKAChU." ; sc:featureList edam:operation_0337, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RanDepict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OBrink/RanDepict" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1708 ; sc:encodingFormat edam:format_2076 ; sc:name "RNA secondary structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Secondary structure calculation of non-coding RNA sequences." ; sc:featureList edam:operation_0278 ; sc:name "Randfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/Randfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3179, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description """A Web Server for Data Randomization. High-throughput DNA methylation arrays are susceptible to bias facilitated by batch effects and other technical noise that can alter DNA methylation level estimates. RANDOMIZE is a user-friendly web application that provides an interactive and flexible graphical user interface (GUI) to randomize relevant metadata. Using this tool will minimize chip and position mediated batch effects in microarray studies for an increased validity in inferences from your methylation data. The tool is very helpful for biologist to perform randomization of test samples and insert controls in the data.""" ; sc:featureList edam:operation_0364, edam:operation_0452, edam:operation_2428 ; sc:name "RANDOMIZE" ; sc:url "https://coph-usf.shinyapps.io/RANDOMIZE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0634, edam:topic_2269, edam:topic_3053 ; sc:description "Software of detecting disease-causing single-locus effects and gene-gene interactions. The method is based on finding differences of genotype pattern frequencies between case and control individuals. Those single-nucleotide polymorphism markers with largest single-locus association test statistics are included in a pattern." ; sc:featureList edam:operation_3659 ; sc:name "randompat" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.jurgott.org/linkage/randompat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2259, edam:topic_3063 ; sc:citation ; sc:description "This package performs Random Walk with Restart on multiplex and heterogeneous networks." ; sc:featureList edam:operation_2454 ; sc:license "GPL-2.0" ; sc:name "RandomWalkRestartMH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RandomWalkRestartMH.html" ; biotools:primaryContact "Alberto Valdeolivas Urbelz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3379 ; sc:citation ; sc:description "A suite of classes and functions for randomizing patients in clinical trials." ; sc:featureList edam:operation_3802 ; sc:license "Artistic-2.0" ; sc:name "randPack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/randPack.html" ; biotools:primaryContact "Robert Gentleman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3056, edam:topic_3299 ; sc:citation ; sc:description """An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species’ responses to environmental changes. RangeShifter-software-and-documentation. An R package as interface to the RangeShifter simulation platform. Executables, manuals and tutorial data for RangeShifter v2 GUI and batch mode application. RangeShiftR workshop at IBS 2022. We’ve been picked to host a RangeShiftR workshop at the IBS 2022 in Vancouver!.""" ; sc:featureList edam:operation_0282, edam:operation_3946 ; sc:name "RangeShifter" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://rangeshifter.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC8464058", "pubmed:34214174" ; sc:description "Rank-In is constructed to analyze the consolidated cancer transcriptomics data cross microarray and RNA-seq technologies." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:name "Rank-In" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.badd-cao.net/rank-in/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3315, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7585212", "pubmed:33097004" ; sc:description """A rank-based marker selection method for high throughput scRNA-seq data. A marker selection method for scRNA-seq data based on rank correlation. See the notebook RankCorr-example.ipynb for a full walkthough of how to run the method; an outline is presented below.""" ; sc:featureList edam:operation_2495, edam:operation_3557, edam:operation_3891, edam:operation_3935 ; sc:name "RANKCORR" ; sc:url "https://github.com/ahsv/RankCorr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3277 ; sc:citation ; sc:description "Analyze gene expression data, feature selection and ranking genes based on the predictive power of each gene to classify samples into functional or disease categories." ; sc:featureList edam:operation_2495 ; sc:name "Rankgene" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.1" ; sc:url "http://genomics10.bu.edu/yangsu/rankgene/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2332 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3299 ; sc:citation , ; sc:description "Report taxonomic abundance, based on BLAST hits." ; sc:featureList edam:operation_3460 ; sc:name "rankoptimizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.5" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/taxonomy_analysis/rankoptimizer/0.0.5" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:12175724" ; sc:description "This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here." ; sc:featureList edam:operation_0416 ; sc:name "Rankpep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://imed.med.ucm.es/Tools/rankpep.html" ; biotools:primaryContact "SECRETARIA GENERAL DE CIENCIA, TECNOLOGIA E INNOVACION OF SPAIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification." ; sc:featureList edam:operation_3223 ; sc:name "RankProd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RankProd.html" ; biotools:primaryContact "Francesco Del Carratore" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:name "Nucleic acid sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3168, edam:topic_3308 ; sc:citation ; sc:description "It is a web tool that performs a quite complete and customizable RNA-Seq pipeline and provides an easy and intuitive access through a web interface to intermediate and final results. The main aim of RAP is to provide to users information about gene and transcript expression, differential expression, alternative splicing, polyA signals, fusion transcripts, etc." ; sc:featureList edam:operation_3198 ; sc:name "RAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-CINECA" ; sc:softwareVersion "1" ; sc:url "https://bioinformatics.cineca.it/rap" ; biotools:primaryContact "Graziano Pesole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Protein Repeats. This server allows the analysis of one protein structure of interested to determine periodicity in protein structures." ; sc:featureList edam:operation_2423 ; sc:name "Raphael" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://protein.bio.unipd.it/raphael/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2814, edam:topic_3538 ; sc:citation "pubmed:23732563" ; sc:description "Server providing fast and accurate sequence based prediction of protein disorder content." ; sc:featureList edam:operation_2479 ; sc:name "RAPID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biomine.cs.vcu.edu/servers/RAPID/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation , "pmcid:PMC5035472", "pubmed:27663265" ; sc:description "We present rapidGSEA – a software suite consisting of two tools for facilitating permutation-based gene set enrichment analysis(GSEA): cudaGSEA and ompGSEA. cudaGSEA is a CUDA-accelerated tool using fine-grained parallelization schemes on massively parallel architectures while ompGSEA is a coarse-grained multi-threaded tool for multi-core CPUs." ; sc:featureList edam:operation_2403 ; sc:license "Unlicense" ; sc:name "rapidGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/gravitino/cudaGSEA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3335, edam:topic_3572 ; sc:citation , "pmcid:PMC8957280", "pubmed:35345583" ; sc:description "A package for preprocessing, analyzing and visualizing cardiac data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RapidHRV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/rapidhrv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Two innovators coming together to transform business analytics. Altair acquires RapidMiner. Altair and RapidMiner share the same vision to make data analytics simple enough for all users, but scalable, governed, and safe enough for all enterprises. RapidMiner is the enterprise-ready data science platform that amplifies the collective impact of your people, expertise and data for breakthrough competitive advanta""" ; sc:featureList edam:operation_2409, edam:operation_3438 ; sc:license "AGPL-3.0" ; sc:name "Rapidminer" ; sc:url "https://rapidminer.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "A tool for fast canonical neighbor-joining tree construction." ; sc:featureList edam:operation_0323 ; sc:name "RapidNJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "birc.au.dk" ; sc:softwareVersion "2.3.0.2" ; sc:url "http://birc.au.dk/software/rapidnj/" ; biotools:primaryContact "Martin Simonsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0097, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:18460546" ; sc:description "RAPIDO conducts 3D alignments of crystal structures of different protein molecules in the presence of conformational change." ; sc:featureList edam:operation_0295, edam:operation_0320, edam:operation_0474, edam:operation_0477 ; sc:name "RAPIDO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://webapps.embl-hamburg.de/rapido" ; biotools:primaryContact "RAPIDO Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3517 ; sc:citation ; sc:description """A rapid polygenic score calculator for summary GWAS data without validation dataset. Polygenic scores (PGS) aim to predict complex traits at an individual level based on genetic data. Computation of PGS is based on simply ascertained genome-wide association summary statistics but typically requires an independent test dataset to tune PGS parameters, and for the more sophisticated methods, the computation of LD matrices. Internally tuned methods have recently been proposed that obviate the need for a test dataset, but they remain computationally intensive to run. Here we present RápidoPGS, a flexible and fast method to compute PGS without the need to compute LD-matrices, requiring only summary-level GWAS datasets. Based on fine-mapping principles, RápidoPGS computes the posterior probability that each variant is causal, which in turn is used to shrink effect sizes adaptively as a function of LD and strength of association""" ; sc:featureList edam:operation_2428, edam:operation_3659, edam:operation_3791 ; sc:name "RapidoPGS" ; sc:url "https://github.com/GRealesM/RapidoPGS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:24990604" ; sc:description "R package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA." ; sc:featureList edam:operation_2423 ; sc:name "RAPIDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/RAPIDR/index.html" ; biotools:primaryContact "Kitty Lo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0176, edam:topic_2814 ; sc:citation ; sc:description "Rapid determination of RMSDs corresponding to motions of flexible molecules." ; sc:featureList edam:operation_0244 ; sc:license "BSD-2-Clause" ; sc:name "RapidRMSD" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://team.inria.fr/nano-d/software/RapidRMSD/" ; biotools:primaryContact "Sergei Grudinin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2269, edam:topic_3321, edam:topic_3518 ; sc:citation "pubmed:12737936" ; sc:description "Run t test on pairs of array experiments." ; sc:featureList edam:operation_0571, edam:operation_2238 ; sc:name "rapier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hpcf.upr.edu/~humberto/cmb/microarray/spatial/index.html" ; biotools:primaryContact "Humberto Ortiz Zuazaga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3308 ; sc:citation , "pmcid:PMC4908361", "pubmed:27307617" ; sc:contributor ; sc:description "RapMap is a tool implementing quasi-mapping and is capable of mapping sequencing reads to a target transcriptome substantially faster than existing alignment tools." ; sc:featureList edam:operation_2520 ; sc:license "GPL-3.0" ; sc:name "RapMap" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/COMBINE-lab/RapMap" ; biotools:primaryContact "Rob Patro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2830, edam:topic_3360 ; sc:citation ; sc:description """a platform of ratiometric bioluminescent sensors for homogeneous immunoassays. Abstract Heterogeneous immunoassays such as ELISA have become indispensable in modern bioanalysis, yet translation into easy-to-use point-of-care assays is hindered by their dependence on external calibration and multiple washing and incubation steps. Here, we introduce RAPPID ( Ra tiometric P lug-and- P lay Immuno d iagnostics), a “mix-and-measure” homogeneous immunoassay platform that combines highly specific antibody-based detection with a ratiometric bioluminescent readout that can be detected using a basic digital camera. The concept entails analyte-induced complementation of split NanoLuc luciferase fragments, photoconjugated to an antibody sandwich pair via protein G adapters. We also introduce the use of a calibrator luciferase that provides a robust ratiometric signal, allowing direct in-sample calibration and quantitative measurements in complex media such as blood plasma""" ; sc:featureList edam:operation_3359, edam:operation_3799 ; sc:name "RAPPID" ; sc:url "https://doi.org/10.1101/2020.10.31.363044" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_3474, edam:topic_3957 ; sc:citation ; sc:description "Regularised Automatic Prediction of Protein-Protein Interactions using Deep Learning" ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3094 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "RAPPPID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jszym/rapppid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation "pubmed:21575167" ; sc:description "Fast protein similarity search tool for short reads that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length." ; sc:featureList edam:operation_0292 ; sc:license "GPL-3.0" ; sc:name "RAPSearch" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://omics.informatics.indiana.edu/mg/RAPSearch2/" ; biotools:primaryContact "Yongan Zhao", "Yuzhen Ye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0632, edam:topic_3168, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "A variational autoencoder with profile hidden Markov model for generative aptamer discovery." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0296 ; sc:license "MIT" ; sc:name "RaptGen" ; sc:url "https://github.com/hmdlab/raptgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_0203, edam:topic_3168, edam:topic_3316 ; sc:citation , "pmcid:PMC8313605", "pubmed:34337360" ; sc:description "A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences." ; sc:featureList edam:operation_0224, edam:operation_3211, edam:operation_3472, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Raptor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/seqan/raptor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_2275, edam:topic_2814 ; sc:citation , ; sc:description "Prediction of 3D structures (secondary and tertiary structures as well as solvent accessibility and disordered regions) for protein sequences without close homologs in the Protein Data Bank (PDB)." ; sc:featureList edam:operation_0271, edam:operation_0474, edam:operation_2423 ; sc:name "RaptorX" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://raptorx.uchicago.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3474 ; sc:citation ; sc:description "The predicting program of ResNet for a target or a list of proteins by using an ensemble of trained models." ; sc:featureList edam:operation_0249, edam:operation_0474, edam:operation_3432 ; sc:name "RaptorX-Angle" ; sc:url "https://github.com/lacus2009/RaptorX-Angle" ; biotools:primaryContact "Yujuan Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3673 ; sc:citation "pubmed:25686638" ; sc:description "Read Pair and Split Read methods are used to identify structural variants in paired-end WGS data." ; sc:featureList edam:operation_3197 ; sc:name "RAPTR-SV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/njdbickhart/RAPTR-SV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0654, edam:topic_3047, edam:topic_3168 ; sc:citation , "pmcid:PMC7641312", "pubmed:32537639" ; sc:description """in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information. Please see the wiki for detail usage. RaptRanker is a software for RNA aptamer selection from HT-SELEX experiment data based on local sequence and structure information.""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_3938 ; sc:license "MIT" ; sc:name "RaptRanker" ; sc:url "https://github.com/hmdlab/RaptRanker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:24894501" ; sc:description "Program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing." ; sc:featureList edam:operation_3197 ; sc:name "RAREMETAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/RAREMETAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2815, edam:topic_3053 ; sc:citation , "pmcid:PMC9069075", "pubmed:35298919" ; sc:description "A simulation method for very rare genetic variants." ; sc:featureList edam:operation_0282 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RAREsim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=35298919" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3168, edam:topic_3325 ; sc:citation ; sc:description "A suite for analysis of rare genomic variants in whole genome sequencing data. It annotates, filters and presents genomic variants in a global, per chromosome way." ; sc:featureList edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "RareVariantVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RareVariantVis.html" ; biotools:primaryContact "Tomasz Stokowy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "This package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples." ; sc:featureList edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "Rariant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rariant.html" ; biotools:primaryContact "Julian Gehring" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3379 ; sc:citation ; sc:description "Provides a SimBiology model implementation of the Renin-Angiotensin-System." ; sc:featureList edam:operation_3891, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "Renin-Angiotensin-System (RAS) model for SimBiology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/37759-renin-angiotensin-system-ras-model-for-simbiology" ; biotools:primaryContact "Sven Mesecke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3175, edam:topic_3512, edam:topic_3930 ; sc:citation , "pmcid:PMC9612819", "pubmed:36251721" ; sc:description "Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL)." ; sc:featureList edam:operation_3227, edam:operation_3472, edam:operation_3962 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "RaScALL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/j-rehn/RaScALL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0769 ; sc:citation ; sc:description "Rapid Assessment Of selection in Clades Through Molecular Sequence Analysis." ; sc:featureList edam:operation_0310, edam:operation_0324, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RASCL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/veg/RASCL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_2640, edam:topic_3305 ; sc:citation , "pubmed:32721138" ; sc:description """Assessing spatial confounding in cancer disease mapping using R. RASCO: An R package to Alleviate the Spatial Confounding.""" ; sc:featureList edam:operation_2429, edam:operation_3435, edam:operation_3659 ; sc:name "RASCO" ; sc:url "https://github.com/douglasmesquita/RASCO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0209, edam:topic_0769, edam:topic_3343, edam:topic_3474 ; sc:citation ; sc:description """Rapid Machine Learned Synthesizability Classification from AI Driven Retrosynthetic Planning. Retrosynthetic Accessibility (RA) score. RAscore is a score learned from the predictions of a computer aided synthesis planning tool (AiZynthfinder: https://github.com/MolecularAI/aizynthfinder). RAscore is intended to be a binary score, indicating whether the underlying computer aided synthesis planning tool can find a route (1) or not (0) to a given compound.""" ; sc:featureList edam:operation_3938 ; sc:license "MIT" ; sc:name "RAscore" ; sc:url "https://github.com/reymond-group/RAscore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0099, edam:topic_2885, edam:topic_3170 ; sc:citation "pubmed:26323713" ; sc:description "Short-read aligner with high accuracy, suitable for applications where SNPs, RNA editing sites or other types of small variants are sought after in RNA-Seq data sets." ; sc:featureList edam:operation_3198 ; sc:name "RASER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.ibp.ucla.edu/research/xiao/RASER.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0092, edam:topic_0166, edam:topic_2275, edam:topic_2815 ; sc:citation "pubmed:10973060", "pubmed:7482707" ; sc:description "3-D structure viewer, web browser helper application." ; sc:featureList edam:operation_0295, edam:operation_0297, edam:operation_0322, edam:operation_0451, edam:operation_2476 ; sc:name "RasMol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bernstein-plus-sons.com/software/rasmol/" ; biotools:primaryContact "Herbert J. Bernstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:19417073" ; sc:description "The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protein structures exhibiting resides of similar topology." ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_0321, edam:operation_2487, edam:operation_2950 ; sc:name "RASMOT-3D PRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodev.extra.cea.fr/rasmot3d/" ; biotools:primaryContact "Philippe Cuniasse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3293 ; sc:citation "pubmed:25819445" ; sc:description "Tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC), BayesTraits and ChromEvol." ; sc:featureList edam:operation_3478 ; sc:name "RASP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mnh.scu.edu.cn/soft/blog/RASP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0621, edam:topic_0632, edam:topic_0780 ; sc:citation , "pubmed:33068412" ; sc:description """an atlas of transcriptome-wide RNA secondary structure probing data. RASP (RNA Alatas of Structure Probing) is a transcriptome-scale RNA structure probing database. Currently, RASP contains 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-Seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data.""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2495, edam:operation_3642 ; sc:name "RASP" ; sc:url "http://rasp.zhanglab.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_2330 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2269, edam:topic_3055, edam:topic_3307 ; sc:author "Natsuhiko Kumasaka" ; sc:citation ; sc:description "Map QTLs for sequenced based cellular traits by combining population and allele-specific signals." ; sc:featureList edam:operation_3232 ; sc:isAccessibleForFree true ; sc:name "RASQUAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "sanger.ac.uk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/dg13/rasqual" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3315 ; sc:citation , "pmcid:PMC3675459", "pubmed:23585278" ; sc:description "RASS is a webserver for RNA alignment in the joint sequence-structure space." ; sc:featureList edam:operation_0278, edam:operation_0302, edam:operation_0502 ; sc:name "RASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cloud.stat.fsu.edu/RASS/" ; biotools:primaryContact "RASS support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3293 ; sc:citation ; sc:description "\"RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree.\"" ; sc:featureList edam:operation_0226 ; sc:name "RAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rast.nmpdr.org/" ; biotools:primaryContact "R.K. Aziz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0654, edam:topic_3301 ; sc:citation "pubmed:17678530" ; sc:description "Automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not." ; sc:featureList edam:operation_2423 ; sc:name "RASTA-Bacteria" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genoweb1.irisa.fr/duals/RASTA-Bacteria/" ; biotools:primaryContact "Emeric Sevin", "Frédérique Hubler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:18488322" ; sc:description "Set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Output is to pixel image files with 24 bits of color information per pixel." ; sc:featureList edam:operation_0570 ; sc:name "Raster3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://skuld.bmsc.washington.edu/raster3d/raster3d.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3293, edam:topic_3306, edam:topic_3315 ; sc:citation ; sc:description """a global view of the free and open source rasterdiv R package under a coding perspective. Stable versions can be installed from the CRAN:. rasterdiv is a package for the R statistical software and environment. It aims to provide functions to apply Information Theory based diversity indexes on RasterLayer or numerical matrices, such as Shannon's entropy or Cumulative Residual Entropy (CRE).""" ; sc:featureList edam:operation_3435 ; sc:name "rasterdiv" ; sc:url "https://github.com/mattmar/rasterdiv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Produces an unbiased subsample of your reads" ; sc:name "rasusa" ; sc:url "https://github.com/mbhall88/rasusa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC7221356", "pubmed:32284342" ; sc:description """A Machine Vision Rodent Tracking Camera and Closed Loop Control System. RAT is a low-cost system to track and report mouse activity while they are contained in a simple arena. The system uses an OpenMV M7 microcontroller to acquire images of the arena and process them in real-time to report mouse centroid data to a text file. This data can be used as a measure of mouse movement (i.e speed and distance traveled) for various activity studies. This project is currently ongoing as we test and perfect the prototypes.""" ; sc:featureList edam:operation_3359 ; sc:name "RAT" ; sc:url "https://hackaday.io/project/162481-rodent-arena-tracker-rat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3673 ; sc:citation ; sc:description """Ratatosk – Hybrid error correction of long reads enables accurate variant calling and assembly. Phased hybrid error correction of long reads using colored de Bruijn graphs. Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.""" ; sc:featureList edam:operation_0524, edam:operation_3195, edam:operation_3227, edam:operation_3454, edam:operation_3798 ; sc:license "BSD-2-Clause" ; sc:name "Ratatosk" ; sc:url "https://github.com/DecodeGenetics/Ratatosk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7237151", "pubmed:32009518" ; sc:description """the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. Rat Atlas of Tissue-specific and Enriched miRs. RATEmiRs- a database of rat microRNA-Seq data in several tissues. 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Organ-specific pipelines detects miRs that are specific for a particular set of tissues that comprise of an organ.""" ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "RATEmiRs" ; sc:url "https://www.niehs.nih.gov/ratemirs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3934 ; sc:description "Data analysis code and example datasets for ratiometric FRET analysis" ; sc:isAccessibleForFree true ; sc:name "Ratiometric FRET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48437-ratiometric-fret" ; biotools:primaryContact "Jakub Nedbal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC7783408", "pubmed:33414703" ; sc:description """A Fully Convolutional Network for Rodent Brain Lesion Segmentation. 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These gene-keyword relationships are presented as an interactive graph and a table.""" ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:license "MIT" ; sc:name "RatsPub" ; sc:url "https://github.com/chen42/ratspub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654 ; sc:citation ; sc:description "Transfer annotation from a reference (annotated) genome to an unannotated query genome. 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RAVE: R Analysis and Visualization of intracranial Electroencephalography. For all RAVE info, including installation instructions, visit https://openwetware.org/wiki/RAVE.""" ; sc:featureList edam:operation_0337, edam:operation_3214 ; sc:name "RAVE" ; sc:url "https://github.com/beauchamplab/rave" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation ; sc:description """a de novo genome assembler for long reads. Raven is a de novo genome assembler for long uncorrected reads.""" ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3219 ; sc:license "MIT" ; sc:name "Raven" ; sc:url "https://github.com/lbcb-sci/raven" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1208 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585, edam:format_3620 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3722 ; sc:encodingFormat edam:format_1957 ; sc:name "Physiology parameter" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2585, edam:format_3620, edam:format_3750 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3307, edam:topic_3398 ; sc:citation , "pmcid:PMC6207324", "pubmed:30335785" ; sc:description "The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology." ; sc:featureList edam:operation_2497, edam:operation_3439, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RAVEN Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/SysBioChalmers/RAVEN" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3710, edam:format_3712 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3621 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:author "Alexandre Burel", "David Bouyssié" ; sc:citation "pmcid:PMC4349994", "pubmed:25505153" ; sc:contributor "ProFI" ; sc:description "An extension of the ProteoWizard framework enabling the support of the mzDB format. This tools is supported by the Proteomics French Infrastructure ProFI." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "raw2mzDB" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.9" ; sc:url "https://github.com/mzdb/pwiz-mzdb" ; biotools:primaryContact "Alexandre Burel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3174, edam:topic_3474 ; sc:citation , "pmcid:PMC6695225", "pubmed:31415569" ; sc:description "End-to-end Deep Learning using raw Multiple Sequence Alignments | In the last decades, huge efforts have been made in the bioinformatics community to develop machine learning-based methods for the prediction of structural features of proteins in the hope of answering fundamental questions about the way proteins function and their involvement in several illnesses. The recent advent of Deep Learning has renewed the interest in neural networks, with dozens of methods being developed taking advantage of these new architectures. However, most methods are still heavily based pre-processing of the input data, as well as extraction and integration of multiple hand-picked, and manually designed features. Multiple Sequence Alignments (MSA) are the most common source of information in de novo prediction methods. Deep Networks that automatically refine the MSA and extract useful features from it would be immensely powerful" ; sc:featureList edam:operation_0267, edam:operation_0476, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rawMSA" ; sc:operatingSystem "Linux" ; sc:url "https://bitbucket.org/clami66/rawmsa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC8041395", "pubmed:33657803" ; sc:description "A Simple, Vendor-Independent, Raw-Data Quality-Control Tool." ; sc:featureList edam:operation_3218, edam:operation_3359, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "RawBeans" ; sc:url "https://bitbucket.org/incpm/prot-qc/downloads/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174 ; sc:citation , "pmcid:PMC10311405", "pubmed:37387139" ; sc:description "Hash-based mechanism to map raw nanopore signals to a reference genome in real-time. To achieve this, it 1) generates an index from the reference genome and 2) efficiently and accurately maps the raw signals to the reference genome such that it can match the throughput of nanopore sequencing even when analyzing large genomes." ; sc:featureList edam:operation_3198, edam:operation_3208, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RawHash" ; sc:url "https://github.com/CMU-SAFARI/RawHash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:35080628" ; sc:description "An R Shiny app for assessing LC–MS system performance by visualising instrument log files and monitoring raw quality control samples within a project." ; sc:featureList edam:operation_0337, edam:operation_3218, edam:operation_3627 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RawHummus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bcdd.shinyapps.io/RawHummus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0196, edam:topic_3520 ; sc:citation ; sc:description """Direct access to raw mass spectrometry data in R. R interface for Thermo Fisher Scientifc raw files branched from rawDiag. This package wraps the functionality of the RawFileReader .NET assembly. Within the R environment spectra and chromatograms are represented by S3 objects. All objects are currently kept in memory. Later versions will support on-disc backend processing and lazy evaluation. Please install the latest release from https://github.com/fgcz/rawR/releases according to the provided instructions.""" ; sc:featureList edam:operation_0310, edam:operation_3436, edam:operation_3860 ; sc:name "rawR" ; sc:url "https://github.com/fgcz/rawR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation , "pubmed:33686856" ; sc:description """Direct Access to Orbitrap Data and Beyond. R interface for Thermo Fisher Scientific raw files branched from rawDiag. This package wraps the functionality of the RawFileReader .NET assembly. Within the R environment, spectra and chromatograms are represented by S3 objects.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3633 ; sc:isAccessibleForFree true ; sc:name "rawrr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fgcz/rawrr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_2330 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:30462513" ; sc:description "A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RawTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "https://github.com/kevinkovalchik/RawTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520 ; sc:citation , "pubmed:32526479" ; sc:description """A data assessment tool for proteomics and cross-linking mass spectrometry experiments. RawVegetable requires Thermo mass spectrometer RAW files, *.mzML or Agilent files for the main feature to function. The chromatography reproducibility feature requires PatternLab for proteomics’ *.xic or *.plp files or a SIM-XL output file. In order to view identifications along the chromatogram, a SIM-XL file is required.""" ; sc:featureList edam:operation_3203, edam:operation_3628, edam:operation_3629 ; sc:name "RawVegetable" ; sc:url "http://patternlabforproteomics.org/rawvegetable" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation , , "pmcid:PMC3998144", "pubmed:16928733", "pubmed:24451623" ; sc:description "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies." ; sc:featureList edam:operation_0324, edam:operation_2403 ; sc:name "RAxML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sco.h-its.org/exelixis/web/software/raxml/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070 ; sc:author "Sébastien Boisvert" ; sc:citation , ; sc:contributor "Canadian Institutes of Health Research (CIHR), and other", "François Laviolette", "Frédéric Raymond", "Jacques Corbeil", "Élénie Godzaridis" ; sc:description "De novoassembly of single genomes and metagenomes. Also analyses microbe abundance and performs taxonomic profiling as well as making gene ontology profiling. It can also compare genomic content between samples." ; sc:featureList edam:operation_0310 ; sc:funder "Canadian Institutes of Health Research (CIHR), and other" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Ray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "Department of Molecular Medicine, Faculty of Medicine, Laval University", "Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "Infectious Diseases Research Center, CHUQ Research Center", "NTNU" ; sc:softwareHelp ; sc:softwareVersion "2.3.1" ; sc:url "http://denovoassembler.sourceforge.net" ; biotools:primaryContact "Animesh Sharma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3382 ; sc:citation , "pmcid:PMC7818000" ; sc:description """Tools and tutorial on practical ray tracing for microscopy. This code aims to provide a simple ray tracing module for calculating various properties of optical paths (object, image, aperture stops, field stops). It makes use of ABCD matrices and does not consider aberrations (spherical or chromatic). Since it uses the ABCD formalism (or Ray matrices, or Gauss matrices) it can perform tracing of rays and gaussian laser beams.""" ; sc:featureList edam:operation_0337, edam:operation_0479 ; sc:license "MIT" ; sc:name "raytracing" ; sc:url "https://github.com/DCC-Lab/RayTracing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation "pubmed:19592482" ; sc:description "RazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds." ; sc:featureList edam:operation_0495, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "RazerS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/seqan/seqan/tree/master/apps/razers" ; biotools:primaryContact "Anne-Katrin Emde", "David Weese" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:description """RazerS 3 is a tool for mapping millions of short genomic reads onto a reference genome. It was designed with focus on mapping next-generation sequencing reads onto whole DNA genomes. RazerS 3 searches for matches of reads with a percent identity above a given threshold (-i X), whereby it detects alignments with mismatches as well as gaps.""" ; sc:featureList edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "razers3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/seqan/seqan/tree/master/apps/razers3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2840, edam:topic_3174, edam:topic_3510 ; sc:citation ; sc:description """Annotating eukaryotic and toxin-specific signal peptides using Razor. Razor is a tool to detect signal peptides for eukaryotic protein sequences. Optimise your protein coding sequences using smarter tools and algorithms!. Razor detects signal peptide in the given sequence. If signal peptide is found, it also checks if the signal peptide carries toxic proteins or is from fungi. This is done using 5 random forest model at each detection step. Consequently, we have 5 scores for each step.""" ; sc:featureList edam:operation_0250, edam:operation_0418, edam:operation_0422 ; sc:name "Razor" ; sc:url "https://tisigner.com/razor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0780, edam:topic_3474, edam:topic_3678 ; sc:citation "pubmed:17083731" ; sc:description "A Support Vector Machine-learned tool to predict rice blast severity based on weather factors." ; sc:featureList edam:operation_2428, edam:operation_2454, edam:operation_3659 ; sc:name "RB-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/rbpred/" ; biotools:primaryContact "Dr. G.P.S. Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3518 ; sc:citation , "pmcid:PMC10439545", "pubmed:37596553" ; sc:description "Simulation of phenotype / genotype data under assortative mating. 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RBCeq is an integrated bioinformatics webserver to characterize blood group profiles from genomics data. The software uses manually curated, publicly available database(s) listing antigen variants and reports known, novel and rare blood group variants. RBCeq is fully automated and allows seamless analysis and visualization through a user-friendly interface.""" ; sc:featureList edam:operation_0252, edam:operation_3192, edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "RBCeq" ; sc:softwareHelp ; sc:url "https://www.rbceq.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3063, edam:topic_3303, edam:topic_3382 ; sc:citation , "pubmed:33119516" ; sc:description """Clustering-Based Dual Deep Learning Architecture for Detecting Red Blood Cells in Malaria Diagnostic Smears. RBCNet for cell detecton using a dual deep learning architecture. Computer-assisted algorithms have become a mainstay of biomedical applications to improve accuracy and reproducibility of repetitive tasks like manual segmentation and annotation.""" ; sc:featureList edam:operation_3432, edam:operation_3552 ; sc:name "RBCNet" ; sc:url "https://github.com/nlm-malaria/RBCNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0736, edam:topic_0820, edam:topic_3542 ; sc:citation "pubmed:10736778", "pubmed:10877849", "pubmed:12824436" ; sc:description "Constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions, free registration is required to use all features." ; sc:featureList edam:operation_0267, edam:operation_2486, edam:operation_2488 ; sc:name "RbDe" ; sc:url "http://icb.med.cornell.edu/crt/RbDe/index.xml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3334, edam:topic_3419 ; sc:citation , "pmcid:PMC9719467", "pubmed:36463304" ; sc:description "An open-source software to detect REM sleep without atonia according to visual scoring criteria." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RBDtector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aroethen/RBDtector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library." ; sc:featureList edam:operation_0224 ; sc:license "Artistic-2.0" ; sc:name "RBGL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RBGL.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3047, edam:topic_3794 ; sc:citation , "pmcid:PMC8164131", "pubmed:34136090" ; sc:description "A user-friendly server for RNA binding site prediction." ; sc:featureList edam:operation_0278, edam:operation_2441, edam:operation_2464, edam:operation_3902, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RBinds" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhaoserver.com.cn/RBinds/RBinds.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3372 ; sc:citation , "pubmed:35323899" ; sc:description "User-Friendly R Interface to Biologic Web Services' API." ; sc:featureList edam:operation_0224, edam:operation_3431, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rbioapi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rbioapi.moosa-r.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_0622, edam:topic_3053, edam:topic_3518 ; sc:citation ; sc:description "Functions and datasets and examples to accompany the monograph R For Bioinformatics." ; sc:featureList edam:operation_2403, edam:operation_2495 ; sc:license "Artistic-2.0" ; sc:name "RBioinf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RBioinf.html" ; biotools:primaryContact "Robert Gentleman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0659, edam:topic_3053 ; sc:citation , "pmcid:PMC5768164", "pubmed:29340253" ; sc:description "Simple to use machine learning-based miRNA gene set analysis." ; sc:featureList edam:operation_2495 ; sc:name "RBiomirGS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jzhangc/git_RBiomirGS" ; biotools:primaryContact "Kenneth B. Storey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , "pubmed:23274212" ; sc:description "Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported." ; sc:featureList edam:operation_1812 ; sc:license "GPL-2.0" ; sc:name "rBiopaxParser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rBiopaxParser.html" ; biotools:primaryContact "Frank Kramer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "RBM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RBM.html" ; biotools:primaryContact "Dongmei Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3305, edam:topic_3517 ; sc:citation ; sc:description "RBMR is a Mendelian randomization (MR) method to estimate the causal effect by accounting for the LD structure, systematic pleiotropy and idiosyncratic pleiotropy simultaneously in a unified framework." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3659 ; sc:name "RBMR" ; sc:url "https://github.com/AnqiWang2021/RBMR" ; biotools:primaryContact "Zhonghua Liu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_1929, edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0659 ; sc:author "Marek Schwarz" ; sc:citation , , "pubmed:33523120" ; sc:contributor ; sc:description "A tool for analyzing BLAST search output for RNA sequences." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "rboAnalyzer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.1.4" ; sc:url "http://rboanalyzer.elixir-czech.cz/" ; biotools:primaryContact "Jiří Vohradský" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2275, edam:topic_2814 ; sc:citation ; sc:description "Fully automated protein structure prediction. 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The package is used by the QuasR bioconductor package. 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RBP2GO is a comprehensive database dedicated to the analysis of RNA-binding proteins, their interactions and functions. RBP2GO offers three search options for each species, which can be accessed via the sidebar under SEARCH SPECIES. More details can be found in the HELP menu.""" ; sc:featureList edam:operation_2421, edam:operation_3901, edam:operation_3902 ; sc:name "RBP2GO" ; sc:url "https://RBP2GO.DKFZ.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3320, edam:topic_3382, edam:topic_3407 ; sc:citation , "pmcid:PMC9825414", "pubmed:36321651" ; sc:description "A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins." ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3553, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "RBP Image Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rnabiology.ircm.qc.ca/RBPImage/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0099, edam:topic_0128, edam:topic_3794 ; sc:description "Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs" ; sc:license "MIT" ; sc:name "RBPBench" ; sc:softwareHelp ; sc:url "https://github.com/michauhl/RBPBench" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0128, edam:topic_3542 ; sc:citation , "pubmed:35662470" ; sc:description "Quantitative Prediction of Protein-RNA Interactions." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2441, edam:operation_3901, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:name "RBPBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioserv.mps.ohio-state.edu/RBPBind/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32191896" ; sc:description "Improved Predicting of The Sequence Specificities of RNA Binding Proteins by Deep Learning." ; sc:featureList edam:operation_0327, edam:operation_0445, edam:operation_3901, edam:operation_3902 ; sc:name "RBPCNN" ; sc:url "https://home.jbnu.ac.kr/NSCL/RBPCNN.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_0749, edam:topic_3656 ; sc:citation "pubmed:21036867" ; sc:description "The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. The database is accessible by a web interface which allows browsing by domain or by organism, searching and export of records, and bulk data downloads. Users can also use RBPDB to scan sequences for RBP-binding sites." ; sc:featureList edam:operation_0239, edam:operation_0303, edam:operation_2575, edam:operation_3092, edam:operation_3222 ; sc:name "RBPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rbpdb.ccbr.utoronto.ca/" ; biotools:primaryContact "RBPDB Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:33780344" ; sc:description "rBPDL is a tool for predicting RNA-binding proteins using deep learning." ; sc:featureList edam:operation_3901, edam:operation_3902, edam:operation_3927 ; sc:name "rBPDL" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/nmt315320/rBPDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0623, edam:topic_0780, edam:topic_3512 ; sc:citation , "pubmed:37158175" ; sc:description "Computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features." ; sc:featureList edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "RBPLight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://iasri-sg.icar.gov.in/rbplight/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3125, edam:topic_3511, edam:topic_3512, edam:topic_3534 ; sc:citation , "pmcid:PMC4086114", "pubmed:24829458" ; sc:description "RBPmap is a web server for mapping binding sites of RNA-binding proteins." ; sc:featureList edam:operation_0445, edam:operation_2429, edam:operation_2575, edam:operation_3092, edam:operation_3222 ; sc:name "RBPmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rbpmap.technion.ac.il/" ; biotools:primaryContact "Yael Mandel Gutfreund's lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0082, edam:topic_0160, edam:topic_0166 ; sc:citation "pubmed:23754853" ; sc:description "Web server for the discovery of sequence and structure preferences of RNA-binding proteins. 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It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing." ; sc:featureList edam:operation_3195 ; sc:name "Rcorrector" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mourisl/Rcorrector/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_2640 ; sc:citation "pubmed:19946373" ; sc:description "Find genes (or miRNAs) that have a consistently high rank across different lists." ; sc:featureList edam:operation_2423 ; sc:name "RCoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.cs.technion.ac.il/people/zohar/RCoS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_3170 ; sc:citation "pubmed:25322836" ; sc:description "Software for simple and flexible RNA-Seq read counting. It allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions." ; sc:featureList edam:operation_3563 ; sc:name "Rcount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.botinst.uzh.ch/research/development/grossnik/rcount.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1196, edam:format_1476, edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196, edam:format_1476, edam:format_1929 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2854 ; sc:encodingFormat edam:format_3033, edam:format_3547 ; sc:name "Position-specific scoring matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2258 ; sc:citation , "pubmed:25246429" ; sc:description "This molecular informatics toolkit offers a comprehensive integration of bioinformatics and chemoinformatics tools for drug discovery." ; sc:featureList edam:operation_0482 ; sc:license "Artistic-2.0" ; sc:name "Rcpi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.6" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rcpi.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_0821, edam:topic_2814, edam:topic_3510 ; sc:citation , , "pmcid:PMC8826025", "pmcid:PMC9825554", "pubmed:34864908", "pubmed:36420884" ; sc:description "Improved Annotation, Search, and Visualization of Membrane Protein Structures Archived in the PDB." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_2421, edam:operation_3431, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:name "RCSB Protein Data Bank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rcsb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:25183487" ; sc:description "The RCSB Protein Data Bank mobile app is the official mobile app of the RCSB PDB. It provides fast, on-the-go access to the RCSB PDB resources. The app enables the general public, researchers and scholars to search the Protein Data Bank and visualize protein structures using either a WiFi or cellular data connection." ; sc:featureList edam:operation_0570 ; sc:name "RCSB PDB Mobile" ; sc:softwareHelp ; sc:url "http://www.rcsb.org/pdb/static.do?p=mobile/RCSBapp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Rank Constrained Similarity Learning (RCSL) is Clustering single-cell RNA-seq data by rank constrained similarity learning. RCSL is an R toolkit for single-cell clustering and trajectory analysis using single-cell RNA-seq data." ; sc:featureList edam:operation_0244, edam:operation_2939, edam:operation_3432 ; sc:name "RCSL" ; sc:url "https://github.com/QinglinMei/RCSL" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Robust decomposition of cell type mixtures in spatial transcriptomics. Robust Cell Type Decomposition (RCTD).""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "RCTD" ; sc:url "https://github.com/dmcable/RCTD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3170 ; sc:citation , "pubmed:33772584" ; sc:description "RcwlPipelines (For users) and Rcwl (For developers) are R and Bioconductor toolchain for bioinformatics tools and workflows. They are an R interface to the Common Workflow Language. The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines." ; sc:featureList edam:operation_0224, edam:operation_3227, edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "RcwlPipelines and Rcwl" ; sc:url "https://rcwl.org" ; biotools:primaryContact , "Qiang Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "RCX – an R package adapting the Cytoscape Exchange format for biological networks." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RCX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/frankkramer-lab/RCX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Vizualize, analyze and explore networks using Cytoscape via R." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "MIT" ; sc:name "RCy3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.84" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RCy3.html" ; biotools:primaryContact "Alexander Pico", "Paul Shannon", "Tanja Muetze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation ; sc:description "Interactive viewing and exploration of graphs, connecting R to Cytoscape.js." ; sc:featureList edam:operation_2940 ; sc:license "GPL-2.0" ; sc:name "RCyjs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RCyjs.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC3751905", "pubmed:23837656" ; sc:description "Interactvive viewing and exploration of graphs, connecting R to Cytoscape." ; sc:featureList edam:operation_0571, edam:operation_2940 ; sc:license "GPL-2.0" ; sc:name "RCytoscape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RCytoscape.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3325, edam:topic_3337 ; sc:citation , "pmcid:PMC4124112", "pubmed:25029978" ; sc:description "Integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research." ; sc:featureList edam:operation_2421, edam:operation_3197, edam:operation_3431, edam:operation_3561, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:name "RD-connect" ; sc:url "http://catalogue.rd-connect.eu" ; biotools:primaryContact "Libby Wood" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3063, edam:topic_3325, edam:topic_3473 ; sc:citation , , "pmcid:PMC4124112", "pubmed:25029978", "pubmed:35178824" ; sc:contributor , "Alberto Corvó", "Anastasios Papakonstantinou", "Carles Garcia-Linares", "Cristina Luengo", "Daniel Picó-Amador", "Davide Piscia", "Gemma Bullich", "Ida Paramonov", "Inés Martínez", "Jean-Rémi Trotta", "Joan Protasio", "Jordi Camps-Puchadas", "Leslie Matalonga", "Marcos Fernández-Callejo", "Mònica Bayés", "Raul Tonda" ; sc:description "An online tool for diagnosis and gene discovery in rare disease research. The platform features allow identifying disease-causing mutations in rare disease patients and linking them with detailed clinical information." ; sc:featureList edam:operation_0361, edam:operation_2403, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "RD-Connect Genome-Phenome Analysis Platform (GPAP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://platform.rd-connect.eu/" ; biotools:primaryContact "Sergi Beltran", "Steven Laurie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3077, edam:topic_3325 ; sc:citation , , , "pmcid:PMC3040526", "pmcid:PMC6419911", "pubmed:17297480", "pubmed:21210979", "pubmed:30165396" ; sc:description """This catalogue is intended to facilitate the discovery of samples and samples data from Rare Diseases biobanks. It also provides information about sample collections and studies done on the registered samples.""" ; sc:featureList edam:operation_2422, edam:operation_3197, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RD-Connect Sample Catalogue" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://samples.rd-connect.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3315 ; sc:citation ; sc:description "rdacca.hp is an R package for generalizing hierarchical and variation partitioning in multiple regression and canonical analysis." ; sc:featureList edam:operation_3659, edam:operation_3799, edam:operation_3936 ; sc:license "GPL-2.0" ; sc:name "rdacca.hp" ; sc:url "http://cran.r-project.org/web/packages/rdacca.hp/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3325, edam:topic_3407, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC6288202", "pubmed:30564269" ; sc:description """A Machine Learning System to Support Phenotype-Based Rare Disease Diagnosis. DNA sequencing has allowed for the discovery of the genetic cause for a considerable number of diseases, paving the way for new disease diagnostics. However, due to the lack of clinical samples and records, the molecular cause for rare diseases is always hard to identify, significantly limiting the number of rare Mendelian diseases diagnosed through sequencing technologies. Clinical phenotype information therefore becomes a major resource to diagnose rare diseases. In this article, we adopted both a phenotypic similarity method and a machine learning method to build four diagnostic models to support rare disease diagnosis. All the diagnostic models were validated using the real medical records from RAMEDIS""" ; sc:featureList edam:operation_2422 ; sc:name "RDAD" ; sc:url "http://www.unimd.org/RDAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3077 ; sc:citation , "pubmed:23958726" ; sc:description "Tool for retrieving data from DAVID database that offers the main functionalities of the website, including a connectivity to upload gene background lists, or the reports of the submitted information." ; sc:featureList edam:operation_0224, edam:operation_0226 ; sc:license "GPL-2.0" ; sc:name "RDAVIDWebService" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RDAVIDWebService.html" ; biotools:primaryContact "Cristobal Fresno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC7126467", "pubmed:32245403" ; sc:description """an improved method to identify the residue-residue pairing in β strands. stand-alone software package for RDB2C2. You can also download the full model package from our website: http://structpred.life.tsinghua.edu.cn/Software.html. A fully featured admin theme which can be used to build CRM, CMS, etc.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0321, edam:operation_0440, edam:operation_0474 ; sc:name "RDb2C2" ; sc:url "http://structpred.life.tsinghua.edu.cn/rdb2c2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3175, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC8504719", "pubmed:34634042" ; sc:description "RDBKE is a breakpoint enhancment pipeline for read-depth (RD) based SV callers using deep segmenation model UNet" ; sc:featureList edam:operation_2426, edam:operation_3196, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RDBKE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yaozhong/deepIntraSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3305, edam:topic_3325, edam:topic_3384 ; sc:citation , "pmcid:PMC10368801", "pubmed:37458501" ; sc:description "Knowledge graph of rare diseases based on large-scale text mining." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RDBridge" ; sc:url "http://rdb.lifesynther.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0593, edam:topic_1317, edam:topic_2814 ; sc:citation "pubmed:19711185" ; sc:description "RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. It is specifically designed for automated NMR NOE assignment and protein structure determination." ; sc:featureList edam:operation_2479 ; sc:name "RDC-PANDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.duke.edu/donaldlab/rdcpanda.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3170 ; sc:description "rddChecker is a program for determining sites of RNA-DNA differences (RDDs) and candidate RNA editing sites from RNA-seq data." ; sc:featureList edam:operation_3096 ; sc:name "rddChecker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ccb.jhu.edu/software/rddChecker/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation "pubmed:26817607" ; sc:description "This is a condition-specific RNA-editing prediction model from RNA-seq data." ; sc:featureList edam:operation_3680 ; sc:name "RDDpred" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://epigenomics.snu.ac.kr/RDDpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3297, edam:topic_3372, edam:topic_3489 ; sc:citation , "pmcid:PMC6657663", "pubmed:31343683" ; sc:description """An effective biomedical data migration tool from resource description framework to JSON. A desktop application for transform RDF files to JSON files.""" ; sc:featureList edam:operation_2422, edam:operation_2429, edam:operation_3436 ; sc:name "RDF2JSON" ; sc:url "https://github.com/lyotvincent/rdf2json" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2259, edam:topic_3070 ; sc:citation "pubmed:18460179" ; sc:description "This is a project that brings Semantic Web “features” to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape." ; sc:featureList edam:operation_0224, edam:operation_3559 ; sc:name "RDFScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/rdfscape/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3343 ; sc:citation ; sc:description "Wrapper for the Drug Gene Interaction Database. For simplicity, its query function and output resembles the user interface and results format provided on the DGIdb website." ; sc:featureList edam:operation_1812, edam:operation_2421 ; sc:license "MIT" ; sc:name "rDGIdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rDGIdb.html" ; biotools:primaryContact "Thomas Thurnherr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation "pubmed:23585274" ; sc:description "rDiff is an open source tool for accurate detection of differential RNA processing from RNA-Seq data. It implements two statistical tests to detect changes of the RNA processing between two samples. rDiff.parametric is a powerful test, which can be applied for well annotated organisms to detect changes in the relative abundance of isoforms. rDiff.nonparametric is an alternative when the annotation is incomplete or missing." ; sc:featureList edam:operation_0292 ; sc:name "RDiff" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://bioweb.me/rdiff" ; biotools:primaryContact "Gunnar Rätsch", "Philipp Boss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation , "pmcid:PMC2639009", "pubmed:19015140" ; sc:description "Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists." ; sc:featureList edam:operation_3214 ; sc:license "GPL-2.0" ; sc:name "Rdisop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rdisop.html" ; biotools:primaryContact "Steffen Neumann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_3325, edam:topic_3407 ; sc:citation ; sc:description """A Map for Exploring Rare Diseases. Disease NameDisorder IDOrpha Code.""" ; sc:featureList edam:operation_2421, edam:operation_2429, edam:operation_3196, edam:operation_3432 ; sc:name "RDmap" ; sc:url "http://rdmap.nbscn.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3056, edam:topic_3796 ; sc:citation ; sc:description """R package for Distinguishing among modes of convergent adaptation using population genomic data. Distinguishing among modes of convergent adaptation using population genomic data. This is the source code page for an R package implementing methods presented in Lee and Coop (2017). 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A table of normalized expression values from a RIP-chip experiment is read (e.g. as produced by the Affymetrix PowerTools) and two main steps are performed: Subtraction of the background of non target genes and secondary normalization for differing IP efficiencies." ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:name "REA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "http://www.bio.ifi.lmu.de/REA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3334, edam:topic_3379 ; sc:citation , "pmcid:PMC9205086", "pubmed:35710503" ; sc:description "The ReACH registry collected clinical information from 51 pediatric ACH patients during its six years of existence, corresponding to ~ 60% of ACH patients aged 3 months to 14 years that were anticipated to live in the Czechia and Slovak Republic" ; sc:name "ReACH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.achondroplasia-registry.cz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description """Format for Reaction Searching, Analysis, Classification, Transform, and Encoding/Decoding. 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The data is curated by biologists and subsequently peer-reviewed for accuracy and consistency. Cross-references with UniProt, PubMed, Ensembl, Gene Ontology and LocusLink are also provided. It supersedes The Genome Knowledgebase project." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2497, edam:operation_3436 ; sc:name "Reactome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.reactome.org" ; biotools:primaryContact "Lincoln Stein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0154, edam:topic_0602, edam:topic_0634 ; sc:citation , "pmcid:PMC10399304", "pubmed:37467006" ; sc:description "Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal." ; sc:featureList edam:operation_2492, edam:operation_3925, edam:operation_3926 ; sc:isAccessibleForFree true ; sc:name "Reactome-IDG" ; sc:url "https://idg.reactome.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0602, edam:topic_3365 ; sc:citation ; sc:description "A tool for accessing Reactome data efficiently." ; sc:featureList edam:operation_2422, edam:operation_2425 ; sc:isAccessibleForFree true ; sc:name "Reactome Graph Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://reactome.org/dev/graph-database" ; biotools:primaryContact "Antonio Fabregat" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3490 ; sc:name "Chemical structure sketch" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0962 ; sc:name "Small molecule report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258 ; sc:author "ChEBI team" ; sc:citation ; sc:description "Launch a search in the ChEBI database of small molecules (also used by RHEA)." ; sc:featureList edam:operation_0339 ; sc:name "Reactome Small Molecule Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "OICR" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.reactome.org/cgi-bin/small_molecule_search?DB=gk_current" ; biotools:primaryContact "Janna Hastings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4184317", "pubmed:25309732" ; sc:description "Perform pathway- and network-based data analysis. It uses highly reliable gene functional interaction network combined with human curated pathways derived from Reactome and other pathway databases. BiIt allows to uncover network and pathway patterns, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes in a list, and integrate multiple genomic data types into a pathway context using probabilistic graphical models." ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439, edam:operation_3501 ; sc:license "CC-BY-4.0" ; sc:name "ReactomeFIViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "7.1.0" ; sc:url "http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3068, edam:topic_3308 ; sc:citation ; sc:description """Efficient Multi-Omics Comparative Pathway Analysis. The ReactomeGSA package is an R client to the Reactome Analysis System. This new analysis system supports multi-species, multi-omics, comparative pathway analyses. Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge. The ReactomeGSA project supports multi-omics, comparative pathway analyses using the Reactome pathway database.""" ; sc:featureList edam:operation_2495, edam:operation_3501, edam:operation_3928 ; sc:name "ReactomeGSA" ; sc:softwareHelp ; sc:url "https://gsa.reactome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene ID (NCBI)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3547 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0862 ; sc:encodingFormat edam:format_3547 ; sc:name "Dotplot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602 ; sc:citation , "pubmed:26661513" ; sc:description "This package provides functions for pathway analysis based on REACTOME pathway database. 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The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening." ; sc:featureList edam:operation_2928, edam:operation_3215, edam:operation_3628, edam:operation_3799, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "recetox-aplcms" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "RECETOX SpecDatRI" ; sc:softwareVersion "0.11.0" ; sc:url "https://github.com/RECETOX/recetox-aplcms" ; biotools:primaryContact "RECETOX SpecDatRI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3172 ; sc:description """This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy. MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rules The program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.""" ; sc:featureList edam:operation_0226 ; sc:license "CC-BY-4.0" ; sc:name "recetox-msfinder" ; sc:softwareVersion "v3.5.2-rcx0" ; sc:url "https://github.com/RECETOX/recetox-msfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Annotation tool for untargeted LCMS1 data. 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Tools for exploring reciprocal space. reciprocalspaceship provides a pandas-style interface for analyzing and manipulating reflection data from crystallography experiments. 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The implementation enables the reconstruction of large volumes (>10243 pixels) using partitioning strategies in forward- and back-projection operations." ; sc:featureList edam:operation_3443 ; sc:name "RecoItTV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "https://github.com/arcosuc3m/recoittv" ; biotools:primaryContact "Manuel Desco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation ; sc:description "Batch effect removal in large-scale, multi-source omics data integration." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "reComBat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BorgwardtLab/reComBat.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3127 ; sc:citation , ; sc:description "recombClust is a R package that groups chromosomes by their recombination history. Recombination history is based on a mixture model that, given a pair of SNP-blocks, separates chromosomes in two populations, one with high Linkage Disequilibrium (LD) and low recombination (linkage) and another with low LD and high recombination. The method use the classification of several SNP-block pairs in a region to group chromosomes in clusters with different recombination history. This package takes as input genotype phased data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "recombClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v0.0.9", "v1.0.0" ; sc:url "https://github.com/isglobal-brge/recombClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3500 ; sc:citation , "pubmed:34482425" ; sc:description "Annotated expression and activity data for murine recombinase alleles and transgenes." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "recombinase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.informatics.jax.org/home/recombinase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_0625, edam:topic_0749 ; sc:citation , "pmcid:PMC9119626", "pubmed:35533184" ; sc:description "A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis." ; sc:featureList edam:operation_0415, edam:operation_0525, edam:operation_2238, edam:operation_3192, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RecombineX" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/yjx1217/RecombineX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC7403290", "pubmed:32754893" ; sc:description """RECOMIA provides academic researchers with AI-based tools for automated quantification of CT, PET/CT, SPECT/CT and MR. 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sc:operatingSystem "Linux" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://www.daimi.au.dk/%7Ecompbio/recpars/recpars.html" ; biotools:primaryContact "Mikkel Heide Schierup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation ; sc:description "Format for reconciled gene trees." ; sc:featureList edam:operation_0335 ; sc:name "RecPhyloXML" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://phylariane.univ-lyon1.fr/recphyloxml/" ; biotools:primaryContact "Wandrille Duchemin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3168, edam:topic_3174, edam:topic_3941 ; 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Lee", "Xun Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3810 ; sc:citation , "pmcid:PMC6820467", "pubmed:31708937" ; sc:description """Identification of Single Nucleotide Polymorphism in Red Clover (Trifolium pratense L.) Using Targeted Genomic Amplicon Sequencing and RNA-seq. Red clover (Trifolium pratense L.) is a diploid, naturally cross-pollinated, cool-season species. As a perennial forage legume, red clover is mostly cultivated in temperate regions worldwide. Being a non-model crop species, genomic resources for red clover have been underdeveloped. Thus far, genomic analysis used in red clover has mainly relied on simple sequence repeat (SSR) markers. However, SSR markers are sparse in the genome and it is often difficult to unambiguously map them using short reads generated by next generation sequencing technology. Single nucleotide polymorphisms (SNPs) have been successfully applied in genomics assisted breeding in several agriculturally important species.""" ; sc:featureList edam:operation_0308, edam:operation_0415, edam:operation_3196, edam:operation_3661 ; sc:name "red clover" ; sc:url "https://github.com/WLpython19/RedClover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation ; sc:description """A novel method for detecting variants in single-cell RNA sequencing. A tool for identifying variants in scRNA-seq. 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Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination by NOEs imposes increasing quantity of data for analysis, increased cost of structure determination and is less available in the study of perdeuterated proteins. 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McGuffin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , ; sc:description "Reformats an input file generated by a MiSeq/HiSeq system, where reads are formatted in a scheme that includes a space-character, which might not correctly be used in downstream operations." ; sc:featureList edam:operation_0335 ; sc:name "reformat_fastq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://bioweb.pasteur.fr/packages/pack@PGP_tools@0.0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330, edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3071 ; sc:citation , ; sc:description "Convert a tabular snpEff file into a SynTView .snp and .indel files." ; sc:featureList edam:operation_0335 ; sc:name "reformat_snpeff_for_syntview" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://bioweb.pasteur.fr/packages/pack@SynTViewTools@0.0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods." ; sc:featureList edam:operation_2495 ; sc:license "GPL-2.0" ; sc:name "RefPlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.44.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RefPlus.html" ; biotools:primaryContact "Kai-Ming Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3377 ; sc:citation , "pmcid:PMC6196526", "pubmed:30282735" ; sc:description """The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis. ReframeDB is an open and extendable drug repurposing database and screening set of 12,000 compounds.""" ; sc:featureList edam:operation_0310, edam:operation_2421, edam:operation_3938 ; sc:name "ReFRAME" ; sc:url "https://reframedb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3407 ; sc:description "ReFramed is a Python 3 library for metabolic model simulation." ; sc:featureList edam:operation_0244, edam:operation_2426, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "reFramed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cdanielmachado/reframed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3168, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC8575030", "pubmed:34402866" ; sc:description "An intelligent genotype imputation reference recommendation method with convolutional neural networks." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "RefRGim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shishuo16/RefRGim" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:name "Protein identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0797 ; sc:citation , , , , , "pmcid:PMC4383986", "pmcid:PMC4702849", "pmcid:PMC5001611", "pubmed:25428358", "pubmed:26553804", "pubmed:27342282" ; sc:description "A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. 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High throughput sequencing of RNA (RNA-Seq) has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts. To enable such an isoform-level analysis, a transcriptome assembly algorithm is utilized to stitch together the observed short reads into the corresponding transcripts. This task is complicated due to the complexity of alternative splicing - a mechanism by which the same gene may generate multiple distinct RNA transcripts. We develop a novel genome-guided transcriptome assembler, RefShannon, that exploits the varying abundances of the different transcripts, in enabling an accurate reconstruction of the transcripts. Our evaluation shows RefShannon is able to improve sensitivity effectively (up to 22%) at a given specificity in comparison with other state-of-the-art assemblers""" ; sc:featureList edam:operation_0232, edam:operation_0524, edam:operation_2495, edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "RefShannon" ; sc:url "https://github.com/shunfumao/RefShannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0659, edam:topic_2640 ; sc:citation , "pubmed:31511901" ; sc:description "whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants | Base-wise aggregation and functional prediction for human non-coding regulatory variants | regBase is a comprehensively integrated non-coding regulatory prediction scores and composite prediction models from existing tools for base-wise annotation of human genome. As such, the regBase resource provides convenience to prioritize functional regulatory SNVs and assist the fine mapping of causal regulatory SNVs without queries from numerus sources" ; sc:featureList edam:operation_3436, edam:operation_3461 ; sc:license "BSD-3-Clause" ; sc:name "regBase" ; sc:url "https://github.com/mulinlab/regBase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2828, edam:topic_3520 ; sc:citation ; sc:description """a general method to deconvolve X-ray scattering data from evolving mixtures. Software package for small angle X-ray scattering (SAXS) mixture deconvolution by REGularized Alternating Least Squares. It has been applied to datasets from chromatography-coupled SAXS, time-resolved SAXS, and equilibrium titrations. See our paper (Meisburger, Xu, & Ando, 2020) for details. matlab/ - MATLAB implementation of the REGALS library. The Python implementation was developed in Python 3. The REGALS library requires numpy and scipy. The demos use Jupyter notebooks with h5py for data import and matplotlib for plotting. The code has been tested with the following versions:.""" ; sc:featureList edam:operation_2940, edam:operation_3431, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "REGALS" ; sc:url "https://github.com/ando-lab/regals" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3489 ; sc:citation "pubmed:19465400" ; sc:description "Web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database)." ; sc:featureList edam:operation_0438, edam:operation_0440 ; sc:name "RegAnalyst" ; sc:url "http://www.nii.ac.in/~deepak/RegAnalyst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3071 ; sc:citation ; sc:description "Command line utility that automates the registration of the tools installed on any given Galaxy portal in ELIXIR bio.tools." ; sc:featureList edam:operation_1812 ; sc:license "GPL-2.0" ; sc:name "ReGaTE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/C3BI-pasteur-fr/ReGaTE" ; biotools:primaryContact "Olivia Doppelt-Azeroual" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3382, edam:topic_3385, edam:topic_3416, edam:topic_3452 ; sc:citation ; sc:description "Comparative analysis of tissue reconstruction algorithms for 3D histology." ; sc:featureList edam:operation_3552 ; sc:name "RegBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioimageInformaticsTampere/RegBenchmark" ; biotools:primaryContact "Pekka Ruusuvuori" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3315 ; sc:citation , "pmcid:PMC10265787", "pubmed:37312038" ; sc:description "Robust regression approach to closing genome gaps." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RegCloser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/csh3/RegCloser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295, edam:topic_3500 ; sc:citation , "pmcid:PMC8724954", "pubmed:35035784" ; sc:description "Identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns between epigenetic marks and TF binding motifs" ; sc:featureList edam:operation_0239, edam:operation_0445, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "regCNN" ; sc:operatingSystem "Linux" ; sc:url "http://cobisHSS0.im.nuk.edu.tw/regCNN/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0749, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC8728239", "pubmed:34591960" ; sc:description "Regeneration Roadmap aims to compile large datasets for gene expression and regulation created by a broad spectrum of high-throughput omics technologies. This one-stop service provides user-friendly functionalities to explore annotated regeneration-related changes in gene expression, as well as raw data downloads from these multi-omics studies. The current implementation includes five modules: Regeneration-related genes, Transcriptomics, Single-cell Transcriptomics, Epigenomics and Pharmacogenomics." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "Regeneration Roadmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/regeneration/index" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:name "Locus ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC9249971", "pubmed:35832616" ; sc:description "A web-based application for plant REGENeration-associated transcriptOMICS analyses." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "REGENOMICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://plantregeneration.snu.ac.kr/regenomics/?species=Ath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3295 ; sc:citation , "pmcid:PMC8752721", "pubmed:35017649" ; sc:description "RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling." ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3223, edam:operation_3741, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RegEnrich" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/RegEnrich.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3174 ; sc:citation "pubmed:22669417" ; sc:description "An R package to calculate risks conferred by genetic factors and multi-level environmental factors.  This is performed at a population level, with the option to also analyse individual-level data.  REGENT incorporates variability in risk factors to calculate confidence intervals for risk estimates and to classify the population into different categories of risk based on significant differences from the baseline average member of the population." ; sc:featureList edam:operation_3461 ; sc:name "REGENT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.kcl.ac.uk/lsm/research/divisions/gmm/departments/mmg/researchgroups/clewis/software/regent/index.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description "A framework and R package for using genomics to study regional pathogen transmission." ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "regentrans" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://snitkin-lab-umich.github.io/regentrans/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3053 ; sc:description "Software to extract a region from hapMapII for MaCH imputation." ; sc:featureList edam:operation_3557 ; sc:name "RegionalHapMapExtractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yunliweb.its.unc.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:22126751" ; sc:description "The software works by quantifying the degree of over-representation of associated SNPs in a pre-defined genomic region, given a specific definition of statistical significance." ; sc:featureList edam:operation_0484 ; sc:name "RegionalP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.statgen.nus.edu.sg/~software/regionalP.html" ; biotools:primaryContact "Dr. Yik Ying Teo", "Wang Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0634, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:33075560" ; sc:description """Rapidly extracting standardized brain connectivity information in voxel-wise neuroimaging studies. The mission of the Magnetic Resonance Imaging Lab at the Illinois Institute of Technology is to develop MRI data acquisition, image reconstruction and processing techniques, and to apply these methods for the diagnosis and monitoring of brain disease. MRIIT is part of the Medical Imaging Research Center and the Pritzker Institute of Biomedical Science and Engineering. IIT Human Brain Atlas v.5.0 Anatomical Templates DTI Template HARDI Template Gray Matter Labels Multi-Layer White Matter Labels Download Now. Postmortem MRI in aging research Find Out More.""" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3443 ; sc:name "regionconnect" ; sc:url "http://www.nitrc.org/projects/iit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3517 ; sc:citation , "pmcid:PMC4708104", "pubmed:26424858" ; sc:description "Offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features." ; sc:featureList edam:operation_3194, edam:operation_3209 ; sc:license "Artistic-2.0" ; sc:name "regioneR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/regioneR.html" ; biotools:primaryContact "Bernat Gel" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1017 ; sc:encodingFormat edam:format_2078 ; sc:name "Sequence range" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331, edam:format_3508 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC5314792", "pubmed:27694310" ; sc:description "Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results." ; sc:featureList edam:operation_3209 ; sc:license "Artistic-2.0" ; sc:name "regionReport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/regionReport.html" ; biotools:primaryContact "Leonardo Collado-Torres" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3064, edam:topic_3314 ; sc:citation ; sc:description """Improved Prediction of the Regioselectivity of Electrophilic Aromatic Substitutions. RegioSQM20 predicts the regioselectivity of electrophilic aromatic substitution reactions in heteroaromatic systems. The reactive sites are identified using semiempirical quantum mechanical calculations based on the open source software package xTB. Use by pasting a SMILES code from ChemDraw to get the regioselective prediction, for example using this SMILES.""" ; sc:license "MIT" ; sc:name "RegioSQM20" ; sc:url "http://regiosqm.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0204, edam:topic_0623, edam:topic_2640, edam:topic_3172 ; sc:citation , "pubmed:35872412" ; sc:description "Molecular regulation data of diverse living systems facilitating current multiomics research." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:name "REGLIV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/regliv/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0128, edam:topic_0203, edam:topic_0602 ; sc:citation "pubmed:21037261" ; sc:description "RegPhos is a database for exploration of the phosphorylation network associated with an input of genes/proteins. Subcellular localization information is also included." ; sc:featureList edam:operation_0276, edam:operation_0314, edam:operation_0417, edam:operation_3083, edam:operation_3439 ; sc:name "RegPhos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://regphos.mbc.nctu.edu.tw/" ; biotools:primaryContact "Hsien-Da Huang", "Tzong-Yi Lee", "Wen-Chi Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:19884135", "pubmed:22700702" ; sc:description "The database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575, edam:operation_3660 ; sc:name "RegPrecise" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://regprecise.lbl.gov" ; biotools:primaryContact "Dmitry A. Rodionov", "Pavel S. Novichkov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0622, edam:topic_0797, edam:topic_2275, edam:topic_3308 ; sc:citation "pubmed:20542910" ; sc:description "Provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics." ; sc:featureList edam:operation_0487, edam:operation_3745 ; sc:name "RegPredict" ; sc:url "http://regpredict.lbl.gov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3056, edam:topic_3168, edam:topic_3324 ; sc:citation ; sc:description "Penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection." ; sc:featureList edam:operation_0487 ; sc:name "RegressHaplo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/SLeviyang/RegressHaplo" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659, edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:16845041" ; sc:description "Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5'-UTR and 3'-UTR, motifs involved in mRNA splicing and transcriptional regulation, other motifs in mRNA such as riboswitches and splice donor/acceptor sites, RNA structural features, and miRNA target sites." ; sc:featureList edam:operation_0264, edam:operation_0438 ; sc:name "RegRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://regrna.mbc.nctu.edu.tw/" ; biotools:primaryContact "RegRNA Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769 ; sc:citation , "pubmed:35333294" ; sc:description "A Regression Approach to Scaffolding." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RegScaf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lemontealala/RegScaf.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:26130577" ; sc:description "This R package  provides a classifier for predicting whether a given oligonucleotide sequence (of length l bp, where l would typically vary from six to as high as 25 bp) is, or is not, a transcription factor (TF) binding site." ; sc:featureList edam:operation_0438 ; sc:name "regshape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ramseylab/regshape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3169, edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC7405637", "pubmed:32850739" ; sc:description """A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data. Expression quantitative trait loci (eQTL) analysis is useful for identifying genetic variants correlated with gene expression, however, it cannot distinguish between causal and nearby non-functional variants. Because the majority of disease-associated SNPs are located in regulatory regions, they can impact allele-specific binding (ASB) of transcription factors and result in differential expression of the target gene alleles. In this study, our aim was to identify functional single-nucleotide polymorphisms (SNPs) that alter transcriptional regulation and thus, potentially impact cellular function. Here, we present regSNPs-ASB, a generalized linear model-based approach to identify regulatory SNPs that are located in transcription factor binding sites""" ; sc:featureList edam:operation_0445, edam:operation_0484, edam:operation_3196, edam:operation_3226 ; sc:name "regSNPs-ASB" ; sc:url "https://github.com/SiwenX/RegSNPs-ASB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2229, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC8710255", "pubmed:35036172" ; sc:description "A visualized application for homology-based gene searching and plotting using multiple reference sequences." ; sc:featureList edam:operation_0490, edam:operation_2421, edam:operation_2422, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "ReGSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ds.mju.ac.kr/regsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Statistical methods for detection of differential exon usage in RNA-seq and exon microarray data sets, using L1 regularization (lasso) to improve power." ; sc:featureList edam:operation_0446 ; sc:license "MIT" ; sc:name "regsplice" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/regsplice.html" ; biotools:primaryContact "Lukas M. Weber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pmcid:PMC3163918", "pubmed:21904427" ; sc:description "Identify differentially expressed proteins based on 2D gel images." ; sc:featureList edam:operation_3443 ; sc:name "RegStatGel" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1211" ; sc:url "http://www.mediafire.com/FengLi/2DGelsoftware" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3308 ; sc:description "Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression." ; sc:featureList edam:operation_2409, edam:operation_2499 ; sc:license "MIT" ; sc:name "regtools" ; sc:url "https://regtools.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3170 ; sc:citation , "pmcid:PMC7706183", "pubmed:33258965" ; sc:description """a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1. regulatory network P. aeruginosa.""" ; sc:featureList edam:operation_1781, edam:operation_2421, edam:operation_2437 ; sc:name "RegulomePA" ; sc:url "http://www.regulome.pcyt.unam.mx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:21051347" ; sc:description "It is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response. It has summaries for every transcription factor (TF) and TF-binding sites with internal symmetry." ; sc:featureList edam:operation_0314, edam:operation_0438, edam:operation_0445, edam:operation_1781, edam:operation_3439 ; sc:name "RegulonDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://regulondb.ccg.unam.mx/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3295 ; sc:citation ; sc:description "Transcriptional regulatory networks inference tool based on Semantic Web technologies." ; sc:featureList edam:operation_2422, edam:operation_2437, edam:operation_3463, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Regulus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/gcollet/regulus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0204, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description """Programmatic access to bacterial regulatory networks with regutools. The goal of regutools is to provide an R interface for extracting and processing data from RegulonDB. This package was created as a collaboration by members of the Community of Bioinformatics Software Developers (CDSB in Spanish). regutools: an R package for data extraction from RegulonDB. RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12.""" ; sc:featureList edam:operation_0372, edam:operation_1781, edam:operation_2422 ; sc:license "Artistic-2.0" ; sc:name "regutools" ; sc:url "http://bioconductor.org/packages/regutools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc:description "Regvar is a deep neural network-based computational server for prioritizing tissue-specific noncoding regulatory variants. RegVar integrates the sequential, epigenetic and evolutionary profiles of single nucleotide polymorphisms (SNPs) and their potential target genes in 17 human tissues, and gives tissue-specific predictions of regulatory probabilities of the provided SNPs on provided genes." ; sc:featureList edam:operation_0331, edam:operation_2437, edam:operation_3226, edam:operation_3232 ; sc:name "RegVar" ; sc:softwareHelp ; sc:url "http://regvar.cbportal.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053 ; sc:description "SAT-based program to compute a haplotype configuration on pedigrees with recombinations, genotyping errors, and missing genotypes." ; sc:featureList edam:operation_0487, edam:operation_3196 ; sc:name "reHCstar" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:softwareVersion "2.1.3" ; sc:url "http://rehcstar.algolab.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation ; sc:description "Search for footprints of selection using Haplotype Homozygosity based tests." ; sc:featureList edam:operation_2421 ; sc:name "Rehh" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.13" ; sc:url "http://cran.r-project.org/web/packages/rehh/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Process and extract clinical information from Electronic Medical Records." ; sc:featureList edam:operation_2421 ; sc:name "rEHR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/rOpenHealth/rEHR" ; biotools:primaryContact "Evangelos Kontopantelis", "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8990463", "pubmed:35414795" ; sc:description "A database for cancer A-to-I RNA editing with interactive analysis." ; sc:featureList edam:operation_0314, edam:operation_3096, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "REIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo-sysu.com/reia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3520 ; sc:citation ; sc:description """efficient indexing of k-mer presence and abundance in sequencing datasets. REINDEER builds a data-structure that indexes k-mers and their abundances in a collection of datasets (raw RNA-seq or metagenomic reads for instance). Then, a sequence (FASTA) can be queried for its presence and abundance in each indexed dataset. While other tools (e.g. SBT, BIGSI) were also designed for large-scale k-mer presence/absence queries, retrieving abundances was so far unsupported (except for single datasets, e.g. using some k-mer counters like KMC, Jellyfish). REINDEER combines fast queries, small index size, and low memory footprint during indexing and queries. We showed it allows to index 2585 RNA-seq datasets (~4 billions k-mers) using less than 60GB of RAM and a final index size lower than 60GB on the disk. Then, a REINDEER index can either be queried on disk (experimental feature, low RAM usage) or be loaded in RAM for faster queries.""" ; sc:featureList edam:operation_0524, edam:operation_2422, edam:operation_3211, edam:operation_3472, edam:operation_3799 ; sc:license "AGPL-3.0" ; sc:name "REINDEER" ; sc:url "https://github.com/kamimrcht/REINDEER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3371, edam:topic_3524 ; sc:citation ; sc:description "Molecular De Novo design using Recurrent Neural Networks and Reinforcement Learning." ; sc:featureList edam:operation_0322 ; sc:license "MIT" ; sc:name "REINVENT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MarcusOlivecrona/REINVENT" ; biotools:primaryContact "Marcus Olivecrona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0209, edam:topic_3474 ; sc:citation , "pubmed:33118816" ; sc:description """An AI Tool for De Novo Drug Design. The application in this repository is described in the paper: "REINVENT 2.0 – an AI tool for de novo drug design". This repository is a collection of useful jupyter notebooks, code snippets and example JSON files illustrating the use of Reinvent 2.0. At the moment, the following notebooks are supported:. Sampling: sampling.json can be used to start sampling. Requires a generative model as an input and produces a file that contains SMILES. We provide a generative model "reinvent/data/augmented.prior". Alternatively focused Agents generated by transfer learning or reinforcement learning can be sampled as well. Example.""" ; sc:featureList edam:operation_0394, edam:operation_3435, edam:operation_3695 ; sc:license "MIT" ; sc:name "REINVENT" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/MolecularAI/Reinvent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Segmentation of retina image to extract complex structure of blood vessel" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Reitna Blood Vessel Segmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/72118-reitna-blood-vessel-segmentation" ; biotools:primaryContact "Gautam Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Search every one of 168,297 protein sequences from 8826 animals, plants and microorganisms and return the protein that contains the closest match to the letters of your sequence." ; sc:featureList edam:operation_0346 ; sc:name "reLATE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/cgi-bin/decode/relate.cgi" ; biotools:primaryContact "Training" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:24215025" ; sc:description "This is a method which estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals." ; sc:featureList edam:operation_0282 ; sc:name "RelateAdmix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.popgen.dk/software/index.php/Relate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:34270436" ; sc:description "Relative Neural Architecture Search via Slow-Fast Learning" ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RelativeNAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EMI-Group/RelativeNAS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3652, edam:format_3712 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3520 ; sc:citation "pubmed:14670053" ; sc:description "Calculation of ion current ratios from LC-MS data (requires Xcalibur)." ; sc:featureList edam:operation_3215, edam:operation_3630, edam:operation_3634, edam:operation_3635, edam:operation_3640, edam:operation_3659, edam:operation_3695, edam:operation_3705, edam:operation_3715 ; sc:name "RelEx" ; sc:url "http://fields.scripps.edu/relex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0749, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC7521704", "pubmed:32936799" ; sc:description """Discovering functional sequences with RELICS. RELICS ✨: Regulatory Element Location Identification in CRISPR screens. RELICS is an analysis method for discovering functional sequences from tiling CRISPR screens. The current version (v.2.0) of RELICS uses a Bayesian hierarchical model and considers the overlapping effects of multiple guides, can jointly analyze multiple pools per replicate, and estimates the number of functional sequences supported by the data.""" ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3802 ; sc:license "MIT" ; sc:name "RELICS" ; sc:url "https://github.com/patfiaux/RELICS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0971 ; sc:encodingFormat edam:format_1964 ; sc:name "Article" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0972 ; sc:encodingFormat edam:format_3464 ; sc:name "Text mining report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068 ; sc:author "Ashish Baghudana", "Juan Miguel Cejuela" ; sc:description "Text mining tool for relation extraction of Protein to DNA and to RNA interactions." ; sc:featureList edam:operation_0306, edam:operation_3280 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "relna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "RostLab", "Technische Universität München" ; sc:softwareHelp , ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/ashishbaghudana/mthesis-ashish" ; biotools:primaryContact "Juan Miguel Cejuela" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1289 ; sc:name "Restriction map" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3125 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display restriction enzyme binding sites in a nucleotide sequence." ; sc:featureList edam:operation_0431, edam:operation_0575 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "remap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/remap.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3407 ; sc:citation ; sc:description """Relabeling Multi-label Pathway Data with Bags to Enhance Predictive Performance. TH138 Virtual Production shell app. Modified NDIIOPlugin for easier run-time control. QLab Cues and other work files for MITHC.""" ; sc:featureList edam:operation_3660, edam:operation_3926, edam:operation_3929 ; sc:name "reMap" ; sc:url "http://github.com/reMap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3303, edam:topic_3379, edam:topic_3395, edam:topic_3934 ; sc:citation , "pmcid:PMC8218701", "pubmed:34156448" ; sc:description "A platform for integrating and sharing published stem cell research data with a focus on iPSC trials." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "ReMeDy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://remedy.mssm.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0204, edam:topic_0622, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC10120424", "pubmed:37083939" ; sc:description "Regulatory mendelian mutation score for GRCh38." ; sc:featureList edam:operation_3208, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ReMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://remm.bihealth.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web API", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0160, edam:topic_3173, edam:topic_3574 ; sc:citation , , "pmcid:PMC5011059", "pubmed:27569544" ; sc:description """ReMM score is a tool that scores the positions in the human genome in terms of their regulatory probability. We use curated regulatory variants involved in Mendelian disease and contrast them with proxy-neutral variants that survived natural selection in a machine learning framework. We use an algorithm for highly imbalanced data, called hyperSMURF, to differentiate deleterious from neutral variants.""" ; sc:license "MIT" ; sc:name "ReMM score" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "v0.3.1.post1", "v0.4" ; sc:url "https://remm.bihealth.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3343, edam:topic_3474 ; sc:citation , "pmcid:PMC9743675", "pubmed:36510307" ; sc:description "A deep learning-based web server for target-specific drug design." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_3216, edam:operation_4008, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ReMODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cadd.zju.edu.cn/relation/remode/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Gene expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data." ; sc:featureList edam:operation_3439 ; sc:name "ReMoDiscovery" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Lemmens_2006/Index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:32710238" ; sc:description """REMoDNaV is a velocity based eye movement event detection algorithm that is based on, but extends the adaptive Nyström & Holmqvist algorithm (Nyström & Holmqvist, 2010). It is built to be suitable for both static and dynamic stimulation, and is capable of detecting saccades, post-saccadic oscillations, fixations, and smooth pursuit events. REMoDNaV is especially suitable for data without a trial structure and performs robustly on data with temporally varying noise level. This repository contains the raw data, the code to generate summary statistics, and raw figures for the manuscript, and the manuscript sources for the publication REMoDNaV: Robust Eye Movement Detection for Natural Viewing.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3357 ; sc:license "CC-BY-4.0" ; sc:name "REMoDNaV" ; sc:url "https://pypi.org/project/remodnav" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0114, edam:topic_3071 ; sc:citation , ; sc:description "Removes the lines containing Exon." ; sc:featureList edam:operation_3695 ; sc:name "removeexonlines" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Remove line artefacts sometimes present in microscopical images" ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "removeLineArtefact" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70388-removelineartefact" ; biotools:primaryContact "Constantino Carlos Reyes-Aldasoro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description "Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE." ; sc:featureList edam:operation_2428, edam:operation_2454, edam:operation_2928, edam:operation_3435, edam:operation_3809 ; sc:license "GPL-3.0" ; sc:name "REMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/REMP.html" ; biotools:primaryContact "Yinan Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3263, edam:topic_3316, edam:topic_3489, edam:topic_3571 ; sc:author "Janne Lauros" ; sc:citation ; sc:contributor "Academy of Finland, grants 271642 and 263164" ; sc:description "Tool that enables a researcher to submit and a Data Access Committee to process Data Access Applications to sensitive datasets." ; sc:featureList edam:operation_2409, edam:operation_3760 ; sc:funder "Academy of Finland, grants 271642 and 263164" ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "REMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CSC - IT Center for Science", "csc.fi" ; sc:softwareHelp ; sc:softwareVersion "1.8" ; sc:url "http://www.csc.fi/rems" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0157, edam:topic_0623 ; sc:citation "pubmed:16433931", "pubmed:16568543", "pubmed:16844991" ; sc:description "REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences." ; sc:featureList edam:operation_0232, edam:operation_3631, edam:operation_3643, edam:operation_3767 ; sc:name "ReMus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biotools.cs.ntou.edu.tw/Remus.asp" ; biotools:primaryContact "ReMus team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_0749, edam:topic_3169, edam:topic_3673 ; sc:citation , "pmcid:PMC7978111", "pubmed:33747049" ; sc:description "Remus is a web application for prioritization of regulatory regions and variants in monogenic diseases." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:name "Remus" ; sc:url "http://remus.btm.umed.pl/" ; biotools:primaryContact "Paweł Sztromwasser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3384, edam:topic_3576 ; sc:description "Renames Dicom Images with Sequential Alpha Numeric Nomenclature." ; sc:isAccessibleForFree true ; sc:name "renamedicom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/6695-renamedicom" ; biotools:primaryContact "Nagi Hatoum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3174 ; sc:citation ; sc:description "RENANO is a reference-based lossless FASTQ data compressor, specifically tailored to compress FASTQ files generated with nanopore sequencing technologies. RENANO improves on its state of the art predecessor ENANO, by providing a more efficient base call sequence compression component. Two compression algorithms are introduced, corresponding to the following scenarios: (1) a reference genome is available without cost to both the compressor and the decompressor; (2) the reference genome is available only on the compressor side, and a compacted version of the reference is included in the compressed file." ; sc:featureList edam:operation_1812, edam:operation_3185, edam:operation_3192 ; sc:license "MIT" ; sc:name "RENANO" ; sc:url "https://github.com/guilledufort/RENANO" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_0749 ; sc:citation "pubmed:22693210" ; sc:description "Network-based analysis web tool for the interpretation and visualization of transcriptional and post-transcriptional regulatory information, designed to identify common regulatory elements in a list of genes. Itmaps these genes to the regulatory network, extracts the corresponding regulatory connections and evaluate each regulator for significant over-representation in the list. Ranked gene lists can also be analysed." ; sc:featureList edam:operation_0438, edam:operation_1781, edam:operation_3439, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RENATO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://renato.bioinfo.cipf.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0749, edam:topic_2259 ; sc:citation "pubmed:18400774" ; sc:description "A C++ based software for automatic generation of ordinary differential equations for gene and protein expression dynamics in artificial regulatory networks." ; sc:featureList edam:operation_3562 ; sc:name "RENCO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/renco/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:25541727" ; sc:description "A new Cytoscape 3.x plugin, which enables integration, merging, enhancement, visualization, and exporting of pathways from multiple repositories." ; sc:featureList edam:operation_3083 ; sc:name "ReNE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sysbio.polito.it/index.php/tools-and-downloads/item/220-rene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0769, edam:topic_2269 ; sc:citation ; sc:description "RENET2 is a tool for high-performance full-text gene-disease relation extraction with iterative training data expansion." ; sc:featureList edam:operation_3280, edam:operation_3625, edam:operation_3778 ; sc:license "BSD-3-Clause" ; sc:name "RENET2" ; sc:url "https://github.com/sujunhao/RENET2" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0622, edam:topic_3068, edam:topic_3297 ; sc:citation , "pubmed:36029977" ; sc:description "Web platform for the improvement of assembly result and annotation of prokaryotic genomes." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ReNoteWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biod.ufpa.br/renoteweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3053, edam:topic_3068, edam:topic_3174, edam:topic_3297 ; sc:citation ; sc:description """An R package for the NCBI eUtils API. WIP on a manuscript for rentrez (at last!). A manuscript for rentrez (at last!). rentrez provides functions that work with the NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases. rentrez is on CRAN, so you can get the latest stable release with install.packages("rentrez"). This repository will sometimes be a little ahead of the CRAN version, if you want the latest (and possibly greatest) version you can install the current github version using Hadley Wickham's devtools""" ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_2422 ; sc:name "rentrez" ; sc:url "https://github.com/dwinter/rentrez_ms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3299, edam:topic_3372 ; sc:citation , "pmcid:PMC9112463", "pubmed:35578161" ; sc:description "An R package for the analysis of enzyme kinetic data." ; sc:featureList edam:operation_0334, edam:operation_0337, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "renz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/jcaledo/renz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0157 ; sc:citation , "pubmed:33972020" ; sc:description "REP2 is a web server to detect common tandem repeats in protein sequences." ; sc:featureList edam:operation_0292, edam:operation_0379, edam:operation_2479 ; sc:name "REP2" ; sc:url "http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/" ; biotools:primaryContact "Miguel A. Andrade-Navarro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9912678", "pubmed:36759904" ; sc:description "Analysis of alternative polyadenylation from RNA-sequencing data." ; sc:featureList edam:operation_0314, edam:operation_0428, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "REPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eddieimada/REPAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3047, edam:topic_3168, edam:topic_3500 ; sc:citation , "pmcid:PMC7574428", "pubmed:33076827" ; sc:description """an improved approach for de novo repeat identification by assembly of the high-frequency reads. RepAHR is used to identify repeats(repetitive sequences) in genome using Next-Generation Sequencing reads. Before running RepAHR, need to edit 2 configure files: parameter_config_file and reads_config_file. Some parameters need to be set in the parameter_config_file.""" ; sc:featureList edam:operation_0310, edam:operation_3096, edam:operation_3228, edam:operation_3472 ; sc:name "RepAHR" ; sc:url "https://github.com/bioinfomaticsCSU/RepAHR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3500 ; sc:author ; sc:citation , "pubmed:33603229" ; sc:description """RePAIR is a statistical method that uses previously obtained information (Bayesian framework) to decrease the number of animals to perform well-powered research. With RePAIR you can 1) determine prior parameters, 2) calculate sample size, and 3) analyze your results.""" ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RePAIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://utrecht-university.shinyapps.io/repair/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3277, edam:topic_3303 ; sc:citation , "pubmed:34997301" ; sc:description "An online database for skeletal injuries of known ages." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "REPAIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://repair.orainc.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0602, edam:topic_0654, edam:topic_2640 ; sc:citation ; sc:description """Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer. Reference implementation of RepairSig, a computational approach that accounts for the non-additivity of DNA damage and repair processes by modeling the composition of primary mutagenic processes corresponding to DNA damage processes with normally functioning DNA repair mechanism and secondary mutagenic processes which correspond to the deficiency of the DNA repair mechanism. RepairSig assumes signatures of the primary processes are known while signatures of the secondary processes are to be inferred.""" ; sc:featureList edam:operation_3227, edam:operation_3435, edam:operation_3629 ; sc:name "RepairSig" ; sc:url "https://github.com/ncbi/RepairSig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_0654 ; sc:citation "pubmed:21051355" ; sc:description "REPAIRtoire is a database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins." ; sc:featureList edam:operation_0224, edam:operation_0331, edam:operation_0477, edam:operation_2409 ; sc:name "REPAIRtoire" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://repairtoire.genesilico.pl/" ; biotools:primaryContact "Contact List", "REPAIRtoire Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC4027187", "pubmed:24634442" ; sc:description "Repetitive motif detection by Assembly of Repetitive K-mers." ; sc:featureList edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RepARK" ; sc:operatingSystem "Mac", "Windows" ; sc:url "https://github.com/PhKoch/RepARK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0749, edam:topic_0780, edam:topic_0798 ; sc:citation , "pmcid:PMC10463291", "pubmed:37608271" ; sc:description "Toolbox for the identification of repetitive elements." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "RepBox" ; sc:operatingSystem "Mac" ; sc:url "https://github.com/shelvasha/RepBox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:26977803" ; sc:description "A new method which assembles repeat sequences directly from raw shotgun sequencing data." ; sc:featureList edam:operation_3472 ; sc:name "REPdenovo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/Reedwarbler/REPdenovo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_2310 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0798, edam:topic_2885 ; sc:author "Jiri Macas", "Pavel Neumann", "Petr Novak" ; sc:citation , ; sc:contributor "Czech Academy of Sciences" ; sc:description "RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering of sequence reads to identify repetitive elements and several additional programs that aid in their annotation and quantification." ; sc:featureList edam:operation_0362, edam:operation_0379 ; sc:funder "Czech Academy of Sciences" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RepeatExplorer" ; sc:operatingSystem "Linux" ; sc:provider "Biology Centre, CAS, Czech Republic", "ELIXIR-CZ" ; sc:softwareHelp ; sc:softwareVersion "0.3.7 (command line)", "2.3.7 (Galaxy server)" ; sc:url "http://repeatexplorer.org" ; biotools:primaryContact "Petr Novak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056, edam:topic_3174 ; sc:citation , "pmcid:PMC4891823", "pubmed:27260942" ; sc:description "RepeatAnalyzer is a software tool capable of tracking, managing, analysing and cataloguing short-sequence repeats and genotypes using Anaplasma marginale as a model species." ; sc:featureList edam:operation_0379 ; sc:license "GPL-3.0" ; sc:name "RepeatAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/repeatgroup/repeatanalyzer/overview" ; biotools:primaryContact "Assefaw H. Gebremedhin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0654, edam:topic_3524 ; sc:citation "pubmed:16854633" ; sc:description "It is designed to find “direct repeats”, “inverted repeats”, “mirror repeats” and “complementary repeats”, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database and several genomes can be input simultaneously. The program provides visualisation of the repeats location in the genomic structure and the search for specific motifs is also possible." ; sc:featureList edam:operation_0237 ; sc:name "RepeatAround" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://portugene.com/repeataround.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3517, edam:topic_3796 ; sc:citation "pubmed:24489372" ; sc:description "An R package of global tests for expression data of high-dimensional sets of molecular features." ; sc:featureList edam:operation_2495 ; sc:name "RepeatedHighDim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ams.med.uni-goettingen.de/software-en.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0605, edam:topic_0749 ; sc:citation , "pubmed:33230554" ; sc:description """a file system providing reproducibility through provenance and automation. RepeatFS is a Python, FUSE-based file system with the goal of promoting scientific informatics reproducibility by recording all file and IO operations during analysis. This provenance record can then be exported and used to replicate the analysis on other systems. During replication, RepeatFS will verify that all software versions, command line parameters, and other relevant attributes match, and will report out any deviation from the original record. While other provenance software often involves learning scripting languages or migrating your workflow to a confined platform, RepeatFS operates invisibily at the file system level, and is compatible with virtually all Linux command-line software.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_1812 ; sc:license "GPL-3.0" ; sc:name "RepeatFS" ; sc:url "https://github.com/ToniWestbrook/repeatfs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157 ; sc:description "A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns)." ; sc:featureList edam:operation_0362 ; sc:license "OSL-2.1" ; sc:name "RepeatMasker" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.repeatmasker.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:description "De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats." ; sc:featureList edam:operation_0379 ; sc:license "OSL-2.1" ; sc:name "RepeatModeler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.repeatmasker.org/RepeatModeler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0157, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:19407343" ; sc:description "A software on a hybrid data set of real genomic DNA with simulated interspersed repeats." ; sc:featureList edam:operation_0451 ; sc:name "Repeatoire" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://wwwabi.snv.jussieu.fr/public/Repeatoire/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0625, edam:topic_0654, edam:topic_3293 ; sc:citation ; sc:description """a pipeline for visualization and comparative analysis of repetitive DNA profiles. A tool for studying repetitive DNA dynamics using low-coverage, short-read data.""" ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3192, edam:operation_3894 ; sc:license "GPL-3.0" ; sc:name "RepeatProfiler" ; sc:url "https://github.com/johnssproul/RepeatProfiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0654 ; sc:citation "pubmed:17137733" ; sc:description "A CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges." ; sc:featureList edam:operation_0379 ; sc:name "RepeatRunner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.yandell-lab.org/software/repeatrunner.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2007 ; sc:encodingFormat edam:format_1964 ; sc:name "UniProt keyword" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_3464 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2814 ; sc:citation , "pmcid:PMC5389603", "pubmed:27928056" ; sc:description "Database of annotated tandem repeat protein structures." ; sc:featureList edam:operation_0224, edam:operation_0564, edam:operation_0570, edam:operation_2406, edam:operation_2996 ; sc:name "RepeatsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp ; sc:softwareVersion "3" ; sc:url "https://repeatsdb.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2206 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_1939 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0157, edam:topic_0654 ; sc:author "URGI" ; sc:citation , , , , , "pmcid:PMC1185648", "pmcid:PMC3031573", "pmcid:PMC4008368", "pubmed:15008403", "pubmed:16110336", "pubmed:21304975", "pubmed:24786468" ; sc:contributor "URGI" ; sc:description """The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.""" ; sc:featureList edam:operation_0237, edam:operation_0379 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.0" ; sc:name "REPET" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "URGI" ; sc:softwareHelp , , , ; sc:softwareVersion "v3.0" ; sc:url "https://urgi.versailles.inrae.fr/Tools/REPET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Protein solenoid repeat detection from sequence." ; sc:featureList edam:operation_2423 ; sc:name "Repetita" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://protein.bio.unipd.it/services" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3360, edam:topic_3473, edam:topic_3474 ; sc:citation "pubmed:25717197" ; sc:description "RepExplore is a web-service for omics data analysis exploiting the information captured in the variance of technical replicates to provide more reliable and informative differential expression and abundance statistics, as well as low-dimensional data visualizations." ; sc:name "RepExplore" ; sc:url "https://lcsb-repexplore.uni.lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3127 ; sc:citation "pubmed:25012182" ; sc:description "A tool for replicability analysis for genome-wide association studies." ; sc:featureList edam:operation_3658 ; sc:name "repfdr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/repfdr/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804, edam:topic_3569 ; sc:citation , "pmcid:PMC4920122", "pubmed:27153709" ; sc:description "repgenHMM is a dynamic programming tool to infer the rules of immune receptor generation from sequence data." ; sc:featureList edam:operation_2403 ; sc:license "Other" ; sc:name "repgenHMM" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/yuvalel/repgenhmm/overview" ; biotools:primaryContact "Yuval Elthanati" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:description "Recursive tree-fitting and search procedure which aims to address the problem of fitting phylogenies to sequence datasets that include both closely and distantly related species." ; sc:featureList edam:operation_2421 ; sc:name "REPHINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.9" ; sc:url "http://www.acaciamulga.net/#!about1/ckzk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0208, edam:topic_2640, edam:topic_3169, edam:topic_3512 ; sc:citation , "pubmed:33713851" ; sc:description "RePhine is a method for identification of drug response related transcriptional regulators by modeling correlation patterns of targets. RePhine takes in pharmacogenomics data containing gene expression, copy number, mutation status, cancer type information and pharmacological profiles for estimation of associations between genes expression and drug response. It also takes in ChIP-seq data for target inference." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "RePhine" ; sc:url "https://github.com/coexps/Rephine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0160, edam:topic_0623, edam:topic_0769 ; sc:citation , "pubmed:34434663" ; sc:description "Rephine.r is a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies. Rephine.r is a command-line R script designed to identify common errors in gene clustering that can arise when building phage pangenomes. These include errors due to distant homologs being separated into multiple gene clusters, or fragmented genes being misidentified as multi-copy genes. Correcting these errors will often make it possible to identify new single-copy core genes that can be used downstream to build phylogenies." ; sc:featureList edam:operation_0323, edam:operation_2454, edam:operation_3216, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "Rephine.r" ; sc:url "https://www.github.com/coevoeco/Rephine.r" ; biotools:primaryContact "Jason W. Shapiro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3173 ; sc:citation , "pmcid:PMC4053803", "pubmed:24517713" ; sc:description "Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc." ; sc:featureList edam:operation_0438, edam:operation_3809 ; sc:license "GPL-2.0" ; sc:name "Repitools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Repitools.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_0821, edam:topic_2885, edam:topic_3125 ; sc:citation "pubmed:17631616" ; sc:description "REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups." ; sc:featureList edam:operation_0323, edam:operation_0431, edam:operation_3192, edam:operation_3223, edam:operation_3695 ; sc:name "REPK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rocaplab.ocean.washington.edu/tools/repk" ; biotools:primaryContact "Gabrielle Rocap" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0605 ; sc:citation , ; sc:description "This tool replaces the string or regular expression given in \"pattern to search\" field by the string given in \"replacing string\" field." ; sc:featureList edam:operation_3096 ; sc:name "replace_regex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/text_manipulation_utilities/replace_regex/0.0.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0634, edam:topic_3300, edam:topic_3379 ; sc:citation , "pubmed:37368794" ; sc:description "A digital twin-based methodology to identify a personalized model from type 1 diabetes data and simulate glucose concentrations to assess alternative therapies." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ReplayBG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gcappon/replay-bg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0659, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """Probability-based methods for outlier detection in replicated high-throughput biological data. This package provides functions for outlier detection in the setting of replicated data. Assuming we have multiple independent measurements (called "replicates") for each data point, we can find which sets of measurements are so different from each other that we can call them outliers. We use the absolute difference and coefficient of variation (Zeta, a kind of relative difference) for each pair of replicates to make our determinations. The function outlier_DZ returns a numeric identifier for the outlier status ( for non-outlier, for large but not , and for outlier).""" ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3799 ; sc:name "replicateOutliers" ; sc:url "http://github.com/matthew-seth-smith/replicateOutliers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3127 ; sc:citation ; sc:description "Tool for classifying replication timing regions." ; sc:featureList edam:operation_2990 ; sc:name "Repliscan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zyndagj/repliscan" ; biotools:primaryContact "Matthew W. Vaughn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0157, edam:topic_0621, edam:topic_0769, edam:topic_3673 ; sc:citation , "pubmed:32591772" ; sc:description """Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage. RepLoc Sequence repetitiveness quantification and de novo repeat detection. We developed a software named Repeat Locator (RepLoc), which quantifies the sequence repetitiveness based on weighted k-mer coverage. The repetitiveness map (Rmap) generated by RepLoc can be used to determine all repetitive sequences in the genome. The potential applications of this method include: de novo repeat detection (both common repeats and segmental duplications), genome structure and genome mappability analysis, etc.""" ; sc:featureList edam:operation_0379, edam:operation_0524, edam:operation_3472, edam:operation_3644, edam:operation_3799 ; sc:name "RepLoc" ; sc:url "http://bis.zju.edu.cn/reploc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3071, edam:topic_3489 ; sc:citation , "pmcid:PMC5314482", "pubmed:28209127" ; sc:description "A data manager meant to avoid manual storage/retrieval of data to/from the file system. It builds one (or more) centralized repository where R objects are stored with rich annotations, including corresponding code chunks, and easily searched and retrieved." ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "repo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.1.3" ; sc:url "https://cran.r-project.org/web/packages/repo/" ; biotools:primaryContact "Francesco Napolitano" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "Protein quantification based on reporter ions." ; sc:featureList edam:operation_3630 ; sc:name "Reporter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "v0.2.7 (beta)" ; sc:url "http://compomics.github.io/projects/reporter.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2332 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2331 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation , "pmcid:PMC5994940", "pubmed:24078713" ; sc:description "This software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page." ; sc:featureList edam:operation_0571 ; sc:license "Artistic-2.0" ; sc:name "ReportingTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ReportingTools.html" ; biotools:primaryContact "Gabriel Becker", "Jason A. Hackney", "Jessica L. Larson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC10273728", "pubmed:37322495" ; sc:description "Surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data." ; sc:featureList edam:operation_0323, edam:operation_0567, edam:operation_3196, edam:operation_3431, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ReporTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/insapathogenomics/ReporTree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_0623, edam:topic_3510 ; sc:citation "pubmed:15980460" ; sc:description "Tool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats." ; sc:featureList edam:operation_0292, edam:operation_0379, edam:operation_0380, edam:operation_2479, edam:operation_3092 ; sc:name "REPPER" ; sc:url "http://protevo.eb.tuebingen.mpg.de/repper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0157 ; sc:citation "pubmed:11203383" ; sc:description "The web application is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments." ; sc:featureList edam:operation_0379, edam:operation_0495 ; sc:name "REPRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/reprowww/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_0769, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description """Workflow for Revised Probe Assignment and Updated Probe-Set Annotation in Microarrays. devtools::install_github("friederhadlich/rePROBE"). Revised probe assignment and updated probe-set annotation in microarrays.""" ; sc:featureList edam:operation_0309, edam:operation_2495, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "rePROBE" ; sc:url "https://github.com/friederhadlich/rePROBE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3379, edam:topic_3397, edam:topic_3420, edam:topic_3500 ; sc:citation , "pubmed:32090407" ; sc:description """approach towards Evidence-based Veterinary Medicine in small animal reproduction. The “Reprocases” project aims to collect case reports of diseases with a low incidence. Especially for diseases that we rarely see in practice and for which performing clinical research is challenging, it is difficult to base our work on reliable research data.""" ; sc:name "REPROCASES" ; sc:url "http://www.evssar.org/reprocases" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6902413", "pubmed:31823809" ; sc:description "Comparison of Dimensionality Reduction Methods for Single Cell RNAseq Analysis." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3680, edam:operation_3891 ; sc:name "reproduce" ; sc:url "http://www.xzlab.org/reproduce.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0219, edam:topic_0621, edam:topic_3957 ; sc:citation , "pubmed:35015827" ; sc:description "Semantic-based detection of redundancies to unify protein-protein interaction databases." ; sc:featureList edam:operation_2422, edam:operation_2492, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "Reproducible interactome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://reproducible-interactome.genouest.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation "pubmed:8345525" ; sc:description "Protein secondary structure and accessibility predictor from the Rost Lab. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance. The language choosen was Perl." ; sc:featureList edam:operation_0267 ; sc:name "reprof" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "tum.de" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/Rostlab/reprof" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3420 ; sc:author "Thomas Darde" ; sc:citation ; sc:description "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "ReproGenomics Viewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "GenOuest", "irisa.fr" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://rgv.genouest.org" ; biotools:primaryContact "Frédéric Chalmel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_2840, edam:topic_3411, edam:topic_3420 ; sc:citation , "pmcid:PMC10352311", "pubmed:37460679" ; sc:description "Toxicology knowledge graph for structural birth defects." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ReproTox-KG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://maayanlab.cloud/reprotox-kg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:11997349" ; sc:description "A WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. The updated version of RePS incorporates some of the ideas introduced by Phusion on clustering" ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3432 ; sc:name "RePS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.genomics.cn/en/navigation/show_navigation?nid=2732" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0659 ; sc:citation "pubmed:21149264" ; sc:description "RepTar is a database of miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites." ; sc:featureList edam:operation_0224, edam:operation_0463, edam:operation_2489, edam:operation_2575 ; sc:name "RepTar" ; sc:url "http://reptar.ekmd.huji.ac.il" ; biotools:primaryContact "RepTar Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "A new algorithm for short read error correction that harvests information from k-spectrum and read decomposition." ; sc:featureList edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "Reptile" ; sc:operatingSystem "Linux" ; sc:url "http://aluru-sun.ece.iastate.edu/doku.php?id=reptile" ; biotools:primaryContact "Xiao Yang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1211, edam:format_1214, edam:format_1925, edam:format_1927, edam:format_1929, edam:format_1930, edam:format_1942, edam:format_2330, edam:format_2332 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_0654 ; sc:citation , "pmcid:PMC92531", "pubmed:11713313" ; sc:description "The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization." ; sc:featureList edam:operation_0379, edam:operation_0573 ; sc:isAccessibleForFree true ; sc:name "REPuter" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BiBiServ" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bibiserv.cebitec.uni-bielefeld.de/reputer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation ; sc:description "Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format." ; sc:featureList edam:operation_3218 ; sc:license "GPL-2.0" ; sc:name "ReQON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ReQON.html" ; biotools:primaryContact "Christopher Cabanski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:author ; sc:citation ; sc:contributor "Arianna Galzerano" ; sc:description "ReRa is a relevance-redundancy feature selection approach that improves the performance of an expression-based predictive model in unbalanced classification." ; sc:name "ReRa" ; sc:url "https://github.com/DEIB-GECO/ReRa" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3175, edam:topic_3334, edam:topic_3512 ; sc:citation , "pubmed:32845284" ; sc:description """inferring repeat expansions and structural variation in paired-end short read sequencing data. git clone https://github.com/rlmcl/rescan. As well as controlling data flow into REscan using SAMtools (see Feed it only the data it needs under Caveats and features, below), you have three options for specifying regions for REscan output:.""" ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "REscan" ; sc:url "https://github.com/rlmcl/rescan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3174, edam:topic_3489, edam:topic_3697 ; sc:citation ; sc:description """Reproducible sequence taxonomy reference database management for the masses. REference Sequence annotation and CuRatIon Pipeline. RESCRIPt is a python 3 package to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data.""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3431, edam:operation_3460 ; sc:license "BSD-3-Clause" ; sc:name "RESCRIPt" ; sc:url "https://github.com/bokulich-lab/RESCRIPt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:12114529", "pubmed:15215377" ; sc:description "Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes." ; sc:featureList edam:operation_0446 ; sc:name "Rescue-ESE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hollywood.mit.edu/burgelab/rescue-ese/" ; biotools:primaryContact "Gene Yeo", "Ru-Fang Yeh", "Will Fairbrother" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3321, edam:topic_3517 ; sc:citation "pubmed:15070404" ; sc:description "An application that uses the Self-Organizing Map neural network algorithm for codon usage anaysis and gene-prediction. In its gene prediction functionality, RescueNet can estimate multiple models of gene codon usage properties during training. This offers advantageous gene-finding performance in cases where a diverse number of codon usage patterns are displayed." ; sc:featureList edam:operation_0286 ; sc:name "RescueNet" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinf.nuigalway.ie/RescueNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3384, edam:topic_3421, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC8633465", "pubmed:34608757" ; sc:description "A tool to automatically segment and characterize lacunas in brain images." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ResectVol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.lniunicamp.com/resectvol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3512, edam:topic_3674 ; sc:citation ; sc:description """ReSeq simulates realistic Illumina high-throughput sequencing data. More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original sequences. Snakemake file to reproduce figures and tables in the ReSeq paper. This included the pipeline used to compare ReSeq, pIRS, NEAT and ART on 8 datasets, a bwa bowtie2 comparison with simulated data using ReSeq and various small things. Apply errors and qualities directly to sequences. Even though sequencing biases and errors have been deeply researched to adequately account for them, comparison studies, e.g. for error correction, assembly or variant calling, face the problem that synthetic datasets resemble the real output of high-throughput sequencers only in very limited ways, resulting in optimistic estimated performance of programs run on simulated data compared to real data.""" ; sc:featureList edam:operation_0363, edam:operation_3192, edam:operation_3216, edam:operation_3359, edam:operation_3435 ; sc:license "MIT" ; sc:name "ReSeq" ; sc:url "https://github.com/schmeing/ReSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation ; sc:description "A simulation toolbox that will help us optimize the combination of different technologies to perform comparative genome re-sequencing, especially in reconstructing large structural variants (SVs)." ; sc:featureList edam:operation_3198 ; sc:name "ReSeqSim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://archive.gersteinlab.org/proj/ReSeqSim/" ; biotools:primaryContact "Jiang Du" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation , "pmcid:PMC3468078", "pubmed:22782487" ; sc:description "Identification of acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria." ; sc:featureList edam:operation_0282 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ResFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://cge.cbs.dtu.dk/services/ResFinder/" ; biotools:primaryContact "Ole Lund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2814 ; sc:citation , "pubmed:26342233" ; sc:description "A method for the identification of dynamic domains, hinges and interfacial regions in proteins" ; sc:featureList edam:operation_0246 ; sc:name "ResiCon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dworkowa.imdik.pan.pl/EP/ResiCon/" ; biotools:primaryContact "Pawel Daniluk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2619 ; sc:name "RESID ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2332 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0601 ; sc:citation ; sc:description "A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications." ; sc:featureList edam:operation_0224 ; sc:name "RESID database of protein modifications" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pir.georgetown.edu/resid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0780, edam:topic_3489, edam:topic_3673 ; sc:citation , "pmcid:PMC7816582", "pubmed:33495705" ; sc:description """ResiDB is a user-friendly sequence similarity-dependent database manager for bacteria, fungi, viruses, protozoa, invertebrate, plants, archaea, environmental and whole genome shotgun sequence data. Create a new database Access existing databases Load sample results. An automated database manager for sequence data. Your rapid sequence similiarity-dependent database manager!.""" ; sc:featureList edam:operation_2422, edam:operation_3096, edam:operation_3482 ; sc:name "resiDB" ; sc:url "https://residb.ait.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3318, edam:topic_3407, edam:topic_3697 ; sc:citation ; sc:description """A residence-time framework for biodiversity. Residence time (τ) is the average amount of time that particles spend in an ecosystem. Often estimated from the ratio of volume to flow rate, τ equates the physical environment with dynamics of growth. We proposed that τ is key to understanding relationships between biodiversity and the physical ecosystem.""" ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "residence-time" ; sc:url "https://github.com/LennonLab/residence-time" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0199, edam:topic_0218 ; sc:citation , "pmcid:PMC8293528", "pubmed:34289903" ; sc:description "ResidueFinder is a simple, effective, and efficient program for finding individual residue mentions in primary literature starting with text files, implemented in Python" ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ResidueFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sourceforge.net/projects/residuefinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_2269, edam:topic_2814 ; sc:citation , "pubmed:32780798" ; sc:description """Residue-Level Functional Site Predictions to Gauge the Accuracies of Protein Structure Prediction Techniques. Assessing the Accuracy of Structure Models Using Functional Predictions. Welcome to ResiRole, a protein structure model assessment technique based on predictions of functional sites mapped to specific residues. functional site motifs. The set of scripts presented here contain a method for assessing the quality of protein homology models based on the precision with which they reconstitute functional site predictions around specific residues as found in their experimentally determined target structures.""" ; sc:featureList edam:operation_0477, edam:operation_1777, edam:operation_3092 ; sc:license "GPL-3.0" ; sc:name "ResiRole" ; sc:url "http://protein.som.geisinger.edu/ResiRole/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3293, edam:topic_3301, edam:topic_3673 ; sc:citation , "pubmed:31980371" ; sc:description """An online tool for prediction of drug resistance patterns of Mycobacterium tuberculosis isolates using next generation sequencing data. Resistance Sniffer: Prediction of Drug Resistance by Sequence Data.""" ; sc:featureList edam:operation_3482, edam:operation_3803 ; sc:name "Resistance Sniffer" ; sc:url "http://resistance-sniffer.bi.up.ac.za/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3174, edam:topic_3299, edam:topic_3474 ; sc:citation , "pmcid:PMC7213576", "pubmed:32391909" ; sc:description "Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples." ; sc:featureList edam:operation_0436, edam:operation_3460, edam:operation_3482 ; sc:name "resistomedb" ; sc:url "http://www.resistomedb.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0593, edam:topic_2640, edam:topic_3292, edam:topic_3398 ; sc:citation , "pmcid:PMC10173857", "pubmed:37115667" ; sc:description "Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR." ; sc:featureList edam:operation_0477, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RESISTOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/donaldlab/OSPREY3/releases/3.3-resistor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description """A web-based tool for visual, statistical and exploratory analysis of resistome data. ResistoXplorer is a web-based, visual analytics tool to assist researchers to perform exploratory data analysis on abundance profiles and resistome signatures generated from AMR metagenomics studies. The key features of ResistoXplorer include:.""" ; sc:featureList edam:operation_2436, edam:operation_2939, edam:operation_3925 ; sc:name "ResistoXplorer" ; sc:url "http://www.resistoxplorer.no/ResistoXplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:35560104" ; sc:description "Residual Learning for Long-tailed Recognition." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ResLT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jiequancui/ResLT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC9416665", "pubmed:36005688" ; sc:description "Web Server for Predicting Residue-Specific Membrane-Association Propensities of Intrinsically Disordered Proteins." ; sc:featureList edam:operation_0470, edam:operation_2476, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "ReSMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pipe.rcc.fsu.edu/ReSMAPidp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3474, edam:topic_3837 ; sc:citation , "pmcid:PMC10174551", "pubmed:37126495" ; sc:description "Increasing the quality of metagenome-assembled genomes with deep learning." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ResMiCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/leylabmpi/ResMiCo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_2229, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC10185920", "pubmed:36880172" ; sc:description "Web server for predicting protein lysine 2-hydroxyisobutylation modification sites." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "ResNetKhib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://resnetkhib.erc.monash.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0634, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:16173164" ; sc:description "Tool for cross-referencing microarray data derived from different species and across different expression analysis platforms. 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PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important.""" ; sc:featureList edam:operation_0331, edam:operation_1777, edam:operation_3196 ; sc:name "RESULTS:SIFT" ; sc:url "http://sift.jcvi.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3518 ; sc:description "Browse the data analysis results of your own microarray experiments." ; sc:featureList edam:operation_2495 ; sc:name "ResultViewer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://bioinformatics.mdanderson.org/main/ResultViewer:Overview" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2050 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular property (general)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3370, edam:topic_3520 ; sc:citation "pubmed:21840007" ; sc:description "A related web utility for projecting/predicting retention times." ; sc:featureList edam:operation_3633 ; sc:name "retentionprediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://retentionprediction.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_3305, edam:topic_3325, edam:topic_3421 ; sc:citation , , "pmcid:PMC7590677", "pubmed:33109251" ; sc:description """Design, development and deployment of a web-based interoperable registry for inherited retinal dystrophies in Portugal. 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If you want to know what will expect you here shortly, check out the reel:. ||| COMMON LINK WITH (PUB. & NAME DIFFERENT) bio.tools/Ribopeaks (COM.) ||| CORRECT NAME OF TOOL COULD ALSO BE 'retina.pt', 'Retina Study Group', 'registries increases', 'Retina Study'""" ; sc:featureList edam:operation_3196 ; sc:name "Retina" ; sc:url "http://retina.com.pt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384 ; sc:description "MATLAB script for extracting blood vessels from a retina image using Kirsch's Templates." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Retinal Blood Vessel Extraction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/24990-retinal-blood-vessel-extraction" ; biotools:primaryContact "Athi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344, edam:topic_3382 ; sc:description "Extraction of blood vessel features in retinal images" ; sc:featureList edam:operation_3443, edam:operation_3695, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Retinal blood vessel extractor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/15411-image-processing" ; biotools:primaryContact "Ebtesam Ahmed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3384, edam:topic_3452, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description "A script for detection of retinal vessels by Gabor transform and machine learning" ; sc:featureList edam:operation_3443, edam:operation_3695, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "Retinal Vessel Detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46082-retinal-vessel-detection-by-gabor-transform-and-machine-learning-a-tutorial" ; biotools:primaryContact "pangyuteng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "This script is for calculating multiple retinal vessel tortuosity measure such as Vessel Torttousity Index (VTI)." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "Retinal Vessel Tortuosity Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/73562-retinal-vessel-tortuosity-analysis" ; biotools:primaryContact "Maz M. Khansari" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3172, edam:topic_3314, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:32390414" ; sc:description """Retention Time Prediction for Compound Annotation in Untargeted Metabolomics. Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis. Retip - Retention Time prediction for Metabolomics. Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.""" ; sc:featureList edam:operation_0335, edam:operation_3431, edam:operation_3629, edam:operation_3633, edam:operation_3860 ; sc:name "Retip" ; sc:url "https://www.retip.app" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_1929, edam:format_2205 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:name "Tool name (FASTA)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:description "Retrieve similar sequences beginning from DNA, RNA or Proteins as well as free text - meaning there is no need to set any preliminary search parameters or filters which restrict the search space. Out of the box your search in parallel 11 of the most popular databases. Average alignment takes less then 3 seconds. 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Accessing the contents of visual short-term memory (VSTM) is compromised by information bottlenecks and visual interference between memorization and recall. Retro-cues, displayed after the offset of a memory stimulus and prior to the onset of a probe stimulus, indicate the test item and improve performance in VSTM tasks. It has been proposed that retro-cues aid recall by transferring information from a high-capacity memory store into visual working memory (multiple-store hypothesis). Alternatively, retro-cues could aid recall by redistributing memory resources within the same (low-capacity) working memory store (single-store hypothesis). If retro-cues provide access to a memory store with a capacity exceeding the set size, then, given sufficient training in the use of the retro-cue, near-ceiling performance should be observed""" ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "retro-cues" ; sc:url "http://github.com/paulzerr/retrocues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0821, edam:topic_2258, edam:topic_3068, edam:topic_3371, edam:topic_3895 ; sc:citation ; sc:description """Computer-Aided Synthesis Planning for Biocatalytic Reactions and Cascades. A collection of tools for automated biocatalytic cascade design. Any feedback is very welcome. Please email william.finnigan@manchester.ac.uk.""" ; sc:featureList edam:operation_2422 ; sc:name "RetroBioCat" ; sc:url "http://retrobiocat.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_0798 ; sc:citation "pubmed:15461796" ; sc:description "An application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner. This is NOT a particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements will be treated as solo LTRs and internal regions depending on how you have set up your element searches." ; sc:featureList edam:operation_0427 ; sc:name "RetroMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.burchsite.com/bioi/RetroMapHome.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_3398, edam:topic_3895 ; sc:citation , "pubmed:31841626" ; sc:description "RetroPath RL performs bio-retrosynthesis using the Monte Carlo Tree Search Reinforcement Learning approach. It is compatible with mono-component reaction rules from RetroRules." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RetroPath RL" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/brsynth/RetroPathRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web service" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_3398, edam:topic_3895 ; sc:citation , "pmcid:PMC6323975", "pubmed:30321422" ; sc:description "RetroRules is a database of reaction rules for metabolic pathway discovery and metabolic engineering. RetroRules provides a complete set of reaction rules, extracted from public databases and expressed in the community-standard SMARTS format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such multiple representation of reactions expands natural chemical diversity by predicting de novo reactions of promiscuous enzymes. Our rules are readily usable by open source cheminformatics tools such as RDKit as well as more complex retrosynthetic codes such as RetroPath2.0." ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RetroRules" ; sc:softwareHelp ; sc:softwareVersion "v1.0.5" ; sc:url "https://retrorules.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3299, edam:topic_3512 ; sc:citation , "pmcid:PMC8415311", "pubmed:34484306" ; sc:description "RetroScan is an easy-to-use tool for retrocopy identification that integrates a series of bioinformatics tools (LAST, BEDtools, ClustalW2, KaKs_Calculator, HISAT2, StringTie, SAMtools and Shiny) and scripts. It scans retrocopies based on alignments between protein-coding genes and whole-genome sequences. This tool can also analyze heterosense substitution and synonymous substitution, compare gene structure between parental genes and retrocopies, and calculate corresponding expression values. Moreover, RetroScan has a user-friendly visualization interface that provides overall statistical information, a retrocopy structure diagram, the nonsynonymous/synonymous substitution (Ka/Ks) ratio distribution and the fragments per kilobase per million (FPKM) heatmap using the Shiny package in R." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RetroScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Vicky123wzy/RetroScan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences." ; sc:featureList edam:operation_2423 ; sc:name "RetroTector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://retrotector.neuro.uu.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_0203 ; sc:citation "pubmed:26898549" ; sc:description "A novel method for the fast automatic prediction of repeat units and repeat classification using an extensive Structure Repeat Unit Library (SRUL) derived from RepeatsDB." ; sc:featureList edam:operation_0379 ; sc:name "ReUPRed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protein.bio.unipd.it/reupred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0749, edam:topic_2269, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc:description "REVA as a Well-curated Database for Human Expression-modulating Variants." ; sc:featureList edam:operation_0308, edam:operation_3227, edam:operation_3435 ; sc:name "REVA" ; sc:softwareHelp ; sc:url "http://reva.gao-lab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation , "pmcid:PMC8085609", "pubmed:33982023" ; sc:description "reval is a Python package to determine best clustering solutions with stability-based relative clustering validation." ; sc:featureList edam:operation_2428, edam:operation_3432, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "reval" ; sc:softwareHelp ; sc:url "https://github.com/IIT-LAND/reval_clustering" ; biotools:primaryContact "Isotta Landi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_2885, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC9822537", "pubmed:36576005" ; sc:description "A comprehensive tool for regulatory variant analysis and visualization of cancer genomes." ; sc:featureList edam:operation_0337, edam:operation_3197, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Revana" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KiTZ-Heidelberg/revana" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3569 ; sc:citation , "pmcid:PMC4911942", "pubmed:27235697" ; sc:contributor ; sc:description "RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful for many complex modeling tasks." ; sc:featureList edam:operation_3664 ; sc:license "GPL-3.0" ; sc:name "RevBayes" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://revbayes.github.io/" ; biotools:primaryContact "Sebastian Höhna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2275, edam:topic_2814, edam:topic_3534 ; sc:citation "pubmed:17518766" ; sc:description "A viewer for automated active-site predictions for polypeptides." ; sc:featureList edam:operation_0250 ; sc:name "Reveal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.cm-uj.krakow.pl/reveal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0622, edam:topic_3697 ; sc:citation , "pmcid:PMC4965897", "pubmed:27473172" ; sc:description "An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis." ; sc:featureList edam:operation_3660 ; sc:license "GPL-2.0" ; sc:name "RevEcoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.99.3" ; sc:url "https://cran.r-project.org/web/packages/RevEcoR/" ; biotools:primaryContact "Yang Cao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168, edam:topic_3516 ; sc:citation "pubmed:26353840" ; sc:description "An ultrafast tool for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage." ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:name "Reveel" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://reveel.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0130, edam:topic_0623, edam:topic_3306, edam:topic_3407 ; sc:citation , "pmcid:PMC7218706", "pubmed:32400867" ; sc:description "Revenant is a database of resurrected proteins coming from extinct organisms. Currently, it contains a manually curated collection of 84 resurrected proteins derived from bibliographic data. Each protein is extensively annotated, including structural, biochemical and biophysical information. Revenant contains a browse capability designed as a timeline from where the different proteins can be accessed. The oldest Revenant entries are between 4200 and 3500 million years ago, while the younger entries are between 8.8 and 6.3 million years ago. These proteins have been resurrected using computational tools called ancestral sequence reconstruction techniques combined with wet-laboratory synthesis and expression" ; sc:featureList edam:operation_0477, edam:operation_3478, edam:operation_3745 ; sc:name "Revenant" ; sc:url "http://revenant.inf.pucp.edu.pe/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC7342053" ; sc:description """Time-Travelling in CSP Computations. reverCSP is a tool that allows us to evaluate a CSP specification in both directions: forwards (traditional computation) and backwards (using our reversible computation framework). reverCSP uses internally csp_tracker to produce tracks of the computation so one can better follows what is being computed so far (or henceforth if going backwards).""" ; sc:featureList edam:operation_1812, edam:operation_3435 ; sc:license "AGPL-3.0" ; sc:name "reverCSP" ; sc:url "https://github.com/tamarit/reverCSP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0593, edam:topic_2275 ; sc:citation , "pmcid:PMC10594994", "pubmed:37881441" ; sc:description "Web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina." ; sc:featureList edam:operation_0482, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ReverseDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://reversedock.biologie.uni-freiburg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description "RevGadgets is an R Package for visualizing Bayesian phylogenetic analyses from RevBayes. Through user-friendly data pipelines, RevGadgets guides users through importing RevBayes output into R, processing the output, and producing figures or other summaries of the results. RevGadgets provide paired processing and plotting functions built around commonly implemented analyses, such as tree building and divergence-time estimation, diversification-rate estimation, ancestral-state reconstruction and biogeographic range reconstruction, and posterior predictive simulations." ; sc:featureList edam:operation_0323, edam:operation_0337, edam:operation_3435 ; sc:name "RevGadgets" ; sc:url "https://github.com/cmt2/RevGadgets" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_0625, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC9367089", "pubmed:35948990" ; sc:description "Haplotype-resolved visualization of read alignments in and around tandem repeats." ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "REViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/illumina/REViewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3063, edam:topic_3263, edam:topic_3337, edam:topic_3577 ; sc:citation ; sc:description "ReviewR is a portable tool to help you explore data across different data models. Within ReviewR, you can browse patient data stored in either the OMOP or MIMIC-III data model." ; sc:featureList edam:operation_2422, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ReviewR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://thewileylab.shinyapps.io/ReviewR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0749, edam:topic_3382 ; sc:citation , "pmcid:PMC8315543", "pubmed:34314456" ; sc:description "Remote visualization environment for large numerical simulation datasets." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "ReVisE" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/deadmorous/revise" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3479 ; sc:encodingFormat edam:format_2200 ; sc:name "Gene order" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2855 ; sc:encodingFormat edam:format_3475 ; sc:name "Distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3945 ; sc:citation , ; sc:description "Various tools for genome rearrangement analysis. CREx, TreeREx, etc" ; sc:featureList edam:operation_3228 ; sc:license "GPL-3.0" ; sc:name "revoluzer" ; sc:operatingSystem "Linux" ; sc:url "https://gitlab.com/Bernt/revoluzer/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Reverse and complement a nucleotide sequence." ; sc:featureList edam:operation_0363 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "revseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/revseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_0154, edam:topic_0199, edam:topic_0654 ; sc:citation "pubmed:12824361" ; sc:description "RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_3216 ; sc:license "Other" ; sc:name "RevTrans" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbs.dtu.dk/services/RevTrans/" ; biotools:primaryContact "Scientific problems: Anders Gorm Pedersen", "Technical problems: Rasmus Wernersson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3325, edam:topic_3512 ; sc:citation , "pmcid:PMC9048665", "pubmed:35289834" ; sc:description "Online scoring system for regulatory variants implicated in rare diseases." ; sc:featureList edam:operation_2422, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:name "RevUP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.revup-classifier.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0602, edam:topic_3295, edam:topic_3518 ; sc:citation , "pmcid:PMC7547494", "pubmed:33036550" ; sc:description """unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm. REW-ISA now supports calling in the form of R packages. The Github link of REW-ISA R package is: https://github.com/cst-cumt/REWISA. REW-ISA is used to find potential local functional blocks (LFB) based on MeRIP-Seq data, where sites are hyper-methylated or hypo-methylated simultaneously across the specific conditions. REW-ISA adopts RNA expression levels of each site as weights to make sites of lower expression level less significant.""" ; sc:featureList edam:operation_2495, edam:operation_3207, edam:operation_3928 ; sc:name "REW-ISA" ; sc:url "https://github.com/cst-cumt/REW-ISA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3071 ; sc:citation , "pmcid:PMC6317226", "pubmed:30622655" ; sc:description "REXdb: a reference database of transposable element protein domains" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "REXdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://repeatexplorer.org/?page_id=918" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344 ; sc:author ; sc:citation , , "pmcid:PMC9678903", "pubmed:31243429", "pubmed:36411288" ; sc:description "Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rexposome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rexposome.html" ; biotools:primaryContact "Juan R Gonzalez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_3511 ; sc:citation "pubmed:19958502" ; sc:description "A web application that provides many functionalities for improved PCR primer design." ; sc:featureList edam:operation_0308 ; sc:name "RExPrimer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www4a.biotec.or.th/rexprimer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0621, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC7160427", "pubmed:32322367" ; sc:description "RF-MaloSite and DL-MaloSite are methods based on random forest and deep learning to identify malonylation sites. The computational methods for malonylation site prediction are based on random forest and deep learning machine learning algorithms, RF-MaloSite and DL-MaloSite, respectively. DL-MaloSite requires the primary amino acid sequence as an input and RF-MaloSite utilizes a diverse set of biochemical, physiochemical and sequence-based features." ; sc:featureList edam:operation_0417, edam:operation_3936, edam:operation_3937 ; sc:name "RF-MaloSite and DL-MaloSite" ; sc:url "https://github.com/dukkakc/DL-MaloSite-and-RF-MaloSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0621, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC7160427", "pubmed:32322367" ; sc:description """Methods based on random forest and deep learning to identify malonylation sites. Dataset is in FASTA format which includes protein window size of 29. Test dataset is provided. There are two dataset for positive and negative examples. Dataset includes all organisms, human, mouse and S-organism. They are provided in separate folder with separate models. The best model has been included. Download all model parts and extracting the 1st part will automatically extract others. The final file is named as .h5.""" ; sc:featureList edam:operation_0417, edam:operation_3936, edam:operation_3937 ; sc:name "RF-MaloSite" ; sc:url "https://github.com/dukkakc/DL-MaloSite-and-RF-MaloSite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3293 ; sc:citation ; sc:description "RF-Net 2 is a tool for fast inference of virus reassortment and hybridization networks. RF-Net is a method for estimation of entangled evolutionary histories of viruses or species. It reconstructs reassortment or hybridization networks from real, error-prone biological data. RF-Net requires rooted gene/locus phylogenetic trees in the Newick format as an input." ; sc:featureList edam:operation_0326, edam:operation_0553, edam:operation_3478 ; sc:license "MIT" ; sc:name "RF-Net 2" ; sc:url "https://github.com/flu-crew/rf-net-2" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3300, edam:topic_3474 ; sc:citation , "pmcid:PMC7054385", "pubmed:32175316" ; sc:description """A Random Forest Predictor for RNA Pseudouridine Sites. One of the ubiquitous chemical modifications in RNA, pseudouridine modification is crucial for various cellular biological and physiological processes. To gain more insight into the functional mechanisms involved, it is of fundamental importance to precisely identify pseudouridine sites in RNA. Several useful machine learning approaches have become available recently, with the increasing progress of next-generation sequencing technology; however, existing methods cannot predict sites with high accuracy. Thus, a more accurate predictor is required. In this study, a random forest-based predictor named RF-PseU is proposed for prediction of pseudouridylation sites. To optimize feature representation and obtain a better model, the light gradient boosting machine algorithm and incremental feature selection strategy were used to select the optimum feature space vector for training the random forest model RF-PseU""" ; sc:featureList edam:operation_0451, edam:operation_0452, edam:operation_3936 ; sc:name "RF-PseU" ; sc:url "http://rfpsu.aibiochem.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3127, edam:topic_3474, edam:topic_3557 ; sc:citation "pubmed:17478517" ; sc:description "This tool predicts recombination hot/cold spots in the yeast genome." ; sc:featureList edam:operation_0451 ; sc:name "RF_DYMHC" ; sc:url "http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3474 ; sc:citation ; sc:description "Ligand-based virtual screening model comprising 1121 target SAR models built using a random forest algorithm." ; sc:featureList edam:operation_0250, edam:operation_2949 ; sc:name "RF QSAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rfqsar.kaist.ac.kr/home.php" ; biotools:primaryContact "Kyoungyeul Lee", "Minho Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0623, edam:topic_0659 ; sc:citation , ; sc:description "Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs)" ; sc:featureList edam:operation_0294, edam:operation_0362 ; sc:isAccessibleForFree true ; sc:name "Rfam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rfam.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0623 ; sc:author "Eric Nawrocki", "Rfam group" ; sc:citation ; sc:description "Search of Rfam's CM collection." ; sc:featureList edam:operation_0346 ; sc:name "Rfam search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "HHMI", "Sanger Institute" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://rfam.xfam.org/search" ; biotools:primaryContact "Rfam group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0623, edam:topic_0659, edam:topic_0749, edam:topic_3293 ; sc:citation , "pmcid:PMC7810343", "pubmed:33449976" ; sc:description """An R client-side interface to facilitate the analysis of the Rfam database of RNA families. rfaRm is an R package providing a client-side interface for the Rfam database of non-coding RNA and other structured RNA elements. The package facilitates the search of the Rfam database by keywords or sequences, as well as the retrieval of all available information about specific Rfam families, such as member sequences, multiple sequence alignments, secondary structures and covariance models. By providing such programmatic access to the Rfam database, rfaRm enables genomic workflows to incorporate information about non-coding RNA, whose potential cannot be fully exploited just through interactive access to the database. The features of rfaRm are demonstrated by using it to analyze the SARS-CoV-2 genome as an example case""" ; sc:featureList edam:operation_0324, edam:operation_0492, edam:operation_2422, edam:operation_3469 ; sc:name "rfaRm" ; sc:url "https://bioconductor.org/packages/release/bioc/html/rfaRm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3474, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC10227442", "pubmed:37260508" ; sc:description "Machine learning approach combined with read-level features to detect somatic mutations." ; sc:featureList edam:operation_3227, edam:operation_3435, edam:operation_3962 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RFcaller" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xa-lab/RFcaller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2269, edam:topic_3384 ; sc:author "Cansu Alakuş" ; sc:citation , "pubmed:33693547" ; sc:description "Random Forest with Canonical Correlation Analysis (RFCCA) is a an R library random forest method for estimating the canonical correlations between two sets of variables depending on the subject-related covariates." ; sc:featureList edam:operation_3359, edam:operation_3463, edam:operation_3659, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "RFCCA" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=RFCCA" ; biotools:primaryContact "Cansu Alakuş" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0736 ; sc:citation "pubmed:25435395" ; sc:description "A predictor that could distinguish parallel dimeric and trimeric coiled coils. It uses the most efficient and non-redundant amino acid indices combined with the state-of-the-art machine learning method Random Forest to make the prediction." ; sc:featureList edam:operation_0474 ; sc:name "RFCoil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://protein.cau.edu.cn/RFCoil/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3512 ; sc:description "This program obtains the numerical solution of ordinary differential equations by means of numerical integration." ; sc:isAccessibleForFree true ; sc:name "Runge-Kutta-Fehlberg (RFK45) solver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/73172-metodos-runge-kutta-4-orden-runge-kutta-fehlberg-rfk45" ; biotools:primaryContact "Alfredo Velazquez Ibañez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3574, edam:topic_3673 ; sc:citation "pubmed:23910464" ; sc:description "Apowerful discriminative modeling approach that is faster (~30×) and more accurate than existing methods. It is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians." ; sc:featureList edam:operation_3745 ; sc:name "RFMix" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/rfmixlocalancestryinference/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3382 ; sc:citation , "pubmed:35767498" ; sc:description "Transformer-Based Generative Adversarial Network for Real Fundus Image Restoration on a New Clinical Benchmark." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RFormer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dengzhuo-AI/Real-Fundus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "RFOVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74200-rfove-cell-segmentation" ; biotools:primaryContact "Costas Panagiotakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3174, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description """Predicting plasmid sequences from short read assembly data using machine learning. Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers. RFPlasmid comes with an option to train your own model if you provide it with contigs of chromosomes and plasmids.""" ; sc:featureList edam:operation_0310, edam:operation_0578, edam:operation_2454, edam:operation_3196, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "RFPlasmid" ; sc:url "http://klif.uu.nl/rfplasmid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3474, edam:topic_3538 ; sc:citation , "pubmed:32112084" ; sc:description """reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins. Protein remote homology detection is one of the fundamental tasks in computational biology, which plays an important role in both basic research and practical applications.""" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0470, edam:operation_0474, edam:operation_3904 ; sc:name "RFPR-IDP" ; sc:url "http://bliulab.net/RFPR-IDP/server" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3475 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation ; sc:description "Based on external numerous data files where scores are pre-calculated on all genomic positions of the human exome, this package gives scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein." ; sc:featureList edam:operation_1777 ; sc:license "GPL-2.0" ; sc:name "rfPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rfPred.html" ; biotools:primaryContact "Hugo Varet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3376 ; sc:citation , "pmcid:PMC9205535", "pubmed:35719742" ; sc:description "An R package for finding higher order interactions, and best subsets for statistical regression models" ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "rFSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/joshuawlambert/rFSA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1212 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3174, edam:topic_3837 ; sc:description "Reference-Free Sequence Classification Tool for DNA sequences in metagenomic samples." ; sc:featureList edam:operation_2995 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RFSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/cobilab/RFSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3170, edam:topic_3314, edam:topic_3320 ; sc:citation ; sc:description "rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments." ; sc:featureList edam:operation_0239, edam:operation_3215, edam:operation_3435 ; sc:name "rG4-seeker" ; sc:url "https://github.com/TF-Chan-Lab/rG4-seeker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_2269, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9723610", "pubmed:36350614" ; sc:description "A convolutional neural network for predicting rG4 folding of any given sequence based on rG4-seq data." ; sc:featureList edam:operation_0303, edam:operation_3901, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "rG4detector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/OrensteinLab/rG4detector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software." ; sc:featureList edam:operation_0239 ; sc:license "Artistic-2.0" ; sc:name "rGADEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rGADEM.html" ; biotools:primaryContact "Arnaud Droit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "rGAI is an R package for fitting the generalised abundance index to seasonal count data. The package provides a user interface for calculating a Generalised Abundance Index (GAI) for seasonal invertebrates, with multiple options for covariate inclusion, seasonal flight patterns and observed count distributions, along with the ability to conduct bootstraps to obtain measures of uncertainty for estimated parameter and GAI values." ; sc:featureList edam:operation_3435 ; sc:name "rGAI" ; sc:url "https://github.com/calliste-fagard-jenkin/rGAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Given an R function and its manual page, make the documented function available in Galaxy." ; sc:featureList edam:operation_1812 ; sc:license "Artistic-2.0" ; sc:name "RGalaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RGalaxy.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:citation "pubmed:24753490" ; sc:description "This package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. 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Glaucoma is a disease associated with the loss of retinal ganglion cells (RGCs), and remains one of the primary causes of blindness worldwide. Major research efforts are presently directed towards the understanding of disease pathogenesis and the development of new therapies, with the help of rodent models as an important preclinical research tool. The ultimate goal is reaching neuroprotection of the RGCs, which requires a tool to reliably quantify RGC survival. Hence, we demonstrate a novel deep learning pipeline that enables fully automated RGC quantification in the entire murine retina. This software, called RGCode (Retinal Ganglion Cell quantification based On DEep learning), provides a user-friendly interface that requires the input of RBPMS-immunostained flatmounts and returns the total RGC count, retinal area and density, together with output images showing the computed counts and isodensity maps""" ; sc:featureList edam:operation_3799 ; sc:license "MIT" ; sc:name "RGCode" ; sc:url "https://gitlab.com/NCDRlab/rgcode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Regularized Copula based Feature Selection- Application on Single cell RNA Sequence Data. The default core, p=20, and Tuning Coefficient-value is (coeff=0.009) for RgCop. Load the dataset from Data folder, and put the codes and Datasets in same path. Muraro Data is in master branch in this github. Run the DataProcessing.R code. Run the FeatureSelection.R in R folder.""" ; sc:featureList edam:operation_0313, edam:operation_3463, edam:operation_3936 ; sc:name "RgCop" ; sc:url "https://github.com/Snehalikalall/RgCop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0634, edam:topic_3298, edam:topic_3335 ; sc:citation "pubmed:11752273", "pubmed:15608243", "pubmed:17151068", "pubmed:18996890" ; sc:description "The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis." ; sc:featureList edam:operation_0282, edam:operation_0485, edam:operation_2429, edam:operation_3196, edam:operation_3197 ; sc:name "Rat Genome Database (RGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rgd.mcw.edu/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8410278", "pubmed:34541090" ; sc:description "Computational tools and libraries for CRISPR/Cas9-derived RNA-guided engineered nucleases (RGENs)." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RGEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rgenome.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0625, edam:topic_2269 ; sc:citation ; sc:description """An R Package for the Exploration of Molecular Convergent Evolution. A Package for Estimating Probability of Convergent Evolution from Genomic Data version 0.1.0 from GitHub. rgenesconverged helps identify instances of convergent evolution by sequence similarity at the molecular level, by finding conserved, similar, and independently arising sequences within user-submitted phylogenetic trees. dinaIssakova/rgenesconverged: A Package for Estimating Probability of Convergent Evolution from Genomic Data""" ; sc:featureList edam:operation_0337, edam:operation_3478 ; sc:name "rgenesconverged" ; sc:url "https://rdrr.io/github/dinaIssakova/rgenesconverged" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3277 ; sc:citation , ; sc:description "Attempts to estimate library complexity from sequence alone. Does so by sorting all reads by the first N bases (5 by default) of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default)." ; sc:featureList edam:operation_0234 ; sc:name "rgestlibcomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:description "C++ implementation of SConES." ; sc:featureList edam:operation_2497 ; sc:license "MIT" ; sc:name "Rgin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rgin.html" ; biotools:primaryContact "Hector Climente" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "This package brings the GenoMetric Query Language functionalities into the R environment. It is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. It adopts algorithms efficiently designed for big data using cloud-computing technologies allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance." ; sc:featureList edam:operation_0224 ; sc:license "Artistic-2.0" ; sc:name "RGMQL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RGMQL.html" ; biotools:primaryContact "Simone Pallotta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10475473", "pubmed:37671241" ; sc:description "Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity." ; sc:featureList edam:operation_2238, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "RgnTX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioconductor.org/packages/RgnTX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3297 ; sc:citation , "pmcid:PMC7273057", "pubmed:32500918" ; sc:description "Database of Root Genes and Promoters in Maize, Soybean, and Sorghum." ; sc:featureList edam:operation_0440, edam:operation_2421, edam:operation_2495 ; sc:name "RGPDB" ; sc:url "http://sysbio.unl.edu/RGPDB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "Ensure that all mate-pair information is in sync between each read and it's mate pair." ; sc:featureList edam:operation_0231 ; sc:name "rgpicfixmate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "https://broadinstitute.github.io/picard/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071 ; sc:citation ; sc:description "Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael." ; sc:featureList edam:operation_0335 ; sc:license "GPL-2.0" ; sc:name "RGraph2js" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RGraph2js.html" ; biotools:primaryContact "Stephane Cano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package." ; sc:featureList edam:operation_3744 ; sc:license "EPL-1.0" ; sc:name "Rgraphviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html" ; biotools:primaryContact "Kasper Daniel Hansen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508, edam:format_3603, edam:format_3604, edam:format_3696 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3508, edam:format_3603, edam:format_3604, edam:format_3696 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3673 ; sc:author "Zuguang Gu" ; sc:description "This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server." ; sc:featureList edam:operation_0362 ; sc:license "GPL-2.0" ; sc:name "rGREAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.13.3" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rGREAT.html" ; biotools:primaryContact "Zuguang Gu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Combining bootstrap aggregating and Gene Set Enrichment Analysis, this software is a classfication algorithm with high robustness and no over-fitting problem. It performs especially well for the data generated from different exprements." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "RGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RGSEA.html" ; biotools:primaryContact "Chengcheng Ma" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2769 ; sc:encodingFormat edam:format_1958 ; sc:name "Transcript ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3752 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation ; sc:description "Bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group." ; sc:featureList edam:operation_2436 ; sc:license "GPL-3.0" ; sc:name "rgsepd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rgsepd.html" ; biotools:primaryContact "Karl Stamm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3379 ; sc:citation , "pubmed:34282646" ; sc:description "An Analysis Tool for Continuous Glucose Monitor Data." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "rGV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny.biostat.umn.edu/GV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_3168 ; sc:citation "pubmed:26568628" ; sc:description "A seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio’s Single Molecule Read-time (SMRT) sequencing reads." ; sc:featureList edam:operation_3182 ; sc:name "rHAT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/derekguan/rHAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "Bernd Fischer", "Gregoire Pau" ; sc:description "This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "rhdf5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.26.0" ; sc:url "http://bioconductor.org/packages/rhdf5/" ; biotools:primaryContact "Mike Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:description "Provides functionality for reading data from h5serv server from within R." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "rhdf5client" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rhdf5client.html" ; biotools:primaryContact "Samuela Pollack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Provides C and C++ hdf5 libraries to R packages in a non-system-dependant manner." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "Rhdf5lib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/Rhdf5lib/" ; biotools:primaryContact "Mike Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3314 ; sc:citation "pmcid:PMC6324061", "pubmed:30272209" ; sc:description """Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest developed by the Swiss-Prot group at SIB Swiss Institute of Bioinformatics. 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To address this issue, we performed a genome-wide transcriptome analysis on R. arenarum larvae through massive RNA sequencing, followed by de novo assembly, annotation, and gene prediction. We obtained 57,407 well-annotated transcripts representing 99.4% of transcriptome completeness (available at http: rhinella.uncoma.edu.ar). 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Make Ribbon automatically go to each variant in a bedpe file and take pictures of the multi-read view and a selection of reads. Instructions: Load a bedpe file and a bam file first, set the settings below and in the right-side panel as you want them and click Run!. Margin around a variant or manually entered coordinate where reads will be pulled from a bam file (use this parameter carefully as importing too much data can crash your web browser due to memory overload).""" ; sc:featureList edam:operation_0337, edam:operation_3198, edam:operation_3227 ; sc:license "MIT" ; sc:name "Ribbon" ; sc:url "http://genomeribbon.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3360 ; sc:citation , "pubmed:36264679" ; sc:description "A Proposed Benchmark for the Standardized Evaluation of Indirect Methods for Reference Interval Estimation." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RIbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=RIbench" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation "pubmed:15980564" ; sc:description "Seach sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved." ; sc:featureList edam:operation_0438 ; sc:name "RibEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibt.unam.mx/biocomputo/RibEx.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0099, edam:topic_0602 ; sc:citation ; sc:description "An ultrafast RNA–RNA interaction prediction system based on a seed-and-extension approach." ; sc:featureList edam:operation_0272 ; sc:license "MIT" ; sc:name "RIblast" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://funpopgen.github.io/veqtl-mapper/" ; biotools:primaryContact "Michiaki Hamada", "Tsukasa Fukunag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:25592593" ; sc:description "Human-computing game that aims to improve the accuracy of RNA alignments already stored in Rfam." ; sc:featureList edam:operation_0292 ; sc:name "Ribo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ribo.cs.mcgill.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "Ribo-ODDR : Based on given pilot sequencing data and rRNA sequences, Ribo-ODDR pipeline designs oligos complementary to rRNA sequences and computes their depleting potentials in pilot Ribo-seq data. The tool outputs all oligo designs that pass user-defined filtering criterias, which are explained in later sections. Oligo designs are reported in FASTA, BED, GFF and CSV formats, and if needed, off-target information is outputted in TXT format." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Ribo-ODDR" ; sc:url "https://github.com/fallerlab/Ribo-ODDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Simple, cost-effective, and widely applicable ribosomal RNA depletion. Snakemake workflow: ribopop_probe_design. This workflow designs oligos that hybridize to rRNA targets. First, a consensus sequence is built for each target. Next, potential probe target sites are screened against the genome and the transcriptome for non-rRNA matches. Finally, probes are selected to cover the targets, while adhering to the specified design parameters and avoiding the predicted non-specific targeting. Snakemake workflow: ribopop_rnaseq. This workflow performs analysis of RNA-Seq data for the Ribo-Pop paper. If you're not using conda, you will need to install snakemake as well as all the other software listed in envs/ribopop_probe_design.yaml in advance of running the workflow using your preferred installation method.""" ; sc:featureList edam:operation_0309, edam:operation_2495, edam:operation_3933 ; sc:license "MIT" ; sc:name "Ribo-Pop" ; sc:url "https://github.com/marykthompson/ribopop_probe_design" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC9825487", "pubmed:36440758" ; sc:description "A comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Ribo-uORF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rnainformatics.org.cn/RiboUORF" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1246 ; sc:name "Sequence cluster (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC6009695", "pubmed:29608703" ; sc:description "Prokaryotic genome assembly polisher -- uses targeted subassembly to resolve gaps caused by repeated rDNA operons." ; sc:featureList edam:operation_0525, edam:operation_3183 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "riboSeed" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.4.90" ; sc:url "https://github.com/nickp60/riboSeed/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC7992832", "pubmed:33765913" ; sc:description "RiboA (Ribo-Seq A-site Identifier) is a web application to identify ribosome A-site locations in ribosome profiling data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3198 ; sc:license "MIT" ; sc:name "RiboA" ; sc:url "https://github.com/obrien-lab/aip_web_docker" ; biotools:primaryContact "Edward P. O’Brien" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0097, edam:topic_0099, edam:topic_3557 ; sc:citation , "pmcid:PMC5238798", "pubmed:27821510" ; sc:description "Capillary electrophoresis data analysis tool for nucleic acid probing." ; sc:featureList edam:operation_2439 ; sc:name "RiboCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238798/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0154, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:36177882" ; sc:description "A database of ribozymes." ; sc:featureList edam:operation_0483, edam:operation_0570, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:name "Ribocentre" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ribocentre.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0605, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:35043169" ; sc:description "A chat-style web interface for analysis and annotation of ribosome profiling data." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "RiboChat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://db.cngb.org/ribobench/chat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7938571", "pubmed:33685493" ; sc:description "riboCIRC is a comprehensive database of translatable circRNAs. Translation of circular RNAs (circRNAs) now has drawn increasing attention from researchers due to their emerging roles of the functional peptides encoded by circRNAs as new players involved in the regulation of gene expression." ; sc:featureList edam:operation_0308, edam:operation_0476, edam:operation_3208, edam:operation_3644 ; sc:name "riboCIRC" ; sc:url "http://www.ribocirc.com" ; biotools:primaryContact , "Zhi Xie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:35731209" ; sc:description "A pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants." ; sc:featureList edam:operation_0314, edam:operation_0435, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "riboCleaner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/basf/riboCleaner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0160, edam:topic_0637 ; sc:citation , "pubmed:27189556" ; sc:description "Fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences." ; sc:featureList edam:operation_2422, edam:operation_3460 ; sc:name "RiboDB" ; sc:softwareHelp , ; sc:softwareVersion "1.0.2" ; sc:url "https://ribodb.univ-lyon1.fr/ribodb/ribodb-in.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "RiboDetector is a software developed to accurately yet rapidly detect and remove rRNA sequences from metagenomeic, metatranscriptomic, and ncRNA sequencing data. It was developed based on LSTMs and optimized for both GPU and CPU." ; sc:featureList edam:operation_2451, edam:operation_3187 ; sc:license "GPL-3.0" ; sc:name "RiboDetector" ; sc:url "https://github.com/hzi-bifo/RiboDetector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_2229, edam:topic_3512 ; sc:citation ; sc:description "A Novel tool for differential pattern analysis in Ribo-seq data." ; sc:featureList edam:operation_1812, edam:operation_3223, edam:operation_3435, edam:operation_3799 ; sc:name "RiboDiPA" ; sc:url "https://github.com/jipingw/RiboDiPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_0203, edam:topic_0769, edam:topic_2229 ; sc:citation , "pmcid:PMC8141510", "pubmed:34093996" ; sc:description "A Docker-based package for ribosome profiling analysis." ; sc:featureList edam:operation_2428, edam:operation_3223, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RiboDoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/equipeGST/RiboDoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0166, edam:topic_0659, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC8515840", "pubmed:34661102" ; sc:description "semiautomated two-dimensional drawing of RNA tertiary structure diagrams." ; sc:featureList edam:operation_0295, edam:operation_2441, edam:operation_2486 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RiboDraw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DasLab/RiboDraw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:33479731" ; sc:description """Riboexp is an interpretable reinforcement learning framework for ribosome density modeling. Train a neural network model to predict ribosome densities across a set of transcripts.""" ; sc:featureList edam:operation_0253, edam:operation_2962, edam:operation_3454, edam:operation_3927 ; sc:name "Riboexp" ; sc:url "https://github.com/Liuxg16/Riboexp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_3297, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """using deep learning to classify riboswitches with ~99% accuracy. Classifying Putative Riboswitch Sequences. RIBOFLOW - classifying riboswitches with >99% accuracy. riboflow is a python package for classifying putative riboswitch sequences into one of 32 classes with > 99% accuracy. It is based on a tensorflow deep learning model. riboflow has been tested using Python 3.5.2""" ; sc:featureList edam:operation_0310, edam:operation_0441, edam:operation_2495 ; sc:license "MIT" ; sc:name "riboflow" ; sc:url "https://pypi.org/project/riboflow" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation "pubmed:26635865" ; sc:description "It is a novel method for microbial profiling based on the identification and classification of 16S rRNA sequences in non targeted metagenomics datasets. Reads overlapping the 16S rRNA genes are identified using Hidden Markov Models and a taxonomic assignment is obtained by naive Bayesian classification. All reads identified as ribosomal are coherently positioned in the 16S rRNA gene, allowing the use of the topology of the gene to instruct the abundance analysis." ; sc:featureList edam:operation_3460 ; sc:name "RiboFrame" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.1" ; sc:url "http://bioserver2.sbsc.unifi.it/bioinfo/riboframe.html" ; biotools:primaryContact "Matteo Ramazzotti" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_1932 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2969 ; sc:encodingFormat edam:format_3603 ; sc:name "Sequence image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3603 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_3006 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , "pmcid:PMC4829337", "pubmed:26821742", "pubmed:37356899" ; sc:contributor "Science Foundation Ireland" ; sc:description "Galaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_2495, edam:operation_2928 ; sc:funder "Science Foundation Ireland" ; sc:isAccessibleForFree true ; sc:name "RiboGalaxy" ; sc:operatingSystem "Mac", "Windows" ; sc:provider "ucc.ie" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://ribogalaxy.ucc.ie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation "pubmed:24833802" ; sc:description "A webserver for the computational design of conformation-based riboregulation." ; sc:featureList edam:operation_2430, edam:operation_2441 ; sc:name "Ribomaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://absynth.issb.genopole.fr/Bioinformatics/tools/Ribomaker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7430821", "pubmed:32738892" ; sc:description """a toolset for mining multi-dimensional features of the translatome with ribosome profiling data. A python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. The RiboMiner is a python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. This package has four function parts:. RiboMiner could offer other useful functions that would help users analyze ribosome profiling data, such as statistics of read coverage, visualization of read density for a single transcript or some transcript sets.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2495, edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "RiboMiner" ; sc:url "https://github.com/xryanglab/RiboMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3174, edam:topic_3308 ; sc:citation "pubmed:22155869" ; sc:description "A tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too." ; sc:featureList edam:operation_3695 ; sc:name "riboPicker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ribopicker.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8650366", "pubmed:34876166" ; sc:description "A Visualization Tool for Periodic Ribo-seq Reads." ; sc:featureList edam:operation_0337, edam:operation_0436, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RiboPlotR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hsinyenwu/RiboPlotR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1017 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence range" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage." ; sc:featureList edam:operation_0286 ; sc:license "GPL-3.0" ; sc:name "RiboProfiling" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RiboProfiling.html" ; biotools:primaryContact "A. Popa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0622, edam:topic_0659 ; sc:citation ; sc:description "Fast and flexible identification of differential translation from Ribo-seq data." ; sc:featureList edam:operation_0438 ; sc:name "Riborex" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/smithlabcode/riborex" ; biotools:primaryContact "Andrew D. Smith", "Weili Wang", "Wenzheng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation , "pubmed:34089018" ; sc:description "Ribose-Map is a user-friendly, standardized bioinformatics toolkit for the comprehensive analysis of ribonucleotide (rNMP) sequencing experiments. It can be applied to data generated using any high-throughput ribonucleotide sequencing technique, including ribose-seq, emRiboSeq, RHII-HydEn-seq, Alk-HydEn-seq, and Pu-seq." ; sc:featureList edam:operation_2520, edam:operation_3192, edam:operation_3196, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Ribose-Map" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/agombolay/ribose-map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments." ; sc:featureList edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "riboSeqR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/riboSeqR.html" ; biotools:primaryContact "Thomas J. Hardcastle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_2229, edam:topic_3512 ; sc:citation , "pubmed:31760685" ; sc:description """Computational methods for ribosome profiling data analysis. Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation. Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.""" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "ribosome profiling" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RiboProfiling.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:16820430" ; sc:description "A user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position." ; sc:featureList edam:operation_0564, edam:operation_2928 ; sc:name "Ribostral" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.bgsu.edu/ribostral/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0204, edam:topic_3407, edam:topic_3512 ; sc:citation "pubmed:15215370" ; sc:description "RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis." ; sc:featureList edam:operation_0239, edam:operation_0314, edam:operation_0438, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Riboswitch finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3673 ; sc:citation "pubmed:26519506" ; sc:description "A new web application which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity." ; sc:featureList edam:operation_0239 ; sc:name "Riboswitch Scanner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://service.iiserkol.ac.in/~riboscan/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2305 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_1929, edam:format_3003, edam:format_3508 ; sc:name "Gene expression profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation ; sc:description "New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions." ; sc:featureList edam:operation_0314 ; sc:name "RiboTaper" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.31a" ; sc:url "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3174, edam:topic_3837, edam:topic_3941 ; sc:citation , "pmcid:PMC9492272", "pubmed:36159175" ; sc:description "RiboTaxa is a complete pipeline to rapidly filter and reconstruct the full length SSU rRNA gene from Illumina (meta)genomic dataset and perform taxonomic classification on the reconstructed sequences." ; sc:featureList edam:operation_3192, edam:operation_3216, edam:operation_3460, edam:operation_3478, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "RiboTaxa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/oschakoory/RiboTaxa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0659, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC7319539", "pubmed:32427338" ; sc:description """an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. Ribosome profiling (Ribo-seq) has revolutionized the translatomics field by mapping the position of ribosome-protected fragments (RPFs), which is typically ranging from 26bp to 34bp, over the entire transcriptome.""" ; sc:featureList edam:operation_0286, edam:operation_2436, edam:operation_3799, edam:operation_3891 ; sc:name "RiboToolkit" ; sc:url "http://rnabioinfor.tch.harvard.edu/RiboToolkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31750902" ; sc:description "A tool for accurately detecting actively translating ORFs from Ribo-seq data." ; sc:featureList edam:operation_0436, edam:operation_3359, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "Ribotricer" ; sc:url "https://github.com/smithlabcode/ribotricer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:25340471" ; sc:description "A visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes." ; sc:featureList edam:operation_0570 ; sc:name "RiboVision" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://apollo.chemistry.gatech.edu/RiboVision/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "riboviz 2 is a flexible and robust ribosome profiling data analysis and visualization workflow. Ribosome profiling provides a detailed global snapshot of protein synthesis in a cell." ; sc:featureList edam:operation_0314, edam:operation_1812, edam:operation_3192, edam:operation_3799, edam:operation_3933 ; sc:license "Apache-2.0" ; sc:name "riboviz 2" ; sc:url "http://github.com/riboviz/riboviz" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Suite" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0219, edam:topic_0659, edam:topic_2229, edam:topic_3174 ; sc:citation ; sc:description """Ribovore is a suite of tools for detecting, classifying and analyzing small subunit ribosomal RNA (SSU rRNA) and large subunit (LSU) rRNA sequences. It is used by GenBank to validate incoming 16S SSU rRNA sequences and to generate high quality datasets of SSU and LSU rRNA sequences for RefSeq and for use as blastn databases. Ribovore is written in Perl. Ribosomal RNA sequence analysis for GenBank submissions and database curation.""" ; sc:featureList edam:operation_3192, edam:operation_3200, edam:operation_3431, edam:operation_3460 ; sc:name "Ribovore" ; sc:url "https://github.com/ncbi/ribovore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "riboWaltz" ; sc:softwareVersion "1.0.0", "1.0.1", "1.1.0", "1.2.0" ; sc:url "https://github.com/LabTranslationalArchitectomics/riboWaltz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3125, edam:topic_3292, edam:topic_3299 ; sc:citation , "pmcid:PMC9825457", "pubmed:36305870" ; sc:description "A comprehensive database for visualizing and analyzing ribosome structures." ; sc:featureList edam:operation_0339, edam:operation_0570, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "RiboXYZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ribosome.xyz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:name "GO-term enrichment data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3148 ; sc:name "Gene family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0780, edam:topic_3293, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Comprehensive pan-genome database for comparative and functional genomics of Asian rice." ; sc:featureList edam:operation_0362, edam:operation_2421, edam:operation_2436, edam:operation_2495, edam:operation_2928, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "Rice Gene Index" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://riceome.hzau.edu.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_2885, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc:description """a comprehensive database of rice long non-coding RNAs. Long non-coding RNAs (lncRNAs) play significant functions in various biological processes including differentiation, development and adaptation to different environments. Although multi research focused on lncRNAs in rice, the systematic identification and annotation of lncRNAs expressed in different tissues, developmental stages under diverse conditions are still scarce. This impacts the elucidation of their functional significance and the further research on them. Here, RiceLncPedia is constructed including rice lncRNAs explored from 2313 publically available rice RNA-seq libraries and characterize them with multi-omics data sets""" ; sc:featureList edam:operation_0313, edam:operation_0463, edam:operation_3792 ; sc:name "RiceLncPedia" ; sc:url "http://218.199.68.191:10092/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170 ; sc:citation , "pubmed:35762882" ; sc:description "A Resource for Rice Non-coding RNA Co-Expression Atlas Based on Massive RNA-seq and Small-RNA seq Data." ; sc:featureList edam:operation_3463, edam:operation_3680, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:name "RiceNCexp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbi.njau.edu.cn/RiceNCexp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3517 ; sc:author ; sc:description "RicePilaf is a web app for post-GWAS/QTL analysis that performs a slew of novel bioinformatics analyses to cross GWAS results and QTL mappings with a host of publicly available rice databases. It integrates pangenomic information from high-quality genome builds of multiple rice varieties, co-expression information from genome-scale co-expression networks, ontology and pathway information, regulatory information from rice transcription factor databases, epigenomic information from multiple high-throughput epigenetic experiments, and text-mining information extracted from scientific abstracts linking genes and traits." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RicePilaf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://github.com/bioinfodlsu/rice-pilaf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3421, edam:topic_3512 ; sc:citation "pubmed:21045061" ; sc:description "It is a gene expression database to provide the transcriptional changes throughout the growth of the rice plant in the field. It contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. Analysis tools facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0315, edam:operation_2495, edam:operation_3463 ; sc:name "RiceXPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ricexpro.dna.affrc.go.jp/" ; biotools:primaryContact "RiceXPro Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3314, edam:topic_3344, edam:topic_3385 ; sc:description "Performs raster image correlation analysis spectroscopy (RICS)" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "Raster Image Correlation Spectroscopy (RICS)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48703-raster-image-correlation-spectroscopy" ; biotools:primaryContact "Molly Rossow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3403, edam:topic_3474 ; sc:description "Focused on (but not exclusive to) data sets hosted on PhysioNet (https://physionet.org), 'ricu' provides utilities for download, setup and access of intensive care unit (ICU) data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented." ; sc:featureList edam:operation_1812, edam:operation_2422, edam:operation_3282 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ricu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.5.4" ; sc:url "https://github.com/eth-mds/ricu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0634, edam:topic_3300, edam:topic_3538 ; sc:citation , "pmcid:PMC9679974", "pubmed:36334049" ; sc:description "Rapid prediction and analysis of protein intrinsic disorder." ; sc:featureList edam:operation_0470, edam:operation_3904, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:name "RIDAO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ridao.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:23268829" ; sc:description "A network-based method for characterizing gene sets. It asks if an input query set is significantly “close” to a known pathway or disease set in the human functional network." ; sc:featureList edam:operation_3672 ; sc:name "RIDDLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.functionalnet.org/riddle/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0160 ; sc:citation , "pubmed:28666322" ; sc:description """an application to protein pairwise alignments. Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions""" ; sc:featureList edam:operation_0295, edam:operation_0303, edam:operation_0491 ; sc:name "Rigapollo" ; sc:url "http://www.ibsquare.be/rigapollo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_3304, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC7363478", "pubmed:32493756" ; sc:description """An Open-Source Toolbox for Probing Neurons and Behavior. Rigbox is a high-performance, open-source MATLAB toolbox for managing behavioral neuroscience experiments. Rigbox's main goals are to simplify hardware/software interfacing, behavioral task design, and visual and auditory stimuli presentation. Additionally, Rigbox can time-align datastreams from multiple sources and communicate with a remote database to manage experiment data. Rigbox is mostly object-oriented and highly modular, which simplifies the process of designing experiments. For detailed information, see the publication.""" ; sc:featureList edam:operation_0337, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "Rigbox" ; sc:url "https://github.com/cortex-lab/Rigbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3512, edam:topic_3810 ; sc:citation , "pmcid:PMC7426402", "pubmed:32849839" ; sc:description """A Database for Intronless Genes in the Rosaceae. RIGD is developed by Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, School of Life Sciences, Anhui Agricultural University. PIGD integrates the intronless genes data of six species of Rosaceae and makes a systematic comparative analysis. PIGD provides a solid platform for the collection, integration and analysis of intronless genes. As such, this database will be useful for researchers to use the database for data mining and analysis in various aspects. Some pictures come from the Internet, please contact us to express our thanks!.""" ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3663 ; sc:name "RIGD" ; sc:url "http://www.rigdb.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3308, edam:topic_3383, edam:topic_3384 ; sc:citation , "pubmed:31860065" ; sc:description "Regional Imaging Genetic Enrichment Analysis." ; sc:featureList edam:operation_3443, edam:operation_3501, edam:operation_3553 ; sc:license "GPL-3.0" ; sc:name "regional imaging genetic associations" ; sc:url "https://github.com/lshen/RIGEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3572 ; sc:citation ; sc:description "Open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a 'Template Creator' to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data." ; sc:featureList edam:operation_0336 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "RightField" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Manchester, UK", "manchester.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "0.22" ; sc:url "http://www.rightfield.org.uk/" ; biotools:primaryContact "RightField" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0089, edam:topic_0605, edam:topic_3473 ; sc:citation "pubmed:21076152" ; sc:description "It integrates not only RIKEN’s original databases, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations." ; sc:featureList edam:operation_0224, edam:operation_0339, edam:operation_2421, edam:operation_2422 ; sc:name "RIKEN integrated database of mammals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metadb.riken.jp/metadb/db/SciNetS_ria254i" ; biotools:primaryContact "RIKEN support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0881 ; sc:name "Secondary structure alignment (RNA)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1708 ; sc:name "RNA secondary structure image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0097 ; sc:author "Peter Menzel" ; sc:citation , "pubmed:22826541" ; sc:description "Command line program and web server to create an RNA-RNA interaction logo from a pair of RNA sequences or alignments." ; sc:featureList edam:operation_0564, edam:operation_0570 ; sc:license "LGPL-2.1" ; sc:name "RILogo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "binf.ku.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://rth.dk/resources/rilogo/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3360 ; sc:citation , "pubmed:36725922" ; sc:description "An R shiny tool for estimating the reference interval from a meta-analysis." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RIMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cers.shinyapps.io/RIMeta/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0804 ; sc:citation ; sc:description "This package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format." ; sc:featureList edam:operation_1812 ; sc:license "GPL-3.0" ; sc:name "RImmPort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RImmPort.html" ; biotools:primaryContact "Ravi Shankar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3174, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC8565308", "pubmed:34417598" ; sc:description "Set of programs to analyze data derived from (Rapid Identification of Methylase Specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities." ; sc:featureList edam:operation_3186, edam:operation_3192, edam:operation_3207 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RIMS-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Ettwiller/RIMS-seq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2275, edam:topic_3314, edam:topic_3371 ; sc:citation ; sc:description "International chemical identifier for reactions ." ; sc:featureList edam:operation_0322 ; sc:license "CC-BY-4.0" ; sc:name "RInChI" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.inchi-trust.org/downloads/" ; biotools:primaryContact "Jonathan M. 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RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu.""" ; sc:featureList edam:operation_2454, edam:operation_3659, edam:operation_3936 ; sc:license "Artistic-2.0" ; sc:name "RLasso-Cox" ; sc:url "http://bioconductor.org/packages/devel/bioc/html/RLassoCox.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0102, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Exploration and analysis of R-loop mapping data with RLBase." ; sc:featureList edam:operation_2422, edam:operation_2429, edam:operation_2939, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RLBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gccri.bishop-lab.uthscsa.edu/rlbase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_2275, edam:topic_3336, edam:topic_3512 ; sc:citation , "pubmed:36398911" ; sc:description "A deep learning method to predict RNA-ligand binding sites." ; sc:featureList edam:operation_0303, edam:operation_0478, edam:operation_2441, edam:operation_2575, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RLBind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KailiWang1/RLBind" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047 ; sc:citation , "pubmed:33549725" ; sc:description """RLDOCK method for predicting RNA-small molecule binding modes. 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Using a large training sample where the genotype labels are known, the algorithm will obtain more accurate classification results on new data. It is based on a linear model, uses the Mahalanobis distance for classification. Non-biological variation is removed through normalization. It captures similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification." ; sc:featureList edam:operation_3196 ; sc:license "GPL-2.0" ; sc:name "RLMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RLMM.html" ; biotools:primaryContact "Nusrat Rabbee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2275, edam:topic_3511 ; sc:citation "pubmed:20427516" ; sc:description "A web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. It allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface." ; sc:featureList edam:operation_0570 ; sc:name "RLooM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rloom.mpimp-golm.mpg.de/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:name "Tool name (FASTA)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0654, edam:topic_3673 ; sc:citation ; sc:description "RLZ-Graph constructs a genome graph by first compressing the input sequences using the relative Lempel-Ziv algorithm. 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A tool for optical map assembly using de Bruijn graph.""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_2429, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "Rmapper" ; sc:url "https://github.com/kingufl/Rmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_0097, edam:topic_0099, edam:topic_3512 ; sc:citation "pubmed:27174931" ; sc:description "A web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions." ; sc:featureList edam:operation_2404, edam:operation_3677 ; sc:name "rMAPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rmaps.cecsresearch.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:encodingFormat edam:format_2332 ; sc:name "Database metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation , "pubmed:23303751" ; sc:description "Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records." ; sc:featureList edam:operation_3432 ; sc:license "Artistic-2.0" ; sc:name "RMassBank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RMassBank.html" ; biotools:primaryContact "RMassBank at Eawag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation ; sc:description "This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and BioConductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments." ; sc:featureList edam:operation_2495 ; sc:license "Artistic-2.0" ; sc:name "rMAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rMAT.html" ; biotools:primaryContact "Arnaud Droit", "Raphael Gottardo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1930, edam:format_2573 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3932 ; sc:name "Q-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , "pmcid:PMC4280593", "pubmed:25480548" ; sc:description "MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data." ; sc:featureList edam:operation_2499 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "rMATS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.1.2" ; sc:url "http://rnaseq-mats.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0622 ; sc:description "RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program \"rmblastn\" for use with RepeatMasker and RepeatModeler." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "OSL-2.1" ; sc:name "RMBlast" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "2.11.0" ; sc:url "http://www.repeatmasker.org/RMBlast.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC8456376", "pubmed:34621514" ; sc:description "This Shiny app computes and visualizes repeated measures correlation (rmcorr). Rmcorr is the common within-individual linear association for paired, repeated measures data. Rmcorr is conceptually similar to a null multilevel model: A fixed slope and varying intercept by participant." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rmcorrShiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lmarusich.shinyapps.io/shiny_rmcorr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33010174" ; sc:description """a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. RMDisease a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge.""" ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_0484, edam:operation_3661 ; sc:name "RMDisease" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/rmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3068, edam:topic_3382 ; sc:citation , "pubmed:33225873" ; sc:description """An R package to assess nonverbal synchronization in motion energy analysis time-series. The goal of rMEA is to provide a suite of tools useful to read, visualize and export bivariate Motion Energy time-series. Lagged synchrony between subjects can be analyzed through windowed cross-correlation. Surrogate data generation allows an estimation of pseudosynchrony that helps to estimate the effect size of the observed synchronization.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3435, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "rMEA" ; sc:url "https://github.com/kleinbub/rMEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2258, edam:topic_3047 ; sc:citation , "pubmed:36799778" ; sc:description "A Public Database of Elementary Radical Reaction Steps." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "RMechDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://deeprxn.ics.uci.edu/rmechdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description "Advances in Automatic Mechanism Generation." ; sc:featureList edam:operation_2426, edam:operation_3642 ; sc:name "RMG" ; sc:url "https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3071 ; sc:citation , "pubmed:36222558" ; sc:description "RMG Database for Chemical Property Prediction." ; sc:featureList edam:operation_0262, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RMG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rmg.mit.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1926 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Useful functions to merge microRNA and respective targets using differents databases." ; sc:featureList edam:operation_0490 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "RmiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RmiR.html" ; biotools:primaryContact "Francesco Favero" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3172, edam:topic_3308 ; sc:citation , "pubmed:34634637" ; sc:description "A robust missing value imputation approach in transcriptomics and metabolomics data." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rMisbeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=rMisbeta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:description "Run rmlst API through python script for species identification of a bacterial assembly." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rmlst_api" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1.3" ; sc:url "https://github.com/domenico-simone/rmlst_api" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:12824429" ; sc:description "Tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS)." ; sc:featureList edam:operation_0238, edam:operation_0438, edam:operation_0445 ; sc:name "rMotif" ; sc:url "http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3315, edam:topic_3512, edam:topic_3518 ; sc:citation , "pubmed:32449749" ; sc:description """differential expression analysis for repeated-measures RNA-seq data. RNA-Seq Analysis for Repeated-Measures Data. A differential expression analysis method for RNA-seq data from repeated-measures design using general linear model framework and parametric bootstrap inference. The method accounts for the dependence of gene expression levels due to the repeated-measures through continuous autoregressive correlation structure.""" ; sc:featureList edam:operation_3435, edam:operation_3463, edam:operation_3680, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "rmRNAseq" ; sc:url "https://cran.r-project.org/web/packages/rmRNAseq/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation , "pubmed:37356900" ; sc:description "Sequence search and alignment algorithm to improve RNA structure modeling." ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0492, edam:operation_0502, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:name "rMSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanggroup.org/rMSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2814 ; sc:description "Redirect protein structure files (PDB files) or RasMol scripts to multiple RasMol sessions." ; sc:featureList edam:operation_0335 ; sc:name "RmscopII" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2" ; sc:url "http://rmscopii.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3383, edam:topic_3384, edam:topic_3520 ; sc:citation ; sc:description "MS imaging data handling and visualization." ; sc:featureList edam:operation_3443, edam:operation_3694 ; sc:name "rMSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/prafols/rMSI" ; biotools:primaryContact "Jesús Brezmes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC8205298", "pubmed:34179452" ; sc:description "RmsiGUI provides a graphical user interface (GUI) to analyze mass spectrometry imaging (MSI) data with the statistical language R. The interface is based on 'shiny' and visualized in a web browser." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RmsiGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/lababi/rmsigui/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:32108859" ; sc:description """an R package for mass spectrometry imaging data processing. Mass spectrometry imaging (MSI) can reveal biochemical information directly from a tissue section. MSI generates a large quantity of complex spectral data which is still challenging to translate into relevant biochemical information. Here, we present rMSIproc, an open-source R package that implements a full data processing workflow for MSI experiments performed using TOF or FT-based mass spectrometers. The package provides a novel strategy for spectral alignment and recalibration, which allows to process multiple datasets simultaneously""" ; sc:featureList edam:operation_3215, edam:operation_3443, edam:operation_3627 ; sc:name "rMSIproc" ; sc:url "https://github.com/prafols/rMSIproc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3316 ; sc:citation , "pmcid:PMC6993073", "pubmed:32038716" ; sc:description """A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data. RMTA: Read Mapping and Transcript Assembly workflow. RMTA can process FASTq files containing paired-end or single-end reads. Alternatively, RMTA can directly process one or more sequence read archives (SRA) from NCBI using a SRA ID.""" ; sc:featureList edam:operation_0523, edam:operation_3192, edam:operation_3198, edam:operation_3258, edam:operation_3563 ; sc:name "RMTA" ; sc:softwareHelp ; sc:url "https://wiki.cyverse.org/wiki/display/DEapps/RMTA+v2.6.3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3320, edam:topic_3512, edam:topic_3517, edam:topic_3912 ; sc:citation , "pubmed:33021671" ; sc:description """RMVar-Database of functional variants involved in RNA modification. We collected millions of variants, as well as thousands of RNA modification sites from 28 miCLIP experiments, 2 PA-m6A-Seq experiments, 2 m6ACE-Seq experiments, 3 DART-Seq experiments, 7 m6A-REF-Seq experiments, 4 MAZTER-seq experiments, 2 m1A-quant-seq experiments, 2 m1A-IP-Seq experiments, 2 m1A-MAP experiments, 5 m7G-seq, 10 BS-Seq experiments, 2 Nm-Seq experiments, 14 RiboMeth-Seq experiments, 2 ψ-Seq experiments, 1 DM-ψ-Seq experiment, 3 Ceu-Seq experiments, 3 RBS-Seq experiments, 2 m6A-Seal-Seq experiments and 507 MeRIP-Seq experiments, together with a large number of predicted RNA modification sites are involved.""" ; sc:featureList edam:operation_0463, edam:operation_3227, edam:operation_3791 ; sc:name "RMVar" ; sc:url "http://rmvar.renlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3315, edam:topic_3318, edam:topic_3517 ; sc:citation ; sc:description "A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study." ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3659, edam:operation_3791, edam:operation_3891 ; sc:license "Apache-2.0" ; sc:name "rMVP" ; sc:url "https://github.com/xiaolei-lab/rMVP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description "A randomized Numerical Aligner for Accurate alignment of NGS reads" ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iga-rna.sourceforge.net/" ; biotools:primaryContact "rNA Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2885, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC8740077", "pubmed:34991454" ; sc:description "A toolkit for comprehensive analyses on transcriptome data from different sequencing platforms." ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3223, edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RNA-combine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dongxuemin666/RNA-combine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:23396121" ; sc:description "A user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis." ; sc:featureList edam:operation_3680 ; sc:name "RNA-eXpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rnaexpress.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:19648138" ; sc:description "A recursive mapping strategy for high-throughput RNA-sequencing data." ; sc:featureList edam:operation_2429 ; sc:name "RNA-MATE" ; sc:url "http://grimmond.imb.uq.edu.au/RNA-MATE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0160, edam:topic_0166 ; sc:citation , "pubmed:33835435" ; sc:description "RNA-MoIP is a web application for automated prediction framework for RNA tertiary structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2441, edam:operation_2476 ; sc:name "RNA-MoIP" ; sc:url "http://rnamoip.cs.mcgill.ca" ; biotools:primaryContact "Jérôme Waldispühl" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_2330 ; sc:name "RNA sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_3542 ; sc:citation , "pmcid:PMC5793723", "pubmed:28525607" ; sc:description "Predicting RNA hybrid 2D–3D structures from sequence data only. Optionally, it can be used for (i) local 3D motif prediction or (ii) the refinement of user-defined secondary structures. Importantly, our web server automatically generates a script for the MC-Sym software, which can be immediately used to quickly predict all-atom RNA 3D models." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0502 ; sc:name "RNA-MolP" ; sc:softwareHelp ; sc:url "http://rnamoip.cs.mcgill.ca/" ; biotools:primaryContact "Jérôme Waldispühl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """RNA-Ribo Explorer (RRE) is an interactive, stand-alone, and graphical software for analysing, viewing and mining both transcriptome (typically RNA-seq) and translatome (typically Ribosome profiling or Ribo-seq) datasets. ||| CORRECT NAME OF TOOL COULD ALSO BE 'RNA-Ribo Explorer'""" ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_0436 ; sc:name "RNA-Ribo Explorer" ; sc:url "https://gite.lirmm.fr/rivals/RRE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170 ; sc:citation ; sc:description "Computes a series of quality control metrics for RNA-seq data." ; sc:featureList edam:operation_2428 ; sc:name "RNA-SeQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.8" ; sc:url "http://www.broadinstitute.org/cancer/cga/rna-seqc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation "pubmed:24931995" ; sc:description "A rapid method for RNA-Seq quantification at transcript level." ; sc:featureList edam:operation_3800 ; sc:name "RNA-Skim" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.csbio.unc.edu/rs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9279659", "pubmed:35846154" ; sc:description "A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data." ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3227, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNA-SSNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pmglab/RNA-SSNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_3170, edam:topic_3308 ; sc:description "Parallel processing framework for large-scale generation of secondary RNA structures and folding statistics for the transcriptome of any species." ; sc:featureList edam:operation_0278, edam:operation_2439 ; sc:name "rna-stability" ; sc:url "https://github.com/nch-igm/rna-stability" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """Here, we have predicted CasRx guide efficiency for all human and mouse RefSeq genes. We have also enabled custom sequence input for CasRx guide design.""" ; sc:featureList edam:operation_0238, edam:operation_0278, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RNA-targeting" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://RNAtargeting.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:22983261" ; sc:description "A structural interface to comparative data. Currently, it presents three-dimensional RNA distances, tertiary interactions, conservation values, motifs, basepair groups, basepair conformations and coaxial stacks on interactive secondary structure models." ; sc:featureList edam:operation_2439 ; sc:name "RNA2DMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rna.icmb.utexas.edu/SIM/4F/RNA2DMap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Quality assessment tool for de novo transcriptome assemblies." ; sc:featureList edam:operation_0524, edam:operation_3180, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "rnaQUAST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cab.spbu.ru/software/rnaquast/" ; biotools:primaryContact "Andrey D. Prjibelski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:12824342" ; sc:description "Searches for known structures and identifies RNA motifs in your input sequence." ; sc:featureList edam:operation_0239, edam:operation_0278, edam:operation_0314, edam:operation_0483, edam:operation_2441 ; sc:name "RNA Analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/" ; biotools:primaryContact "Thomas Dandekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC10202958", "pubmed:37217540" ; sc:description "Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNA-Bloom2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/RNA-Bloom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0798, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10205464", "pubmed:37221043" ; sc:description "Manually curated analytical database of RNA-chromatin interactome." ; sc:featureList edam:operation_2480, edam:operation_3208, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "RNA-Chrom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rnachrom2.bioinf.fbb.msu.ru/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3324 ; sc:citation , "pmcid:PMC3934900", "pubmed:24586784" ; sc:description "A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets." ; sc:featureList edam:operation_3461, edam:operation_3680 ; sc:name "RNA CoMPASS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://rnacompass.sourceforge.net/" ; biotools:primaryContact "Guorong Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0166, edam:topic_3542 ; sc:citation "pubmed:22127861" ; sc:description "Characterization of Secondary Structure Motifs: a searchable database of secondary structure motifs in RNA three-dimensional structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "RNA CoSSMos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cossmos.slu.edu/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation ; sc:description "An engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation." ; sc:featureList edam:operation_2421 ; sc:name "RNA FRABASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://rnafrabase.ibch.poznan.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0621, edam:topic_0659 ; sc:citation "pubmed:21112871" ; sc:description "Integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. The database is structured according to the most recent helicase classification into helicase superfamilies and families, emphasizes phyologenetic relations." ; sc:featureList edam:operation_0224, edam:operation_0339, edam:operation_0360, edam:operation_2422 ; sc:name "RNA helicase database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rnahelicase.org" ; biotools:primaryContact "Eckhard Jankowsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3500, edam:topic_3542 ; sc:citation "pubmed:10068690", "pubmed:17567618" ; sc:description "RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "RNA Movies" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/rnamovies/" ; biotools:primaryContact "Jan Krüger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:12824414" ; sc:description "RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_2441 ; sc:name "RNA Studio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html" ; biotools:primaryContact "Biefeld University Bioinformatics Server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description """A multi-tissue transcriptional age calculator. An R package for the analysis of tiling array data that incorporates the correlation structures among probe measurements.""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3659 ; sc:name "RNAAgeCalc" ; sc:url "http://www.ams.sunysb.edu/~pfkuan/softwares.html#RNAAgeCalc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097 ; sc:citation ; sc:description "Predict a consensus secondary structure of a set of aligned sequences." ; sc:featureList edam:operation_0278, edam:operation_2478 ; sc:name "RNAalifoldWS" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:25273103" ; sc:description "A tool for secondary structure prediction, using shape abstraction. Input is a multiple sequence alignment. Pseudoknots are not considered at all." ; sc:featureList edam:operation_2441 ; sc:name "RNAalishapes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv2.cebitec.uni-bielefeld.de/rnaalishapes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_3336 ; sc:citation , "pubmed:36146935" ; sc:description "RNA aptamer 3D-structural modeling database." ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_2441, edam:operation_2476, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "RNAapt3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rnaapt3d.medals.jp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:16790841", "pubmed:17483510" ; sc:description "A server for analyzing and predicting RNA binding sites in proteins." ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_2575, edam:operation_3092 ; sc:name "RNABindR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ailab1.ist.psu.edu/RNABindR/" ; biotools:primaryContact "RNABindR team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:citation , "pmcid:PMC4028231", "pubmed:24846307" ; sc:contributor ; sc:description "RNABindRPlus predicts RNA-binding residues from protein sequences by combining the output from a Support Vector Machine (SVM) classifier with the output from a Homology-based method." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "RNABindRPlus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://ailab1.ist.psu.edu/RNABindRPlus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0092, edam:topic_0099 ; sc:citation ; sc:description "Flexible multiple target nucleic acid sequence design." ; sc:featureList edam:operation_3095 ; sc:name "RNAblueprint" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ViennaRNA/RNAblueprint" ; biotools:primaryContact "Ivo L. 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The program reads RNA structures generated from RNAsubopt, calculates their equilibrium distribution and outputs the graph-distances in a tab delimited list or in the terminal." ; sc:featureList edam:operation_0262, edam:operation_0278 ; sc:name "RNAgraphdist" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www.rna.uni-jena.de/en/software/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1210, edam:format_1925, edam:format_1927, edam:format_1929, edam:format_1930, edam:format_1942, edam:format_2330, edam:format_2332 ; sc:name "Nucleic acid sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1210, edam:format_1925, edam:format_1927, edam:format_1929, edam:format_1930, edam:format_1942, edam:format_2330, edam:format_2332 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3128 ; sc:name "Nucleic acid structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:name "RNA secondary structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1584 ; sc:name "Nucleic acid enthalpy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1584 ; sc:name "Nucleic acid enthalpy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0160 ; sc:author "Marc Rehmsmeier" ; sc:citation ; sc:description "Tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. 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Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis." ; sc:featureList edam:operation_0337 ; sc:license "Artistic-2.0" ; sc:name "RNAinteract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RNAinteract.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2078 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3604 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "This tool analyzes cell-based RNAi screens, including quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "RNAither" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RNAither.html" ; biotools:primaryContact "Lars Kaderali" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2546 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099 ; sc:author ; sc:citation , "pmcid:PMC5041467", "pubmed:27330139" ; sc:description "RNAlien is a tool for automatic construction of RNA family models from a single sequence. Results include a covariance model, structural alignment and consensus secondary structure." ; sc:featureList edam:operation_0338, edam:operation_0504, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNAlien" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.3.7" ; sc:url "https://github.com/eggzilla/RNAlien" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9851306", "pubmed:36464487" ; sc:description "A machine learning model to identify nucleotide features determining RNA subcellular localization." ; sc:featureList edam:operation_0278, edam:operation_0418, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RNAlight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YangLab/RNAlight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_3170 ; sc:citation ; sc:description """RNAlign2D – a novel RNA structural alignment tool based on pseudo-amino acid substitution matrix. 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The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. 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A tool for coding potential prediction. 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It takes into consideration the isosteric (both canonical and non-canonical) base-pairs and multi-pairings in RNA tertiary motifs." ; sc:featureList edam:operation_0239, edam:operation_0240 ; sc:name "RNAMotifScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/RNAMotifScan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3511 ; sc:citation "pubmed:25595715" ; sc:description "RNAMotifScanX is a motif search tool based on a base-interaction graph alignment algorithm." ; sc:featureList edam:operation_0239 ; sc:name "RNAMotifScanX" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/RNAMotifScanX/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_2269, edam:topic_3170 ; sc:citation , "pmcid:PMC6980424", "pubmed:31978147" ; sc:description """Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. RNA sequence/structure alignment. RNAmountAlign is a novel algorithm for RNA sequence structure pairwise alignment, that runs in O(n 3 ) time and O(n 2 ) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.""" ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_0496, edam:operation_0503, edam:operation_0510 ; sc:name "RNAmountAlign" ; sc:url "http://bioinformatics.bc.edu/clotelab/RNAmountAlign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0166, edam:topic_0659 ; sc:citation "pubmed:16845040" ; sc:description "Tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences." ; sc:featureList edam:operation_0239, edam:operation_0278, edam:operation_0502, edam:operation_2439, edam:operation_2441 ; sc:name "RNAMST" ; sc:url "http://bioinfo.csie.ncu.edu.tw/~rnamst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0199, edam:topic_3542 ; sc:citation "pubmed:19531740" ; sc:description "A web server to explore the effect of mutations on the RNA secondary structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "RNAmutants" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.bc.edu/clotelab/RNAmutants/" ; biotools:primaryContact "Jérôme Waldispühl (questions about the RNAmutants software)", "Peter Clote (questions about the web server)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0199, edam:topic_3542 ; sc:citation "pubmed:21478166" ; sc:description "RNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "RNAmute" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.cs.bgu.ac.il/~RNAMute/" ; biotools:primaryContact "D. Barash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3474 ; sc:citation , "pubmed:33135044" ; sc:description """an automatically built dual-source dataset integrating homologous sequences and RNA structures. A major part of any data-science work consists in finding appropriate data which contains enough signal to tackle the problem we are interested in. 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Database Summary Paper Categories. Publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic aci. We use cookies to enhance your experience on our website. NAR Database Summary Paper Category List.""" ; sc:featureList edam:operation_2421, edam:operation_2996, edam:operation_3208 ; sc:name "RNArchitecture" ; sc:url "https://academic.oup.com/nar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_3511 ; sc:citation "pubmed:27188396" ; sc:description "An RNA structural motif search tool. Itcan search sequence databases in FASTA format for a motif defined by a descriptor, which can specify primary and secondary structure constraints." ; sc:featureList edam:operation_0239 ; sc:name "RNArobo" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://compbio.fmph.uniba.sk/rnarobo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation ; sc:description "Compute RNA secondary structure with user-input chemical/enzymatic probing data, especially Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) or inline-probing data." ; sc:featureList edam:operation_0271, edam:operation_0278, edam:operation_2423 ; sc:name "RNAsc" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.bc.edu/clotelab/RNAsc/index.spy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3170, edam:topic_3511 ; sc:citation ; sc:description "Clustering RNA sequences using structure conservation and graph based motifs." ; sc:featureList edam:operation_0291 ; sc:license "GPL-3.0" ; sc:name "RNAscClust" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.bioinf.uni-freiburg.de/Software/RNAscClust/" ; biotools:primaryContact "Jan Gorodkin", "Rolf Backofen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:16597240" ; sc:description "A program for RNA consensus folding for a set of unaligned RNA sequences." ; sc:featureList edam:operation_0278 ; sc:name "RNAscf" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.ucf.edu/RNAscf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation , "pmcid:PMC4355470", "pubmed:25766521" ; sc:contributor ; sc:description "Visualization tool that incorporates and extends the functionality of the UCSC genome browser." ; sc:featureList edam:operation_3208 ; sc:name "RNASeqBrowser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "V2" ; sc:url "http://www.australianprostatecentre.org/research/software/rnaseqbrowser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC10267603", "pubmed:37172729" ; sc:description "A web-based integrative transcriptome analysis, RNAseqChef, uncovers the cell/tissue type-dependent action of sulforaphane." ; sc:featureList edam:operation_3223, edam:operation_3680, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNAseqChef" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://imeg-ku.shinyapps.io/RNAseqChef/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC5045616", "pubmed:27716375" ; sc:description "Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation." ; sc:featureList edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "rnaseqcomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rnaseqcomp.html" ; biotools:primaryContact "Mingxiang Teng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3170, edam:topic_3308, edam:topic_3518, edam:topic_3678 ; sc:citation , "pmcid:PMC7941184", "pubmed:33692596" ; sc:description "RNASeqDesign is a framework for RNA-Seq genome-wide power calculation and study design issues." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3800 ; sc:name "RNASeqDesign" ; sc:url "https://github.com/MasakiLin/RNASeqDesign" ; biotools:primaryContact "George C. Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "A tool for evaluating RNA seq mapping." ; sc:featureList edam:operation_0292 ; sc:name "RNAseqEval" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/kkrizanovic/RNAseqEval" ; biotools:primaryContact "Mile Šikić" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation "pubmed:24812338" ; sc:description "A graphical user interface for the identification of differentially expressed genes from RNA-Seq experiments." ; sc:featureList edam:operation_2495 ; sc:name "RNASeqGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.na.iac.cnr.it/RNASeqGUI/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1921 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "A library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time." ; sc:featureList edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "rnaSeqMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.html" ; biotools:primaryContact "Michal Okoniewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0199, edam:topic_3170 ; sc:description "RNASeqMut is an easy-to-use program to detection variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a single or multiple RNA-Seq BAM files." ; sc:featureList edam:operation_2423, edam:operation_3096, edam:operation_3202 ; sc:name "RNASeqMut" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.7" ; sc:url "http://allaboutbioinfo.blogspot.ca/2013/09/detecting-mutations-from-rna-seq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Sample size and power computation for RNA-seq studies." ; sc:featureList edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "RNASeqPower" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RNASeqPower.html" ; biotools:primaryContact "Terry M Therneau" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:25246651" ; sc:description "The tool captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments." ; sc:featureList edam:operation_3680 ; sc:name "RNASeqPowerCalculator" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www2.hawaii.edu/~lgarmire/RNASeqPowerCalculator.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:22199257" ; sc:description """An R package for automated two-group RNA-Seq analysis workflow. This R package is designed for case-control RNA-Seq analysis (two-group). There are six steps: "RNASeqRParam S4 Object Creation", "Environment Setup", "Quality Assessment", "Reads Alignment & Quantification", "Gene-level Differential Analyses" and "Functional Analyses". Each step corresponds to a function in this package. After running functions in order, a basic RNASeq analysis would be done easily.""" ; sc:featureList edam:operation_2939, edam:operation_3185, edam:operation_3198, edam:operation_3680, edam:operation_3800, edam:operation_3891 ; sc:name "RNASEQR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/release/bioc/html/RNASeqR.html" ; biotools:primaryContact "Leroy E. Hood" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , ; sc:description "This package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data." ; sc:featureList edam:operation_3223, edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "RnaSeqSampleSize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RnaSeqSampleSize.html" ; biotools:primaryContact "Shilin Zhao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3489 ; sc:citation , "pubmed:36806691" ; sc:description "An end-to-end reproducible RNAseq data analysis and publishing framework." ; sc:featureList edam:operation_2939, edam:operation_3223, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RNASequest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/interactivereport/RNASequest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation ; sc:description "Integration of tools for RNA abstract shape analysis." ; sc:featureList edam:operation_0474, edam:operation_2423 ; sc:name "RNAshapes" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "3.3.0" ; sc:url "http://bibiserv2.cebitec.uni-bielefeld.de/rnashapes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0209, edam:topic_3170 ; sc:citation , "pubmed:33416863" ; sc:description """Recognition of small molecule-RNA binding sites using RNA sequence and structure. RNA-ligand binding sites prediction. RNAsite is a novel method to predict small molecule-RNA binding sites. We first developed a structure-based method (RNAsite_str) by designing a group of novel structure-based features that effectively captured the perferences towards small molecule-RNA binding sites. Second, a sequence profile-based predictor (RNAsite_seq) was designed to deal with the cases where no structure is available. These two methods are combined, yielding to the final approach RNAsite. Read more about the RNAsite algorithm...""" ; sc:featureList edam:operation_2441, edam:operation_2575, edam:operation_4009 ; sc:name "RNAsite" ; sc:url "http://yanglab.nankai.edu.cn/RNAsite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0166, edam:topic_0659, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC9876829", "pubmed:36733704" ; sc:description "A integrated tool for comparing RNA secondary structure and evaluating allosteric effects." ; sc:featureList edam:operation_0314, edam:operation_0502, edam:operation_0570, edam:operation_3469 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RNAsmc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=RNAsmc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0203, edam:topic_0659, edam:topic_3474 ; sc:citation , "pubmed:33106872" ; sc:description """Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. RNA solvent accessibility, similar to protein solvent accessibility, reflects the structural regions that are accessible to solvents or other functional biomolecules, and plays an important role for structural and functional characterization. Unlike protein solvent accessibility, only a few tools are available for predicting RNA solvent accessibility despite the fact that millions of RNA transcripts have unknown structures and functions. Also, these tools have limited accuracy. Here, we have developed RNAsnap2 that employs a dilated convolutional neural network (Figure 1) with a new feature, based on predicted base-pairing probabilities from LinearPartition[4].""" ; sc:featureList edam:operation_0278, edam:operation_0300, edam:operation_2441, edam:operation_3431 ; sc:license "MPL-2.0" ; sc:name "RNAsnap2" ; sc:url "https://sparks-lab.org/server/rnasnap2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:20015949" ; sc:description "A tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. It implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant." ; sc:featureList edam:operation_0483 ; sc:name "RNAsnoop" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinf.uni-leipzig.de/~htafer/RNAsnoop/RNAsnoop.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2885 ; sc:citation "pubmed:23315997" ; sc:description "A web software for efficient detection of local RNA secondary structure changes induced by SNP's." ; sc:featureList edam:operation_0278 ; sc:name "RNAsnp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rth.dk/resources/rnasnp" ; biotools:primaryContact "Sabarinathan R", "Tafer H" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_3542 ; sc:citation "pubmed:12824338", "pubmed:15095976" ; sc:description "Software for RNA/DNA secondary structure prediction and design." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_2441, edam:operation_2442 ; sc:name "RNAsoft" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.rnasoft.ca/" ; biotools:primaryContact "Anne Condon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0611 ; sc:citation , "pmcid:PMC9272803", "pubmed:35674373" ; sc:description "A repository of cleaned PDB-derived RNA 3D structures." ; sc:featureList edam:operation_0502, edam:operation_0570, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:name "RNAsolo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rnasolo.cs.put.poznan.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099 ; sc:description "Post-processing tool of a structural clustering pipeline for structured RNAs (e.g. RNAclust). It requires as input a binary cluster-tree, the minimum free energy (MFE) of the consensus secondary structure for each internal node, and a FASTA file of the input sequences. It detects the optimal partition (i.e. finding the optimal number of clusters/groups) into distinct subtrees where each subtree contains structurally related RNA sequences." ; sc:featureList edam:operation_2409, edam:operation_3432 ; sc:name "RNAsoup" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0a" ; sc:url "http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAsoup/?p=index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0219, edam:topic_0659 ; sc:citation "pubmed:21947200" ; sc:description "A platform which aims at providing an integrated environment for non-coding RNA annotation. The platform allows running in an integrated environment a variety of ncRNA gene finders, to explore results with dedicated tools for comparison, visualization and edition of putative ncRNAs and to export them in various formats." ; sc:featureList edam:operation_0361 ; sc:name "RNAspace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rnaspace.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:citation , , ; sc:description "Pipeline for de novo transcriptome assembly from RNA-Seq." ; sc:featureList edam:operation_0524, edam:operation_3258 ; sc:name "rnaspades" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.9.0" ; sc:url "http://cab.spbu.ru/software/spades/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_1476 ; sc:name "RNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_0593 ; sc:citation , "pubmed:35349710" ; sc:description "A webserver to analyze entanglements in RNA 3D structures." ; sc:featureList edam:operation_0278, edam:operation_0295, edam:operation_0570, edam:operation_2441, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "RNAspider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rnaspider.cs.put.poznan.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659, edam:topic_3572 ; sc:citation , "pmcid:PMC4489242", "pubmed:26068469" ; sc:description "A web server for quality assessment of RNA 3D structure." ; sc:featureList edam:operation_2439, edam:operation_3218 ; sc:name "RNAssess" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rnassess.cs.put.poznan.pl/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:34570193" ; sc:description "Synthesizing Information to Support Transcriptomics (RNASSIST)." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3766, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RNASSIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://figshare.com/articles/software/RNAssist_Software_and_Data/16617250" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0166, edam:topic_0593 ; sc:citation , "pmcid:PMC9580920", "pubmed:36303785" ; sc:description "An Integrated Tool for Statistical Analysis of RNA 3D Structures." ; sc:featureList edam:operation_0250, edam:operation_0278, edam:operation_0502, edam:operation_2441, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RNAStat" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/RNA-folding-lab/RNAStat" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:encodingFormat edam:format_2330 ; sc:name "RNA secondary structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "RNAstrand predicts the reading direction of a structured RNA in a multiple sequence alignment by employing a support vector machine (SVM)" ; sc:featureList edam:operation_0253 ; sc:name "RNAstrand" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://www.bioinf.uni-leipzig.de/Software/RNAstrand/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0654 ; sc:citation "pubmed:26589271" ; sc:description "A complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target." ; sc:featureList edam:operation_0278 ; sc:name "RNAstructure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.urmc.rochester.edu/RNAstructure.html" ; biotools:primaryContact "David Mathews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3524 ; sc:citation , "pmcid:PMC3981793", "pubmed:24718440" ; sc:description "Direct Temperature Simulations for Predicting the Location of RNA Thermometers." ; sc:featureList edam:operation_2476 ; sc:name "RNAthermsw" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.cs.bgu.ac.il/~rnathemsw/RNAthemsw/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0632, edam:topic_3170 ; sc:citation , "pmcid:PMC7529196", "pubmed:33002005" ; sc:description """fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis. RNAthor is a tool for the fully automated normalization and analysis of SHAPE/DMS data resolved by capillary electrophoresis (CE) and processed in ShapeFinder or QuShape. RNAthor significantly reduces the time required for data analysis and provides tools for fast and easy data visualization and statistical analysis. Main functions of RNAthor:.""" ; sc:featureList edam:operation_0278, edam:operation_0570, edam:operation_2441, edam:operation_2495, edam:operation_3435 ; sc:name "RNAthor" ; sc:url "http://rnathor.cs.put.poznan.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0621, edam:topic_0781 ; sc:citation "pubmed:23766288" ; sc:description "Web server that takes in RNA sequences of the same length and a temperature range to predict regions with high likelihood of temperature induced structural changes." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RNAtips" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webclu.bio.wzw.tum.de/cgi-bin/RNAtips/start.cgi" ; biotools:primaryContact "Dmitrij Frishman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3308, edam:topic_3941 ; sc:description "rnaviralSPAdes - de novo assembler for transcriptomes, metatranscriptomes and metaviromes" ; sc:featureList edam:operation_0310, edam:operation_3258 ; sc:name "rnaviralSPAdes" ; sc:url "http://cab.spbu.ru/software/spades/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2784 ; sc:name "RNAVirusDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2530 ; sc:encodingFormat edam:format_2331 ; sc:name "Organism report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation , "pmcid:PMC2686580", "pubmed:18948277" ; sc:description "RNA virus genome database." ; sc:featureList edam:operation_0224 ; sc:name "RNA virus genome database (RNAVirusDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioafrica.mrc.ac.za/rnavirusdb/" ; biotools:primaryContact "Tulio de Oliveira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation , ; sc:description "This tool and MC-Fold-DP are two programs (rather, collections of a library and several programs, each) that deal with RNA secondary structure prediction." ; sc:featureList edam:operation_0278 ; sc:name "RNAwolf" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.3.2" ; sc:url "http://www.tbi.univie.ac.at/software/rnawolf/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3068, edam:topic_3320 ; sc:citation , "pmcid:PMC7327530", "pubmed:32608478" ; sc:description """a resource of writers, readers and erasers of RNA modifications. RNA modifications are involved in various kinds of cellular biological processes. Accumulated evidences have demonstrated that the functions of RNA modifications are determined by the effectors that can catalyze, recognize and remove RNA modifications. They are called 'writers', 'readers' and 'erasers'. The identification of RNA modification effectors will be helpful for understanding the regulatory mechanisms and biological functions of RNA modifications. In this work, we developed a database called RNAWRE that specially deposits RNA modification effectors. The current version of RNAWRE stored 2045 manually curated writers, readers and erasers for the six major kinds of RNA modifications, namely Cap, m1A, m6A, m5C, ψ and Poly A. The main modules of RNAWRE not only allow browsing and downloading the RNA modification effectors but also support the BLAST search of the potential RNA modification effectors in other species""" ; sc:featureList edam:operation_0443, edam:operation_2421, edam:operation_3431 ; sc:name "RNAWRE" ; sc:url "http://rnawre.bio2db.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0736, edam:topic_3277 ; sc:citation ; sc:description """Harnessing the Power of Guiding Potentials to Sample RNA Landscapes. RNAxplorer is a multitool, that offers different methods to explore RNA energy landscapes. The main use case is sampling of representative structures of the RNA conformation space, in order to compute RNA folding kinetics.""" ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_0303 ; sc:license "GPL-3.0" ; sc:name "RNAxplorer" ; sc:url "https://github.com/ViennaRNA/RNAxplorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:12079347", "pubmed:15665081", "pubmed:17452347" ; sc:description "Detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0502, edam:operation_2439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "RNAz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.tbi.univie.ac.at/cgi-bin/RNAz/RNAz.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003, edam:format_3578 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3173 ; sc:citation "pubmed:25262207" ; sc:description "An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution." ; sc:featureList edam:operation_0531, edam:operation_3204 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RnBeads" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.0" ; sc:url "http://rnbeads.mpi-inf.mpg.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_0602, edam:topic_2640, edam:topic_3336 ; sc:citation , "pubmed:32577712" ; sc:description "RNCE: Network Integration with Reciprocal Neighbors Contextual Encoding for Multi-modal Drug Community Study." ; sc:featureList edam:operation_3432, edam:operation_3925, edam:operation_3938 ; sc:name "RNCE" ; sc:url "https://github.com/WINGHARE/RNCE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:author "Giulio Pavesi" ; sc:citation ; sc:contributor "Graziano Pesole" ; sc:description "A methodology for the identification of genes showing a significant variation of expression across multiple conditions. Given expression estimates from any number of RNA-Seq samples and conditions identifies genes or transcripts with a significant variation of expression across all the conditions studied, together with the samples in which they are over- or under-expressed." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RNentropy" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareVersion "1.1.2" ; sc:url "http://www.beaconlab.it/RNentropy" ; biotools:primaryContact "Federico Zambelli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26353839" ; sc:description "A generic format for assigning names to simulated Next-Generation Sequencing (NGS) reads." ; sc:featureList edam:operation_3219 ; sc:name "RNF" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://karel-brinda.github.io/rnftools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "R/BioConductor package for normalization, curve registration and inference in time course gene expression data." ; sc:featureList edam:operation_3435, edam:operation_3658 ; sc:license "GPL-3.0" ; sc:name "Rnits" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rnits.html" ; biotools:primaryContact "Dipen P. Sangurdekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0654, edam:topic_2640 ; sc:citation , "pubmed:35575002" ; sc:description "A practical framework RNMF for exploring the association between mutational signatures and genes using gene cumulative contribution abundance." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RNMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhenzhang-li/RNMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0593 ; sc:citation ; sc:description "Open source software package for visualizing and interpreting one and two dimensional NMR data." ; sc:featureList edam:operation_0337 ; sc:name "rNMR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rnmr.nmrfam.wisc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3837 ; sc:citation , "pubmed:33315571" ; sc:description """a deep learning method for identification of short viral sequences from metagenomes. To utilize RNN-VirSeeker, Python packages "sklearn", "numpy" and "matplotlib" are needed to be previously installed. To make a prediction, users' own query contigs should be edited into a ".csv" file, where every line contains a single query contig. Through test.py, RNN-VirSeeker will give a set of scores to each query contig, higher of which represents its classification result.""" ; sc:featureList edam:operation_0224, edam:operation_3096 ; sc:name "RNN-VirSeeker" ; sc:url "https://github.com/crazyinter/RNN-VirSeeker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "RNN-IMP is a recurrent neural network based genotype imputation program implemented in Python. RNN-IMP takes phased genotypes in HAP/LEGEND format as input data and outputs imputation results in Oxford GEN format." ; sc:featureList edam:operation_3196, edam:operation_3454, edam:operation_3557 ; sc:name "rnnimp" ; sc:url "https://github.com/kanamekojima/rnnimp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:21106091" ; sc:description "Automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome" ; sc:featureList edam:operation_0524 ; sc:name "Rnnotator" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/a/lbl.gov/rnnotator/" ; biotools:primaryContact "David Gilbert", "Jeff Martin", "Xiandong Meng", "Zhong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_1775 ; sc:citation "pubmed:15180928" ; sc:description "This tool efficiently partitions networks into clusters using a cost function. Used to detect known and predict still undiscovered protein complexes within the cell's protein-protein interaction (PPI) network. The increasing amount of available PPI data necessitates an accurate and scalable approach to protein complex identification." ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3432, edam:operation_3439 ; sc:name "RNSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.utoronto.ca/~juris/data/rnsc/" ; biotools:primaryContact "Dr. Igor Jurisica" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3070, edam:topic_3344 ; sc:description "The Regularized Optimal Affine Discriminant (ROAD) is a powerful method for binary classification in high dimensional space" ; sc:featureList edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "The Regularized Optimal Affine Discriminant (ROAD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/40047-a-road-to-classification-in-high-dimensional-space-the-regularized-optimal-affine-discriminant" ; biotools:primaryContact "Yang Feng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments." ; sc:featureList edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "roar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/roar.html" ; biotools:primaryContact "Elena Grassi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0654 ; sc:citation , "pubmed:26198102" ; sc:description "A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome." ; sc:featureList edam:operation_0525 ; sc:name "Roary" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://sanger-pathogens.github.io/Roary/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3377 ; sc:citation ; sc:description "Tool to assess risk of bias due to missing evidence in network meta-analysis (ROB-MEN)." ; sc:featureList edam:operation_3927 ; sc:name "ROB-MEN" ; sc:url "https://cinema.ispm.unibe.ch/rob-men/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0593, edam:topic_1317, edam:topic_2275 ; sc:citation "pubmed:15215442" ; sc:description "Provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations." ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_0474, edam:operation_0476, edam:operation_0477 ; sc:name "Robetta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://robetta.bakerlab.org/" ; biotools:primaryContact "David Baker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description "Java GUI that enables the user to graphically call differentially expressed genes. For read mapping it relies on bowtie and for the differntial expression analysis it builds on an R backbone running DESeq and edgeR." ; sc:featureList edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "RobiNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mapman.gabipd.org/web/guest/robin" ; biotools:primaryContact "M. Lohse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3303 ; sc:citation ; sc:description """an R package for robust, flexible and high dimensional mixture regression. Finite mixture models are a popular technique for modelling unobserved heterogeneity or to approximate general distribution functions in a semi-parametric way.""" ; sc:featureList edam:operation_3192, edam:operation_3659, edam:operation_3936 ; sc:license "GPL-2.0" ; sc:name "RobMixReg" ; sc:url "https://CRAN.R-project.org/package=RobMixReg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3169, edam:topic_3173, edam:topic_3176 ; sc:citation , "pmcid:PMC8373080", "pubmed:34255854" ; sc:description "Multivariate state space model that integrates nucleotide sequence and chromatin accessibility data (currently uses only with MNase-seq or ATAC-seq) to compute genome-wide probabilistic occupancy landscape of nucleosomes and transciption factors (collectively known as DNA-binding factors or DBFs)." ; sc:featureList edam:operation_0432, edam:operation_0445, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RoboCOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/HarteminkLab/RoboCOP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3173 ; sc:citation ; sc:description """A convex optimization framework for gene-level tissue network estimation with missing data and its application in understanding disease architecture. An R package for Robust Estimation of covariance and precision matrices when the data has missing entries. Observe that Robocov correlation and partial correlation estimators are visually more interpretable and less cluttered than the standard estimator. We also show in our manuscript that our method has better false positivity rate than standard approach and CorShrink.""" ; sc:featureList edam:operation_2937, edam:operation_3196, edam:operation_3463, edam:operation_3557, edam:operation_3659 ; sc:name "Robocov" ; sc:url "https://github.com/kkdey/Robocov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_3047, edam:topic_3315 ; sc:citation , "pubmed:32298789" ; sc:description "A rigid-body molecular simulation program based on robot mechanics." ; sc:featureList edam:operation_2238, edam:operation_2476 ; sc:name "Robosample" ; sc:url "https://github.com/spirilaurentiu/Robosample" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3569, edam:topic_3570 ; sc:citation ; sc:description "R Program to compute algebric formulas in references to the article “Inuence of population structure on power and robustness of current association mapping tests”." ; sc:featureList edam:operation_2426 ; sc:name "RobPower" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=54&Itemid=59" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_3344 ; sc:citation , "pubmed:34984440" ; sc:description "Robust disease module mining via enumeration of diverse prize-collecting Steiner trees." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ROBUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bionetslab/robust-eval" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0634 ; sc:citation , "pmcid:PMC10246579", "pubmed:37233198" ; sc:description "Online bias-aware disease module mining with ROBUST-Web." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ROBUST-Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://robust-web.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10400800", "pubmed:37547470" ; sc:description """Robustness evaluation tool for cell-cell communication methods. RobustCCC offers the following capabilities: 1) generating simulated data, including replicated data, transcriptomic data noise and prior knowledge noise, with a single step, 2) installing and executing 14 cell-cell communication methods in a single step and 3) generating robustness evaluation reports in tabular form for easy interpretation.""" ; sc:featureList edam:operation_3435, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RobustCCC" ; sc:url "https://github.com/GaoLabXDU/RobustCCC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_2640 ; sc:citation , "pubmed:32159762" ; sc:description """A robust PCA method of tumor clone and evolution inference from single-cell sequencing data. We many thank to the article for their available source code. The input data is SNV data or CNV data. For SNV data, it can be either binary or ternary data. If it is binary data, 0 represents non-mutation site, 1 represents mutation site, 3 represents missing; if ternary data, 0 represents non-mutation site, 1 represents mutation heterozygous site, 2 represents mutation homozygous site and 3 represents missing,for example, ‘example.csv’ in the above list. Run the matlab script file, named "carryout_RPCA.m" to recover the genotype matrix.""" ; sc:featureList edam:operation_3196, edam:operation_3478, edam:operation_3891 ; sc:license "MIT" ; sc:name "RobustClone" ; sc:url "https://github.com/ucasdp/RobustClone" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:name "ID list" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:name "ID list" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3366 ; sc:citation ; sc:description "Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation (RRA) and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that isrobust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking." ; sc:featureList edam:operation_3436 ; sc:name "RobustRankAggregation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-EE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cran.r-project.org/web/packages/RobustRankAggreg/" ; biotools:primaryContact "Raivo Kolde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3068 ; sc:citation , "pubmed:32336025" ; sc:description """An R package and Shiny web app for visualizing risk-of-bias assessments. Robvis now exists as a web-app, aimed at those who are not familiar with R or who want to explore the package’s functionality before installing it locally. Visualize the Results of Risk-of-Bias (ROB) Assessments. Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review.""" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "robvis" ; sc:url "https://www.riskofbias.info/welcome/robvis-visualization-tool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Various functionals of receiver operating characteristic curves." ; sc:featureList edam:operation_2403 ; sc:license "Artistic-2.0" ; sc:name "ROC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ROC.html" ; biotools:primaryContact "Vince Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "ROC curves of one or more experiments and the area under of each curve can be computed with this cod." ; sc:isAccessibleForFree true ; sc:name "ROC Curves and Area under ROC curve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/21318-roc-curves-and-area-under-of-them" ; biotools:primaryContact "Cuneyt Mertayak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474 ; sc:description "MATLAB function which performs a ROC curve of two-class data." ; sc:isAccessibleForFree true ; sc:name "ROC Curve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/52442-roc-curve" ; biotools:primaryContact "Víctor Martínez-Cagigal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0797 ; sc:author "Roland Wittler" ; sc:citation ; sc:description "Reconstruct ancestral gene orders of a phylogenetic tree. Given the topology of a phylogenetic tree and the gene orders of the leaf nodes, it calculates sets of gene orders for the inner nodes, represented by conserved intervals." ; sc:featureList edam:operation_0325 ; sc:isAccessibleForFree true ; sc:name "Roci" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bibiserv.cebitec.uni-bielefeld.de/roci" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3336, edam:topic_3373, edam:topic_3512 ; sc:citation , "pmcid:PMC10734502", "pubmed:37975659" ; sc:description "Translational launchpad for miRNA-based antimicrobial drug development." ; sc:featureList edam:operation_0463, edam:operation_3461, edam:operation_3482, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Rocket-miR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://scangeo.dartmouth.edu/RocketmiR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3444 ; sc:citation , "pmcid:PMC4466867", "pubmed:26076957" ; sc:description "ROCKETSHIP, an open-source software for dynamic contrast-enhanced magnetic resonance imaging analysis." ; sc:featureList edam:operation_3443 ; sc:license "GPL-2.0" ; sc:name "ROCKETSHIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/petmri/ROCKETSHIP" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_0749, edam:topic_3474 ; sc:citation ; sc:description "De novo protein structure prediction by incremental inter-residue geometries prediction and model quality assessment using deep learning." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0476, edam:operation_0477, edam:operation_2415 ; sc:isAccessibleForFree true ; sc:name "RocketX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://zhanglab-bioinf.com/RocketX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation ; sc:description "Sampling-based protein complex prediction method, which exploits, as part of the whole scoring function, a regularization term for the overlaps of predicted complexes and that for the distribution of sizes of predicted complexes." ; sc:featureList edam:operation_2464 ; sc:name "RocSampler" ; sc:operatingSystem "Linux" ; sc:url "http://imi.kyushu-u.ac.jp/~om/software/RocSampler/" ; biotools:primaryContact "Osamu Maruyama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3170, edam:topic_3365, edam:topic_3673 ; sc:citation , "pmcid:PMC9020074", "pubmed:35443610" ; sc:description "A fully convolutional architecture for basecalling nanopore RNA sequencing data." ; sc:featureList edam:operation_3185, edam:operation_3198 ; sc:license "MIT" ; sc:name "RODAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biodlab/RODAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2259 ; sc:author "Philip R. Kensche" ; sc:description "Roddy is a workflow management system for large scale NGS processing pipelines on Petabyte scale. It is used for Pan-Cancer Analysis of Whole Genomes (PCAWG) project and has a focus on high-throughput computing infrastructures." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Roddy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "3+ versions" ; sc:url "https://github.com/TheRoddyWMS/Roddy" ; biotools:primaryContact "German Cancer Research Center (DKFZ)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0622, edam:topic_0623 ; sc:citation ; sc:description "Rapid ORF Description & Evaluation Online- an algorithm to help biosynthetic gene cluster (BGC) analysis, with an emphasis on ribosomal natural product (RiPP) discovery." ; sc:featureList edam:operation_1777 ; sc:name "RODEO" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://www.ripp.rodeo" ; biotools:primaryContact "Prof. Douglas Mitchell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_2640 ; sc:citation ; sc:description """Robust differential protein co-expression analysis for cancer complexome. devtools::install_github("ymatts/RoDiCE").""" ; sc:featureList edam:operation_3435, edam:operation_3463, edam:operation_3741 ; sc:name "RoDiCE" ; sc:softwareHelp ; sc:url "https://github.com/ymatts/RoDiCE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3452 ; sc:citation , "pubmed:33169367" ; sc:description """A validated software for radiomics analysis of medical images in radiation oncology. ROdiomiX is a MATLAB-based framework for the computation of radiomic features and feature aggregation techniques in compliance with the Image-Biomarker-Standardization-Initiative (IBSI) guidelines, which includes preprocessing protocols and quantitative benchmark results for analysis of computational phantom images.""" ; sc:featureList edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:name "ROdiomiX" ; sc:url "https://github.com/Ebadian-HFHS/ROdiomiX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3366 ; sc:citation , "pmcid:PMC7498900" ; sc:description "The Real-time Outbreak and Disease Surveillance (RODS) system was initiated by the RODS Laboratory at the University of Pittsburgh in 1999. The system is now an open source project under the GNU license. The RODS development effort has been organized into seven functional areas: overall design, data collection, syndrome classification, database and data warehousing, outbreak detection algorithms, data access, and user interfaces. Each functional area has a coordinator for the open source project, and there is an overall coordinator responsible for the architecture, overall integration of components, and overall quality of the JAVA source code. Figure 8-1 illustrates the RODS' system architecture. The RODS system as a syndromic surveillance application was originally deployed in Pennsylvania, Utah, and Ohio" ; sc:name "RODS" ; sc:url "https://www.rods.pitt.edu/content/view/15/36/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3360 ; sc:citation , "pmcid:PMC10386769", "pubmed:37516886" ; sc:description "R Shiny app for RNA sequencing analysis and biomarker discovery." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3680, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "ROGUE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://marisshiny.research.chop.edu/ROGUE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0199, edam:topic_0625, edam:topic_3676 ; sc:citation ; sc:description "A Flexible Hidden Markov Model Framework To Detect Runs of Homozygosity From Genotyping Data." ; sc:featureList edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ROHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gokalpcelik/ROHMMCLI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305, edam:format_2306, edam:format_3003 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160 ; sc:citation , ; sc:description "Region Of Interest Projection." ; sc:featureList edam:operation_0337 ; sc:name "roi_feature_projection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2.1" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_feature_projection/0.2.2.1" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Filter ROI files." ; sc:featureList edam:operation_3695 ; sc:name "roi_filter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_filter/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3071 ; sc:citation , , ; sc:description "Compute metrics for records in an ROI file." ; sc:featureList edam:operation_2409 ; sc:name "roi_metrics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_metrics/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , , ; sc:description "Compute PCA-based metric for records in an ROI file." ; sc:featureList edam:operation_2939 ; sc:name "roi_pca" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_pca/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071 ; sc:citation , ; sc:description "Create ROI thumbnail plot grids." ; sc:featureList edam:operation_0337 ; sc:name "roi_plot_thumbnails" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_plot_thumbnails/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , ; sc:description "ROI Overview Report." ; sc:featureList edam:operation_2409 ; sc:name "roi_report" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_report/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3365 ; sc:citation , , ; sc:description "Sort ROI file." ; sc:featureList edam:operation_3802 ; sc:name "roi_sort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_sort/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071 ; sc:citation , , ; sc:description "ROI Overview Report." ; sc:featureList edam:operation_0337 ; sc:name "roi_table" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.2" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/screno/ngs_roi2/roi_table/0.2.2" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0153, edam:topic_3172, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC10087011", "pubmed:37039115" ; sc:description "Spatial segmentation, obtained by clustering MSI pixels according to their mass spectral similarities, is a popular approach to automate ROI definition. Here we report a multimodal fusion strategy to enable an objective and trustworthy selection of \\#Clusters by utilizing additional information from corresponding histology images. Our work will greatly facilitate MSI-mediated spatial lipidomics, metabolomics, and proteomics research by providing intelligent software to automatically and reliably generate ROIs." ; sc:featureList edam:operation_3214, edam:operation_3432, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ROIforMSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/guoang4github/ROIforMSI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0634, edam:topic_3520 ; sc:citation ; sc:description """Robust Inference of Kinase Activity Using Functional Networks. RoKAI is a computation tool for inferring kinase activity in a robust manner using functional networks. RoKAI operates on a heterogeneous network having kinases and phosphosites as nodes and available functional associations as edges, including protein-protein interactions, kinase-substrate annotations, co-evolution and structure distance evidence between phosphosites. The key idea of RoKAI is to propagate the phosphosite quantifications on this heterogeneous network to capture the coordinated changes in the signaling, which are used to infer the kinase activities in a more robust manner.""" ; sc:featureList edam:operation_0417, edam:operation_3799, edam:operation_3896 ; sc:name "RoKAI" ; sc:url "http://rokai.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602 ; sc:citation , "pmcid:PMC4027195", "pubmed:24609385" ; sc:description "Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. It operates in two phases by inferring the probability of mRNA being the targets of miRNA, considering the expression of all the mRNAs due to their potential competition for the same miRNA. It assumes that the total transcribed mRNA levels are higher than the observed mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference." ; sc:featureList edam:operation_3792 ; sc:license "GPL-2.0" ; sc:name "Roleswitch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Roleswitch.html" ; biotools:primaryContact "Yue Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:18851737" ; sc:description "Allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots." ; sc:featureList edam:operation_3185 ; sc:name "Rolexa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://master.bioconductor.org/packages//2.10/bioc/html/Rolexa.html" ; 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0621 ; sc:citation , "pubmed:34387349" ; sc:description "A script to calculate the rootstrap support values for all the branches" ; sc:featureList edam:operation_0323, edam:operation_0552, edam:operation_3359 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "rootstrap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/suhanaser/Rootstrap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "Discovering the source of all reads originating from complex RNA molecules." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "ROP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/smangul1/rop/wiki" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:25107872" ; sc:description "A tool for constructing the FM-index for a collection of DNA sequences. 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Rosaceae Nemesis: Cherry Powdery Mildew. Cherry powdery mildew is a major problem in sweet cherry growing regions in the U.S. Pacific Northwest (PNW), but much less so in the eastern part of the country.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3920 ; sc:name "RosBREED" ; sc:url "http://www.rosbreed.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0605, edam:topic_0749, edam:topic_0780 ; sc:citation , "pmcid:PMC10348015", "pubmed:37457357" ; sc:description "RoseAP is an analytical platform for gene function of Rosa rugosa . Users can submit locus IDs to quickly search for co-expression networks, expression profile. Additionally, the basic structural and functional annotations of each gene can be obtained, such as Pfam domains, gene families, KEGG metabolic pathways, GO terms, InterPro annotation, trEMBL annotation, SwissProt annotation and orthologues in 11 species. 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ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3695, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ROSeq" ; sc:url "http://www.bioconductor.org/packages/release/bioc/html/ROSeq.html" ; biotools:primaryContact "Debarka Sengupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2275 ; sc:citation "pubmed:21622962" ; sc:description "Rosetta FlexPepDock web server is a high resolution peptide docking protocol for modeling of peptide-protein complexes." ; sc:featureList edam:operation_0478, edam:operation_0482 ; sc:name "Rosetta FlexPepDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://flexpepdock.furmanlab.cs.huji.ac.il/" ; biotools:primaryContact "Yuval Sedan" . a sc:SoftwareApplication ; 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sc:license "GPL-3.0" ; sc:name "RosettaDDGPrediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ELELAB/RosettaDDGPrediction" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0593, edam:topic_0736 ; sc:citation "pubmed:10984534", "pubmed:11427890", "pubmed:11526208", "pubmed:11786026", "pubmed:12948494", "pubmed:14631033", "pubmed:16845000" ; sc:description "RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_0480 ; sc:name "RosettaDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rosettadesign.med.unc.edu" ; biotools:primaryContact "Brian Kuhlman" . a sc:SoftwareApplication ; 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sc:encodingFormat edam:format_1476 ; sc:name "Structure image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:encodingFormat edam:format_2032 ; sc:name "Structural profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0611, edam:topic_1317 ; sc:citation ; sc:description "An automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3–5-Å resolution." ; sc:featureList edam:operation_2480, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RosettaES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.rosettacommons.org/" ; biotools:primaryContact "Frank Dimaio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3314, edam:topic_3930 ; sc:citation ; sc:description """Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens. RosettaMHC models of SARS-CoV-2 peptide/HLA-A02 antigens.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0477 ; sc:name "RosettaMHC" ; sc:url "https://rosettamhc.chemistry.ucsc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0166, edam:topic_3930 ; sc:citation ; sc:description "RosettaSurf is a surface-centric computational design approach" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0479, edam:operation_0480, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "RosettaSurf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LPDI-EPFL/RosettaSurf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3512 ; sc:citation , "pmcid:PMC8479477", "pubmed:34583245" ; sc:description "Reliable gene expression signature scoring of cancer models and patients." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "RosettaSX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rosettasx.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3810 ; sc:citation , "pmcid:PMC5353781", "pubmed:28331535" ; sc:description "A high-throughput affordable in vitro growth assay for Arabidopsis." ; sc:featureList edam:operation_2425 ; sc:license "GPL-3.0" ; sc:name "rosettR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hredestig.github.io/rosettR/" ; biotools:primaryContact "Filipa Tomé" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_3293 ; sc:citation , "pmcid:PMC6700492", "pubmed:31453286" ; sc:description "Genome assembly and phylogenomic data analyses using plastid data | Code used in the analyses of Gonçalves et al. (2019) | Here you will find all the code used in the analyses of Gonçalves et al. 2019 and the tutorials presented in Gonçalves et al. in review | In this first pipeline, we present the code used to processes Illumina reads using bbtools software to remove adaptors, phix, quality trim and to assemble reads into contigs | Here we aligned genes from the plastid genome using two software, MAFFT and MACSE. Then the alignments were used as input in a series of phylogenetic analyses using Maximum Likelihood and Multispecies Coalescent methods" ; sc:featureList edam:operation_0525, edam:operation_0551, edam:operation_3192 ; sc:name "rosids" ; sc:url "https://github.com/deisejpg/rosids" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0160, edam:topic_0736, edam:topic_3474 ; sc:citation ; sc:description "Rossmann-toolbox is a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann-fold proteins." ; sc:featureList edam:operation_0303, edam:operation_0478, edam:operation_3907 ; sc:license "MIT" ; sc:name "Rossmann-toolbox" ; sc:url "https://lbs.cent.uw.edu.pl/rossmann-toolbox" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_3318 ; sc:citation , "pubmed:33213140" ; sc:description """A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. The Rotational Profiler attempts to facilitate the task of performing this overall fit. The functional torsional form used in the code is. There is a very fundamental difference in the use of torsional potential functions as compared to bond length and angle potentials. Only a small subset of the full potential energy domain, around the minumum, is realized in the parabolic-like bond length and angle potentials. Therefore the emphasis in fitting these potentials is to reproduce potential near the minimum, with not so much concern about the functional form, or parameterization, or large excursions from equilibrium because they are energetically disallowed. On the other hand, torsional potentials are evaluated over the full 360° of rotation around a bond.""" ; sc:featureList edam:operation_0249, edam:operation_1844, edam:operation_3454, edam:operation_3659, edam:operation_3893 ; sc:name "Rotational Profiler" ; sc:url "http://rotprof.lncc.br" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "RotaVirusPred is a machine learning based tool to predict the zoonotic host tropism of Rotavirus A with the help of its genome sequences, stating whether a viral strain has the potential to infect human hosts." ; sc:featureList edam:operation_2945 ; sc:name "rotavpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/rotavpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_3050, edam:topic_3293 ; sc:citation , ; sc:description """R package to interact with the Open Tree of Life data. Interface to Open Tree of Life API. Interface to the 'Open Tree of Life' API. rotl is an R package to interact with the Open Tree of Life data APIs. It was initially developed as part of the NESCENT/OpenTree/Arbor hackathon. rotl is an R package that can be used to query and download subsets of the synthetic Open Tree of Life directly in R. This repository contains a manuscript describing this package and how to get started with it. An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species. Then explore how you can use rotl with other packages to combine your data with trees from the Open Tree of Life project by typing: vignette("data_mashups", package="rotl")""" ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:license "BSD-2-Clause" ; sc:name "rotl" ; sc:url "https://cran.r-project.org/package=rotl" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330, edam:format_3033 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2330 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3391 ; sc:citation ; sc:description "Calculates the Reproducibility-Optimized Test Statistic for differential testing in omics data." ; sc:featureList edam:operation_2238, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ROTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ROTS.html" ; biotools:primaryContact "Fatemeh Seyednasrollah" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2393 ; sc:name "mFLJ/mKIAA number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621 ; sc:citation ; sc:description "A sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs)." ; sc:featureList edam:operation_0224 ; sc:name "Rouge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.kazusa.or.jp/rouge/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3500 ; sc:description "The M-file with Round-Variance is to check for the difference among corona virus clade." ; sc:isAccessibleForFree true ; sc:name "Round Variance of SARS-COV-2 Gene Sequence for COVID-19" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75280-round-variance-of-sars-cov-2-gene-sequence-for-covid-19" ; biotools:primaryContact "steed huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3168, edam:topic_3516, edam:topic_3518 ; sc:citation , "pmcid:PMC10161648", "pubmed:37147657" ; sc:description "Pangenomic genotyping with the marker array." ; sc:featureList edam:operation_0292, edam:operation_0524, edam:operation_3196, edam:operation_3211, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rowbowt" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/alshai/rowbowt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3170, edam:topic_3303 ; sc:citation , "pmcid:PMC8346655", "pubmed:34252940" ; sc:description "RowDiff transform for sparsification of graph annotations" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0362, edam:operation_0524 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "RowDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ratschlab/row_diff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9579745", "pubmed:36299497" ; sc:description "An open-source cloud-enabled framework for reproducible ribosomal profiling data processing, analysis, and result reporting." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RP-REP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/emmesgit/RPREP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3752 ; sc:name "Pathway or network" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:encodingFormat edam:format_3475 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3752 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_2258, edam:topic_3407, edam:topic_3895 ; sc:citation ; sc:description "Pathway enumeration from RetroPath2.0 retrosynthesis output" ; sc:featureList edam:operation_3642, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rp2paths" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.3" ; sc:url "https://github.com/brsynth/rp2paths" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:21071809" ; sc:description "Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. \"Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays\", TCBB/IEEE, 2011." ; sc:featureList edam:operation_3223 ; sc:license "BSD-4-Clause" ; sc:name "RPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RPA.html" ; biotools:primaryContact "Leo Lahti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3299 ; sc:citation ; sc:description "Open access database of Integral Projection Models." ; sc:featureList edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Rpadrino" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/padrinoDB/Rpadrino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "rPanglaoDB is an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. A meta-analysis database for single cell RNA sequencing data. Search across datasets, studies, download data, and perform advanced visualization. PanglaoDB is a database for the scientific community interested in exploration of single cell RNA sequencing experiments from mouse and human. We collect and integrate data from multiple studies and present them through a unified framework." ; sc:featureList edam:operation_2421, edam:operation_3223, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "rPanglaoDB" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=rPanglaoDB" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:26166713" ; sc:description "A computational pipeline to identify differentially and coherently processed transcripts using RNA-seq data obtained from multiple tissue or cell lines." ; sc:featureList edam:operation_3680 ; sc:name "RPASuite" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://rth.dk/resources/rpa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3308, edam:topic_3336 ; sc:citation ; sc:description "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery." ; sc:featureList edam:operation_2422, edam:operation_3629, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RPath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/enveda/RPath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0154, edam:topic_3510 ; sc:citation "pubmed:10089205", "pubmed:10373380", "pubmed:15588112", "pubmed:15724288", "pubmed:15980507", "pubmed:3678489", "pubmed:7583694", "pubmed:8019863", "pubmed:8683588" ; sc:description "Structural bioinformatics resource" ; sc:name "RPBS" ; sc:url "http://bioserv.rpbs.jussieu.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_2814 ; sc:citation "pubmed:22570414" ; sc:description "RPF webserver uses RECALL, PRECISION, and F-MEASURE (RPF) for calculating global NMR structure quality scores, or how well a query 3D structure(s) fit to the experimental NOESY peak list and resonance assignment data." ; sc:featureList edam:operation_0224, edam:operation_0250, edam:operation_0320, edam:operation_0321, edam:operation_2429 ; sc:name "RPF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nmr.cabm.rutgers.edu/rpf" ; biotools:primaryContact "RPF Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "A fold recognition server for searching protein fold in PDB. It is based on sequence similarity search and secondary structure alignment technique." ; sc:featureList edam:operation_2945 ; sc:name "rpfold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/rpfold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3304, edam:topic_3382 ; sc:citation ; sc:description """A low-cost, open-source, high-performance solution for displaying visual stimuli. A high performance python library for displaying visual stimuli on the Raspberry Pi 3 and 4. $ git clone https://github.com/bill-connelly/rpg. Move to your home directory, and clone the repository. RPG is designed to run in response to 3.3 volt triggers from other hardware, or in a free running mode, where it will provide a 3.3V output when it displays each frame. There are several examples scripts in the examples folder. But briefly, to confirm that RPG has been install successfully, and to show its functionality, the following lines of code can be run.""" ; sc:featureList edam:operation_0337 ; sc:name "RPG" ; sc:url "https://github.com/bill-connelly/rpg" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:name "Tool name (FASTA)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0821, edam:topic_3520, edam:topic_3922 ; sc:citation , "pmcid:PMC7671371", "pubmed:33575558" ; sc:description """fast and efficient in silico protein digestion. Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-induced cleavage sites on amino acid sequences. https://rapid-peptide-generator.readthedocs.io.""" ; sc:featureList edam:operation_0366, edam:operation_0398, edam:operation_0418, edam:operation_0422 ; sc:name "RPG" ; sc:url "https://gitlab.pasteur.fr/nmaillet/rpg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0780, edam:topic_3170, edam:topic_3810 ; sc:citation , "pmcid:PMC8141123", "pubmed:34022814" ; sc:description "Rhododendron Plant Genome Database (RPGD) is a comprehensive online omics database for Rhododendron." ; sc:featureList edam:operation_0308, edam:operation_0314, edam:operation_0525, edam:operation_2421, edam:operation_3216 ; sc:name "RPGD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfor.kib.ac.cn/RPGD/" ; biotools:primaryContact "Chengjun Zhang", "Jihua Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_0769, edam:topic_0780, edam:topic_3382 ; sc:citation ; sc:description "An R package for fetching, transforming, and visualising PhyloPic silhouettes." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rphylopic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.phylopic.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3474 ; sc:citation , "pmcid:PMC7029608", "pubmed:32070279" ; sc:description """a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. The interactions between non-coding RNAs and proteins play an essential role in many biological processes.""" ; sc:featureList edam:operation_0303, edam:operation_3891, edam:operation_3901 ; sc:name "RPI-SE" ; sc:url "https://github.com/haichengyi/RPI-SE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_3474 ; sc:citation , "pubmed:27134008" ; sc:description "In Silico RNA-protein interaction detection using random forest." ; sc:featureList edam:operation_0272 ; sc:name "rpiCOO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biocool.ir/softs/rpicool.html" ; biotools:primaryContact "Zahiri J." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3474, edam:topic_3794 ; sc:citation , "pubmed:32092438" ; sc:description """An online toolbox to extract features for predicting RNA-protein interactions. Explore and create dataset.""" ; sc:featureList edam:operation_0224, edam:operation_3901, edam:operation_3937 ; sc:name "RPINBASE" ; sc:url "http://rpinbase.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC8323483", "pubmed:34058988" ; sc:description "A tool for analyzing and visualizing ribo-seq data at the isoform level." ; sc:featureList edam:operation_0314, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RPiso" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://cosbi6.ee.ncku.edu.tw/RPiso/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3511 ; sc:citation "pubmed:25583120" ; sc:description "A parallel MCMC algorithm for discovering diverse motifs from large sequence sets." ; sc:featureList edam:operation_0238 ; sc:name "RPMCMC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://daweb.ism.ac.jp/yoshidalab/motif/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7366700", "pubmed:32678114" ; sc:description """Reciprocal Perspective improves miRNA targeting prediction. RPmirDIP Predictions of ~6 Million miRNA-Gene Pairs.""" ; sc:featureList edam:operation_0463, edam:operation_2492, edam:operation_3792, edam:operation_3802 ; sc:name "RPmirDIP" ; sc:url "http://cu-bic.ca/RPmirDIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_3336 ; sc:citation , "pmcid:PMC8424408", "pubmed:34496744" ; sc:description "An intuitive database of RNA pocket topology information with RNA-ligand data resources." ; sc:featureList edam:operation_0278, edam:operation_0478, edam:operation_0570, edam:operation_2441, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "RPocket" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhaoserver.com.cn/RPocket/RPocket.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , ; sc:description "Infer haplotypes from genotype data (by pseudo-Boolean optimization) using the pure parsimony criterion." ; sc:featureList edam:operation_0487 ; sc:name "RPOLY" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "1.2.1" ; sc:url "http://sat.inesc-id.pt/software/rpoly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:34890793" ; sc:description "Robust PET-only processing of community acquired heterogeneous amyloid-PET data." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "rPOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/leoiacca/rPOP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3518 ; sc:citation , "pmcid:PMC9665860", "pubmed:36205581" ; sc:description "An R package for normalization and quantitation of Reverse-Phase Protein Array data." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "RPPA SPACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/RPPASPACE/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:24951946" ; sc:description "Pipeline for the analysis of reverse-phase protein array data." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "RPPApipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ra.cs.uni-tuebingen.de/software/RPPApipe/" ; biotools:primaryContact "Johannes Eichner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_2275, edam:topic_3512 ; sc:citation , "pmcid:PMC9266927", "pubmed:35805909" ; sc:description "An RNA-Protein Intuitive Database with RNA Pocket Topology Resources." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0278, edam:operation_0570, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:name "RPpocket" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://zhaoserver.com.cn/RPpocket/RPpocket.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:encodingFormat edam:format_1457, edam:format_2331, edam:format_3464, edam:format_3604, edam:format_3752 ; sc:name "RNA secondary structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0880 ; sc:encodingFormat edam:format_1457, edam:format_2331, edam:format_3604 ; sc:name "RNA secondary structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:author "Josef Pánek" ; sc:citation , , , , "pmcid:PMC5641303", "pmcid:PMC5688744", "pmcid:PMC6482342", "pubmed:29067038", "pubmed:29141608", "pubmed:31032840" ; sc:description "A web database for prediction, analysis and storage of secondary structures of RNAs." ; sc:featureList edam:operation_0278, edam:operation_0361, edam:operation_0570, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "rPredictorDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ" ; sc:softwareHelp , , , , ; sc:softwareVersion "1.0" ; sc:url "http://rpredictordb.elixir-czech.cz" ; biotools:primaryContact "David Hoksza", "Josef Pánek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description """a web-based tool for the inference of potential roles of plant microRNAs in human body. RPRH is a database for predicted plant microRNA Functions in human. MicroRNAs are a class of small non-coding RNA molecules involved in gene expression regulation. Since the finding of cross-kingdom regulation of plant microRNA in 2012 by Zhang et al., increasing evidences suggest that microRNAs could affect gene expression in an inter-species manner. Here we developed the tool for predicting this kind of interactions between plant and human.""" ; sc:featureList edam:operation_0463, edam:operation_2436, edam:operation_3792 ; sc:name "RPRH" ; sc:url "http://www.rnanut.net/rprh/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_0769, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC9206141", "pubmed:35717145" ; sc:description "rprimer is an R package that designs degenerate oligos and PCR assays from a multiple DNA sequence alignment of target sequences of interest. The package is specifically designed for sequence variable viruses." ; sc:featureList edam:operation_0292, edam:operation_0308, edam:operation_0337, edam:operation_0363, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rprimer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioconductor.org/packages/rprimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Set of routines for analyzing proteomics data, an XML database to store the results and a user interface." ; sc:featureList edam:operation_3741 ; sc:name "Rproteomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/NCIP/cagrid-general/tree/master/demos/06annual/workflow/JRProteomicsGridSkeletonValue-1.0/src/org/globus/cagrid/RProteomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:description "This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against." ; sc:featureList edam:operation_2409 ; sc:license "BSD-3-Clause" ; sc:name "RProtoBufLib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html" ; biotools:primaryContact "Mike Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation ; sc:description "Computes reproducibility probability score to select differentially expressed genes." ; sc:featureList edam:operation_2428, edam:operation_2495 ; sc:name "RPS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://systemsbio.ucsd.edu/rps/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:encodingFormat edam:format_3464 ; sc:name "Ecological data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0914 ; sc:encodingFormat edam:format_2331 ; sc:name "Codon usage data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "a database of llps rna" ; sc:featureList edam:operation_0292 ; sc:name "RPS" ; sc:url "https://bio.tools/register" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8728229", "pubmed:34718734" ; sc:description "A comprehensive database of RNAs involved in liquid-liquid phase separation." ; sc:featureList edam:operation_0278, edam:operation_2441, edam:operation_3216, edam:operation_3454, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:name "RPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rps.renlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously." ; sc:featureList edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "RpsiXML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RpsiXML.html" ; biotools:primaryContact "Jitao David Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:31581757" ; sc:description "The rptR package offers easy-to-use functions for estimating R and its uncertainty. The package includes estimates of the repeatability (and also raw variances and marginal R2) for Gaussian traits, binomial and Poisson-distributed traits. The theory for the quantification of the repeatability for non-Gaussian traits." ; sc:featureList edam:operation_3435 ; sc:name "rptR" ; sc:url "https://cran.r-project.org/web/packages/rptR/vignettes/rptR.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "This package implements an interface to proteomics data submitted to the ProteomeXchange consortium." ; sc:featureList edam:operation_0224 ; sc:license "GPL-2.0" ; sc:name "rpx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rpx.html" ; biotools:primaryContact "Laurent Gatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0160, edam:topic_0196, edam:topic_0611, edam:topic_2275 ; sc:citation , "pmcid:PMC10237659", "pubmed:37216343" ; sc:description "Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock." ; sc:featureList edam:operation_2404, edam:operation_3216, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "RPXDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/willsheffler/rpxdock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3572 ; sc:citation ; sc:description "Optimised tool designed for quality control and assessment of high-throughput sequencing data that performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics." ; sc:featureList edam:operation_3218 ; sc:license "GPL-2.0" ; sc:name "Rqc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rqc.html" ; biotools:primaryContact "Welliton Souza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3517 ; sc:citation , "pmcid:PMC5860520", "pubmed:28633423" ; sc:description "Gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone." ; sc:featureList edam:operation_0253 ; sc:isAccessibleForFree true ; sc:license "GPL-1.0" ; sc:name "rqt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.6.0" ; sc:url "https://github.com/izhbannikov/rqt" ; biotools:primaryContact "Ilya Zhbannikov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Interactive environment for mapping quantitative trait loci (QTL) in experimental crosses." ; sc:featureList edam:operation_0282, edam:operation_2429 ; sc:name "Rqtl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.rqtl.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC2731891", "pubmed:19509312" ; sc:description "This package implements the QUBIC algorithm for the qualitative biclustering with gene expression data." ; sc:featureList edam:operation_0313 ; sc:license "GPL-2.0" ; sc:name "rqubic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rqubic.html" ; biotools:primaryContact "Jitao David Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allows you to predict the residue-residue contact in proteins from its amino acid sequence." ; sc:featureList edam:operation_2945 ; sc:name "rrcpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/rrcpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC9122960", "pubmed:35607618" ; sc:description "Relevance, redundancy, and complementarity trade-off (RRCT)." ; sc:featureList edam:operation_3891, edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RRCT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ThanasisTsanas/RRCT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_2275 ; sc:citation ; sc:description "Comprehensive and non-redundant benchmark for RNA–RNA docking and scoring." ; sc:featureList edam:operation_2421 ; sc:name "RRDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://huanglab.phys.hust.edu.cn/RRDbenchmark/" ; biotools:primaryContact "Sheng-You Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33417543" ; sc:description "Enhanced Restoration-Reconstruction Deep Neural Network for Down-Sampling-Based Video Coding." ; sc:featureList edam:operation_3435 ; sc:name "RRDnCNN" ; sc:softwareVersion "2.0" ; sc:url "https://minhmanho.github.io/rrdncnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3301 ; sc:citation ; sc:description "Seamlessly interfaces RDP classifier." ; sc:featureList edam:operation_2995 ; sc:license "GPL-2.0" ; sc:name "rRDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rRDP.html" ; biotools:primaryContact "Michael Hahsler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3489 ; sc:citation ; sc:description "Extract non-coding regions associated to annotated genes." ; sc:featureList edam:operation_2422 ; sc:name "RRE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "20040401" ; sc:url "http://www.bioinformatica.unito.it/bioinformatics/rre/rre.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0632, edam:topic_0736, edam:topic_0821 ; sc:citation ; sc:description """A Genome-Mining Tool for Class-Independent RiPP Discovery. Bioinformatic application for the detection of RREs in protein sequences of interest. Install the included conda environment with "conda env create -f RREfinder.yml" Or make sure the following packages/programs are installed and in your path. Databases need to be downloaded independently from https://zenodo.org/record/3733240#.XoRkIUEzbCI. Please download all the files, except the folder with the seed sequences, and place them into the data/database folder within the downloaded repository. RREFinder accepts both protein .fasta files and .genbank files. Alternatively, you can use '--antismash ripp' and let the --infile point to a .final.gbk file from antiSMASH analysis. This way all the antiSMASH RiPP gene clusters will be analyzed.""" ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_2422 ; sc:name "RRE-Finder" ; sc:url "https://github.com/Alexamk/RREFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3569 ; sc:citation , "pmcid:PMC4570700", "pubmed:26379782" ; sc:description "RRegrs is an integrated framework for creating multiple regression models." ; sc:featureList edam:operation_3659 ; sc:license "BSD-2-Clause" ; sc:name "RRegrs" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.5" ; sc:url "https://github.com/enanomapper/RRegrs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC9215042", "pubmed:35729491" ; sc:description "Efficient short-read repeat resolution within ABySS." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3472, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "RResolver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/abyss/tree/master/RResolver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "RRHO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RRHO.html" ; biotools:primaryContact "Jonathan Rosenblatt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC6936067", "pubmed:31888606" ; sc:description """Region-based interaction detection in genome-wide case-control studies. In genome-wide association study (GWAS), we aim at detecting single nucleotide polymorphisms (SNPs) that are associated with diseases. Conventional SNP interaction detection methods like PLINK [1] and BOOST [2] are based on SNP-SNP interactions. Although single nucleotides are the building blocks of human genome, SNPs are not necessarily the smallest functional unit for complex phenotypes. Region-based strategies have been successful in studies aiming at marginal effects (the effect of a single SNP regardless of other SNPs). In this paper, we have developed RRIntCC [3], a novel region-region interaction detection method for case-control studies, by utilizing the correlations between individual SNP-SNP interactions based on linkage disequilibrium (LD) contrast test.""" ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_3196, edam:operation_3661 ; sc:name "RRIntCC" ; sc:url "http://bioinformatics.ust.hk/RRIntCC.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation , "pubmed:33094318" ; sc:description """Prognostic outcome prediction by semi-supervised least squares classification. Although great progress has been made in prognostic outcome prediction, small sample size remains a challenge in obtaining accurate and robust classifiers. We proposed the Rescaled linear square Regression based Least Squares Learning (RRLSL), a jointly developed semi-supervised feature selection and classifier, for predicting prognostic outcome of cancer patients. RRLSL used the least square regression to identify the scale factors and then rank the features in available multiple types of molecular data. We applied the unlabeled multiple molecular data in conjunction with the labeled data to develop a similarity graph. RRLSL produced the constraint with kernel functions to bridge the gap between label information and geometry information from messenger RNA and microRNA expression profiling""" ; sc:featureList edam:operation_0417, edam:operation_2495, edam:operation_3659 ; sc:name "RRLSL" ; sc:url "https://github.com/ShiMGLab/RRLSL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc:citation , "pmcid:PMC9894542", "pubmed:36689472" ; sc:description "RRMScorer provides quick predictions for any RNA recognition motif (RRM) and any RNA target purely based on their sequences." ; sc:featureList edam:operation_0337, edam:operation_0492, edam:operation_3438 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RRMScorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.8" ; sc:url "https://bio2byte.be/rrmscorer/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308 ; sc:citation ; sc:description "A computer program for selecting rRNA genes from metagenomic and metatranscriptomic sequences." ; sc:featureList edam:operation_2403 ; sc:name "rRNASelector" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hpc.ilri.cgiar.org/rrnaselector-software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0602, edam:topic_0654, edam:topic_0798 ; sc:citation ; sc:description "A tool to detect RRNPP quorum sensing systems in chromosomes, plasmids and phages of gram-positive bacteria." ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "RRNPP_detector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TeamAIRE/RRNPP_detector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC7937228", "pubmed:33676405" ; sc:description "R.ROSETTA is an R package for constructing and analyzing rule-based classification models. R.ROSETTA is designed to support the overall data mining and knowledge discovery process. The presented tool is a more accessible and extended version of ROSETTA system. In addition to all the existing ROSETTA functionalities, we have added new functions such as: balancing data with undersampling, estimating rule P values, retrieving support sets from rules, mergind rule-based models, predicting external classes, visualizing rule-based model and generating synthetic data." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:name "R.ROSETTA" ; sc:url "https://github.com/komorowskilab/R.ROSETTA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_3474 ; sc:citation , "pubmed:35751651" ; sc:description "Protein contact map quality estimation by deep evolutionary reconciliation." ; sc:featureList edam:operation_0272, edam:operation_0392, edam:operation_2429, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rrQNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Bhattacharya-Lab/rrQNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "This tool plots the Rosin-Rammler Diagram (RRSB) and calculates various related parameters." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Rosin-Rammler Diagram plotting tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.16.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28013-rosin-rammler-diagram-plotting-tool" ; biotools:primaryContact "Ivan Brezani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0204, edam:topic_0602 ; sc:citation , "pmcid:PMC10155054", "pubmed:37151216" ; sc:description "Bioconductor package for interpreting lists of Gene Ontology terms." ; sc:featureList edam:operation_2942, edam:operation_3432, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rrvgo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioconductor.org/packages/rrvgo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network" ; sc:featureList edam:operation_0276 ; sc:license "GPL-3.0" ; sc:name "RS-ExpNet-CRNMF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/USTC-HIlab/RS-ExpNet-CRNMF" ; biotools:primaryContact "Minghui Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description "RS-FISH is a tool for precise, interactive and scalable single-molecule FISH spot detection using Radial Symmetry." ; sc:name "RS-FISH" ; sc:url "https://github.com/PreibischLab/RadialSymmetryLocalization" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_3373, edam:topic_3375 ; sc:citation , "pmcid:PMC3570214", "pubmed:23242264" ; sc:description "Server for predicting CYP-mediated sites of metabolism on drug-like molecules." ; sc:featureList edam:operation_3092, edam:operation_3660 ; sc:name "RS-WebPredictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://reccr.chem.rpi.edu/Software/RS-WebPredictor/" ; biotools:primaryContact "Curt M. Breneman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3301, edam:topic_3697 ; sc:citation , "pmcid:PMC5714482", "pubmed:29084818" ; sc:description "An R Tool for the Luria-Delbruck Fluctuation Assay." ; sc:featureList edam:operation_2426 ; sc:name "rSalvador" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.7" ; sc:url "https://eeeeeric.com/rSalvador/" ; biotools:primaryContact "Qi Zheng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929, edam:format_2572, edam:format_2573, edam:format_3020, edam:format_3616 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_3327 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3327 ; sc:name "Sequence coordinates" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files." ; sc:featureList edam:operation_0227, edam:operation_3219, edam:operation_3563 ; sc:license "Artistic-2.0" ; sc:name "Rsamtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.26.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_3125, edam:topic_3512 ; sc:citation "pubmed:10641039", "pubmed:12824373", "pubmed:18495751", "pubmed:9719638" ; sc:description "Regulatory Sequence Analysis Tools (RSAT) is a software suite combining specialised tools for the detection of regulatory signals in non-coding sequences. It includes tools for sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows." ; sc:featureList edam:operation_0238, edam:operation_0438, edam:operation_0441, edam:operation_2422 ; sc:license "Other" ; sc:name "RSAT suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rsat.eu" ; biotools:primaryContact "Jacques van Helden" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_2330 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3511 ; sc:author , ; sc:citation , "pubmed:19720677" ; sc:description """Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database. Multi-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.""" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "RSAT retrieve-ensembl-seq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , , ; sc:url "http://rsat.sb-roscoff.fr/retrieve-ensembl-seq_form.cgi" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0204, edam:topic_3169, edam:topic_3173 ; sc:citation "pubmed:21715389" ; sc:description "A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240 ; sc:name "RSAT peak-motifs" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://floresta.eead.csic.es/rsat/peak-motifs_form.cgi" ; biotools:primaryContact "Jacques van Helden" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3452, edam:topic_3810 ; sc:citation , "pmcid:PMC8390230", "pubmed:34433428" ; sc:description "RSAtrace3D is a vectorization software to measure RSA (root system architecture) traits of monocot plants from 3D volume data such as X-ray CT images." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "RSAtrace3D" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/st707311g/RSAtrace3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models." ; sc:featureList edam:operation_0335 ; sc:license "Artistic-2.0" ; sc:name "rsbml" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rsbml.html" ; biotools:primaryContact "Michael Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0749, edam:topic_3308 ; sc:citation , "pmcid:PMC10017096", "pubmed:36857576" ; sc:description "Rapid assessment and visualization of RNA structure content." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570 ; sc:isAccessibleForFree true ; sc:name "RSCanner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pylelab/RSCanner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:author "Alessandra Breschi" ; sc:description "Various R scripts for exploratory biological sequence-derived data analysis." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2403, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Rscripts for data analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/abreschi/Rscripts" ; biotools:primaryContact "Alessandra Breschi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3577 ; sc:citation , "pubmed:32399554" ; sc:description """an R package for classification of molecular profiles using rank-based signatures. Signature-based Clustering for Diagnostic Purposes. SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. BiomedicalInformatics, Classification, Clustering, DifferentialExpression, FeatureExtraction, GeneExpression, GraphAndNetwork, Network, Proteomics, Software, SystemsBiology, Transcriptomics.""" ; sc:featureList edam:operation_0313, edam:operation_2428, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "rScudo" ; sc:url "https://bioconductor.org/packages/rScudo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0797, edam:topic_1775, edam:topic_3293, edam:topic_3299 ; sc:citation , , "pubmed:15593400", "pubmed:18025688" ; sc:description "The reciprocal smallest distance (RSD) algorithm (Wall, et al., 2003.) accurately infers orthologs between pairs of genomes by considering global sequence alignment and maximum likelihood evolutionary distance between sequences." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Reciprocal Smallest Distance (RSD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v1.1.7" ; sc:url "https://github.com/todddeluca/reciprocal_smallest_distance" ; biotools:primaryContact "Dennis Wall" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1001 ; sc:name "Chemical name (synonymous)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3668 ; sc:name "Disease name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:name "Phenotype name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0625, edam:topic_3325, edam:topic_3373 ; sc:citation , "pmcid:PMC9418253", "pubmed:36028515" ; sc:description "A rare skin disease database to link drugs with potential drug targets for rare skin diseases." ; sc:featureList edam:operation_3925, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "RSDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rsdb.cmdm.tw" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:21134892" ; sc:description "This tool allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains." ; sc:featureList edam:operation_0484 ; sc:name "Rseg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.au.dk/~plamy/Rseg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation ; sc:description "Analyzes ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications." ; sc:featureList edam:operation_2495 ; sc:name "RSEG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://smithlabresearch.org/software/rseg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:20022975" ; sc:description "We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels." ; sc:featureList edam:operation_3800 ; sc:name "RSEM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://deweylab.github.io/RSEM/" ; biotools:primaryContact "Bo Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0102, edam:topic_3170 ; sc:description "Set of tools for RNA-Seq data analysis. It consists of programs that deal with many aspects of RNA-Seq data analysis, such as reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) computation, etc." ; sc:featureList edam:operation_0230, edam:operation_2871, edam:operation_3680 ; sc:name "rSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "0.2.1" ; sc:url "http://www-personal.umich.edu/~jianghui/rseq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:description "Headers from the SeqAn C++ library for easy of usage in R." ; sc:featureList edam:operation_2409 ; sc:license "BSD-3-Clause" ; sc:name "RSeqAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RSeqAn.html" ; biotools:primaryContact "August Guang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc." ; sc:featureList edam:operation_2409 ; sc:name "RSeQC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://rseqc.sourceforge.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "Workflow which can implement a set of RNA-Seq analysis, such as performing quality control (QC) for sequencing data, generating signal tracks of mapped reads, calculating expression levels, and identifying differentially expressed genes by just providing sequencing RNA-Seq datasets." ; sc:featureList edam:operation_2428, edam:operation_3680 ; sc:name "RseqFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genomics.isi.edu/rnaseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8024626", "pubmed:33841507" ; sc:description "RSEQNORM is a fast and accurate RNA-seq data normalization for formalin-fixed paraffin-embedded samples. 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It works with unstranded, stranded, and paired-end sequence FASTQ files. 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Through RT-NET, it is possible to enable source-based neurofeedback experiments in one or two brain areas, and to visualize in 2D and 3D (on a 3D cortical model) the online brain activity.""" ; sc:featureList edam:operation_3659, edam:operation_3695 ; sc:name "RT-NET" ; sc:url "https://www.nitrc.org/projects/rtnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3489 ; sc:citation , "pubmed:33852697" ; sc:description "The rtabnetsp package enables retrieval of health indicators data from São Paulo's TABNET system." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3436 ; sc:name "rtabnetsp" ; sc:url "https://github.com/joaohmorais/rtabnetsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_0798, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc:description "RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures." ; sc:featureList edam:operation_0239, edam:operation_0427, edam:operation_0452, edam:operation_2421 ; sc:name "RTAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ismailoglu.github.io/RT-analyzer/" ; biotools:primaryContact "Contact Form", "RT-analyzer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0798 ; sc:citation "pubmed:17545202" ; sc:description "It looks for a target site duplication, a polyA in 3′ and an endonuclease cleavage site in 5′ to calculate an overall score of retrotransposition. 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We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies." ; sc:featureList edam:operation_0224 ; sc:license "GPL-2.0" ; sc:name "RTCGAToolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RTCGAToolbox.html" ; biotools:primaryContact "Mehmet Kemal Samur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_2640 ; sc:citation , "pubmed:35912447" ; sc:description "Open-source software for radiotherapy dose-surface map generation and analysis." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "rtdsm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/McGillMedPhys/rtdsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3300, edam:topic_3444 ; sc:citation ; sc:description """The effects of multi-echo fMRI combination and rapid T2*-mapping on offline and real-time BOLD sensitivity. 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The manual for the package: rtmpt_manual.""" ; sc:featureList edam:operation_2422, edam:operation_2426 ; sc:license "GPL-2.0" ; sc:name "rtmpt" ; sc:url "https://github.com/RaphaelHartmann/rtmpt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3308 ; sc:citation , "pmcid:PMC3778544", "pubmed:24043118" ; sc:description "This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies." ; sc:featureList edam:operation_2497 ; sc:license "Artistic-2.0" ; sc:name "RTN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RTN.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204 ; sc:citation ; sc:description "RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer 'dual regulons', a new concept that tests whether regulon pairs agree on the predicted downstream effects." ; sc:featureList edam:operation_2497 ; sc:license "Artistic-2.0" ; sc:name "RTNduals" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RTNduals.html" ; biotools:primaryContact "Clarice Groeneveld", "Mauro Castro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204 ; sc:citation ; sc:description "It is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort." ; sc:featureList edam:operation_2436, edam:operation_2497 ; sc:license "Artistic-2.0" ; sc:name "RTNsurvival" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RTNsurvival.html" ; biotools:primaryContact "Clarice Groeneveld", "Mauro A. A. Castro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pmcid:PMC3333775", "pubmed:22018358" ; sc:description "Package designed to perform and integrate gene set enrichment results across multiple genomic platforms." ; sc:featureList edam:operation_2436 ; sc:license "GPL-3.0" ; sc:name "RTopper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RTopper.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:14639705" ; sc:description "A C code for calculating significance of truncated products of P-values" ; sc:featureList edam:operation_2238 ; sc:name "RTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/fdudbridge/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3315 ; sc:citation ; sc:description "rTPC is an R package that helps fit thermal performance curves (TPCs) in R. rTPC contains 24 model formulations previously used to fit TPCs and has helper functions to help set sensible start parameters, upper and lower parameter limits and estimate parameters useful in downstream analyses, such as cardinal temperatures, maximum rate and optimum temperature." ; sc:featureList edam:operation_2426, edam:operation_3659, edam:operation_3799 ; sc:name "rTPC" ; sc:url "https://padpadpadpad.github.io/rTPC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128 ; sc:citation , "pubmed:32717044" ; sc:description "R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions." ; sc:featureList edam:operation_2492, edam:operation_2495, edam:operation_3741 ; sc:license "GPL-3.0" ; sc:name "Rtpca" ; sc:url "https://bioconductor.org/packages/Rtpca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC8963181", "pubmed:35360171" ; sc:description "A library for fMRI real-time processing systems in python (RTPSpy) with comprehensive online noise reduction, fast and accurate anatomical image processing, and online processing simulation." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "RTPSpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mamisaki/RTPSpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7470976", "pubmed:32749457" ; sc:description """A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts""" ; sc:featureList edam:operation_0264, edam:operation_0446, edam:operation_2495, edam:operation_3223 ; sc:name "RTR" ; sc:url "http://www.unimd.org/rtr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """A toolkit for the analysis of paths from spatial tracking experiments (such as the Morris water maze) and calculation of goal-finding strategies. This package is centered on an approach using machine learning for path classification. Rtrack is a package to process raw spatial tracking data (such as from the Morris water maze task) and calculate behavioural strategies. The core Rtrack classifier provided by this package assigns one of 9 strategies to each path. A core functionality of the Rtrack package is the calculation of metrics from the path coordinates.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "Rtrack" ; sc:softwareHelp , ; sc:url "https://rupertoverall.net/Rtrack" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2305, edam:format_3003, edam:format_3005 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2305, edam:format_3003, edam:format_3005 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3053 ; sc:citation , "pmcid:PMC2705236", "pubmed:19468054" ; sc:description "Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport." ; sc:featureList edam:operation_0362, edam:operation_3208 ; sc:license "Artistic-2.0" ; sc:name "rtracklayer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.34.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rtracklayer.html" ; biotools:primaryContact "Michael Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Analyze relative risk and conducts sib pair linkage analysis using tree-based methods." ; sc:featureList edam:operation_0283, edam:operation_2990 ; sc:name "RTREE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://c2s2.yale.edu/software/rtree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "Package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. 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This allows for a vastly simplified approach as recursive peak splitting procedures and repeated re-estimation of the background model are avoided. 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The tool substitutes genotype calls by their expected values given observed sequence data and implements a robust variance estimate for the score statistic." ; sc:featureList edam:operation_3197 ; sc:name "RVS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://strug.ccb.sickkids.ca/rvs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC6330140", "pubmed:30246882" ; sc:description """Inferring disease risk genes from sequencing data in multiplex pedigrees through sharing of rare variants. Computes estimates of the probability of related individuals sharing a rare variant. Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3791 ; sc:license "GPL-2.0" ; sc:name "RVs-r" ; sc:url "http://bioconductor.org/packages/release/bioc/html/RVS.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3325 ; sc:citation , "pmcid:PMC6612888", "pubmed:30500888" ; sc:description """Detection of rare disease variants in extended pedigrees using RVS. Computes estimates of the probability of related individuals sharing a rare variant. Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test). ExomeSeq, Genetics, GenomeWideAssociation, ImmunoOncology, Software, VariantDetection, WholeGenome.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3791 ; sc:license "GPL-2.0" ; sc:name "RVS" ; sc:url "https://bioconductor.org/packages/release/bioc/html/RVS.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:24755303" ; sc:description "A R package for rare variants selection with sequence data. The most outome-related rare variants are selected within a gene or a genetic region. The selection procedure is based on the power set of the subset of the rare variants." ; sc:featureList edam:operation_3197 ; sc:name "rvsel" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.columbia.edu/~sw2206/softwares.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:24740360" ; sc:description "The tool computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them." ; sc:featureList edam:operation_3197 ; sc:name "RVsharing" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.crulrg.ulaval.ca/pages_perso_chercheurs/bureau_a/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168, edam:topic_3574 ; sc:citation "pubmed:27153000" ; sc:description "A flexible software package for genetic association studies. It is designed to support unrelated individual or related (family-based) individuals. Both quantitative trait and binary trait are supported" ; sc:featureList edam:operation_3197 ; sc:name "RvTests" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanxw.github.io/rvtests/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3299 ; sc:citation , "pubmed:37289204" ; sc:description "Companion R package for the world checklist of vascular plants." ; sc:isAccessibleForFree true ; sc:name "rWCVP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/rWCVP/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3063, edam:topic_3303, edam:topic_3360, edam:topic_3379 ; sc:citation , "pubmed:35266872" ; sc:description "The RWD app provides a platform to view and search for quality-scored real-world datasets." ; sc:featureList edam:operation_2421, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "RWD-Cockpit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://rwd.aihealth.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3325 ; sc:citation , "pmcid:PMC5753270", "pubmed:29136241" ; sc:description "Use this package to interface with the WikiPathways API." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "rWikiPathways" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/rWikiPathways.html" ; biotools:primaryContact , "Alexander Pico" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3295, edam:topic_3512, edam:topic_3577 ; sc:citation , "pmcid:PMC7912853", "pubmed:33639858" ; sc:description "Random Walk with Restart for multi-dimensional data Fusion (RWRF). 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Recently, we have proposed a computational method based on a random walk framework on a miRNA-target gene network to predict disease-associated miRNAs. The prediction performance of our method is better than that of some existing state-of-the-art network- and machine learning-based methods since it exploits the mutual regulation between miRNAs and their target genes in the miRNA-target gene interaction networks. To facilitate the use of this method, we have developed a Cytoscape app, named RWRMTN, to predict disease-associated miRNAs.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0463, edam:operation_3792, edam:operation_3927 ; sc:name "RWRMTN" ; sc:url "http://apps.cytoscape.org/apps/rwrmtn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0623, edam:topic_2259 ; sc:citation "pubmed:19695104" ; sc:description "An R Package for Relative expression analysis of gene expession profiles." ; sc:featureList edam:operation_2495 ; sc:name "RXA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://jshare.johnshopkins.edu/dnaiman1/public_html/rxa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3068, edam:topic_3397, edam:topic_3407 ; sc:citation , "pubmed:33350578" ; sc:description """An online compendium of treatable genetic disorders. Treatments for genetic disorders – A compendium of treatments for genetic conditions. Treatments for genetic disorders. A compendium of treatments for genetic conditions. Search for treatments for genetic disorders. The rx-genes.com site does not provide medical advice. It is intended for informational purposes only. It should not be used in place of professional medical advice, diagnosis or treatment. There is no substitute for the astute physician.""" ; sc:featureList edam:operation_2421, edam:operation_3920 ; sc:name "Rx-genes" ; sc:url "https://www.rx-genes.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC7680896", "pubmed:33240070" ; sc:description """Rxnat: Query and retrieves neuroimaging sets from XNAT projects. XNAT is an extensible open-source imaging informatics software platform dedicated to imaging-based research. To use system environment variables we need to add them to the .Renviron file located in the user's home folder. Use Sys.getenv("HOME") to get the path (for unix/osx users the location can be easily accessed with ~, eg. vi ~/.Renviron). The Rxnat package will be able to automatically read / use a system environment variable provided the following format is used: XXXX_RXNAT_USER and XXXX_RXNAT_PASS. XXXX is provided as an argument when an XNAT connection is initiated.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3283, edam:operation_3435 ; sc:name "Rxnat" ; sc:url "https://github.com/adigherman/Rxnat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_3303, edam:topic_3314 ; sc:citation , "pubmed:31950996" ; sc:description """molecular scaffold and reactive chemical environment feature extractor for biochemical reactions. RxnBLAST as a web-based tool for analyzing scaffold transformations and reactive chemical environment fea-tures in bioreactions. RxnBLAST extracts chemical features from bioreactions including atom–atom mapping, reaction centers, functional groups, and rules to help understand chemical compositions and reaction patterns. Core-to-Core is proposed, which can be utilized in scaffold networks and for constructing a reac-tion space, as well as provide guidance for subsequent biosynthesis efforts.""" ; sc:featureList edam:operation_0337, edam:operation_3216 ; sc:name "RxnBLAST" ; sc:url "http://design.rxnfinder.org/rxnblast/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, Gold Standard Drug Database, and Multum. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary." ; sc:featureList edam:operation_2422 ; sc:name "RxNorm API" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.nlm.nih.gov/research/umls/rxnorm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3334, edam:topic_3375, edam:topic_3379, edam:topic_3403 ; sc:citation ; sc:description "Pharmacological Management of Acute Spinal Cord Injury." ; sc:featureList edam:operation_0337, edam:operation_2424 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "RXSCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://jutzelec.shinyapps.io/RxSCI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170 ; sc:citation , "pubmed:34255826" ; sc:description "Ryuto is a tool for exact and fast transcript assembly and quantification, using network flows and a novel extension of splice-graphs." ; sc:featureList edam:operation_0310, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Ryuto" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/studla/RYUTO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation "pubmed:12096903" ; sc:description "A program that identifies and characterizes Ribose zippers in an RNA structure given an appropriate PDB formatted file as input.  It also generates PyMol scripts to assist in the visualization of identified ribose zippers." ; sc:featureList edam:operation_0278 ; sc:name "RZParser" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.softpedia.com/get/Science-CAD/RZparser.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3474, edam:topic_3572 ; sc:citation , "pubmed:34464837" ; sc:description "Self-cleansing unsupervised domain adaptation for medical image segmentation." ; sc:featureList edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "S-CUDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zzdxjtu/S-cuda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32790629" ; sc:description "Super Lightweight Super-Resolution Network." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:license "MIT" ; sc:name "s-LWSR" ; sc:url "https://github.com/Sudo-Biao/s-LWSR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3169, edam:topic_3170 ; sc:citation "pubmed:21998740" ; sc:description "This tool manages your RNA-Seq and ChIP-seq data." ; sc:featureList edam:operation_0564 ; sc:name "S-MART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://urgi.versailles.inra.fr/Tools/S-MART" ; biotools:primaryContact "Matthias Zytnicki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC9381718", "pubmed:35974061" ; sc:description "Protein structural property prediction using MSA transformer." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0474, edam:operation_3454, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "S-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/arontier/S_Pred_Paper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229 ; sc:citation "pubmed:26363175" ; sc:description "A novel cell structure-driven classifier construction approach for predicting image-based protein subcellular location by employing the prior biological structural information." ; sc:featureList edam:operation_2489 ; sc:name "S-PSorter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/shaoweinuaa/S-PSorter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation , "pubmed:25534081" ; sc:description "s2D is a computational method to predict secondary-structure populations from amino acid sequences, which simultaneously characterizes structure and disorder in a unified statistical mechanics framework." ; sc:featureList edam:operation_2423, edam:operation_2480 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "s2D" ; sc:operatingSystem "Linux" ; sc:softwareVersion "v1.1" ; sc:url "http://www-mvsoftware.ch.cam.ac.uk/index.php/s2D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082 ; sc:citation , "pubmed:34170287" ; sc:description "A supervised two-layer search framework based on PSI-BLAST for protein remote homology detection." ; sc:featureList edam:operation_0477, edam:operation_2421, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "S2L-PSIBLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/S2L-PSIBLAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3063, edam:topic_3071 ; sc:citation , "pmcid:PMC5219713", "pubmed:28061771" ; sc:description "Convert data collections based on IBM SPSS Statistics to the data standard for definition and exchange of clinical trials." ; sc:featureList edam:operation_0335 ; sc:license "LGPL-2.0" ; sc:name "S2O" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/s2o/" ; biotools:primaryContact "Martin Dugas", "Philipp Bruland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0108 ; sc:citation ; sc:description "S2P is an open source application for fast and accurate processing of 2D-gel and MALDI-based mass spectrometry protein data." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "S2P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://sing-group.org/s2p" ; biotools:primaryContact "S2P" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2258, edam:topic_2830 ; sc:citation ; sc:description "Sigma-2 receptor selective Ligands Database is an online ligand database consisting of the Sigma-2 selective receptor ligand published since 1993. The S2RSLDB is based on structural 2D information as well as pharmacological and computed physicochemical properties and experimental procedures, retrieved from the literature." ; sc:featureList edam:operation_0224 ; sc:name "S2RSLDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.researchdsf.unict.it/S2RSLDB/" ; biotools:primaryContact "Emanuele Amata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3173 ; sc:citation ; sc:description """a package for normalizing, denoising and integrating epigenomic datasets across different cell types. In the package, it can first normalize average read counts signal by S3norm ver2 and then use IDEAS to either to do genome segmentations or to call master peaks list across multiple datasets. This package will use bigWig file as input files.""" ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3935 ; sc:license "MIT" ; sc:name "S3V2-IDEAS" ; sc:url "https://github.com/guanjue/S3V2_IDEAS_ESMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3334, edam:topic_3474 ; sc:citation , "pubmed:32466691" ; sc:description "Temporal Backpropagation for Spiking Neural Networks with One Spike per Neuron." ; sc:featureList edam:operation_3450, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "S4NN" ; sc:url "https://github.com/SRKH/S4NN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3569 ; sc:citation ; sc:description "Defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the package itself (many more are implemented in the IRanges package and in other BioConductor infrastructure packages)." ; sc:featureList edam:operation_3664 ; sc:license "Artistic-2.0" ; sc:name "S4Vectors" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.12.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/S4Vectors.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3512 ; sc:citation , , "pmcid:PMC4702841", "pubmed:26527729" ; sc:description "Repository of small open reading frames identified by ribosome profiling in a database of over 3 million sORFs across 78 datasets from six species." ; sc:featureList edam:operation_2422, edam:operation_2929, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "sORFs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://www.sorfs.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068, edam:topic_3304 ; sc:citation , "pmcid:PMC6257411", "pubmed:30524220" ; sc:description "Software Package for Running PyNN Simulations on SpiNNaker." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sPyNNaker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SpiNNakerManchester/sPyNNaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC6765109", "pubmed:31392979" ; sc:description "AGO-unbound cytosolic pool of mature miRNAs in plant cells reveals a novel regulatory step at AGO1 loading | Small RNAs were sequenced from FPLC-fractionated Arabidopsis leaf and flower crude extracts | Here we provide the scripts that reproduce the results and figures of the paper Dalmadi et al. 2019. These scripts are not meant to be reusable. Most of the figures and tables underwent post-processing in Excel, Powerpoint, or other GUI softwares, therefore the results will not exactly be the same as they appear in the paper | Download this directory and run the sRNA_analysis.sh script which downloads sRNA-seq reads from the SRA database and processes them. The results are placed in the 'sRNA-seq' directory | Linux operation system with zsh shell" ; sc:featureList edam:operation_0463, edam:operation_1812, edam:operation_3792 ; sc:name "sRNA" ; sc:url "https://github.com/gyulap/sRNA_content_of_FPLC_fractions" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780 ; sc:description "The plant sRNA portal is a a database of annotated sRNAs integrating the miRPursuit pipeline to identify, predict and annotate plant small RNAs (sRNA)." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sRNA plant portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://srna-portal.biodata.pt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3168 ; sc:citation ; sc:description "a database repository of uniformly-annotated small RNAs in plants | Abstract Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Except miRNAs, the other two classes are not well-annotated and collected in public databases for most sequenced plant genomes. We performed comprehensive sRNA annotation for 138 plant species, which have fully sequenced genomes and public next-generation-sequencing (NGS) sRNA data available. The results are available via an online repository called sRNAanno ( www.plantsRNAs.org )" ; sc:featureList edam:operation_3431, edam:operation_3454, edam:operation_3792 ; sc:name "sRNAanno" ; sc:url "http://www.plantsrnas.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3519 ; sc:citation , "pmcid:PMC6602500", "pubmed:31114926" ; sc:description "Web-server tool and standalone application for processing small-RNA data obtained from next generation sequencing platforms such as Illumina or SOLiD." ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "sRNAbench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinfo5.ugr.es/srnatoolbox/srnabench/" ; biotools:primaryContact "Michael Hackenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3519 ; sc:citation , "pmcid:PMC6602500", "pubmed:31114926" ; sc:description "Intuitive fast small RNA profiling and differential expression." ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "sRNAtoolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://arn.ugr.es/srnatoolbox/" ; biotools:primaryContact "Michael Hackenberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31885040" ; sc:description """Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. sRNAtools at this site is under construction ... Coming soon!""" ; sc:featureList edam:operation_0282, edam:operation_2495, edam:operation_3454 ; sc:name "sRNAtools" ; sc:url "https://bioinformatics.caf.ac.cn/sRNAtools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC10318387", "pubmed:37354496" ; sc:description "Efficient downsampling method for large high-throughput sequencing data." ; sc:featureList edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "s-leaping" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hkuwahara/sleaping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0130, edam:topic_2814 ; sc:citation ; sc:description "Quantify the structural variability of a multiple target conformations (MTC) set and localize the structural variable positions and regions of the target." ; sc:featureList edam:operation_0474 ; sc:name "SA-CONF" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels" ; biotools:primaryContact "Anne-Claude Camproux", "Leslie Regad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_0736 ; sc:citation "pubmed:21665924" ; sc:description "SA-Mot is a wbe server for the extraction and location of structural motifs of interest from protein loops. Recurrent and conserved structural motifs involved in structural redundancy of loops are considered." ; sc:featureList edam:operation_0238, edam:operation_0245, edam:operation_0321, edam:operation_0481, edam:operation_2415 ; sc:name "SA-Mot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sa-mot.mti.univ-paris-diderot.fr" ; biotools:primaryContact "Adrien Saladin", "Julien Maupetit", "Leslie Regad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:15215446" ; sc:description "Tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment." ; sc:featureList edam:operation_0346, edam:operation_0360, edam:operation_0477, edam:operation_2487 ; sc:name "SA-Search" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search" ; biotools:primaryContact "Frédéric Guyon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:27170037" ; sc:description "A software tool developed to find Simple Sequence Repeats (SSRs) in a sequence (presumably of DNA or RNA)." ; sc:featureList edam:operation_0415 ; sc:name "SA-SSR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://github.com/ridgelab/SA-SSR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC7827184", "pubmed:33435356" ; sc:description """A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability. SAAFEC-SEQ: an online application for calculating folding free energy changes in proteins caused by missense mutations. SAAFEC-SEQ uses the PsePSSM algorithm to predict the stability changes upon a single mutation in protein. SAAFEC-SEQ uses gradient boosting decision tree repressor to encode physicochemical properties, sequence features and evolutionary information to compute the change in stability free energy resulting from single mutations. SAAFEC-SEQ outperforms all existing state-of-the-art sequence-based methods in both the Pearson correlation coefficient and root-mean-squared-error parameters for several independent datasets.""" ; sc:featureList edam:operation_0253, edam:operation_0303, edam:operation_0331 ; sc:name "SAAFEC-SEQ" ; sc:url "http://compbio.clemson.edu/SAAFEC-SEQ/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_2533 ; sc:citation "pubmed:27077847" ; sc:description "This method addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast (<< 1 minute) modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points." ; sc:featureList edam:operation_0250 ; sc:name "SAAMBE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.clemson.edu/saambe_webserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199, edam:topic_0749, edam:topic_3474, edam:topic_3957 ; sc:citation , "pmcid:PMC7177817", "pubmed:32272725" ; sc:description """Predicting Effect of Mutations on Protein-Protein Interactions. #SAMMBE 3D can be used to i) calculate the binding free energy caused by single mutation and ii) predict whether a particular mutation is disruptive or non-disruptive. User need to download the script and two models. Regression.model is the model for predicting binding free energy due to mutation and classification.model is the model #to identify disruptive/non-disruptive mutation.""" ; sc:featureList edam:operation_0331, edam:operation_2464, edam:operation_2492 ; sc:license "GPL-3.0" ; sc:name "SAAMBE-3D" ; sc:url "https://github.com/delphi001/SAAMBE-3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0199, edam:topic_3318, edam:topic_3957 ; sc:citation , "pubmed:32866236" ; sc:description "A Sequence-based Method for Predicting Mutation Effect on Protein-protein Binding Affinity." ; sc:featureList edam:operation_0331, edam:operation_2464, edam:operation_2492 ; sc:name "SAAMBE-SEQ" ; sc:url "http://compbio.clemson.edu/saambe_webserver/indexSEQ.php#started" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168, edam:topic_3295 ; sc:citation "pubmed:22689387" ; sc:description "Streamlined Analysis and Annotation Pipeline for Reduced Representation Bisulfite Sequencing) offers an end-to-end solution for analyzing and interpreting next-generation methylation sequencing data." ; sc:featureList edam:operation_0361, edam:operation_2478 ; sc:name "SAAP-BS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformaticstools.mayo.edu/research/saap-rrbs/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1470 ; sc:encodingFormat edam:format_1476 ; sc:name "C-alpha trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation "pubmed:16844979" ; sc:description "Tool for the reconstruction of complete protein structures from their alpha-carbon descriptions." ; sc:featureList edam:operation_0479 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "SABBAC" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1476 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0154, edam:topic_2830, edam:topic_3374, edam:topic_3400 ; sc:citation , "pmcid:PMC8728266", "pubmed:34986602" ; sc:description "SAbDab is a database containing all the antibody structures available in the PDB, annotated and presented in a consistent fashion." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "SAbDab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://opig.stats.ox.ac.uk/webapps/newsabdab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:16773560" ; sc:description "The tool implements a Markov-Hidden Markov Model for inferring locus-specific ancestry in admixed individuals" ; sc:featureList edam:operation_3745 ; sc:name "SABER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://med.stanford.edu/tanglab/software/saber.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_1775, edam:topic_2814 ; sc:citation "pubmed:21153777" ; sc:description "Software for protein structure alignment based on the internal coordinates (i.e. bond lengths, bond angles and torsion angles) of structure representation." ; sc:featureList edam:operation_0295 ; sc:name "SABIC" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://doc.aporc.org/wiki/SABIC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1011 ; sc:name "EC number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2648 ; sc:name "Reaction kinetics ID (SABIO-RK)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2309 ; sc:name "Reaction ID (SABIO-RK)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2978 ; sc:encodingFormat edam:format_2331 ; sc:name "Reaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2024 ; sc:encodingFormat edam:format_2331 ; sc:name "Enzyme kinetics data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_2331 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3070, edam:topic_3292, edam:topic_3344, edam:topic_3473 ; sc:citation , ; sc:description "Curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "SABIO-RK: biochemical reactions and their kinetics" ; sc:operatingSystem "Linux" ; sc:provider "HITS" ; sc:softwareHelp , ; sc:url "http://sabiork.h-its.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2259 ; sc:citation ; sc:description "Data in the database can be accessed via web-based user interfaces and web-services offering the possibility of submitting complex searches by defining various search criteria. Currently the database has two different versions of web-based user interface, due to a transition process. The new user interface enables to show the user beforehand how many results can be expected for a given set of search criteria." ; sc:featureList edam:operation_2422 ; sc:name "SABIO-RK API" ; sc:operatingSystem "Linux" ; sc:provider "HITS" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://sabiork.h-its.org/layouts/content/docuRESTfulWeb/manual.gsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:20865514" ; sc:description "This server can be used for predicting real valued relative solvent possibilities of amino acid residues in proteins, and for improved prediction of secondary structures using evolutionary profiles and predicted relative solvent accessibility of an amino acid residue as a fingerprint of the overall packing." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "SABLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sable.cchmc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3572 ; sc:description "A tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file." ; sc:featureList edam:operation_3192, edam:operation_3218 ; sc:license "MIT" ; sc:name "sabre" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/najoshi/sabre" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Make Sabund and Rabund files from a CD-HIT cluster output." ; sc:featureList edam:operation_0335 ; sc:name "sabund" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1 beta" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/Sabund/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196, edam:format_3815 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3343, edam:topic_3373 ; sc:author , "Miroslav Kratochvíl" ; sc:citation ; sc:description "PostgreSQL extension suitable for storing small molecules and searching them using substructure or similarity search" ; sc:featureList edam:operation_2483 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Sachem" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo.uochb.cas.cz/sachem/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3168, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc:description """identifying sequence-based determinants of chromosomal compartments. Sequence-based predictor of chromosomal compartments. The 'Sequence-based Annotator of Chromosomal Compartments by Stacked Artificial Neural Networks' or SACSANN is a machine learning approach to predicting A/B compartment annotations using only features derived from a reference genome. SACSANN has been tested on both Linux and MacOS environments.""" ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3927 ; sc:license "GPL-2.0" ; sc:name "SACSANN" ; sc:url "https://github.com/BlanchetteLab/SACSANN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0108, edam:topic_0196, edam:topic_0736 ; sc:citation , "pubmed:35962986" ; sc:description "Structural analogue-based protein structure domain assembly assisted by deep learning." ; sc:featureList edam:operation_0303, edam:operation_0310, edam:operation_0476, edam:operation_0477 ; sc:isAccessibleForFree true ; sc:name "SADA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://zhanglab-bioinf.com/SADA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2828, edam:topic_3678 ; sc:citation , "pubmed:36037090" ; sc:description "A deep learning framework for protein crystallization propensity prediction using self-attention and auto-encoder networks." ; sc:featureList edam:operation_0477, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SADeepcry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhc940702/SADeepcry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:23333734" ; sc:description "This server is able to calculate the atom depth value for every atom of a protein structure, giving a lot of intrinsic information of 3D composition of the macromolecule and its core." ; sc:featureList edam:operation_0250 ; sc:name "Sadic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sbl.unisi.it/prococoa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0160, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:32960943" ; sc:description """A novel sequence alignment algorithm based on deep learning of the protein folding code. 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Barry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_2533 ; sc:citation "pubmed:27070572" ; sc:description "A web applicatin for calculating folding free energy changes caused by missense mutations in proteins." ; sc:featureList edam:operation_0250 ; sc:name "SAFEEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.clemson.edu/SAAFEC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Script package for quantifying bacterial load within cells using images from an ArrayScan microscope. 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We have integrated 6 datasets encompassing 1213 human genome and exome data to create a compendium of 154 million genetic variants. The resource has immense applications in understanding the allelic frequencies, carrier rates for rare genetic diseases and genetic traits including pharmacogenetics, apart from prioritising and discovering novel disease associated variants. The variants were systematically annotated, integrated with other public databases and and allele frequencies are available in this browsable resource. 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Lash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0204, edam:topic_0634, edam:topic_3512 ; sc:citation "pubmed:7570003" ; sc:description "Simultaneous expression and map information." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "SAGE Home Page" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sagenet.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. 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It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400,000). SAIGE performs single-variant association tests for binary traits and quantitative traits. For binary traits, SAIGE uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) to account for case-control imbalance. SAIGE-GENE (implemented in the SAIGE R package) performs gene- or region-based association tests (Burde, SKAT, SKAT-O) for binary traits and quantitative traits. Note: SAIGE-GENE accounts for case-control imbalance in gene-based tests (>= 0.35.8.5)""" ; sc:featureList edam:operation_2928 ; sc:name "SAIGE" ; sc:url "https://github.com/weizhouUMICH/SAIGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3337, edam:topic_3517, edam:topic_3577 ; sc:citation ; sc:description "SAIGE-Biobank Re-Usable SAIGE Helper (SAIGE-BRUSH) is an efficient, user-friendly and low cost cloud implementation for genome-wide association studies. SAIGE-BRUSH is an implementation of the popular SAIGE GWAS software." ; sc:license "MIT" ; sc:name "SAIGE-BRUSH" ; sc:softwareHelp ; sc:url "https://github.com/tbrunetti/SAIGE-BRUSH" ; biotools:primaryContact "Nicholas Rafaels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3337, edam:topic_3517 ; sc:citation , "pubmed:32898220" ; sc:description """Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies. Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests in large-scale phenome-wide association studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the original SAIGE R package (v0.29.4.4). SAIGEgds also implements some of the SPAtest functions in C to speed up the calculation of Saddlepoint approximation. Benchmarks show that SAIGEgds is 5 to 6 times faster than the original SAIGE R package.""" ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "SAIGEgds" ; sc:url "https://bioconductor.org/packages/SAIGEgds" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0749, edam:topic_2229, edam:topic_3173, edam:topic_3474 ; sc:citation ; sc:description "Scalable and Accurate Invariant Representation Learning for Single-Cell ATAC-Seq Processing and Integration." ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3935 ; sc:license "MIT" ; sc:name "SAILER" ; sc:url "https://github.com/uci-cbcl/SAILER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:24752080" ; sc:description "A software tool that implements a novel, is an alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads." ; sc:featureList edam:operation_3680 ; sc:name "Sailfish" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.cs.cmu.edu/~ckingsf/software/sailfish/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0749 ; sc:citation ; sc:description "Pipeline for quantification of circular RNA." ; sc:featureList edam:operation_2441, edam:operation_3800 ; sc:name "Sailfish-cir" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zerodel/Sailfish-cir" ; biotools:primaryContact "Musheng Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3520 ; sc:citation ; sc:description "Filter high confidence interactions from spectral count data in affinity purification–mass spectrometry." ; sc:featureList edam:operation_2945, edam:operation_3695 ; sc:name "SAINT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "3.6.1" ; sc:url "http://saint-apms.sourceforge.net/Main.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0160, edam:topic_3474, edam:topic_3542 ; sc:citation , "pmcid:PMC10115468", "pubmed:37092035" ; sc:description "Self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction." ; sc:featureList edam:operation_0249, edam:operation_0267, edam:operation_0474, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SAINT-Angle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bayzidlab/SAINT-Angle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0593, edam:topic_2828, edam:topic_3474, edam:topic_3542 ; sc:citation ; sc:description "SAINT stands for Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_2488, edam:operation_3904 ; sc:name "SAINT" ; sc:url "https://github.com/SAINTProtein/SAINT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31891535" ; sc:description """Fast Approximation of Frequent k-Mers and Applications to Metagenomics. Sampling Algorithm for K-mers Approximation (Pellegrina, Pizzi, Vandin). SAKEIMA is a sampling-based algorithm for computing an approximation of the most frequent k-mers from a dataset of reads or a sequence. It's implementation is based on Jellyfish (version 2 https://github.com/gmarcais/Jellyfish ).""" ; sc:featureList edam:operation_3472, edam:operation_3800, edam:operation_3802 ; sc:name "SAKEIMA" ; sc:url "https://github.com/VandinLab/SAKEIMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0621, edam:topic_0780 ; sc:citation "pubmed:19854933" ; sc:description "It is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences." ; sc:featureList edam:operation_0240, edam:operation_0325, edam:operation_3432 ; sc:name "SALAD" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://salad.dna.affrc.go.jp/salad/en/" ; biotools:primaryContact "M. Mihara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC9486591", "pubmed:36124792" ; sc:description "Species-agnostic local ancestry inference network." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SALAI-Net" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/AI-sandbox/SALAI-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:19465380" ; sc:description "The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity and sequence alignments." ; sc:featureList edam:operation_0292, edam:operation_0294, edam:operation_0346, edam:operation_0360 ; sc:name "SALAMI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://flensburg.zbh.uni-hamburg.de/~wurst/salami/" ; biotools:primaryContact "T. Margraf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_0621, edam:topic_3315, edam:topic_3957 ; sc:citation , "pmcid:PMC7640460", "pubmed:33148180" ; sc:description """structure aware method for global PPI network alignment. To reproduce the results reported in SAlign paper, use "Reproduce_Paper_Results" folder. This folder contains all the files that are used in alignment generation and evaluation. "SAlign and SAlign_mc Code" folder contains code with test example. If you want to run SAlign on your own collected datasets please run "SAlign and SAlign_mc Code" folder.""" ; sc:featureList edam:operation_0491, edam:operation_0495, edam:operation_0496, edam:operation_0503, edam:operation_0510 ; sc:name "SAlign" ; sc:url "https://github.com/cbrl-nuces/SAlign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "SalivaDB is a comprehensive and manually-curated database for salivary biomarkers found in Homo sapiens. 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biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3500 ; sc:author "Amine Namouchi" ; sc:citation ; sc:description "SalmoBase 2.0: An integrative genomic data resource for salmonids" ; sc:isAccessibleForFree true ; sc:name "salmobase2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://salmobase.org/" ; biotools:primaryContact "Amine Namouchi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:encodingFormat edam:format_1929 ; sc:name "Data reference" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A tool for transcript expression quantification from RNA-seq data" ; sc:featureList edam:operation_0236, edam:operation_2495, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Salmon" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://combine-lab.github.io/salmon" ; biotools:primaryContact "Rob Patro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence motif (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3301 ; sc:citation ; sc:description "This tool gets a CRISPR profile by identifying the presence of known spacers and direct repeats (DRs) in a given sequence based on a catalogue." ; sc:featureList edam:operation_0239 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Salmonella CRISPR typing" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Bioinformatics and Biostatistics Hub", "C3BI", "Enteric Bacterial Pathogens", "Institut Pasteur" ; sc:softwareHelp ; sc:softwareVersion "v.1.0.0" ; sc:url "https://research.pasteur.fr/team/enteric-bacterial-pathogens/" ; biotools:primaryContact "Kenzo Hugo Hillion", "Laetitia Fabre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0736, edam:topic_3170 ; sc:citation "pubmed:23782615" ; sc:description "This tool can accurately and sensitivity classify short reads of NGS into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families." ; sc:featureList edam:operation_0246, edam:operation_2996 ; sc:name "SALT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/salt1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC8386087", "pubmed:34433415" ; sc:description "A SNP-aware short read aligner" ; sc:featureList edam:operation_0292, edam:operation_1839, edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SALT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/weiquan/SALT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3473, edam:topic_3518 ; sc:citation "pubmed:22127579" ; sc:description "This tool is a statistical technique for finding significant genes in a set of microarray experiments, a supervised learning software for genomic expression data mining." ; sc:featureList edam:operation_0571 ; sc:name "SAM" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://statweb.stanford.edu/~tibs/SAM/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0202, edam:topic_3336 ; sc:citation , "pubmed:36545795" ; sc:description "A sequence-agnostic model for drug-target binding affinity prediction." ; sc:featureList edam:operation_2940, edam:operation_3092, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SAM-DTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/huzqatpku/SAM-DTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:19483096" ; sc:description "The SAM-T08 web server is a 3D protein structure prediction server. The server also provides 3 multiple sequence alignments of putative homologs, prediction of local structural features including backbone and burial properties and residue-residue contact predictions." ; sc:featureList edam:operation_0245, edam:operation_0267, edam:operation_0474, edam:operation_3092 ; sc:name "SAM-T08" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html" ; biotools:primaryContact "SAM-T08 support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2572 ; sc:name "File name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_1929 ; sc:name "File name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2330 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Prints the SAM alignments as a TAB delimited file." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Sam2Tsv" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/Sam2Tsv" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3325, edam:topic_3379 ; sc:citation , , "pubmed:37668049", "pubmed:37721513" ; sc:description "Self-adapting mixture prior to dynamically borrow information from historical data in clinical trials." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3436 ; sc:license "BSD-3-Clause" ; sc:name "SAM" ; sc:url "https://cran.r-project.org/web/packages/SAMprior" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0821, edam:topic_3334, edam:topic_3474 ; sc:citation , "pubmed:35288360" ; sc:description "A computational prediction of S-Adenosyl methionine (SAM) interacting proteins and their interaction sites through primary structures." ; sc:featureList edam:operation_0253, edam:operation_2492, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sites.google.com/view/wajidarshad/software" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Converts SAM format to BAM format." ; sc:featureList edam:operation_0335 ; sc:name "sam_to_bam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.19" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation "pubmed:15945370" ; sc:description "SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type." ; sc:featureList edam:operation_0310, edam:operation_0523, edam:operation_0525, edam:operation_3180 ; sc:name "SAM - Sequence Assembly Manager" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/sam" ; biotools:primaryContact "SAM Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC8849508", "pubmed:35120119" ; sc:description "The SAMBA tool uses long reads to improve the contiguity of genome assemblies." ; sc:featureList edam:operation_0525, edam:operation_3216, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SAMBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alekseyzimin/masurca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3170 ; sc:citation "pubmed:25697820" ; sc:description "This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats." ; sc:featureList edam:operation_0292, edam:operation_2403 ; sc:name "Sambamba" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "http://www.open-bio.org/wiki/Sambamba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24812344" ; sc:description "A tool to mark duplicates and extract discordant and split reads from SAM files." ; sc:featureList edam:operation_3199 ; sc:name "SAMBLASTER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GregoryFaust/samblaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0736, edam:topic_3315, edam:topic_3542 ; sc:citation , "pubmed:33325494" ; sc:description """from regular bundles to peculiar twists. Explore CCdb or measure your structure. Non-redundant database of coiled-coil structures measured with SamCC-Turbo. Software for automatic detection and measurement of coiled coils in PDB structures.""" ; sc:featureList edam:operation_0268, edam:operation_0303, edam:operation_0479, edam:operation_3216 ; sc:license "MIT" ; sc:name "SamCC-Turbo" ; sc:url "https://lbs.cent.uw.edu.pl/samcc_turbo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0623, edam:topic_3168 ; sc:citation "pubmed:12724290" ; sc:description "An integrated scheme and corresponding program for automatic discovery of sample classes based on gene expression profile." ; sc:featureList edam:operation_2995 ; sc:name "SamCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biosun.org.cn/SamCluster/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:34490909" ; sc:description "Spectrum analysis for multiple exponentials via experimental condition oriented simulation (SAME-ECOS)." ; sc:featureList edam:operation_2426, edam:operation_3214, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SAME-ECOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hanwencat/SAME-ECOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3170, edam:topic_3518, edam:topic_3520 ; sc:citation ; sc:description """An experimentally-derived measure of inter-replicate variation in reference samples. Example Dataset Download. Multiple Test Correction Method""" ; sc:featureList edam:operation_2409, edam:operation_3435, edam:operation_3799 ; sc:name "same-same" ; sc:url "https://peptidewitch.shinyapps.io/samesame" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_2533, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3673 ; sc:citation , "pubmed:27402900" ; sc:description "This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread." ; sc:featureList edam:operation_0362, edam:operation_2928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "samExploreR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/samExploreR.html" ; biotools:primaryContact "shailesh tripathi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2572 ; sc:name "File name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_2572 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Filters a BAM using javascript." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SamJavascript" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/SamJavascript" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170 ; sc:citation "pubmed:21232146" ; sc:description "GUI for processing SAM/BAM and BED files. The software allows users to accurately estimate gene expression scores using short reads originating from both exons and exon-exon junctions, to generate wiggle files for visualization in UCSC genome browser, and to generate an alignment statistics report." ; sc:featureList edam:operation_0310, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "SAMMate" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sammate.sourceforge.net/" ; biotools:primaryContact "Dongxiao Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3379, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC7270712", "pubmed:32547380" ; sc:description """A Library for Processing SmAll-MaMmal BrAin MRI Data in Python. Sammba-MRI:Small mammals NeuroImaging in Python — Multimodal Imaging of Neurodegenerative Diseases and Therapies.""" ; sc:featureList edam:operation_3443 ; sc:name "Sammba-MRI" ; sc:url "http://sammba-mri.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0203, edam:topic_2259, edam:topic_3168 ; sc:citation "pubmed:25414365" ; sc:description "A web-based tool that enables functional enrichment analysis and visualization of high-throughput datasets. Itcan analyse two distinct data types (e.g. mRNA expression and global proteomics) simultaneously across multiple experimental systems to identify pathways activated in these experiments and then visualize the pathways in a single interaction network." ; sc:featureList edam:operation_0314, edam:operation_2403, edam:operation_2492 ; sc:name "SAMNetWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fraenkel-nsf.csbi.mit.edu/samnetweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:34849586" ; sc:description "Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks." ; sc:featureList edam:operation_0478, edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "sAMP-PFPDeep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WaqarHusain/sAMP-PFPDeep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3050, edam:topic_3299 ; sc:citation ; sc:description """method for quantifying geographic sampling biases in species distribution data. Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "sampbias" ; sc:url "https://github.com/azizka/sampbias" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3306, edam:topic_3534 ; sc:citation ; sc:description "Single Amino acid Mutation binding free energy change of Protein–DNA Interaction." ; sc:featureList edam:operation_0248 ; sc:name "SAMPDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.clemson.edu/SAMPDI/" ; biotools:primaryContact "Emil Alexov" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1464 ; sc:encodingFormat edam:format_1476 ; sc:name "DNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:34343273" ; sc:description "SAMPDI-3D uses a gradient boosting decision tree machine learning algorithm with features as physicochemical properties, structure of mutation site and protein-DNA interactions to predict the change of binding free energy." ; sc:featureList edam:operation_0331, edam:operation_3900, edam:operation_3903 ; sc:isAccessibleForFree true ; sc:name "SAMPDI-3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://compbio.clemson.edu/SAMPDI-3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3407, edam:topic_3520, edam:topic_3922 ; sc:citation , , "pubmed:33749263" ; sc:description """Discovery of protein modifications using high resolution differential mass spectrometry proteomics. 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SQL-like query language for the SAM/BAM file format.""" ; sc:featureList edam:operation_0224, edam:operation_0335, edam:operation_3695 ; sc:license "MIT" ; sc:name "SamQL" ; sc:url "https://github.com/maragkakislab/samql/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0625, edam:topic_0634, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC9252818", "pubmed:35524573" ; sc:description "SAMS is a database and phenotyping tool for precision medicine. Physicians can enter clinical signs from the Human Phenotype Ontology as well complete diagnoses, and patients can be involved by sharing the symptoms they encounter." ; sc:featureList edam:operation_2421, edam:operation_3559 ; sc:isAccessibleForFree true ; sc:name "SAMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.genecascade.org/SAMS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308 ; sc:citation ; sc:description "The purpose of this pipeline is to handle beginning-to-end metatranscriptome analysis. 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It provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.""" ; sc:featureList edam:operation_0226, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SAMSA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://transcript.github.io/samsa2/" ; biotools:primaryContact "Danielle G. LemayEmail author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Lightweight SAM/BAM file viewer that makes visually exploring NGS data intuitively. It uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ features like polarity from as many files as you like. The paging-friendly binary file layout makes it feasible to browse data sets far larger than the system's available RAM." ; sc:featureList edam:operation_0337, edam:operation_3198 ; sc:license "AGPL-3.0" ; sc:name "Samscope" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://samscope.dna.bio.keio.ac.jp/" ; biotools:primaryContact "Admin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation ; sc:description "Solver for sample sequence selection from large DNA datasets for quorum planted motif search" ; sc:featureList edam:operation_0238 ; sc:name "SamSelect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/qyu071/samselect" ; biotools:primaryContact "Hongwei Huo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC2923634", "pubmed:20667133" ; sc:description "Given a matrix of coordinates, this tool constructs the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find and combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample." ; sc:featureList edam:operation_3214 ; sc:license "GPL-2.0" ; sc:name "SamSPECTRAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SamSPECTRAL.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation "pubmed:21088025" ; sc:description "Efficient C program for displaying statistics of large sequence files." ; sc:featureList edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "SAMStat" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://samstat.sourceforge.net/#usage" ; biotools:primaryContact "Timo Lassmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26419425" ; sc:description "Applying the LIBSVM, a package of support vector machine, this tool was developed to correctly detect and filter the misaligned reads of SAM format. Such filtration can reduce false positives in alignment and the following variant analysis." ; sc:featureList edam:operation_2945, edam:operation_3187 ; sc:name "SAMSVM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/samsvm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3071, edam:topic_3300 ; sc:citation , "pmcid:PMC7771161", "pubmed:33552471" ; sc:description """Establishing the South Australian Macrobenthic Traits (SAMT) database. The South Australian Macrobenthic Traits. SAMT is an R package that contains different functions to manipulate and analyse trait information of marine macrobenthic fauna (SAMT database).""" ; sc:featureList edam:operation_3460 ; sc:name "SAMT" ; sc:url "https://github.com/OrlandoLam/SAMT" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572, edam:format_2573, edam:format_3462 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3168, edam:topic_3325 ; sc:citation , , , "pmcid:PMC2723002", "pmcid:PMC3198575", "pmcid:PMC7931819", "pubmed:19505943", "pubmed:21903627", "pubmed:33590861" ; sc:contributor "Richard Durbin" ; sc:description "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods." ; sc:featureList edam:operation_0227, edam:operation_0335, edam:operation_0337, edam:operation_1812, edam:operation_3096, edam:operation_3695, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SAMtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Wellcome Sanger Institute" ; sc:softwareHelp , , ; sc:softwareVersion "1.0", "1.1", "1.10", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.16.1", "1.17", "1.18", "1.19", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Wellcome Sanger Institute" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , ; sc:description "Uses the samtools view command in SAMTools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region." ; sc:featureList edam:operation_3695 ; sc:name "samtools_filter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.19" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , , ; sc:description "Simple statistics calculation on BAM files." ; sc:featureList edam:operation_0236 ; sc:name "samtools_flagstat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation , , ; sc:description "Run the samtools idxstats command in the SAMtools toolkit." ; sc:featureList edam:operation_2429 ; sc:name "samtools_idxstats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , , ; sc:description "Slice BAM by provided regions." ; sc:featureList edam:operation_0232 ; sc:name "samtools_slice_bam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.1" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3168 ; sc:citation , , ; sc:description "This tool uses the SAMTools toolkit to produce an indexed BAM file based on a sorted input SAM file." ; sc:featureList edam:operation_0335 ; sc:name "samtools_sort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.18" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2814 ; sc:citation "pubmed:20127263" ; sc:description "An algorithm for the alignment of two proteins. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring, geometrically compatible aligned fragment pairs (AFPs). The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments." ; sc:featureList edam:operation_0295 ; sc:name "SANA" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://doc.aporc.org/wiki/SANA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3524 ; sc:citation ; sc:description "Simulated annealing far outperforms many other search algorithms for biological network alignment." ; sc:featureList edam:operation_2497 ; sc:name "SANA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sana.ics.uci.edu/" ; biotools:primaryContact "Wayne B. Hayes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_2258, edam:topic_3050, edam:topic_3336 ; sc:citation , "pmcid:PMC8097257", "pubmed:33952332" ; sc:description "South African Natural Compounds Database (SANCDB) is the sole and a fully referenced database of natural chemical compounds of South African biodiversity." ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3891, edam:operation_3938 ; sc:name "SANCDB" ; sc:url "https://sancdb.rubi.ru.ac.za/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2091 ; sc:name "Accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "A web resource for interrogating public shotgun metagenome datasets" ; sc:featureList edam:operation_0337, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:name "Sandpiper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sandpiper.qut.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0736, edam:topic_3301 ; sc:citation ; sc:description "Specificity of AdenylatioN Domain Prediction Using Multiple Algorithms." ; sc:featureList edam:operation_0246 ; sc:license "GPL-3.0" ; sc:name "SANDPUMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/chevrm/sandpuma" ; biotools:primaryContact "Marc G. Chevrette", "Marnix H. Medema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_3168 ; sc:citation ; sc:description """sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R. This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads.""" ; sc:featureList edam:operation_0452, edam:operation_3192, edam:operation_3203 ; sc:license "MIT" ; sc:name "sangeranalyseR" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/sangeranalyseR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC4525701", "pubmed:25160973" ; sc:description "This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms." ; sc:featureList edam:operation_3203 ; sc:license "GPL-2.0" ; sc:name "sangerseqR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sangerseqR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3365, edam:topic_3474 ; sc:citation , "pmcid:PMC7924704", "pubmed:33816922" ; sc:description "GoSAN is the discrete-event based simulator with reinforcement learning support. It is a storage infrastructure simulator with reinforcement learning support." ; sc:featureList edam:operation_2426, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "SANgo" ; sc:url "https://github.com/HSE-LAMBDA/sango" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082 ; sc:citation "pubmed:22434533" ; sc:description "A web server for prediction of protein solvent accessibility by nearest neighbor method." ; sc:featureList edam:operation_0384, edam:operation_2479 ; sc:name "Sann" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lee.kias.re.kr/~newton/sann/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3474, edam:topic_3500, edam:topic_3512 ; sc:citation , "pubmed:31904817" ; sc:description """a deep learning method for identifying Poly(A) signals. Polyadenylation plays a regulatory role in transcription. The recognition of polyadenylation signal (PAS) motif sequence is an important step in polyadenylation. In the past few years, some statistical machine learning-based and deep learning-based methods have been proposed for PAS identification. Although these methods predict PAS with success, there is room for their improvement on PAS identification.""" ; sc:featureList edam:operation_0239, edam:operation_0428, edam:operation_0440 ; sc:name "SANPolyA" ; sc:url "https://github.com/yuht4/SANPolyA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1919 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1919 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_3475 ; sc:name "Phylogenetic data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3272 ; sc:encodingFormat edam:format_1910 ; sc:name "Species tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3293 ; sc:citation , "pmcid:PMC7137503", "pubmed:32280365" ; sc:description """SANS is a freely available command line tool for phylogenetic reconstruction. It is alignment- and reference-free, and accepts (multiple) FASTA or FASTQ files containing complete genomes, assembled contigs, or raw reads as input. Sequence segments (in terms of k-mers) that are shared by a set of genomes are used as indicators for phylogenetic splits. Splits are combined, weighted, filtered and output in tab separated format or Newick format. They can visualized as a phylogenetic tree or network using existing tools such as SplitsTree. SANS is implemented in C++.""" ; sc:featureList edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SANS" ; sc:provider "Bielefeld University", "Genome Informatics" ; sc:softwareHelp ; sc:url "https://gitlab.ub.uni-bielefeld.de/gi/sans" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3510 ; sc:citation "pubmed:25855811" ; sc:description "This tool takes a protein sequence as input and returns a set of similar sequences from Uniprot databases." ; sc:featureList edam:operation_0346 ; sc:name "SANSparallel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625 ; sc:citation , "pmcid:PMC4161294", "pubmed:25210953" ; sc:description "This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode)." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "SANTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SANTA.html" ; biotools:primaryContact "Alex J. Cornish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444, edam:topic_3474 ; sc:citation , "pmcid:PMC8292498", "pubmed:34283328" ; sc:description "SANTIA is a Matlab-based open-source toolbox for artifact detection and removal from extracellular neuronal signals. Neuronal signals generally represent activation of the neuronal networks and give insights into brain functionalities. They are considered as fingerprints of actions and their processing across different structures of the brain. These recordings generate a large volume of data that are susceptible to noise and artifacts. Therefore, the review of these data to ensure high quality by automatically detecting and removing the artifacts is imperative. Toward this aim, this work proposes a custom-developed automatic artifact removal toolbox named, SANTIA (SigMate Advanced: a Novel Tool for Identification of Artifacts in Neuronal Signals). Developed in Matlab, SANTIA is an open-source toolbox that applies neural network-based machine learning techniques to label and train models to detect artifacts from the invasive neuronal signals known as local field potentials." ; sc:name "SANTIA" ; sc:url "https://github.com/IgnacioFabietti/SANTIAtoolbox" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC7655839", "pubmed:33173130" ; sc:description """Enhancing protein backbone angle prediction by using simpler models of deep neural networks. This project provides the programs and related files of the Simple Angle Predictor (SAP) that predicts protein backbone angles phi, psi, theta, and tau.""" ; sc:featureList edam:operation_0249, edam:operation_0267, edam:operation_0321, edam:operation_0476, edam:operation_0479 ; sc:name "SAP" ; sc:url "https://gitlab.com/mahnewton/sap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0108, edam:topic_0736, edam:topic_3474, edam:topic_3542 ; sc:citation , "pmcid:PMC8728911", "pubmed:34983370" ; sc:description "Secondary structure specific simpler prediction models for protein backbone angles." ; sc:featureList edam:operation_0249, edam:operation_0267, edam:operation_0479, edam:operation_0502, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SAP4SS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/mahnewton/sap4ss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_3071 ; sc:citation , "pubmed:33892308" ; sc:description "SAPdb (Self Assembling Peptides Database) is a database of short peptides and the corresponding nanostructures formed by self-assembly." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3646 ; sc:name "SAPdb" ; sc:url "https://webs.iiitd.edu.in/raghava/sapdb" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3379, edam:topic_3421 ; sc:citation , "pmcid:PMC10296656", "pubmed:37370744" ; sc:description "Web-based application for peritoneal surface area quantification." ; sc:featureList edam:operation_0387, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "SAPESUCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://taja.shinyapps.io/sapesuca-app/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Tool developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics." ; sc:featureList edam:operation_0224, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "sapFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sapFinder.html" ; biotools:primaryContact "Bo Wen", "Shaohang Xu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2298 ; sc:name "Gene ID (HGNC)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0749, edam:topic_3320, edam:topic_3510, edam:topic_3512 ; sc:citation , "pmcid:PMC9229502", "pubmed:35751026" ; sc:description "A webserver for the identification of alternative protein features." ; sc:featureList edam:operation_0264, edam:operation_0303, edam:operation_0433, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SAPFIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-scottgroup.med.usherbrooke.ca/sapfir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC8078219", "pubmed:33968376" ; sc:description "SAPHIR (Shiny Analytical Plot of Histological Image Results) is a Shiny application to analyze tissue section images." ; sc:featureList edam:operation_2940, edam:operation_2943, edam:operation_3553, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SAPHIR" ; sc:url "https://github.com/elodiegermani/SAPHIR" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0780, edam:topic_3474 ; sc:citation ; sc:description """SAPLING: Suffix Array Piecewise Linear INdex for Genomics. A method for achieving faster suffix array queries compared to binary search.""" ; sc:featureList edam:operation_2421, edam:operation_3198, edam:operation_3211 ; sc:license "MIT" ; sc:name "Sapling" ; sc:url "https://github.com/mkirsche/sapling" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1936, edam:format_2305, edam:format_3255 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1927, edam:format_1929, edam:format_1936, edam:format_3255 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3307, edam:topic_3391 ; sc:citation ; sc:description "SAPP is a Semantic Annotation Platform with Provenance and is designed on the basis of Semantic Web and is FAIR by design. The platform and corresponding modules allows you to annotate genomes of various qualities with the full chain of provenance. Resulting is a RDF genome data model which you can query and analyse using SPARQL. Various modules are available which allows you to annotate, visualise and export to various formats." ; sc:featureList edam:operation_0224, edam:operation_0233, edam:operation_0338, edam:operation_0362, edam:operation_0436, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SAPP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sapp.gitlab.io" ; biotools:primaryContact "Jasper Koehorst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3474, edam:topic_3576 ; sc:citation , "pmcid:PMC7510298", "pubmed:32962628" ; sc:description """a neural network based classifier for σ70 promoter prediction in Pseudomonas. Sequence Analyser for the Prediction of Prokaryote Homology Inferred Regulatory Elements. For sequences longer than 5k basepairs, it is advisable to download SAPPHIRE and run it locally.""" ; sc:featureList edam:operation_0440, edam:operation_2437 ; sc:name "SAPPHIRE" ; sc:url "http://www.biosapphire.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification." ; sc:license "Apache-2.0" ; sc:name "Sapporo-service" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "1.4.8" ; sc:url "https://github.com/sapporo-wes/sapporo-service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "A web application for managing and executing WES services." ; sc:license "Apache-2.0" ; sc:name "Sapporo-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/sapporo-wes/sapporo-web" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3343, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC9326022", "pubmed:35910729" ; sc:description "An Expert System for Screening Chemicals Against Structural Alerts." ; sc:featureList edam:operation_0303, edam:operation_0337, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "SApredictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sapredictor.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3053 ; sc:author "Andrew Beck [aut]", "Benjamin Haibe-Kains [aut]", "Daniel Schmolze [aut", "cre]" ; sc:citation ; sc:description "Functions implementing the Significance Analysis of Prognostic Signatures method that provides a robust method for identifying biologically significant gene sets associated with patient survival. 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sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "SAS is an integrated system of software that enables you to do everything from accessing data across multiple sources to performing sophisticated analyses and delivering information across your organization. SAS foundation products are available as individual software modules, and they serve as the foundation for SAS solutions." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "SAS" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://www.sas.com/en_us/software/foundation.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:citation , "pubmed:37022274" ; sc:description "Spatial-aware self-attention mechanism for building protein 3D structure directly from inter-residue distances." ; sc:featureList edam:operation_0476, edam:operation_0477, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SASA-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gongtiansu/SASA-Net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation , "pubmed:32805010" ; sc:description """Simulated Annealing Single Cell inference (SASC) tool -- cancer progression inference. SASC is a new model and a robust framework based on Simulated Annealing for the inference of cancer progression from the SCS data. The main objective is to overcome the limitations of the Infinite Sites Assumption by introducing a version of the k-Dollo parsimony model which indeed allows the deletion of mutations from the evolutionary history of the tumor.""" ; sc:featureList edam:operation_3227, edam:operation_3435, edam:operation_3478 ; sc:license "MIT" ; sc:name "SASC" ; sc:url "https://github.com/sciccolella/sasc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3053 ; sc:citation "pubmed:25934800" ; sc:description "Software to identify regions of interest with a higher than expected number of mutations than the near-by regions." ; sc:featureList edam:operation_3202 ; sc:name "SASE-hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sjdlab.org/resources/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Gene segregation and linkage analysis in breeding population." ; sc:featureList edam:operation_0283 ; sc:name "SASGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3361, edam:topic_3810 ; sc:citation , "pmcid:PMC7327187", "pubmed:32656159" ; sc:description """Validation of "sasLM," an R package for linear models with type III sum of squares. This is a core implementation of 'SAS' procedures for linear models - GLM, REG, and ANOVA. Some packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "sasLM" ; sc:url "http://CRAN.R-project.org/package=sasLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_2640 ; sc:citation , "pubmed:33416828" ; sc:description "A Method for Subtype Analysis with Somatic Mutations." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:name "SASOM" ; sc:url "https://github.com/rksyouyou/SASOM-pkg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0622, edam:topic_3673 ; sc:citation , "pubmed:35385055" ; sc:description "Analysis of missing genomic regions in draft genomes of prokaryotes." ; sc:featureList edam:operation_0310, edam:operation_1812, edam:operation_3472, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SASpector" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LoGT-KULeuven/SASpector" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3055, edam:topic_3056 ; sc:citation "pubmed:17602177" ; sc:description "A SAS computer program for analysis of quantitative genetic data." ; sc:featureList edam:operation_0282 ; sc:name "SASQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275 ; sc:citation ; sc:description "Set of software routines that can be used to analyze SAXS data, build molecular shapes from SAXS data and further refine existing atomic models." ; sc:featureList edam:operation_0322 ; sc:isAccessibleForFree true ; sc:name "SASTBX" ; sc:operatingSystem "Mac" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://sastbx-document.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0084, edam:topic_3293 ; sc:citation "pubmed:20430824" ; sc:description "Web server for simultaneous estimation of protein multiple sequence alignments and phylogenetic trees. Input is a FASTA file of sequences, and output is a phylogenetic tree and multiple sequence alignment." ; sc:featureList edam:operation_0292, edam:operation_0323, edam:operation_0492, edam:operation_0499 ; sc:isAccessibleForFree true ; sc:name "SATCHMO-JS" ; sc:url "http://phylogenomics.berkeley.edu/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0114, edam:topic_0121, edam:topic_0623, edam:topic_0749 ; sc:citation , "pubmed:36869669" ; sc:description "Identification and characterization of thousands of bacteriophage satellites across bacteria." ; sc:featureList edam:operation_0314, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "SatelliteFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/fmareuil/satellitefinder/SatelliteFinder/0.9" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0199, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation "pubmed:15949044" ; sc:description "Database for the identification and prioritization of satellite repeats in disease association studies." ; sc:featureList edam:operation_0237, edam:operation_0314, edam:operation_0379, edam:operation_0380, edam:operation_3202 ; sc:name "Satellog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://satellog.bcgsc.ca/" ; biotools:primaryContact "Perseus I Missirlis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "An automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SATINN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/conradlab/SATINN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:27166378" ; sc:description "A pipeline that uses Evolutionary Placement Algorithm (EPA) to identify taxonomically mislabeled sequences and suggest corrections." ; sc:featureList edam:operation_3195 ; sc:name "SATIVA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/amkozlov/sativa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description """A Self-Attention Model for Inferring Cooperativity between Regulatory Features. SATORI is a Self-ATtentiOn based deep learning model to capture Regulatory element Interactions in genomic sequences. It can be used to infer a global landscape of interactions in a given genomic dataset, without a computationally-expensive post-processing step.""" ; sc:featureList edam:operation_0239, edam:operation_0438, edam:operation_3891 ; sc:license "MIT" ; sc:name "SATORI" ; sc:url "https://github.com/fahadahaf/SATORI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC4702810", "pubmed:26527728" ; sc:description "SATPdb is a database of structurally annotated therapeutic peptides curated from twenty public domain peptide databases and two datasets." ; sc:featureList edam:operation_2945 ; sc:name "satpdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/satpdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "A SOLiD assembly translation program." ; sc:featureList edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "SATRAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "http://satrap.cribi.unipd.it/cgi-bin/satrap.pl" ; biotools:primaryContact "Davide Campagna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2269, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications. satuRn is a highly performant and scalable method for performing differential transcript usage analyses.""" ; sc:featureList edam:operation_0264, edam:operation_2436, edam:operation_3223, edam:operation_3658, edam:operation_3800 ; sc:name "satuRn" ; sc:url "https://github.com/statOmics/satuRn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8153189", "pubmed:34046647" ; sc:description "SAU-Net is a unified network for cell counting in 2D and 3D microscopy images." ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3925 ; sc:name "SAU-Net" ; sc:url "https://github.com/mzlr/sau-net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_2258, edam:topic_3168 ; sc:citation , "pmcid:PMC9917004", "pubmed:36768784" ; sc:description "A Freely Available Web Application for the Prediction of Pathogenic Amino Acid Substitutions for Monogenic Hereditary Diseases Studied in Newborn Screening." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "SAV-Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.way2drug.com/SAV-Pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3168 ; sc:citation "pubmed:22638571" ; sc:description "Allows for visualization of genomic data. Developed for visualizing high throughput (next generation) sequencing data, it can also be used to visualize virtually any genome-based sequence, point, interval, or continuous dataset." ; sc:featureList edam:operation_3196, edam:operation_3208 ; sc:name "Savant Genome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.savantbrowser.com" ; biotools:primaryContact "Savant Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3336, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC7987121", "pubmed:33757425" ; sc:description "SAveRUNNER (Searching off-lAbel dRUg aNd NEtwoRk) is an R-based tool for drug repurposing." ; sc:license "AGPL-3.0" ; sc:name "SAveRUNNER" ; sc:softwareHelp ; sc:url "https://github.com/sportingCode/SAveRUNNER" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0659, edam:topic_3170 ; sc:citation "pubmed:22492627" ; sc:description "SAVoR webserver allows the user to visualize RNA-seq data and other genomic annotations on RNA secondary structures. SAVoR is designed to help researchers visualize sequencing data in the context of RNA secondary structures. Useful if you want to see the distribution of smRNA-seq reads along a microRNA precursor, how a set of SNPs might impact RNA structure, or in a control vs. treatment sequencing experiments you would like to see regions of enrichment along an RNA structure." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "SAVoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tesla.pcbi.upenn.edu/savor" ; biotools:primaryContact "SAVoR Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots." ; sc:featureList edam:operation_2403, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "savR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/savR.html" ; biotools:primaryContact "R. Brent Calder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315 ; sc:citation , "pmcid:PMC7363216" ; sc:description """A Tool for Safety Analysis of Weakly-Hard Systems. The virtual machine where the tool is ready to run can be found at https://www.csie.ntu.edu.tw/~r08922054/SAW.ova. To reproduce the results of all the examples in the paper, please follow the instruction in ./artifact_evaluation_readme.txt.""" ; sc:name "SAW" ; sc:url "https://github.com/551100kk/SAW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation , "pmcid:PMC5541358", "pubmed:28808439" ; sc:description "SAXS4COLL is an integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems." ; sc:featureList edam:operation_3443 ; sc:license "Other" ; sc:name "SAXS4COLL" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://figshare.com/s/7be18c69b8b0bd113db7" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:22261066" ; sc:description "A new algorithm to combine small-angle x-ray scattering data and threading for high-resolution protein structure determination." ; sc:featureList edam:operation_0303, edam:operation_0474 ; sc:name "SAXSTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/SAXSTER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24532721" ; sc:description "A bioinformatics tool for searching of different types of long repeats in sequences comparable by size with chromosomes." ; sc:featureList edam:operation_0379 ; sc:name "SBARS" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://mpyatkov.github.io/sbars/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0602, edam:topic_0821, edam:topic_3068 ; sc:citation , "pubmed:36111865" ; sc:description "Biochemical Reaction Networks with Definable Degree Distributions." ; sc:featureList edam:operation_1781, edam:operation_3431, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBbadger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sys-bio/SBbadger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0160, edam:topic_0623 ; sc:citation "pubmed:16343337", "pubmed:16361270", "pubmed:16845078" ; sc:description "Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality." ; sc:featureList edam:operation_0292, edam:operation_0447, edam:operation_0492 ; sc:name "SBC tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://msa.cgb.ki.se/cgi-bin/msa.cgi" ; biotools:primaryContact "Oliver Frings" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269, edam:topic_3070, edam:topic_3299 ; sc:citation "pubmed:24027418" ; sc:description "Systems Biology and Evolution Toolbox is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc.), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc." ; sc:featureList edam:operation_2238 ; sc:name "SBEToolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/biocoder/SBEToolbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0108, edam:topic_0602, edam:topic_2259, edam:topic_3407 ; sc:citation , "pmcid:PMC7756621", "pubmed:32568733" ; sc:description "The aim is to provide the most accurate translation for metabolic networks between GraphML (yEd) and SBGN-ML Process Description file formats. Translation in both direction is possible. This project should ultimately be integrated into the SBFC." ; sc:featureList edam:operation_0337, edam:operation_0533, edam:operation_3096 ; sc:license "GPL-2.0" ; sc:name "SBGN" ; sc:url "http://sbgn.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0749, edam:topic_2259, edam:topic_3407 ; sc:citation ; sc:description """SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. SBGN Bricks aims at facilitating the development of new tools for the template-based construction of molecular networks and for their semantic annotation. It is also intended as a teaching aid for those learning SBGN and systems biology. SBGN bricks are building blocks representing basic biological patterns. They can be used for assembly into different kinds of networks (metabolic, regulatory networks).""" ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_2429 ; sc:name "SBGN bricks" ; sc:url "http://sbgnbricks.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3068 ; sc:citation , "pubmed:31070720" ; sc:description "TikZ library to draw Systems Biology Graphical Notation (SBGN) maps." ; sc:featureList edam:operation_0573, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sbgntikz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Adrienrougny/sbgntikz/" ; biotools:primaryContact "Adrien Rougny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3407, edam:topic_3518 ; sc:citation ; sc:description "SBGNview is an R package, which adopts Systems Biology Graphical Notation (SBGN) and greatly extends the Pathview package by supporting multiple major pathway databases beyond KEGG." ; sc:featureList edam:operation_0533, edam:operation_0573, edam:operation_1812, edam:operation_3926 ; sc:name "SBGNview" ; sc:url "https://github.com/datapplab/SBGNview" ; biotools:primaryContact "Weijun Luo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:author "Nan Xiao ", "Tengfei Yin " ; sc:citation ; sc:description "R client for Seven Bridges Genomics API." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "sbgr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioConductor" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://www.bioconductor.org/packages/3.2/bioc/html/sbgr.html" ; biotools:primaryContact "Nan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_3542 ; sc:citation , "pmcid:PMC10589914", "pubmed:37796837" ; sc:description "SBILib Python library provides an integrated platform for the analysis of macromolecular structures and interactions. It combines simple 3D file parsing and workup methods with more advanced analytical tools. SBILib includes modules for macromolecular interactions, loops, super-secondary structures, and biological sequences, as well as wrappers for external tools with which to integrate their results and facilitate the comparative analysis of protein structures and their complexes. The library can handle macromolecular complexes formed by proteins and or nucleic acid molecules (i.e. DNA and RNA). It is uniquely capable of parsing and calculating protein super-secondary structure and loop geometry. We have compiled a list of example scenarios which SBILib may be applied to and provided access to these within the library." ; sc:featureList edam:operation_0249, edam:operation_0268, edam:operation_0303, edam:operation_0477, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBILib" ; sc:url "https://github.com/structuralbioinformatics/SBILib" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3375 ; sc:description "MATLAB tool for importing Ordinary Differential Equation models in the BerkeleyMadonna(TM) format into a SimBiology(R) model." ; sc:isAccessibleForFree true ; sc:name "sbioimportBerkeleyMadonna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/39719-sbioimportberkeleymadonna" ; biotools:primaryContact "Jeremy Huard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0821, edam:topic_2259 ; sc:citation ; sc:description "A Framework for Evaluating Quality of Annotations in Systems Biology Models." ; sc:featureList edam:operation_2422, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/woosubs/SBMate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2229, edam:topic_2640, edam:topic_3174 ; sc:citation , "pmcid:PMC7355247", "pubmed:32657385" ; sc:description """Identifying tumor clones in sparse single-cell mutation data. SBMClone is a tool that uses stochastic block model (SBM) inference methods to identify clonal structure (groups of cells that share groups of mutations) in low-coverage single-cell DNA sequencing data. While SBMClone was originally designed for single-nucleotide variants, it can also be applied to other types of mutations such as structural variants.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3432 ; sc:license "BSD-3-Clause" ; sc:name "SBMClone" ; sc:url "https://github.com/raphael-group/SBMClone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , ; sc:description "Project that develops and makes available a number of software resources in addition to the homonimous .org portal." ; sc:featureList edam:operation_2409, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "SBML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbml.org/Software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3474 ; sc:citation , "pmcid:PMC9889961", "pubmed:36661327" ; sc:description "Python interface for Systems Biology Markup Language (SBML) compatible hybrid modelling." ; sc:featureList edam:operation_0336, edam:operation_2426, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sbml2hyb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/r-costa/sbml2hyb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3068, edam:topic_3070 ; sc:citation "pubmed:19307240" ; sc:description "A tool to convert files in the System Biology Markup Language (SBML) format into LATEX files." ; sc:featureList edam:operation_0335, edam:operation_3434 ; sc:name "SBML2LATEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/sbml2latex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3372, edam:topic_3500 ; sc:citation , "pmcid:PMC9805581", "pubmed:36370074" ; sc:description "A python package to process and visualize SBML layout and render." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBMLDiagrams" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://github.com/sys-bio/SBMLDiagrams" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation ; sc:description "SBMLeditor is a portable (written in Java), low-level, tree-structured editor for SBML. It supports annotations and validation." ; sc:featureList edam:operation_2428 ; sc:name "SBMLeditor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0-b1" ; sc:url "http://www.ebi.ac.uk/compneur-srv/SBMLeditor.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3366 ; sc:citation , "pmcid:PMC5483284", "pubmed:28646877" ; sc:description "A web application that allows the integration of various data into a given SBML model. Accepted data cover common gene expression, proteomics or metabolomics data." ; sc:featureList edam:operation_3431 ; sc:name "SBMLmod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbmlmod.uit.no:8000/sbmlmod/" ; biotools:primaryContact "Ines Heiland" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation ; sc:description "This package contains a systems biology markup language (SBML) interface to R." ; sc:featureList edam:operation_2426 ; sc:license "GPL-2.0" ; sc:name "SBMLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.70.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SBMLR.html" ; biotools:primaryContact "Tomas Radivoyevitch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3068, edam:topic_3524 ; sc:citation , "pmcid:PMC7093077", "pubmed:32211200" ; sc:description """A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. SBMLsimulator is a fast, accurate, and easily usable program for dynamic model simulation and heuristic parameter optimization of models encoded in the Systems Biology Markup Language (SBML). For simulation it contains the Systems Biology Simulation Core Library, which has been benchmarked against the entire SBML Test Suite and all models from the Biomodels.net database. It includes a large collection of nature-inspired heuristic optimization procedures for efficient model calibration. SBMLsimulator provides an intuitive Graphical User Interface (GUI) and several command-line options to be suitable for large-scale batch processing and model calibration. SBMLsimulator runs on all platforms that provide a standard Java Virtual Machine and is based on the open-source library JSBML.""" ; sc:featureList edam:operation_2426, edam:operation_3927, edam:operation_3928 ; sc:name "SBMLsimulator" ; sc:url "http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsimulator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0821, edam:topic_2259, edam:topic_3292 ; sc:citation ; sc:description "Generates kinetic equations for biochemical networks according to context of each reaction." ; sc:featureList edam:operation_0334 ; sc:name "SBMLsqueezer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/" ; biotools:primaryContact "Andreas Dräger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3315 ; sc:citation ; sc:description "Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models." ; sc:featureList edam:operation_2426, edam:operation_3660, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBMLWebApp" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/TakahiroYamada/SBMLWebApp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3047, edam:topic_3343, edam:topic_3474 ; sc:citation , "pubmed:34242036" ; sc:description "Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_3927, edam:operation_4008, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBMolGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/clinfo/SBMolGen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_0736, edam:topic_3068, edam:topic_3306 ; sc:citation , "pubmed:34251801" ; sc:description "SBMOpenMM is a Python library to facilitate the creation of Structure Based Model simulations using the OpenMM library. It contains several methods that connect the structural information of a protein system with the necessary objects to aid in the creation of an SBM force field compatible with the OpenMM simulation engine." ; sc:featureList edam:operation_0244, edam:operation_2415, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SBMOpenMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/CompBiochBiophLab/sbm-openmm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3071 ; sc:citation ; sc:description "This ontology project goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling." ; sc:featureList edam:operation_2422 ; sc:name "SBO WS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/sbo/SBOWSLib/docwsdl/wsdldoc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3047, edam:topic_3398, edam:topic_3474, edam:topic_3895 ; sc:citation , "pmcid:PMC7516281", "pubmed:33015004" ; sc:description """The Synthetic Biology Open Language (SBOL) Version 3. The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings""" ; sc:featureList edam:operation_0310, edam:operation_3435 ; sc:name "SBOL" ; sc:softwareVersion "3.0" ; sc:url "https://github.com/SynBioDex/SBOLTestSuite/tree/master/SBOL3/multicellular" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3382, edam:topic_3895 ; sc:citation , "pubmed:34152132" ; sc:description "SBOLCavas is a web application for creation and editing of genetic constructs using the SBOL data and visual standard. SBOLCanvas allows a user to create a genetic design from start to finish, with the option to incorporate existing SBOL data from a SynBioHub repository." ; sc:featureList edam:operation_0337, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SBOLCanvas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sbolcanvas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3524 ; sc:citation ; sc:description "Allows mathematical modellers to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis." ; sc:featureList edam:operation_3762 ; sc:license "MIT" ; sc:name "SBpipe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://pdp10.github.io/sbpipe/" ; biotools:primaryContact "Piero Dallepezze" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0160 ; sc:citation , "pmcid:PMC5570206", "pubmed:28460065" ; sc:description "Structure-based genome mining and analysis of polyketide and non-ribosomal peptide biosynthetic pathways in chemical space." ; sc:featureList edam:operation_3280, edam:operation_3631, edam:operation_3803 ; sc:name "SBPKS2" ; sc:url "http://www.nii.ac.in/sbspks2.html" ; biotools:primaryContact "Debasisa Mohanty" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1046 ; sc:encodingFormat edam:format_3016, edam:format_3752 ; sc:name "Strain name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1353 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence motif" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0659, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC8500130", "pubmed:34606615" ; sc:description "An online service for somatic binding sequence annotation." ; sc:featureList edam:operation_0361, edam:operation_0445, edam:operation_3096, edam:operation_3227, edam:operation_3901 ; sc:isAccessibleForFree true ; sc:name "SBSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://innovebioinfo.com/Annotation/SBSA/SBSA.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3524, edam:topic_3569 ; sc:citation ; sc:description "Provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution." ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "Systems Biology Simulation Core Library" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://draeger-lab.github.io/SBSCL/" ; biotools:primaryContact "Andreas Dräger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2814 ; sc:citation "pubmed:20444870" ; sc:description "A webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of pharmaceutically important secondary metabolites." ; sc:featureList edam:operation_2406, edam:operation_2479 ; sc:name "SBSPKS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.nii.ac.in/~pksdb/sbspks/homepage.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_2815, edam:topic_2830, edam:topic_3512 ; sc:citation "pubmed:15215374" ; sc:description "Tool accompanying the NCBI&apos,s Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments." ; sc:featureList edam:operation_2928 ; sc:name "The SBT (Sequencing-based typing) interface " ; sc:url "http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2259, edam:topic_3070 ; sc:citation "pubmed:14683609" ; sc:description "An open source framework connecting heterogeneous software application components-written in diverse programming languages and running on different platforms-to communicate and use each others' capabilities via a fast binary encoded-message system." ; sc:featureList edam:operation_3562 ; sc:name "SBW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbw.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:27412087" ; sc:description "A Burrows–Wheeler transformation BWT based fast indexer/aligner specialized in parallelized indexing and searching for Next Generation Sequencing data." ; sc:featureList edam:operation_0292, edam:operation_2403, edam:operation_3211 ; sc:name "sBWT" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jhhung.github.io/sBWT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description "A topology preserving graph convolution network for clustering of single-cell RNA seq data" ; sc:featureList edam:operation_3432, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "sc-CGconv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Snehalikalall/CopulaGCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33961321" ; sc:description "SC-GAN is a tool for 3D self-attention conditional GAN with spectral normalization for multi-modal neuroimaging synthesis. SC-GAN was assessed for positron emission tomography (PET), Fractional anisotropy (FA) and mean diffusivity (MD) synthesis from tasks using T1w and FLAIR magnetic resonance images (MRI)." ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3927 ; sc:name "SC-GAN" ; sc:url "https://github.com/Haoyulance/SC-GAN" ; biotools:primaryContact "Haoyu Lan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3940 ; sc:citation , "pmcid:PMC7412809", "pubmed:32767996" ; sc:description """Integrative analyses of single-cell transcriptome and regulome using MAESTRO. MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. Benchmark codes used in MAESTRO paper. We provided the codes used in evaluating scATAC-seq clustering, automatic cell-type annotation, integration between scRNA-seq and scATAC-seq using different methods, and integration evaluation using different peak-RP model in this repository.""" ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3432, edam:operation_3799, edam:operation_3933 ; sc:license "GPL-3.0" ; sc:name "sc-MAESTRO" ; sc:url "http://github.com/liulab-dfci/MAESTRO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "An Entropy Based Feature Selection- Application on Single cell RNA Sequence Data." ; sc:featureList edam:operation_3432, edam:operation_3936 ; sc:name "sc-REnF" ; sc:url "https://github.com/Snehalikalall/sc-REnF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0769, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "SC1 (scRNA-Seq analysis pipeline) is a tool for interactive web-based single cell RNA-seq data analysis." ; sc:featureList edam:operation_0313, edam:operation_2938, edam:operation_3223, edam:operation_3557, edam:operation_3891 ; sc:name "SC1" ; sc:url "https://sc1.engr.uconn.edu" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Computational cell cycle analysis of single cell RNA-Seq data. SC1: scRNA-Seq Analysis Pipeline.""" ; sc:featureList edam:operation_1812, edam:operation_2495, edam:operation_3432, edam:operation_3454, edam:operation_3891 ; sc:name "SC1CC" ; sc:url "https://sc1.engr.uconn.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3170, edam:topic_3308, edam:topic_3517 ; sc:citation , "pubmed:33010177" ; sc:description """a manually curated database of single-cell transcriptome for human diseases. The transcriptome plays a crucial role in the maintenance of cell identity and the spatiotemporal specificity in the process of cell differentiation, which consequently produces a profound impact in the formation of any organism and regulatory complex.""" ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_3435 ; sc:name "SC2disease" ; sc:url "http://easybioai.com/sc2disease/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3360 ; sc:citation ; sc:description "A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data." ; sc:featureList edam:operation_3223, edam:operation_3557, edam:operation_3935, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "SC2MeNetDrug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fuhaililab.github.io/sc2MeNetDrug/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC9835482", "pubmed:36576008" ; sc:description "A scaffold-based two-step molecule generator with variational autoencoder and transformer." ; sc:featureList edam:operation_0479, edam:operation_3216, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Sc2Mol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhiruiliao/Sc2Mol" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , "pmcid:PMC9387141", "pubmed:35980286" ; sc:description "Sepsis single-cell whole gene expression database." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "SC2sepsis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rjh-sc2sepsis.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , "pmcid:PMC5410170", "pubmed:28346451" ; sc:description "A tool for unsupervised clustering and analysis of single cell RNA-Seq data." ; sc:featureList edam:operation_0291, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "SC3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.11" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SC3.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9743492", "pubmed:36503522" ; sc:description "Efficient scaling of single cell consensus clustering to millions of cells." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SC3s" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hemberg-lab/sc3s/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0121, edam:topic_3170 ; sc:citation ; sc:description "> HOMEPAGE MISSING! | a unifying tool based on autoencoders for the analysis of single-cell RNA sequencing data | Autoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of single-cell RNA sequencing (scRNA-Seq) data. However, their integration with the common scRNA-Seq bioinformatics pipelines still poses a challenge. Here, we introduce scAEspy, a unifying tool that embodies five of the most advanced AEs and different loss functions, including two novel AEs that we developed. scAEspy allows the integration of data generated using different scRNA-Seq platforms. We benchmarked scAEspy against principal component analysis (PCA) on five public datasets, showing that our new AEs outperform the existing solutions, achieving more than 20% increase of the Rand Index in the identification of cell clusters" ; sc:featureList edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:name "scAEspy" ; sc:url "https://gitlab.com/cvejic-group/scaespy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc:description """a comprehensive workbench for single-cell chromatin accessibility sequencing data. single cell ATAC-seq processing pipeline. scATAC-pro incorporates two main steps, preprocessing and downstream analysis. The preprocessing step takes raw fastq files as input and outputs peak-by-cell count matrix. It consists of demultiplexing, adaptor trimming, mapping, peak calling, cell calling, signal generating and quality controlling modules. The downstream analysis is comprised of dimension reduction, cell clustering, differential accessibility analysis, TF motif enrichment analysis and footprinting analysis. We provide flexible options for most of the modules. A comprehensive pipeline for single cell ATAC-seq data processing and analysis""" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3436 ; sc:name "scATAC-pro" ; sc:url "https://github.com/tanlabcode/scATAC-pro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0204, edam:topic_0769, edam:topic_3295, edam:topic_3308 ; sc:citation , "pmcid:PMC6859644", "pubmed:31739806" ; sc:description """Assessment of computational methods for the analysis of single-cell ATAC-seq data. ATAC-seq Data Standards and Prototype Processing Pipeline – ENCODE. ATAC-seq Data Standards and Prototype Processing Pipeline. The Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) experiment provides genome-wide profiles of chromatin accessibility. Briefly, the ATAC-seq method works as follows: loaded transposase inserts sequencing primers into open chromatin sites across the genome, and reads are then sequenced. The ends of the reads mark open chromatin sites. In its current form, the ATAC-seq pipeline is a prototype and will likely undergo substantial change within the next year""" ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3222, edam:operation_3432, edam:operation_3891 ; sc:name "scATAC-seq" ; sc:url "https://www.encodeproject.org/atac-seq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6693154", "pubmed:31412909" ; sc:description "a tool for alignment, integration, and rare cell identification from scRNA-seq data | An alignment and integration method for single cell genomics | An unsupervised deep learning method for data alignment, integration and estimation of per-cell differences in -omic data (e.g. gene expression) across datasets (conditions, tissues, species). See Johansen and Quon (2019) for more details | DimensionReduction, NeuralNetwork, SingleCell, Software, Transcriptomics" ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "scAlign" ; sc:url "https://bioconductor.org/packages/release/bioc/html/scAlign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6734238", "pubmed:31500668" ; sc:description "modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data | A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq | This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis | Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data | Single cell Binary Factor Analysis (scBFA) and Binary PCA - These are tools for performing dimensionality reduction in large scRNA-seq datasets, as described in: Li, R., Quon, G. (2018) Gene detection models outperform gene expression for large-scale scRNA-seq analysis. bioRxiv doi: https://doi.org/10.1101/454629" ; sc:featureList edam:operation_2495, edam:operation_3799, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "scBFA" ; sc:url "https://bioconductor.org/packages/devel/bioc/html/scBFA.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3324 ; sc:author "Amit Frishberg", "Irit Gat-Viks", "Naama Peshes-Yaloz" ; sc:citation , "pubmed:30886410" ; sc:description "R pacakge containing a repository of methods aiming to understand complex processes related to the cellular variability within tissues." ; sc:featureList edam:operation_3196, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "scBio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.1.5" ; sc:url "https://github.com/amitfrish/scBio/blob/master/README.md" ; biotools:primaryContact "Amit Frishberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6929272", "pubmed:31870278" ; sc:description "Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis." ; sc:featureList edam:operation_2939, edam:operation_3432, edam:operation_3680 ; sc:name "scCCESS" ; sc:url "https://github.com/gedcom/scCCESS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """a package for automated processing of single cell RNA-seq data in cancer. The scCancer package focuses on processing and analyzing droplet-based scRNA-seq data for cancer research. Except basic data processing steps, this package takes several special considerations for cancer-specific features""" ; sc:featureList edam:operation_2428, edam:operation_3223, edam:operation_3659 ; sc:name "scCancer" ; sc:url "http://lifeome.net/software/sccancer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:31557285" ; sc:description "detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data | Detection and visualization of dynamic alternative polyadenylation | scDAPA - a tool for detection and visualization of dynamic alternative polyadenylation from scRNA-seq data" ; sc:featureList edam:operation_0428, edam:operation_3501 ; sc:name "scDAPA" ; sc:url "https://scdapa.sourceforge.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_3308, edam:topic_3678 ; sc:citation , "pmcid:PMC6612870", "pubmed:31510652" ; sc:description "A statistical simulator scDesign for rational scRNA-seq experimental design | scDesign: a statistical simulator for rational scRNA-seq experimental design | Wei Vivian Li, Jingyi Jessica Li 2019-03-18" ; sc:featureList edam:operation_3557, edam:operation_3799, edam:operation_3891 ; sc:name "scDesign" ; sc:url "https://github.com/Vivianstats/scDesign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC6413955", "pubmed:30818329" ; sc:description "Suite of MATLAB functions to perform a single-cell Flux Balance Analysis (scFBA)" ; sc:featureList edam:operation_2495, edam:operation_3660, edam:operation_3803 ; sc:isAccessibleForFree true ; sc:name "scFBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BIMIB-DISCo/scFBA" ; biotools:primaryContact "BIMIB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0769, edam:topic_3170, edam:topic_3344 ; sc:citation , "pubmed:31697351" ; sc:description """a Matlab toolbox for single-cell RNA sequencing data analysis. scGEAToolbox: Matlab toolbox for single-cell gene expression analyses. scGEAToolbox - a Matlab toolbox for single-cell RNA-seq data analyses. Results: I developed scGEAToolbox—a Matlab toolbox for scRNA-seq data analysis. It contains a comprehensive set of functions for data normalization, feature selection, batch correction, imputation, cell clustering, trajectory/pseudotime analysis, and network construction, which can be combined and integrated to building custom workflow. While most of the functions are implemented in native Matlab, wrapper functions are provided to allow users to call the “third-party” tools developed in Matlab or other languages. Furthermore, scGEAToolbox is equipped with sophisticated graphical user interfaces (GUIs) generated with App Designer, making it an easy-to-use application for quick data processing""" ; sc:featureList edam:operation_0244, edam:operation_3435, edam:operation_3557 ; sc:license "GPL-3.0" ; sc:name "scGEAToolbox" ; sc:url "https://github.com/jamesjcai/scGEAToolbox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:31363220" ; sc:description "scGen predicts single-cell perturbation responses | Single cell perturbation prediction | Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species | This repository includes python scripts in code and notebooks in the Jupyter Notebooks folder to reproduce figures from the paper (bioRxiv, 2018) according to the table bellow | A tensorflow implementation of scGen. scGen is a generative model to predict single-cell perturbation response across cell types, studies and species (Nature Methods, 2019) | Jupyter Notebooks/SupplFig1.ipynb | Jupyter Notebooks/SupplFig2.ipynb" ; sc:featureList edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "scGen" ; sc:url "https://github.com/theislab/scgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2830, edam:topic_3170 ; sc:citation ; sc:description "Allele-specific HLA expression from single-cell gene expression data | Count HLA alleles in single-cell RNA-seq data | scHLAcount allows you to count molecules in single-cell RNA-seq data for class I genes HLA-A, B, and C; and class II genes DPA1, DPB1, DRA1, DRB1, DQA1, and DQB1 using a personalized reference genome. You can either use provided HLA types determined by alternative methods or call HLA types with this tool then quantify against those calls. See the Using scHLAcount section for more details" ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3800 ; sc:license "MIT" ; sc:name "scHLAcount" ; sc:url "https://github.com/10XGenomics/scHLAcount" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , "pubmed:31392316" ; sc:description "Imputing dropout events for single-cell RNA-seq data with limited sample size | scHinter is a Matlab package for imputing dropout events for scRNA-seq with special emphasis on data with limited sample size. scHinter consists of three modules (Figure 1), incorporates a voting-based consensus distance and leverages the synthetic minority over-sampling technique for random interpolation. A hierarchical framework is also embedded in scHinter to increase the reliability of the imputation for small samples. The imputed expression matrix from scHinter can be used for as inputs for other existing scRNA-seq pipelines or tools for downstream analyses, such as cell type clustering, dimension reduction, and visualization" ; sc:featureList edam:operation_3557 ; sc:name "scHinter" ; sc:url "https://github.com/BMILAB/scHinter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2229, edam:topic_3168, edam:topic_3173, edam:topic_3176 ; sc:citation , "pubmed:31836865" ; sc:description """Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq. This repository includes codes for data analysis in scMNase paper""" ; sc:featureList edam:operation_0308, edam:operation_3198, edam:operation_3802 ; sc:name "scMNase-seq" ; sc:url "https://github.com/binbinlai2012/scMNase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Single-cell gene expression profile annotation tool using reference datasets." ; sc:featureList edam:operation_0315, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scMatch" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/forrest-lab/scMatch" ; biotools:primaryContact "Rui Hou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6748759", "pubmed:31531674" ; sc:description "Evaluating stably expressed genes in single cells | Single Cell Stably Express Gene Index — scSEGIndex | Merging multiple batches of scRNA-seq data | Single Cell Stably Express Gene Index | scMerge is a R package for merging and normalising single-cell RNA-Seq datasets | We recommend using either the pre-computed genes (see \"See Also\" below) or the top SEG genes from an user's own data as the control genes in the scMerge function (see the ctl argument in the scMerge function) | This function computes the single-cell Stably Expressed Gene (scSEG) index from Lin. et al. (2019) for a given single-cell count data matrix | If you have any enquries, especially about performing scMerge integration on your own data, then please contact bioinformatics@maths.usyd.edu.au" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3435 ; sc:name "scMerge" ; sc:url "https://sydneybiox.github.io/scMerge/reference/scSEGIndex.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6505295", "pubmed:31068142" ; sc:description "R package for pre-processing of single-cell RNA-seq data by leveraging the context-specific topology inherent in the given data and the network information from priori gene-gene interaction networks." ; sc:featureList edam:operation_3463, edam:operation_3557, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "scNPF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/BMILAB/scNPF" ; biotools:primaryContact "Wenbin Ye", "Xiaohui Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "scNTImpute is an imputation model for scRNA-seq data. 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Based on your location, we recommend that you select:""" ; sc:featureList edam:operation_3216, edam:operation_3755 ; sc:name "scafSLICR" ; sc:url "http://www.mathworks.com/matlabcentral/fileexchange/72856-scafslicr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "SCAFE (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’end RNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3799, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCAFE" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/chung-lab/scafe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:description "Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads." ; sc:featureList edam:operation_0525 ; sc:name "Scaff10X" ; sc:softwareVersion "4.1" ; sc:url "https://sourceforge.net/projects/phusion2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3125, edam:topic_3168 ; sc:citation "pubmed:25890305" ; sc:description "A novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs)." ; sc:featureList edam:operation_3216 ; sc:name "ScaffMatch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3067, edam:topic_3125, edam:topic_3314 ; sc:citation , "pmcid:PMC9650898", "pubmed:36357931" ; sc:description "A Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)." ; sc:featureList edam:operation_0444, edam:operation_0479, edam:operation_3216, edam:operation_3432, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "Scaffold Generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Julian-Z98/ScaffoldGenerator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2258, edam:topic_3336 ; sc:citation ; sc:description "ava-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets. 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Per-base quality values in NGS sequencing data take a significant portion of storage even after compression. Lossy compression technologies could further reduce the space used by quality values. However, in many applications lossless compression is still desired. Hence, sequencing data in multiple file formats have to be prepared for different applications. Results We developed a scalable lossy to lossless compression solution for quality values named ScaleQC. ScaleQC is able to provide bit-stream level scalability. More specifically, the losslessly compressed bit-stream by ScaleQC can be further truncated to lower data rates without re-encoding. 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ScanEV - Extracellular Vesicle Scanner. Upload up to 10 images for detection.""" ; sc:featureList edam:operation_3457 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ScanEV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://bioeng.ru/scanev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9620817", "pubmed:36099042" ; sc:description "A computational workflow for exitron splicing identification in long-read RNA-seq data." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ScanExitronLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ylab-hi/ScanExitronLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3512, edam:topic_3673 ; sc:citation , "pmcid:PMC6507043", "pubmed:30982610" ; sc:description """Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole-Genome Sequencing Studies. This is an R package for performing SCANG procedure in whole genome sequencing studies. 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A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data." ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_3501 ; sc:name "SCANNER" ; sc:url "https://www.thecailab.com/scanner/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_1476, edam:format_3752 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_2830, edam:topic_3474, edam:topic_3534 ; sc:citation ; sc:description "An interpretable geometric deep learning model for structure-based protein binding site prediction." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0477, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "ScanNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo3d.cs.tau.ac.il/ScanNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3500 ; sc:citation , "pubmed:37183449" ; sc:description "Deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3629, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "scAnno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liuhong-jia/scAnno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC10027414", "pubmed:36949780" ; sc:description "Automated cell-type annotation tool for single-cell RNA-sequencing data." ; sc:featureList edam:operation_0490, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scAnnotate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/package=scAnnotate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC8762856", "pubmed:35038984" ; sc:description "The scAnnotatR package automatically classifies cells in scRNA-seq datasets. 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Alexander Wolf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0160, edam:topic_0602, edam:topic_3510 ; sc:citation "pubmed:11283593", "pubmed:12824383", "pubmed:15064475", "pubmed:7874496" ; sc:description "Searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains." ; sc:featureList edam:operation_0239, edam:operation_0240, edam:operation_0246, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Scansite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "4.0" ; sc:url "http://scansite.mit.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3360 ; sc:citation "pubmed:10931953" ; sc:description "The tool finds a set of contiguous SNPs that jointly are associated with disease." ; sc:featureList edam:operation_0282 ; sc:name "SCANSTAT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.jurgott.org/linkage/scanstat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC8048404", "pubmed:33954036" ; sc:description "scAnt is an open-source, low-cost macro 3D scanner, designed to automate the creation of digital 3D models of insects of various sizes in full colour. scAnt provides example configurations for the scanning process, as well as scripts for stacking and masking of images to prepare them for the photogrammetry software of your choice." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:license "MIT" ; sc:name "scAnt" ; sc:url "http://github.com/evo-biomech/scAnt" ; biotools:primaryContact "David Labonte" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6821429", "pubmed:31501864" ; sc:description "Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data | This is a package and a shell script for alternative polyadenylation (APA) analysis of 3' tag single-cell RNA-seq data | This is a package and a shell script for alternative polyadenylation (APA) analysis of 3' tag single-cell RNA-seq data. 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Furthermore, scASK is also a generic ensemble classifier for any supervised classification problem, such as classifying cancer types based on gene expression data or DNA methylation data. scASKcmd is the command line version of scASK in a batch-processing manner, which can perform the whole process without intervention.""" ; sc:featureList edam:operation_3454, edam:operation_3935 ; sc:name "scASK" ; sc:url "https://github.com/liubo2358/scASKcmd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0769, edam:topic_0780, edam:topic_3940 ; sc:citation , "pmcid:PMC9551270", "pubmed:36238687" ; sc:description "A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data." ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3891, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scATACpipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hukai916/scATACpipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3321, edam:topic_3393 ; sc:citation ; sc:description "Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data." ; sc:featureList edam:operation_0564, edam:operation_3218, edam:operation_3219 ; sc:name "scater" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/release/bioc/html/scater.html" ; biotools:primaryContact "Davis McCarthy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2828, edam:topic_3316, edam:topic_3318, edam:topic_3448 ; sc:citation , "pmcid:PMC9533759", "pubmed:36249495" ; sc:description "An approximate method for fast wide-angle scattering simulations." ; sc:featureList edam:operation_2422, edam:operation_3453, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Scatman" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://gitlab.ethz.ch/nux/numerical-physics/pyscatman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC7299405", "pubmed:32502143" ; sc:description """Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers. Single Cell Analysis of Transcript Splicing (SCATS). A statistical tool to detect differential alternative splicing events using single-cell RNA-seq.""" ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0446 ; sc:name "SCATS" ; sc:url "https://github.com/huyustats/SCATS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation ; sc:description "The goal of scatterHatch is to create scatter plots that visually distinguish groups of data using color and texture in sparse or dense datasets." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "scatterHatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FertigLab/scatterHatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:description "R library for fast plotting of scatterplots with millions of points" ; sc:featureList edam:operation_2940 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scattermore" ; sc:url "https://github.com/exaexa/scattermore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9805575", "pubmed:36383176" ; sc:description "An adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scAWMV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pengchengzeng/scAWMV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0654, edam:topic_3170 ; sc:citation , "pmcid:PMC7336184", "pubmed:32627830" ; sc:description """comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. Sequence Compression Benchmark (SCB). This repository contains all code used for constructing Sequence Compression Benchmark.""" ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_3436 ; sc:name "SCB" ; sc:url "http://kirr.dyndns.org/sequence-compression-benchmark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3173, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:35941239" ; sc:description "Sequence-based modeling of single-cell ATAC-seq using convolutional neural networks." ; sc:featureList edam:operation_0314, edam:operation_3436, edam:operation_3891, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "scBasset" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/calico/scBasset" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC7214039", "pubmed:32053185" ; sc:description """batch-effect correction of RNA-seq data through sample distance matrix adjustment. Correct scRNA-seq count matrix subject to batch effects by sample distance matrix adjustment. scBatch utilizes previous correction on sample distance matrices, such as QuantNorm, to further correct the count matrix. We implemented the method with RcppArmadillo for higher efficiency. The manuscript associated with this tool has been published on Bioinformatics.""" ; sc:featureList edam:operation_2937, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "scBatch" ; sc:url "http://github.com/tengfei-emory/scBatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3940 ; sc:citation , "pubmed:34585247" ; sc:description "Scbean integrates a range of models for single-cell data analysis, including dimensionality reduction, remvoing batch effects, and transferring well-annotated cell type labels from scRNA-seq to scATAC-seq and spatial resoved transcriptomics." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scbean" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/jhu99/scbean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC9925104", "pubmed:36734596" ; sc:description "Deep Single-cell Clustering Analysis via Dual Denoising Autoencoder with Bipartite Graph Ensemble Clustering." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scBGEDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wangyh082/scBGEDA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3752 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:37015596" ; sc:description "A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scBKAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YuBinLab-QUST/scBKAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3063, edam:topic_3304, edam:topic_3308 ; sc:citation , "pmcid:PMC10191140", "pubmed:37195696" ; sc:description "A landscape for cell types and associated genetic markers in the brain." ; sc:featureList edam:operation_0224, edam:operation_0415, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "scBrainMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://scbrainmap.sysneuro.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation ; sc:description """An accurate imputation method for scRNA-seq dropouts based on a mixture model. SCC (scRNA-seq complementation). SCC can recover the gene expression of scRNA-seq data. Users can download the package and install SCC in Rstudio or R software. There are two functions in SCC.""" ; sc:featureList edam:operation_0313, edam:operation_3557 ; sc:name "SCC" ; sc:url "https://github.com/nwpuzhengyan/SCC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3673 ; sc:citation ; sc:description "A tool for Identifying single nucleotide variations (SNVs) and short insertions and deletions (INDELs) from single cell sequencing data." ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SCcaller" ; sc:softwareHelp ; sc:url "https://github.com/biosinodx/SCcaller/" ; biotools:primaryContact "Xiao Dong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0605, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC9206025", "pubmed:35715568" ; sc:description "Single-cell clustering using autoencoder and network fusion." ; sc:featureList edam:operation_0314, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.0" ; sc:name "scCAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/package=scCAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3055, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC7031312", "pubmed:32062421" ; sc:description """Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data. The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database. To address these problems, we introduce a single cell Cluster-based Annotation Toolkit for Cellular Heterogeneity (scCATCH) from cluster marker genes identification to cluster annotation based on evidence-based score by matching the identified potential marker genes with known cell markers in tissue-specific cell taxonomy reference database (CellMatch). Recent advance in single-cell RNA sequencing (scRNA-seq) has enabled large-scale transcriptional characterization of thousands of cells in multiple complex tissues, in which accurate cell type identification becomes the prerequisite and vital step for scRNA-seq studies.""" ; sc:featureList edam:operation_3432, edam:operation_3561, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "scCATCH" ; sc:url "https://github.com/ZJUFanLab/scCATCH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Framework to accurately classify cell types in single-cell RNA-sequencing data. The scClassifR package automatically classifies cells in scRNA-seq datasets. It is simple to use with a clear infrastructure to easily add additional cell type classification models. scClassifR support both Seurat and SingleCellExperiment objects as input.""" ; sc:featureList edam:operation_3435 ; sc:name "scClassifR" ; sc:url "https://github.com/grisslab/scClassifR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3316 ; sc:citation ; sc:description """Evaluating single-cell cluster stability using the Jaccard similarity index. Snakemake workflow for subsampling and repeat clustering. A snakemake pipeline to scatter and gather Seurat@ident by subsampling the cells and repeat for multiple times. This is useful for evaluating the cluster stability using different parameters. The goal of scclusteval(Single Cell Cluster Evaluation) is to evaluate the single cell clustering stability by subsampling the cells and provide many visualization methods for comparing clusters.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3432 ; sc:license "MIT" ; sc:name "scclusteval" ; sc:url "https://github.com/crazyhottommy/scclusteval" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3301, edam:topic_3673 ; sc:citation , "pmcid:PMC5812897", "pubmed:29468193" ; sc:description "It identifies SCCmec elements in sequenced S. aureus isolates." ; sc:featureList edam:operation_2403 ; sc:name "SCCmecFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cge.cbs.dtu.dk/services/SCCmecFinder/" ; biotools:primaryContact "Scientific Support", "Technical support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0157, edam:topic_2229, edam:topic_3168 ; sc:citation ; sc:description """A Bayesian model for compositional single-cell data analysis. scCODA - Single-cell differential composition analysis. scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq. It also provides a framework for integration of results directly from scanpy and other sources. This repository contains the code that was used to produce the results and plots for scCODA: A Bayesian model for compositional single-cell data analysis (Büttner and Ostner et al., 2020). The package containing the model can be found here.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3435 ; sc:license "BSD-3-Clause" ; sc:name "scCODA" ; sc:url "https://github.com/theislab/scCODA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "An R package for personalized differentially expressed gene detection on single-cell RNA-sequencing data." ; sc:featureList edam:operation_2454, edam:operation_3223, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scCODE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/XZouProjects/scCODE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:33974001" ; sc:description "A method for exploratory analysis of cell-cell communication based on single cell RNA sequencing data." ; sc:featureList edam:operation_0314, edam:operation_0571, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scConnect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JonETJakobsson/scConnect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data. An approach combining semi-supervised and unsupervised clustering for cell type annotation in single-cell RNA-seq data.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3432, edam:operation_3766 ; sc:name "scConsensus" ; sc:url "https://github.com/prabhakarlab/scConsensus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC8740455", "pubmed:34996359" ; sc:description "An R package for A graph-based k-partitioning approach for single-cell analysis" ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3432, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scCorr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CBIIT-CGBB/scCorr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25135945" ; sc:description "Computational software developed to detect recent positive selection using deep sequencing data. It’s robust to various demographic events and also robust to the variations of mutation rates and recombination rates." ; sc:featureList edam:operation_0324 ; sc:name "SCCT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wavefancy/scct" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8187165", "pubmed:34141142" ; sc:description "Single cell discriminant analysis for single-cell RNA sequencing data." ; sc:featureList edam:operation_0314, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scDA" ; sc:softwareHelp ; sc:url "https://github.com/ZCCQQWork/scDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3295 ; sc:citation , "pmcid:PMC8734213", "pubmed:34991671" ; sc:description "scDALI (single-cell differential allelic imbalance) is a statistical model and analysis framework that leverages allele-specific analyses of single-cell data to decode cell-state-specific genetic regulation." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3799, edam:operation_3802, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "scDALI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pmbio.github.io/scdali/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3940 ; sc:citation ; sc:description "scDART (single cell Deep learning model for ATAC-Seq and RNA-Seq Trajectory integration) is a scalable deep learning framework that embed the two data modalities of single cells, scRNA-seq and scATAC-seq data, into a shared low-dimensional latent space while preserving cell trajectory structures. Furthermore, scDART learns a nonlinear function represented by a neural network encoding the cross-modality relationship simultaneously when learning the latent space representations of the integrated dataset." ; sc:featureList edam:operation_2939, edam:operation_3890 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scDART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PeterZZQ/scDART" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_2885, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC7265634", "pubmed:32487193" ; sc:description """an integrated database of stomach cancer. Stomach cancer (SC) is a type of cancer, which is derived from the stomach mucous membrane. As there are non-specific symptoms or no noticeable symptoms observed at the early stage, newly diagnosed SC cases usually reach an advanced stage and are thus difficult to cure. Therefore, in this study, we aimed to develop an integrated database of SC. METHODS:SC-related genes were identified through literature mining and by analyzing the publicly available microarray datasets. Using the RNA-seq, miRNA-seq and clinical data downloaded from The Cancer Genome Atlas (TCGA), the Kaplan-Meier (KM) survival curves for all the SC-related genes were generated and analyzed. The miRNAs (miRanda, miRTarget2, PicTar, PITA and TargetScan databases), SC-related miRNAs (HMDD and miR2Disease databases), single nucleotide polymorphisms (SNPs, dbSNP database), and SC-related SNPs (ClinVar database) were also retrieved from the indicated databases""" ; sc:featureList edam:operation_0224, edam:operation_0306, edam:operation_0463, edam:operation_3196 ; sc:name "SCDb" ; sc:url "http://www.stomachcancerdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions." ; sc:featureList edam:operation_0337, edam:operation_2424, edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "scDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scDD.html" ; biotools:primaryContact "Keegan Korthauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "This package implements a set of statistical methods for analyzing single-cell RNA-seq data by fitting individual error models for single-cell RNA-seq measurements. These models can then be used for the assessment of DE between groups of cells, as well as other types of analysis. This package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures." ; sc:featureList edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "scde" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scde.html" ; biotools:primaryContact "Jean Fan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_2640, edam:topic_3303, edam:topic_3678 ; sc:citation "pubmed:22121217" ; sc:description "Database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2424, edam:operation_2436, edam:operation_3431 ; sc:name "Stem Cell Discovery Engine (SCDE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://discovery.hsci.harvard.edu/" ; biotools:primaryContact "SCDE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3173, edam:topic_3308, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:36458445" ; sc:description "Deep generative modeling and clustering of single cell Hi-C data." ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scDEC-Hi-C" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/kimmo1019/scDEC-Hi-C" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_3170, edam:topic_3295, edam:topic_3308 ; sc:citation , "pubmed:35453146" ; sc:description "An R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scDeconv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yuabrahamliu/scDeconv" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3590 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description "scDeepCluster is a model-based deep embedding clustering for single cell RNA-seq data." ; sc:featureList edam:operation_0313 ; sc:license "Apache-2.0" ; sc:name "scDeepCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ttgump/scDeepCluster_pytorch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network. To addresses this challenge, we developed a reference-free cell-type annotation method, namely scDeepSort, using a state-of-the-art deep learning algorithm, i.e. a modified graph neural network (GNN) model. Recent advance in single-cell RNA sequencing (scRNA-seq) has enabled large-scale transcriptional characterization of thousands of cells in multiple complex tissues, in which accurate cell type identification becomes the prerequisite and vital step for scRNA-seq studies.""" ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "scDeepSort" ; sc:url "https://github.com/ZJUFanLab/scDeepSort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34048541" ; sc:description "A rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer that can be used across different data platforms, using a combination of gene expression rank-based method and majority vote ensemble machine-learning probability-based prediction method." ; sc:featureList edam:operation_0314, edam:operation_2454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scDetect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/IVDgenomicslab/scDetect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7884436", "pubmed:33589635" ; sc:description """Fast and precise single-cell data analysis using a hierarchical autoencoder. The scDHA software package can perform cell segregation through unsupervised learning, dimension reduction and visualization, cell classification, and time-trajectory inference on single-cell RNA sequencing data. The scDHA package is a complete pipeline for single-cell RNA sequencing (scRNA-seq) analysis. scDHA supports various analyses.""" ; sc:featureList edam:operation_0337, edam:operation_2939, edam:operation_3432, edam:operation_3435, edam:operation_3891, edam:operation_3935 ; sc:name "scDHA" ; sc:url "http://scdha.tinnguyen-lab.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3590 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3391, edam:topic_3474 ; sc:citation "pubmed:36849204" ; sc:description "Model-based deep hyperbolic manifold learning for visualizing complex hierarchical structures in single-cell genomics data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "scDHMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ttgump/scDHMap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC8734364", "pubmed:34991457" ; sc:description "scDIOR software was developed for single-cell data transformation between platforms of R and Python based on Hierarchical Data Format Version 5" ; sc:featureList edam:operation_3435, edam:operation_3629, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scDIOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JiekaiLab/scDIOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC9281153", "pubmed:35831808" ; sc:description "scDLC is a deep learning classifier (scDLC) for large sample scRNA-seq data, based on the long short-term memory recurrent neural networks (LSTMs). This classifier does not require a prior knowledge on the scRNA-seq data distribution and it is a scale invariant method which does not require a normalization procedure for scRNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scDLC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/scDLC-code/scDLC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC6929335", "pubmed:31870280" ; sc:description "scdney is a R package with collection of single cell RNA-sequencing (scRNA-seq) data analysis functions developed by team of Sydney Precision Bioinformatics Research Group at The University of Sydney." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:name "scdney" ; sc:url "https://github.com/SydneyBioX/scdney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32365169" ; sc:description """correcting drop-out events in single-cell RNA-seq data. Drop-out correction for single cell RNA_seq data.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3557 ; sc:name "scDoc" ; sc:url "https://github.com/anlingUA/scDoc" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3590 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_3308 ; sc:description """Scdrake is a highly scalable, reproducible and configurable pipeline for scRNA-seq data prepared by a popular 10x Genomics droplet-based technology. Scdrake is implemented as a package for the R language and is built on top of the drake package, a Make-like pipeline toolkit. Scdrake currently provides common steps of scRNA-seq data analysis: quality control and filtering of cells and genes, normalization, dimensionality reduction, clustering, finding of cluster markers and differentially expressed genes between clusters, and integration of multiple datasets. All pipeline steps are accompanied by rich graphical outputs and reports in HTML format. Thanks to the drake package, all intermediate results can be reused, and the pipeline can be easily extended by users to incorporate custom analyses. Also, drake analyzes which parts of the pipeline are already done or haven't changed since the last run, and which can be run in parallel, resulting in great execution speed.""" ; sc:featureList edam:operation_0313, edam:operation_0531, edam:operation_2935, edam:operation_2938, edam:operation_2940, edam:operation_2943, edam:operation_3223, edam:operation_3435, edam:operation_3563, edam:operation_3695, edam:operation_3744, edam:operation_3935, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scdrake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , , , , ; sc:softwareVersion "1.0.1" ; sc:url "https://bioinfocz.github.io/scdrake" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0208, edam:topic_0769, edam:topic_3170, edam:topic_3336, edam:topic_3360 ; sc:citation , "pmcid:PMC9747355", "pubmed:36544472" ; sc:description "From single-cell RNA-seq to drug response prediction." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scDrug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ailabstw/scDrug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation , "pubmed:31501871" ; sc:description "Computational Annotation of Doublets in Single-Cell RNA Sequencing Data | Instructions to create figures / tables from the scds manuscript | The scds_manuscript/data folder contains directories for each of the four data sets. Each directory contains two files, getRawData.sh and processRawData.R. getRawData.sh downloads the data sets (or contains instructions on how to do so), while processRawData.R can be run to process the input data and generate SingleCellExperiments that contain experimental doublet annotations. For each data set, these annotations are stored in the colData slot" ; sc:featureList edam:operation_3501, edam:operation_3891 ; sc:name "scds" ; sc:url "https://github.com/kostkalab/scds_manuscript" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3384, edam:topic_3517 ; sc:citation , "pubmed:32634825" ; sc:description """an efficient and scalable algorithm for genome-wide association studies on longitudinal outcomes with mixed-effects modeling. SCEBE is a R package that conducts high-dimension Genome-Wide Association Study (GWAS) for dynamic traits. The main function in SCEBE package is scebe_sim. Four approaches are included in SCEBE: (1) lme in R package 'lme4' (standard approach), (2) nebe, representing naive empirical Bayes estimation (Londono et al. 2013 and Meirelles et al. 2013), (3) gallop, representing Genome-wide Analysis of Largescale Longitudinal Outcomes using Penalization (GALLOP) (Sikorska et al. 2015), and scebe, representing the proposed two-step simultaneous correction method.""" ; sc:featureList edam:operation_3196, edam:operation_3658, edam:operation_3659 ; sc:name "SCEBE" ; sc:url "https://github.com/Myuan2019/SCEBE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_3168 ; sc:citation "pubmed:18293306" ; sc:description "This server is designed for the prediction of 4 types of structural classes (all-α,all-β,α/β, and α+β) based on a protein sequence." ; sc:featureList edam:operation_0474 ; sc:name "SCEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC7217489", "pubmed:32339163" ; sc:description """A scalable Python package for single-cell RNA-seq exploratory data analysis. Single-cell exploratory data analysis for RNA-Seq. Scedar (Single-cell exploratory data analysis for RNA-Seq) is a reliable and easy-to-use Python package for efficient visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering of large-scale single cell RNA-seq (scRNA-seq) datasets.""" ; sc:featureList edam:operation_0337, edam:operation_0372, edam:operation_3432, edam:operation_3557, edam:operation_3680 ; sc:license "MIT" ; sc:name "scedar" ; sc:url "https://pypi.org/project/scedar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3315 ; sc:citation , "pmcid:PMC9108753", "pubmed:35615016" ; sc:description "Accurate single-cell RNA-seq data analysis via ensemble consensus clustering based on multiple feature selections." ; sc:featureList edam:operation_3223, edam:operation_3432, edam:operation_3454, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scEFSC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Conan-Bian/scEFSC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9692209", "pubmed:36438203" ; sc:description "Supervised Contrastive Learning for Clinical Risk Prediction using Electronic Health Records." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCEHR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/calvin-zcx/SCEHR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development. Scellnetor is a Single Cell Network Profiler for Extraction of Systems Biology Patterns from scRNAseq Trajectories. First time using Scellnetor or need help?. Scellnetor is a novel clustering tool for scRNA-seq data that takes Scanpy generated AnnData objects in H5AD file-format as input. With Scellnetor you can compare two sets of cells that you manually select on one of your Scanpy-generated plots. The output will be connected components of genes where the genes are either differently or similarly expressed in the two sets. You can also do a clustering of a single set, where the genes in the connected components are similarly expressed. For every cluster, you get a plot showing mean gene expression and the genes' 95 % confidence intervals and a table with statistically significant GO-terms.""" ; sc:featureList edam:operation_0244, edam:operation_0313, edam:operation_3223 ; sc:license "MIT" ; sc:name "Scellnetor" ; sc:url "https://exbio.wzw.tum.de/scellnetor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC7035868", "pubmed:32117635" ; sc:description "SCelVis: Easy Single-Cell Visualization is a tool exploratory single cell data analysis on the desktop and in the cloud." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3223 ; sc:license "MIT" ; sc:name "SCelVis" ; sc:softwareHelp ; sc:url "https://github.com/bihealth/scelvis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_2330 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2331, edam:format_3166, edam:format_3477, edam:format_3604 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0804, edam:topic_2269, edam:topic_3307 ; sc:citation , "pmcid:PMC5570263", "pubmed:28525568" ; sc:contributor "European Research Council within the CausalPath project" ; sc:description "Apply standard pre-processing, statistical analysis, advanced visualization methods and network reconstruction methods on single-cell cytometry data. It has an open architecture that allows power users to extend its functionalities by submitting their own machine learning methods." ; sc:featureList edam:operation_3083, edam:operation_3435, edam:operation_3439, edam:operation_3658, edam:operation_3659, edam:operation_3664 ; sc:funder "European Research Council within the CausalPath project" ; sc:isAccessibleForFree true ; sc:name "SCENERY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://scenery.csd.uoc.gr" ; biotools:primaryContact "Giorgos Papoutsoglou", "Ioannis Tsamardinos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_2885, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC8728125", "pubmed:34761274" ; sc:description "The database provides single-cell enhancer annotation in three species, including human (hg19), mouse (mm9), and fly (dm3)." ; sc:featureList edam:operation_0440, edam:operation_2421, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scEnhancer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://enhanceratlas.net/scenhancer/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2032 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_3170 ; sc:citation , "pubmed:32561888" ; sc:description "A computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data." ; sc:featureList edam:operation_1781, edam:operation_2495, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SCENIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.2" ; sc:url "http://scenic.aertslab.org" ; biotools:primaryContact "Stein Aerts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data." ; sc:featureList edam:operation_3680 ; sc:name "scEpath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sqjin/scEpath" ; biotools:primaryContact "Qing Nie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3940 ; sc:citation , "pmcid:PMC10069468", "pubmed:36653120" ; sc:description "Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "scEpiSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.scepisearch.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3173, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:37769837" ; sc:description "Database to comprehensively interrogate analytic tools for single-cell epigenomic data." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "scEpiTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://health.tsinghua.edu.cn/scepitools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC7216638", "pubmed:32393315" ; sc:description """an R package for identifying eQTL from single-cell parallel sequencing data. SCeQTL is an R package that uses zero-inflated negative binomial regression to do eQTL analysis on single-cell data. It can distinguish two type of gene-expression differences among different genotype groups. It’s more suitable to use SCeQTL to identify eQTLs from single-cell data. It can also be used for finding gene expression variations associated with other grouping factors like cell lineages. Following is the detail information and usage of this program. You can also found them in READ.ME. R Packages is a book based around this workflow.""" ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3659 ; sc:name "SCeQTL" ; sc:url "https://github.com/XuegongLab/SCeQTL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749 ; sc:citation "pubmed:22140105" ; sc:description "ScerTF catalogs over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors." ; sc:featureList edam:operation_0441, edam:operation_0445 ; sc:name "ScerTF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stormo.wustl.edu/ScerTF/" ; biotools:primaryContact "Gary D. Stormo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_3299, edam:topic_3308 ; sc:citation , "pmcid:PMC9990205", "pubmed:36879200" ; sc:description "A gradient boosting-based method for prediction of cell state evolution." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scEvoNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/monsoro/scEvoNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3374 ; sc:description "Writes SCF formatted files." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:name "SCF writer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/7389-scf-writer" ; biotools:primaryContact "Lucio Cetto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0634, edam:topic_2640 ; sc:citation , "pmcid:PMC7344292", "pubmed:32714868" ; sc:description """A Novel Method for Cancer Subtyping and Risk Prediction Using Consensus Factor Analysis. Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in order to reliably identify cancer subtypes and accurately predict risk scores of patients.""" ; sc:featureList edam:operation_0555, edam:operation_3891, edam:operation_3947 ; sc:name "SCFA" ; sc:url "http://scfa.tinnguyen-lab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269 ; sc:citation , "pmcid:PMC9805561", "pubmed:36394263" ; sc:description "A scalable python package for advanced pseudotime and bifurcation analysis from single cell data." ; sc:featureList edam:operation_3223, edam:operation_3359, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "scFates" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/scFates/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3308, edam:topic_3407, edam:topic_3955 ; sc:citation , "pmcid:PMC10320190", "pubmed:37216602" ; sc:description "A webserver for predicting metabolic flux and variations using transcriptomics data." ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "scFEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://scFLUX.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scFeatureFilter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scFeatureFilter.html" ; biotools:primaryContact "Guillaume Devailly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_2229 ; sc:citation , "pubmed:36040148" ; sc:description "scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types belonging to the following six categories." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scFeatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SydneyBioX/scFeatures" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3332 ; sc:citation "pubmed:23160142" ; sc:description "Software to calculate RNA structural entropies through stochastic context free grammars." ; sc:featureList edam:operation_0455 ; sc:name "SCFG Structural Entropy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://rna-informatics.uga.edu/malmberg/rlmlab/programs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Recently a very large collection of single-cell RNA-seq datasets has been generated and publicly released. For the collection to be useful, the information must be organized in a way that supports queries that are relevant to researchers. `scfind` builds an index from scRNA-seq datasets which organizes the information in a suitable and compact manner so that the datasets can be very efficiently searched for either cells or cell types in which a given list of genes is expressed." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scfind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scfind.html" ; biotools:primaryContact "Vladimir Kiselev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3316 ; sc:citation , ; sc:description "The scFlow R package provides the analytical back-end to the nf-core/scflow Nextflow pipeline for the orchestration of automated, scalable, and reproducible single-cell RNA sequencing analyses." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3891, edam:operation_3933, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://combiz.github.io/scFlow/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2533, edam:topic_2640 ; sc:citation ; sc:description "A new statistical model and machine learning inference algorithm designed to determine the pattern of how DNA mutations are distributed in individual cells of a tumour. The software provides implementation of several probabilistic models for clustering single cell (nucleus) data and inferring clonal genotypes." ; sc:featureList edam:operation_3504 ; sc:license "GPL-3.0" ; sc:name "Single Cell Genotyper (SCG)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shahlab.ca/projects/scg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2229, edam:topic_3053 ; sc:citation ; sc:description "single-cell gene associating domain scores for exploratory analysis of scHi-C data." ; sc:featureList edam:operation_3432, edam:operation_3799, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sshen82.github.io/BandNorm/articles/scGAD-tutorial.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3934 ; sc:citation , "pubmed:35258562" ; sc:description "Marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets." ; sc:featureList edam:operation_0314 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/carmonalab/scGate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2269, edam:topic_3170 ; sc:citation , "pubmed:36825817" ; sc:description "An imputation method for scRNA-seq data based on Graph Contrastive Learning." ; sc:featureList edam:operation_0313, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGCL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zehaoxiong123/scGCL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3068, edam:topic_3308, edam:topic_3474 ; sc:citation ; sc:description """a Graph Convolutional Networks Algorithm for Knowledge Transfer in Single Cell Omics. single cell graph convolutional network (scGCN). This is a TensorFlow implementation of scGCN for leveraging differnt single cell datasets, which is described in our paper:.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3436 ; sc:license "MIT" ; sc:name "scGCN" ; sc:url "https://github.com/QSong-github/scGCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC9405199", "pubmed:36004879" ; sc:description "A Single-Cell Gene Coexpression Network Analysis Framework for Clustering Cell Types and Revealing Biological Mechanisms." ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3463, edam:operation_3557, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGENA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zpliulab/scGENA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3512 ; sc:citation , "pmcid:PMC8864248", "pubmed:34954425" ; sc:description "Predicting Cell Fate Transition During Early Embryonic Development by Single-cell Graph Entropy." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhongjiayuna/scGET_Project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269, edam:topic_3170 ; sc:citation , "pubmed:33300547" ; sc:description """a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder. The rapid development of single-cell RNA sequencing (scRNA-Seq) technology provides strong technical support for accurate and efficient analyzing single-cell gene expression data. However, the analysis of scRNA-Seq is accompanied by many obstacles, including dropout events and the curse of dimensionality. Here, we propose the scGMAI, which is a new single-cell Gaussian mixture clustering method based on autoencoder networks and the fast independent component analysis (FastICA). Specifically, scGMAI utilizes autoencoder networks to reconstruct gene expression values from scRNA-Seq data and FastICA is used to reduce the dimensions of reconstructed data. The integration of these computational techniques in scGMAI leads to outperforming results compared to existing tools, including Seurat, in clustering cells from 17 public scRNA-Seq datasets""" ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3891 ; sc:name "scGMAI" ; sc:url "https://github.com/QUST-AIBBDRC/scGMAI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:35394015" ; sc:description "A graph neural network-based approach to automatically identify cell types." ; sc:featureList edam:operation_3436, edam:operation_3501, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scGraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://figshare.com/articles/software/scGraph/17157743" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3173, edam:topic_3308 ; sc:citation , "pmcid:PMC10767939", "pubmed:37889053" ; sc:description "Comprehensive single-cell gene regulatory network platform of human and mouse." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2437, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "scGRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bio.liclab.net/scGRN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_0749, edam:topic_3173 ; sc:citation , "pmcid:PMC8161957", "pubmed:34044854" ; sc:description "A computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks." ; sc:featureList edam:operation_0438, edam:operation_1781, edam:operation_2437, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scGRNom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/daifengwanglab/scGRNom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269 ; sc:citation ; sc:description "Single-cell generalized trendmodel (scGTM): a flexible and interpretable model for gene expression along cell pseudotime. This is a Python package for modeling the statistical relationship between pseudotime and gene expression data." ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scGTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ElvisCuiHan/scGTM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3170, edam:topic_3308, edam:topic_3517 ; sc:citation , "pmcid:PMC9575201", "pubmed:36253801" ; sc:description "Landscape of trait-cell type associations by integrating single-cell transcriptomics-wide and genome-wide association studies." ; sc:featureList edam:operation_2436, edam:operation_3659, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bsml320/scGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0634, edam:topic_3305, edam:topic_3406, edam:topic_3474 ; sc:citation ; sc:description "Sch-net is a deep learning architecture for automatic schizophrenia setection." ; sc:name "Sch-net" ; sc:url "https://github.com/Scu-sen/Sch-net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_0654, edam:topic_3168, edam:topic_3324 ; sc:citation , "pmcid:PMC6995221", "pubmed:32007105" ; sc:description """haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data. Haplotyping reveals chromosome blocks inherited from parents to in vitro fertilized (IVF) embryos in preimplantation genetic diagnosis (PGD), enabling the observation of the transmission of disease alleles between generations. However, the methods of haplotyping that are suitable for single cells are limited because a whole genome amplification (WGA) process is performed before sequencing or genotyping in PGD, and true haplotype profiles of embryos need to be constructed based on genotypes that can contain many WGA artifacts. RESULTS:Here, we offer scHaplotyper as a genetic diagnosis tool that reconstructs and visualizes the haplotype profiles of single cells based on the Hidden Markov Model (HMM). scHaplotyper can trace the origin of each haplotype block in the embryo, enabling the detection of carrier status of disease alleles in each embryo.""" ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_3196 ; sc:name "scHaplotyper" ; sc:url "https://github.com/yzqheart/scHaplotyper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3400, edam:topic_3452 ; sc:citation , "pmcid:PMC9174863", "pubmed:35711832" ; sc:description "A new classifier constructed with platelet features for malignant and benign pulmonary nodules based on prospective real-world data." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "SCHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://i.uestc.edu.cn/SCHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3263, edam:topic_3382 ; sc:citation , "pmcid:PMC7183633", "pubmed:32334522" ; sc:description """an open-source, distributed mobile platform for deploying mHealth research tools and interventions. schema is a cross-platform mobile application for deploying mHealth monitoring and intervention studies.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3561 ; sc:license "MIT" ; sc:name "schema" ; sc:url "https://github.com/schema-app/schema" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Ontology" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0749, edam:topic_0780, edam:topic_3324, edam:topic_3400 ; sc:citation , "pmcid:PMC10116472", "pubmed:37081398" ; sc:description "Tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3435, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Schema Playground" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://Schema.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:31794001" ; sc:description """Schex avoids overplotting for large single cell RNA-sequencing datasets. It builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment and SeuratObject. The goal of schex is to provide easy plotting of hexagon cell representations of single cell data stored in SingleCellExperiment or Seurat objects.""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Schex" ; sc:url "http://bioconductor.org/packages/release/bioc/html/schex.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_3170 ; sc:citation , "pmcid:PMC10598576", "pubmed:37847655" ; sc:description "scHiCDiff software tool provides both nonparametric tests and parametirc models to detect differential chromatin interactions (DCIs) from single-cell Hi-C data." ; sc:featureList edam:operation_2945, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scHiCDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wmalab/scHiCDiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3168, edam:topic_3572 ; sc:citation , "pmcid:PMC5860379", "pubmed:29186290" ; sc:description "Software package for eliminating systematic biases in single-cell Hi-C data. Considering that single-cell Hi-C data are zero-inflated, here we use zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, including cutting sites, GC content, and mappability." ; sc:featureList edam:operation_3218 ; sc:name "scHiCNorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dna.cs.miami.edu/scHiCNorm/" ; biotools:primaryContact "Zheng Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3170, edam:topic_3295, edam:topic_3315 ; sc:citation , "pubmed:36205615" ; sc:description "Unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data." ; sc:featureList edam:operation_2940, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scHiCPTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lhqxinghun/scHiCPTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3306 ; sc:citation ; sc:description "A Self-Representation Smoothing Method with Gaussian Mixture Model for Imputing single cell Hi-C Data." ; sc:featureList edam:operation_3432, edam:operation_3436, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scHiCSRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sl-lin/scHiCSRS.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0919 ; sc:encodingFormat edam:format_2330 ; sc:name "Chromosome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3474, edam:topic_3810, edam:topic_3940 ; sc:citation , "pubmed:34553746" ; sc:description "A stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding." ; sc:featureList edam:operation_3435, edam:operation_3659, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scHiCStackL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hww.sdu.edu.cn:8002/scHiCStackL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3940 ; sc:citation , "pmcid:PMC8162587", "pubmed:34003823" ; sc:description "scHiCTools is a computational toolbox for analyzing single cell Hi-C (high-throughput sequencing for 3C) data which includes functions for Loading single-cell HiC datasets, Screening valid single-cell data, Smoothing the contact maps with linear convolution, random walk or network enhancing, Calculating pairwise similarity using measures include InnerProduct, HiCRep and Selfish, Calculating embeddings for single cell HiC datasets efficiently with MDS, t-SNE and PHATE, Clustering the cells using scHiCluster, k-means and spectral clustering, and Visualizing embedded cells via 2-D or 3-D scatter plot." ; sc:featureList edam:operation_2940, edam:operation_3432, edam:operation_3435 ; sc:license "MIT" ; sc:name "scHiCTools" ; sc:url "https://github.com/liu-bioinfo-lab/scHiCTools" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3305 ; sc:citation , "pmcid:PMC7897994", "pubmed:33665519" ; sc:description "Schistoxpkg.jl is a Julia package to run an individual based model of a schistosomiasis outbreak based on original code from this paper. Generally people uptake larvae based on a contact rate defined by their age, along with some predisposition which is chosen from a gamma distribution with mean 1, but some specified level of variance." ; sc:featureList edam:operation_2426, edam:operation_2428 ; sc:license "MIT" ; sc:name "SCHISTOX.jl" ; sc:softwareHelp ; sc:url "https://github.com/mattg3004/Schistoxpkg.jl" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0780 ; sc:author ; sc:citation , "pmcid:PMC5408801", "pubmed:28172591" ; sc:description "Prediction of protein sub-chloroplastinc localization." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SChloro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://busca.biocomp.unibo.it/schloro" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "Joint estimation of contamination for ancient DNA and endogenous mitochondrial genome inference" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "schmutzi" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://grenaud.github.io/schmutzi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3934 ; sc:citation ; sc:description "Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3432, edam:operation_3435 ; sc:license "LGPL-2.1" ; sc:name "SCHNAPPs" ; sc:softwareHelp ; sc:url "https://c3bi-pasteur-fr.github.io/UTechSCB-SCHNAPPs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3934 ; sc:citation ; sc:description """Scalable clustering of high dimensional single-cell data. Scalable Clustering of Hierarchical Stochastic Neighbour Embedding hierarchies using Louvain community detection. Clustering of high dimensional data using manifold learning and subsampling. Clustering is performed on a small representative subset of the data and translated back to the full dataset. See the notebooks in the Python Parser folder for explanation on the HSNE datastructure, how to parse the HSNE hierarchy into a python object and a clustering example.""" ; sc:featureList edam:operation_1812, edam:operation_3432, edam:operation_3435, edam:operation_3891, edam:operation_3935 ; sc:name "SCHNEL" ; sc:url "https://github.com/paulderaadt/HSNE-clustering" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3500 ; sc:citation , "pubmed:32661426" ; sc:description """Investigating higher-order interactions in single-cell data with scHOT. Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.""" ; sc:featureList edam:operation_2436, edam:operation_3359, edam:operation_3463 ; sc:license "MIT" ; sc:name "scHOT" ; sc:url "https://github.com/MarioniLab/scHOT2019" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC8121839", "pubmed:33990598" ; sc:description "scHPL is a hierarchical progressive learning method which automatically finds relationships between cell populations across multiple datasets and uses this to construct a hierarchical classification tree. For each node in the tree either a linear SVM or one-class SVM, which enables the detection of unknown populations, is trained. The trained classification tree can be used to predict the labels of a new unlabeled dataset." ; sc:featureList edam:operation_0553, edam:operation_3478, edam:operation_3891 ; sc:license "MIT" ; sc:name "scHPL" ; sc:url "https://github.com/lcmmichielsen/scHPL" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3577 ; sc:citation , "pmcid:PMC9881140", "pubmed:36350625" ; sc:description "A single-cell network analysis platform for the study of cell-type specificity of disease genes." ; sc:featureList edam:operation_3216, edam:operation_3223, edam:operation_3557, edam:operation_3629, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scHumanNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/netbiolab/scHumanNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3168, edam:topic_3293, edam:topic_3474 ; sc:citation "pubmed:17708678" ; sc:description "A software of tree construction and subfamily detection." ; sc:featureList edam:operation_0324 ; sc:name "SCI-PHY" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://phylogenomics.berkeley.edu/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3170, edam:topic_3474 ; sc:citation , "pubmed:34913057" ; sc:description "An integrative autoencoder-based ensemble classification framework for single-cell RNA-seq data." ; sc:featureList edam:operation_3799, edam:operation_3891, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scIAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JGuan-lab/scIAE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC9848058", "pubmed:36548380" ; sc:description "A simple method for removing batch effects from single-cell RNA-sequencing data." ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCIBER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/SCIBER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:32603812" ; sc:description """An open-source toolbox for measuring dynamic video framerates and synchronizing video stimuli with neural and behavioral responses. The Schultz Cigarette Burn Toolbox is a series of Python, MATLAB, and Arduino scripts designed to measure veridical video framerates and onset times. It uses visual markers ("Cigarette Burns") on the corners of the screen which can be synchronized with EEG and/or response data using an analog input box or an Arduino microcontroller (or similar).""" ; sc:name "SCiBuT" ; sc:url "http://www.band-lab.com/scibut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """High-throughput paired profiling of transcriptomes and DNA copy number variations at single cell resolution. This file provides an overview of the Tiedemann Lab scRNA-seq normalization and inferred CNV pipeline that includes:. Chromosome copy number variations (CNVs) are a near-universal feature of cancer however their specific effects on cellular function are poorly understood.""" ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_3233, edam:operation_3435, edam:operation_3933 ; sc:name "sciCNV" ; sc:url "https://www.github.com/TiedemannLab/sciCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3173, edam:topic_3656 ; sc:citation , "pubmed:33232443" ; sc:description """Fast detection of differential chromatin domains with SCIDDO. The generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing is a standard approach to dissect the complexity of the epigenome. Interpretation and differential analysis of histone datasets remains challenging due to regulatory meaningful co-occurrences of histone marks and their difference in genomic spread. To ease interpretation, chromatin state segmentation maps are a commonly employed abstraction combining individual histone marks. We developed the tool SCIDDO as a fast, flexible and statistically sound method for the differential analysis of chromatin state segmentation maps. RESULTS:We demonstrate the utility of SCIDDO in a comparative analysis that identifies differential chromatin domains (DCD) in various regulatory contexts and with only moderate computational resources""" ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3463 ; sc:name "SCIDDO" ; sc:url "http://github.com/ptrebert/sciddo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing. Cell atlas projects and single-cell CRISPR screens hit the limits of current technology, as they require cost-effective profiling for millions of individual cells""" ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scifi-RNA-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scifi-rna-seq.computational-epigenetics.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1957, edam:format_3982 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229 ; sc:description "SCIGA is a software for 10X single cell immunoglobulin repertoires analysis. It uses raw reads or output of Cellranger as input, and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCIGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sciensic/SCIGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC7470961", "pubmed:32588900" ; sc:description """single-cell RNA-seq imputation using generative adversarial networks. Generative adversarial networks for single-cell RNA-seq imputation. The data and codes for reproducing all Figures and Tables in the manuscript of scIGANs. scIGANs is a computational tool for single-cell RNA-seq imputation and denoise using Generative Adversarial Networks (GANs). Build on PyTorch, scIGNAs enables GPU acceleration inaddition to CPU computing as long as the GPUs are available.""" ; sc:featureList edam:operation_0313, edam:operation_3557, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "scIGANs" ; sc:url "https://github.com/xuyungang/scIGANs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC10374128", "pubmed:37498822" ; sc:description "A sidekick for workflow clarity and reproducibility during extensive data analysis." ; sc:featureList edam:operation_3435, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Scikick" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/matthewcarlucci/scikick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation ; sc:description "scikit-activeml is a Python module for active learning on top of SciPy and scikit-learn. The following code implements an Active Learning Cycle with 20 iterations using a Logistic Regression Classifier and Uncertainty Sampling. To use other classifiers, you can simply wrap classifiers from scikit-learn or use classifiers provided by scikit-activeml. Note that the main difficulty using active learning with scikit-learn is the ability to handle unlabeled data which we denote as a specific value (MISSING_LABEL) in the label vector y_true." ; sc:featureList edam:operation_0224, edam:operation_3659 ; sc:license "BSD-3-Clause" ; sc:name "scikit-activeml" ; sc:softwareHelp ; sc:url "https://github.com/scikit-activeml/scikit-activeml" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3068, edam:topic_3474 ; sc:citation , "pmcid:PMC8534554", "pubmed:34682092" ; sc:description "A Python Package for Intrinsic Dimension Estimation." ; sc:featureList edam:operation_3435, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "scikit-dimension" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/j-bac/scikit-dimension" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3372, edam:topic_3382 ; sc:citation , "pmcid:PMC4081273", "pubmed:25024921" ; sc:description "Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3443, edam:operation_3553 ; sc:license "BSD-3-Clause" ; sc:name "scikit-image" ; sc:softwareHelp ; sc:url "http://scikit-image.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3474 ; sc:citation ; sc:description "scikit-learn is a Python module for machine learning built on top of SciPy and is distributed under the 3-Clause BSD license." ; sc:featureList edam:operation_2990, edam:operation_3432, edam:operation_3659, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "scikit-learn" ; sc:softwareHelp , ; sc:softwareVersion "1.1.1" ; sc:url "https://scikit-learn.org/stable/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3379, edam:topic_3384, edam:topic_3421, edam:topic_3954 ; sc:citation , "pmcid:PMC7316849", "pubmed:32436132" ; sc:description """Compact libraries for surgical navigation. This paper introduces the SciKit-Surgery libraries, designed to enable rapid development of clinical applications for image-guided interventions. SciKit-Surgery implements a family of compact, orthogonal, libraries accompanied by robust testing, documentation, and quality control. SciKit-Surgery libraries can be rapidly assembled into testable clinical applications and subsequently translated to production software without the need for software reimplementation. The aim is to support translation from single surgeon trials to multicentre trials in under 2 years. METHODS:At the time of publication, there were 13 SciKit-Surgery libraries provide functionality for visualisation and augmented reality in surgery, together with hardware interfaces for video, tracking, and ultrasound sources. The libraries are stand-alone, open source, and provide Python interfaces""" ; sc:featureList edam:operation_0337 ; sc:name "SciKit-Surgery" ; sc:url "https://scikit-surgerytutorial01.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3316 ; sc:citation , "pmcid:PMC5123367", "pubmed:27942268" ; sc:description "Scientific Luigi (SciLuigi for short) is a light-weight wrapper library around Spotify's Luigi workflow system that aims to make writing scientific workflows more fluent, flexible and modular." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SciLuigi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9.5" ; sc:url "https://github.com/pharmbio/sciluigi" ; biotools:primaryContact "Samuel Lampa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3168, edam:topic_3934 ; sc:citation ; sc:description """Universal Single-Cell Matching with Unpaired Feature Sets. Code for Universal Single-Cell Matching with Unpaired Feature Sets. Integrates datasets from multiple single cell 'omics technologies in two steps. CyTOF data: The sample was profiled with CyTOF using a 41-markers panel designed for an in-depth characterization of the immune compartment of a sample. Data preprocessing was performed following the workflow described in (Chevrier et al., 2017, 2018). Cell-type assignment was performed using a Random Forest classifier trained on multiple manually gated samples. In the SCIM manuscript, we utilize a subset comprising B-Cells and T-Cells only, for a total of 135,334 cells.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "LGPL-3.0" ; sc:name "SCIM" ; sc:url "https://github.com/ratschlab/scim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9122610", "pubmed:35524568" ; sc:description "A platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "scIMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://server.wei-group.net/scIMC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "Unsupervised clustering of metagenomic sequences using interpolated Markov models." ; sc:featureList edam:operation_0291, edam:operation_3432 ; sc:name "Scimm" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "0.3.0" ; sc:url "http://www.cbcb.umd.edu/software/scimm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3391 ; sc:description "SCIMO a prototype of a 2-D Gel Electrophoresis image analysis system. Being a prototype, some errors may be found that we would appreciate to be informed of. Currently, this software detects the protein spots in the gel and will present the area and volume of each spot." ; sc:featureList edam:operation_3443 ; sc:name "SCIMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20100824" ; sc:url "http://w3.ualg.pt/~aanjos/prototypes.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3500, edam:topic_3676 ; sc:citation , "pmcid:PMC10317120", "pubmed:37308294" ; sc:description "Accurate integration of multiple heterogeneous single-cell RNA-seq data sets by learning contrastive biological variation." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "scInt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Jinsl-lab/scInt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_2229, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """A scalable and accurate cell-type identification method for scRNA-seq data with application to integration of multiple donors. scintegral can be installed using pip.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3799 ; sc:license "GPL-2.0" ; sc:name "scIntegral" ; sc:url "https://github.com/hanbin973/scIntegral" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:32706854" ; sc:description """Scalable machine learning-assisted model exploration and inference using Sciope. Scalable inference, optimization and parameter exploration (sciope) is a Python 3 package for performing machine learning-assisted inference and model exploration by large-scale parameter sweeps. Please see the documentation for examples.""" ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_3658 ; sc:name "Sciope" ; sc:url "https://github.com/Sciope/Sciope" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3806 ; sc:name "3D EM Mask" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0889 ; sc:name "Structural profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Workbench" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0611 ; sc:citation ; sc:description "A software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. 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A powerful tool for comparative genomics." ; sc:featureList edam:operation_2421 ; sc:name "SciRoKo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.4" ; sc:url "http://www.kofler.or.at/bioinformatics/SciRoKo/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3324 ; sc:citation ; sc:description """A Scanpy extension for analyzing single-cell T-cell receptor sequencing data. Scirpy: A Scanpy extension for analyzing single-cell immune-cell receptor sequencing data. Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization. Tutorials — scirpy documentation.""" ; sc:featureList edam:operation_0337 ; sc:license "BSD-3-Clause" ; sc:name "Scirpy" ; sc:softwareHelp ; sc:url "https://github.com/icbi-lab/scirpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "Package to create In Silico Interactomes." ; sc:featureList edam:operation_2492 ; sc:license "GPL-3.0" ; sc:name "ScISI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ScISI.html" ; biotools:primaryContact "Tony Chiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3304, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9237735", "pubmed:35604081" ; sc:description "Visualizing Differential Isoform Expression in Single-Cell Long-Read Data." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ScisorWiz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/ans4013/ScisorWiz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:citation ; sc:description "To perform analysis of live imaging under the ppH assay." ; sc:isAccessibleForFree true ; sc:name "scission_analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.21" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/72744-scission_analysis" ; biotools:primaryContact "David Perrais" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3175, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC7804101", "pubmed:33436599" ; sc:description """SCISSOR is a framework for identifying structural changes in RNA transcripts. Shape Changes In Selecting Sample Outliers in RNA-seq. SCISSOR (shape changes in selecting sample outliers in RNA-seq) aims for unsupervised screening of a range of structural alterations in RNA-seq data. SCISSOR considers a novel shape property of aligned short read data through a base-level pileup file. This intact and uncompressed view of RNA-seq profile enables the unbiased discovery of structural alterations by looking for anomalous shapes in expression. This approach holds promise for identifying otherwise obscured genetic aberrations. As a result, SCISSOR identifies known as well as novel aberrations including abnormal splicing, intra-/intergenic deletions, small indels, alternative transcription start/termination.""" ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_3435 ; sc:name "SCISSOR" ; sc:url "https://github.com/hyochoi/SCISSOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3934 ; sc:citation , "pmcid:PMC10412410", "pubmed:37498558" ; sc:description "Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCISSORS" ; sc:url "https://github.com/jr-leary7/SCISSORS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8428296", "pubmed:34514416" ; sc:description "S ingle C ell I nferred S ite S pecific O mics R esources for T umor M icroenvironments Single Cell Inferred Site Specific Omics Resource for Tumor Microenvironment (SCISSORTM) is an online open resource to investigate the association between the composition of tisssue-specific cell types and tumor omics data. SCISSORTM combines large scale TCGA bulk tumor multi-omics data and high-resolution single cell transcriptomics data and infers the abundance of cell type-specific expression profile in heterogeneous samples." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCISSORTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://thecailab.com/scissor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:citation "pubmed:15215438" ; sc:description "Set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure." ; sc:featureList edam:operation_0331, edam:operation_0480, edam:operation_2406, edam:operation_3080, edam:operation_3096 ; sc:name "SCit" ; sc:url "http://bioserv.rpbs.jussieu.fr/cgi-bin/SCit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3293, edam:topic_3474 ; sc:citation ; sc:description "Compute mutation histories of somatic cells. Given noisy mutation profiles of single cells, this performs a stochastic search to find the Maximum Likelihood (ML) or Maximum aposterori (MAP) tree and/or to sample from the posterior probability distribution." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "SCITE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/cbg-ethz/SCITE" ; biotools:primaryContact "Niko Beerenwinkel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3297, edam:topic_3308, edam:topic_3934 ; sc:citation , "pubmed:34354295" ; sc:description "single-cell combinatorial indexed cytometry sequencing." ; sc:featureList edam:operation_0314, edam:operation_0480, edam:operation_3200, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:name "SCITO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yelabtools.herokuapp.com/scSeqCostCalc/scito.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Library aimed at application developers writing scientific software to support this tracking of scientific computation. The library provides elementary functionality to support logging. The primary capabilities concern generating checksums on input and output files and facilitating logging of the computational environment. If the optional dependency mpiutils is installed, then logging can be done safely in a parallel computation environment." ; sc:featureList edam:operation_3435 ; sc:name "SciTrack" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bitbucket.org/gavin.huttley/scitrack" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "This is an interactive viewer for 2D embeddings such as UMAP or tSNE of high dimensional single-cell RNA-seq data that is run directly out of the Jupyter Notebook environment." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Sciviewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/colabobio/sciviewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """Learning association for single-cell transcriptomics by integrating profiling of gene expression and alternative polyadenylation. Learning association for single-cell transcriptomics by integrating single-cell profiling of gene expression and alternative polyadenylation. High variability and dropout rate inherent in scRNA-seq confounds the reliable quantification of cell-cell associations based on the gene expression profile alone.""" ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3799, edam:operation_3935 ; sc:name "scLAPA" ; sc:url "https://github.com/BMILAB/scLAPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0208, edam:topic_0749, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC9619308", "pubmed:36325065" ; sc:description "SCLC CellMiner Cross Database (SclcCellMinerCDB) allows translational researchers to conduct analyses across all major SCLC cancer cell line pharmacogenomic data sources from NCI, Sanger GDSC, and Broad CCLE/CTRP." ; sc:featureList edam:operation_0337, edam:operation_0417, edam:operation_0440, edam:operation_3207, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "SCLC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://discover.nci.nih.gov/SclcCellMinerCDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0208, edam:topic_2640, edam:topic_3295, edam:topic_3308 ; sc:citation ; sc:description """Integrated Genomics and Therapeutics Predictors of Small Cell Lung Cancer Cell Lines based on their genomic signatures. CellMiner Cross Database (CellMinerCDB) is the first web application to allow translational researchers to conduct analyses across all major cancer cell line pharmacogenomic data sources from NCI-DTP NCI-60, Sanger GDSC, and Broad CCLE/CTRP.""" ; sc:featureList edam:operation_3196, edam:operation_3233, edam:operation_3463 ; sc:name "SCLCCellMiner" ; sc:url "https://discover.nci.nih.gov/SclcCellMinerCDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2229, edam:topic_2815, edam:topic_3395 ; sc:citation "pubmed:20972216" ; sc:description "User-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells." ; sc:featureList edam:operation_0314, edam:operation_2429, edam:operation_2495, edam:operation_3223 ; sc:name "SCLD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scld.mcb.uconn.edu" ; biotools:primaryContact "Craig E. Nelson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3360 ; sc:citation , "pubmed:35914950" ; sc:description "Learning discriminative and structural samples for rare cell types with deep generative model." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scLDS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xkmaxidian/scLDS2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0804, edam:topic_3170 ; sc:citation , "pubmed:34481921" ; sc:description "scLINE is an R package for dimension reduction of single-cell RNA-seq data. scLINE integrates the single-cell RNA-seq data and multiple gene networks collated from public databases, supplementing inter-gene interactions to solve the problem of missing information caused by drop-out events." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scLINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BMILAB/scLINE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3295 ; sc:citation ; sc:description """Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. scLink: Inferring gene networks from single-cell gene expression data.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3463 ; sc:name "scLink" ; sc:url "https://github.com/Vivianstats/scLink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2229, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description """automatic detection of consensus gene clusters across multiple single-cell datasets. A R-based tool to do the automatic identification of co-expressed genes across mulitple single cell RNA-seq datasets simultaneously. scLM works with multiple single cell RNA-seq dataset as inputs. It also works with one single cell dataset. Bascially, the format looks like the following. Example data files can be found in the Data folder.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3766 ; sc:name "scLM" ; sc:url "https://github.com/QSong-WF/scLM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:32142105" ; sc:description """subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks. SCLpred-EMS: Prediction of protein subcellular localization.""" ; sc:featureList edam:operation_0418, edam:operation_2489, edam:operation_3928 ; sc:name "SCLpred-EMS" ; sc:url "http://distilldeep.ucd.ie/SCLpred2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0820, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:33983651" ; sc:description "SCLpred-MEM is a web application for subcellular localization prediction of membrane proteins by deep N-to-1 convolutional neural networks." ; sc:featureList edam:operation_0267, edam:operation_0418, edam:operation_2489, edam:operation_4009 ; sc:name "SCLpred-MEM" ; sc:url "http://distilldeep.ucd.ie/SCLpred-MEM/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9191214", "pubmed:35482476" ; sc:description "A method to test dysregulated ligand-receptor interactions from single cell transcriptomics." ; sc:featureList edam:operation_3223, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cyhsuTN/scLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8628418", "pubmed:34844559" ; sc:description "scLRTC is a Matlab package for imputing for scRNA-seq. The imputed expression matrix from scLRTC can be used as inputs for other existing scRNA-seq pipelines or tools for downstream analyses, such as cell type clustering, dimension reduction, and visualization." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scLRTC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jianghuaijie/scLRTC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:25599176" ; sc:description "Modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation." ; sc:featureList edam:operation_3680 ; sc:name "scLVM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PMBio/scLVM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC9071478", "pubmed:34986249" ; sc:description "A robust and accurate cell type classifier for single cell RNA-seq data" ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3703 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scMAGIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TianLab-Bioinfo/scMAGIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2229, edam:topic_3308 ; sc:citation , "pubmed:36774895" ; sc:description "Marker gene selection from scRNA-seq data for spatial transcriptomics studies." ; sc:featureList edam:operation_0314 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "scMAGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/doganlab/scmags" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2032 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3166 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0607, edam:topic_2229, edam:topic_3308 ; sc:citation ; sc:description "a method for projecting cells from an scRNA-seq data set onto cell types or individual cells from other experiments" ; sc:featureList edam:operation_0335, edam:operation_2495, edam:operation_3436, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.sanger.ac.uk/science/tools/scmap" ; biotools:primaryContact "Martin Hemberg", "Vladimir Kiselev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Alternative polyadenylation (APA) causes shortening or lengthening of the 3ʹ-untranslated region (3ʹ-UTR), widespread in complex tissues. To detect APA and identify cell-type-specific APA in a multi-cluster setting, we developed a model-based method, scMAPA. The first part of scMAPA is coded as shell scripts, which can 1) divide the aligned read data by the cell cluster[1] and remove PCR duplicates by UMI-tools; 2) Pad the 3'biased reads and convert BAM to Bedgraph file; 3) estimate the abundance of 3ʹ-UTR long and short isoform of genes in each cluster-bulk data using linear regression and quadratic programming implemented in DaPars2. The second part of scMAPA is coded as an R package, which can 4) fit a logistic regression model for each gene and estimate the significance of APA; 5) Identify cluster-specific 3'UTR shortening and lengthening; 6) Do visualization to show the APA dynamics." ; sc:name "scMAPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ybai3/scMAPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0625, edam:topic_3170, edam:topic_3517 ; sc:citation ; sc:description """using scRNA-seq to infer cell-type specificities of differentially expressed genes. Description of scMappR R package adapted from pre-print. single-cell mapper (scMappR) data repository.""" ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "scMappR" ; sc:url "https://cran.r-project.org/web/packages/scMappR/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3306, edam:topic_3374, edam:topic_3474 ; sc:citation , "pubmed:36284036" ; sc:description "Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "SCMB3PP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/SCMB3PP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:36848584" ; sc:description "A high-precision cell clustering algorithm integrating marker gene set with single-cell RNA sequencing data." ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCMcluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HaoWuLab-Bioinformatics/SCMcluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0621, edam:topic_3382, edam:topic_3473 ; sc:citation "pubmed:14681423", "pubmed:15290760", "pubmed:15980577" ; sc:description "Collection of micrographs of budding yeast mutants, visualization and data mining tools are provided." ; sc:featureList edam:operation_0306 ; sc:name "SCMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scmd.gi.k.u-tokyo.ac.jp/" ; biotools:primaryContact "Yoshikazu Ohya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229 ; sc:citation , "pmcid:PMC10234764", "pubmed:37220900" ; sc:description "Dual-modality factor model for single-cell multiomics embedding." ; sc:featureList edam:operation_3432, edam:operation_3436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "scME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bucky527/scME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_3170 ; sc:citation , "pmcid:PMC10210493", "pubmed:37231345" ; sc:description "Fast and clustering-independent method for detecting differentially expressed genes in single-cell RNA-seq data." ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "scMEB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/FocusPaka/scMEB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC9853317", "pubmed:36698768" ; sc:description "Single-cell multi-omic enhancer-based gene regulatory network inference." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scMEGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://costalab.github.io/scMEGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation ; sc:description """Bayesian modelling of DNA methylation heterogeneity at single-cell resolution. Here we introduce scMET, a Bayesian framework for the analysis of single cell DNA methylation data. This modelling approach combines a hierarchical beta-binomial specification with a generalised linear model framework with the aim of capturing biological overdispersion and overcome data sparsity by sharing information across cells and genomic features.""" ; sc:featureList edam:operation_3204, edam:operation_3659, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "scMET" ; sc:url "https://github.com/andreaskapou/scMET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3295 ; sc:description "Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report." ; sc:featureList edam:operation_2428, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "scmeth" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scmeth.html" ; biotools:primaryContact "Divy Kangeyan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0654, edam:topic_3173, edam:topic_3674, edam:topic_3974 ; sc:citation , "pubmed:34570235" ; sc:description "A database of single-cell methylation maps for human and mouse." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3186, edam:operation_3207, edam:operation_3919 ; sc:isAccessibleForFree true ; sc:name "scMethBank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ngdc.cncb.ac.cn/methbank/scm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "Similarity constrained matrix factorization method for the drug-disease association prediction, which makes use of known drug-disease associations, drug features and disease semantic information. It projects the drug-disease association relationship into two low-rank spaces, which uncover latent features for drugs and diseases, and then introduces drug feature-based similarities and disease semantic similarity as constraints for drugs and diseases in low-rank spaces." ; sc:featureList edam:operation_2409 ; sc:name "SCMFDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfotech.cn/SCMFDD/" ; biotools:primaryContact "Feng Liu", "Wen Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:33341869" ; sc:description """Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. scMLnet is an R package developed to construct inter-/intracellular multilayer singaling network based on single-cell RNA-seq expression data. scMLnet constructs the multilayer network by integrating intercellular pathways (ligand-receptor interactions) and intracellular subnetworks (receptor-TF pathways and TF-target gene interactions) based on cell-type specific gene expression, prior network information and statistical inference. scMLnet can also visualize the constructed inter-/intracellular signaling pathways between the central cell and neighboring cells. scMLnet is implemented using R (version 3.6.0) and Python (version 3.7).""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3463 ; sc:name "scMLnet" ; sc:url "https://github.com/SunXQlab/scMLnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9481959", "pubmed:36124302" ; sc:description "Single-cell multi-modal GAN reveals spatial patterns in single-cell data from triple-negative breast cancer." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3435, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scMMGAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/KrishnaswamyLab/scMMGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0122, edam:topic_0123, edam:topic_0820 ; sc:citation "pubmed:26677931" ; sc:description "A novel method  based on the scoring card method (SCM) using dipeptide composition to identify and characterize MTPs from an existing dataset." ; sc:featureList edam:operation_0269 ; sc:name "SCMMTP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iclab.life.nctu.edu.tw/iclab_webtools/SCMMTP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3308 ; sc:citation ; sc:description """Single-Cell Multi-omics clustering. It is an approach to identify cell clusters from data with co-measurements of scRNA-seq and scATAC-seq from the same cell. We overcome the high sparsity of the scATAC-seq data by using an imputation strategy that exploits the less-sparse scRNA-seq data available from the same cell. Subsequently, scMoC identifies clusters of cells by merging clusterings derived from both data domains individually. We tested scMoC on datasets generated using different protocols with variable data sparsity levels. We show that, due to its imputation scheme, scMoC 1) is able to generate informative scATAC-seq data due to its RNA guided imputation strategy, and 2) results in integrated clusters based on both RNA and ATAC information that are biologically meaningful either from the RNA or from the ATAC perspective.""" ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3557 ; sc:name "scMoC" ; sc:url "https://github.com/meltager/scmoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Inference of Cell-Type-Specific Regulatory Networks and Energy Landscapes. A method to infer Gene Regulatory Networks (GRNs) and reconstruct developmental energy landscapes directly from single-cell RNA-seq data.""" ; sc:featureList edam:operation_0279, edam:operation_2437, edam:operation_3431 ; sc:name "scMomentum" ; sc:url "https://github.com/larisa-msoto/scMomentum.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description """Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data. scMontage is a system for searching gene expression databases for similar cells to the query gene expression profile. Please enter your profile in the blank space or try sample queries.""" ; sc:featureList edam:operation_2421, edam:operation_2495 ; sc:name "scMontage" ; sc:url "https://scmontage.stemcellinformatics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0123, edam:topic_0780 ; sc:citation "pubmed:25708243" ; sc:description "A novel bioinformatics method of predicting and characterizing PSPs based on scoring card method." ; sc:featureList edam:operation_3092 ; sc:name "SCMPSP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://iclab.life.nctu.edu.tw/SCMPSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:34623390" ; sc:description "scMRA is a robust deep learning method to annotate scRNA-seq data with multiple reference datasets. Single-cell RNA-seq (scRNA-seq) has been widely used to resolve cellular heterogeneity. After collecting scRNA-seq data, the natural next step is to integrate the accumulated data to achieve a common ontology of cell types and states. Thus, an effective and efficient cell-type identification method is urgently needed. Meanwhile, high quality reference data remain a necessity for precise annotation. However, such tailored reference data are always lacking in practice. 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sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0610 ; sc:citation , "pmcid:PMC9476499", "pubmed:36120041" ; sc:description "A New Approach for Identifying and Analyzing Anti-MRSA Peptides Using Estimated Propensity Scores of Dipeptides." ; sc:featureList edam:operation_3454, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "SCMRSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/SCMRSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9440561", "pubmed:36056412" ; sc:description "A statistical multidimensional imputation method for single-cell RNA-seq data leveraging transcriptome dynamic information." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scMTD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Jinsl-lab/scMTD" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3306, edam:topic_3474, edam:topic_3930 ; sc:citation , "pmcid:PMC8779003", "pubmed:35057016" ; sc:description "A New Approach for Identifying and Characterizing of Tumor-Homing Peptides Using Estimated Propensity Scores of Amino Acids." ; sc:featureList edam:operation_0252, edam:operation_3631, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "SCMTHP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/SCMTHP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0736, edam:topic_3474 ; sc:citation , "pmcid:PMC8664844", "pubmed:34893688" ; sc:description "A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides." ; sc:featureList edam:operation_0303, edam:operation_0480, edam:operation_1839 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCMTPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/SCMTPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:34999761" ; sc:description "Neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scNAME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aster-ww/scNAME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3063, edam:topic_3384 ; sc:citation , "pubmed:32224471" ; sc:description "A Novel UGI Cancer Screening Framework Based on Semantic-Level Multimodal Data Fusion." ; sc:name "SCNET" ; sc:url "https://github.com/netflymachine/SCNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0749, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8019823", "pubmed:33828580" ; sc:description "scNET is a tool for evaluating the reproducibility of single-cell gene regulatory network inference algorithms. Here three single-cell network inference algorithms is benchamrk based on their reproducibility, i.e. their ability to infer similar networks once applied to two independent datasets from the same biological condition." ; sc:featureList edam:operation_3258, edam:operation_3463, edam:operation_3927 ; sc:name "scNET" ; sc:url "https://github.com/ComputationalSystemsBiology/scNET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "Single-Cell RNA Seq analysis and visualization package for Cytoscape" ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3501, edam:operation_3680, edam:operation_3741 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "scNetViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.cgl.ucsf.edu/cytoscape/scNetViz/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3174, edam:topic_3697 ; sc:citation ; sc:description "Sparse Correlation Network Investigation for Compositional Data." ; sc:featureList edam:operation_3463, edam:operation_3766, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SCNIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lozuponelab/SCNIC" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2032, edam:format_3033 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3033, edam:format_3617 ; sc:name "Gene expression profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "A tool for normalization of single-cell RNA-seq data." ; sc:featureList edam:operation_3435, edam:operation_3563, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SCnorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "https://www.biostat.wisc.edu/~kendzior/SCNORM/" ; biotools:primaryContact "Rhonda Bacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3168, edam:topic_3308, edam:topic_3474 ; sc:citation , "pubmed:33627475" ; sc:description """scNym - Semi-supervised adversarial neural networks for single cell classification. scNym is a neural network model for predicting cell types from single cell profiling data (e.g. scRNA-seq) and deriving cell type representations from these models. While cell type classification is the main use case, these models can map single cell profiles to arbitrary output classes (e.g. experimental conditions).""" ; sc:featureList edam:operation_0303, edam:operation_0314, edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "scNym" ; sc:url "https://github.com/calico/scnym" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3752 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0621, edam:topic_0625, edam:topic_3517 ; sc:author "Ola Brynildsrud" ; sc:citation ; sc:contributor "Vegard Eldholm" ; sc:description "Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Scoary" ; sc:operatingSystem "Linux" ; sc:provider "Norwegian Institute of Public Health", "UiO" ; sc:softwareHelp , ; sc:softwareVersion "1.6.11" ; sc:url "https://github.com/AdmiralenOla/Scoary" ; biotools:primaryContact "Ola Brynildsrud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3940 ; sc:citation , "pmcid:PMC10450184", "pubmed:37403780" ; sc:description "Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCOIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/deepomicslab/SCOIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3170 ; sc:citation , "pmcid:PMC7237818", "pubmed:32431014" ; sc:description "we generate independent single-cell RNA-seq and single-cell ATAC-seq atlases of the Drosophila eye-antennal disc and spatially integrate the data into a virtual latent space that mimics the organization of the 2D tissue using ScoMAP (Single-Cell Omics Mapping into spatial Axes using Pseudotime ordering)." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ScoMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/aertslab/ScoMAP" ; biotools:primaryContact "Stein Aerts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3299, edam:topic_3673 ; sc:citation ; sc:description "A method for profiling Copy Number Alterations in Cancer Evolution using Single Cell Whole Genome Sequencing." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCONCE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NielsenBerkeleyLab/sconce" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:18166073" ; sc:description "This tool reports position-specific measures of conservation." ; sc:featureList edam:operation_0448 ; sc:name "SCONE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genetics.bwh.harvard.edu/scone/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:description "A package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses." ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "scone" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scone.html" ; biotools:primaryContact "Michael Cole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "SConES (Selecting Connected Explanatory SNPs) is a network-guided multi-locus association mapping methods. It allows for the discovery genetic loci that are maximally associated with a phenotype, and tend to be connected on an underlying network. This network can be constructed from a gene-gene interaction network (based on proximity), or in any way such that you believe that neighboring SNPs should tend to be selected together." ; sc:featureList edam:operation_2429 ; sc:name "SConES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/scones.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps\"fold change\" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold." ; sc:featureList edam:operation_0337, edam:operation_2424 ; sc:license "Artistic-2.0" ; sc:name "Sconify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Sconify.html" ; biotools:primaryContact "Tyler J Burns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:15980446" ; sc:description "Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_0408, edam:operation_0474, edam:operation_2487 ; sc:name "Scooby Domain Prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ibivu.cs.vu.nl/programs/scoobywww/" ; biotools:primaryContact "Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation , "pubmed:33135074" ; sc:description """a new data storage format for single-cell Hi-C data. Single-cell Hi-C research currently lacks an efficient, easy to use and shareable data storage format. Recent studies have used a variety of sub-optimal solutions: publishing raw data only, text based interaction matrices, or reusing established Hi-C storage formats for single interaction matrices. These approaches are storage and pre-processing intensive, require long labour time and are often error-prone. RESULTS:The single-cell cooler file format (scool) provides an efficient, user-friendly and storage-saving approach for single-cell Hi-C data. It is a flavour of the established cooler format and guarantees stable API support. AVAILABILITY:The single-cell cooler format is part of the cooler file format as of API version 0.8.9. It is available via pip, conda and github. ||| CORRECT NAME OF TOOL COULD ALSO BE 'cooler'""" ; sc:featureList edam:operation_0335 ; sc:name "scool" ; sc:url "https://github.com/open2c/cooler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0623, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:10592240", "pubmed:11752311", "pubmed:14681400", "pubmed:18000004", "pubmed:7723011", "pubmed:9847194" ; sc:description "Database created by a combination of manual inspection and automated methods. 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It is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. It can also identify other genes in the genome that might be coregulated with the original gene set." ; sc:featureList edam:operation_0238, edam:operation_0438, edam:operation_0445, edam:operation_3501 ; sc:name "SCOPE" ; sc:url "http://genie.dartmouth.edu/scope/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315 ; sc:description "Implemented bootstrapping by Monte Carlo sampling with replacement for ROC areas." ; sc:isAccessibleForFree true ; sc:name "SCOPE: bootstrapping the ROC areas and errors in two ways" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/37366-scope-bootstrapping-the-roc-areas-and-errors-in-two-ways" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0153, edam:topic_0625, edam:topic_2258, edam:topic_2840 ; sc:citation , "pmcid:PMC7695036", "pubmed:33094747" ; sc:description """a cheminformatics toolbox for investigating lipidomic changes in complex systems. . To run any of the r scripts provided, clone the repository and open the SCOPE_Lipid_Analysis.Rproj file in Rstudio. Run the scripts within the project, so that they can find the relevant paths on your machine. Example data files for dual Case vs. Control comparison are included for building biological-structure relationships.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3196, edam:operation_3432 ; sc:name "SCOPE" ; sc:url "https://github.com/BakerLabNCSU/SCOPE" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3590 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:author "Kristofer Davie", "Lukasz Kreft", "Maxime De Waegeneer" ; sc:citation , "pubmed:29909982" ; sc:contributor ; sc:description "SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom. This file format for very large omics datasets is maintained by the Linnarsson Lab through the loompy Python package (https://github.com/linnarsson-lab/loompy)." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCope" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.2", "1.8.2" ; sc:url "http://scope.aertslab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315 ; sc:description "SCOPE (SEER (Surveillance, Epidemiology, and End Results) Clinical Outcome Prediction Expert) optimizes risk factors using binary fusion with Area of ROC as a metric." ; sc:isAccessibleForFree true ; sc:name "SCOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/37259-scope-v-1-0-seer-clinical-outcome-prediction-expert" ; biotools:primaryContact "Rex Cheung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081 ; sc:author "Lukasz Kreft" ; sc:citation , "pubmed:30540477" ; sc:description "Scop3D is a tool that automatically annotates protein structure with sequence conservation starting from a set of protein sequence variants." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Scope3D" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://iomics.ugent.be/scop3d/#/home" ; biotools:primaryContact "Elien Vandermarliere" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0623, edam:topic_0736, edam:topic_3474 ; sc:citation , , "pmcid:PMC3965108", "pmcid:PMC8728185", "pubmed:24304899", "pubmed:34850923" ; sc:description "Extended database to facilitate variant interpretation and machine learning." ; sc:featureList edam:operation_2996, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "SCOPe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://scop.berkeley.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3512 ; sc:citation ; sc:description "Accurately identifying homopolymers in cDNA sequences using Hidden Markov Models. This can be extended to trimming poly(A)/poly(T) tails, or identifying A,C,G,T,or N homopolymer sequences." ; sc:featureList edam:operation_2990, edam:operation_2995, edam:operation_3192 ; sc:name "SCOPE++" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20130523" ; sc:url "http://code.google.com/p/scopeplusplus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3343 ; sc:citation , "pubmed:32892221" ; sc:description """an integrated negative design python library for desirable HTS/VS database design. Scopy (Screnning COmpounds in PYthon), an integrated negative design python library designed for screening out undesirable compounds in the early drug discovery. Scopy includes six modules, covering data preparation, screening filters, the calculation of scaffolds and descriptors, and the visualization analysis.""" ; sc:featureList edam:operation_3216, edam:operation_3695, edam:operation_3938 ; sc:license "MIT" ; sc:name "Scopy" ; sc:url "https://github.com/kotori-y/Scopy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0593, edam:topic_0659 ; sc:citation "pubmed:11752346", "pubmed:14681389" ; sc:description "Database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships." ; sc:featureList edam:operation_0278, edam:operation_0570, edam:operation_2441, edam:operation_2996 ; sc:name "SCOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://scor.berkeley.edu/" ; biotools:primaryContact "Peter S. Klosterman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC6792129", "pubmed:31649721" ; sc:description """Comprehensive Analysis of Human microRNA-mRNA Interactome. Our services require cookies to keep track of your submissions and find your results. Submissions expire after 24 hours.""" ; sc:featureList edam:operation_0463, edam:operation_3792 ; sc:name "score" ; sc:url "http://score.generesearch.ru/services/mirna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0769, edam:topic_3170 ; sc:citation , "pubmed:32717040" ; sc:description """a consensus tool for detecting differentially expressed genes in bacteria. Smart Consensus Of RNA Expression pipelines.""" ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3680, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "SCORE" ; sc:url "https://github.com/SiWolf/SCORE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2269, edam:topic_3053, edam:topic_3168, edam:topic_3678 ; sc:citation ; sc:description "Detect disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The association testing is based on score-type statistics. Statistical significance can be assessed by using asymptotic normal approximation or resampling." ; sc:featureList edam:operation_3659 ; sc:name "SCORE-Seq" ; sc:operatingSystem "Linux" ; sc:softwareVersion "5.3" ; sc:url "http://dlin.web.unc.edu/software/score-seq/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A program to score residue conservation in a multiple sequence alignment." ; sc:featureList edam:operation_0448 ; sc:name "Scorecons" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Data analysis toolkit designed for large sets of gene expressions over various experiments. Includes methods for evaluating data sets, discovering informative genes that are differentially expressed across the classes, classifying the experiments using supervised learning algorithms, and clustering the genes using semi-supervised learning method." ; sc:featureList edam:operation_2495, edam:operation_3432 ; sc:name "ScoreGene" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.cs.huji.ac.il/labs/compbio/scoregenes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:description "It can get the samples' inversion status of known inversions. It uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for two well known inversions and for two additional regions." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "scoreInvHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scoreInvHap.html" ; biotools:primaryContact "Carlos Ruiz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation ; sc:description """a computer-aided scoring tool for resting-state M/EEG epochs. scorEpochs: a computer aided scoring tool for resting-state M/EEG epochs. Scorepochs aims to represent a simple tool for automatic scoring of resting-state M/EEG epochs to provide an accurate yet objective method to aid M/EEG experts during epoch selection procedure.""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Scorepochs" ; sc:url "https://github.com/matteogithub/scorepochs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_2258, edam:topic_2814 ; sc:citation ; sc:description "Python package for manipulating three dimensional molecular data. Unlike similar packages, it is written in pure Python and so requires no dependencies or installation. One can incorporate the source code directly into their own programs. But it is not designed to compete with other similar packages." ; sc:featureList edam:operation_0570 ; sc:license "Apache-2.0" ; sc:name "Scoria" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://durrantlab.com/scoria/" ; biotools:primaryContact "Jacob D. Durrant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3299 ; sc:author ; sc:citation , , "pubmed:32556216" ; sc:description """SCORPiOs - Synteny-guided CORrection of Paralogies and Orthologies SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event. SCORPiOs identifies gene trees where the whole-genome duplication is missing or incorrectly placed, based on the genomic locations of the duplicated genes across the different species. SCORPiOs then builds an optimized gene tree consistent with the known WGD event, the species tree, local synteny context, as well as gene sequence evolution.""" ; sc:featureList edam:operation_0326 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCORPiOs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/DyogenIBENS/SCORPIOS" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3474, edam:topic_3940 ; sc:citation ; sc:description """Gromov-Wasserstein optimal transport to align single-cell multi-omics data. Single-Cell alignment using Optimal Transport (SCOT). SCOT is a python tool for performing unsupervised alignment of single-cell multi-omics datasets. Its methodology is detailed in the pre-print "Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data".""" ; sc:featureList edam:operation_0303, edam:operation_0496, edam:operation_3435 ; sc:license "MIT" ; sc:name "SCOT" ; sc:url "https://github.com/rsinghlab/SCOT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0203, edam:topic_0634, edam:topic_3305 ; sc:citation , "pmcid:PMC5106001", "pubmed:27835644" ; sc:description "Structured COalescent Transmission Tree Inference. BEAST 2 package to reconstruct transmission trees from genetic data of the pathogen and epidemiological data simultaneously." ; sc:featureList edam:operation_0323, edam:operation_2426, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "SCOTTI" ; sc:url "https://bitbucket.org/nicofmay/scotti/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation "pubmed:23314327" ; sc:description "A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims." ; sc:featureList edam:operation_3680 ; sc:name "Scotty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scotty.genetics.utah.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3474, edam:topic_3955 ; sc:citation , "pmcid:PMC8268592", "pubmed:34238207" ; sc:description "A stepwise machine learning framework for predicting metabolite-dependent regulatory interactions." ; sc:featureList edam:operation_0478, edam:operation_2437, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SCOUR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/gtStyLab/SCOUR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3170, edam:topic_3934 ; sc:citation ; sc:description """Single-cell outlier analysis in cancer. SCOUTS - Single Cell Outlier Selector. SCOUTS — SCOUTS 2019 documentation. SCOUTS is a tool that quickly finds OUTLIERS in single-cell datasets, especially those obtained by mass cytometry (CyToF) and single-cell RNA sequencing (scRNA-Seq) platforms.""" ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3907 ; sc:license "MIT" ; sc:name "SCOUT" ; sc:softwareHelp ; sc:url "http://www.ufrgs.br/labsinal/scouts" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1042 ; sc:name "SCOP sunid" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128 ; sc:description "PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent." ; sc:featureList edam:operation_0224 ; sc:name "SCOWL" ; sc:url "http://www.scowlp.org" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170 ; sc:citation ; sc:description "A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. 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It provides an efficient description of structural motifs based on simple geometrical assumptions." ; sc:featureList edam:operation_2479 ; sc:name "ScrewFit" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0.4" ; sc:url "http://dirac.cnrs-orleans.fr/plone/software/screwfit/screwfit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """Single-cell identity definition using random forests and recursive feature elimination. scRFE (single-cell identity definition using random forests and recursive feature elimination) is a Python package that uses a one versus all random forest classifier with recursive feature elimination to identify the set of genes necessary and sufficient to describe the different features of your single-cell RNA sequencing data. 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It can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file." ; sc:featureList edam:operation_0310 ; sc:name "Scribl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.1.4" ; sc:url "http://chmille4.github.com/Scribl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:34874992" ; sc:description "An accurate simulator for single-cell RNA sequencing data." ; sc:featureList edam:operation_0244, edam:operation_0314, edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SCRIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=SCRIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Scriptella is an open source ETL (Extract-Transform-Load) and script execution tool written in Java. Our primary focus is simplicity. You don't have to study yet another complex XML-based language - use SQL (or other scripting language suitable for the data source) to perform required transformations.""" ; sc:featureList edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "Scriptella" ; sc:softwareHelp , , ; sc:softwareVersion "1.2" ; sc:url "https://scriptella.org/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:20436462" ; sc:description "Tool for assembling transcriptome from paired-end Illumina RNA-Seq data" ; sc:featureList edam:operation_2495, edam:operation_3258, edam:operation_3680 ; sc:name "Scripture" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/software/scripture/" ; biotools:primaryContact "Manuel Garber", "Mitchell Guttman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2229, edam:topic_3170, edam:topic_3676 ; sc:citation , "pubmed:32119079" ; sc:description """imputation for single cell RNA-seq data via robust matrix decomposition. scRMD: Imputation for single cell RNA-seq data via restricted robust matrix decomposition. Chong Chen, Changjing Wu 2017-9-14. scRMD is developed to impute single cell RNA data with dropouts. scRMD assumes the the underlying expression profile of genes is low rank and the dropout events are rare compared with true zero expression.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3557 ; sc:name "scRMD" ; sc:url "https://github.com/XiDsLab/scRMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3304, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC6937257", "pubmed:31889137" ; sc:description """Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data. scRNA - Transfer learning for clustering single-cell RNA-Seq data. A Python framework for single-cell RNA-Seq clustering with special focus on transfer learning. This package contains methods for generating artificial data, clustering, and transfering knowledge from a source to a target dataset. from sklearn.model_selection import train_test_split. def recursive_dirichlet(cluster_spec, num_cells,.""" ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3891 ; sc:license "MIT" ; sc:name "scRNA-Seq" ; sc:url "https://github.com/nicococo/scRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3316, edam:topic_3512 ; sc:citation , "pmcid:PMC10155351", "pubmed:37131143" ; sc:description "Ecosystem of scRNA-seq analysis, visualization, and publishing." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scRNASequest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/interactivereport/scRNASequest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229 ; sc:description "ScRNAX: cross-species transfer of high quality 3’UTR annotation for single cell RNA-Seq" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scRNAx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bi-compbio/scrnax/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3179 ; sc:citation , "pmcid:PMC10191611", "pubmed:36961334" ; sc:description "A fast and memory-frugal genomic sequence aligner for CPUs, GPUs and ASICs." ; sc:featureList edam:operation_0491, edam:operation_3182, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Scrooge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/CMU-SAFARI/Scrooge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC6498700", "pubmed:31046658" ; sc:description "R/Bioconductor package for preprocessing single-cell RNA-sequencing data." ; sc:featureList edam:operation_3198, edam:operation_3219, edam:operation_3563 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scruff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/scruff.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "SCWRL4.0 is the most recent version of the SCWRL program for prediction of protein side-chain conformations. SCWRL4.0 is based on an algorithm based on graph theory that solves the combinatorial problem in side-chain prediction more rapidly than many other available program." ; sc:featureList edam:operation_0480 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "SCRWL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "4.0" ; sc:url "http://dunbrack.fccc.edu/scwrl4/SCWRL4.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "SPARQL endpoint", "Web API", "Workbench" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3316 ; sc:author "Bas Stringer" ; sc:contributor "Albert Meroño Peñuela" ; sc:description "SPARQL Compatible seRvice laYer. Integrate analytic procedures in standard-compliant SPARQL queries." ; sc:featureList edam:operation_0224, edam:operation_2945, edam:operation_3429 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCRY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Centre for Integrative Bioinformatics", "Vrije Universiteit Amsterdam" ; sc:softwareHelp ; sc:softwareVersion "1.2.5" ; sc:url "https://pypi.python.org/pypi/scry" ; biotools:primaryContact "Bas Stringer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:37429992" ; sc:description "Subcellular spatial transcriptomics cell segmentation (SCS), which combines imaging data with sequencing data to improve cell segmentation accuracy. SCS assigns spots to cells by adaptively learning the position of each spot relative to the center of its cell using a transformer neural network." ; sc:featureList edam:operation_0314, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCS" ; sc:url "https://github.com/chenhcs/SCS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:35426898" ; sc:description "scSampler is a Python pacakge for fast diversity-preserving subsampling of large-scale single-cell transcriptomic data." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SONGDONGYUAN1994/scsampler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10166880", "pubmed:37180117" ; sc:description "Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets." ; sc:featureList edam:operation_0337, edam:operation_3446, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "scSELpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MarkDedden/scSELpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9069784", "pubmed:35513780" ; sc:description "A deep model with semi-supervised learning for single-cell transcriptomics." ; sc:featureList edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scSemiAE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PlusoneD/scSemiAE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3315, edam:topic_3474 ; sc:citation , "pubmed:33098418" ; sc:description """Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation. The identification of cell types plays an essential role in the analysis of scRNA-seq data, which, in turn, influences the discovery of regulatory genes that induce heterogeneity. Here, we propose a flexible single cell semi-supervised clustering and annotation framework, scSemiCluster. Notably, without explicit feature alignment and batch effect correction, scSemiCluster outperforms other state-of-the-art, single-cell supervised classification and semi-supervised clustering annotation algorithms in both simulation and real data. In addition, scSemiCluster is suitable for cell annotation on single data and cross-data.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3891 ; sc:name "scSemiCluster" ; sc:url "https://github.com/xuebaliang/scSemiCluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_3170, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:36193998" ; sc:description "A single-cell semi-supervised annotation and dimensionality reduction framework based on generative adversarial network." ; sc:featureList edam:operation_0337, edam:operation_3778, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scSemiGAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rafa-nadal/scSemiGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC8063398", "pubmed:33888056" ; sc:description "scSensitiveGeneDefine is a tool for sensitive gene detection in single-cell RNA sequencing data by Shannon entropy." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_2436, edam:operation_3891 ; sc:name "scSensitiveGeneDefine" ; sc:url "https://github.com/Zechuan-Chen/scSensitiveGeneDefine" ; biotools:primaryContact "Pei Hao", "Xiaoming Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:35043939" ; sc:description "Identify, quantify and characterize cellular communication from single cell RNA sequencing data with scSeqComm." ; sc:featureList edam:operation_3196, edam:operation_3223, edam:operation_3557, edam:operation_3565, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scSeqComm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sysbiobig.dei.unipd.it/software/#scSeqComm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3315, edam:topic_3474, edam:topic_3518 ; sc:citation ; sc:description "Graph signal processing based signed graph learning for gene regulatory inference from single cell RNA-seq data." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scSGL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Single-Cell-Graph-Learning/scSGL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3315 ; sc:citation ; sc:description "scShaper is a tool for linear trajectory inference from single-cell RNA-seq data through discrete pseudotime estimation using Shortest HAmiltonian path PERmuted clustering. scShaper is an R package implementing a new trajectory inference method, which enables accurate and fast linear trajectory inference from single-cell RNA-seq (scRNA-seq) data." ; sc:featureList edam:operation_3890, edam:operation_3891, edam:operation_3935 ; sc:name "scShaper" ; sc:url "https://github.com/elolab/scshaper" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "A novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). Each gene is modelled independently under each treatment condition using the error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion and likelihood ratio test statistic." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scShapes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://github.com/Malindrie/scShapes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3958 ; sc:citation , "pmcid:PMC9092674", "pubmed:35546390" ; sc:description "A tool for synthetic single-cell DNA sequencing data generation." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SCSilicon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xikanfeng2/SCSilicon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0654, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. SCSIM: Jointly Simulating Correlated single-cell and bulk next-generation sequencing data. This is a tool for simulating next-generation sequencing data from a hierarchical sampling arrangement with single-cell and bulk samples.""" ; sc:featureList edam:operation_0244, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "SCSIM" ; sc:url "https://github.com/flahertylab/scsim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "scSimClassify is a reference-free method for multi-class cell type classification based on k-mer level information." ; sc:featureList edam:operation_0314, edam:operation_3436, edam:operation_3472, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "scSimClassify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/digi2002/scSimClassify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2885, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC8103760", "pubmed:33962667" ; sc:description "scSNV is an accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing. scSNV is an alternative to Cell Ranger + velocyto for the alignment, quantification and SNV calling of 10X Single Cell RNA-seq data. Currently, scSNV supports 10X 5-prime and 3-prime 10X version 2 and 3 libraries." ; sc:featureList edam:operation_3200, edam:operation_3227, edam:operation_3463, edam:operation_3799, edam:operation_3933 ; sc:license "MIT" ; sc:name "scSNV" ; sc:url "https://github.com/GWW/scsnv" ; biotools:primaryContact "Gavin W. Wilson", "Jonathan C. Yeung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0108, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33787873" ; sc:description "scSO is a single-cell data clustering based on sparse optimization and low-rank matrix factorization. scSO is a algorithm for scRNA-seq data clustering based on Sparse Optimization and low-rank matrix factorization." ; sc:featureList edam:operation_3432 ; sc:license "BSD-2-Clause" ; sc:name "scSO" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/QuKunLab/scSO" ; biotools:primaryContact , "Falai Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC7898451", "pubmed:33618746" ; sc:description """scSorter is a tool for assigning cells to known cell types according to marker genes. On single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods""" ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3435 ; sc:name "scSorter" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/scSorter/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Corrects genome-wide siRNA screens for seed mediated off-target effect. Suitable functions to identify the effective seeds/miRNAs and to visualize their effect are also provided in the package." ; sc:featureList edam:operation_0231 ; sc:license "GPL-2.0" ; sc:name "scsR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/scsR.html" ; biotools:primaryContact "Andrea Franceschini", "Christian von Mering", "Roger Meier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2830, edam:topic_3170, edam:topic_3277 ; sc:citation , "pmcid:PMC9264648", "pubmed:35799304" ; sc:description "Single cell STEM (scSTEM) is a shiny app based R package for visualizing and clustering genes in pseudotime ordered single cell RNA-seq data. scSTEM is a GUI based tool and thus does not require any coding experience." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0337, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "scSTEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alexQiSong/scSTEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0602, edam:topic_2640, edam:topic_3299, edam:topic_3382, edam:topic_3958 ; sc:citation ; sc:description "scSVAS is an online platform for single cell DNA visualization. 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SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size." ; sc:featureList edam:operation_3214, edam:operation_3223 ; sc:license "GPL-1.0" ; sc:name "SDAMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SDAMS.html" ; biotools:primaryContact "Yuntong Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_2640, edam:topic_3295 ; sc:citation , "pmcid:PMC8897669", "pubmed:35284049" ; sc:description "An integrated database for sex differences in cancer." ; sc:featureList edam:operation_0463, edam:operation_3503, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SDC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sdc.anticancer.xyz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_0749 ; sc:citation ; sc:description "Program that uses a stochastic dictionary model to search for transcription factor binding sites (motifs) in DNA sequences. The algorithm is capable of detecting multiple motif sites of multiple types, gapped motifs, finding the optimal motif width, and calculating motif significance through a MAP score and the Bayes factor using computational methods." ; sc:featureList edam:operation_0445 ; sc:name "SDDA" ; sc:operatingSystem "Linux" ; sc:url "http://www.stats.gla.ac.uk/~mgupta/publications.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3678 ; sc:citation "pubmed:20487547" ; sc:description "The tool performs two tests to evaluate if the experiments are associated and returns a list of interesting features common to all the experiments." ; sc:featureList edam:operation_2424 ; sc:name "sdef" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/sdef/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275, edam:topic_3047 ; sc:citation , "pmcid:PMC8757437", "pubmed:34932340" ; sc:description "sdfconf is a python package aimed to be used as a manipulation and analysis tool when working with .sdf files. High emphasis is on files with multiple conformations of molecules." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sdfconf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.utu.fi/sdfconf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0154, edam:topic_0202, edam:topic_0203, edam:topic_3071 ; sc:citation , "pmcid:PMC6985572", "pubmed:32038710" ; sc:description """Quantifying Gene Essentiality Based on the Context of Cellular Components. SDI Database for the subcellular diversity index. Database for the subcellular diversity index.""" ; sc:featureList edam:operation_0224, edam:operation_2489, edam:operation_3463 ; sc:name "SDI" ; sc:url "http://www.cuilab.cn/sdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8266063", "pubmed:34138847" ; sc:description "SDImpute is an implement block imputation for dropout events in scRNA-seq data. 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In this GitHub project, we give a demo to show how SDLDA works. In data_processing folder, we give following datasets we used in our study.""" ; sc:featureList edam:operation_0306 ; sc:license "MIT" ; sc:name "SDLDA" ; sc:url "https://github.com/CSUBioGroup/SDLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0623 ; sc:citation "pubmed:21593128" ; sc:description "Site Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. 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User-friendly framework that enables the training and the evaluation of species distribution models (SDMs).""" ; sc:featureList edam:operation_3659, edam:operation_3936, edam:operation_3946 ; sc:license "GPL-3.0" ; sc:name "SDMtune" ; sc:url "https://consbiol-unibern.github.io/SDMtune/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0218, edam:topic_0736, edam:topic_3398, edam:topic_3474 ; sc:citation , "pmcid:PMC7201018", "pubmed:32411695" ; sc:description """An Integrated Deep Learning Model for Protein Function Prediction. A Deep Learning Model for Protein Function Prediction. SDNGO is a deep learning model for predicting protein functions using protein sequences, protein domains, and protein-protein interaction (PPI) networks.""" ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_1777, edam:operation_3935 ; sc:name "SDN2GO" ; sc:url "https://github.com/Charrick/SDN2GO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3376, edam:topic_3474 ; sc:citation , "pmcid:PMC8714298", "pubmed:34610645" ; sc:description "SDNDL (Software Defined Networking Description Language) - CAO (CUREX Asset Discovery Tool) Ontology has been developed to give support to the inclusion of information about devices." ; sc:featureList edam:operation_2422, edam:operation_3283, edam:operation_3436, edam:operation_3559, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "SDNDL-CAO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://medal.ctb.upm.es/projects/CUREX/ontologies/sdndlcao/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC8764118", "pubmed:35039537" ; sc:description "Scrutinised distance predictor for protein structures" ; sc:featureList edam:operation_0248, edam:operation_0272, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:name "SDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/mahnewton/sdp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:16379533" ; sc:description "The tool formulates the haplotype inference problem as the following integer quadratic programming (IQP) problem. 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This is done for every pair of sequences in the input file, and, in addition, average values across all pairs are calculated. The output is written as tab-delimited text." ; sc:featureList edam:operation_0335 ; sc:name "SDSW" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.03" ; sc:url "http://www.famd.me.uk/AGL/AGL_sw.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2229, edam:topic_3382 ; sc:citation , "pubmed:34329378" ; sc:description "Cell Tracking and Shape Retrieval in Membrane-labeled Embryos." ; sc:featureList edam:operation_2422, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SDT-PICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wimthiels/SDT-PICS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:32700238" ; sc:description """An R package for the signal detection analysis of eyewitness lineup data. In a standard eyewitness lineup scenario, a witness observes a culprit commit a crime and is later asked to identify the culprit from a set of faces, the lineup. Signal detection theory (SDT), a powerful modeling framework for analyzing data, has recently become a common way to analyze lineup data. The goal of this paper is to introduce a new R package, sdtlu (Signal Detection Theory - LineUp), that streamlines and automates the SDT analysis of lineup data. sdtlu provides functions to process lineup data, determine the best-fitting SDT parameters, compute model-based performance measures such as area under the curve (AUC) and diagnosticity, use bootstrapping to determine uncertainty intervals around these parameters and measures, and compare parameters across two different data sets""" ; sc:featureList edam:operation_3435, edam:operation_3791, edam:operation_3799 ; sc:name "sdtlu" ; sc:url "https://osf.io/mfk4e/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3063, edam:topic_3325 ; sc:citation "pubmed:29678099" ; sc:description "Mapping of Health Care Providers for People with Rare Diseases." ; sc:featureList edam:operation_2429 ; sc:name "se-atlas" ; sc:url "http://www.se-atlas.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3517, edam:topic_3518 ; sc:citation ; sc:description "Tool for sex inference from genotype arrays." ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "seXY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Christopher-Amos-Lab/seXY" ; biotools:primaryContact "Christopher I. Amos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308, edam:topic_3365 ; sc:citation "pubmed:20525784" ; sc:description "Serial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "SEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sea.bioinfo.cipf.es" ; biotools:primaryContact "SEA Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295 ; sc:citation , "pmcid:PMC4702879", "pubmed:26578594" ; sc:description "Super-Enhancer Archive. Integrates super-enhancers in multiple species and annotates their potential roles in the regulation of cell identity gene expression." ; sc:featureList edam:operation_0430, edam:operation_3501 ; sc:name "SEA" ; sc:url "http://sea.edbc.org" ; biotools:primaryContact "Zhang Yan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0092, edam:topic_0769 ; sc:description "A web server that integrates techniques, such as docking and QSAR for structure analysis." ; sc:featureList edam:operation_0478, edam:operation_0570 ; sc:name "SeaBed" ; sc:url "http://www.bsc.es/SEABED" ; biotools:primaryContact "Institute for Research in Biomedicine Barcelona" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "This page provides access to Zostera muelleri genome assembly and annotation data." ; sc:featureList edam:operation_0224 ; sc:name "Seagrass Zmu Genome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:url "http://appliedbioinformatics.com.au/index.php/Seagrass_Zmu_Genome" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3050 ; sc:description """SeagrassTraitDB is a global data base of seagrass traits. It integrates world-wide seagrass trait data in one consistent format. SeagrassTraitDB is based on data sets contributed by seagrass scientists. Plant Traits are any morphological, anatomical, biochemical, physiological or phenological feature measurable at the individual level, from the cell to the whole organism. The aim of SeagrassTraitDB is to integrate and make available global empirical data of seagrass traits.""" ; sc:isAccessibleForFree true ; sc:name "SeagrassTraitDB" ; sc:softwareVersion "beta01" ; sc:url "http://seagrasses.ccmar.ualg.pt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2269 ; sc:citation ; sc:description """lasso, group lasso and sparse-group lasso regularisation for linear regression models via proximal gradient descent. This package provides regularization paths for the lasso, group lasso, and sparse-group lasso. The underlying mathematical model is a mixed model, i.e., a model with fixed and random effects. (Whereas it is actually optional to include any fixed effect.). Lasso, Group Lasso, and Sparse-Group Lasso for Mixed Models. Proximal gradient descent solver for the operators lasso, group lasso, and sparse-group lasso. The implementation involves backtracking line search and warm starts. Input data needs to be clustered/grouped for the (sparse-)group lasso before calling these algorithms. The sparse-group lasso contains two penalty terms, which are combined via a mixing parameter 0 <= alpha <= 1. The lasso, group lasso, and sparse-group lasso are implemented via proximal gradient descent.""" ; sc:featureList edam:operation_3196, edam:operation_3432, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "seagull" ; sc:url "https://CRAN.R-project.org/package=seagull" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168 ; sc:citation "pubmed:21697132" ; sc:description "Seal is a suite of distributed applications for aligning short DNA reads, manipulating and analyzing short read alignments. It is generally run on the Hadoop framework, which makes it particularly well suited for processing large data sets." ; sc:featureList edam:operation_0258, edam:operation_0292, edam:operation_0335, edam:operation_3438, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "SEAL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://biodoop-seal.sourceforge.net/" ; biotools:primaryContact "Luca Pireddu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:21856737" ; sc:description "A comprehensive sequencing simulation and alignment tool evaluation suite." ; sc:featureList edam:operation_0292, edam:operation_2426 ; sc:name "Seal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.case.edu/seal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_3179, edam:topic_3474, edam:topic_3500 ; sc:citation , "pmcid:PMC9047973", "pubmed:35505998" ; sc:description "Facial recognition software for ecological studies of harbor seals." ; sc:featureList edam:operation_2423, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SealNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zbirenbaum/SealFaceRecognition" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_1196, edam:format_1476, edam:format_3814, edam:format_3816 ; sc:name "Structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2275, edam:topic_3068, edam:topic_3336 ; sc:citation , "pmcid:PMC8484321", "pubmed:34604303" ; sc:description "An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "SeamDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioserv.rpbs.univ-paris-diderot.fr/services/SeamDock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "Fast and accurate large-scale de novo motif discovery in nucleic acid sequences." ; sc:featureList edam:operation_0238, edam:operation_2403, edam:operation_3501 ; sc:name "SeAMotE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://s.tartaglialab.com/new_submission/seamote" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_2885, edam:topic_3277 ; sc:citation , "pmcid:PMC10320134", "pubmed:37194711" ; sc:description "Comprehensive super-enhancer regulatory network analysis tool for human and mouse." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "SEanalysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://licpathway.net/SEanalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3293, edam:topic_3360 ; sc:citation , "pmcid:PMC4265393", "pubmed:25433763" ; sc:description "Reference-based phylogenetic analysis for 18S rRNA studies." ; sc:featureList edam:operation_0324, edam:operation_3680 ; sc:name "Seance" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://wasabiapp.org/software/seance/" ; biotools:primaryContact "Contact form", "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:32092001" ; sc:description """Soft-edge Assisted Network for Single Image Super-Resolution. The task of single image super-resolution (SISR) is a highly ill-posed inverse problem since reconstructing the highfrequency details from a low-resolution image is challenging. Most previous CNN-based super-resolution (SR) methods tend to directly learn the mapping from the low-resolution image to the high-resolution image through some complex convolutional neural networks. However, the method of blindly increasing the depth of the network is not the best choice because the performance improvement of such methods is marginal but the computational cost is huge. A more efficient method is to integrate the image prior knowledge into the model to assist the image reconstruction. Indeed, the soft-edge has been widely applied in many computer vision tasks as the role of an important image feature""" ; sc:name "SeaNet" ; sc:url "https://gitlab.com/junchenglee/seanet-pytorch" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:encodingFormat edam:format_1930 ; sc:name "Nucleic acid sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3301 ; sc:citation ; sc:description "Construct full-length, horizontally acquired Antibiotic Resistance Genes (ARGs) from sequencing datasets. It has been designed with environmental metagenomics and microbiome experiments in mind, where the diversity and relative abundance of ARGs need to be determined both quickly and easily." ; sc:featureList edam:operation_3482 ; sc:name "SEAR: Search Engine for Antimicrobial Resistance" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "cam.ac.uk" ; sc:softwareHelp ; sc:url "http://www.github.com/wpmr2/SEAR" ; biotools:primaryContact "Will Rowe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , "pubmed:15980457" ; sc:description "Tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs." ; sc:featureList edam:operation_0224, edam:operation_2403, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SEARCHGTr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://clustermine360.ca/antiSMASH/Sequences/116/searchgtr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3651 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247, edam:format_3711 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Graphical user interface for proteomics identification search engines" ; sc:featureList edam:operation_3631, edam:operation_3644, edam:operation_3646, edam:operation_3647, edam:operation_3648, edam:operation_3694, edam:operation_3767 ; sc:name "SearchGUI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "2.2.2" ; sc:url "http://compomics.github.io/projects/searchgui.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3676 ; sc:citation , "pmcid:PMC8375142", "pubmed:34412594" ; sc:description "Automated bulk RNA-seq exploration and visualisation using dynamically generated R-scripts." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3192, edam:operation_3223, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Searchlight2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Searchlight2/Searchlight2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:12824387" ; sc:description "Program for the detection and analysis of Polyketide Synthase (PKS) domains." ; sc:featureList edam:operation_0451, edam:operation_0452 ; sc:name "SEARCHPKS" ; sc:url "http://www.nii.res.in/searchpks.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0749, edam:topic_0769, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description """SearcHPV detects HPV fusion sites on both human genome and HPV genome. SearcHPV is able to provide locally assembled contigs for each integration events. It will report at least one and at most two contigs for each integration sites. The two contigs will provide information captured for left and right sides of the event. SearcHPV is a novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer.""" ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3228 ; sc:license "MIT" ; sc:name "SearcHPV" ; sc:url "https://github.com/mills-lab/SearcHPV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2259, edam:topic_3301 ; sc:citation "pubmed:21799897" ; sc:description "A computational tool for pathway enrichment analysis over a given set of genes in a specified organism against pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes in a bacterium to genes currently covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes." ; sc:featureList edam:operation_2497 ; sc:name "SEAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csbl.bmb.uga.edu/~xizeng/research/seas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3277, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC8481385", "pubmed:34604741" ; sc:description "Statistical Enrichment Analysis of Samples (SEAS): a general-purpose tool to annotate metadata neighborhoods of biological samples." ; sc:featureList edam:operation_2238, edam:operation_3432, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SEAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://aimed-lab.shinyapps.io/SEAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3176, edam:topic_3940 ; sc:citation , "pmcid:PMC10204251", "pubmed:37218013" ; sc:description "Tool for exploring the chromatin landscape and the role of pioneer factors." ; sc:featureList edam:operation_0432, edam:operation_0490, edam:operation_3222 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeATAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gongx030/seatac" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2885 ; sc:description "Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans." ; sc:featureList edam:operation_0224 ; sc:name "SeattleSNPs variation discovery resource" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pga.gs.washington.edu/" ; biotools:primaryContact "Colleen Davis" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:name "Phylogenetic tree image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1711 ; sc:name "Sequence alignment image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0092 ; sc:citation ; sc:description "Multiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences." ; sc:featureList edam:operation_0326, edam:operation_0492, edam:operation_0540, edam:operation_0564, edam:operation_0567, edam:operation_3081 ; sc:name "SeaView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "IFB ELIXIR-FR" ; sc:softwareHelp ; sc:softwareVersion "4" ; sc:url "http://doua.prabi.fr/software/seaview" ; biotools:primaryContact "Manolo Gouy" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2305, edam:format_2306, edam:format_3003 ; sc:name "Sequence features" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2305, edam:format_2306 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC3882232", "pubmed:24400097" ; sc:description "Self-Estimation Based Novel lincRNA Filter. Discovery of bona fide novel lincRNAs that are suitable for further functional characterization. Specifically, it implements an algorithm for identifying high-quality single-exonic lincRNAs that were often omitted in many studies." ; sc:featureList edam:operation_0314, edam:operation_3192, edam:operation_3501 ; sc:license "BSL-1.0" ; sc:name "Sebnif" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.3rc" ; sc:url "http://sunlab.lihs.cuhk.edu.hk/sebnif/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:24695403" ; sc:description "A user-friendly web-based application to perform SNP effect concordance analysis using GWA summary results." ; sc:featureList edam:operation_3661 ; sc:name "SECA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://neurogenetics.qimrberghofer.edu.au/SECA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2229, edam:topic_3168 ; sc:citation ; sc:description "SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SECEDO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ratschlab/secedo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0869 ; sc:name "Sequence-profile alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Charles Chapple" ; sc:citation ; sc:contributor "Marco Mariotti" ; sc:description "Predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements." ; sc:featureList edam:operation_0361 ; sc:name "SECISaln" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareVersion "1" ; sc:url "http://big.crg.cat/services/secisaln" ; biotools:primaryContact "Didac Santesmasses & Charles Chapple" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author , "Anke Busch" ; sc:citation , "pubmed:15919727" ; sc:description "Insert SECIS-elements in coding mRNAs." ; sc:featureList edam:operation_0365 ; sc:isAccessibleForFree true ; sc:name "SECISDesign web server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://rna.informatik.uni-freiburg.de/SECISDesign/" ; biotools:primaryContact , "Anke Busch" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:author "Marco Mariotti" ; sc:citation ; sc:contributor "Didac Santesmasses" ; sc:description "In this web server we provide public access for two new computational methods for selenoprotein identification and analysis. This tool replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements and becomes a new method for selenoprotein gene detection that predicts selenoprotein sequences encoded upstream of SECIS elements. It is able to both identify known selenoproteins and predict new selenoproteins." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SECISearch3 Seblastian" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://seblastian.crg.es/" ; biotools:primaryContact "Didac Santesmasses & Marco Mariotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168, edam:topic_3958 ; sc:citation , "pubmed:35801503" ; sc:description "Resolving single-cell copy number profiling for large datasets." ; sc:featureList edam:operation_3233, edam:operation_3798, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SeCNV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/deepomicslab/SeCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2830, edam:topic_3930, edam:topic_3948 ; sc:citation ; sc:description """In silico secretome characterization of clinical Mycobacterium abscessus isolates provides insights into antigenic differences. The secretome contains all the Excreted Secreted (ES) proteins of a cell.""" ; sc:featureList edam:operation_0303, edam:operation_3192, edam:operation_3196, edam:operation_3431, edam:operation_3461 ; sc:name "Secret-AAR" ; sc:url "http://microbiomics.ibt.unam.mx/tools/aar/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0196, edam:topic_0621, edam:topic_3068, edam:topic_3697 ; sc:citation , "pubmed:36346548" ; sc:description "A comprehensive resource of bacterial Type VI Secretion Systems." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:name "SecReT6" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinfo-mml.sjtu.edu.cn/SecReT6/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:15115854", "pubmed:16212653" ; sc:description "Predictions of non-classical (i.e. not signal peptide triggered) protein secretion." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SecretomeP" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/SecretomeP/" ; biotools:primaryContact "Henrik Nielsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0121, edam:topic_3308, edam:topic_3520 ; sc:citation , "pubmed:37429152" ; sc:description "Web-based database on mycobacteria secreted proteins and structure-based homology identification using bio-informatics tools." ; sc:featureList edam:operation_0303, edam:operation_0418, edam:operation_0477 ; sc:isAccessibleForFree true ; sc:name "SecretoMyc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://secretomyc.cbs.cnrs.fr/myc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0602, edam:topic_0820 ; sc:citation ; sc:description "Flexible pipelines for functional secretome prediction." ; sc:featureList edam:operation_1777 ; sc:name "SecretSanta" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/gogleva/SecretSanta" ; biotools:primaryContact "Anna Gogleva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9754601", "pubmed:36469543" ; sc:description "Ultrafast, scalable and accurate clustering of single-cell RNA-seq data." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Secuer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nanawei11/Secuer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:25147357" ; sc:description "A secure framework for performing multi-site genetic association studies across large consortia, without violating privacy/confidentiality of individual participants or substudy sites. It aims at addressing various attacks on genomic privacy, and provides comprehensive protection over genomic data without impeding scientific endeavor." ; sc:featureList edam:operation_0253 ; sc:name "SecureMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/XieConnect/SecureMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26873931" ; sc:description "A suite of secure sequencing analysis tools." ; sc:featureList edam:operation_2403 ; sc:name "secureSeq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.hcbravo.org/projects/secureseq/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:citation , , "pubmed:30511150" ; sc:description "SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences." ; sc:featureList edam:operation_0231, edam:operation_0335, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SEDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5.1" ; sc:url "http://www.sing-group.org/seda/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:citation "pubmed:24264942" ; sc:description "A global machine learning based scoring function for protein structure prediction. The package was designed using the GEneral Neural Network program." ; sc:featureList edam:operation_0474 ; sc:name "Seder" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://mamiris.com/services.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3170, edam:topic_3474, edam:topic_3934 ; sc:citation , "pubmed:34553763" ; sc:description "High-throughput single-cell RNA-seq data imputation and characterization with surrogate-assisted automated deep learning." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SEDIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/li-shaochuan/SEDIM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3299 ; sc:citation "pubmed:26358728" ; sc:description "A forward-in-time simulator of segmental duplications undergoing concerted evolution." ; sc:featureList edam:operation_2426 ; sc:name "SeDuS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.biologiaevolutiva.org/sedus/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0958 ; sc:name "Tool metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find programs with similar function to a specified program." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seealso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seealso.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:23558750" ; sc:description "Sequence error correction for RNA-Seq data." ; sc:featureList edam:operation_3195 ; sc:name "SEECER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sb.cs.cmu.edu/seecer/" ; biotools:primaryContact "Hai-Son Le", "Marcel H. Schulz", "Ziv Bar-Joseph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0632, edam:topic_2885, edam:topic_3337, edam:topic_3518 ; sc:citation ; sc:description """a method to assess CNV calls from SNP arrays using trio data. SeeCiTe is a novel CNV quality control tool that post-processes output from current CNV calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. It utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artefacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies.""" ; sc:featureList edam:operation_0337, edam:operation_0484, edam:operation_3196, edam:operation_3359 ; sc:license "MIT" ; sc:name "SeeCiTe" ; sc:url "https://github.com/aksenia/SeeCiTe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation "pubmed:21810899" ; sc:description "Tool to cluster sequence reads prior to assembly or other operations." ; sc:featureList edam:operation_0291 ; sc:name "SEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://manuals.bioinformatics.ucr.edu/home/seed" ; biotools:primaryContact "Thomas Girke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0610, edam:topic_3365 ; sc:citation "pubmed:25332377" ; sc:description "An R/Shiny package for visualizing ecological data. It provides a visual interface for generating a wide variety of plots, including histograms, scatterplots, bar plots, stacked bar plots, PCoA plots, cluster dendrograms, and heatmaps." ; sc:featureList edam:operation_0337 ; sc:name "Seed" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/danlbek/Seed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0621, edam:topic_0654 ; sc:citation , "pmcid:PMC10444664", "pubmed:37621456" ; sc:description "Optimizing alignment parameters for sensitive sequence comparison." ; sc:featureList edam:operation_0259, edam:operation_0491, edam:operation_0496 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Seedability" ; sc:url "https://github.com/lorrainea/Seedability" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382, edam:topic_3517 ; sc:citation ; sc:description "an open-source GUI for seed image analysis." ; sc:featureList edam:operation_3443 ; sc:name "SeedExtractor" ; sc:url "https://cse.unl.edu/~fzhu/SeedExtractor.zip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3474, edam:topic_3810 ; sc:citation , "pubmed:32533857" ; sc:description """a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination. SeedGerm: automated seed phenotyping. Contribute to Crop-Phenomics-Group/SeedGerm development by creating an account on GitHub.""" ; sc:featureList edam:operation_0484 ; sc:name "SeedGerm" ; sc:url "https://github.com/Crop-Phenomics-Group/SeedGerm/releases" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3365, edam:topic_3511 ; sc:citation , ; sc:description "Creates the seed from -15 to -25 bp before ATG." ; sc:featureList edam:operation_3095 ; sc:name "seedgff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2533 ; sc:citation , "pmcid:PMC4467979", "pubmed:26075402" ; sc:description "SEEDY (Simulation of Evolutionary and Epidemiological Dynamics) is an R package that can be used to follow the accumulation of within-host mutation in pathogens." ; sc:featureList edam:operation_0449 ; sc:license "GPL-3.0" ; sc:name "SEEDY" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "https://cran.r-project.org/web/packages/seedy/" ; biotools:primaryContact "Colin J. Worby" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3071 ; sc:citation ; sc:description "Web-based cataloguing and commons platform, for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes." ; sc:featureList edam:operation_3431 ; sc:license "BSD-2-Clause" ; sc:name "SEEK" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.seek4science.org/" ; biotools:primaryContact "Contact list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "SEEK developers" ; sc:citation , , ; sc:description "Web-based resource for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "FAIRDOM-SEEK" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Heidelberg Institute for Theoretical Studies, Germany", "The University of Manchester, UK", "manchester.ac.uk" ; sc:softwareHelp ; sc:softwareVersion "1", "1.11", "1.11.1", "1.12.2" ; sc:url "http://seek4science.org/" ; biotools:primaryContact "SEEK", "SEEK developers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7598922", "pubmed:33079938" ; sc:description """Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data. NOTE: UNDER CONSTRUCTION, the actual software is NOT released yet. seek for circular RNA in transcriptome (identifies deferentially expressed circRNAs between two samples). git clone https://github.com/UofLBioinformatics/seekCRIT.git. Run testrun.sh to test the installation and the dependencies of seekCRIT and also it will test the installation with CRTL12.fastq and IR12.fastq by specifying the path for FASTA and gtf files:.""" ; sc:featureList edam:operation_0264, edam:operation_3431, edam:operation_3435 ; sc:license "MIT" ; sc:name "seekCRIT" ; sc:url "https://github.com/UofLBioinformatics/seekCRIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3174, edam:topic_3474, edam:topic_3957 ; sc:citation ; sc:description """Alignment-free identification of bacteriophage genomes by deep learning. Seeker is a python library for discriminating between bacterial and phage genomes. Seeker is based on an LSTM deep-learning models and does not rely on a reference genome, genomic alignment or any direct genome comparison. Alignment free identification of novel phages via a deep learning framework. Maximum file size is 10MB. For large-scale datasets, please use the accompanying Python package. The MATLAB and Python model types differ in how they represent the DNA sequences. They are largely equivalent in their performance. The default recommendation is to use the Python model, as it uses fewer parameters.""" ; sc:featureList edam:operation_0362, edam:operation_0553, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "Seeker" ; sc:url "http://seeker.pythonanywhere.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC9648347", "pubmed:36389425" ; sc:description "Simplified fetching and processing of transcriptome data." ; sc:featureList edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "seeker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://seeker.hugheylab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_3524, edam:topic_3534 ; sc:citation , "pmcid:PMC5562489", "pubmed:28191969" ; sc:description "Simulation Enabled Estimation of Kinetic Rates- A Computational Tool to Estimate Molecular Kinetics and its Application to Trypsin-Benzamidine Binding." ; sc:featureList edam:operation_0334 ; sc:name "SEEKR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://amarolab.ucsd.edu/seekr/" ; biotools:primaryContact "Rommie E. Amaro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_0166, edam:topic_0623, edam:topic_2814 ; sc:citation "pubmed:19477961" ; sc:description "Allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB)." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240, edam:operation_0245, edam:operation_2404 ; sc:name "seeMotif" ; sc:url "http://seemotif.csie.ntu.edu.tw" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:encodingFormat edam:format_1999 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_3308 ; sc:citation , "pmcid:PMC6127256", "pubmed:30190516" ; sc:description "A Web Application for Predicting Cell-fate Determinants in Cell Differentiation" ; sc:featureList edam:operation_2437 ; sc:license "AGPL-3.0" ; sc:name "SeesawPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.1" ; sc:url "http://seesaw.lcsb.uni.lu" ; biotools:primaryContact "Antonio del Sol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0610, edam:topic_3500 ; sc:citation , "pubmed:31539165" ; sc:description "Identifying stationary phases in multivariate time series for highlighting behavioural modes and home range settlements | Bivariate Segmentation/Clustering Methods and Tools | Provides two methods for segmentation and joint segmentation clustering of bivariate time-series" ; sc:featureList edam:operation_3432, edam:operation_3446, edam:operation_3454 ; sc:license "GPL-3.0" ; sc:name "segclust2d" ; sc:url "http://cran.r-project.org/package=segclust2d" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2533, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:22539397" ; sc:description "A software package, to detect germline copy number variations in SNP array data. Currently, SegCNV supports Illumina 550K and 610K genotyping platforms." ; sc:featureList edam:operation_3233 ; sc:name "SegCNV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dceg.cancer.gov/tools/analysis/segcnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621, edam:topic_0622, edam:topic_3169 ; sc:citation , "pmcid:PMC9805567", "pubmed:36394233" ; sc:description "SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data." ; sc:featureList edam:operation_3216, edam:operation_3222, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SEGCOND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AntonisK95/SEGCOND" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:33120283" ; sc:description """Automatic segmentation of prostate magnetic resonance imaging using generative adversarial networks. This repository is the official repository of the article "Automatic Segmentation of Prostate Magnetic Resonance Imaging Using Generative Adversarial Networks" To train a model use the train.py file, you can use the following commands line to get the important arguments. You can config the detailed parameters in the config.py. To do the inference, use the test.py file, you can use the following commands line to get the important arguments.""" ; sc:featureList edam:operation_3799, edam:operation_3927, edam:operation_3937 ; sc:name "SegDGAN" ; sc:url "https://github.com/w3user/SegDGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24626854" ; sc:description "A software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, this tool is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly." ; sc:featureList edam:operation_2520 ; sc:name "segemehl" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hoffmann.bioinf.uni-leipzig.de/LIFE/segemehl.html" ; biotools:primaryContact "segemehl Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation , "pmcid:PMC5998006", "pubmed:29946440" ; sc:description "Convert segments between genome assemblies, without breaking them apart. Part of its functionality is based on re-conversion by locus approximation" ; sc:featureList edam:operation_2403, edam:operation_3096 ; sc:license "MIT" ; sc:name "segment_liftover" ; sc:softwareHelp ; sc:url "https://github.com/baudisgroup/segment-liftover" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3307 ; sc:citation ; sc:description "A novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations" ; sc:featureList edam:operation_2426 ; sc:name "SEGMEnT_HPC" ; sc:operatingSystem "Linux" ; sc:url "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122192" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Presented Algorithm segments blood vessels of retinal image with a high degree of accuracy using maximum principal curvature." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Segmentation of blood vessels in retinal fundus images using maximum principal curvature" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/64884-segmentation-of-blood-vessels-in-retinal-fundus-images-using-maximum-principal-curvature" ; biotools:primaryContact "Achintha Iroshan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444, edam:topic_3474 ; sc:description "MATLAB tool for Automatic segmentation of brain tumor in MRI images." ; sc:isAccessibleForFree true ; sc:name "Automatic segmentation of brain tumor in MRI images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/51153-automatic-segmentation-of-brain-tumor-in-mr-images" ; biotools:primaryContact "Chandra Sekhar Ravuri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "Gets label matrix of a tissue in segmented and ground truth and returns similarity indices." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "segmentation evaluatation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/29737-segmentation-evaluatation" ; biotools:primaryContact "M. A Balafar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384 ; sc:description "Segmentation of locally darker somewhat circular regions using a morphology based method" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Segmentation using morphology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/41799-segmentation-using-morphology" ; biotools:primaryContact "Benjamin I" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description "The algorithm identifies nuclei in images of cells stained with a DNA-specific dye (e.g. DAPI)." ; sc:featureList edam:operation_3432, edam:operation_3443, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "Segmentation of nuclei (Waahlby algorithm)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63070-segmentation-of-nuclei-wahlby-algorithm" ; biotools:primaryContact "Peter Nagy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description "The algorithm identifies nuclei in images of cells stained with a DNA-specific dye (e.g. DAPI)." ; sc:featureList edam:operation_3432, edam:operation_3443, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "Segmentation of nuclei (Wahlby algorithm)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63070-segmentation-of-nuclei-wahlby-algorithm" ; biotools:primaryContact "Peter Nagy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3452, edam:topic_3500 ; sc:citation , "pmcid:PMC8919404", "pubmed:35291672" ; sc:description "A Tool for Measuring Second Moment of Area in 3D Slicer." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SegmentGeometry" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jmhuie/Slicer-SegmentGeometry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3382 ; sc:citation ; sc:description """A tool for manual refinement of 3D microscopy annotations. Segmentation tool for 3D tissue cleared microscopy images of nuclei. See the wiki for more information on installing and using Segmentor.""" ; sc:featureList edam:operation_3096, edam:operation_3359, edam:operation_3553 ; sc:license "MIT" ; sc:name "Segmentor" ; sc:softwareHelp ; sc:url "https://github.com/RENCI/Segmentor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3475, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "This package allows the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery." ; sc:featureList edam:operation_0292 ; sc:license "GPL-3.0" ; sc:name "segmentSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/segmentSeq.html" ; biotools:primaryContact "Thomas J. Hardcastle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_3168 ; sc:citation "pubmed:20637422" ; sc:description "A segmental threading algorithm designed to recoginzing substructure motifs from the Protein Data Bank (PDB) library." ; sc:featureList edam:operation_0245, edam:operation_2479 ; sc:name "SEGMER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/SEGMER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:citation , , , ; sc:contributor "Thomas Wollmann" ; sc:description "Image segmentation and object detection performance measures" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SegMetrics" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BMCV/segmetrics.py" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:19043412" ; sc:description "An algorithm to identify chromosomal breakpoints using massively parallel sequence data." ; sc:featureList edam:operation_2429, edam:operation_3233 ; sc:name "SegSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=182" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3344, edam:topic_3382 ; sc:description "Segshow_3D is the visualization GUI which shows cell segmentation result in 3D view" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Segshow_3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/59878-cell-3d-segmentation-display-gui" ; biotools:primaryContact "Tzu-Ching Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:32421654" ; sc:description """Super-resolution and segmentation using generative adversarial networks. Segmentation and super resolution GAN network. This algorithm is based on the method proposed by Chi-Hieu Pham in 2019. More information about the SEGSRGAN algorithm can be found in the associated article.""" ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3443 ; sc:name "SegSRGAN" ; sc:url "http://pypi.org/project/SegSRGAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description "Tools for exploratory analysis of genomic segmentations." ; sc:featureList edam:operation_0362, edam:operation_2495 ; sc:name "Segtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.pmgenomics.ca/hoffmanlab/proj/segtools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation "pubmed:22069465" ; sc:description "A software tool to annotate large sets of genomic coordinates, intervals, SNVs, indels and translocations with respect to known genes." ; sc:featureList edam:operation_3661 ; sc:name "Segtor" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BioNica/Segtor" ; biotools:primaryContact "F. Passetti" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2919 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2919 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085, edam:topic_3173 ; sc:author , "Eric Roberts" ; sc:citation , "pmcid:PMC3340533", "pubmed:22426492", "pubmed:23221638" ; sc:description "Novel method for analyzing multiple tracks of functional genomics data which uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling." ; sc:featureList edam:operation_0362, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "Segway" ; sc:operatingSystem "Linux" ; sc:provider "Princess Margaret Cancer Centre", "University of Toronto" ; sc:softwareHelp , , ; sc:softwareVersion "1.4.0" ; sc:url "http://segway.hoffmanlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "Simulation of an epidemic by classical deterministic models: SI, SIS, SIR, SIRS, SEIR, SEIRS." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "SEIRS epidemic model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75321-seirs-epidemic-model" ; biotools:primaryContact "milan batista" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3334, edam:topic_3500, edam:topic_3676 ; sc:citation , "pmcid:PMC6122958", "pubmed:29718741" ; sc:description """High-throughput behavioral assay to investigate seizure sensitivity in zebrafish implicates ZFHX3 in epilepsy. Studying Epilepsy In Zebrafish using R.""" ; sc:name "SEIZR" ; sc:url "https://tyson-fuller.shinyapps.io/SEIZR_Tracking_App/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3524 ; sc:citation , "pubmed:12642649" ; sc:description "Predicts response to selection for multiple traits and rates of inbreeding for practical livestock improvement programs. To keep computation time short, it uses deterministic simulation so that it can be used as an interactive optimization tool." ; sc:featureList edam:operation_2426 ; sc:license "Not licensed" ; sc:name "SelAction" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.wur.nl/en/Expertise-Services/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genetics-Group/Research/Software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3056, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC7410354", "pubmed:32785571" ; sc:description """A database of exonic variants in a Brazilian population referred to a quaternary medical center in São Paulo. High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases""" ; sc:featureList edam:operation_3227, edam:operation_3431, edam:operation_3675, edam:operation_3891 ; sc:name "SELAdb" ; sc:url "http://intranet.fm.usp.br/sela" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3524 ; sc:citation ; sc:description "Simulation of stochastic multidimensional Gene Regulatory Networks (GRNs)." ; sc:featureList edam:operation_3562 ; sc:name "SELANSI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/selansi" ; biotools:primaryContact "Antonio A Alonso" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Select the best hit for each query sequence in a Blast tabular file." ; sc:featureList edam:operation_3695 ; sc:name "selectbesthit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1 beta" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/SelectBestHit/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:33016991" ; sc:description """a general algorithm to enhance the performance of variable selection methods. A General Algorithm to Enhance the Performance of Variable Selection Methods in Correlated Datasets. Deciphering Biological Networks with Patterned Heterogeneous Measurements. An implementation of the selectboost algorithm (Bertrand et al. 2020, ), which is a general algorithm that improves the precision of any existing variable selection method. This algorithm is based on highly intensive simulations and takes into account the correlation structure of the data. It can either produce a confidence index for variable selection or it can be used in an experimental design planning perspective. A modeling tool dedicated to biological network modeling.""" ; sc:featureList edam:operation_2495, edam:operation_3659, edam:operation_3927, edam:operation_3936 ; sc:license "GPL-3.0" ; sc:name "SelectBoost" ; sc:url "https://cran.r-project.org/package=SelectBoost" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2306 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622 ; sc:citation , ; sc:description "Keeps the genomic coordinates such that a value of a given tag." ; sc:featureList edam:operation_2409 ; sc:name "selectbytag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "Blast-hits filter for each line in a Blast file." ; sc:featureList edam:operation_3695 ; sc:name "selecthitscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1 beta" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/SelectHitScore/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3474, edam:topic_3517, edam:topic_3810 ; sc:citation , "pmcid:PMC10443705", "pubmed:37614817" ; sc:description """Package for performing and optimising genomic prediction using machine learning. Genomic prediction attempts to predict a phenotypic value given an individuals genetic data and other context. This package provides a range of models, feature selection methods, and data transformers following the scikit-learn API tailored specifically for genomic prediction.""" ; sc:featureList edam:operation_0418, edam:operation_3196, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SelectML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/darcyabjones/selectml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1075 ; sc:name "Protein family identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:name "Taxon" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:name "Identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation , "pmcid:PMC3964977", "pubmed:24225318" ; sc:description "Database of positive selection based on a rigorous branch-site specific likelihood test." ; sc:featureList edam:operation_0224 ; sc:license "CC0-1.0" ; sc:name "Selectome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "https://selectome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation "pubmed:15647294", "pubmed:17586822" ; sc:description "Selecton is a server for the identification of site-specific positive selection and purifying selection." ; sc:featureList edam:operation_0554 ; sc:name "Selecton" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://selecton.tau.ac.il/" ; biotools:primaryContact "SELECTON Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0082 ; sc:citation "pubmed:19055744" ; sc:description "A novel structure-based model selection method derived from an energy function comprising physical, statistical, and predicted structural terms. Novel and unique energy terms include predicted secondary structure, predicted solvent accessibility, predicted contact map, beta-strand pairing, and side-chain hydrogen bonding." ; sc:featureList edam:operation_0477 ; sc:name "SELECTpro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.igb.uci.edu/~baldig/selectpro.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3174, edam:topic_3315, edam:topic_3673, edam:topic_3697 ; sc:citation , "pmcid:PMC8978828", "pubmed:35387076" ; sc:description "A Simultaneous Feature Selection and Compositional Association Test for Detecting Sparse Associations in High-Dimensional Metagenomic Data." ; sc:featureList edam:operation_3557, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SelEnergyPerm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/andrew84830813/selEnergyPermR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Marco Mariotti" ; sc:citation ; sc:contributor "Didac Santesmasses" ; sc:description "Pipeline for profile-based protein finding in genomes." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Selenoprofiles3" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://big.crg.cat/services/selenoprofiles" ; biotools:primaryContact "Didac Santesmasses & Marco Mariotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3297, edam:topic_3398 ; sc:citation ; sc:description "Enzyme selection tool for pathway design." ; sc:featureList edam:operation_3660 ; sc:name "Selenzyme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://selenzyme.synbiochem.co.uk/" ; biotools:primaryContact "Pablo Carbonell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:24361938" ; sc:description "Software to detect signatures of selection from gene frequency data and measure the selection intensity." ; sc:featureList edam:operation_3197 ; sc:name "SelEstim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1930, edam:format_2000, edam:format_2332 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_3033, edam:format_3475, edam:format_3547 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3125 ; sc:citation ; sc:description "Tools for quantifying DNA binding specificities based on SELEX-seq data." ; sc:featureList edam:operation_0238 ; sc:license "GPL-2.0" ; sc:name "SELEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SELEX.html" ; biotools:primaryContact "Harmen Bussemaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33523807" ; sc:description """Self-supervision for Classification of Pathology Images with Limited Annotations. While high-resolution pathology images lend themselves well to 'data hungry' deep learning algorithms, obtaining exhaustive annotations on these images for learning is a major challenge. In this paper, we propose a self-supervised convolutional neural network (CNN) frame-work to leverage unlabeled data for learning generalizable and domain invariant representations in pathology images. Our proposed framework, termed as Self-Path, employs multi-task learning where the main task is tissue classification and pretext tasks are a variety of self-supervised tasks with labels inherent to the input images. We introduce novel pathology-specific self-supervision tasks that leverage contextual, multi-resolution and semantic features in pathology images for semi-supervised learning and domain adaptation. We investigate the effectiveness of Self-Path on 3 different pathology datasets ||| HOMEPAGE MISSING!""" ; sc:featureList edam:operation_3553 ; sc:name "Self-Path" ; sc:url "https://warwick.ac.uk/fac/cross_fac/tia/software/selfpath/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0166, edam:topic_0218, edam:topic_0736 ; sc:citation , "pubmed:33090951" ; sc:description """protein fold recognition based on residue-based and motif-based self-attention networks. 1. The similarities between the self-attention mechanism for natural language processing (a) and the self-attention mechanism based on the structure motifs for protein fold recognition (b). The lines represent the attention weights. The darker the line is, the higher the corre-sponding attention weight is. 2. The flowchart of the motif-based self-attention network (MSAN) for extracting fold-specific attention features. (a) the motif convolution layer, (b) the self-attention layer, and (c) the full connected layer.""" ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_0303 ; sc:name "SelfAT-Fold" ; sc:url "http://bliulab.net/selfAT_fold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC10408573", "pubmed:38013816" ; sc:description """Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation. A main objective is to use SELFIES as direct input into machine learning models, in particular in generative models, for the generation of molecular graphs which are syntactically and semantically valid.""" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SELFIES" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aspuru-guzik-group/selfies" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0749, edam:topic_2815, edam:topic_3168 ; sc:citation "pubmed:20529878" ; sc:description "Web server identifies degenerate lox-like sites within genomic sequences." ; sc:featureList edam:operation_0237, edam:operation_0451, edam:operation_3209, edam:operation_3211 ; sc:name "SeLOX" ; sc:url "http://selox.mpi-cbg.de/cgi-bin/selox/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0602, edam:topic_0821 ; sc:citation , "pmcid:PMC4489257", "pubmed:25948583" ; sc:description "Correlation-based identification of kinase-associated networks from global phospho-proteomics data sets." ; sc:featureList edam:operation_2497 ; sc:name "SELPHI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rothwebprod.mshri.on.ca:8081/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Calculate EHH-based scans for positive selection in genomes currently implementing EHH, iHS, XP-EHH and nSL." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "selscan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/szpiech/selscan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3524 ; sc:citation ; sc:description "A program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection." ; sc:featureList edam:operation_2426 ; sc:license "Not licensed" ; sc:name "SelSim" ; sc:softwareHelp ; sc:url "https://popmodels.cancercontrol.cancer.gov/gsr/packages/selsim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2830, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:19820113" ; sc:description "Curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite instability (MSI) -H tumor entities indicating statistically deviant mutation frequencies predict genes that are shown or highly suspected to be involved in MSI tumorigenesis." ; sc:featureList edam:operation_0252, edam:operation_0314, edam:operation_0331, edam:operation_3202, edam:operation_3659 ; sc:name "SelTarbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.seltarbase.org" ; biotools:primaryContact "Stefan M. Woerner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0157, edam:topic_0611, edam:topic_2275 ; sc:citation "pubmed:12824326" ; sc:description "Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization, some configuration necessary." ; sc:featureList edam:operation_0279, edam:operation_0297, edam:operation_0322, edam:operation_3429 ; sc:name "SEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dicsoft2.physics.iisc.ernet.in/sem/" ; biotools:primaryContact "K. Sekar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0637, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC7466824", "pubmed:32905086" ; sc:description """Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. sem1R is a machine learning algorithm that finds interesting, hidden, and non-trivial semantic patterns in omics data.""" ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3802 ; sc:name "sem1R" ; sc:url "http://github.com/fmalinka/sem1r" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3170, edam:topic_3172, edam:topic_3308 ; sc:citation , "pmcid:PMC9252823", "pubmed:35580059" ; sc:description "Expression-based exploration tool for increased secondary metabolite production in bacteria." ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "SeMa-Trap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sema-trap.ziemertlab.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_2830, edam:topic_3400, edam:topic_3474, edam:topic_3966 ; sc:citation , "pmcid:PMC9523212", "pubmed:36189325" ; sc:description "Antigen B-cell conformational epitope prediction using deep transfer learning.'" ; sc:featureList edam:operation_0252, edam:operation_0272, edam:operation_0416, edam:operation_0480 ; sc:isAccessibleForFree true ; sc:name "SEMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sema.airi.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444, edam:topic_3474 ; sc:description "Semantic Breast Tumor Segmentation by Convolutional Neural Network in MRI images" ; sc:isAccessibleForFree true ; sc:name "Semantic Breast Tumor Segmentation by CNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74106-semantic-breast-tumor-segmentation-by-cnn" ; biotools:primaryContact "Majid Farzaneh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3300, edam:topic_3500 ; sc:citation "pubmed:25344497" ; sc:description "A web application for intuitively exploring the body of an organism from the organ to the sub-cellular level and visualising expression profiles by means of semantically annotated illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users." ; sc:featureList edam:operation_0337 ; sc:name "Semantic Body Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbb.cellfinder.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_3125, edam:topic_3474, edam:topic_3518 ; sc:citation , "pubmed:33571101" ; sc:description """Quantifying intensities of transcription factor-DNA binding by learning from an ensemble of protein binding microarrays. SemanticBI: prediction of DNA-TF binding intensities (trained on DREAM5 PBM data sets).""" ; sc:featureList edam:operation_0253, edam:operation_0420, edam:operation_0445 ; sc:name "SemanticBI" ; sc:url "http://qianglab.scst.suda.edu.cn/semantic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3474 ; sc:citation , "pubmed:32976105" ; sc:description """Learning useful representations of DNA sequences from ChIP-seq datasets for exploring transcription factor binding specificities. SemanticCS: prediction of TF-DNA binding probability (trained on ChIP-seq datasets).""" ; sc:featureList edam:operation_0337, edam:operation_0372, edam:operation_0445 ; sc:name "SemanticCS" ; sc:url "http://qianglab.scst.suda.edu.cn/semanticCS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780, edam:topic_3053 ; sc:citation , "pubmed:32563466" ; sc:description """a tool for gene functional similarity analysis in Arabidopsis thaliana and rice. Semantic analysis of Arabidopsis thaliana genes function.""" ; sc:featureList edam:operation_2436, edam:operation_3463 ; sc:name "SemanticGO" ; sc:url "http://bioinformatics.fafu.edu.cn/semanticGO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2533, edam:topic_3534 ; sc:citation "pubmed:25777526" ; sc:description """A program for analyzing the binding affinity of amyloid proteins. It uses an energy function that computes the Lennard-Jones, Coulomb, and solvation energies to determine the effect of a mutation on a protein’s stability.""" ; sc:featureList edam:operation_0331, edam:operation_2575 ; sc:name "SEMBA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://amyloid.cs.mcgill.ca/semba.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3063, edam:topic_3474 ; sc:citation , "pubmed:31980104" ; sc:description """A semantic biomedical question answering system for retrieving exact and ideal answers to natural language questions. SemBioNLQA - Semantic Biomedical Natural Language Question Answering - has the ability to handle the kinds of yes/no questions, factoid questions, list questions and summary questions that are commonly asked in the biomedical domain. It consists of question classification, document retrieval, passage retrieval and answer extraction modules. It is aimed to be able to accept a variety of natural language questions and to generate appropriate natural language answers by providing both exact and ideal answers (paragraph-sized summaries). It provides exact answers “yes” or “no” for yes/no questions, biomedical named entities for factoid questions, and a list of biomedical named entities for list questions. In addition to exact answers for yes/no, factoid and list questions, SemBioNLQA also returns ideal answers, while it retrieves only ideal answers for summary questions.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3280 ; sc:name "SemBioNLQA" ; sc:url "https://github.com/sarrouti/sembionlqa" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3475 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0582 ; sc:encodingFormat edam:format_2330, edam:format_3475 ; sc:name "Ontology" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3572 ; sc:citation ; sc:description "This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor." ; sc:featureList edam:operation_2428, edam:operation_3352 ; sc:license "GPL-2.0" ; sc:name "SemDist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SemDist.html" ; biotools:primaryContact "Ian Gonzalez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; 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Sample size estimation for single cell studies. Unpaired t-Test Paired t-Test Instructions. The graph will update when the Beta-distributions change. False negative rates. Lower is better. Each row correponds to a fixed number of control samples. Each row correponds to a fixed number of experimental samples. 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In photon-limited imaging, the pixel intensities are affected by photon count noise. Many applications require an accurate estimation of the covariance of the underlying 2-D clean images. For example, in X-ray free electron laser (XFEL) single molecule imaging, the covariance matrix of 2-D diffraction images is used to reconstruct the 3-D molecular structure. Accurate estimation of the covariance from low-photon-count images must take into account that pixel intensities are Poisson distributed, hence the classical sample covariance estimator is highly biased. Moreover, in single molecule imaging, including in-plane rotated copies of all images could further improve the accuracy of covariance estimation. 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It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data." ; sc:featureList edam:operation_2403 ; sc:name "SePIA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://anduril.org/sepia/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3168, edam:topic_3384, edam:topic_3444 ; sc:citation ; sc:description """SEPIA (SuscEptibility mapping PIpeline tool for phAse images). SEPIA is designed to provide a platform for easy access to different QSM processing methods in the field. To achieve this, most of the codes were written for data flow and algorithm parameter control. Through SEPIA, I hope researchers who are not expert in QSM will also be able to use QSM for their research.""" ; sc:featureList edam:operation_2429, edam:operation_3431, edam:operation_3454 ; sc:license "MIT" ; sc:name "SEPIA" ; sc:softwareHelp ; sc:url "https://github.com/kschan0214/sepia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """SEPIA (Simulation-based Evaluation of Prioritization Algorithms) is a framework for comparing the accuracies of algorithms that prioritize individuals by risk of transmitting HIV (Human Immunodeficiency Virus). SEPIA (Simulation-based Evaluation Of PriorIzation Algorithms). SEPIA.py matches all individuals in the user's ordering along with the number of people each individual infected during a specified period of time. Then, computes the Kendall Tau-b correlation coefficient between the user's ordering and the optimal ordering. Note that SEPIA can use any dataset produced by FAVITES: we just happened to reuse this dataset in the SEPIA manuscript. SEPIA itself is completely generalizable to any simulation conditions. ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/sepia-phase ||| NAME (SEPIA) SIMILAR TO (PUB. 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This is a preliminary version of code that does not call SNP variants inside the EM algorithm." ; sc:featureList edam:operation_3663 ; sc:name "SEQ-EM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cs.tau.ac.il/~heran/cozygene/software/seqem.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0199, edam:topic_0593, edam:topic_3542 ; sc:citation , "pubmed:34849579" ; sc:description "Directly exploiting multiple sequence alignment for protein secondary structure prediction." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_0504, edam:operation_2488, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Seq-SetNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fusong-ju/Seq-SetNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0637, edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC7578641", "pubmed:33087810" ; sc:description """a random forest model predicts potential miRNA-disease associations based on information of sequences and clinical symptoms. disease name.txt--339 diseases name including in our dataset. miRNA name.txt--917 miRNAs name including in our dataset. MDA.mat-- a binary matrix that represents the known miRNA-disease association from HMDD3.0. (2)Run the Seq-SymRF.m to construct the RF model and test the performance.""" ; sc:featureList edam:operation_0451, edam:operation_0463, edam:operation_3938 ; sc:name "Seq-SymRF" ; sc:url "https://github.com/LeeKamlong/Seq-SymRF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0821, edam:topic_2814, edam:topic_3500 ; sc:citation , "pubmed:34624539" ; sc:description "An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction." ; sc:featureList edam:operation_0267, edam:operation_0476, edam:operation_3431, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "Seq2Enz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.scfbio-iitd.res.in" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_0196, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC8015844", "pubmed:33731361" ; sc:description "Seq2Fun is an ultra-fast, all-in-one functional profiling tool for RNA-seq data analysis for organisms without reference genomes. Seq2Fun can finish a typical RNA-seq dataset within several hours on a standard PC in stead of several days or even weeks by conventional RNA-seq workflow on a high-performance server." ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3258, edam:operation_3800 ; sc:name "Seq2Fun" ; sc:url "https://www.seq2fun.ca" ; biotools:primaryContact "Jianguo Xia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3308 ; sc:citation "pubmed:22866951" ; sc:description """seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.""" ; sc:featureList edam:operation_3197, edam:operation_3198 ; sc:name "Seq2HLA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/sebastian_boegel/seq2hla" ; biotools:primaryContact "Sebastian Boegel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0781, edam:topic_3053 ; sc:citation "pubmed:26607834" ; sc:description "A web server of a dual-model approach, support vector machines (SVM) and a Mahalanobis distance discriminant (MD), to infer potential hosts of coronaviruses based on mononucleotide and dinucleotide biases of spike gene of coronaviruses." ; sc:featureList edam:operation_2423 ; sc:name "Seq2Hosts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ihb.ac.cn/seq2hosts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_3510 ; sc:citation "pubmed:22638583" ; sc:description "A web-based sequence logo generation method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion." ; sc:featureList edam:operation_2406, edam:operation_2575 ; sc:license "Other" ; sc:name "Seq2Logo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbs.dtu.dk/biotools/Seq2Logo/" ; biotools:primaryContact "Scientific problems: Morten Nielsen", "Technical problems and suggestions: Martin Thomsen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640, edam:topic_3512, edam:topic_3930 ; sc:citation , "pmcid:PMC9569519", "pubmed:36232923" ; sc:description "A comprehensive pipeline for cancer neoantigen immunogenicity prediction." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "AFL-3.0" ; sc:name "Seq2Neo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/XSLiuLab/Seq2Neo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3033 ; sc:name "Sequence coordinates" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2725 ; sc:encodingFormat edam:format_3033 ; sc:name "Ensembl transcript ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3517 ; sc:citation , "pmcid:PMC3266878", "pubmed:22291585" ; sc:description "This functional gene-set tool for the analysis of NGS data consists of \"seq2gene\" and \"gene2path\" components. The seq2gene component links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2path feature summarizes gene scores to pathway-scores for each sample." ; sc:featureList edam:operation_2497, edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "seq2pathway" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seq2pathway.html" ; biotools:primaryContact "Ana Marija Sokovic", "Xinan Yang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_1775 ; sc:citation "pubmed:23356573" ; sc:description "A web server designed to facilitate functional interpretation by retrieving and ranking the reference proteins in the BLAST result." ; sc:featureList edam:operation_2423 ; sc:name "Seq2Ref" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://prodata.swmed.edu/seq2ref/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3473, edam:topic_3474 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'pre-trained', 'generalizable', 'assays', 'Boosting' | Machine Learning in Quality Assessment of Early Stage Next-Generation Sequencing Data | Machine Learning Quality Assessment of NGS Data | seqQscorer is a python implementation that handles quality statistics or report summaries (quality features) as input to calculate a probability of an input sample to be of low quality. This probability is calculated with pre-trained classification models. The quality features are derived from FastQ and BAM files as shown in the Figure below and described in detail in our preprint on bioRxiv" ; sc:featureList edam:operation_3192, edam:operation_3218, edam:operation_3798 ; sc:name "seqQscorer" ; sc:url "https://github.com/salbrec/seqQscorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Jupyter notebook-based educational pipeline for RNA-Seq and epigenomic data analysis. Easy-to-use tutorial that outlines the complete RNA-Seq and ChIP-Seq analysis workflow and requires no prior programming experience." ; sc:featureList edam:operation_0445, edam:operation_2403, edam:operation_3222 ; sc:license "MIT" ; sc:name "SeqAcademy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.seqacademy.org/" ; biotools:primaryContact "Syed Hussain Ather" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2181, edam:format_2182, edam:format_2205 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0797, edam:topic_3174, edam:topic_3308, edam:topic_3372 ; sc:author "Mailing list answered by the developers" ; sc:citation , ; sc:description "An open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. The library is easy to use and simplifies the development of new software tools with a minimal loss of performance. Additionally, it includes several ready-made command line tools for common tasks in sequence analysis." ; sc:featureList edam:operation_0292, edam:operation_2403, edam:operation_2478, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SeqAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Freie Universität Berlin", "cibi" ; sc:softwareHelp , , ; sc:softwareVersion "2.4.0", "3.1.0" ; sc:url "https://www.seqan.de" ; biotools:primaryContact "Mailing list answered by the developers" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1179 ; sc:name "NCBI taxonomy ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2327 ; sc:name "GI number (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2275, edam:topic_2840, edam:topic_3314 ; sc:citation , , "pubmed:36825751", "pubmed:36847398" ; sc:description "A web-based tool for addressing the challenges of cross-species extrapolation of chemical toxicity." ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "SeqAPASS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://seqapass.epa.gov/seqapass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation , "pmcid:PMC5860110", "pubmed:28334390" ; sc:description "Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in the corresponding files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language." ; sc:featureList edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "SeqArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SeqArray.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3572 ; sc:description "Molecular sequence assembly software, proof-reading of trace file data, contig building." ; sc:featureList edam:operation_0310 ; sc:name "SeqAssem 200807- Molecular Sequence Assembly" ; sc:operatingSystem "Windows" ; sc:url "http://www.sequentix.de/software_seqassem.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation , "pmcid:PMC4251038", "pubmed:25349885" ; sc:description "Valuable “assistant” to a broad range of investigators who conduct genome re-sequencing, RNA-Seq, or de novo genome sequencing and assembly experiments. It takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data." ; sc:featureList edam:operation_2238, edam:operation_2409 ; sc:license "Other" ; sc:name "seqassist" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://orca.st.usm.edu/cbbl/seqassist/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3168 ; sc:citation "pubmed:18463137" ; sc:description "SEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in the BLAST output are replaced with the corresponding subsequence from the original FASTA files)." ; sc:featureList edam:operation_0368, edam:operation_2406, edam:operation_2479 ; sc:name "SEQATOMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinformatics.nl/tools/seqatoms" ; biotools:primaryContact "SEQATOMs Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_3676 ; sc:citation , "pmcid:PMC3898724", "pubmed:24444368" ; sc:description "Management and analysis of exome sequencing data. Provides a user friendly data acquisition module to facilitate comprehensive and intuitive data handling. Provides also direct access to the analysis pipeline SIMPLEX, which can be configured to run locally, on a cluster, or in the cloud." ; sc:featureList edam:operation_3227, edam:operation_3229, edam:operation_3799 ; sc:license "AGPL-3.0" ; sc:name "SeqBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.icbi.at/software/seqbench/seqbench.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC3315719", "pubmed:22285831" ; sc:description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "seqbias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqbias.html" ; biotools:primaryContact "Daniel Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description "Cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform." ; sc:featureList edam:operation_3222, edam:operation_3680 ; sc:name "SeqBox" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html" ; biotools:primaryContact "Marco Beccuti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3308 ; sc:citation "pubmed:20008100" ; sc:description "SeqBuster, a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs and the discovering of new small RNAs." ; sc:featureList edam:operation_3198 ; sc:name "SeqBuster" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/lpantano/seqbuster" ; biotools:primaryContact "Lorena Pantano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_0157 ; sc:citation "pubmed:21364786" ; sc:description "This tool assists the research personnel in computational sequence analysis and automated experimental calculations." ; sc:featureList edam:operation_2403 ; sc:name "SeqCalc" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/seqcalc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description "This package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours." ; sc:featureList edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "seqCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqCAT.html" ; biotools:primaryContact "Erik Fasterius" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2190 ; sc:name "Sequence checksum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071 ; sc:citation ; sc:description "Generation of checksums for protein and nucleotide sequences." ; sc:featureList edam:operation_3348 ; sc:name "SeqCksum (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/so/seqcksum" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (pair)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308 ; sc:author "Francisco Pantano Rubino", "Judith Flo Gaya" ; sc:citation , "pubmed:21976421", "pubmed:26530722" ; sc:description "Analysis of small RNA sequencing data. It detect unit of transcription over the genome, annotate them and create an HTML interactive report that helps to explore the data quickly." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "seqcluster" ; sc:operatingSystem "Linux" ; sc:provider "Center of Genomic Regulation", "Harvard Chan School", "hsph.harvard.edu" ; sc:softwareHelp , ; sc:softwareVersion "1.1.14" ; sc:url "http://seqcluster.readthedocs.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC4022175", "pubmed:24597965" ; sc:description "Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization." ; sc:featureList edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "seqCNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqCNA.html" ; biotools:primaryContact "David Mosen-Ansorena" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3674 ; sc:citation , "pmcid:PMC8486768", "pubmed:34599234" ; sc:description "Productive visualization of high-throughput sequencing data using the SeqCode open portable platform." ; sc:featureList edam:operation_0327, edam:operation_0337, edam:operation_3222, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeqCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eblancoga/seqcode" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "Provides useful functions for visualizing sequence recombination and virus reassortment events." ; sc:featureList edam:operation_0337, edam:operation_2928 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "seqcombo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqcombo.html" ; biotools:primaryContact "Guangchuang Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:19269990" ; sc:description "SeqCons is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly." ; sc:featureList edam:operation_0310 ; sc:name "SeqCons" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/gkno/seqan/tree/master/core/apps/seqcons" ; biotools:primaryContact "T. Rausch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25173705" ; sc:description "A set of Perl and R scripts designed to assess the quality of sequencing data using multiple quality metrics." ; sc:featureList edam:operation_3218 ; sc:name "SeqControl" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://labs.oicr.on.ca/Boutros-lab/software/SeqControl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0625, edam:topic_3474 ; sc:citation , "pubmed:33451939" ; sc:description "SeqCor is a tool for correcting the effect of guide RNA sequences in clustered regularly interspaced short palindromic repeats/Cas9 screening by machine learning algorithm." ; sc:featureList edam:operation_3432 ; sc:name "SeqCor" ; sc:url "https://github.com/wangyi-fudan/SeqCor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and count sequences." ; sc:featureList edam:operation_0231, edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqcount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqcount.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0601, edam:topic_2814, edam:topic_3398 ; sc:citation , "pmcid:PMC9763678", "pubmed:36582435" ; sc:description "A sequence-based algorithm for searching circularly permuted proteins." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "SeqCP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pcnas.life.nthu.edu.tw/SeqCP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information." ; sc:featureList edam:operation_2422, edam:operation_2479 ; sc:name "SeqDepot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://seqdepot.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0659, edam:topic_3174, edam:topic_3293 ; sc:citation ; sc:description "A tools to calculate the distance among sequence." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeqDistK" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/htczero/SeqDistK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0632, edam:topic_0654, edam:topic_3168, edam:topic_3324 ; sc:citation , "pubmed:33079985" ; sc:description """an application for primer design and sequence analysis with or without GTF/GFF files. SeqEditor is a Sequence Browser for the management and analysis of nucleotide and protein sequences of up to 300 megabases. This enables it to manage the largest chromosomes currently known. SeqEditor is an updated version of TIME, a former sequence editor (Muñoz et a.l 2011) also implemented as a sequence editor in the former release of GPRO (Futami et al. 2011). The new version provides improved updates of the functions (translation of nucleotide sequences into proteins, editing of sequences, changes in the geometry and orientation of the sequences etc.) and also provides new utilities for the searching and filtering of sequences, ORFs and motifs, managing multiple files simultaneously, primer design, metrics inference, and more.""" ; sc:featureList edam:operation_0231, edam:operation_0308, edam:operation_3216 ; sc:name "SeqEditor" ; sc:url "https://gpro.biotechvana.com/tool/seqeditor/manual" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation "pubmed:20861027" ; sc:description "Genotype-calling algorithm that estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm applies the well-known EM algorithm to an appropriate likelihood for a sample of unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype probabilities and the nucleotide-read error rate." ; sc:featureList edam:operation_3197 ; sc:name "SeqEM" ; sc:url "http://hihg.med.miami.edu/software-download/seqem-version-1.0" ; biotools:primaryContact "M. Schmidt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_2229, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """sequence-based classification of cell type-specific enhancers using deep learning models. Deep learning and SVM models for kmer-based enhancer classification. Utility programs for data processing are also provided. Usage of each program (excluding wrapper scripts) can be displayed by typing a command line without any option. python3, g++, perl, tensorflow, sklearn, numpy, pandas. mask_seq.pl Mask regions of chromosomal sequences: repeat sequences by 'N's, and other masked sequences by 'X's. Testing data for single cell type enhancer classifier (hepg2). Testing data for two cell types' enhancer classifier (gm12878 & hepg2). Testing data can be download from http://www.bdxconsult.com/SeqEnhDL.""" ; sc:featureList edam:operation_0368, edam:operation_2422, edam:operation_3695 ; sc:name "SeqEnhDL" ; sc:url "https://github.com/wyp1125/SeqEnhDL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23544073" ; sc:description "Assessmemt tool of sequence repeats for short read sequencing." ; sc:featureList edam:operation_0379 ; sc:name "SeqEntropy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/seqentropy/?source=navbar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203 ; sc:description "Comprehensive analysis and visualisation package for gene expression experiments. It is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages." ; sc:featureList edam:operation_3501, edam:operation_3559 ; sc:name "SeqExpress" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.2" ; sc:url "http://www.seqexpress.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "Analysis of next generation sequencing (NGS) DNA data from families with known pedigree information in order to identify rare variants that are potentially causal of a disease/trait of interest. It can be used to verify pedigree information, to perform Monte Carlo gene dropping, to undertake regression-based gene burden testing, and to identify variants which segregate by affection status in families via user-defined pattern of occurrence rules." ; sc:featureList edam:operation_0310, edam:operation_2403, edam:operation_2520, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "seqfam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/mframpton/seqfam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_3174 ; sc:citation , "pmcid:PMC4701496", "pubmed:26731669" ; sc:description "SeqFeatR has been developed to identify associations between mutation patterns in biological sequences and specific selection pressures (“features”)." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "SeqFeatR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.7" ; sc:url "https://seqfeatr.zmb.uni-due.de/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0194, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:22693213" ; sc:description "Web tool for extracting regions of interest from a mulitple sequence alignment. From a multiple sequence alignment, it can search for and extract regions that contain insertions and deletions (indels), and output details of the indels, as well as a binary character matrix of conserved clean indels for use in phylogenetic analysis. It can also extract blocks of conserved columns from a sequence alignment, output for phylogenetic analysis." ; sc:featureList edam:operation_0448, edam:operation_0452, edam:operation_0492, edam:operation_0499 ; sc:name "SeqFIRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.seqfire.org" ; biotools:primaryContact "Pravech AJAWATANAWONG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_3308 ; sc:citation ; sc:description "RNA secondary structure prediction from experimental data. Given high-throughput data, it can reconstruct the secondary structures of the whole transcriptome, termed the RNA structurome." ; sc:featureList edam:operation_0271, edam:operation_0278, edam:operation_2423 ; sc:name "SeqFold" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://ouyanglab.jax.org/seqfold/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2545 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2545 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:citation , "pmcid:PMC8148589", "pubmed:34066939" ; sc:description "A collection of utilities to manipulate FASTA and FASTQ files, supporting Gzipped input." ; sc:featureList edam:operation_3187, edam:operation_3695 ; sc:name "seqfu" ; sc:softwareHelp ; sc:softwareVersion "1.10.0", "1.11.0", "1.12.0", "1.13.0", "1.14.0", "1.15.0", "1.16.0" ; sc:url "https://telatin.github.io/seqfu2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2269, edam:topic_3170 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'seqgendiff R' | Data-based RNA-seq Simulations by Binomial Thinning | RNA-Seq Generation/Modification for Simulation | Generates/modifies RNA-seq data for use in simulations. We provide a suite of functions that will add a known amount of signal to a real RNA-seq dataset. The advantage of using this approach over simulating under a theoretical distribution is that common/annoying aspects of the data are more preserved, giving a more realistic evaluation of your method. The main functions are select_counts(), thin_diff(), thin_lib(), thin_gene(), thin_2group(), thin_all(), and effective_cor(). See Gerard (2019) for details on the implemented methods" ; sc:featureList edam:operation_2929, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "seqgendiff" ; sc:url "https://cran.r-project.org/package=seqgendiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , "pubmed:24535097" ; sc:description "The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively." ; sc:featureList edam:operation_2436 ; sc:license "GPL-3.0" ; sc:name "SeqGSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0089, edam:topic_0091, edam:topic_0219, edam:topic_3168 ; sc:citation "pubmed:12401134" ; sc:description "A freely available bioinformatics database warehouse resource that collects bioinformatics data from a number of sources including the National Center for Biotechnology Information and the Gene Ontology Consortium. It is designed for programmers who need unrestricted access to up-to-date data." ; sc:featureList edam:operation_2421 ; sc:name "SeqHound" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/slritools/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3489 ; sc:citation , "pmcid:PMC5051824", "pubmed:27706213" ; sc:description "FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations." ; sc:featureList edam:operation_0233, edam:operation_0371, edam:operation_0372, edam:operation_3192 ; sc:name "seqkit" ; sc:url "https://bioinf.shenwei.me/seqkit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_3474, edam:topic_3518 ; sc:description "Sequential KNN imputation method (SeqKNN) estimates missing values sequentially from the gene that has least missing rate." ; sc:featureList edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "SeqKNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/60128-sequential-knn-imputation-method" ; biotools:primaryContact "Shujaat Khan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3068 ; sc:citation ; sc:description "Implementation of a greedy coordinate-wise gradient descent technique for efficiently learning sequence classifiers." ; sc:featureList edam:operation_2990, edam:operation_2995, edam:operation_3659 ; sc:name "SEQL" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2.0" ; sc:url "http://daimi.au.dk/~ifrim//seql/seql.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3510, edam:topic_3534 ; sc:citation , "pubmed:26471456" ; sc:description "This toll predicts the substrate of non-ribosomal peptide synthetases A-domains using Sequence Learner (SEQL), a discriminative classification method for sequences." ; sc:featureList edam:operation_0238 ; sc:isAccessibleForFree true ; sc:name "SEQL-NRPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://services.birc.au.dk/seql-nrps/" ; biotools:primaryContact , "Dan Søndergaard" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "An R package for identification of differentially methylated regions (DMRs) from high density chip, for example Illumina 450K, data." ; sc:featureList edam:operation_3204 ; sc:name "seqlm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-EE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/raivokolde/seqlm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description "This tool takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990)." ; sc:featureList edam:operation_2520 ; sc:license "GPL-2.0" ; sc:name "seqLogo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqLogo.html" ; biotools:primaryContact "Oliver Bembom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_3070, edam:topic_3344 ; sc:description "Generates a sequence logo as a true colour array." ; sc:isAccessibleForFree true ; sc:name "seqlogo generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28700-seqlogo-generator" ; biotools:primaryContact "Malcolm McLean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3070, edam:topic_3344 ; sc:description "This is a wrapper around the bioinformatics SeqLogo function that creates a REAL matlab figure." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:name "SeqLogoFig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/27124-seqlogofig" ; biotools:primaryContact "Will Dampier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3169, edam:topic_3170, edam:topic_3673 ; sc:citation "pubmed:20950480" ; sc:description "Sequence assembly software using traditional and next-gen techonologies. Subsequent analysis of the assembly, including variant discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene." ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3198 ; sc:name "SeqMan NGen" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dnastar.com/t-nextgen-seqman-ngen.aspx" ; biotools:primaryContact "DNASTAR Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation "pubmed:18697769" ; sc:description "SeqMap is a tool for mapping large amount of short sequences to the genome." ; sc:featureList edam:operation_2520, edam:operation_3198 ; sc:name "SeqMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-personal.umich.edu/~jianghui/seqmap/" ; biotools:primaryContact "Hui Jiang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "All-against-all word comparison of a sequence set." ; sc:featureList edam:operation_0288 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqmatchall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqmatchall.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Takes a set of sequences and does an all-against-all pairwise comparison of words (fragments of the sequences of a specified fixed size) in the sequences, finding regions of identity between any two sequences." ; sc:featureList edam:operation_2403 ; sc:name "seqmatchall WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/seqmatchall.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_3169, edam:topic_3473 ; sc:citation "pubmed:21177645" ; sc:description "An integrated platform for ChIP-Seq data interpretation. SeqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative information. It also allows visualization and modelling of general as well as specific patterns in a given dataset." ; sc:featureList edam:operation_0571, edam:operation_2403, edam:operation_3198, edam:operation_3695 ; sc:name "seqMINER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bips.u-strasbg.fr/seqminer/tiki-index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053 ; sc:citation , "pubmed:26394715" ; sc:description "An R package for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases." ; sc:featureList edam:operation_0361, edam:operation_2403 ; sc:name "SEQMINER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://seqminer.genomic.codes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3337 ; sc:citation , "pubmed:32756942" ; sc:description """an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset. Seqminer is a highly efficient R-package for retrieving sequence variants from biobank scale datasets of millions of individuals and billions of genetic variants. It supports all variant types, including multi-allelic variants and imputation dosages. It takes VCF/BCF/BGEN/PLINK format as input file, indexes, queries them based upon variant-based index and loads them as R data types such as list or matrix. cfh2 <- seqminer::createSingleChromosomeVCFIndex(vcf.ref.file, vcf.idx.file). vcf.idx.file <- "input.vcf.scIdx".""" ; sc:featureList edam:operation_1812, edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3557 ; sc:name "seqminer2" ; sc:url "https://github.com/zhanxw/seqminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3173 ; sc:citation "pubmed:20098412" ; sc:description "A tool to visualise and analyse high throughput mapped sequence data" ; sc:featureList edam:operation_0337, edam:operation_0564, edam:operation_2238, edam:operation_3184 ; sc:license "GPL-3.0" ; sc:name "SeqMonk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/" ; biotools:primaryContact "Simon Andrews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "de novo sequencing by tandem mass spectrometry" ; sc:featureList edam:operation_3644 ; sc:name "SeqMS" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/10870956/" ; biotools:primaryContact "Jorge Fernandez-de-Coss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation "pubmed:26381817" ; sc:description "An automated pipeline to generate variant calls from FASTQ or BAM files, using more than 10 popular alignment and variant calling tools." ; sc:featureList edam:operation_0292, edam:operation_0564, edam:operation_2478, edam:operation_3227 ; sc:name "SeqMule" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://seqmule.openbioinformatics.org/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC8315007", "pubmed:34321962" ; sc:description "An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data." ; sc:featureList edam:operation_3566, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeqNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tgrimes/SeqNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "seqpac is a framework for small RNA analysis in R using sequence-based counts." ; sc:featureList edam:operation_2995, edam:operation_3192, edam:operation_3792 ; sc:license "GPL-3.0" ; sc:name "seqpac" ; sc:url "https://github.com/Danis102/seqpac" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation ; sc:description """a self-consistent metric of similarity between genomic interval sets. Seqpare is a self-consistent metric and tool for comparing sequences based on the total effective overlaps of their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, which directly represents the percentage of their effective overlapping: a similarity index of zero indicates totally unrelated sequences, and an index of one means that the interval sets are exactly the same. Seqpare tool provides functions for both searching and mapping large-scale interval datasets. The seqpare code is based on ailist.""" ; sc:featureList edam:operation_0335, edam:operation_2421 ; sc:license "MIT" ; sc:name "Seqpare" ; sc:url "https://github.com/deepstanding/seqpare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "seqPattern" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqPattern.html" ; biotools:primaryContact "Vanja Haberle" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2305, edam:format_3003, edam:format_3005 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2305, edam:format_3003, edam:format_3005 ; sc:name "Annotation track" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3508 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622 ; sc:citation ; sc:description "Tool for plotting NGS based experiments' signal tracks, e.g. reads coverage from ChIP-seq, RNA-seq and DNA accessibility assays like DNase-seq and MNase-seq, over user specified genomic features, e.g. promoters, gene bodies, etc. It can also calculate sequence motif density profiles from a reference genome." ; sc:featureList edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "seqplots" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqplots.html" ; biotools:primaryContact "Przemyslaw Stempor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3517 ; sc:citation "pubmed:24778108" ; sc:description "A tool that provides statistical power analysis and sample size estimation for sequence-based association studies." ; sc:featureList edam:operation_2478 ; sc:name "SEQPower" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/spower/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0632, edam:topic_3168 ; sc:citation ; sc:description "Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads." ; sc:featureList edam:operation_3095 ; sc:license "MIT" ; sc:name "SeqPrep" ; sc:softwareHelp ; sc:url "https://github.com/jstjohn/SeqPrep" ; biotools:primaryContact "S. C. Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0634, edam:topic_0654, edam:topic_3169, edam:topic_3474 ; sc:citation , "pmcid:PMC8527647", "pubmed:34670493" ; sc:description "Fast activation maximization for molecular sequence design." ; sc:featureList edam:operation_0479, edam:operation_0480, edam:operation_4008, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SeqProp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.github.com/johli/seqprop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3168, edam:topic_3325 ; sc:description "Open source software platform for rare disease genomics, which enables to analyze NGS data. Its integration with PhenoTips allows the collection of detailed phenotype information to be entered for individuals and integration with igv.js allows for interactive visualization of read-level data." ; sc:featureList edam:operation_2403, edam:operation_3197, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqr" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://seqr.broadinstitute.org/" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3168 ; sc:citation ; sc:description """A system for managing local collections biological sequences. Python package for writing and reading a local collection of biological sequences. The repository is non-redundant, compressed, and journalled, making it efficient to store and transfer multiple snapshots. A "fully-qualified" identifier includes a namespace to disambiguate accessions (e.g., "1" in GRCh37 and GRCh38). If the namespace is provided, seqrepo uses it as-is. If the namespace is not provided and the unqualified identifier refers to a unique sequence, it is returned; otherwise, ambiguous identifiers will raise an error.""" ; sc:featureList edam:operation_2422, edam:operation_3227, edam:operation_3435 ; sc:license "Apache-2.0" ; sc:name "SeqRepo" ; sc:url "https://github.com/biocommons/biocommons.seqrepo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and write (return) sequences." ; sc:featureList edam:operation_2422, edam:operation_3096 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqret" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqret.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3071 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Sequence format coversion tool." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:name "seqret (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/sfc/emboss_seqret" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and write (return) many sets of sequences." ; sc:featureList edam:operation_0224, edam:operation_0231 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqretsetall" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqretsetall.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read sequences and write them to individual files." ; sc:featureList edam:operation_0231, edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqretsplit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqretsplit.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:21575597" ; sc:description "A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "SeqSaw" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:url "http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/" ; biotools:primaryContact "seqsaw team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0637, edam:topic_0654, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description "SeqScreen sensitively assigns taxonomic classifications, functional annotations, and biological processes of interest to short DNA sequences." ; 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sc:license "Other" ; sc:name "SeqSeg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=182" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169 ; sc:description "seqsetvis enables the visualization and analysis of multiple genomic datasets. 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It first detects transcription factor binding regions by clustering tags and statistical hypothesis testing, and locates every binding site in detected binding regions by modeling the tag profiles. It can pinpoint closely spaced adjacent binding sites from ChIP-seq data. This software is coded in C/C++, and supports major computer platforms." ; sc:featureList edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "SeqSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.au.tsinghua.edu.cn/software/seqsite/" ; biotools:primaryContact "Xi Wang (Software details/bugs)", "Xuegong Zhang (Corresponding)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation "pubmed:20671709" ; sc:description "Simple analysis of Next Generation Sequencing data." ; sc:featureList edam:operation_2428, edam:operation_3662 ; sc:name "SeqSolve" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://www.asebio.com/en/member_product_item.cfm?iid=64" ; biotools:primaryContact "ASEBIO Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC5501866", "pubmed:28669402" ; sc:description "Analysis tool for large-scale rare variant association studies using whole-genome and exome sequence data." ; sc:featureList edam:operation_3197 ; sc:license "Apache-2.0" ; sc:name "SEQSpark" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/statgenetics/seqspark" ; biotools:primaryContact "Suzanne M. Leal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3301 ; sc:citation "pubmed:23563421" ; sc:description "This software is designed for distributed work-groups (client/server model) and allows automatic processing, assembling and analyzing NGS (e.g., Illumina, Ion Torrent or PacBio) and Sanger capillary-electrophoresis sequence data. 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It parses both FASTA and FASTQ files which can also be optionally compressed by gzip." ; sc:featureList edam:operation_2121, edam:operation_2409 ; sc:license "MIT" ; sc:name "seqtk" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/lh3/seqtk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "seqtk-trinity is a toolkit for processing sequences in FASTA/Q formats." ; sc:featureList edam:operation_2409 ; sc:license "MIT" ; sc:name "seqtk-trinity" ; sc:url "https://github.com/trinityrnaseq/seqtk-trinity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files." ; sc:featureList edam:operation_2478 ; sc:license "Artistic-2.0" ; sc:name "seqTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/seqTools.html" ; biotools:primaryContact "Wolfgang Kaisers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:22942788" ; sc:description "Application for viewing and processing DNA sequencing chromatograms (trace files). 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A straightforward desktop app for third generation sequencing read analysis — sequ-into latest documentation. Third generation sequencing techniques rapidly evolved as a common practice in molecular biology. Free document hosting provided by Read the Docs.""" ; sc:featureList edam:operation_3185, edam:operation_3198, edam:operation_3933 ; sc:license "MIT" ; sc:name "sequ-into" ; sc:softwareHelp ; sc:url "https://github.com/mjoppich/sequ-into" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168, edam:topic_3297 ; sc:citation , "pmcid:PMC10612204", "pubmed:37891497" ; sc:description "Big Data tool to perform quality control operations of NGS datasets in a scalable way, supporting single-end and paired-end reads in FASTQ/FASTA formats." ; sc:featureList edam:operation_0282, edam:operation_3218, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SeQual-Stream" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UDC-GAC/SeQual-Stream" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2854 ; sc:encodingFormat edam:format_2572, edam:format_3003, edam:format_3475 ; sc:name "Position-specific scoring matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3316 ; sc:author "Dimitri Desvillechabrol", "Thomas Cokelaer" ; sc:citation "pubmed:30192951" ; sc:description "Show coverage and interval of confidence to identify under and over represented genomic regions. The tool also creates an HTML report with various images showing the coverage and GC versus coverage plots. It also provides a set of CSV files with low or high coverage regions (as compared to the average coverage)." ; sc:featureList edam:operation_0253 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "sequana_coverage" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Bioinformatics and Biostatistics Hub", "Institut Pasteur" ; sc:softwareHelp ; sc:softwareVersion "0.15.1" ; sc:url "http://sequana.readthedocs.io" ; biotools:primaryContact "Thomas Cokelaer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Graphical user interface (PyQt) for Snakemake workflows." ; sc:featureList edam:operation_3184 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "sequanix" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.5.0" ; sc:url "http://sequana.readthedocs.io" ; biotools:primaryContact "Cokelaer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:22925230" ; sc:description "Sequedex classifies short reads for phylogeny and function at high speed" ; sc:featureList edam:operation_0361, edam:operation_2403 ; sc:name "Sequedex" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sequedex.lanl.gov" ; biotools:primaryContact "Sequedex Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0780, edam:topic_3168 ; sc:citation , "pmcid:PMC7532105", "pubmed:33004007" ; sc:description """a suite of tools for working with PacBio Sequel raw sequence data. For more information please read our paper found at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03751-8. Whenever using this software or presenting data generated from this software you are obligated to cite this paper. This work is protected by an open source GNU general public liscence. SequelTools is a fast and easy to install command-line program that provides a collection of tools for working with multiple SMRTcells of BAM format PacBio Sequel raw sequece data.""" ; sc:featureList edam:operation_3218, edam:operation_3435, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "SequelTools" ; sc:url "https://github.com/ISUgenomics/SequelTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0196, edam:topic_3168, edam:topic_3794 ; sc:description "Assemble overlapping sequences according to reference" ; sc:featureList edam:operation_0310, edam:operation_0495, edam:operation_0496 ; sc:isAccessibleForFree true ; sc:name "Sequence Assembly App" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/46071-sequence-assembly-app" ; biotools:primaryContact "Turner Conrad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_0160, edam:topic_3168 ; sc:citation "pubmed:17130172", "pubmed:17584793" ; sc:description "Detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings." ; sc:featureList edam:operation_0292, edam:operation_0492, edam:operation_0499, edam:operation_3186 ; sc:name "Sequence Harmony" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/seqharmwww/" ; biotools:primaryContact "K. Anton Feenstra" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author "Thomas Haschka" ; sc:citation ; sc:description "Finds a accurate nucleic subsequences within in a sequence. On whole chromosome / genome levels, within seconds." ; sc:featureList edam:operation_0238, edam:operation_0240 ; sc:isAccessibleForFree true ; sc:license "Zlib" ; sc:name "sequence_in_sequence_finder" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/haschka/sequence_in_sequence_finder" ; biotools:primaryContact "Thomas Haschka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23275734" ; sc:description "The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism." ; sc:featureList edam:operation_0338, edam:operation_2478 ; sc:name "Sequence Maneuverer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0654 ; sc:description "Easy-to-use Java tool for searching protein and DNA sequences for user specified sequence motifs.  The Sequence Searcher can search multiple sequences in a single pass.  The target sequences may be imported from your computer in FASTA format or you can manually paste the sequence(s) into a text window." ; sc:featureList edam:operation_2421 ; sc:name "Sequence Searcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://athena.bioc.uvic.ca/virology-ca-tools/sequence-searcher/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2229, edam:topic_3053 ; sc:citation , "pubmed:34875773" ; sc:description "Concatenation software for the fast assembly of multi-gene datasets with character set and codon information." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SequenceMatrix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.ggvaidya.com/taxondna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2229, edam:topic_3168 ; sc:citation , "pmcid:PMC7829059", "pubmed:33487172" ; sc:description "SequencErr is a tool for measuring and suppressing sequencer errors in next-generation sequencing data." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3218 ; sc:name "SequencErr" ; sc:url "https://platform.stjude.cloud/workflows/sequencerr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0867 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence alignment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091 ; sc:author "WurmLab" ; sc:citation ; sc:description "BLAST is the most commonly used bioinformatics tool. But setting it up for private data and using it is counter-intuitive. We developed this tool to make BLAST easy to use." ; sc:featureList edam:operation_0346 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SequenceServer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0.9" ; sc:url "http://www.sequenceserver.com" ; biotools:primaryContact "Anurag Priyam", "Yannick Wurm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622, edam:topic_3577 ; sc:citation ; sc:description "Software tool that we have been developing to analyze the genetic variants identified from whole-genome sequencing studies." ; sc:featureList edam:operation_0484, edam:operation_3208 ; sc:name "SequenceVariantAnalyzer" ; sc:operatingSystem "Linux" ; sc:url "http://www.omicsexpress.com/sva.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation ; sc:description "Desktop alignment software now with plugins to MAQ and GSNAP for NGS sequence date" ; sc:featureList edam:operation_0292, edam:operation_0310 ; sc:name "Sequencher" ; sc:operatingSystem "Mac", "Windows" ; sc:url "http://genecodes.com/" ; biotools:primaryContact "Contact Form", "Technical support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3344, edam:topic_3518 ; sc:description "Sequenom2pedfile creates a pedfile from the genotyping info generated from Sequenom Mass Array runs." ; sc:featureList edam:operation_3196, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Sequenom2pedfile" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/41569-sequenom2pedfile" ; biotools:primaryContact "Ismael Huertas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170 ; sc:citation ; sc:description "Algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn’t assume uniform distribution of count within transcripts." ; sc:featureList edam:operation_2409 ; sc:name "Sequgio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.99.0" ; sc:url "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6680061", "pubmed:31378808" ; sc:description "A fast and scalable library for depth of coverage calculations" ; sc:featureList edam:operation_3192, edam:operation_3680, edam:operation_3800 ; sc:name "SeQuiLa" ; sc:softwareHelp ; sc:url "https://github.com/biodatageeks/sequila" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_2275 ; sc:description "Performs sequence validation by comparing the model side chains against the electron density. It may be run with phases from experimental phasing, or it can calculate its own phases using a side-chain-omit process. In this case it can be used after molecular replacement, or to validate structures in the PDB." ; sc:featureList edam:operation_2451 ; sc:name "sequins" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "20070909" ; sc:url "http://www.ysbl.york.ac.uk/~cowtan/sequins/sequins.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC7324041" ; sc:description """A Playground for Logicians. Sequent calculus proof construction tool. git clone git@github.com:meta-logic/sequoia.git. These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. Design, play with, and analyze sequent calculus proof systems. Investigate meta-theoretical properties for your calculus systems (such as identity expansion, weakening admissibility, and permutability of rules). Sequoia is able to infer most of the trivial cases automatically. Create, save, modify, and manage your own calculi. Bower (note that Bower can be installed via npm once Node.js is installed).""" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "Sequoia" ; sc:url "https://github.com/meta-logic/sequoia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_3170, edam:topic_3398, edam:topic_3512 ; sc:citation , "pmcid:PMC8262049", "pubmed:34233619" ; sc:description "An interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets." ; sc:featureList edam:operation_0337, edam:operation_3185, edam:operation_3695, edam:operation_3802, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Sequoia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dnonatar/Sequoia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3372 ; sc:citation , "pubmed:32315391" ; sc:description """multiobjective multiple sequence alignment in Python. Sequoya is an open source software tool aimed at for solving Multiple Sequence Alignment problems with multi-objective metaheuristics.""" ; sc:featureList edam:operation_0337, edam:operation_0492 ; sc:license "MIT" ; sc:name "Sequoya" ; sc:url "https://github.com/benhid/Sequoya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation ; sc:description "An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "SeqVarTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html" ; biotools:primaryContact "Adrienne Stilp", "Stephanie M. Gogarten", "Xiuwen Zheng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0749, edam:topic_3510, edam:topic_3512 ; sc:citation "pubmed:12513700", "pubmed:15215387" ; sc:description "Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister." ; sc:featureList edam:operation_0253, edam:operation_0256, edam:operation_3092 ; sc:name "SeqVISTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zlab.bu.edu/SeqVISTA/" ; biotools:primaryContact "Martin Frith", "Tianhua Niu", "Zhenjun Hu", "Zhiping Weng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web API", "Workbench" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:author "Brian O'Connor", "Denis Yuen", "Morgan Taschuk", "Solomon Shorser" ; sc:citation ; sc:description "Portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "SeqWare" ; sc:operatingSystem "Linux" ; sc:provider "Ontario Institute for Cancer Research", "ucla.edu" ; sc:softwareHelp , ; sc:softwareVersion "1.1.1" ; sc:url "http://seqware.io/" ; biotools:primaryContact "Brian O'Connor", "Denis Yuen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3168 ; sc:citation ; sc:description "SeqWho is a reliable and extremely rapid program designed to determin a FASTQ(A) sequencing file identity, both sourse protocol and species of origin. This is accomplished using an alignment-free algorithm that leverages a Random Forest classifier that learns from biases in k-mer frequencies and repeat sequence identity. SeqWho is capable of achieving greater than 96% accuracy in it’s ability to classify files." ; sc:featureList edam:operation_2995, edam:operation_3218, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "SeqWho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DaehwanKimLab/seqwho" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0659, edam:topic_0749, edam:topic_3489 ; sc:citation , "pmcid:PMC10189941", "pubmed:37194023" ; sc:description "Modularized toolkit for next-generation protein sequence database management and analysis." ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SeqWiz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.websdoor.net/goto/seqwiz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Featherweight object for the calculation of n-mer word occurrences in a single sequence." ; sc:featureList edam:operation_3472 ; sc:name "SeqWords" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://search.cpan.org/dist/BioPerl-1.6.924/Bio/Tools/SeqWords.pm" ; biotools:primaryContact "SeqWords Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Retrieve all database cross-references for a sequence entry." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqxref" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqxref.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2093 ; sc:name "Data reference" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3077 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Retrieve all cross-referenced data for a sequence entry." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "seqxrefget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/seqxrefget.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3299, edam:topic_3305, edam:topic_3855 ; sc:citation , "pmcid:PMC10008288", "pubmed:36919015" ; sc:description "An R package to characterize environmental regimes, calculating Short-period Environmental Regime (SER)." ; sc:featureList edam:operation_0337, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:name "SER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kun-ecology/SER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3299 ; sc:citation , "pubmed:33120029" ; sc:description "an R package for ShortlivEd RAdionuclide chronology of recent sediment cores." ; sc:featureList edam:operation_3431, edam:operation_3435 ; sc:license "MIT" ; sc:name "serac" ; sc:url "https://github.com/rosalieb/serac" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3068, edam:topic_3518 ; sc:citation "pubmed:18480123" ; sc:description "This tool helps users select the GO annotation or list analysis tools which best suit their needs. It may also be used to compare the capabilities of the various GO tools in the context of the users' experiment." ; sc:featureList edam:operation_3501, edam:operation_3672 ; sc:name "SerbGO" ; sc:url "http://www.geneontology.org/GO.tools.microarray.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7530147", "pubmed:32871105" ; sc:description """SERGIO (Single-cell ExpRession of Genes In silicO). A Single-Cell Expression Simulator Guided by Gene Regulatory Networks. SERGIO is a simulator for single-cell expression data guided by gene regulatory networks. A command-line, easy-to-use version of SERGIO will be soon uploaded to PyPI. Here is the documentation for using SERGIO v1.0.0 as a module in python.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3891, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "SERGIO" ; sc:url "https://github.com/PayamDiba/SERGIO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description "This figure display aspect of seri fourier." ; sc:isAccessibleForFree true ; sc:name "Seri Fourier Gui" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/8376-seri-fourier-gui" ; biotools:primaryContact "Sayed Meysam Hosseini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3452 ; sc:citation ; sc:description "Acquire tilt series for electron tomography on Tecnai and JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. It does not count on the microscope or the specimen being particularly well-behaved, so unless a prediction appears reliable, it falls back to measuring and adjusting defocus and/or specimen position when necessary." ; sc:featureList edam:operation_2423, edam:operation_3443 ; sc:name "SerialEM" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "3.4.8" ; sc:url "http://bio3d.colorado.edu/SerialEM/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1413 ; sc:name "Sequence similarity" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pmcid:PMC4508402", "pubmed:25972421" ; sc:description "SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli." ; sc:featureList edam:operation_3198 ; sc:isAccessibleForFree true ; sc:name "SerotypeFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://cge.cbs.dtu.dk/services/SerotypeFinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0157, edam:topic_3168 ; sc:citation , "pmcid:PMC7320618", "pubmed:32311033" ; sc:description """a flexible 2D binning method for differential Hi-C analysis. Locally smearing noisy regions in Hi-C contact maps as a prelude to differential analyses. trend, threshold = sp.MDbefore(A, B, show=False). sA, sB, sK = sp.serpentin_binning(A, B, threshold, threshold / 5). Executing the command serpentine --help will give you a brief help of the command line tool. For a detailed reference to the python library functions, please read the documentation.""" ; sc:featureList edam:operation_2429, edam:operation_3435, edam:operation_3798 ; sc:name "Serpentine" ; sc:softwareHelp ; sc:url "https://github.com/koszullab/serpentine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0634, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9277798", "pubmed:35821062" ; sc:description "Mutation update of SERPING1 related to hereditary angioedema in the Chinese population" ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "SERPING1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://databases.lovd.nl/shared/variants/SERPING1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654, edam:topic_0736, edam:topic_3047 ; sc:citation ; sc:description """a program to determine nucleic acids elasticity from simulation data. SerraNA is composed by three executables: SerraNA, Analysis and Extract.""" ; sc:featureList edam:operation_3454, edam:operation_3659, edam:operation_3891 ; sc:license "LGPL-3.0" ; sc:name "SerraNA" ; sc:url "https://github.com/agnesnoy/SerraNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0611, edam:topic_2828, edam:topic_3448 ; sc:citation ; sc:description "Servalcat is a tool for structure refinement and validation for crystallography and single particle analysis. It is used for Cryo-EM single particle structure refinement and map calculation using Servalcat. Servalcat makes refinement by REFMAC5 easy for single particle analysis. 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Hydrography are input from a polyline shapefile and intersected with a structured grid defined using a shapefile or a Flopy StructuredGrid instance" ; sc:license "CC0-1.0" ; sc:name "SFRmaker" ; sc:softwareHelp ; sc:url "https://github.com/usgs/sfrmaker" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3524 ; sc:citation "pubmed:18842601" ; sc:description "This tool can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects." ; sc:featureList edam:operation_0554, edam:operation_2426 ; sc:name "SFS_CODE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sfscode.sourceforge.net/SFS_CODE/index/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Automated analysis of mtDNA variations from NGS data." ; sc:featureList edam:operation_0361 ; sc:name "SG-ADVISER" ; sc:softwareHelp ; sc:url "https://genomics.scripps.edu/mtdna/" ; biotools:primaryContact "Ali Torkamani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33039787" ; sc:description """Self-grouping convolutional neural networks. Although group convolutions are increasingly used on deep convolutional neural networks to improve the computation efficiency and to reduce the number of parameters, most existing methods construct their group convolution architectures by predefinedly partitioning the filters of each convolutional layer into multiple regular filter groups with equally spatial group size and data-independence, which is disadvantageous to fully exploit their potential abilities.""" ; sc:featureList edam:operation_3192, edam:operation_3432, edam:operation_3695 ; sc:name "SG-CNN" ; sc:url "https://github.com/QingbeiGuo/SG-CNN.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:32181478" ; sc:description "a computational frame using sequence and geometrical information via LSTM to predict miRNA-gene associations." ; sc:featureList edam:operation_0463, edam:operation_3659 ; sc:name "SG-LSTM" ; sc:url "https://github.com/Xshelton/SG_LSTM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3673 ; sc:citation "pubmed:16204131" ; sc:description "SGA is a de novo assembler designed to assemble large genomes from high coverage short read data." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "SGA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jts/sga" ; biotools:primaryContact "Jared Simpson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2229 ; sc:citation "pubmed:23677617" ; sc:description "A single stop solution for analysing data from genetic screens. There are three steps to the analysis pipeline, each of which can also be run separately from the rest. First, images of plates with colonies are processed to give quantified colony sizes for the screen. 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Louis", "Richard Durbin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2572 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320 ; sc:citation , "pmcid:PMC4878813", "pubmed:27218464" ; sc:description "Package for analyzing splice events from RNA-seq data. Input data are sequence reads mapped to a reference genome in BAM format. Genes are represented as a genome-wide splice graph, which can be obtained from existing annotation or can be predicted from the data. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant." ; sc:featureList edam:operation_0564 ; sc:license "Artistic-2.0" ; sc:name "SGSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SGSeq.html" ; biotools:primaryContact "Leonard Goldstein" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0154, edam:topic_1317, edam:topic_3168 ; sc:citation "pubmed:16844998" ; sc:description "sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties." ; sc:featureList edam:operation_0477 ; sc:name "sgTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ysbl.york.ac.uk/sgTarget/" ; biotools:primaryContact "A. P. C. Rodrigues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382 ; sc:citation , "pubmed:33595304" ; sc:description """A Python Code for Calculating the Interfacial Properties of Fluids Based on the Square Gradient Theory Using the SAFT-VR Mie Equation of State. SGTPy is an open-source python package of SAFT-VR-Mie Equation of State (EOS). SGTPy allows to work with pure fluids and fluid mixtures, additionally the fluids can be modeled considering association, cross-association and polar contributions. SGTPy was built on top of phasepy's phase equilibrium and Square Gradient Theory (SGT) functions. These functions were updated to speed-up calculations of associative mixtures.""" ; sc:featureList edam:operation_3454, edam:operation_3455 ; sc:name "SGTPy" ; sc:url "https://github.com/gustavochm/SGTPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:description "R package to visualize results from population genomics analyses. The package implements low-level function to generate genomics plots and high-level functions to visualize results from the Sex Genomics Toolkit." ; sc:featureList edam:operation_0282, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "sgtr" ; sc:url "https://github.com/SexGenomicsToolkit/sgtr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:36288230" ; sc:description "Semantic Attention Guided Underwater Image Enhancement with Multi-Scale Perception." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SGUIE-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://trentqq.github.io/SGUIE-Net.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """Privacy-Preserving Genotype Imputation in a Trusted Execution Environment. SMac: Secure Genotype Imputation in Intel SGX.""" ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3557 ; sc:name "SGX" ; sc:url "https://github.com/ndokmai/sgx-genotype-imputation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0209, edam:topic_0736, edam:topic_2640 ; sc:citation , "pmcid:PMC10320075", "pubmed:37207333" ; sc:description "Information system for the SH2 domain." ; sc:featureList edam:operation_0246, edam:operation_0294, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "SH2db" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sh2db.ttk.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_0736, edam:topic_3510 ; sc:citation "pubmed:10764600", "pubmed:16870929", "pubmed:17485474" ; sc:description "SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_2479, edam:operation_2949, edam:operation_3092 ; sc:name "SH3-Hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbm.bio.uniroma2.it/SH3-Hunter/" ; biotools:primaryContact "Enrico Ferraro" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1872 ; sc:encodingFormat edam:format_2331, edam:format_3475 ; sc:name "Taxonomic classification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3050 ; sc:description "UNITE SH matching analysis is a digital service for the global species discovery from eDNA (environmental DNA). SH matching service is based on the UNITE (https://unite.ut.ee) datasets hosted in PlutoF (https://plutof.ut.ee). Its output includes information about what species are present in eDNA samples, are they potentially undescribed new species, where are they found in other studies, are they alien or threatened species, etc. The output will provide DOI (Digital Object Identifier) based stable identifiers for the communicating species found in eDNA. DOIs are connected to the taxonomic backbone of PlutoF and GBIF (https://gbif.org)." ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "CC-BY-SA-4.0" ; sc:name "SH matching" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/TU-NHM/sh_matching_pub" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3293, edam:topic_3407 ; sc:citation , "pmcid:PMC7397055", "pubmed:32645885" ; sc:description """Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes. A python implementation of a hybrid approach for the detection of horizontal gene transfer events in prokaryotes.""" ; sc:featureList edam:operation_0327, edam:operation_0544, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "ShadowCaster" ; sc:softwareHelp ; sc:url "https://github.com/dani2s/ShadowCaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3343 ; sc:citation "pubmed:19434847" ; sc:description "This tool aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay. It can be used for the virtual screening of libraries of chemical structures against a known active molecule, or as a preparative step for 3D QSAR methods." ; sc:featureList edam:operation_3666 ; sc:name "ShaEP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://users.abo.fi/mivainio/shaep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC7320600", "pubmed:32315385" ; sc:description """detection of homologous recombination deficiency from shallow whole genome sequencing. This method uses shallow Whole Genome Sequencing (sWGS ~ 0.4-1x) and the segmentation of a tumor genomic profile to infer the Homologous Recombination status of a breast, ovarian tumor based on the number of Large-scale Genomic Alterations (LGAs), evaluated in a similar way to LSTs (Large-scale State Transitions) but independent of the ploidy, with no reference to an absolute copy number. This can also be applied to pancreatic and prostate tumor. shallowHRD is a R script that can be launched from the command line. It relies on a ratio file characterizing the normalized read counts of a shallow Whole Genome Sequencing (0.4-1x) in sliding windows along the genome and its segmentation. It was developped on the output of ControlFREEC (Boeva,V. et al., 2012) but is adapted to similar softwares (see sections "run shallowHRD" and "Nota Bene").""" ; sc:featureList edam:operation_0451 ; sc:name "shallowHRD" ; sc:url "https://github.com/aeeckhou/shallowHRD" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3475 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:author "Amine Ghozlane", "Hugo Varet", "Pierre Lechat", "Stevenn Volant" ; sc:citation , "pmcid:PMC4878514", "pubmed:27140611" ; sc:description "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. 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The SHAPER model is an updated version of 3DSSR model, which takes RNA sequence-dependent bias into consideration. 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It takes as input a set of initial network estimates for each cell type in a dataset, computed using a user's network inference algorithm of choice, and then outputs a corresponding set of revised networks." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ShareNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alexw16/sharenet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7050522", "pubmed:31992615" ; sc:description """Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection. SHARP, short for Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection, is a bioinformatics tool to process and analyze single-cell RNA-seq (scRNA-seq) data. Algorithmically, SHARP is based on ensemble random projection (RP) and multi-layer meta-clustering which can well preserve cell-to-cell distance in reduced-dimensional space. Compared to other existing tools, it has the following advantages:. Number of Random-Projection Applications. Processing 1.3 Million Single Cells.""" ; sc:featureList edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:name "SHARP" ; sc:url "https://github.com/shibiaowan/SHARP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation , "pmcid:PMC7483855", "pubmed:32686750" ; sc:description "De novo assembly from Oxford Nanopore reads." ; sc:featureList edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Shasta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://github.com/chanzuckerberg/shasta" . a sc:SoftwareApplication ; 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biotools:primaryContact "Eric Alm", "Shandrina Burns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24476358" ; sc:description "A tool for next-generation sequencing data analysis that predicts sequence variations, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis." ; sc:featureList edam:operation_3228 ; sc:name "SHEAR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://vk.cs.umn.edu/SHEAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:22809339" ; sc:description "The tool displays schemes of β-sheet called, draws β-sheet maps." ; sc:featureList edam:operation_0474 ; sc:name "SheeP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=sheep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154, edam:topic_1317 ; sc:citation , , , , , "pubmed:12351820", "pubmed:18156677", "pubmed:20383001", "pubmed:25567568" ; sc:description "Suite of programs for small molecule crystallography, direct method and refinement." ; sc:featureList edam:operation_0474 ; sc:isAccessibleForFree true ; sc:name "SHELX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://shelx.uni-goettingen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0749, edam:topic_3520 ; sc:citation , "pmcid:PMC10423030", "pubmed:37540173" ; sc:description "Modular and extensible software architecture for analysing and annotating large protein datasets." ; sc:featureList edam:operation_0417, edam:operation_1812, edam:operation_2422, edam:operation_3216, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "SHEPHARD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/holehouse-lab/shephard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC9344852", "pubmed:35708611" ; sc:description "Accurate Clustering for Correcting DNA Barcode Errors." ; sc:featureList edam:operation_3200, edam:operation_3432, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Shepherd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.github.com/Nik-Tavakolian/Shepherd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Sherenga de novo sequencing" ; sc:featureList edam:operation_3631 ; sc:name "Sherenga" ; sc:url "http://proteomics.broadinstitute.org/millhtml/batchsherengaframe.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2259, edam:topic_3071 ; sc:citation ; sc:description "Sherlock is an open-source data platform to store, analyze and integrate Big Data for biology." ; sc:featureList edam:operation_0224, edam:operation_3282, edam:operation_3802 ; sc:name "Sherlock" ; sc:url "https://earlham-sherlock.github.io/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:encodingFormat edam:format_3859 ; sc:name "NMR spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0621, edam:topic_3047 ; sc:citation , "pmcid:PMC9920390", "pubmed:36771127" ; sc:description "Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3215, edam:operation_3465, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Sherlock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/michaelwenk/sherlock" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3295 ; sc:citation ; sc:description "bisulfite-treated Read FastQ Simulator" ; sc:featureList edam:operation_2426 ; sc:license "GPL-3.0" ; sc:name "Sherman" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.bioinformatics.babraham.ac.uk/projects/sherman/" ; biotools:primaryContact "Simon Andrews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0593, edam:topic_3314 ; sc:citation ; sc:description """A General Code for Calculating Molecular Thermochemistry Properties. Shermo is essentially open-source. The source code (written in Fortran) can be freely obtained by simply sending an E-mail to me, the only requirement is clearly indicating your name and affiliation in the mail.""" ; sc:featureList edam:operation_0455, edam:operation_0475, edam:operation_3891 ; sc:name "Shermo" ; sc:url "http://sobereva.com/soft/shermo" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0870 ; sc:encodingFormat edam:format_1912 ; sc:name "Sequence distance matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0972 ; sc:encodingFormat edam:format_2332 ; sc:name "Text mining report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3747 ; sc:name "Protein report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1174 ; sc:encodingFormat edam:format_3475 ; sc:name "ChEBI ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0870 ; sc:encodingFormat edam:format_1991 ; sc:name "Sequence distance matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_3475 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2872 ; sc:encodingFormat edam:format_3475 ; sc:name "ID list" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_3475 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:description "shic is a collection of shims for use in automated workflow composition" ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "shic" ; sc:softwareHelp ; sc:url "https://github.com/magnuspalmblad/shic" ; biotools:primaryContact "Magnus Palmblad" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_2275 ; sc:citation "pubmed:12652131" ; sc:description "The tool compares, identifies, corrects and re-referencs 1H, 13C and 15N backbone chemical shifts of peptides and proteins by comparing the observed chemical shifts with the predicted chemical shifts derived from the 3D structure (PDB corrdinates) of the protein(s)of interest." ; sc:featureList edam:operation_0250 ; sc:name "Shiftcor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shifty.wishartlab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0601, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC7319548", "pubmed:32459331" ; sc:description """a web server to understand and biophysically align proteins through their NMR chemical shift values. ShiftCrypt: Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index. These are the oxidised thioredoxins shown in the ShiftCrypt paper, the first one is bmr6318 (A. thaliana), the second one bmr25703 (S. cervisiae). You can then upload and align these proteins.""" ; sc:featureList edam:operation_0491, edam:operation_3214 ; sc:name "ShiftCrypt" ; sc:softwareHelp ; sc:url "http://www.bio2byte.be/shiftcrypt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0593, edam:topic_2275 ; sc:citation "pubmed:16823900" ; sc:description "A program for predicting φ, ψ, χ1, and ω torsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology." ; sc:featureList edam:operation_0474 ; sc:name "SHIFTOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/shiftor/cgi-bin/shiftor_1f.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0593, edam:topic_3168 ; sc:citation "pubmed:9460240" ; sc:description "With this tool you can predict 1H, 13C, and 15N chemical shifts for your favourite protein using only its amino acid sequence as input. The technique uses dynamic programming to detect sequence homologies between your query and sequences of hundreds of previously assigned protiens in the BioMagResBank." ; sc:featureList edam:operation_0250 ; sc:name "Shifty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shifty.wishartlab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3293, edam:topic_3305, edam:topic_3673 ; sc:citation ; sc:description """Shigella EIEC Cluster Enhanced Serotyper Finder. Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping. This is a tool that is used to identify differentiate Shigella/EIEC using cluster-specific genes and identify the serotype using O-antigen/H-antigen genes. This pipeline can serotype over 59 Shigella and 22 EIEC serotypes using either assembled whole genomes or Whole Genome Sequencing (WGS) reads. The results are output in a tabular format which if saved as a file can be opened in Excel or other tabular programs. Also available as an online tool.""" ; sc:featureList edam:operation_0415, edam:operation_0525, edam:operation_3211, edam:operation_3431, edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "ShigEiFinder" ; sc:url "https://github.com/LanLab/ShigEiFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3444 ; sc:citation , "pubmed:36441743" ; sc:description "An open-source software toolbox for B0 and B1 shimming in MRI." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Shimming Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shimming-toolbox.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3489, edam:topic_3810 ; sc:citation ; sc:description """A web tool dedicated to seed lots history, phenotyping and cultural practices. In 2005, a collaboration started between INRA and the french farmers' seed network Réseau Semences Paysannes (RSP) on bread wheat. In this project, researchers and farmers' organizations needed to map the history and life cycle of the population-varieties using the network formalism. All this information needed to be centralized and stored in a database. Thus, we developed SHiNeMaS (Seeds History and Network Management System) a database with its web interface, dedicated to the management of the history of seed lots and related data like phenotyping, environment and cultural practices. SHiNeMaS is freely available and distributed under GNU Affero GPL Licence. La forge Enseignement supérieur et Recherche.""" ; sc:featureList edam:operation_3431 ; sc:license "AGPL-3.0" ; sc:name "SHiNeMaS" ; sc:url "https://sourcesup.renater.fr/projects/shinemas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3382 ; sc:citation , "pubmed:32666343" ; sc:description "A Web Application to Analyze and Visualize Differentially Expressed Genes in RNA-seq." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3680 ; sc:name "Shiny-DEG" ; sc:url "https://github.com/sufangwang-npu/shiny-DEG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Advanced Guided Transcriptome Analysis. Abstract Objective A comprehensive analysis of RNA-Seq data uses a wide range of different tools and algorithms, which are normally limited to R users only. While several tools and advanced analysis pipelines are available, some require programming skills and others lack the support for many important features that enable a more comprehensive data analysis. There is thus, a need for a guided and easy to use comprehensive RNA-Seq data platform, which integrates the state of the art analysis workflow. Results We present the tool Shiny-Seq, which provides a guided and easy to use comprehensive RNA-Seq data analysis pipeline""" ; sc:featureList edam:operation_3463, edam:operation_3680, edam:operation_3766, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "Shiny-Seq" ; sc:url "https://beta.fastgenomics.org/analyses/detail-analysis-25cfdf63ed984ac3a3101de6b9253f0a#Run" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3299, edam:topic_3673 ; sc:citation , "pmcid:PMC7451576", "pubmed:32853264" ; sc:description """A web-based performance calculator for somatic structural variant detection. Shiny-SoSV provides an interactive and visual platform for users to easily explore the impact of different parameters on the power to detect somatic structural variants derived from short-read shole genome sequencing. Therefore, it enables users to rapidly address essential questions related to their study design.""" ; sc:featureList edam:operation_0331, edam:operation_0337, edam:operation_3227, edam:operation_3659 ; sc:license "MIT" ; sc:name "Shiny-SoSV" ; sc:url "https://hcpcg.shinyapps.io/Shiny-SoSV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3382 ; sc:citation , "pmcid:PMC6916222", "pubmed:31842743" ; sc:description """an online application for interactive Bayesian network inference and visualization. shinyBN is an R/Shiny application for interactive construction, inference and visualization of Bayesian Network, which provide friendly GUI for users lacking of programming skills. It's mainly based on five R packages: bnlearn for structure learning, parameter training, gRain for network inference, and visNetwork for network visualization, pROC and rmda for receiver operating characteristic (ROC) curve and decision curves analysis (DCA) , respectively, which was further wrapped by Shiny, a framework to build interactive web application straight by R""" ; sc:featureList edam:operation_3083, edam:operation_3439, edam:operation_3562 ; sc:license "Apache-2.0" ; sc:name "shinyBN" ; sc:url "https://jiajin.shinyapps.io/shinyBN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3940 ; sc:citation ; sc:description "ShinyArchR.UiO (ShinyArchR User interface Open) is an user-friendly, integrative, and open-source shiny-based web app using R programming for visualization of massive single-cell chromatin accessibility data (scATAC-seq) based on ArchR, (Granja et al, 2021)." ; sc:featureList edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ShinyArchR UiO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/EskelandLab/ShinyArchRUiO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC7750682", "pubmed:33376806" ; sc:description """Interactive NMF-based decomposition workflow of genome-scale datasets. ShinyButchR is an interactive R/Shiny app to perform NMF on an input matrix. ShinyButchR uses ButchR (https://github.com/wurst-theke/ButchR) to run the matrix decomposition and generate diagnostic plots and visualizations that helps to find association of the NMF signatures to known biological factors. ButchR is an R package providing functions to perform non-negative matrix factorization and postprocessing using TensorFlow.""" ; sc:featureList edam:operation_0337, edam:operation_3501, edam:operation_3937 ; sc:license "GPL-3.0" ; sc:name "ShinyButchR" ; sc:url "https://hdsu-bioquant.shinyapps.io/shinyButchR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description """Simple and sharable visualisation of single-cell gene expression data. ShinyCell is a R package that allows users to create interactive Shiny-based web applications to visualise single-cell data via (i) visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, (ii) visualising the distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots and (iii) visualising the expression of multiple genes using bubbleplots / heatmap.""" ; sc:featureList edam:operation_0571, edam:operation_2422, edam:operation_2943, edam:operation_3431 ; sc:name "ShinyCell" ; sc:url "https://github.com/SGDDNB/ShinyCell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_0654, edam:topic_0659, edam:topic_3382 ; sc:citation , "pmcid:PMC7056921", "pubmed:31931182" ; sc:description """An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes. ShinyChromosome is an Shiny application for interactive creation of non-circular plots of whole genomes within the web browser. shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinychromosome.ncpgr.cn/ and https://yimingyu.shinyapps.io/shinychromosome/, for online use. interactive creation of non-circular whole genome diagram.""" ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3182 ; sc:name "shinyChromosome" ; sc:url "https://yimingyu.shinyapps.io/shinychromosome/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:citation ; sc:description "Graphical user interface for interactive creation of Circos plot." ; sc:featureList edam:operation_3208 ; sc:name "shinyCircos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/venyao/shinyCircos" ; biotools:primaryContact "Wen Yao", "Yidan Ouyang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3519 ; sc:citation ; sc:description """shiny web application to analyse multisource qPCR amplification data. Quantitative RT-PCR amplification has been the gold-standard tool for viral detection during the SARS-CoV-2 pandemic. However, the desperate rush for a quick diagnosis led the use of very different types of machines and proprietary software, leading thus to an unbearable complexity of data analysis with a limited parameter setup. Here, we present shinyCurves, a shiny web application created to analyse multisource qPCR amplification data from independent multi-plate format. Furthermore, our automated system allows the classification of the results as well as the plot of both amplification and melting curves. Altogether, our web application is an automated qPCR analysis resource available to the research community.""" ; sc:featureList edam:operation_0458, edam:operation_3799 ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "shinyCurves" ; sc:url "https://biosol.shinyapps.io/shinycurves/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3305, edam:topic_3382, edam:topic_3517 ; sc:citation , "pmcid:PMC9908040" ; sc:description "ShinyDataSHIELD—an R Shiny application to perform federated non-disclosive data analysis in multicohort studies." ; sc:featureList edam:operation_2940, edam:operation_3431, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "ShinyDataSHIELD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://datashield-demo.obiba.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_3053, edam:topic_3577 ; sc:citation , "pmcid:PMC7924953", "pubmed:33554860" ; sc:description """A web-tool to explore the Cancer Dependency Map (DepMap) project. This is a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. A shiny-based interactive web tool to analyze DepMap data (based on their 19q3 release). A resource of data and computational tools to expose the vulnerabilities of cancer, and for identifying targets for therapeutic development and designing strategies to optimize patient responses.""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3432, edam:operation_3802 ; sc:name "shinyDepMap" ; sc:url "https://labsyspharm.shinyapps.io/depmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3056, edam:topic_3697 ; sc:citation ; sc:description "Interactive application to explore various ecological diversity metrics" ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "ShinyDiversity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://erictleung.shinyapps.io/shinydiversity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web API" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0769, edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pubmed:33416853" ; sc:description """A graphical pipeline to analyze Illumina DNA methylation arrays. ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis. ShinyÉPICo is a web interface based on Shiny that makes it easy to do differentially methylated CpGs analysis from Illumina EPIC or 450k DNA methylation arrays. ShinyÉPICo can run in GNU Linux, Windows or macOS. DNAMethylation, DifferentialMethylation, Microarray, Preprocessing, QualityControl, Software.""" ; sc:featureList edam:operation_2940, edam:operation_3204, edam:operation_3435 ; sc:license "AGPL-3.0" ; sc:name "shinyEPICo" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/shinyepico/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_3053, edam:topic_3360 ; sc:citation "pubmed:27503226" ; sc:description "A web-based application for performing differential expression and survival analysis on Gene Expression Omnibus datasets." ; sc:featureList edam:operation_3223 ; sc:name "shinyGEO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gdancik.github.io/shinyGEO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_0622 ; sc:citation , "pmcid:PMC5426587", "pubmed:28493881" ; sc:description "Ultra fast low memory heatmap web interface for big data genomics." ; sc:featureList edam:operation_0531 ; sc:name "shinyheatmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shinyheatmap.com/" ; biotools:primaryContact "Bohdan Khomtchouk" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3273 ; sc:name "Sample ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269 ; sc:citation ; sc:description "A web application for sample size and power calculation in case-control microbiome studies" ; sc:featureList edam:operation_2238 ; sc:name "ShinyMB" ; sc:provider "Ghent University", "ugent.be" ; sc:softwareVersion "1" ; sc:url "https://fedematt.shinyapps.io/shinyMB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3518, edam:topic_3674 ; sc:citation , "pmcid:PMC4176427", "pubmed:25285208" ; sc:description "Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported." ; sc:featureList edam:operation_2939, edam:operation_3204 ; sc:license "Artistic-2.0" ; sc:name "shinyMethyl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/shinyMethyl.html" ; biotools:primaryContact "Jean-Philippe Fortin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC6969480", "pubmed:31952481" ; sc:description """collaborative exploration of omics-data. This app allows exploratory data analysis on any 'Omics' dataset, e.g. Transcriptomics, proteomics, phenotypic screens. It comes with pre-loaded datasets from the human pathogens Streptococcus pneumoniae and Mycobacterium tuberculosis. The S. pneumoniae set includes RNA-Seq and Tn-seq data from Zhu et al 2019 (under review) where two strains (19F and T4) were treated with 5 different antibiotics (KAN, LVX, VNC, RIF, PEN). The M. tuberculosis datasets are microarray and proteomic screens under hypoxic conditions ShinyOmics: Exploration of 'Omics' data.""" ; sc:featureList edam:operation_2495, edam:operation_2939, edam:operation_2940, edam:operation_3359, edam:operation_3891 ; sc:license "AGPL-3.0" ; sc:name "ShinyOmics" ; sc:url "http://bioinformatics.bc.edu/shiny/ShinyOmics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2815 ; sc:citation , "pubmed:35015561" ; sc:description "User-Friendly R Shiny Application for Visualizing Cancer Risk Factors and Mortality Across the University of Kansas Cancer Center Catchment Area." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "shinyOPTIK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://optik.shinyapps.io/OPTIK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3172, edam:topic_3520, edam:topic_3855 ; sc:citation ; sc:description """Shinyscreen R package is an application intended to give the user a first look into raw mass-spectrometry data. This currently means that, given the input of data files and a list of masses of know, or unknown compounds, the application is going to produce the MS1 and MS2 chromatograms of the substances in the list, as well as the MS2 spectra. None of these features have been post-processed in the slightest. However, there is a built-in prescreening aid that will help the user assess the quality of the spectra.""" ; sc:featureList edam:operation_3215, edam:operation_3627, edam:operation_3860 ; sc:name "Shinyscreen" ; sc:url "https://git-r3lab.uni.lu/eci/shinyscreen/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3678 ; sc:citation ; sc:description "Sample Integrated Set Profile Analysis. Define sample groups using gene sets from multiple-omics data. Define sample groups with similar gene set enrichment profiles" ; sc:featureList edam:operation_0253 ; sc:name "shinySISPA" ; sc:operatingSystem "Mac", "Windows" ; sc:url "http://bbisr.shinyapps.winship.emory.edu/shinySISPA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3382 ; sc:citation , "pubmed:35866686" ; sc:description "A Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ShinySyn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/obenno/ShinySyn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files." ; sc:featureList edam:operation_0237 ; sc:license "GPL-3.0" ; sc:name "shinyTANDEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/shinyTANDEM.html" ; biotools:primaryContact "Frederic Fournier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_3301 ; sc:citation "pubmed:22589098" ; sc:description "A Salmonella/Host Protein-Protein Interaction predictions browser." ; sc:featureList edam:operation_2464 ; sc:name "SHIPREC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sbi.imim.es/web/index.php/research/databases/shiprec" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0780, edam:topic_3293, edam:topic_3500 ; sc:citation ; sc:description """SHOOT.bio is a phylogenetic search engine It searches your query sequence against a database of gene families and provides you with a phylogenetic tree with your query sequence grafted into it. You can use SHOOT to: Find similar sequences in other organisms (just like BLAST), Produce a phylogenetic tree of your gene and its relatives, Find the orthologs of your gene in other species, Map the evolutionary history of your gene and Find the gene family of your gene.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0552, edam:operation_0556, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SHOOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.shoot.bio" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_3016, edam:format_3752 ; sc:name "Genotype/phenotype report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1863 ; sc:encodingFormat edam:format_1929 ; sc:name "Haplotype map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3168, edam:topic_3174 ; sc:author , , , "Kerensa McElroy" ; sc:citation , , , , "pmcid:PMC2995073", "pmcid:PMC3113935", "pmcid:PMC3848937", "pubmed:20377454", "pubmed:20671025", "pubmed:21521499", "pubmed:23879730" ; sc:description "Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes." ; sc:featureList edam:operation_0487, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ShoRAH" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1.3", "1.99.0" ; sc:url "https://github.com/cbg-ethz/shorah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:18818371" ; sc:description "Analysis suite for short read data." ; sc:featureList edam:operation_2429 ; sc:name "Shore" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://1001genomes.org/downloads/shore.html" ; biotools:primaryContact "Jörg Hagmann.", "Stephan Ossowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625 ; sc:citation "pubmed:19644454" ; sc:description "Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants." ; sc:featureList edam:operation_2520 ; sc:license "GPL-3.0" ; sc:name "SHOREmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://1001genomes.org/software/shoremap.html" ; biotools:primaryContact "Contact form", "Hequan Sun", "Korbinian Schneeberger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:21330288" ; sc:description "Method for using paired-end reads to find fusion transcripts without requiring unique mappings or additional single read sequencing" ; sc:featureList edam:operation_0491, edam:operation_2429 ; sc:name "ShortFuse" ; sc:softwareHelp ; sc:url "https://bitbucket.org/mckinsel/shortfuse" ; biotools:primaryContact "Marcus Kinsella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , "pmcid:PMC2752612", "pubmed:19654119" ; sc:description "This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats." ; sc:featureList edam:operation_0231, edam:operation_1812, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "ShortRead" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ShortRead.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:19208115" ; sc:description "Targetted for de novo assembly of microreads with mate pair information and sequencing errors. It has some novel approach and features in addressing the short read assembly problem." ; sc:featureList edam:operation_0310 ; sc:name "SHORTY" ; sc:softwareHelp ; sc:url "http://www.cs.sunysb.edu/%7Eskiena/shorty/" ; biotools:primaryContact "Anand Sagar Kothapalli", "Bala Nagi Reddy M", "Chandrakanth Reddy B" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:11858840" ; sc:description "A web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer." ; sc:featureList edam:operation_3478 ; sc:name "SHOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bork.embl-heidelberg.de/~korbel/SHOT_v2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3524 ; sc:description "Convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation." ; sc:featureList edam:operation_0230, edam:operation_0484, edam:operation_3227 ; sc:license "Not licensed" ; sc:name "ShotGun" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://yunliweb.its.unc.edu//shotgun.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769 ; sc:citation ; sc:description """Bashing irreproducibility with shournal. A (file-) journal for your shell. Note: for a more formal introduction please read Bashing irreproducibility with shournal on bioRxiv. Using the external software shournal-to-snakemake an observed shell-command-series can be directly transformed into rules for the Snakemake workflow engine, a tool to create reproducible and scalable data analyses.""" ; sc:featureList edam:operation_0224 ; sc:license "GPL-3.0" ; sc:name "shournal" ; sc:url "https://github.com/tycho-kirchner/shournal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3301 ; sc:author ; sc:description "Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too." ; sc:featureList edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "shovill" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.0.0", "1.0.1", "1.0.2", "1.0.3", "1.0.4", "1.0.5", "1.0.6", "1.0.7", "1.0.8", "1.0.9" ; sc:url "https://github.com/tseemann/shovill" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0654, edam:topic_3320, edam:topic_3372 ; sc:description "Enables self-learning of HMM on a set of sequences, sequence segmentation based on the Baum-Welch or the Viterbi algorithms,and sequence simulation under a given HMM. Allows the user to specify any highly structured model and also to process large sets of sequences. Successfully used in diverse tasks such as DNA segmentation in homogeneous segments, bacterial gene prediction and human splice sites detection." ; sc:featureList edam:operation_2423, edam:operation_2454 ; sc:name "SHOW" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20111109" ; sc:url "http://genome.jouy.inra.fr/ssb/SHOW/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:name "Statistical estimate score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "This tool enables to fit an Hiden Markov Model on sequences using EM algorithm (learning) and to reconstruct the hidden state path using forward-backward algorithm (segmentation). When used with fixed parameters, it only produces the sequence segmentation with the forward-backward algorithm." ; sc:featureList edam:operation_0361, edam:operation_0436, edam:operation_2425 ; sc:name "show_emfit" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "IFB ELIXIR-FR" ; sc:softwareHelp ; sc:softwareVersion "20111109" ; sc:url "http://genome.jouy.inra.fr/ssb/SHOW/" ; biotools:primaryContact "Pierre Nicolas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1249 ; sc:name "Sequence length" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "This tool enables to simulate a hidden state sequence and a DNA sequence under a specified Hidden Markov Model." ; sc:featureList edam:operation_2426 ; sc:name "show_simul" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "IFB ELIXIR-FR" ; sc:softwareHelp ; sc:softwareVersion "20111109" ; sc:url "http://genome.jouy.inra.fr/ssb/SHOW/" ; biotools:primaryContact "Pierre Nicolas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1364 ; sc:name "Hidden Markov model" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "This tool implements the viterbi algorithm to find the most probable hidden path given the observed sequence (segmentation). The Hidden Markov Model parameters can first be learned with show_emfit." ; sc:featureList edam:operation_0361, edam:operation_0436 ; sc:name "show_viterbi" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "IFB ELIXIR-FR" ; sc:softwareHelp ; sc:softwareVersion "20111109" ; sc:url "http://genome.jouy.inra.fr/ssb/SHOW/" ; biotools:primaryContact "Pierre Nicolas" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display a multiple sequence alignment in pretty format." ; sc:featureList edam:operation_0564, edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showalign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "This tool displays an aligned set of protein or a nucleic acid sequences in a style suitable for publication." ; sc:featureList edam:operation_2403 ; sc:name "showalign WS (husar)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/showalign.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display information on configured databases." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showdb.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display features of a sequence in pretty format." ; sc:featureList edam:operation_0564 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showfeat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showfeat.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display a nucleotide sequence and translation in pretty format." ; sc:featureList edam:operation_0371, edam:operation_0436, edam:operation_0564 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showorf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showorf.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display protein sequences with features in pretty format." ; sc:featureList edam:operation_0564 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showpep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showpep.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display sequences with features in pretty format." ; sc:featureList edam:operation_0371, edam:operation_0564, edam:operation_0571 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showseq.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display information on configured servers." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "showserver" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/showserver.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:19542152" ; sc:description "A new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure" ; sc:featureList edam:operation_3195, edam:operation_3218 ; sc:name "SHREC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/shrec-ec/" ; biotools:primaryContact "Schröder J" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:19461883" ; sc:description "Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. Works with data in letterspace (Roche, Illumina), colourspace (AB) and Helicos space." ; sc:featureList edam:operation_0310 ; sc:name "SHRiMP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/compbio-UofT/shrimp" ; biotools:primaryContact "Shrimp Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_3053, edam:topic_3500 ; sc:citation , "pmcid:PMC4094775", "pubmed:24952385" ; sc:description "Gene and protein annotation tool for knowledge sharing and gene discovery in shrimp." ; sc:featureList edam:operation_0361 ; sc:name "ShrimpGPAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://shrimpgpat.sc.mahidol.ac.th/ShrimpGPATV2/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2573 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2573 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "C++ program to shrink the SAM file after a read-mapping" ; sc:featureList edam:operation_0233 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "shrinksam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcthomas/shrinksam" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Shuffle a set of sequences maintaining composition." ; sc:featureList edam:operation_0367 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "shuffleseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/shuffleseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3512, edam:topic_3523 ; sc:citation , "pmcid:PMC6704232", "pubmed:31475020" ; sc:description "> MEDIUM CONFIDENCE! | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction | siFi: Software for long double-stranded RNAi-target design and off-target prediction | RNA interference (RNAi) is a nucleic acid complementarity-based biological phenomenon and a widespread natural mechanism for the inhibition or regulation of gene expression" ; sc:featureList edam:operation_2008, edam:operation_3095, edam:operation_3192 ; sc:license "CC-BY-SA-4.0" ; sc:name "si-Fi" ; sc:url "https://github.com/snowformatics/siFi21" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2914 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence features metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3174 ; sc:citation , , "pmcid:PMC4299606", "pubmed:25432777" ; sc:description "SIAMCAT is a modular R toolbox, which offers machine learning and statistical testing workflows enabling the user to associate microbial community profiles with host phenotypes, such as disease states in clinical case-control studies. SIAMCAT combines statistical rigor with flexible customization for training and evaluating several machine learning classifiers. From these, microbiome biomarkers or signatures can be extracted and validated." ; sc:featureList edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SIAMCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "HD-HuB" ; sc:softwareHelp ; sc:softwareVersion "1.9.0" ; sc:url "http://siamcat.embl.de/" ; biotools:primaryContact "Georg Zeller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3332, edam:topic_3524 ; sc:citation ; sc:description "Computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution." ; sc:featureList edam:operation_2426 ; sc:name "SIApopr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/olliemcdonald/siapopr" ; biotools:primaryContact "Franziska Michor" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2275, edam:topic_3168, edam:topic_3315 ; sc:citation "pubmed:19429693" ; sc:description "SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection." ; sc:featureList edam:operation_0292, edam:operation_0346 ; sc:name "SIB-BLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserv.mps.ohio-state.edu/sib-blast/" ; biotools:primaryContact "Ralf Bundschuh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Sibelia: A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms." ; sc:featureList edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "Sibelia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinf.spbau.ru/sibelia" ; biotools:primaryContact "Sibelia team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_0196, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7728760", "pubmed:33303762" ; sc:description """Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ. SibeliaZ is a whole-genome alignment and locally-coliinear blocks construction pipeline. The blocks coordinates are output in GFF format and the alignment is in MAF.""" ; sc:featureList edam:operation_0492, edam:operation_0524, edam:operation_3182, edam:operation_3216 ; sc:name "SibeliaZ" ; sc:url "https://github.com/medvedevgroup/SibeliaZ/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0769, edam:topic_3068, edam:topic_3577 ; sc:citation , "pmcid:PMC7319474", "pubmed:32379317" ; sc:description """RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. COVID-19 outbreak: explore our literature triage interface and APIs.""" ; sc:featureList edam:operation_0305, edam:operation_1812, edam:operation_2422, edam:operation_3625 ; sc:name "SIBiLS" ; sc:url "https://candy.hesge.ch/SIBiLS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:24825613" ; sc:description "The tool designed to detect inconsistencies based on the evolutionary information in multiple sequence alignments. A Bayesian framework, combined with Dirichlet mixture models, is used to estimate the probability of observing specific amino acids and to detect inconsistent or erroneous sequence segments." ; sc:featureList edam:operation_0447 ; sc:name "SIBIS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.lbgi.fr/~julie/SIBIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3053 ; sc:citation ; sc:description "Perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors." ; sc:featureList edam:operation_0283 ; sc:name "SIBLINK" ; sc:operatingSystem "Linux" ; sc:softwareVersion "3.0" ; sc:url "http://dmpi.duke.edu/siblink-v-30" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625, edam:topic_2269, edam:topic_3053 ; sc:citation ; sc:description "Identifiy likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. Using a hidden Markov model, the program calculates the posterior probability of genotyping error or mutation for each sib-pair-marker combination, given all the available marker data, an assumed genotype-error rate, and a known genetic map." ; sc:featureList edam:operation_2423, edam:operation_2429, edam:operation_3196 ; sc:name "SIBMED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "http://csg.sph.umich.edu/boehnke/sibmed.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:description "SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence." ; sc:featureList edam:operation_0292 ; sc:name "SIBsim4" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/sibsim4/" ; biotools:primaryContact "Christian Iseli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:33003198" ; sc:description """short indel call filtering with boosting. Despite impressive improvement in the next-generation sequencing technology, reliable detection of indels is still a difficult endeavour. Recognition of true indels is of prime importance in many applications, such as personalized health care, disease genomics and population genetics. Recently, advanced machine learning techniques have been successfully applied to classification problems with large-scale data. In this paper, we present SICaRiO, a gradient boosting classifier for the reliable detection of true indels, trained with the gold-standard dataset from 'Genome in a Bottle' (GIAB) consortium. Our filtering scheme significantly improves the performance of each variant calling pipeline used in GIAB and beyond. SICaRiO uses genomic features that can be computed from publicly available resources, i.e. it does not require sequencing pipeline-specific information (e.g. read depth)""" ; sc:featureList edam:operation_0452, edam:operation_3196, edam:operation_3675, edam:operation_3695 ; sc:name "SICaRiO" ; sc:url "https://bitbucket.org/islam2059/sicario/src/master/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3173 ; sc:citation "pubmed:19505939" ; sc:description "A clustering approach for identification of enriched domains from histone modification ChIP-seq data." ; sc:featureList edam:operation_3187 ; sc:name "SICER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://home.gwu.edu/%7Ewpeng/Software.htm" ; biotools:primaryContact "Weiqun Peng" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:description "A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads." ; sc:featureList edam:operation_3192 ; sc:license "MIT" ; sc:name "sickle" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/najoshi/sickle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC8491382", "pubmed:34607568" ; sc:description "A deep-learning-driven text-mining tool to abridge disease-disease associations." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SicknessMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MoreiraLAB/SicknessMiner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_2330 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168 ; sc:citation ; sc:description "This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region." ; sc:featureList edam:operation_2238, edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "SICtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SICtools.html" ; biotools:primaryContact "Xiaobin Xing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_3172 ; sc:citation , "pmcid:PMC10353719", "pubmed:37137236" ; sc:description "Online implementation of distance correlation and partial distance correlation for data-driven network analysis." ; sc:featureList edam:operation_2937, edam:operation_3435, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:name "SiDCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://complimet.ca/sidco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3336, edam:topic_3423 ; sc:citation ; sc:description "Algorithm for predicting adverse drug reactions." ; sc:featureList edam:operation_3439 ; sc:name "side-effects" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/poleksic/side-effects" ; biotools:primaryContact "Aleksandar Poleksic", "Lei Xie" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0984 ; sc:name "Molecule name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3668 ; sc:name "Disease name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3275 ; sc:name "Phenotype name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3303 ; sc:author "Michael Kuhn" ; sc:citation , "pmcid:PMC4702794", "pubmed:23632385", "pubmed:26481350" ; sc:contributor "Peer Bork" ; sc:description "Contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "HD-HuB" ; sc:softwareHelp ; sc:url "http://sideeffects.embl.de/" ; biotools:primaryContact "Michael Kuhn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3512, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description """a pipeline for identifying somatic and dimorphic insertions of processed pseudogenes or retrocopies. A pipeline for detecting Somatic Insertion of DE novo RETROcopies. sideRETRO is a bioinformatic tool devoted for the detection of somatic retrocopy insertion, also known as retroCNV, in whole genome and whole exome sequencing data (WGS, WES). The program has been written from scratch in C, and uses HTSlib and SQLite3 libraries, in order to manage SAM/BAM/CRAM reading and data analysis.""" ; sc:featureList edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "sideRETRO" ; sc:softwareHelp ; sc:url "https://github.com/galantelab/sideRETRO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659, edam:topic_3170 ; sc:citation "pubmed:14769950", "pubmed:15215364" ; sc:description "Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates." ; sc:featureList edam:operation_2008 ; sc:name "siDirect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://design.RNAi.jp/" ; biotools:primaryContact "K. Ui-Tei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "Tool to filter Next Generation Sequencing (NGS) data based on a chosen target organism. It uses data fron BLAST (or similar classifiers) to train a Decision Tree model to classify sequence data as either belonging to the target organism, or belonging to something else. This classification can be used to filter the data for later assembly." ; sc:featureList edam:operation_3460 ; sc:name "SIDR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sidr.readthedocs.io/en/latest/" ; biotools:primaryContact "Janna L. Fierst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444 ; sc:description "Converts Siemens MRI DICOM data into NIfTI format, and/or anonymises and sorts into scan directories" ; sc:featureList edam:operation_0335, edam:operation_3283, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "Siemens DICOM sort and convert to NIfTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.27" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/22508-siemens-dicom-sort-and-convert-to-nifti" ; biotools:primaryContact "Simon Robinson" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:name "Sequence alignment (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1497 ; sc:name "Root-mean-square deviation" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3336, edam:topic_3534 ; sc:citation , ; sc:description "Search for homologous protein binding sites structures in the Protein Data Bank. The tool allows an automated assembly and preprocessing of protein structure ensembles supporting protein flexibility and point mutation analyses as well as structure-based virtual screening." ; sc:featureList edam:operation_0244, edam:operation_0295, edam:operation_0310, edam:operation_0339, edam:operation_3432 ; sc:name "SIENA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Hamburg - Center for Bioinformatics" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de/#siena" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0611, edam:topic_0621, edam:topic_3372 ; sc:citation , "pubmed:32486661" ; sc:description """Recent developments and applications. SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3891 ; sc:name "Siesta" ; sc:softwareHelp ; sc:url "https://launchpad.net/siesta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC8974938", "pubmed:35402832" ; sc:description "Identifying robust single cell variable genes for single-cell RNA sequencing data." ; sc:featureList edam:operation_0313, edam:operation_3435, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SIEVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YinanZhang522/SIEVE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_1775, edam:topic_3325, edam:topic_3473 ; sc:citation , , "pmcid:PMC311071", "pmcid:PMC3394338", "pubmed:11337480", "pubmed:22689647" ; sc:description "Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function." ; sc:featureList edam:operation_0477, edam:operation_0484, edam:operation_1777, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SIFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sift-dna.org" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0821, edam:topic_3299, edam:topic_3398 ; sc:citation ; sc:description "Sift-PUL database is a public repository providing predicted PULs with specific functional annotations. 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Contains functions for manipulation of objects, various analysis types, and some visualization." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "sigaR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sigaR.html" ; biotools:primaryContact "Wessel N. van Wieringen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "While gene signatures are frequently used to predict phenotypes, it is not always clear how optimal or meaningful they are. Based on suggestions in that paper, this tool accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata." ; sc:featureList edam:operation_3224 ; sc:license "Artistic-2.0" ; sc:name "SigCheck" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SigCheck.html" ; biotools:primaryContact "Rory Stark" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Report on signal cleavage sites in a protein sequence." ; sc:featureList edam:operation_0418 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sigcleave" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/sigcleave.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0202, edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation , "pmcid:PMC9252724", "pubmed:35524556" ; sc:description "Data and metadata search engine for a million gene expression signatures." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2436, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "SigCom LINCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://maayanlab.cloud/sigcom-lincs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC7169426", "pubmed:32346383" ; sc:description """Novel Significant Feature Selection Method for Classification of Gene Expression Data Using Support Vector Machine and t Statistic. sigFeature: Significant feature selection using SVM-RFE & t-statistic. This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy.""" ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3936 ; sc:license "GPL-3.0" ; sc:name "sigFeature" ; sc:url "https://bioconductor.org/packages/sigFeature/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_2640 ; sc:citation ; sc:description """an automated and comprehensive pipeline for cancer genome mutational signature analysis. Sigflow: Streamline Analysis Workflows for Mutational Signatures. Sigflow provides useful mutational signature analysis workflows. It can auto-extract mutational signatures, fit mutation data to all/specified COSMIC reference signatures (SBS/DBS/INDEL) and run bootstrapping analysis for studying signature stability.""" ; sc:featureList edam:operation_1812, edam:operation_3227, edam:operation_3907 ; sc:license "AFL-3.0" ; sc:name "Sigflow" ; sc:url "https://github.com/ShixiangWang/sigminer.workflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099, edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Algorithm for testing significance of clustering in RNA-seq data." ; sc:featureList edam:operation_3432 ; sc:license "GPL-3.0" ; sc:name "SigFuge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SigFuge.html" ; biotools:primaryContact "Patrick Kimes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation ; sc:description "Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM)." ; sc:featureList edam:operation_2238, edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "siggenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/siggenes.html" ; biotools:primaryContact "Holger Schwender" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Suite" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3343, edam:topic_3572 ; sc:citation ; sc:description "Suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "sights" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sights.html" ; biotools:primaryContact "Elika Garg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:24371153" ; sc:description "A tool that analyses genomic signature of a DNA sequence and outputs the score DIAS." ; sc:featureList edam:operation_2454 ; sc:name "SigHunt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iba.muni.cz/index-en.php?pg=research--data-analysis-tools--sighunt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC7368050", "pubmed:32681003" ; sc:description """Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood. Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood. SigLASSO considers both sampling error (especially important when the mutation count is low) and signature fitting. Moreover, it parameterizes the model empirically. Let the data speak for itself. Moreover, you will be able to feed prior knowledge of the signatures into the model in a soft thresholding way. No more picking up signature subsets by hand! SigLASSO achieves signature selection by using L1 regularization.""" ; sc:featureList edam:operation_1812, edam:operation_3435, edam:operation_3891 ; sc:name "sigLASSO" ; sc:url "http://github.com/gersteinlab/siglasso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:25266224" ; sc:description "A novel sequence similarity-based approach for strain-level identification of genomes from metagenomic analysis for biosurveillance." ; sc:featureList edam:operation_0314 ; sc:name "SIGMA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sigma.omicsbio.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3344 ; sc:description "Given nonnegative integers k and n, sigma(k,n) is the sum of the kth powers of the divisors of n." ; sc:isAccessibleForFree true ; sc:name "sigma M" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/4967-sigma-m" ; biotools:primaryContact "David Terr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3512 ; sc:citation ; sc:description "A highly accurate method for predicting sigma70 promoter in prokaryotic genome." ; sc:featureList edam:operation_0440, edam:operation_0441, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "Sigma70Pred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/sigma70pred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0622, edam:topic_0654, edam:topic_0797, edam:topic_3678 ; sc:citation ; sc:description "Alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence." ; sc:featureList edam:operation_0292, edam:operation_0492 ; sc:name "Sigma 2.0 BETA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.imsc.res.in/~rsidd/sigma/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2533, edam:topic_2640, edam:topic_3175, edam:topic_3391 ; sc:author ; sc:description "Sigminer: Mutational Signature Analysis and Visualization in R." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sigminer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ShixiangWang/sigminer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3517 ; sc:citation ; sc:description "Exact and efficient method to identify a strongly interconnected disease-associated module in a gene network ." ; sc:featureList edam:operation_0253 ; sc:name "SigMod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YuanlongLiu/SigMod" ; biotools:primaryContact "Yuanlong Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3374, edam:topic_3409 ; sc:description "MATLAB script that creates a Sigmoid function using parameters: amplitude, phase, and slope." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "sigmoid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/19173-sigmoid" ; biotools:primaryContact "Shmuel Dr. Naaman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_2640 ; sc:citation , "pmcid:PMC10165836", "pubmed:37158829" ; sc:description "Model selection and robust inference of mutational signatures using negative binomial non-negative matrix factorization." ; sc:featureList edam:operation_0321, edam:operation_3359, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "SigMoS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MartaPelizzola/SigMoS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , ; sc:description """Multimodal single-cell chromatin analysis with Signac. A New Algorithm for Finding Marker Genes in Single-Cell Transcriptomic Data. Signac - A versatile package for Single-cell RNA-Seq analysis. We introduce Signac, a versatile R package to facilitate the analysis workflow for single-cell data. It helps to find marker genes faster and more accurate, search for cells with similar expression profiles, integrate multiple datasets in the BioTuring Browser database (know more about BioTuring Browser), etc. For users with a limited computational resource, we provide the helper functions to exercise all analyses for the large-scale datasets from disk. Because of its speed and flexibility, it can be adapted to any existing R analysis pipeline to help explore single-cell data more efficient. Signac is an extension of Seurat for the analysis of single-cell chromatin data.""" ; sc:featureList edam:operation_2495, edam:operation_3196, edam:operation_3222, edam:operation_3891, edam:operation_3935 ; sc:name "Signac" ; sc:url "https://satijalab.org/signac/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation , ; sc:description """Cell type classification and discovery across diseases, technologies and tissues reveals conserved gene signatures and enables standardized single-cell readouts. Get the most out of your single cell data. SignacX is software developed and maintained by the Savova lab at Sanofi with a focus on single cell genomics for clinical applications. SignacX classifies the cellular phenotype for each individual cell in single cell RNA-sequencing data using neural networks trained with sorted bulk gene expression data from the Human Primary Cell Atlas. To learn more, check out the pre-print, website and code base.""" ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SignacX" ; sc:url "https://github.com/mathewchamberlain/SignacX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_2229 ; sc:citation , "pubmed:33894945" ; sc:description "SIGNAL (Selection by Iterative pathway Group and Network Analysis Looping) is a web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays." ; sc:featureList edam:operation_3927, edam:operation_3928 ; sc:name "SIGNAL" ; sc:url "https://signal.niaid.nih.gov" ; biotools:primaryContact "Iain D.C. 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Dutilh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:31504185" ; sc:description "Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes." ; sc:featureList edam:operation_0289, edam:operation_2239, edam:operation_3629 ; sc:name "signature matrix" ; sc:url "https://github.com/wuaipinglab/ImmuCC/tree/master/tissue_immucc/SignatureMatrix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0203, edam:topic_0769, edam:topic_3374 ; sc:citation , "pmcid:PMC7708038", "pubmed:33068417" ; sc:description """Environment for Gene Expression Searching Combined with Functional Enrichment Analysis. 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Functionalities to characterize signatures or genome samples according to exposure patterns are also provided." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "signeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/signeR.html" ; biotools:primaryContact "Renan Valieris" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "An R package to detect selection in biological pathways. 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sc:license "Other" ; sc:name "SigniSite" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "2.1" ; sc:url "http://cbs.dtu.dk/services/SigniSite/" ; biotools:primaryContact "Morten Nielsen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3242 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3325 ; sc:author "Alberto Calderone", "Leonardo Briganti", "Prisca Lo Surdo" ; sc:citation , , , "pubmed:28654729", "pubmed:31665520" ; sc:contributor , "Gianni Cesareni", "Marta Iannuccelli" ; sc:description "A tool collects manually-annotated logic relationships between molecules that participate in signal transduction." ; 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biotools:primaryContact "Weil Lai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_2640 ; sc:description "Framework for Deciphering Mutational Signatures from Mutational Catalogues of Cancer Genomes" ; sc:isAccessibleForFree true ; sc:name "SigProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.5.1.9" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/38724-sigprofiler" ; biotools:primaryContact "Ludmil Alexandrov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0632, edam:topic_3308, edam:topic_3500, edam:topic_3518 ; sc:citation "pubmed:21930501" ; sc:description "Re-annotating oligo sets used for expression microarrays is essential to supply biologists with up-to-date annotations. 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It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one." ; sc:featureList edam:operation_0224, edam:operation_0309, edam:operation_2419, edam:operation_3695 ; sc:name "SigReannot-mart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sigreannot-mart.toulouse.inra.fr/biomart/martview/430b028768948e41c781761b26ba2cc6" ; biotools:primaryContact "François Moreews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168 ; sc:description "By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error." ; sc:featureList edam:operation_2238 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sigsquared" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sigsquared.html" ; biotools:primaryContact "UnJin Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3173 ; sc:citation ; sc:description "Sigtools is an R-based visualization package, designed to enable the users with limited programming experience to produce statistical plots of continuous genomic data. 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Stevens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:20886857" ; sc:description "Software for automated protein turnover analysis and method refinement for SILAC data." ; sc:featureList edam:operation_3638 ; sc:name "SILACtor" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://brucelab.gs.washington.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3053 ; sc:citation "pubmed:7581446" ; sc:description "This tool is designed to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. 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To facilitate the studies of silencers and their potential roles in transcriptional control during normal development and disease, we developed this comprehensive database of silencers, SilencerDB. 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Resources related to design, use, and sharing of silicon microprobes developed by the Masmanidis lab""" ; sc:featureList edam:operation_3431, edam:operation_3454 ; sc:name "silicon microprobes" ; sc:url "https://github.com/sotmasman/Silicon-microprobes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3295, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9216573", "pubmed:35670730" ; sc:description "An integrated transcriptomic and genomic database for Bombyx mori and related species." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_2421, edam:operation_3258 ; sc:isAccessibleForFree true ; sc:name "SilkBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://silkbase.ab.a.u-tokyo.ac.jp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0203, edam:topic_3512, edam:topic_3518 ; sc:citation "pubmed:19793867" ; sc:description "The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). SilkDB contains the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently." ; sc:featureList edam:operation_0310, edam:operation_0314, edam:operation_0525, edam:operation_0527, edam:operation_2871 ; sc:name "SilkDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://silkworm.genomics.org.cn/" ; biotools:primaryContact "xiaqy@swu.edu.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Compares sRNA expression levels in multiple samples by grouping sRNAs into loci based on genomic location" ; sc:featureList edam:operation_0314 ; sc:name "SiLoCo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://srna-workbench.cmp.uea.ac.uk" ; biotools:primaryContact "Forum" . a sc:SoftwareApplication ; 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The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user." ; sc:featureList edam:operation_3215, edam:operation_3649 ; sc:license "GPL-2.0" ; sc:name "SIMAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SIMAT.html" ; biotools:primaryContact "Mo R. Nezami Ranjbar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3940 ; sc:citation ; sc:description """A Single-cell ATAC-seq Simulation Framework. simATAC is a framework provided as an R package that generates a single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) count matrix, highly resembling real scATAC-seq datasets in library size, sparsity, and averaged chromatin accessibility signals. simATAC deploys statistical functions derived from analyzing 90 real scATAC-seq cell groups to model read distributions. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with cell labels for a comprehensive tool assessment.""" ; sc:featureList edam:operation_3219, edam:operation_3222, edam:operation_3798 ; sc:license "GPL-3.0" ; sc:name "simATAC" ; sc:url "https://github.com/bowang-lab/simATAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pmcid:PMC5249034", "pubmed:28105921" ; sc:description "Web interface for managing assembly projects of bacterial genomes. 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Azevedo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170 ; sc:citation ; sc:description "Methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines." ; sc:featureList edam:operation_2426, edam:operation_3680 ; sc:name "SimBA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cractools.gforge.inria.fr/softwares/simba/" ; biotools:primaryContact "CracTools Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_3295, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:37248389" ; sc:description "Single-cell embedding along with features." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SIMBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://simba-bio.readthedocs.io" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_3475 ; sc:name "Microarray hybridisation data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_3475 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3125, edam:topic_3518 ; sc:citation ; sc:description "This tool identifies common and unique binding regions in genome tiling array data. It does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It also implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding." ; sc:featureList edam:operation_2442 ; sc:license "GPL-3.0" ; sc:name "SimBindProfiles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SimBindProfiles.html" ; biotools:primaryContact "Bettina Fischer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344 ; sc:description """A representation of the predation model in SimBiology (works in R2016b) Modelling and Optimization, curve fit.""" ; sc:isAccessibleForFree true ; sc:name "SimBiology" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/63049-simbiology" ; biotools:primaryContact "Takafumi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3375 ; sc:description "This package contains an example of a MATLAB® application built using GUIDE for simulating a SimBiology® model. The SimBiology® model that is included is based on a tumor growth model developed by Koch, Walz, Lahu, and Schropp. Users can use the app as an example interface for entering an initial tumor weight, cell line, and dosing schedule, in order to simulate tumor growth inhibition in response to different drug therapies and generate a report. Using MATLAB Compiler®, the SimBiology® model can be deployed as part of a standalone MATLAB® app for distribution to other users." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "Example Deployable SimBiology App for Evaluating PK PD Drug Efficacy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48078-example-deployable-simbiology-app-for-evaluating-pk-pd-drug-efficacy" ; biotools:primaryContact "Anita" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "SimBiology implementations of COVID-19 SEIR models from literature" ; sc:isAccessibleForFree true ; sc:name "SimBiologyCOVID-19 SEIR Model Examples" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; 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To install SimiC in Python, go to the repository folder, and run:. Please make sure that you are using Python 3.x, and the packages in requirements.txt are properly installed. If you are using pip then you can run:. To run SimiC with Single-cell RNA-seq of a small test example, go to folder exmaple. The test data provided here is a subsample of the hepatocypte dataset we used in our paper. 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Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them." ; sc:featureList edam:operation_0289 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Simka" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/GATB/simka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3524 ; sc:citation "pubmed:21234669" ; sc:description "A software package to simulate realistic linkage disequilibrium patterns based on HapMap data." ; sc:featureList edam:operation_0488, edam:operation_2426 ; sc:name "SIMLD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/simld/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_3474 ; sc:citation ; sc:description "Novel similarity-learning framework, which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. It can separate known subpopulations more accurately in single-cell data sets than do existing dimension reduction methods. 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It allows researchers to decide on various parameters before they conduct an MSG experiment." ; sc:featureList edam:operation_3566 ; sc:name "simMSG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/melop/simMSG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2259, edam:topic_3524 ; sc:citation "pubmed:23508970" ; sc:description "Suite of software tools that guides the user through the multiple hierarchical scales of cellular behavior, facilitating the generation of comprehensive models. It was originally created to simulate immunological phenomena, but it is applicable to a very broad class of cell biological models." ; sc:featureList edam:operation_2476 ; sc:name "Simmune" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.niaid.nih.gov/labsandresources/labs/aboutlabs/lsb/Pages/simmuneproject.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:description "simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data (“dust”, bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied." ; sc:featureList edam:operation_3185 ; sc:license "GPL-3.0" ; sc:name "simNGS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20130502" ; sc:url "http://www.ebi.ac.uk/goldman-srv/simNGS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3524 ; sc:citation , "pmcid:PMC8978263", "pubmed:35380031" ; sc:description "An open-source toolkit for simulation and image processing for photonics and acoustics." ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SIMPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/IMSY-DKFZ/simpa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_0634, edam:topic_3474, edam:topic_3577 ; sc:citation ; sc:description "Pathway-based classifier exploits patient similarity network paradigm for interpretability and explainability" ; sc:featureList edam:operation_3501, edam:operation_3927, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Simpati" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/LucaGiudice/Simpati" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC3558011", "pubmed:23088386" ; sc:description "A server-based software for time course monitoring of Orbitrap LC-MS performance." ; sc:featureList edam:operation_2428 ; sc:name "SimpatiQCo" ; sc:softwareVersion "1.3.2c" ; sc:url "https://ms.imp.ac.at/?action=simpatiqco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:16224189" ; sc:description "Program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies." ; sc:featureList edam:operation_0487 ; sc:name "SimPed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/simped/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3325, edam:topic_3517, edam:topic_3676 ; sc:citation , "pubmed:29790190" ; sc:description """Simulation-based power estimation for sequencing studies of low-prevalence conditions. SimPEL is short for Simulation-based Power Estimation for sequencing studies of Low-prevalence conditions. SimPEL addresses the need for power estimation in low-prevalence condition studies, taking into account their inherently small sample sizes and analytical procedures. SimPEL integrates customizable parameters to realistically model study design outcomes and provide applicable information towards further refinement of experimental procedure. SimPEL is implemented as a function of the established JAWAMix5 tool (Long et al., 2013) , an HDF5-based Java implementation for association mapping.""" ; sc:featureList edam:operation_3196, edam:operation_3791 ; sc:name "SimPEL" ; sc:url "https://github.com/precisionomics/SimPEL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:33713354" ; sc:description "SimPET is an open online platform for the Monte Carlo simulation of realistic brain PET data. SimPET is a free cloud-based platform for the generation of realistic brain positron emission tomography (PET) data." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:name "SimPET" ; sc:url "http://simpetweb.uma.es:8020" ; biotools:primaryContact "Jesús Silva-Rodríguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:26526427" ; sc:description "A program for the simulation of gene family evolution under incomplete lineage sorting (ILS), gene duplication and loss (GDL), replacing horizontal gene transfer (HGT) and gene conversion (GC)." ; sc:featureList edam:operation_2426 ; sc:name "SimPhy" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/adamallo/SimPhy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "A simple BLAST algorithm based on a simple dynamic programming strategy." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "A simple BLAST algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/49003-a-simple-blast-algorithm" ; biotools:primaryContact "Ligong Han" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344, edam:topic_3570 ; sc:description "Explore solutions the Bailey's simple epidemic model." ; sc:isAccessibleForFree true ; sc:name "Simple Epidemic Model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/64768-simple-epidemic-model" ; biotools:primaryContact "Crista Arangala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3070, edam:topic_3344 ; sc:description "Simple leaf disease analysis based on histogram method using MATLAB SIMULINK" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Simple leaf disease detection" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/49616-simple-leaf-disease-detection" ; biotools:primaryContact "NAGARATHNA RAMESH" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1442 ; sc:name "Phylogenetic tree distances" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293 ; sc:author "Des Higgins" ; sc:citation , ; sc:description "Phylogenetic tree generation using the ClustalW2 program." ; sc:featureList edam:operation_0324 ; sc:name "Simple Phylogeny (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/phylogeny/simple_phylogeny" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_1637, edam:format_1638 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3518 ; sc:citation ; sc:description "Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures." ; sc:featureList edam:operation_0491, edam:operation_2495, edam:operation_2940 ; sc:license "GPL-2.0" ; sc:name "simpleaffy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.50.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/simpleaffy.html" ; biotools:primaryContact "Crispin Miller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3344, edam:topic_3452 ; sc:description "Matlab toolbox for Computed Tomography (CT) image processing." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "simpleCT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70572-simplect" ; biotools:primaryContact "Gianluca Iori" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0130 ; sc:citation , "pmcid:PMC6933846", "pubmed:31394001" ; sc:description "For characterizing protein thermal stability in different temperature" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SimpleDSFviewer" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://doi.org/10.1002/pro.3703" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780 ; sc:citation ; sc:description "SimpleForest is a comprehensive tool for 3D reconstruction of trees from forest plot point clouds." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "SimpleForest" ; sc:url "https://gitlab.com/SimpleForest/computree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0769 ; sc:citation , "pubmed:33228304" ; sc:description """A Pipeline to Streamline High-Density Linkage Map Construction. A tool to streamline high density genetic linkage group constrcution. A Usefull tool to assist likage mapping software with the construction of high density linkage groups.""" ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3282 ; sc:license "AFL-3.0" ; sc:name "SimpleMap" ; sc:url "http://simplemap-aj.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3382 ; sc:description "Basic (demo) 2-photon microscope scanning software" ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "SimpleMScanner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.52.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/57220-simplemscanner" ; biotools:primaryContact "Rob Campbell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """SIMulation of Pleiotropic, Linked and Epistatic PHENOTYPES. Multiple Traits: Partial Pleiotropy Architecture. In order to install simplePHENOTYPES, the following r packages will also be installed:. Note that the data set used in all vignettes is already in numeric format. In addition to the numeric format, simplePHENOTYPES’ parameter geno_obj also takes an R object in HapMap format as input. Other input options are VCF, GDS, and Plink bed/ped. These last formats should be loaded from file with geno_file or geno_path.""" ; sc:featureList edam:operation_0282, edam:operation_2426, edam:operation_3196 ; sc:license "MIT" ; sc:name "simplePHENOTYPES" ; sc:url "https://github.com/samuelbfernandes/simplePHENOTYPES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3372, edam:topic_3678 ; sc:citation , "pmcid:PMC7808115", "pubmed:33443729" ; sc:description """An open-source tool for quick online perception experiments. Because of the COVID-19 pandemic, researchers are facing unprecedented challenges that affect our ability to run in-person experiments. With mandated social distancing in a controlled laboratory environment, many researchers are searching for alternative options to conduct research, such as online experimentation. However, online experimentation comes at a cost; learning online tools for building and publishing psychophysics experiments can be complicated and time-consuming. This learning cost is unfortunate because researchers typically only need to use a small percentage of these tools' capabilities, but they still have to deal with these systems' complexities (e.g., complex graphical user interfaces or difficult programming languages). Furthermore, after the experiment is built, researchers often have to find an online platform compatible with the tool they used to program the experiment""" ; sc:name "SimplePhy" ; sc:url "https://simplephy.psych.ucsb.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_3056 ; sc:citation , "pmcid:PMC4987899", "pubmed:27141960" ; sc:description "Visualization of microsynteny across multiple species." ; sc:featureList edam:operation_3744 ; sc:name "SimpleSynteny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.dveltri.com/simplesynteny/" ; biotools:primaryContact "Dan Veltri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3300, edam:topic_3500, edam:topic_3697 ; sc:citation ; sc:description "An individual-based platform for ecological modeling." ; sc:featureList edam:operation_0310, edam:operation_2426, edam:operation_3891 ; sc:name "simplex" ; sc:url "https://github.com/LennonLab/Emergence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2229, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotyping at single-cell resolution. SIMPLI is a platform agnostic pipeline for the analysis of highly multiplexed histological imaging data. This will run SIMPLI on minimal example dataset distributed in this repository. For more details on the example dataset and the associated analysis workflow see the example-workflow page.""" ; sc:featureList edam:operation_0314, edam:operation_3443, edam:operation_3799 ; sc:name "SIMPLI" ; sc:url "https://github.com/ciccalab/SIMPLI" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23275695" ; sc:description "A stand-alone software that selectively eliminates redundant sequences from the collection of contigs generated by ab initio assembly of genomes." ; sc:featureList edam:operation_0290 ; sc:name "Simplifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genoma.ufpa.br/rramos/softwares/simplifier.xhtml" ; biotools:primaryContact "Prof. Artur Silva", "Prof. Rommel Ramos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_2269 ; sc:citation ; sc:description """an R/Bioconductor package for Clustering and Visualizing Functional Enrichment Results. Simplify Functional Enrichment Results. A new method (binary cut) is proposed to effectively cluster GO terms into groups from the semantic similarity matrix. Summaries of GO terms in each cluster are visualized by word clouds. Compare similarity measurements for functional terms. Compare partitioning methods in binary cut clustering. Clustering, GO, GeneSetEnrichment, Software, Visualization.""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3501 ; sc:license "MIT" ; sc:name "simplifyEnrichment" ; sc:url "https://simplifyenrichment.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_0623, edam:topic_0736, edam:topic_3293 ; sc:citation , "pubmed:35668544" ; sc:description "Generalizable strategy to analyze domains in the context of parent protein architecture." ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_0337, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SimpLogo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.github.com/clayfos/SimpLogo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0781, edam:topic_3127 ; sc:citation "pubmed:9847317" ; sc:description "A popular tool for recombination analysis." ; sc:featureList edam:operation_0337, edam:operation_0451 ; sc:name "SimPlot" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sray.med.som.jhmi.edu/SCRoftware/simplot/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_3293 ; sc:citation , "pubmed:35451456" ; sc:description "A Python application for representing sequence similarity and detecting recombination." ; sc:featureList edam:operation_0289, edam:operation_0337, edam:operation_0451 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SimPlot++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Stephane-S/Simplot_PlusPlus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3299, edam:topic_3810, edam:topic_3974 ; sc:citation , "pmcid:PMC10169377", "pubmed:37161307" ; sc:description "R package to simulate honeybee populations and breeding programs." ; sc:featureList edam:operation_3196, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SIMplyBee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.SIMplyBee.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056, edam:topic_3299 ; sc:citation "pubmed:26644417" ; sc:description "A framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture." ; sc:featureList edam:operation_2426 ; sc:name "SimRA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ComputationalGenomics/SimRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:2914216" ; sc:description "A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits" ; sc:featureList edam:operation_3196 ; sc:name "SimRare" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/simrare/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3512, edam:topic_3517 ; sc:citation "pubmed:21835306" ; sc:description "A tool to perform maker-set association analysis. Association analysis at gene, pathway, or exon levels (here by marker-set analysis) hold great promise in evaluating modest etiological effects of genes with GWAS or sequence data." ; sc:featureList edam:operation_2403 ; sc:name "SIMreg" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www4.stat.ncsu.edu/~jytzeng/software.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099 ; sc:citation ; sc:description "Simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and RNA 3D structure prediction." ; sc:featureList edam:operation_0271, edam:operation_2423 ; sc:name "SimRNA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "3.20" ; sc:url "http://genesilico.pl/software/stand-alone/simrna" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3325, edam:topic_3676 ; sc:citation ; sc:description """Simulating Pedigrees Ascertained for Multiple Disease-Affected Relatives. Simulate Pedigrees Ascertained for Rare Disease. Please note: this version of SimRVPedigree may be under construction. For the latest stable version of SimRVPedigree please visit https://CRAN.R-project.org/package=SimRVPedigree.""" ; sc:featureList edam:operation_3226, edam:operation_3432, edam:operation_3436 ; sc:name "SimRVPedigree" ; sc:url "https://github.com/cnieuwoudt/SimRVPedigree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2640, edam:topic_3293 ; sc:citation , "pubmed:35311947" ; sc:description "A simulator of single-cell DNA sequencing data." ; sc:featureList edam:operation_0323, edam:operation_3359, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SimSCSnTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/compbiofan/SimSCSnTree.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168, edam:topic_3173, edam:topic_3473 ; sc:citation , "pmcid:PMC7574191", "pubmed:33076821" ; sc:description """Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks. SimSearch is an IGB http://bioviz.org/igb/ plugin to identify and compare occurrences of (epi)genomics feature patterns in multiple genome browser tracks. It is based on a pattern-search algorithm that provides biologists with the ability, once they identify an interesting genomic pattern, to look for similar occurrences in the data, thus facilitating genomic data access and use. 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Simulate pangenomes according to the IMG + Neutral models. simurg: Simulate a Bacterial Pangenome in R""" ; sc:featureList edam:operation_2426, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "simurg" ; sc:url "https://github.com/iferres/simurg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7379788", "pubmed:32703148" ; sc:description """reliably simulate Illumina sequencing data based on position and context dependent profiles. a novel tool to reliably Simulate Illumina Sequencing data based on position and Context dependent Profiles. More details about the software can be found from here. a novel next-generation sequencing simulator using position and genomic contexts based error profiles.""" ; sc:featureList edam:operation_2426, edam:operation_3185, edam:operation_3219, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "SimuSCoP" ; sc:softwareHelp ; sc:url "https://github.com/qasimyu/simuscop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Statistical analysis for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. Uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms." ; sc:featureList edam:operation_2238, edam:operation_2945 ; sc:name "SimWalk" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.91" ; sc:url "http://watson.hgen.pitt.edu/docs/simwalk2.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_0637, edam:topic_3168 ; sc:citation , "pubmed:22556368" ; sc:description """Aligns and optionally taxonomically classifies your rRNA gene sequences. Reference based multiple sequence alignment""" ; sc:featureList edam:operation_0258, edam:operation_0294, edam:operation_0492, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SINA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.1", "1.5.0" ; sc:url "https://sina.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_3400 ; sc:citation , "pmcid:PMC8966674", "pubmed:35239339" ; sc:description "A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations." ; sc:featureList edam:operation_0570, edam:operation_2476, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SINAPs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ParImmune/SINAPs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0780, edam:topic_3053 ; sc:citation , "pubmed:25480115" ; sc:description "Integrated database to study genomics, genetics and comparative genomics in Sesamum indicum." ; sc:featureList edam:operation_2421, edam:operation_3197 ; sc:name "Sinbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ocri-genomics.org/Sinbase/" ; biotools:primaryContact "Zhang X" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "A computational framework to predict cell identities in single cell transcriptomes using bulk atlases as references." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3436, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Sincast" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/meiosis97/Sincast" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2572 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2589 ; sc:encodingFormat edam:format_2067 ; sc:name "Hierarchy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0637, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC4595899", "pubmed:26099264" ; sc:description "This package implements a methodological toolbox allowing flexible workflows under such framework and it contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies." ; sc:featureList edam:operation_3680 ; sc:license "GPL-2.0" ; sc:name "sincell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sincell.html" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "Toolbox for single cell heterogeneity analysis in cancer." ; sc:featureList edam:operation_3209 ; sc:name "SinCHet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://labpages2.moffitt.org/chen/software/" ; biotools:primaryContact "Y. Ann Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3306, edam:topic_3315, edam:topic_3361, edam:topic_3474 ; sc:citation , "pmcid:PMC9424817", "pubmed:36060282" ; sc:description "Enhancing nonlinear system identification with sensitivity analysis." ; sc:featureList edam:operation_2426, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SINDy-SA framework" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tmglncc/SINDy-SA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3334, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC7904048", "pubmed:33507271" ; sc:description """database for eukaryotic single-exon coding sequences. Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological developmental disorders, and many exhibit tissue-specific transcription.""" ; sc:featureList edam:operation_0525, edam:operation_2421, edam:operation_3663 ; sc:name "SinEx" ; sc:url "https://v2.sinex.cl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3382 ; sc:citation , "pmcid:PMC9954745", "pubmed:36831270" ; sc:description "Scalable Identification of Spatially Variable Genes for Deciphering Spatial Domains." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SINFONIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BioX-NKU/SINFONIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC9060378", "pubmed:35500005" ; sc:description "Synthetic training data generation for medical image segmentation." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SinGAN-Seg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://pypi.org/project/singan-seg-polyp/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3934 ; sc:citation , "pmcid:PMC9580930", "pubmed:36304292" ; sc:description "Interactive Analysis of Single Cell RNA-Seq Data on the Cloud." ; sc:featureList edam:operation_2436, edam:operation_3192, edam:operation_3891, edam:operation_3933, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "SingleCAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://singleCAnalyzer.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3341 ; sc:description "Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries." ; sc:featureList edam:operation_0224 ; sc:license "GPL-3.0" ; sc:name "SingleCellExperiment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html" ; biotools:primaryContact "Davide Risso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3473 ; sc:citation , "pmcid:PMC7455704", "pubmed:32859930" ; sc:description """A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data. singleCellHaystack is a package for predicting differentially expressed genes (DEGs) in single cell transcriptome data. It does so without relying on clustering of cells into arbitrary clusters! Single-cell RNA-seq (scRNA-seq) data is often processed to fewer dimensions using Principal Component Analysis (PCA) and represented in 2-dimensional plots (e.g. t-SNE or UMAP plots). singleCellHaystack uses Kullback-Leibler Divergence to find genes that are expressed in subsets of cells that are non-randomly positioned in a these multi-dimensional spaces or 2D representations. Finding Needles (=differentially Expressed Genes) in Haystacks (=single Cell Data). Identification of differentially expressed genes (DEGs) is a key step in single-cell transcriptomics data analysis. 'singleCellHaystack' predicts DEGs without relying on clustering of cells into arbitrary clusters.""" ; sc:featureList edam:operation_0313, edam:operation_2939, edam:operation_3223, edam:operation_3891 ; sc:license "MIT" ; sc:name "singleCellHaystack" ; sc:url "https://CRAN.R-project.org/package=singleCellHaystack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Run common single cell analysis directly through your browser including differential expression, downsampling analysis, and clustering." ; sc:featureList edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "singleCellTK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "http://bioconductor.org/packages/release/bioc/html/singleCellTK.html" ; biotools:primaryContact "David Jenkins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description """interactive visualization of single-cell data in virtual reality. Single cell visualization using Virtual Reality (VR). It can be used with our preprocessed datasets found at the link above or by following the steps below to process your own dataset.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3432 ; sc:license "MIT" ; sc:name "singlecellVR" ; sc:url "http://www.singlecellvr.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_3752 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Novelty-inclusive microbial community profiling of shotgun metagenomes" ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SingleM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://wwood.github.io/singlem/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:description "A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level." ; sc:featureList edam:operation_2238, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "singscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/singscore.html" ; biotools:primaryContact "Ruqian Lyu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3524 ; sc:citation ; sc:description "Framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers." ; sc:featureList edam:operation_2409 ; sc:name "Singularity Hub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://singularity-hub.org/" ; biotools:primaryContact "Vanessa V. Sochat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0625, edam:topic_2269, edam:topic_2885, edam:topic_3957 ; sc:citation , "pubmed:32573681" ; sc:description """Network-guided search for genetic heterogeneity between gene pairs. This repository contains the code for the Significant Network Interval Mining approach, short SiNIMin, and its permutation-testing based counterpart SiNIMin-WY. The methods are described in Network-guided detection of candidate intervals that exhibit genetic heterogeneity (under review).""" ; sc:featureList edam:operation_2421, edam:operation_3196, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "SiNIMin" ; sc:url "https://github.com/BorgwardtLab/SiNIMin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation , "pmcid:PMC7393544", "pubmed:32428603" ; sc:description """An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples. SinoDuplex is an improved duplex consensus sequence generation module. It increased the output of duplex sequencing technology and thus made it more cost effective.""" ; sc:featureList edam:operation_0363, edam:operation_3192, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "SinoDuplex" ; sc:url "https://github.com/SinOncology/sinoduplex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3303, edam:topic_3335, edam:topic_3376 ; sc:citation , "pmcid:PMC5604194", "pubmed:28923061" ; sc:description "Advanced tool for heart rate variability analysis." ; sc:featureList edam:operation_3214 ; sc:name "SinusCor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rhenanbartels.github.io/SinusCor/" ; biotools:primaryContact "Rhenan Bartels" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3169, edam:topic_3382 ; sc:citation , "pmcid:PMC7111518", "pubmed:32127418" ; sc:description """SIP: Significant Interaction Peak caller.Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals. If you want run SIP with mcool file you need to install cooler: https://github.com/mirnylab/cooler (version >= 0.8.6) and cooltools: https://github.com/mirnylab/cooltools (version >= 0.3.0) . Not working with dev version of cooler and cooltools.""" ; sc:featureList edam:operation_0337, edam:operation_0481, edam:operation_3222 ; sc:name "SIP" ; sc:url "https://github.com/PouletAxel/SIP/releases" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2755 ; sc:encodingFormat edam:format_3475 ; sc:name "Transcription factor name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_3780 ; sc:name "Compound name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:encodingFormat edam:format_3780 ; sc:name "Protein name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3307, edam:topic_3308 ; sc:citation , "pubmed:36400030" ; sc:description "A single cell-based computational platform to identify chemical compounds targeting desired sets of transcription factors for cellular conversion" ; sc:featureList edam:operation_2423, edam:operation_2426 ; sc:name "SiPer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://siper.uni.lu/" ; biotools:primaryContact "Antonio del Sol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:22102913" ; sc:description "This tool utilizes two layers of support vector regression (SVR) to predict the efficacy of an siRNA." ; sc:featureList edam:operation_0465 ; sc:name "siPRED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://predictor.nchu.edu.tw/siPRED/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0219 ; sc:citation "pubmed:23793753" ; sc:description "A database-searching algorithm for peptide and protein identification in shotgun proteomics/metaproteomics." ; sc:featureList edam:operation_3646 ; sc:name "Sipros" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://siprosensemble.omicsbio.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3511 ; sc:citation , "pmcid:PMC9442499", "pubmed:36071722" ; sc:description "Easy quantitative measurement of mutation profiles in sequencing data." ; sc:featureList edam:operation_0308, edam:operation_2422, edam:operation_3096, edam:operation_3196, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "SIQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://siq.researchlumc.nl/SIQPlotteR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3344 ; sc:description "This is a live script that explores the SIR model in order to simulate the spread of a virus over time." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "SIR Epidemic Spread Model" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75100-sir-epidemic-spread-model" ; biotools:primaryContact "Giovanni Valentini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3305, edam:topic_3344 ; sc:description "The code app implement the SIR model for the estimation of COVID19 epidemy evolution in India." ; sc:isAccessibleForFree true ; sc:name "SIR Model of COVID19 for India with real time tracking" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/75082-sir-model-of-covid19-for-india-with-real-time-tracking" ; biotools:primaryContact "Siddharth Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3315, edam:topic_3324, edam:topic_3344 ; sc:description "Introductory model of infectious disease spread. Social distancing and social isolation affects beta (transmission rate)." ; sc:isAccessibleForFree true ; sc:name "SIR Model of Virus Spread" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.20" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74697-sir-math-model-of-virus-spread-coronavirus-or-other" ; biotools:primaryContact "Tom Beekhuysen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2258, edam:topic_2275 ; sc:citation "pubmed:26773132" ; sc:description "The tool comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the force field." ; sc:featureList edam:operation_2476 ; sc:name "SIRAH" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.sirahff.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0654, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:18635569" ; sc:description "An application written in python that detects and visualises alternative splicing events using spliced alignments.Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription. Such transcript models may come from the gene prediction pipelines of genome databases or from spliced alignments of ESTs or proteins against the genome." ; sc:featureList edam:operation_0433 ; sc:name "Sircah" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bork.embl.de/Sircah/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3305, edam:topic_3315, edam:topic_3324, edam:topic_3344 ; sc:citation ; sc:description "The Italian SIRD model for COVID-19." ; sc:featureList edam:operation_3946 ; sc:isAccessibleForFree true ; sc:name "SIRD model for COVID-19 outbreaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74838-sird-model-for-covid-19-outbreaks" ; biotools:primaryContact "Diego Caccavo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3305, edam:topic_3324, edam:topic_3577 ; sc:citation , "pubmed:33347459" ; sc:description """Estimating individuals' genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data. Susceptibility Infectivity and Recoverability Estimation (SIRE). Illustrative screenshots - SIRE features an easy to use point and click interface that facilitates data input and displays a variety of output visualisations that aid interpretation of the results. SIRE allows for simultaneous estimation of single nucleotide polymorphism (SNP) and treatment effects on these host traits (so identifying potential pleiotropic effects). SIRE implements a Bayesian algorithm which makes use of temporal data (consisting of any combination of recorded infection times, recovery times or disease status measurements) from multiple epidemics whose dynamics can be represented by the susceptible-infectious-recovered (SIR) model.""" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:name "SIRE" ; sc:url "http://theITEAM.github.io/SIRE.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0736, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:20460462" ; sc:description "SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags." ; sc:featureList edam:operation_0278, edam:operation_0303, edam:operation_0438, edam:operation_0483 ; sc:name "SIREs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://www.sires-webserver.eu/" ; biotools:primaryContact "Mayka Sanchez (For questions regarding IREs)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "SIRFindeR is an R package for detecting and quantifying Intron Retention levels using Second and Third Generation RNA-Sequencing data." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:name "SIRFindeR" ; sc:url "https://github.com/lbroseus/SIRFindeR/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3651, edam:format_3752 ; sc:name "Peptide mass fingerprint" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0944 ; sc:encodingFormat edam:format_3467, edam:format_3579, edam:format_3603 ; sc:name "Peptide mass fingerprint" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0846 ; sc:encodingFormat edam:format_3752 ; sc:name "Chemical formula" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "Tool for metabolite identification using mass spectrometry." ; sc:featureList edam:operation_3553, edam:operation_3632, edam:operation_3694, edam:operation_3803 ; sc:name "Sirius" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bio.informatik.uni-jena.de/sirius" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3305, edam:topic_3324, edam:topic_3344 ; sc:description "This file simulates SIR model for the spread of infectious diseases" ; sc:isAccessibleForFree true ; sc:name "SIRModelSimulation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74762-sirmodelsimulation" ; biotools:primaryContact "Lateef Adewale Kareem" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find siRNA duplexes in mRNA." ; sc:featureList edam:operation_2008 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sirna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/sirna.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0130, edam:topic_0659, edam:topic_2885 ; sc:citation "pubmed:15215365" ; sc:description "Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA." ; sc:featureList edam:operation_0465, edam:operation_2008 ; sc:name "siRNA Selection Server" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://jura.wi.mit.edu/bioc/siRNA" ; biotools:primaryContact "siRNA Selection Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659, edam:topic_3489, edam:topic_3512 ; sc:citation "pubmed:15608162" ; sc:description "This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs)." ; sc:featureList edam:operation_0338, edam:operation_0349, edam:operation_0465, edam:operation_2008, edam:operation_2421 ; sc:name "siRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sirna.cgb.ki.se/" ; biotools:primaryContact "Erik Sonnhammer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "siRNApred: Support vector machine based methods for predicting actual efficacy of both 21mer and 19mer siRNAs with high accuracy." ; sc:featureList edam:operation_2945 ; sc:name "sirnapred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/sirnapred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0091, edam:topic_0160 ; sc:citation "pubmed:12824415" ; sc:description "SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif." ; sc:featureList edam:operation_0224, edam:operation_0239, edam:operation_0253, edam:operation_2422 ; sc:name "SIRW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sirw.embl.de/" ; biotools:primaryContact "Ramu C." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC7046343", "pubmed:32059026" ; sc:description """Machine learning for accurate prediction of hospitalization in subjects suspected of arboviral infection. Machine learning project to predict subject hospitalization.""" ; sc:featureList edam:operation_3927 ; sc:name "SISA" ; sc:url "https://github.com/rsippy/SISASISAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:10842742" ; sc:description "SISEQ has been developed to extract sequence informations from large database entries and to manipulate sequence informations for input to various sequence analysis software." ; sc:featureList edam:operation_0335, edam:operation_2403, edam:operation_2945 ; sc:name "SISEQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.59.4" ; sc:url "http://nsato4.c.u-tokyo.ac.jp/old/Siseq.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0601, edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:citation , "pubmed:31960894" ; sc:description """simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. A tool for the simulation of gene expression profiles for in silico regulatory networks. 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sc:isAccessibleForFree true ; sc:name "SISPRO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/sispro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:26062548" ; sc:description "Novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome." ; sc:featureList edam:operation_0540 ; sc:name "SISRS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/rachelss/SISRS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3125, edam:topic_3168, edam:topic_3169, edam:topic_3308 ; sc:citation "pubmed:18684996" ; sc:description "Produce a list of peakmaxima from aligned positions." ; sc:featureList edam:operation_0445, edam:operation_3222 ; sc:name "SISSRs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://sissrs.rajajothi.com/" ; biotools:primaryContact "Raja Jothi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0634, edam:topic_3170, edam:topic_3308, edam:topic_3336, edam:topic_3395 ; sc:citation , "pmcid:PMC8271161", "pubmed:34278269" ; sc:description "A large and standardized collection of transcriptome data sets for human pluripotent stem cell research." ; sc:featureList edam:operation_0314, edam:operation_3431, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SISTEMA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sistema.ens-lyon.fr" . a sc:SoftwareApplication ; 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:15215382" ; sc:description "Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575, edam:operation_3222 ; sc:name "SITECON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/" ; biotools:primaryContact "Oshchepkov Dmitry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:15147845" ; sc:description "The tool predicts regions that can potentially function as binding sites. The methods is based on recognition of geometrical and physico-chemical environments that are similar to known binding sites." ; sc:featureList edam:operation_2575 ; sc:name "SiteEngine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinfo3d.cs.tau.ac.il/SiteEngine/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2814, edam:topic_3125, edam:topic_3511, edam:topic_3534 ; sc:citation "pubmed:19398430" ; sc:description "SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (i.e. carbon probe, phosphate probe) and displays the putative sites in interactive 3D representation." ; sc:featureList edam:operation_0320, edam:operation_0389, edam:operation_2487, edam:operation_2575, edam:operation_3222 ; sc:name "SITEHOUND-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sitehound.sanchezlab.org" ; biotools:primaryContact "SiteHound Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_2830, edam:topic_3293 ; sc:citation , "pmcid:PMC9701067", "pubmed:36434502" ; sc:description "A visual tool to identify polymorphism clades and help find fixed and parallel mutations." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sitePath" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/wuaipinglab/sitePath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0654 ; sc:citation "pubmed:20795783" ; sc:description "Java application that can sample the sites of a sequence alignment to produce replicate data sets." ; sc:featureList edam:operation_0449 ; sc:name "SiteSampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/simon-ho/sitesampler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_3125 ; sc:citation "pubmed:12824368" ; sc:description "SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0445, edam:operation_2429, edam:operation_2575 ; sc:name "SiteSeer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rocky.bms.umist.ac.uk/SiteSeer/" ; biotools:primaryContact "Paul Boardman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_3510, edam:topic_3512, edam:topic_3534 ; sc:citation "pubmed:22139920" ; sc:description "Database that contains information on functional site amino acid positions in the exon structure of encoding gene. 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Implements a three-dimensional stochastic model of cancer growth and mutation similar to the one described in Waclaw et al. (2015) . Allows for interactive 3D visualizations of the simulated tumor. Provides a comprehensive summary of the spatial distribution of mutants within the tumor. Contains functions which create synthetic sequencing datasets from the generated tumor.""" ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:license "GPL-2.0" ; sc:name "SITH" ; sc:url "https://CRAN.R-project.org/package=SITH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3168, edam:topic_3308, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """IBEX – A versatile multi-plex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. SITK-IBEX: Aligning images acquired with the IBEX microscopy imaging technique. This Python package was implemented as part of the development of the Iterative Bleaching Extends Multiplexity (IBEX) imaging technique. It enables the alignment of multiple cycles of fluorescence images, acquired using IBEX. A repeated marker is used to register all panels to a selected panel (in the registration nomenclature this is the fixed image). After registration all panels are resampled onto the fixed image.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "SITK-IBEX" ; sc:url "http://github.com/niaid/sitk-ibex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3305, edam:topic_3500, edam:topic_3673 ; sc:citation , "pmcid:PMC8962452", "pubmed:35028657" ; sc:description "Publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "SITVITBovis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3173, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9940350", "pubmed:36803416" ; sc:description "Interpretable deep generative models for single-cell transcriptomes." ; sc:featureList edam:operation_3463, edam:operation_3891, edam:operation_3925, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "siVAE" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/quon-titative-biology/siVAE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0659, edam:topic_0781 ; sc:citation "pubmed:16845046" ; sc:description "siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference." ; sc:featureList edam:operation_2008 ; sc:name "siVirus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sivirus.rnai.jp/" ; biotools:primaryContact "siVirus Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3360 ; sc:citation , "pubmed:34270690" ; sc:description "SIVS is an acronym of Stable Iterative Variable Selection, and as the name suggests is a feature selection method that is robust to the variations that cross-validation can have on various methods with embedded feature selection. This method hired an iterative approach and internally utilizes varius Machine Learning methods which have embedded feature reduction in order to shrink down the feature space into a small and yet robust set." ; sc:featureList edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SIVS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/web/packages/sivs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053 ; sc:citation ; sc:description "Scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets." ; sc:featureList edam:operation_2421 ; sc:name "SIXPAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "http://www.cs.columbia.edu/~snehitp/sixpac/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display a DNA sequence with 6-frame translation and ORFs." ; sc:featureList edam:operation_0371, edam:operation_0436, edam:operation_0564 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sixpack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/sixpack.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Six frame nucleotide sequence translation, with ORF finding. The tool reads a DNA sequence and outputs the three forward and (optionally) three reverse translations in a visual manner." ; sc:featureList edam:operation_0371, edam:operation_0436 ; sc:name "sixpack (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/st/emboss_sixpack" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Display DNA sequences with 6-frame translation and ORFs." ; sc:featureList edam:operation_0371, edam:operation_0436 ; sc:name "sixpack (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/st/emboss_sixpack" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC8928875", "pubmed:35342569" ; sc:description "The goal of SizeExtractR is to facilitate scientific projects that have research questions relating to size, from pure biology to ecology on individual to landscape scales, by providing a protocol with a user-friendly set of interactive tools for image analysis (ImageJ-macros) and database formation and quality checking (R-package)." ; sc:featureList edam:operation_2428, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SizeExtractR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liamlachs/SizeExtractR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "sizepower" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.44.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sizepower.html" ; biotools:primaryContact "Weiliang Qiu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Sort sequences by size." ; sc:featureList edam:operation_0231 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "sizeseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/sizeseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077 ; sc:author "Dmitri Pervouchine" ; sc:description "A utility for fast SJ (splice-junction) quantification. It is an annotation-agnostic offset-aware version of bam2ssj." ; sc:featureList edam:operation_2478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SJcount" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "3.1" ; sc:url "https://github.com/pervouchine/sjcount-full" ; biotools:primaryContact "Dmitri Pervouchine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_3297, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC7217484", "pubmed:32352965" ; sc:description """Insight into the protein solubility driving forces with neural attention. Protein solubility is a key aspect for many biotechnological, biomedical and industrial processes, such as the production of active proteins and antibodies. In addition, understanding the molecular determinants of the solubility of proteins may be crucial to shed light on the molecular mechanisms of diseases caused by aggregation processes such as amyloidosis. Here we present SKADE, a novel Neural Network protein solubility predictor and we show how it can provide novel insight into the protein solubility mechanisms, thanks to its neural attention architecture. First, we show that SKADE positively compares with state of the art tools while using just the protein sequence as input. Then, thanks to the neural attention mechanism, we use SKADE to investigate the patterns learned during training and we analyse its decision process""" ; sc:featureList edam:operation_0409, edam:operation_0474, edam:operation_3436, edam:operation_3891 ; sc:name "SKADE" ; sc:url "https://bitbucket.org/eddiewrc/skade/src" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation ; sc:description "A SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes, SKAT aggregates individual score test statistics of SNPs in a SNP set and computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies." ; sc:featureList edam:operation_2429 ; sc:license "GPL-3.0" ; sc:name "SKAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.hsph.harvard.edu/skat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_3512 ; sc:citation ; sc:description "An R package for SNP-based Kinship Analysis, Testing, and Evaluation.." ; sc:featureList edam:operation_1812, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "skater" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://signaturescience.github.io/skater" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:32407111" ; sc:description """A Web Application for Scaffold Docking in PlayMolecule. An online platform for drug discovery applications.""" ; sc:featureList edam:operation_0482, edam:operation_3216, edam:operation_3899 ; sc:name "SkeleDock" ; sc:url "https://playmolecule.org/SkeleDock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3056 ; sc:citation , "pmcid:PMC5161633", "pubmed:27736016" ; sc:contributor ; sc:description "skeleSim guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment." ; sc:featureList edam:operation_3664 ; sc:license "GPL-2.0" ; sc:name "skeleSim" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/skeleSim/index.html" ; biotools:primaryContact "Allan Strand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Calculates the 3D skeleton of an arbitrary binary volume using parallel medial axis thinning." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Skeleton3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.12.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/43400-skeleton3d" ; biotools:primaryContact "Philip Kollmannsberger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0199 ; sc:author , , ; sc:citation , "pmcid:PMC6361233", "pubmed:30020414" ; sc:description "The new version of the SKEMPI database, with more than 7000 mutation data. The SKEMPI2 database contains data on the changes in thermodynamic parameters and kinetic rate constants upon mutation, for protein-protein interactions for which a structure of the complex has been solved and is available in the protein databank." ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SKEMPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Barcelona Supercomputing Center" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://life.bsc.es/pid/skempi2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "Sketching and sampling approaches for fast and accurate long read classification." ; sc:featureList edam:operation_0224, edam:operation_3198, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sketching-based" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/arun96/sketching" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0654 ; sc:citation ; sc:description "A free database of GC and many other skews for over 30,200 chromosomes and plasmids." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SkewDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://skewdb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:24925680" ; sc:description "Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3219, edam:operation_3237 ; sc:name "Skewer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/skewer/" ; biotools:primaryContact "Jiang Hongshan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_0654, edam:topic_3293 ; sc:citation ; sc:description """Skew Index Test for detecting mis-assembled bacterial genomes. SkewIT (Skew Index Test) is a tool for analyzing GC Skew in bacterial genomes. GC Skew is a phenomenon observed in many bacterial genomes wherein the two strands of the chromosome contain different proportions of guanine/cytosine nucleotides. SkewIT quantifies GC Skew using a single metric that can then be compared/analyzed across thousands of bacterial genomes.""" ; sc:featureList edam:operation_0525, edam:operation_3211, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "SkewIT" ; sc:url "https://github.com/jenniferlu717/SkewIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3295, edam:topic_3572 ; sc:citation ; sc:description "Tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II. The remaining three distributions give the density of the Beta-values for these same three subsets." ; sc:featureList edam:operation_0337, edam:operation_3218 ; sc:license "GPL-2.0" ; sc:name "skewr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/skewr.html" ; biotools:primaryContact "Ryan Putney" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3297, edam:topic_3407 ; sc:citation ; sc:description "Intuitive modeling of large-scale biological kinetic models." ; sc:featureList edam:operation_2426, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SKiMpy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EPFL-LCSB/SKiMpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:description "Classify the different type of skin cancers" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Skin lesion melanoma classification using neural networks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/68199-skin-lesion-melanoma-classification-using-neural-networks" ; biotools:primaryContact "Matlab Mebin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382 ; sc:description "This Script is useful in finding symmetry lines in Skin Lesions with extensions to any binary masks." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Novel Method for Determining Symmetry of Skin Lesions using the Jaccard Index" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50903-novel-method-for-determining-symmetry-of-skin-lesions-using-the-jaccard-index" ; biotools:primaryContact "Tyler Coye" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3404 ; sc:citation , "pubmed:34969031" ; sc:description "Reliability Assessment and Validation of the Skin Hyperpigmentation Index Compared to the Physician Global Assessment Score." ; sc:featureList edam:operation_2428, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "skin hyperpigmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shi.skinimageanalysis.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0821, edam:topic_3404, edam:topic_3407, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC7772573", "pubmed:33385118" ; sc:description """an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics. SkinBug can predict the metabolism and biotransformation of any molecule by the human skin microbiota. It can predict all possible reactions with reaction centers, corresponding enzymes, microbial species, and skin sites capable of metabolizing the input molecule.""" ; sc:featureList edam:operation_3660, edam:operation_3891, edam:operation_3929 ; sc:name "SkinBug" ; sc:url "http://metagenomics.iiserb.ac.in/skinbug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3510, edam:topic_3542 ; sc:citation "pubmed:24532729" ; sc:description "The web server classifies given alpha-helical sequences into kinked and canonical helices based on a specified support vector machine (SVM) model." ; sc:featureList edam:operation_2479, edam:operation_2996 ; sc:name "SKINK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biows-inf.zdv.uni-mainz.de/skink/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2258, edam:topic_3300, edam:topic_3371 ; sc:citation ; sc:description "Curated database for skin sensitization assays." ; sc:featureList edam:operation_0224 ; sc:name "SkinSensDB" ; sc:softwareHelp ; sc:url "http://cwtung.kmu.edu.tw/skinsensdb" ; biotools:primaryContact "Chun-Wei Tung" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove redundant sequences from an input set." ; sc:featureList edam:operation_0231, edam:operation_0290, edam:operation_0491 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "skipredundant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/skipredundant.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Read and write (return) sequences, skipping first few." ; sc:featureList edam:operation_0231, edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "skipseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/skipseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0780 ; sc:author , "Vid Podpečan" ; sc:contributor "Kristina Gruden", "Živa Ramšak" ; sc:description "Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network." ; sc:featureList edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "SKM" ; sc:provider "National Institute of Biology, Department of Biotechnology and Systems Biology" ; sc:softwareHelp ; sc:url "https://skm.nib.si/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3175 ; sc:citation , "pubmed:33963826" ; sc:description "SKSV is a ultrafast structural variation detection from circular consensus sequencing reads. Circular consensus sequencing (CCS) reads are promising for the comprehensive detection of structural variants (SVs). However, alignment-based SV calling pipelines are computationally intensive due to the generation of complete read-alignments and its post-processing. Herein, we propose a SKeleton-based analysis toolkit for Structural Variation detection (SKSV). Benchmarks on real and simulated datasets demonstrate that SKSV has an order of magnitude of faster speed than state-of-the-art SV calling ap-proaches, moreover, it enables to well-handle various types of SVs with higher F1 scores." ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3211, edam:operation_3227, edam:operation_3228 ; sc:license "MIT" ; sc:name "SKSV" ; sc:url "https://github.com/ydLiu-HIT/SKSV" ; biotools:primaryContact "Bo Liu", "Tianyi Zang", "Yadong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092 ; sc:citation , "pmcid:PMC3893531", "pubmed:24410852" ; sc:description "Create informative, interactive logos representing sequence alignments and profile hidden Markov models." ; sc:featureList edam:operation_0292, edam:operation_0564 ; sc:name "Skylign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://skylign.org/" ; biotools:primaryContact "Skylign Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation , , "pubmed:35831612" ; sc:description "Builds SRM/MRM methods and analyzes resulting data." ; sc:featureList edam:operation_2409, edam:operation_3636, edam:operation_3694, edam:operation_3801 ; sc:name "Skyline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3520 ; sc:citation , "pmcid:PMC8749956", "pubmed:34919405" ; sc:description "Skyline Batch is an application that automates a common Skyline workflow for batch processing Skyline documents. It interacts with Skyline through the command-line, allowing it to import data into a template document, export reports, and run R scripts on those reports without bringing up the Skyline user interface." ; sc:featureList edam:operation_3096 ; sc:isAccessibleForFree true ; sc:name "Skyline Batch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://skyline.ms/batch.url" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC6668092", "pubmed:31362713" ; sc:description "Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models | Stochastic Lanczos REML algorithms for genomic variance component estimation | Stochastic Lanczos REML algorithms | Code accompanying Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models | L_Seed constructs bases for Krylov subspaces: B, (A+σI)B, (A+σI)²B, .." ; sc:featureList edam:operation_3192, edam:operation_3196 ; sc:name "SL_REML" ; sc:url "https://github.com/rborder/SL_REML" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_0769, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:34995394" ; sc:description "A program for seeded local assembly of genes in complex genomes" ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "slag" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/cfcrane/SLAG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:description "Scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "slalom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/slalom.html" ; biotools:primaryContact "Davis McCarthy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3293 ; sc:citation , "pmcid:PMC9215276", "pubmed:35774992" ; sc:description "SLANG (Simple Long-read loci Assembly of Nanopore data for Genotyping) is a Python script pipeline for locus assembly, orthology estimation and SNP extraction of Nanopore-sequenced multi-locus data." ; sc:featureList edam:operation_0310, edam:operation_0323, edam:operation_0484, edam:operation_3196, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SLANG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DorfnerM/SLANG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3324, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """A Containerized Tool for Predicting Combination Monoclonal Broadly Neutralizing Antibody Sensitivity. 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The slapnap container is a tool for using the Compile, Analyze and Tally NAb Panels (CATNAP) database to develop predictive models of HIV-1 neutralization sensitivity to one or several broadly neutralizing antibodies (bnAbs).""" ; sc:featureList edam:operation_3659 ; sc:name "SLAPNAP" ; sc:url "https://benkeser.github.io/slapnap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3172, edam:topic_3316, edam:topic_3520 ; sc:citation , "pubmed:34735114" ; sc:description "A Scalable and Self-Optimizing Processing Workflow for Untargeted LC-MS." ; sc:featureList edam:operation_2422, edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SLAW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zamboni-lab/SLAW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3053 ; sc:citation "pubmed:19168911" ; sc:description "Software for testing the significance of Gene Pathways when signal is relatively weak. 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The user can perform queries with one or more sequences at a time and then receive the results by e-mail." ; sc:featureList edam:operation_0224, edam:operation_0346, edam:operation_2421 ; sc:name "SledgeHMMER" ; sc:url "http://bioapps.rit.albany.edu/sledgeHMMER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3300, edam:topic_3334 ; sc:citation , "pmcid:PMC5613192", "pubmed:28983246" ; sc:description "Open-Source Python Software for Visualization, Analysis, and Staging of Sleep Data." ; sc:featureList edam:operation_3744 ; sc:name "Sleep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://visbrain.org/sleep" ; biotools:primaryContact "Etienne Combrisson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC8374325", "pubmed:34434837" ; sc:description "Detects Sleep Cycles according to modified Feinberg & Floyd (1979) criteria." ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SleepCycles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ChristineBlume/SleepCycles" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC7263188", "pubmed:32430339" ; sc:description """Exploring dimension-reduced embeddings with Sleepwalk. 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SlicerDMRI, an open-source software suite that enables research using diffusion magnetic resonance imaging (dMRI), the only modality that can map the white matter connections of the living human brain. SlicerDMRI enables analysis and visualization of dMRI data and is aimed at the needs of clinical research users. SlicerDMRI is built upon and deeply integrated with 3D Slicer, a National Institutes of Health-supported open-source platform for medical image informatics, image processing, and three-dimensional visualization. Integration with 3D Slicer provides many features of interest to cancer researchers, such as real-time integration with neuronavigation equipment, intraoperative imaging modalities, and multimodal data fusion""" ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:name "SlicerDMRI" ; sc:url "http://dmri.slicer.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3421, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pmcid:PMC9485637", "pubmed:36148054" ; sc:description "An open-source computing platform for cardiac image analysis and modeling." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SlicerHeart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.slicer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3050, edam:topic_3384, edam:topic_3452 ; sc:citation ; sc:description """An open and extensible platform to retrieve, visualize and analyze 3D morphology. SlicerMorph enable biologists to retrieve, visualize, measure and annotate high-resolution specimen data both from volumetric scans (CTs and MRs) as well as from 3D surface scanners more effectively within 3D Slicer. 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For alignment it uses base probabilities instead of sequences. It also enambles SNP prediction." ; sc:featureList edam:operation_0292, edam:operation_0484, edam:operation_3227 ; sc:license "AFL-3.0" ; sc:name "Slider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/slider" ; biotools:primaryContact "Slider support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3372, edam:topic_3474 ; sc:citation ; sc:description "Tool to visualize WSI and navigate through their zones at different zoom levels." ; sc:featureList edam:operation_3552, edam:operation_3553 ; sc:name "Slides Viewer" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "v1" ; sc:url "http://telemed.uca.es:443/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0769 ; sc:citation "pubmed:21148542" ; sc:description "An algorithm that finds all similar pairs from a string pool in terms of edit distance." ; sc:featureList edam:operation_0288, edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SlideSort" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://cbrc3.cbrc.jp/~shimizu/slidesort/index.php" ; biotools:primaryContact "Kana Shimizu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation "pubmed:24876376" ; sc:description "The tool is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads." ; sc:featureList edam:operation_2451 ; sc:name "SlideSort-BPR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ewijaya/slidesort-bpr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC10406329", "pubmed:37549131" ; sc:description "SliDL: a Python library of pre- and post-processing tools for applying deep learning to whole-slide images." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SliDL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/markowetzlab/slidl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0621, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. SLIDR and SLOPPR: A suite of two pipelines for flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. SLIDR and SLOPPR identify spliced leaders (SLs) from 5'-tails of RNA-Seq reads that are soft-clipped after read alignment to a reference genome or transcriptome.""" ; sc:featureList edam:operation_0433, edam:operation_0435, edam:operation_0524, edam:operation_3192, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "SLIDR" ; sc:url "https://github.com/wenzelm/slidr-sloppr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_3318 ; sc:citation , "pubmed:35642445" ; sc:description "An integrative web server for exploring short linear motif-mediated interactions in interactomes." ; sc:featureList edam:operation_2949 ; sc:isAccessibleForFree true ; sc:name "SLiMAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sliman.cbs.cnrs.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3518 ; sc:citation "pubmed:17147785" ; sc:description "Web application that allows microarray facilities to track inventories of arrays, hybridizations performed and charge accrued for services by their customers. Beyond just tracking these separate pieces of information, it provides added value by utilizing the relationships between them. For instance, when hybridizations are entered, transactions are automatically created to deduct used microarrays from the proper inventories and appropriate charges are recorded." ; sc:featureList edam:operation_2409, edam:operation_2495 ; sc:name "SLIMarray" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://slimarray.systemsbiology.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0166, edam:topic_0602, edam:topic_3510 ; sc:citation "pubmed:16855291", "pubmed:17576682" ; sc:description "Tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240, edam:operation_0245 ; sc:name "SLiMDisc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioware.ucd.ie/~slimdisc/" ; biotools:primaryContact "User Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0166, edam:topic_3168, edam:topic_3510 ; sc:citation "pubmed:20497999" ; sc:description "De novo motif discovery tool for short linear motifs (SLiMs). Statistically over represented motifs within a set of protein sequences are identified and scored. Users have numerous masking options to control the contextual information to be analyzed." ; sc:featureList edam:operation_0238, edam:operation_0476, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SLiMFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.slimsuite.unsw.edu.au/servers/slimfinder.php" ; biotools:primaryContact "Richard Edwards" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_0769, edam:topic_3056, edam:topic_3796 ; sc:citation ; sc:description "An R package for integrating data and tailor-made population genomic simulations over space and time." ; sc:featureList edam:operation_0244, edam:operation_2422, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "slimr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://rdinnager.github.io/slimr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140 ; sc:citation , "pmcid:PMC4670012", "pubmed:26674271" ; sc:contributor ; sc:description "Perform short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. This aims to aid in the discovery of novel short linear motifs, as well as visualisation of the distribution of known motifs." ; sc:featureList edam:operation_0238, edam:operation_2492, edam:operation_3083 ; sc:license "GPL-3.0" ; sc:name "SLiMScape 3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.1" ; sc:url "http://apps.cytoscape.org/apps/slimscape" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0166, edam:topic_0601 ; sc:citation , , "pmcid:PMC5570202", "pubmed:21622654", "pubmed:28387819" ; sc:description "Short Linear Motifs Search. Proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. Scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. 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It can be downloaded from GitHub, and some tools are available as REST servers." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLiMSuite" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of New South Wales", "unimelb.edu.au" ; sc:softwareHelp , , , ; sc:softwareVersion "1" ; sc:url "http://slimsuite.blogspot.com.au/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3053, edam:topic_3524 ; sc:citation "pubmed:21734403" ; sc:description "The program does calculations by simulating genotypes at one locus given the phenotypes at another locus linked with the first locus." ; sc:featureList edam:operation_0283, edam:operation_2426 ; sc:name "SLINK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://watson.hgen.pitt.edu/docs/SLink.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC8749905", "pubmed:35035899" ; sc:description "Visualising novel splicing events in RNA-Seq data." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_0446 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Slinker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Oshlack/Slinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769 ; sc:citation , "pubmed:30629124" ; sc:description "R package for L1000 data set to streamline the process of identifying samples of interest and their corresponding control samples, and loading their associated expression data and metadata." ; sc:featureList edam:operation_1812, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "slinky" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "https://bioconductor.org/packages/slinky/" ; biotools:primaryContact "Eric J. Kort" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3125 ; sc:citation "pubmed:23057825" ; sc:description "A set of simple linear inequalities derived from the geometry of contigs on the line, can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph." ; sc:featureList edam:operation_0525 ; sc:name "SLiQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.rutgers.edu/Software/SLiQ/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3534, edam:topic_3678 ; sc:citation "pubmed:19433508" ; sc:description "SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile." ; sc:featureList edam:operation_0249, edam:operation_0250, edam:operation_0387, edam:operation_2574 ; sc:name "SLITHER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.mc.ntu.edu.tw/slither/" ; biotools:primaryContact "Jung-Hsin Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2885, edam:topic_3325, edam:topic_3676 ; sc:citation ; sc:description """Effective variant filtering and expected candidate variant yield in studies of rare human disease. slivar: filter/annotate variants in VCF/BCF format with simple expressions. 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A pipeline is also available" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SLKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://slkb.osubmi.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3474 ; sc:citation , "pubmed:33974548" ; sc:description "SLMGAE is a tool for the prediction of synthetic lethal interactions in human cancers using multi-view graph auto-encoder." ; sc:name "SLMGAE" ; sc:url "https://github.com/DiNg1011/SLMGAE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3518 ; sc:citation , "pmcid:PMC5490196", "pubmed:28659129" ; sc:description "A suite of algorithms for segmenting genomic profiles." ; sc:featureList edam:operation_3202 ; sc:name "SLMSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/slmsuite/" ; biotools:primaryContact "Alberto Magi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3299, edam:topic_3500 ; sc:citation ; sc:description "Filters a high-quality set of lncRNA from reconstructed RNA-seq data and searches for conserved lncRNAs using a sensitive noncoding aligning method." ; sc:featureList edam:operation_0238 ; sc:license "MIT" ; sc:name "slncky" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://slncky.github.io/" ; biotools:primaryContact "Manuel Garber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation , "pmcid:PMC6923828", "pubmed:31856716" ; sc:description "LncRNA-miRNA interaction prediction through sequence-derived linear neighborhood propagation method with information combination." ; sc:featureList edam:operation_0463, edam:operation_3439, edam:operation_3792 ; sc:name "SLNPM" ; sc:url "https://github.com/BioMedicalBigDataMiningLab/SLNPM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640, edam:topic_3512, edam:topic_3974 ; sc:citation , "pmcid:PMC9419874", "pubmed:36029479" ; sc:description "A comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis." ; sc:featureList edam:operation_2421, edam:operation_3223, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "SLOAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.tmliang.cn/SLOAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3676 ; sc:citation "pubmed:20876606" ; sc:description "Detects structural variants from targeted short DNA reads" ; sc:featureList edam:operation_3228 ; sc:name "SLOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-genepi.med.utah.edu/suppl/SLOPE/index.html" ; biotools:primaryContact "Abel HJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0621, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. SLIDR and SLOPPR: A suite of two pipelines for flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. SLIDR and SLOPPR identify spliced leaders (SLs) from 5'-tails of RNA-Seq reads that are soft-clipped after read alignment to a reference genome or transcriptome.""" ; sc:featureList edam:operation_0433, edam:operation_0435, edam:operation_0524, edam:operation_3192, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "SLOPPR" ; sc:url "https://github.com/wenzelm/slidr-sloppr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A command line tool and a library and for fetching reads from remote BLOW5 files." ; sc:name "slow5curl" ; sc:url "https://github.com/BonsonW/slow5curl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. About SLOW5 format: SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard FAST5 signal data format that prevent efficient, scalable analysis and cause many headaches for developers. SLOW5 can be encoded in human-readable ASCII format, or a more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format supports zlib (DEFLATE) compression, or other compression methods, thereby minimising the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5.""" ; sc:name "slow5tools" ; sc:url "https://github.com/hasindu2008/slow5tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102 ; sc:citation ; sc:description "Single-linkage preclustering for improved OTU (Operational Taxonomic Units) clustering based on pairwise distances." ; sc:featureList edam:operation_3432 ; sc:name "SLP" ; sc:operatingSystem "Linux" ; sc:url "http://vamps.mbl.edu/resources/software.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0780 ; sc:citation ; sc:description "Predictor for subcellular location of proteins. Uses feature vectors based on amino acid composition (frequency) and sequence alignment." ; sc:featureList edam:operation_0292, edam:operation_2423, edam:operation_2428, edam:operation_2479 ; sc:name "SLPFA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/slpfa.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0820, edam:topic_2229, edam:topic_2269 ; sc:citation , "pubmed:35801913" ; sc:description "A Multi-view Subcellular Localization Prediction Tool for Multi-location Human Proteins." ; sc:featureList edam:operation_0224, edam:operation_2489, edam:operation_3092 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SLPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://slpred.kansil.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3519 ; sc:citation ; sc:description "Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH." ; sc:featureList edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "SLqPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SLqPCR.html" ; biotools:primaryContact "Matthias Kohl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3569 ; sc:citation "pubmed:19856275" ; sc:description "A software of fitting smoothed logistic regression with Cauchy-Normal Random Probes Effects with application to aCGH data." ; sc:featureList edam:operation_3659 ; sc:name "SLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://fafner.meb.ki.se/personal/yudpaw/?page_id=13" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3125 ; sc:citation , "pmcid:PMC6820941", "pubmed:31666010" ; sc:description "SLR is a scaffolding tool based on long reads and contig classification." ; sc:featureList edam:operation_0525, edam:operation_3198, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "SLR" ; sc:url "https://github.com/luojunwei/SLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0092 ; sc:citation ; sc:description "A slush generator for BioJS modules." ; sc:featureList edam:operation_3429 ; sc:name "slush-biojs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "BioJS" ; sc:softwareHelp ; sc:softwareVersion "0.4.1" ; sc:url "https://github.com/biojs/slush-biojs" ; biotools:primaryContact "BioJS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2815, edam:topic_3954 ; sc:citation , "pmcid:PMC7015391", "pubmed:32049973" ; sc:description "An ImageJ macro tool to automate measurements in B-mode ultrasound scans." ; sc:featureList edam:operation_0247, edam:operation_3443, edam:operation_3695 ; sc:name "Simple Muscle Architecture Analysis" ; sc:url "https://sites.imagej.net/SMA/plugins/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0654, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """SMAca: SMA Carrier Analysis tool. SMN1 copy-number and sequence variant analysis from next generation sequencing data. SMAca is a python tool to detect putative SMA carriers and estimate the absolute SMN1 copy-number in a population. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify the so-called “silent carriers” (i.e. individuals with two copies of SMN1 on one chromosome, but none on the other).""" ; sc:featureList edam:operation_2428, edam:operation_3196, edam:operation_3233 ; sc:license "GPL-3.0" ; sc:name "SMAca" ; sc:url "http://www.github.com/babelomics/SMAca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_3047, edam:topic_3303, edam:topic_3336 ; sc:citation , "pubmed:37169224" ; sc:description "Comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "SMACC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://smacc.mml.unc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0621, edam:topic_2640, edam:topic_3315, edam:topic_3500 ; sc:citation ; sc:description "A benchmark text corpus for evaluation of approaches to relevance ranking and knowledge discovery in the biomedical domain." ; sc:featureList edam:operation_2422, edam:operation_3280 ; sc:name "SMAFIRA" ; sc:url "https://github.com/SMAFIRA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0128, edam:topic_0602 ; sc:citation "pubmed:27378297" ; sc:description "The web-server is a public, open-source, web-based application for creating multiple network alignments (MNAs) from existing pairwise alignments (PNAs)." ; sc:featureList edam:operation_0276, edam:operation_2928 ; sc:name "SMAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://haddock6.sfsu.edu/smal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC8082881", "pubmed:33910505" ; sc:description "SMALF is a miRNA-disease associations prediction tool based on stacked autoencoder and XGBoost. Identifying miRNA and disease associations helps us understand disease mechanisms of action from the molecular level. However, it is usually blind, time-consuming, and small-scale based on biological experiments. Hence, developing computational methods to predict unknown miRNA and disease associations is becoming increasingly important." ; sc:featureList edam:operation_0463 ; sc:license "MIT" ; sc:name "SMALF" ; sc:url "https://github.com/dayunliu/SMALF" ; biotools:primaryContact "Lei Deng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Plug-in" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC5011339", "pubmed:27597889" ; sc:description "smallAnimalMRgHIFU is a hardware and software package that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner." ; sc:featureList edam:operation_3436 ; sc:license "CC-BY-NC-4.0" ; sc:name "smallAnimalMRgHIFU" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/poormanme/smallAnimalMRgHIFU" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_0634, edam:topic_2640, edam:topic_3305 ; sc:citation , "pmcid:PMC9627310", "pubmed:36338766" ; sc:description "Small area disease mapping of cancer incidence in British Columbia using Bayesian spatial models and the smallareamapp R Package." ; sc:featureList edam:operation_0321, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "smallareamapp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jdsimkin04/smallareamapp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2305, edam:format_2306 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_2572 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10234390", "pubmed:37094819" ; sc:description "Pipeline for siRNA discovery and 3' tail identification." ; sc:featureList edam:operation_2008, edam:operation_3192, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:name "smalldisco" ; sc:operatingSystem "Linux" ; sc:url "https://doi.org/10.5281/zenodo.7799621" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "Processing, analysis and curation of DNA sequence data. Most of these tools are genome-agnostic, with two tools specifically designed for hepatitis B virus sequence data." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:name "SmallGenomeTools" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://hvdr.bioinf.wits.ac.za/SmallGenomeTools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , , "pmcid:PMC4051166", "pubmed:24708189", "pubmed:28286147" ; sc:description "Aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms can be processed except for SOLiD reads." ; sc:featureList edam:operation_0292 ; sc:license "GPL-3.0" ; sc:name "Smalt" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/science/tools/smalt-0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3518 ; sc:citation ; sc:description "Functions and classes for DNA copy number profiling of array-CGH data." ; sc:featureList edam:operation_3197 ; sc:license "GPL-2.0" ; sc:name "SMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.38.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SMAP.html" ; biotools:primaryContact "Robin Andersson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0632, edam:topic_0780, edam:topic_3168 ; sc:citation , "pubmed:36718951" ; sc:description "A multiplex PCR amplicon and gRNA design tool to screen for natural and CRISPR-induced genetic variation." ; sc:featureList edam:operation_0308, edam:operation_3196, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SMAP design" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://gitlab.com/ilvo/smap-design" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3277, edam:topic_3520, edam:topic_3922 ; sc:citation ; sc:description "A pipeline to validate and correct sample identity based on a combination of concordance and specificity scores. SMAP first detects variant peptides from multiplexed isobaric labeling-based quantitative proteomics data using the proteogenomics approach, and then infers allelic information for each sample based on its expression level of the variant peptides." ; sc:featureList edam:operation_3196, edam:operation_3630, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/XWangLab/SMAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0130, edam:topic_0602, edam:topic_3678 ; sc:citation "pubmed:20484373" ; sc:description "Provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics." ; sc:featureList edam:operation_0482, edam:operation_2949 ; sc:name "SMAP WS" ; sc:url "http://kryptonite.ucsd.edu/opal2/GetServicesList.do" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1139 ; sc:name "SMART accession number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2782 ; sc:name "SMART domain name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein structure report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0736 ; sc:citation , , , , , , , , , "pmcid:PMC5753352", "pubmed:10592234", "pubmed:11752305", "pubmed:14681379", "pubmed:16381859", "pubmed:18978020", "pubmed:22053084", "pubmed:29040681", "pubmed:9600884" ; sc:description "SMART protein domain database." ; sc:featureList edam:operation_0224 ; sc:name "Simple modular architecture research tool (SMART)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smart.embl.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC8497366", "pubmed:34390311" ; sc:description "SMART-HF is an online AI app for risk stratification of heart failure patients, based on the Japanese heart failure registry (JROADHF) of ten thousands of people. SMART-HF predicts the prognosis of one-year survival ratio after hospitalization due to acute decompensated heart failure. This app is designed for not only healthcare providers but also non-healthcare providers." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMART-HF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://hfriskcalculator.herokuapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3077, edam:topic_3382 ; sc:citation , "pmcid:PMC9352634", "pubmed:35927517" ; sc:description "A software for generating and processing smart line recording trajectories for population two-photon calcium imaging." ; sc:featureList edam:operation_2939, edam:operation_3443, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SmaRT2P" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/moni90/SmART2P" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0769, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC9070730", "pubmed:35396258" ; sc:description "An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://smartrpackage.shinyapps.io/smart_sample_dataset" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379, edam:topic_3577 ; sc:citation , "pmcid:PMC7808267", "pubmed:33510969" ; sc:description "an R package for designing and analyzing Sequential Multiple Assignment Randomized Trials." ; sc:featureList edam:operation_3435 ; sc:name "SMARTAR" ; sc:url "https://cran.r-project.org/web/packages/SMARTAR/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2259 ; sc:citation "pubmed:17052123" ; sc:description "A program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, the program needs multiple runs to have mean results." ; sc:featureList edam:operation_3562 ; sc:name "SmartCell v4.3" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://software.crg.es/smartcell/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0769, edam:topic_3336 ; sc:citation , "pmcid:PMC6974502" ; sc:description "a network pharmacology investigation platform." ; sc:featureList edam:operation_3216, edam:operation_3629, edam:operation_3925, edam:operation_3928 ; sc:license "MIT" ; sc:name "SmartGraph" ; sc:url "https://smartgraph.ncats.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099 ; sc:citation ; sc:description "Discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. Predicts motifs from enriched k-mers that combine information from ranked RNA sequences and their predicted secondary structure, obtained using various folding methods. Consequently, SMARTIV generates Position Weight Matrices (PWMs) in a combined sequence and structure alphabet with assigned P-values." ; sc:featureList edam:operation_0238, edam:operation_0278, edam:operation_3501 ; sc:name "SMARTIV" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "http://choosealicense.com" ; biotools:primaryContact "Maya Polishchuk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0769, edam:topic_3172, edam:topic_3520, edam:topic_3955 ; sc:citation , "pubmed:33269929" ; sc:description """SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments. The software is based on the OpenMS toolkit.""" ; sc:featureList edam:operation_2409, edam:operation_3215, edam:operation_3799 ; sc:license "MIT" ; sc:name "SmartPeak" ; sc:url "https://github.com/AutoFlowResearch/SmartPeak" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3170, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC7032729", "pubmed:32032351" ; sc:description """Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases. SmartPhase is a phasing tool tailored for clinical use in genetic diagnosis pipelines. It accurately and efficiently reduces the number of possible compound heterozygous variant pairs being examined around either predefined genetic loci or from a list of preselected variant pairs. To achieve this, SmartPhase is able to incorporate parental genotype information as well as reads generated from DNA- or RNA-sequencing. Furthermore, it incorporates existing haplotype information and applies logical rules to exclude variant constellations that cannot be disease causing.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3454 ; sc:name "SmartPhase" ; sc:url "http://ibis.helmholtz-muenchen.de/smartphase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3071, edam:topic_3379 ; sc:citation , "pmcid:PMC9615349", "pubmed:36303168" ; sc:description "An online repository of randomized controlled clinical trials of smartphone applications for chronic conditions." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Smartphone-RCCT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://osf.io/hvf8x" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2259 ; sc:citation "pubmed:25480376" ; sc:description "A method integrating static and time series data from multiple individuals to reconstruct condition specific response networks in an unsupervised way." ; sc:featureList edam:operation_3660 ; sc:name "SMARTS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sb.cs.cmu.edu/smarts/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3305, edam:topic_3474 ; sc:citation , "pubmed:31647520" ; sc:description "SMARTS is a social media-based addiction recovery and intervention targeting server." ; sc:featureList edam:operation_0337 ; sc:name "SMARTS" ; sc:url "http://haddock9.sfsu.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0637, edam:topic_0654, edam:topic_3301 ; sc:citation "pubmed:25568281" ; sc:description "A taxa tree based variable grouping and model selection method for identifying phenotype-assocaited microbiome variables." ; sc:featureList edam:operation_3460 ; sc:name "SMARTscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://dsgwebwp.wustl.edu/methods-software/smartscan/" ; biotools:primaryContact "Qunyuan Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0209, edam:topic_2258, edam:topic_3343 ; sc:citation , "pmcid:PMC7757167", "pubmed:32997890" ; sc:description """A Toolbox for Chemical Pattern Design. A network error occured. Please click on the reload button. If this error continues, contact smartsview[at]zbh.uni-hamburg.de. Create an easy to comprehend visualization for your SMARTS expression. Compare two SMARTS expression with respect to subset relation (Does expression A match whenever B matches?) or similarity and receive a visualization of the node mapping.""" ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3695 ; sc:name "SMARTSplus" ; sc:url "https://smarts.plus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3120 ; sc:citation "pubmed:24894505" ; sc:description "A benchmarking methodology for evaluating germline variant calling algorithms." ; sc:featureList edam:operation_2409 ; sc:name "SMaSH" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://smash.cs.berkeley.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_2885, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC6936078", "pubmed:31888490" ; sc:description """Sample matching using SNPs in humans. A tool for sample swap identification in high throughput sequencing studies. Sample swaps are a real concern in high throughput sequencing studies. SMaSH helps detect such sample swaps by integrating the information from over 6000 carefully selected single nucleotide polymorphism (SNP) sites from across the human genome to identify which samples in a group of sequencing data sets are derived from the same human individual. Importantly, SMaSH is able to verify sample identity between different data types, such as RNA-Seq, exome, and MethylCap-Seq data.""" ; sc:featureList edam:operation_0484, edam:operation_2428, edam:operation_3196, edam:operation_3661 ; sc:name "SMASH" ; sc:url "http://github.com/rbundschuh/SMaSH" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_2571 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0950 ; sc:encodingFormat edam:format_2032 ; sc:name "Mathematical model" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0196, edam:topic_3174, edam:topic_3697 ; sc:citation "pubmed:20959381" ; sc:description "A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2423 ; sc:license "Other" ; sc:name "SmashCommunity" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.bork.embl.de/software/smash" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1212 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:description "Find and visualize rearrangements in DNA sequences" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Smash++" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/smortezah/smashpp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation , "pmcid:PMC9361618", "pubmed:35941549" ; sc:description "A scalable, general marker gene identification framework for single-cell RNA-sequencing." ; sc:featureList edam:operation_0314, edam:operation_3891, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SMaSH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/cvejic-group/smash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0128, edam:topic_0769, edam:topic_2828 ; sc:citation , "pubmed:32070491" ; sc:description """SMAtool reveals sequences and structural principles of protein-RNA interaction. pipeline for integrated analysis of eCLIP and DMS/PARS.""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_2488, edam:operation_2495 ; sc:name "SMAtool" ; sc:url "https://github.com/QuKunLab/SMAtool" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3989 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3464 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3796 ; sc:citation , "pmcid:PMC5470542", "pubmed:28024154" ; sc:description "SMC++ is a program for estimating the size history of populations from whole genome sequence data." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SMC++" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/popgenmethods/smcpp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8335569", "pubmed:34368166" ; sc:description "A computing tool is developed to automated identify somatic mutation-driven immune cells." ; sc:featureList edam:operation_0252, edam:operation_0314, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SMDIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://CRAN.R-project.org/package=SMDIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0820, edam:topic_3382 ; sc:citation ; sc:description """Total workflows of the single-molecule imaging analysis in living cells. The smDynamicsAnalyzer is an open-source macro that can determine a series of dynamics parameters from the single-molecule tracking dataset simply by following the designated steps after building an appropriate folder structure.""" ; sc:featureList edam:operation_0269, edam:operation_3443, edam:operation_3799 ; sc:name "smDynamicsAnalyzer" ; sc:url "https://github.com/masataka-yanagawa/IgorPro8-smDynamicsAnalyzer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_2885, edam:topic_3305, edam:topic_3517 ; sc:citation , "pmcid:PMC8947622", "pubmed:35286307" ; sc:description "A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMetABF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sunjianle-sjtu.shinyapps.io/analycode/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3277, edam:topic_3295 ; sc:citation ; sc:description "Spatial normalisation method for ILLumina InfinIUM HumanMethylation BeadChip to correct the spatial background noise which affect the signal-to-noise ratio. Outperforms BeadStudio to predict the methylation status of a given locus." ; sc:featureList edam:operation_2423, edam:operation_3435 ; sc:name "SMETHILLIUM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://bioinfo-out.curie.fr/projects/smethillium/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3047, edam:topic_3382 ; sc:citation ; sc:description """an open-source platform for single-molecule FRET. (change this slider to rotate the smfBox). Single molecule Förster Resonance Energy Transfer (smFRET) can be used to obtain a unique level of information for dynamic processes involving biological molecules, as well as revealing structural information. The Craggs Lab of The University of Sheffield has developed an open-source microscopy platform for making smFRET measurements at a fraction of the price of typical commercial systems. The smfBox system can be built for around 40,000 GBP using commercially available parts and fabrication of a simple microscope body. It requires a relatively small footprint on an optics bench or optical breadboard. When complete can be used as a class 1 laser product; all beams are enclosed, and a mechanical shutter connected to the lid prevents laser light from entering the box when the lid is open""" ; sc:featureList edam:operation_0310 ; sc:name "smfBox" ; sc:url "https://craggslab.github.io/smfBox/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3520 ; sc:citation , "pubmed:32501676" ; sc:description """Small Molecules Finder for Metabolomics and Lipidomics Analysis. SMfinder is a free software for the analysis of small molecule. It allows identification and quantification of metabolites and lipids, and provides an easy-to-expand MS/MS database for compound identification.""" ; sc:featureList edam:operation_0337, edam:operation_3799, edam:operation_3803 ; sc:name "SMfinder" ; sc:url "http://www.ifom.eu/SMfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0204, edam:topic_0749, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9836277", "pubmed:36520922" ; sc:description "Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework." ; sc:featureList edam:operation_2404, edam:operation_3891, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMFM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/no-banana/SMFM-master" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474 ; sc:citation , "pubmed:33296311" ; sc:description """A New Ensemble Adversarial Attack Powered by Long-Term Gradient Memories. Deep neural networks are vulnerable to adversarial attacks. More importantly, some adversarial examples crafted against an ensemble of source models transfer to other target models and, thus, pose a security threat to black-box applications (when attackers have no access to the target models). Current transfer-based ensemble attacks, however, only consider a limited number of source models to craft an adversarial example and, thus, obtain poor transferability. Besides, recent query-based black-box attacks, which require numerous queries to the target model, not only come under suspicion by the target model but also cause expensive query cost. In this article, we propose a novel transfer-based black-box attack, dubbed serial-minigroup-ensemble-attack (SMGEA)""" ; sc:name "SMGEA" ; sc:url "https://github.com/CZHQuality/AAA-Pix2pix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3314, edam:topic_3315 ; sc:citation ; sc:description "Synthetic Models of biological systems Generator (SMGen) automatically generates synthetic models of biochemical reaction networks that, by construction, are characterized by both features (e.g. system connectivity, reaction discreteness) and emergent dynamics \\textcolor{red}{that do not exhaust all the reactants, a non-trivial behavior that often characterizes} real biochemical networks." ; sc:featureList edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SMGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/sgr34/smgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0160, edam:topic_0623, edam:topic_0637, edam:topic_0736 ; sc:citation , "pubmed:32898222" ; sc:description """a novel supervised search framework based on PSI-BLAST for protein remote homology detection. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. BLAST finds regions of similarity between biological sequences. Results: To uncover the reasons, we figured out three types of Incorrectly Selected Homology (ISH) errors in PSSMs.""" ; sc:featureList edam:operation_0303, edam:operation_0308, edam:operation_0495, edam:operation_0496, edam:operation_2421 ; sc:name "SMI-BLAST" ; sc:url "http://bliulab.net/SMI-BLAST/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3442 ; sc:encodingFormat edam:format_3548 ; sc:name "MRI image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3442 ; sc:encodingFormat edam:format_3548 ; sc:name "MRI image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "Suite of service applications used to catalogue and anonymise DICOM files for the Scottish Medical Imaging (SMI) project" ; sc:featureList edam:operation_0227, edam:operation_2421, edam:operation_3283 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SMI Services" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/SMI/SmiServices" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3299, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC8161935", "pubmed:34049495" ; sc:description "Systems Metabolomics using Interpretable Learning and Evolution (SMILE) is a framework for for supervised metabolomics data analysis. SMILE package implements Linear Genetic Programming (LGP) algorithm in python, with a scikit-learn style API. It is mainly used in data mining and finding feature interactions. Note it currently only support binary classification data." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3435 ; sc:license "MIT" ; sc:name "SMILE" ; sc:softwareHelp ; sc:url "https://github.com/MIB-Lab/SMILE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3314, edam:topic_3474 ; sc:citation ; sc:description """A Data-Driven Substructure Tokenization Algorithm for Deep Learning. SMILES Pair Encoding (ChemRxiv) first learns a vocabulary of high frequency SMILES substrings from a large chemical dataset (e.g., ChEMBL) and then tokenizes SMILES based on the learned vocabulary for deep learning models. SMILES Pair Encoding is inspired by byte-pair-encoding (BPE).""" ; sc:featureList edam:operation_3927 ; sc:license "Apache-2.0" ; sc:name "SMILES Pair Encoding" ; sc:url "https://github.com/XinhaoLi74/SmilesPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3314, edam:topic_3474 ; sc:citation , "pmcid:PMC10498440", "pubmed:37604495" ; sc:description "SMiPoly (Small Molecules into Polymers)\" is rule-based virtual library generator for discovery of functional polymers. It is consist of two submodules, \"monc.py\" and \"polg.py\"." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SMiPoly" ; sc:url "https://github.com/PEJpOhno/SMiPoly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:citation ; sc:description "smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs)." ; sc:featureList edam:operation_0337 ; sc:name "smirnaDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:url "http://www.mirz.unibas.ch/cloningprofiles/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation ; sc:description "This package builds on the Epimods framework which facilitates finding weighted subnetworks (\"modules\") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules." ; sc:featureList edam:operation_0362, edam:operation_3223, edam:operation_3809 ; sc:license "GPL-2.0" ; sc:name "SMITE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SMITE.html" ; biotools:primaryContact "Andrew Damon Johnston", "Neil Ari Wijetunga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3520, edam:topic_3524 ; sc:citation , "pmcid:PMC8000309", "pubmed:33799543" ; sc:description "SMITER (Synthetic mzML writer) is a python-based command-line tool designed to simulate LC-MS/MS runs." ; sc:featureList edam:operation_0337, edam:operation_3631, edam:operation_3633, edam:operation_3799, edam:operation_3860 ; sc:license "MIT" ; sc:name "SMITER" ; sc:softwareHelp ; sc:url "http://github.com/LeidelLab/SMITER" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3299 ; sc:citation , "pmcid:PMC10010604", "pubmed:36825830" ; sc:description "Spatially constrained stochastic model for simulation of intra-tumour heterogeneity." ; sc:featureList edam:operation_0244, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SMITH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/schwarzlab/smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_3474 ; sc:citation , "pmcid:PMC9755196", "pubmed:36531225" ; sc:description "Prediction of potential small molecule−miRNA associations based on heterogeneous network representation learning." ; sc:featureList edam:operation_0463, edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SMMA-HNRL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SMMA-HNRL/SMMA-HNRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3067, edam:topic_3954 ; sc:citation , "pubmed:32925586" ; sc:description """An Open Architecture Development Platform for Modular, Mixed, and Augmented Reality Procedural and Interventional Simulators. The CSSALT Software Development Kit (SDK) connects Unity Technology’s Unity 3D game engine with CSSALT's SMMARTS platform.""" ; sc:featureList edam:operation_0337 ; sc:name "SMMARTS-SDK" ; sc:url "https://github.com/UF-CSSALT/SMMARTS-SDK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0632, edam:topic_0769, edam:topic_3168, edam:topic_3577 ; sc:citation ; sc:description "A computational toolset for processing and analysis of single-molecule molecular inversion probes derived data." ; sc:featureList edam:operation_0308, edam:operation_0452, edam:operation_0484, edam:operation_2422, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SmMIP-tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/abelson-lab/smMIP-tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3336 ; sc:citation , "pmcid:PMC8083326", "pubmed:33839740" ; sc:description "SMMPPI (Predicting Small-Molecule Modulators Of Protein-Protein Interactions) is a machine learning based tool to predict small molecule based modulators of Protein-Protein Interactions. It involves two-stages: At First, it predicts the compounds with potential to act as PPI modulators. In the next stage, PPI family specific predictors can be used to predict modulators for 11 clinically important PPI familes." ; sc:featureList edam:operation_0482, edam:operation_2492, edam:operation_3216, edam:operation_4009 ; sc:name "SMMPPI" ; sc:url "http://www.nii.ac.in/smmppi.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0128, edam:topic_0154, edam:topic_0199 ; sc:citation , "pmcid:PMC3965028", "pubmed:24163098" ; sc:description "An interactive database, with special focus on small molecule ligands targeting RNA." ; sc:featureList edam:operation_2439 ; sc:name "SMMRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rdb.vlifesciences.com/homepage.php" ; biotools:primaryContact "Raman Parkesh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3334, edam:topic_3382 ; sc:citation , "pubmed:32854096" ; sc:description """SmoCuDa - The Open Smoking Cue Database. A Validated Smoking Cue Database to Reliably Induce Craving in Tobacco Use Disorder. SmoCuDa is a free open access database of 250 smoking-related images. All images were taken from open and free-to-use photo websites (creative commons license) and were chosen to cover a widespread variety of cigarette-associated content (e.g. cigarettes, ashtrays, smokers of different ages and genders). Further, all images have been rated, tested and validated by, to date, 40 mild to heavy smokers. These ratings demonstrate that SmoCuDa images cover a wide range of intensities along the stimulus dimensions “craving”, “arousal”, and “valence”. Thus, SmoCuDa images are suited particularly well to investigate cue-induced behavior and neural activity over a large continuum of intensities.""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "SmoCuDa" ; sc:url "https://smocuda.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0176, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:20525782" ; sc:description "SMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials." ; sc:featureList edam:operation_0477, edam:operation_2415, edam:operation_2426, edam:operation_2476 ; sc:name "SMOG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://smog-server.org/" ; biotools:primaryContact "SMOG Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3306 ; sc:citation ; sc:description "A spatial stochastic simulator for chemical reaction networks. 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Ryan", "Thomas Manke" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0196, edam:topic_0769, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC9978240", "pubmed:36875992" ; sc:description "A simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "CECILL-2.1" ; sc:name "SnakeMAGs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Nachida08/SnakeMAGs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3372 ; sc:citation "pubmed:22908215" ; sc:description "Workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style." ; sc:featureList edam:operation_3762 ; sc:name "Snakemake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://snakemake.readthedocs.io/en/stable/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Implements snakes for active contour models for image segmentation." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Snakes: Active Contour Models" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28109-snakes-active-contour-models" ; biotools:primaryContact "Ritwik Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3315, edam:topic_3382, edam:topic_3500, edam:topic_3520 ; sc:citation , "pmcid:PMC7416652", "pubmed:32848652" ; sc:description """A Low-Cost Open-Source High-Speed Multi-Camera Motion Capture System. 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Column Options Reset Filters Refresh Table. snoTHAW is a tool to help visualize snoRNA expression data from snoDB""" ; sc:featureList edam:operation_0571, edam:operation_2421, edam:operation_3695 ; sc:name "snoDB" ; sc:url "http://scottgroup.med.usherbrooke.ca/snoDB/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9226514", "pubmed:35657102" ; sc:description "The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets." ; sc:featureList edam:operation_0433, edam:operation_0443, edam:operation_3902 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "snoGloBe" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/scottgroup/snoGloBe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:15306656", "pubmed:15980563" ; sc:description "snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence" ; sc:featureList edam:operation_0239, edam:operation_0314, edam:operation_0464, edam:operation_2454 ; sc:name "snoGPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lowelab.ucsc.edu/snoGPS/" ; biotools:primaryContact "snoGPS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3303, edam:topic_3452 ; sc:citation , "pubmed:35612169" ; sc:description "Implementing SNOMED CT in Open Software Solutions to Enhance the Findability of COVID-19 Questionnaires." ; sc:featureList edam:operation_3435, edam:operation_3695, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SNOMED CT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BIH-CEI/SNOMEDCT_OPAL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0797, edam:topic_3053 ; sc:citation "pubmed:19687029" ; sc:description "A desktop application for visualising and exploring comparative genomic hybridization (CGH) data. The software allows the user to interactively analyse several sets of data simultaneously. The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples." ; sc:featureList edam:operation_3233 ; sc:name "SnoopCGH Beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snoopcgh.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168 ; sc:citation , "pmcid:PMC5109690", "pubmed:27842494" ; sc:contributor ; sc:description "A machine learning-based method for somatic variant identification from low-pass next-generation sequencing." ; sc:featureList edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "SNooPer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.somaticsnooper.com/" ; biotools:primaryContact "Jean-Francois Spinella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2275, edam:topic_3524 ; sc:citation , "pmcid:PMC5534078", "pubmed:28754122" ; sc:description "Tool to construct and simulate hybrid biological models." ; sc:featureList edam:operation_3562 ; sc:name "Snoopy hybrid simulator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy" ; biotools:primaryContact "Mostafa Herajy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_3053 ; sc:citation , "pmcid:PMC4015994", "pubmed:24148649" ; sc:description "Small nucleolar RNA orthological gene database." ; sc:featureList edam:operation_2421 ; sc:name "snOPY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snoopy.med.miyazaki-u.ac.jp/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3295, edam:topic_3674 ; sc:citation "pubmed:10024243" ; sc:description "Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence" ; sc:featureList edam:operation_3204 ; sc:name "snoscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lowelab.ucsc.edu/snoscan/" ; biotools:primaryContact "Snoscan Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2354 ; sc:encodingFormat edam:format_1920, edam:format_2200 ; sc:name "RNA family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A free web server for the analysis of small nucleolar RNAs (snoRNAs) in fungi genomes." ; sc:featureList edam:operation_0362 ; sc:name "snoStrip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snostrip.bioinf.uni-leipzig.de/index.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622 ; sc:citation ; sc:description "The tool supports metadata and file submission, a database used for metadata storage, web pages for displaying the metadata and a robust API for querying the metadata." ; sc:featureList edam:operation_2409 ; sc:name "SnoVault" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ENCODE-DCC/snovault/" ; biotools:primaryContact "J. Michael Cherry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_2269, edam:topic_3557 ; sc:citation "pubmed:19454602" ; sc:description "SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance estimates." ; sc:featureList edam:operation_0276, edam:operation_2949, edam:operation_3083, edam:operation_3216, edam:operation_3439 ; sc:name "SNOW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snow.bioinfo.cipf.es" ; biotools:primaryContact "BABELOMICS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3444, edam:topic_3524 ; sc:citation , "pmcid:PMC7530342", "pubmed:33071741" ; sc:description """A Model Order Free Independent Component Analysis Strategy for Functional Magnetic Resonance Imaging Data. Snowball ICA: A Model order free Independent Component Analysis Scenario for Functional Magnetic Resonance Imaging Data.""" ; sc:featureList edam:operation_3443, edam:operation_3891, edam:operation_3935 ; sc:name "Snowball ICA" ; sc:url "https://github.com/GHu-DUT/Snowball-ICA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053, edam:topic_3170 ; sc:description "Gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models." ; sc:featureList edam:operation_2454 ; sc:name "SnowyOwl" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.4" ; sc:url "https://sourceforge.net/projects/snowyowl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3168, edam:topic_3512, edam:topic_3912 ; sc:citation , "pubmed:31822517" ; sc:description """A Web Tool for SNP-Specific Genome Editing. SNP-targeted CRISPR design pipeline. CRISPR/Cas9 target online predictor. DRSC tool for designing SNP-targetted CRISPR guides. Are you interested in targeting SNP or INDEL variants in your experiment? Look no further! We can help you find CRISPR guide designs (both -NGG and -NAG) in Fly, Human, Mouse, Zebrafish, and Rat genomes. Each guide will be given an efficiency and off-target score based on our algorithms so that you can plan accordingly. Targeting multiple variants within the same guide is also available (select the checkbox)!. Online version available at: https://www.flyrnai.org/tools/snp_crispr. DRSC tool for search and view of pre-computed CRISPR designs for genome engineering (knock-out or knock-in) in Drosophila. DRSC/TRiP Functional Genomics Resources. — Rational design of CRISPR/Cas target. Enter an accession number (e.g""" ; sc:featureList edam:operation_2421, edam:operation_3096, edam:operation_3227 ; sc:license "MIT" ; sc:name "SNP-CRISPR" ; sc:url "https://www.flyrnai.org/tools/snp_crispr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3293 ; sc:author ; sc:description "snpgenie is a tool for microbial variant calling and phylogenetic analysis from raw read data. It was primarily written to be used with bacterial isolates of M. Bovis but can be applied to any relevant bacterial species." ; sc:featureList edam:operation_0484 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "snpgenie" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dmnfarrell/snpgenie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3314, edam:topic_3517 ; sc:description "Returns the contingency tables for several markers in case control study." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:name "SNP marker(s) contingency table(s)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/35664-genome-snp-marker-s-contingency-table-s" ; biotools:primaryContact "Mohammed Sadeq Al-Rawi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Generate mutated sequence files from a reference genome." ; sc:featureList edam:operation_0364 ; sc:name "snp-mutator" ; sc:url "https://github.com/CFSAN-Biostatistics/snp-mutator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102 ; sc:citation "pubmed:19574284" ; sc:description "Fast, memory-efficient and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping." ; sc:featureList edam:operation_3196, edam:operation_3198 ; sc:name "SNP-o-matic" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://snpomatic.sourceforge.net/" ; biotools:primaryContact "SNP-o-matic Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3053 ; sc:citation ; sc:description "Impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6." ; sc:featureList edam:operation_3557 ; sc:name "SNP2HLA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.3" ; sc:url "http://www.broadinstitute.org/mpg/snp2hla/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "The resource is based on a new 'in silico' approach for identifying regulatory variants. The transcription factor (TF) binding score is computed in both the reference (hg19) and alternate human genome assemblies. The alternate genome assembly is generated by incorporating the alternate allele of common genetic variants (AF>=0.001) from the 1000 Genomes Project. Interesting candidate variants are those SNPs that disrupt, create or change the TF binding score/affinity between the two genomes." ; sc:featureList edam:operation_0445, edam:operation_3197 ; sc:name "SNP2TFBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epd.expasy.org/snp2tfbs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2885, edam:topic_3516, edam:topic_3518 ; sc:citation "pubmed:15980518" ; sc:description "Tool that automates PCR-RFLP assay design for SNP genotyping." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:license "Unlicense" ; sc:name "SNP Cutter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Pipeline to directly connect SNP (Single Nucleotide Polymorphism) data and linkage analysis program." ; sc:featureList edam:operation_0283 ; sc:name "SNP HiTLink" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5.1" ; sc:url "http://www.dynacom.co.jp/u-tokyo.ac.jp/snphitlink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:19620097" ; sc:description "This can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses." ; sc:featureList edam:operation_2238 ; sc:name "SNP ratio test" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/snpratiotest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3053 ; sc:citation "pubmed:24250114" ; sc:description "A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5’UTR, etc)." ; sc:featureList edam:operation_0361, edam:operation_3197 ; sc:name "SNPAAMapper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://isu.indstate.edu/ybai2/SNPAAMapper2/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2885, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC9510352", "pubmed:36171799" ; sc:description "A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data." ; sc:featureList edam:operation_0331, edam:operation_3196, edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SNPAAMapper-Python" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BaiLab/SNPAAMapper-Python" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "C++ library with novel algorithms and a novel file format for compressing and retrieving SNP data, specifically designed for large-scale association studies. The algorithm is based on two main ideas: (i) compress linkage disequilibrium blocks in terms of differences with a reference SNP and (ii) compress reference SNPs exploiting information on their call rate and minor allele frequency." ; sc:featureList edam:operation_2422 ; sc:license "GPL-3.0" ; sc:name "SNPack" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://sysbiobig.dei.unipd.it/?q=Software#SNPack" ; biotools:primaryContact "Francesco Sambo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0736, edam:topic_2815, edam:topic_2885 ; sc:citation "pubmed:16845090" ; sc:description "Identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_0331, edam:operation_0484, edam:operation_3661 ; sc:name "SNPaDomain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://snpnavigator.net/" ; biotools:primaryContact "Sungsam Gong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:12522686" ; sc:description "The tool is able to import many specific types of Genotyping data files and analyze them.When case-control studies are analyzed, in addition to the columns with genotyping data, extra columns for cases and controls are necessary in order to distinguish the groups." ; sc:featureList edam:operation_3196 ; sc:name "SNPALYZE" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.dynacom.co.jp/english/snpalyze_e/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:17267436" ; sc:description "The tool contains classes and methods to help the analysis of whole genome association studies. It utilizes S4 classes and extends haplo.stats R package to facilitate haplotype analyses. The package is useful to carry out most common analysis when performing whole genome association studies." ; sc:featureList edam:operation_0484 ; sc:name "SNPAssoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.iconcologia.net/es/SNPassoc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_3517, edam:topic_3572 ; sc:author "Angel Carreño Torres", "Arcadi Navarro Cuartiellas", "Carlos Morcillo Suarez", "José Marí­a Heredia Genestar", "Pep Alegre", "Ricard Sangrós", "Tere Páramo Prieto" ; sc:citation , "pubmed:18515823" ; sc:contributor "Mireia Utzet Sadurní­", "Urko Martí­nez" ; sc:description "Our application was originally designed to help CeGen users to handle, retrieve, transform and analyze the genetic data generated by the genotyping facilities of the institution. Hoewever, it is also open to external users who may want to upload their own genotyped data in order to take advantage its data processing features. Users will be able to perform a set of operations which may range from very simple format transformations to some complex biostatistical calculations." ; sc:featureList edam:operation_0335, edam:operation_3675, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "SNPator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instituto Nacional de Bioinformática (INB)", "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.snpator.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3168, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:15215373" ; sc:description "Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed results for all Ensembl exons are also available on the server." ; sc:featureList edam:operation_0308, edam:operation_2419, edam:operation_3237 ; sc:name "SNPbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.SNPbox.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Set of routines for making genotype calls from raw intensity data using mixture models for disomic or trisomic data" ; sc:featureList edam:operation_3432 ; sc:name "SNPCaller" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://watson.hgen.pitt.edu/register/soft_doc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885 ; sc:citation , "pubmed:17204461" ; sc:description "Functions for plotting SNP array data; maintained for historical reasons." ; sc:featureList edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "SNPchip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SNPchip.html" ; biotools:primaryContact "Robert Scharpf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pmcid:PMC29783", "pubmed:11125122" ; sc:description "Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants." ; sc:featureList edam:operation_0224 ; sc:license "Other" ; sc:name "SNPdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/snp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2815, edam:topic_3077, edam:topic_3517 ; sc:citation ; sc:description "Displays pre-compute deleterious effects of noncoding variants using a large panel of currently available methods and summarizes this information in an interactive, easy to use website." ; sc:featureList edam:operation_0236 ; sc:name "SNPDelScore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/research/snpdelscore/" ; biotools:primaryContact "Ivan Ovcharenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:19696932" ; sc:description "Provides an analysis of Single Nucleotide Polymorphism (SNP) data between any two individuals. It has been designed based on data exported from Affymetrix CNAT 4.0 or Illumina Beadstudio, as well as data downloaded from the HapMap project. However, provided that the data is formatted correctly the tool can analyze any SNP data." ; sc:featureList edam:operation_0484 ; sc:name "SNPduo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pevsnerlab.kennedykrieger.org/SNPduo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2885, edam:topic_3053, edam:topic_3574 ; sc:citation "pubmed:22140107" ; sc:description "Wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA." ; sc:featureList edam:operation_0308, edam:operation_0484, edam:operation_3196, edam:operation_3197 ; sc:name "SNPedia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.snpedia.com/index.php/SNPedia" ; biotools:primaryContact "Greg Lennon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "Provides some tools for downloading and parsing data from the SNPedia web site. The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way." ; sc:featureList edam:operation_2421 ; sc:license "GPL-2.0" ; sc:name "SNPediaR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SNPediaR.html" ; biotools:primaryContact "David Montaner" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305, edam:format_2306 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330, edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3511 ; sc:citation "pubmed:22728672" ; sc:description "Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes)." ; sc:featureList edam:operation_0484 ; sc:name "snpEff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://snpeff.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0601, edam:topic_0625 ; sc:citation "pubmed:22075996" ; sc:description "This database uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0474, edam:operation_3092 ; sc:name "SNPeffect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://snpeffect.switchlab.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3053, edam:topic_3056 ; sc:citation ; sc:description "Library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals’ phenotypes, etc. in an I/O efficient binary file format." ; sc:featureList edam:operation_2429 ; sc:license "GPL-3.0" ; sc:name "SNPFile" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.1" ; sc:url "http://daimi.au.dk/~mailund/SNPfile/index.html" ; biotools:primaryContact "Thomas Mailund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0610, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pubmed:35398990" ; sc:description "An R package for interactive and reproducible SNP filtering." ; sc:featureList edam:operation_0484, edam:operation_2939, edam:operation_3196, edam:operation_3695, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SNPfiltR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://devonderaad.github.io/SNPfiltR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:23527209" ; sc:description "A freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists." ; sc:featureList edam:operation_2428 ; sc:name "SNPflow" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://genepi-snpflow.i-med.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622, edam:topic_3517 ; sc:citation , "pmcid:PMC5144977", "pubmed:27807048" ; sc:description "snpGeneSets is a package that simplifies annotation and analysis of GWS results. The package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data." ; sc:featureList edam:operation_3661 ; sc:license "Other" ; sc:name "snpGeneSets" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "V1.12" ; sc:url "https://www.umc.edu/SoPH/Departments-and-Faculty/Data-Science/Research/Services/Software.html" ; biotools:primaryContact "Hao Mei" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3168, edam:topic_3299 ; sc:citation "pubmed:26227143" ; sc:description "A program to estimate evolutionary parameters from pooled next-generation sequencing (NGS) data." ; sc:featureList edam:operation_2403 ; sc:name "SNPGenie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hugheslab/snpgenie" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572, edam:format_3003 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3547 ; sc:name "P-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3169 ; sc:citation ; sc:description "This R package investigates and visualizes the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or TF binding sites from ChIP-Seq or RNA-Seq experiments. It comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SNPhood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SNPhood.html" ; biotools:primaryContact "Christian Arnold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:15774022" ; sc:description "Tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering." ; sc:featureList edam:operation_0484 ; sc:name "SNPHunter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.softsea.com/review/SNPHunter.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:18828861" ; sc:description "Predicts the location of SNPs from clusters of ESTs produced by the program CAP3. It is designed for ESTs without accompanying chromatogram sequence quality information, and therefore it performs quality control checks on all data." ; sc:featureList edam:operation_0484 ; sc:name "SNPidentifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.animalgenome.org/tools/share/SNPidentifier/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0204, edam:topic_0659, edam:topic_1775, edam:topic_2885 ; sc:citation "pubmed:19417063" ; sc:description "A suite of web-based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated." ; sc:featureList edam:operation_0474, edam:operation_0484, edam:operation_1777, edam:operation_2575 ; sc:name "SNPinfo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://snpinfo.niehs.nih.gov/" ; biotools:primaryContact "Z. Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_3974 ; sc:citation , "pubmed:33733347" ; sc:description "SNPInt-GPU is a software providing several methods for statistical epistasis testing. SNPInt-GPU supports GPU acceleration, but can also be used without GPU hardware. The software implements logistic regression (as in PLINK epistasis testing), BOOST, log-linear regression, mutual information (MI) and information gain (IG) for pairwise testing as well as mutual information and information gain for third-order tests." ; sc:featureList edam:operation_0488, edam:operation_2428, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "SNPInt-GPU" ; sc:url "https://github.com/ikmb/snpint-gpu" ; biotools:primaryContact "Lars Wienbrandt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053 ; sc:author "Job van Riet" ; sc:citation , "pmcid:PMC7821318", "pubmed:29305224" ; sc:contributor "Harmen van de Werken" ; sc:description "Visualization tool for displaying loss-of-heterozygosity and/or allelic imbalance (LOH/AI) by making use of VCF files originating from primarily diagnostic panels, although it works on any input." ; sc:featureList edam:operation_0564 ; sc:name "SNPitty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Cancer Computational Biology Center", "Department of Urology, Erasmus University Medical Center, Rotterdam,", "Erasmus MC" ; sc:softwareHelp , ; sc:url "https://ccbc.erasmusmc.nl/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0949 ; sc:name "Workflow metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1068 ; sc:name "Phylogenetic tree ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:encodingFormat edam:format_2049, edam:format_2556, edam:format_2557 ; sc:name "Phylogenetic data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293 ; sc:description "A Modular/Scalable workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction." ; sc:featureList edam:operation_0326, edam:operation_0451, edam:operation_0555, edam:operation_3227, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "snpkit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://alipirani88.github.io/snpkit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3320 ; sc:citation , "pmcid:PMC4393518", "pubmed:25481010" ; sc:description "A software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads." ; sc:featureList edam:operation_2499, edam:operation_3202 ; sc:license "GPL-3.0" ; sc:name "SNPlice" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.7.2" ; sc:url "https://code.google.com/archive/p/snplice/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259, edam:topic_3336 ; sc:citation "pubmed:26833341" ; sc:description "A package to integrate pairwise gene expression and drug response data as well as a gene interaction network for identifying joint gene-drug co-modules in a regression manner." ; sc:featureList edam:operation_3463 ; sc:name "SNPLS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://page.amss.ac.cn/shihua.zhang/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_2885, edam:topic_3517, edam:topic_3577 ; sc:citation , "pmcid:PMC9437274", "pubmed:36061173" ; sc:description "Integrated visual SNP interpretation tool." ; sc:featureList edam:operation_0331, edam:operation_0337, edam:operation_0484, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "SNPMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://snp.nbscn.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_2885 ; sc:citation ; sc:description "Comprehensive web interface for masking SNPs and all low-complexity regions or repeats found in large eukaryotic genomes." ; sc:featureList edam:operation_0368 ; sc:name "SNPmasker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-EE" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinfo.ut.ee/snpmasker/" ; biotools:primaryContact "Reidar Andreson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0199, edam:topic_2814, edam:topic_3120, edam:topic_3419 ; sc:citation , "pmcid:PMC7051086", "pubmed:32119710" ; sc:description "SNPMOL- Protein Structures and Genetic Variants Database. In silico analysis of the tryptophan hydroxylase 2 (TPH2) protein variants related to psychiatric disorders." ; sc:featureList edam:operation_0331, edam:operation_0394, edam:operation_2476, edam:operation_2939, edam:operation_3891 ; sc:name "SNPMOL" ; sc:url "http://www.snpmol.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3337 ; sc:citation , , , "pmcid:PMC7641476", "pubmed:32989444", "pubmed:33095761", "pubmed:34146108" ; sc:description "Efficient Lasso Solver for Large-scale SNP Data." ; sc:featureList edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "snpnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/junyangq/snpnet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2885, edam:topic_3175, edam:topic_3308 ; sc:citation "pubmed:22544707" ; sc:description "Webserver allows for significance assessment of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models so to identify phenotypically important variants. Other variations have been included like insertions/deletions, block substitutions, etc." ; sc:featureList edam:operation_0438, edam:operation_2422, edam:operation_3196, edam:operation_3197 ; sc:name "SNPnexus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.snp-nexus.org" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3168, edam:topic_3360 ; sc:citation ; sc:description """Facilitating the analysis of COVID-19 host genetics. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has demanded an unprecedented scientific response, with researchers collaborating on a global scale to better understand how host genetics can influence susceptibility to coronavirus infection and the severity of COVID-19 symptoms. The number of projects directed towards sequencing patients’ genomes has increased rapidly during this time with the rate of data generation outpacing the resources available for analysis and biological interpretation of these datasets. SNPnexus COVID is a cutting-edge web-based analytical platform that allows researchers to analyse and interpret the functional implications of genetic variants in COVID-19 patient genomes and to prioritise those that demonstrate clinical utility for the prevention, management and or treatment of COVID-19""" ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3226 ; sc:name "SNPnexus COVID" ; sc:url "https://www.snp-nexus.org/v4/covid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0749, edam:topic_2885, edam:topic_3068, edam:topic_3673 ; sc:citation ; sc:description """identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Data and scripts for testing SNPPar with either simulated or empirical datasets. SNPPar is designed to find homoplasic SNPs based on a user-defined phylogenetic tree - more specifically, it searches for those SNPs that are: parallel - same mutation (eg. A ~> T) @ same position in two (or more) unrelated groups/isolates; convergent - different mutation in resulting in same base (eg. A ~> T, C ~> T) @ same position in two (or more) unrelated groups/isolates; and/or revertant - mutation back to ancestral state (eg. A ~> T ~> A). These are self-contained datasets, including reference(s), tree and snp_table(s) required to run SNPPar. The instructions for each are below in 10. Published Datasets.""" ; sc:featureList edam:operation_0484, edam:operation_3182, edam:operation_3661, edam:operation_3745, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SNPPar" ; sc:url "https://github.com/d-j-e/SNPPar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:25040453" ; sc:description "An R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data." ; sc:featureList edam:operation_3197 ; sc:name "snpQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-personal.une.edu.au/~cgondro2/snpQC.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "Flexible, reproducible, and comprehensive quality control and imputation of genomic data." ; sc:featureList edam:operation_0484, edam:operation_2428, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "snpQT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nebfield/snpQT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3796 ; sc:citation , "pubmed:36239472" ; sc:description """user friendly population genomics for SNP datasets with categorical metadata. The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread out across programs, each of which require their own input formats, and data must often be. this is for holding javascript data. The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers.""" ; sc:featureList edam:operation_3359 ; sc:name "snpR" ; sc:url "https://rdrr.io/github/hemstrow/snpR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Eigenvector centrality algorithm that ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN)." ; sc:featureList edam:operation_2497 ; sc:name "SNPrank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "http://insilico.utulsa.edu/snprank.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625 ; sc:citation ; sc:description "SnpRecode is a tool meant to be implemented with the Fimpute imputation software. SnpRecode allows for fast and seamless conversion of genotypes to and from a format acceptable by Fimpute software. It also implements a fast genotype correlation function to estimate and plot the imputation accuracy. SnpRecode is implemented in Python." ; sc:featureList edam:operation_0484, edam:operation_0526, edam:operation_3196, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SnpRecode" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/AMarete/fimpute-utils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation , "pmcid:PMC3519454", "pubmed:23060615" ; sc:description "Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits." ; sc:featureList edam:operation_2238, edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "SNPRelate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SNPRelate.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3518 ; sc:citation ; sc:description "Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach | Predicting Human Disease-related Mutations in Proteins with Functional Annotations | SNPs &GO is a server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans" ; sc:featureList edam:operation_0331, edam:operation_0484, edam:operation_3661 ; sc:name "SNPs and GO" ; sc:url "https://snps-and-go.biocomp.unibo.it/snps-and-go/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:encodingFormat edam:format_2330 ; sc:name "UniProt accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325, edam:topic_3473, edam:topic_3510 ; sc:citation ; sc:description "A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.s." ; sc:featureList edam:operation_2414, edam:operation_2422, edam:operation_3225 ; sc:isAccessibleForFree true ; sc:name "SNPs and GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://snps-and-go.biocomp.unibo.it/snps-and-go/index.html" ; biotools:primaryContact , "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:19514061" ; sc:description "A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans." ; sc:featureList edam:operation_3461 ; sc:name "SNPs GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snps-and-go.biocomp.unibo.it/snps-and-go/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:16420694" ; sc:description "A web-accessible tool for the analysis of single nucleotide polymorphism (SNP) array data." ; sc:featureList edam:operation_0484 ; sc:name "SNPscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pevsnerlab.kennedykrieger.org/php/?q=node/101" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation "pubmed:24813542" ; sc:description "SNPsea is an algorithm to identify cell types and pathways likely to be affected by risk loci." ; sc:featureList edam:operation_2436 ; sc:license "GPL-3.0" ; sc:name "SNPsea" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://pubs.broadinstitute.org/mpg/snpsea/" ; biotools:primaryContact "SNPsea Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:19405095" ; sc:description "A program for manipulating Affymetrix SNP metadata. SNPsetter will filter the SNPs exported, by chromosome, by allele frequency, or by distance from the last-exported SNP." ; sc:featureList edam:operation_2409, edam:operation_3197 ; sc:name "SNPsetter" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dna.leeds.ac.uk/snpsetter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3365 ; sc:citation ; sc:description "Toolbox that allows you to filter and manipulate annotated vcf files." ; sc:featureList edam:operation_3675 ; sc:license "LGPL-3.0" ; sc:name "SnpSift" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://snpeff.sourceforge.net/SnpSift.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3056, edam:topic_3524 ; sc:citation "pubmed:12538254" ; sc:description "A population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes." ; sc:featureList edam:operation_0367 ; sc:name "SNPsim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/p/phylosoftware/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0622, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:25316677" ; sc:description "A webserver that enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations." ; sc:featureList edam:operation_0362, edam:operation_3209 ; sc:name "SNPsnap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/mpg/snpsnap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:14997420" ; sc:description "A method of correcting for non-independence of SNPs in LD with each other." ; sc:featureList edam:operation_3195 ; sc:name "SNPSpD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://neurogenetics.qimrberghofer.edu.au/SNPSpD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:16937379" ; sc:description "Program for the systematic analysis of SNP-dependent splicing in genotyped cDNAs." ; sc:featureList edam:operation_3197 ; sc:name "SNPSplicer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.ikmb.uni-kiel.de/resources/download-tools/software/snpsplicer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_2885, edam:topic_3512, edam:topic_3517 ; sc:citation , "pubmed:36546757" ; sc:description "Optimized high-throughput screening of non-coding variants identified from genome-wide association studies." ; sc:featureList edam:operation_0484, edam:operation_3661, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "snpSTARRseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mortunco/snp-starrseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "snpStats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/snpStats.html" ; biotools:primaryContact "David Clayton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2885, edam:topic_3293 ; sc:description "A pattern discovery tool that takes as input a phylogenetic tree and a table of SNP data and outputs SNP solutions for every branch in the phylogenetic tree." ; sc:featureList edam:operation_2429 ; sc:name "SNPSTI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ubccr/SNPSTI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2885, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:21576219" ; sc:description "Tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network." ; sc:featureList edam:operation_0276, edam:operation_0484, edam:operation_2436, edam:operation_3501 ; sc:name "SNPsyn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snpsyn.biolab.si" ; biotools:primaryContact "Tomaz Curk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , , , "pubmed:20517342" ; sc:description "Program for the analysis of single SNP association in genome-wide studies. The tests implemented include: Binary (case-control) phenotypes, single and multiple quantitative phenotypes, Bayesian and Frequentist tests, the ability to condition ypon an arbitrary set of covariates and/or SNPs, and various methods for dealing with imputed SNPs." ; sc:featureList edam:operation_2429 ; sc:license "Other" ; sc:name "SNPTEST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:23296920" ; sc:description "A suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calls in an efficient way." ; sc:featureList edam:operation_0484, edam:operation_3197 ; sc:name "SNPTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.hgsc.bcm.edu/software/snptools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:26585827" ; sc:description "A small tool to extract the latest version rsID and genomic coordinates of SNPs given any version of rs ID(s)." ; sc:featureList edam:operation_2422, edam:operation_3197 ; sc:name "SnpTracker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://statgenpro.psychiatry.hku.hk/limx/snptracker/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_2546 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2006 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3293 ; sc:citation ; sc:description "SNPs phylogenetic tree from assembled genomes or sets of reads." ; sc:featureList edam:operation_0323 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "snpTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://cge.cbs.dtu.dk/services/snpTree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3053 ; sc:citation "pubmed:17661425" ; sc:description "This tool offers an additional category of SNP information by visualizing and analyzing inheritance patterns in trios (mother, father, and child)." ; sc:featureList edam:operation_3197 ; sc:name "SNPtrio" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://pevsnerlab.kennedykrieger.org/SNPtrio.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_0625, edam:topic_2885 ; sc:citation , "pmcid:PMC5912076", "pubmed:29688387" ; sc:description "Consists of a HDF5 database back-end for SNPs, a data exchange layer powered by TASSEL libraries that represent data in JSON format, and an interface layer using PHP to visualize SNP information. It displays data in real-time through a web browser in grids that are color-coded according to a given SNP’s allelic status and mutational state." ; sc:featureList edam:operation_0564 ; sc:name "SNPversity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.maizegdb.org/snpversity" ; biotools:primaryContact "Contact form", "Taner Z Sen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description """a web application to explore SNP-associations and annotate SNP-sets. snpXplorer is an online open source web-server to explore associations from Genome-Wide Association Studies (GWAS). snpXplorer offers a wide range of possibilities, including overlap of multiple studies. Please see the documentation in this repository to get more information about how to run snpXplorer and its options.""" ; sc:featureList edam:operation_0488, edam:operation_2436, edam:operation_3227 ; sc:name "snpXplorer" ; sc:softwareHelp ; sc:url "http://snpxplorer.eu.ngrok.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_2885, edam:topic_3517 ; sc:citation , "pubmed:34048563" ; sc:description """snpXplorer is a web application to explore human SNP-associations and annotate SNP-sets. snpXplorer is an online open source web-server to explore associations from Genome-Wide Association Studies (GWAS). snpXplorer offers a wide range of possibilities, including overlap of multiple studies. Please see the documentation in this repository to get more information about how to run snpXplorer and its options. ||| NAME EQUAL TO (PUB. DIFFERENT) bio.tools/snpxplorer""" ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3661 ; sc:name "snpXplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://snpxplorer.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC6346532", "pubmed:30678634" ; sc:description "Visualization tool for large scale RNA-Seq data." ; sc:featureList edam:operation_3223, edam:operation_3431, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "snr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/snr-vis/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_3168 ; sc:citation "pubmed:19887339" ; sc:description "A tool developed in perl, used to align the protein sequences by combining sequence and structure information at an instance. Given a protein sequence of an organism, the tool is used to identify its homologue(s) in the evolutionarily distant organisms, which might not be found from either sequence alone or structure alone comparisons." ; sc:featureList edam:operation_0292, edam:operation_0295 ; sc:name "SnS-Align" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.ccmb.res.in/rakeshmishra/snsalign-tool.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:22426435" ; sc:description "A method to construct a supernetwork from partial trees based on simulated annealing." ; sc:featureList edam:operation_0323 ; sc:name "SNSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bs.ipm.ir/softwares/snsa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3304, edam:topic_3382, edam:topic_3512 ; sc:citation ; sc:description """A Unifying Toolbox for Quantification of Neuronal Anatomy. This repository hosts the scripts that were used to assemble the figures of the SNT publication. The ImageJ framework for quantification of neuronal anatomy. These scripts are intended to run from a Fiji installation subscribed to the Neuroanatomy update site, as detailed in the SNT documentation. Scripts relying on sciview/Cx3D functionality, also require the optional subscription to the SciView-Unstable update site. Since data is frequently downloaded from external servers, an internet connection is required. SNT is ImageJ's framework for semi-automated tracing, visualization, quantitative analyses and modeling of neuronal morphology.""" ; sc:featureList edam:operation_0337, edam:operation_3359, edam:operation_3450, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SNT" ; sc:softwareHelp ; sc:url "https://imagej.net/SNT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2640, edam:topic_3053 ; sc:citation "pubmed:25398608" ; sc:description "A fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny." ; sc:featureList edam:operation_0323 ; sc:name "SNV-PPILP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.helsinki.fi/en/gsa/snv-ppilp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation "pubmed:21813454" ; sc:description "Tool for variant calling in pooled or individual sequence data." ; sc:featureList edam:operation_3227 ; sc:name "SNVer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://snver.sourceforge.net/" ; biotools:primaryContact "Wei Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_2885, edam:topic_3168 ; sc:citation "pubmed:20130035" ; sc:description "Detects single nucleotide variants from next generation sequencing data derived from tumor tissues." ; sc:featureList edam:operation_0484, edam:operation_2238, edam:operation_3695 ; sc:license "MIT" ; sc:name "SNVMix" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://shahlab.ca/projects/snvmix/" ; biotools:primaryContact "Contact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , , "pubmed:18227114" ; sc:contributor ; sc:description "Short Oligonucleotide Analysis Package. Efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences and full solution to next generation sequencing data analysis." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "SOAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/" ; biotools:primaryContact "SOAP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , , "pmcid:PMC3694458", "pubmed:19497933", "pubmed:23758764" ; sc:description "Program for faster and efficient alignment for short oligonucleotide onto reference sequences. SOAPaligner/soap2 is compatible with numerous applications, including single-read or pair-end resequencing." ; sc:featureList edam:operation_0292 ; sc:name "SOAP2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.21" ; sc:url "http://soap.genomics.org.cn/soapaligner.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3673 ; sc:citation ; sc:description "SOAP3 is a GPU-based software for aligning short reads to a reference sequence." ; sc:featureList edam:operation_0292, edam:operation_3198 ; sc:license "GPL-2.0" ; sc:name "SOAP3" ; sc:operatingSystem "Linux" ; sc:url "https://i.cs.hku.hk/2bwt-tools/soap3/index.html" ; biotools:primaryContact "Ruiqiang Li", "Tak-Wah Lam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0621 ; sc:citation "pubmed:18487276" ; sc:description "Web application for the generation and organization of saved PDB searches as well email notifications." ; sc:featureList edam:operation_3429 ; sc:name "soaPDB" ; sc:url "http://soapdb.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:20019144" ; sc:description "SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "SOAPdenovo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/soapdenovo.html" ; biotools:primaryContact "SOAP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174 ; sc:author "Ruibang Luo" ; sc:citation ; sc:description "SOAPdenovo2 is a next generation sequencing reads de novo assembler." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3216, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SOAPdenovo2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/aquaskyline/SOAPdenovo2" ; biotools:primaryContact "Jun Wang", "Tak-Wah Lam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by “finding fusions directly and verifying them”, differentiating it from all other existing tools by “finding the candidate regions and searching for the fusions afterwards”. This enables the fusion discovery process to be more effective and sensitive, also with a specular performance under low coverage of sequencing far more better than other tools. http://soap.genomics.org.cn/SOAPfusion.html""" ; sc:featureList edam:operation_0282, edam:operation_3197 ; sc:name "SOAPfusion" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/SOAPfusion.html" ; biotools:primaryContact "SOAP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pmcid:PMC3530679", "pubmed:22972939" ; sc:description "Developed to find the insertion and deletion specially for re-sequence technology." ; sc:featureList edam:operation_0452 ; sc:license "GPL-3.0" ; sc:name "SOAPindel" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0637, edam:topic_3168, edam:topic_3174 ; sc:citation , "pubmed:32766813" ; sc:description """Profiling large metagenome datasets efficiently on distributed clusters. An Apache SparkTM based tool for profiling large metagenome datasets accurately on distributed cluster. "meph" mode reference (recommended for new microbe communities where MetaPhlAn2 is preferable). "comg" mode reference (recommended for new samples of known microbe communities which has known gene set). SOAPMetaS has been tested in the environments of local, Spark standalone cluster as well as YARN cluster. Users should download Spark and use spark-submit file to launch SOAPMetaS.""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SOAPMetaS" ; sc:url "https://github.com/BGI-flexlab/SOAPMetaS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3174, edam:topic_3572 ; sc:citation ; sc:description "A MapReduce Acceleration supported Software for integrated Quality Control and Preprocessing of High-Throughput Sequencing Data." ; sc:featureList edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "SOAPnuke" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BGI-flexlab/SOAPnuke" ; biotools:primaryContact "Lin Fang", "Qiang Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2815, edam:topic_2885 ; sc:citation "pubmed:19420381" ; sc:description "Accurate consensus sequence builder based on soap1 and SOAPaligner/soap2's alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs." ; sc:featureList edam:operation_3227 ; sc:name "SOAPsnp" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/soapsnp.html" ; biotools:primaryContact "SOAP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3320 ; sc:citation , , "pmcid:PMC3268599", "pmcid:PMC5792058", "pubmed:22303342", "pubmed:27941783" ; sc:description "Designed to use RNA-Seq reads for genome-wide ab initio detection of splice junction sites and identification of alternative splicing (AS) events." ; sc:featureList edam:operation_0433 ; sc:license "GPL-3.0" ; sc:name "SOAPsplice" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pubmed:21785424" ; sc:description "A program for detecting structural variation." ; sc:featureList edam:operation_2480 ; sc:license "GPL-3.0" ; sc:name "SOAPsv" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://soap.genomics.org.cn/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0632, edam:topic_2830, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC7646500", "pubmed:32640979" ; sc:description """an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. SOAPTyping is a novel HLA genotyping tool capable of producing accurate predictions from Sanger sequencing data files of both HLA classes I and II (Table1) by comparison to the IMGT/HLA database.""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3283 ; sc:license "GPL-3.0" ; sc:name "SOAPTyping" ; sc:url "https://github.com/BGI-flexlab/SOAPTyping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0089, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:20494974" ; sc:description "Provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison." ; sc:featureList edam:operation_0362, edam:operation_3209, edam:operation_3352 ; sc:name "SOBA: Sequence Ontology Bioinformatics Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sequenceontology.org/cgi-bin/soba.cgi" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0632, edam:topic_2269, edam:topic_3676 ; sc:citation , "pubmed:34015811" ; sc:description "Strand Orientation Bias Detector (SOBDetector) is a tool that reanalyzes the mutations stored in a VCF (by any mutation caller), and evaluates whether the reads which support the alternate alleles have a strand orientation bias using the original binary alignment (BAM) files. This method was designed on Illumina-like paired-end sequencing data. Although it was created for human somatic mutation filtration, it can be used on samples of any species and in a germline variant calling analysiss as well." ; sc:featureList edam:operation_3227, edam:operation_3659, edam:operation_3695 ; sc:license "MIT" ; sc:name "SOBDetector" ; sc:url "http://www.github.com/mikdio/SOBDetector" ; biotools:primaryContact "Zoltan Szallasi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pmcid:PMC4760270", "pubmed:26949516" ; sc:description "Creates visual summaries of individuals connected by co-authorship links in academia, created from bibliographic databases like PubMed, Scopus and InCites." ; sc:featureList edam:operation_0337, edam:operation_2497, edam:operation_3465 ; sc:license "GPL-2.0" ; sc:name "Social Network" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3.0" ; sc:url "http://baderlab.org/Software/SocialNetworkApp" ; biotools:primaryContact "Victor Kofia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3386, edam:topic_3406, edam:topic_3500 ; sc:citation , "pmcid:PMC9348686", "pubmed:35921355" ; sc:description "An R package for determining the social hierarchy of animals using data from individual electronic bins." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "socialh" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/socialh/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:11292353" ; sc:description "The tool finds the Knobs-into-Holes mode of packing between alpha-helices which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script if required." ; sc:featureList edam:operation_0474 ; sc:name "SOCKET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://coiledcoils.chm.bris.ac.uk/socket/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0797, edam:topic_3512 ; sc:citation , "pmcid:PMC479126", "pubmed:15123592" ; sc:description "Sockeye is a visualization tool allowing one to assemble and analyze genomic information in a three dimensional workspace. It can be used to view features at various levels, ranging from SNPs to karyotypes. Sockeye displays genomic features along tracks, and links to the Ensembl database." ; sc:featureList edam:operation_0491, edam:operation_3194, edam:operation_3209 ; sc:name "Sockeye" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bcgsc.ca/gc/bomge/sockeye/" ; biotools:primaryContact "Steven J.M. Jones" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3295 ; sc:citation "pubmed:18842598" ; sc:description "SOLiD reference based, un-gapped alignment with bisulfite capability" ; sc:featureList edam:operation_3186, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "SOCS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/socs/" ; biotools:primaryContact "Nicholas H. Bergman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:18518943" ; sc:description "Predict if a target sequence corresponds to an Fe/Mn Superoxide dismutases (SODs) ." ; sc:featureList edam:operation_2479, edam:operation_2492 ; sc:name "SODa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://babylone.ulb.ac.be/SODa/index3.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3053, edam:topic_3299, edam:topic_3676 ; sc:citation , "pubmed:33555318" ; sc:description "SODA is a tool for species delimitation using only gene tree topologies. It's a fast way of doing species delimitation and relies on a polytomy test developed by Sayyari et. al implemented inside ASTRAL package. SODA has been in our tests slightly less accurate than BPP but it is far faster." ; sc:featureList edam:operation_3478, edam:operation_3942, edam:operation_3947 ; sc:name "SODA" ; sc:url "https://github.com/maryamrabiee/SODA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_2814, edam:topic_3510, edam:topic_3538 ; sc:citation , "pubmed:28505312" ; sc:description "Protein SOlubility based on Disorder and Aggregation" ; sc:featureList edam:operation_0267, edam:operation_3092 ; sc:license "CC-BY-NC-ND-4.0" ; sc:name "SODA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://protein.bio.unipd.it/soda/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3391 ; sc:description "SODAR (system for omics data access and retrieval) is a software package for teh management of meta and mass data for (multi) omics experiments. Users can model their experiments using the ISA-tab (Investigation-Study-Assay) data model using SODAR's web based user interface. SODAR integrates with the the iRODS (integrated rules oriented data system) software for mass data management." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SODAR" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/bihealth/sodar-server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0593, edam:topic_0769, edam:topic_3172, edam:topic_3308 ; sc:citation , , "pubmed:36797409", "pubmed:36797411" ; sc:description "SODB facilitates comprehensive exploration of spatial omics data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SODB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/TencentAILabHealthcare/pysodb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3510, edam:topic_3524, edam:topic_3534 ; sc:citation "pubmed:17186483" ; sc:description "An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO is a population-based search algorithm." ; sc:featureList edam:operation_0482 ; sc:name "SODOCK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://140.113.239.45/sodock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0203, edam:topic_0736, edam:topic_3297 ; sc:citation ; sc:description """fast and accurate prediction of protein solubility. TISIGNER (tie-SIGN-er) includes TIsigner, SoDoPE and Razor, the protein expression optimisation, solubility optimisation and signal peptides prediction tools, respectively. Optimise your protein coding sequences using smarter tools and algorithms!""" ; sc:featureList edam:operation_0244, edam:operation_0303, edam:operation_0409 ; sc:name "SoDoPE" ; sc:url "https://tisigner.com/sodope" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:10631988" ; sc:description "A program for use in evaluating and refining atomic models of protein structures. The program calculates an estimated prior probability of the interatomic distances in the structure by reference to an interatomic distance probability density function (PDF) database compiled from known structures. It also calculates derivatives with respect to atomic position vectors for use in molecular dynamics simulations and structure refinement." ; sc:featureList edam:operation_0474 ; sc:name "SOESA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://code.google.com/p/soesa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3385 ; sc:citation , "pmcid:PMC5008722", "pubmed:27583365" ; sc:description "A software tool for a simple qualitative comparison of super-resolution optical fluctuation imaging (SOFI) images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample." ; sc:featureList edam:operation_3443 ; sc:license "GPL-1.0" ; sc:name "SOFI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/lob-epfl/sofitool" ; biotools:primaryContact "Theo Lasser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0634, edam:topic_3053 ; sc:citation , "pmcid:PMC4820874", "pubmed:27044653" ; sc:description "Website for grouping diseases and related disorders for generation of customized panels." ; sc:featureList edam:operation_2995 ; sc:license "GPL-3.0" ; sc:name "SoftPanel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.isb.pku.edu.cn/SoftPanel/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3293 ; sc:citation "pubmed:16830091" ; sc:description "A java package that uses ’soft parsimony’ to root gene trees by mapping them on to a species tree." ; sc:featureList edam:operation_0323 ; sc:name "Softparsmap" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://liberles.cst.temple.edu/Software/Softparsmap/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3299, edam:topic_3372 ; sc:citation ; sc:description """SoftWipe – a tool and benchmark to assess scientific software quality. This tool is a follow-up to our work on code quality in the field of Bioinformatics published here. It automatically checks and scores the software quality of your C or C++ program based on several criteria relative to other C and C++ program and calculates a relative ranking of scientific software tools.""" ; sc:name "SoftWipe" ; sc:url "https://github.com/adrianzap/SoftWipe/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0160, edam:topic_3169 ; sc:citation ; sc:description "Provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments BioConductor objects. It allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "soGGi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/soGGi.html" ; biotools:primaryContact "Tom Carroll" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3314, edam:topic_3810 ; sc:citation , "pmcid:PMC6814045", "pubmed:31651356" ; sc:description "Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota." ; sc:license "GPL-3.0" ; sc:name "soil domestication" ; sc:url "https://github.com/bulksoil/SoilDomestication" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm)." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "SoilGrids" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://soilgrids.org" ; biotools:primaryContact "Tomislav Hengl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092 ; sc:citation ; sc:description "Global predictions for standard numeric soil properties (organic carbon, bulk density, Cation Exchange Capacity (CEC), pH, soil texture fractions and coarse fragments) at seven standard depths (0, 5, 15, 30, 60, 100 and 200 cm)." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "SoilGrids250m" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://soilgrids.org" ; biotools:primaryContact "Tomislav Hengl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_3170 ; sc:citation "pubmed:20935049" ; sc:description "The Sol Genomics Network is a clade-oriented database containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato reference genome. A new transcriptome component has been added to store RNA-seq and microarray data." ; sc:featureList edam:operation_2429, edam:operation_2495, edam:operation_2871, edam:operation_3096, edam:operation_3282 ; sc:name "Sol Genomics Network" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://solgenomics.net/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:citation , "pmcid:PMC4387079", "pubmed:25747917" ; sc:description "A software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening." ; sc:featureList edam:operation_2429 ; sc:license "Other" ; sc:name "SOLAR-eclipse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://solar-eclipse-genetics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769 ; sc:citation ; sc:description """A 3D Extension of GRASS GIS r.sun for Estimating Solar Radiation in Urban Environments. Solar3D is a software application designed to interactively calculate solar irradiation and sky view factor at points on 3D surfaces. It is essentially a 3D extension of the GRASS GIS r.sun solar radiation model.""" ; sc:featureList edam:operation_0573, edam:operation_1816, edam:operation_3435 ; sc:license "MIT" ; sc:name "Solar3D" ; sc:url "https://github.com/jian9695/Solar3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3473 ; sc:citation "pubmed:20150413" ; sc:description "An R package that allows prediction and quantification of alternative isoforms from exon expression levels in RNA-Seq data." ; sc:featureList edam:operation_0415, edam:operation_2499, edam:operation_3680, edam:operation_3800 ; sc:name "Solas" ; sc:softwareHelp ; sc:url "http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/" ; biotools:primaryContact "Hugues Richard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3572 ; sc:citation "pubmed:20875133" ; sc:description "User-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads." ; sc:featureList edam:operation_0564, edam:operation_3192, edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "SolexaQA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://solexaqa.sourceforge.net/" ; biotools:primaryContact "Murray P. Cox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080, edam:topic_3168 ; sc:description "Project to create a tool set to work with a Solexa genome sequencer. It includes multiple components including a LIMS system, pipeline and other tools to support end-users and researchers setting up a Solexa environment." ; sc:featureList edam:operation_2403 ; sc:name "SolexaTools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/SeqWare" ; biotools:primaryContact "SeqWare Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation ; sc:description "An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps | This site uses cookies to provide logins and other features. Please accept the use of cookies by clicking Accept | Welcome to the Solanaceae Genomics Network | Genomes and annotation of 13 diverse tomato accessions" ; sc:featureList edam:operation_0523, edam:operation_3216, edam:operation_3644 ; sc:name "solgenomics" ; sc:url "https://solgenomics.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0622, edam:topic_3299 ; sc:citation , "pmcid:PMC4269960", "pubmed:25495537" ; sc:description "A web-based tool for genomic selection." ; sc:featureList edam:operation_0323 ; sc:name "solGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cassavabase.org/solgs" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation , ; sc:description "SOLiD output to fastq." ; sc:featureList edam:operation_0335 ; sc:name "solid2fastq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation , ; sc:description "Creates a boxplot graph for the quality scores in the library." ; sc:featureList edam:operation_2428 ; sc:name "solid_qual_boxplot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation , ; sc:description "Creates quality statistics report for the given SOLiD quality score file." ; sc:featureList edam:operation_2428 ; sc:name "solid_qual_stats" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/galaxyproject/galaxy/tree/dev/tools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:description "Suite of software tools for data processing and analysis generated on the SOLiD® Analyzer." ; sc:featureList edam:operation_2403 ; sc:name "SOLID software tools" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://www.thermofisher.com/cz/en/home/technical-resources/software-downloads/solid-software.html" ; biotools:primaryContact "Thermo Fisher help desk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32592658" ; sc:description "Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning." ; sc:featureList edam:operation_3200, edam:operation_3800, edam:operation_3933 ; sc:license "MIT" ; sc:name "Solo" ; sc:url "https://github.com/calico/solo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26071141" ; sc:description "A somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples." ; sc:featureList edam:operation_3227 ; sc:name "SoloDel" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/solodel/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9537157", "pubmed:36202992" ; sc:description "SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SoloTE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bvaldebenitom/SoloTE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:34038123" ; sc:description "SolTranNet is a machine learning tool for fast aqueous solubility prediction." ; sc:featureList edam:operation_3216, edam:operation_3359, edam:operation_3938 ; sc:license "Apache-2.0" ; sc:name "SolTranNet" ; sc:url "https://github.com/gnina/SolTranNet" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_2275, edam:topic_3510 ; sc:citation "pubmed:27284085" ; sc:description "A method to identify stabilizing mutations that reduce the aggregation tendency of a protein." ; sc:featureList edam:operation_3197 ; sc:name "SolubiS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://solubis.switchlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0736, edam:topic_2229, edam:topic_3300 ; sc:citation , "pubmed:30341620" ; sc:description """Optimizing Protein Solubility by Minimal Point Mutations. Protein solubility is adapted to endogeneous protein abundance in the cell where protein folding is also assisted by multiple chaperones. During recombinant protein production, purification and storage proteins are frequently handled at concentrations that are several orders of magnitude above their physiological concentration, often resulting in protein aggregation. Here we describe SolubiS, a method allowing for (1) detection of aggregation prone linear segments within a protein sequence and (2) identification of mutations that abolish the aggregation propensity of these segments without affecting the thermodynamic stability of the protein""" ; sc:featureList edam:operation_0409, edam:operation_3436, edam:operation_3767 ; sc:name "Solubis 2" ; sc:url "https://solubis.switchlab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_3538 ; sc:citation , "pubmed:33098409" ; sc:description """A Server to Predict the pH-dependent Aggregation of Intrinsically Disordered Proteins. pH-dependent solubility predictor. SolupHred is the first phenomenological predictor that considers protein environment pH when calculating aggregation propensity of Intrinsically Disordered Proteins (IDPs).""" ; sc:featureList edam:operation_0400, edam:operation_0409, edam:operation_3436, edam:operation_3904 ; sc:name "SolupHred" ; sc:url "https://ppmclab.pythonanywhere.com/SolupHred" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1524 ; sc:name "Protein solubility" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0123, edam:topic_3474 ; sc:author , "Martin Marusiak" ; sc:contributor , , , "Tomas Martinek" ; sc:description """SoluProt is a web application for prediction of soluble protein expression in Escherichia coli. SoluProt is one of the latest additions to the family of solubility predictors based on machine learning. The training set is based on the TargetTrack database, which was carefully filtered to keep only targets expressed in Escherichia coli. The negative and positive samples were balanced and equalized for the protein lengths. The independent validation set is derived from the NESG dataset. The predictor is in its current version based on random forest regression model and employs 36 sequence-based features, e.g., amino acid content, predicted disorder, alpha-helix and beta-sheet content, sequence identity to PDB and several aggregated physico-chemical properties. SoluProt currently achieves accuracy 58.2%, higher than other comparable tools, and is a subject of further active development.""" ; sc:featureList edam:operation_0409 ; sc:isAccessibleForFree true ; sc:license "Proprietary" ; sc:name "SoluProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Brno University of Technology, Brno, Czech Republic", "ELIXIR-CZ", "International Centre for Clinical Research, Brno, Czech Republic", "Loschmidt Laboratories", "Masaryk University, Brno, Czech Republic" ; sc:softwareVersion "1.0" ; sc:url "https://loschmidt.chemi.muni.cz/soluprot/" ; biotools:primaryContact "SoluProt team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0219, edam:topic_3068, edam:topic_3474 ; sc:citation , "pmcid:PMC9678803", "pubmed:36420168" ; sc:description "A manually curated database of protein solubility changes upon mutations." ; sc:featureList edam:operation_0331, edam:operation_0409, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "SoluProtMutsupDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://loschmidt.chemi.muni.cz/soluprotmutdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC7534448", "pubmed:32759330" ; sc:description """Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum). Solyntus genome sequence consortium. Genome sequence of the diploid potato cultivar Solyntus. A growing collection of datasets, data-mining tools (under development) and genetic resources for the highly homozygous, relatively vigorous and self-compatible potato genotype Solyntus.""" ; sc:featureList edam:operation_0525, edam:operation_3196, edam:operation_3208, edam:operation_3216, edam:operation_3472 ; sc:name "Solyntus" ; sc:url "https://www.plantbreeding.wur.nl/Solyntus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3168 ; sc:description "A set of programs to exploit optical maps for assembly to finish a genome and move it from a draft stage (the result of sequencing and initial assembly) to a complete genome." ; sc:featureList edam:operation_0310, edam:operation_2429, edam:operation_3216 ; sc:name "SOMA" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2.0" ; sc:url "http://www.cbcb.umd.edu/finishing/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_2640, edam:topic_3170, edam:topic_3676 ; sc:citation ; sc:description """rapid relatedness estimation for cancer and germline studies using efficient genome sketches. fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs. somalier: extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Note that the somalier relate command runs extremely quickly (< 2 seconds for 600 samples and ~1 minute for 4,500 samples) so it's possible to add/remove samples or adjust a pedigree file and re-run iteratively""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:name "somalier" ; sc:url "http://github.com/brentp/somalier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0634, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC8728264", "pubmed:34634815" ; sc:description "A database of somatic mutations in normal human tissues." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "SomaMutDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vijglab.einsteinmed.org/SomaMutDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3170, edam:topic_3511 ; sc:citation "pubmed:22268718" ; sc:description "A web server for miRNA/tasiRNA analysis resources and tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs that potentially regulate genes of interest." ; sc:featureList edam:operation_3680 ; sc:name "SoMART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bakerlab.berkeley.edu/somart-webserver-mirna-sirna-analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640 ; sc:description "The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences." ; sc:featureList edam:operation_3227 ; sc:name "somatic-sniper" ; sc:url "https://github.com/genome/somatic-sniper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2269, edam:topic_3168 ; sc:citation , "pmcid:PMC4817139", "pubmed:26163694" ; sc:description "This package identifies mutational signatures of single nucleotide variants (SNVs)." ; sc:featureList edam:operation_3197 ; sc:license "MIT" ; sc:name "SomaticSignatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0654, edam:topic_3277, edam:topic_3474 ; sc:citation , "pubmed:35258549" ; sc:description "SomaticSiMu generates single and double base pair substitutions, and single base pair insertions and deletions of biologically representative mutation signature probabilities and combinations." ; sc:featureList edam:operation_0337, edam:operation_2995, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-4.0" ; sc:name "SomaticSiMu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HillLab/SomaticSiMu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC7936459", "pubmed:33676403" ; sc:description "SomatoSim is a tool that simulates single nucleotide variants at any variant allele fraction and depth of coverage. SomatoSim takes an analysis ready BAM file as input and SomatoSim outputs a BAM file containing simulated variants. Use SomatoSim to evaluate variant calling tools, algorithms, and pipelines." ; sc:featureList edam:operation_3196, edam:operation_3198, edam:operation_3227 ; sc:name "SomatoSim" ; sc:url "https://github.com/BieseckerLab/SomatoSim" ; biotools:primaryContact "Celine S. Hong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:citation ; sc:description "Motif-finder that is based on the Self-Organizing Map neural network algorithm." ; sc:featureList edam:operation_0238, edam:operation_2409, edam:operation_2423, edam:operation_3432 ; sc:name "SOMBRERO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://bioinf.nuigalway.ie/sombrero/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3308 ; sc:citation ; sc:description """SOMDE: A scalable method for identifying spa-tially variable genes with self-organizing map. A scalable method for identifying spatially variable genes with self-organizing map. Algorithm for finding gene spatial pattern based on Gaussian process accelerated by SOM.""" ; sc:featureList edam:operation_0313, edam:operation_2429, edam:operation_3463 ; sc:license "MIT" ; sc:name "SOMDE" ; sc:url "https://pypi.org/project/somde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1775 ; sc:author "Peter Hoenigschmid" ; sc:citation ; sc:description "Protein DNA/RNA binding predictor." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SomeNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "RostLab" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://github.com/Rostlab/someNA" ; biotools:primaryContact "RostLab" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2538 ; sc:name "Mutation identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1246 ; sc:name "Sequence cluster (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "Detection of cancer genes based on somatic mutation patterns of inactivation and clustering." ; sc:featureList edam:operation_0484 ; sc:name "SomInaClust" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.intec.ugent.be/sominaclust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3295, edam:topic_3474 ; sc:citation , "pubmed:32413127" ; sc:description """a second-order Markov model for DNA N4-methylcytosine site prediction in six species. With Cluvio you can run SQL queries against your database and visualize the results as beautiful interactive dashboards that can easily be shared with your team. Cluvio supports all major SQL databases like Postgres, MySQL, Redshift, Athena, BigQuery, Snowflake, Presto, Microsoft SQL Server, Oracle, Google Cloud Platform and Exasol. A web server for Identifying Family of Efflux Proteins in Transporters using Convolutional Neural Networks Model. We proposed a new identification method nemed SOMM4mC based on a Markov model which makes use of the transition probability between adjacent nucleotides to identify 4mC site. DNA N4-methylcytosine (4mC) modification occurs mainly in prokaryotic DNA.""" ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_3927 ; sc:name "SOMM4mC" ; sc:url "http://www.insect-genome.com/SOMM4mC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0820, edam:topic_2814, edam:topic_3474 ; sc:citation "pubmed:21695537" ; sc:description "A novel model for prediction of TMH that features by minimal parameter assumptions requirement and high computational efficiency. In this model, a self-organizing map (SOM) is used to adaptively learn the helices distribution knowledge hidden in the training data, and then a probabilistic neural network (PNN) is adopted to predict TMH segments based on the knowledge learned by SOM." ; sc:featureList edam:operation_0269 ; sc:name "SOMPNN" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/SOMPNN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0820, edam:topic_2814 ; sc:citation "pubmed:21742571" ; sc:description "A novel TMH predictor with excellent interpretability while possessing high prediction accuracy." ; sc:featureList edam:operation_0269 ; sc:name "SOMRuler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/SOMRuler/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:26589277" ; sc:description "A computational method for detecting somatic variants using high throughput sequencing data from unpaired tissue samples." ; sc:featureList edam:operation_3227 ; sc:name "SomVarIUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kylessmith/SomVarIUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3500, edam:topic_3520 ; sc:citation ; sc:description "SongExplorer is a deep learning workflow for discovery and segmentation of animal acoustic communication signals." ; sc:featureList edam:operation_0337, edam:operation_3891, edam:operation_3935 ; sc:license "BSD-3-Clause" ; sc:name "SongExplorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JaneliaSciComp/SongExplorer" ; biotools:primaryContact "David L. Stern" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3174, edam:topic_3673 ; sc:description "Scripts for parsing Mykrobe predict results for Shigella sonnei." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sonneityping" ; sc:softwareVersion "20210201" ; sc:url "https://github.com/katholt/sonneityping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3412, edam:topic_3452, edam:topic_3474, edam:topic_3794, edam:topic_3954 ; sc:citation , "pmcid:PMC7266063", "pubmed:32320551" ; sc:description """Internet-based digital video atlas of sonographic findings for clinical and educational purposes. Metastasis of Neuroendocrine Tumor (NET). Cholecystitis, Stones in Gallbladder (Ch... Gallbladder Tumor, Stone in Gallbladder ... ||| CORRECT NAME OF TOOL COULD ALSO BE 'portal', 'video'""" ; sc:featureList edam:operation_3283 ; sc:name "sono" ; sc:url "http://www.sono.gallery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3384, edam:topic_3393 ; sc:citation , "pubmed:31487752" ; sc:description "Web-Based GPU-Accelerated Application for Multiplanar Reconstructions from Conventional 2D Ultrasound | ImagingAnatomy.com is an interactive atlas of normal imaging anatomy for the radiologist as well as a learning device for health professionals in general studying anatomy for any reason | Sonoviewer is an open access web application developed as an extension of the Mulrecon web-based viewer" ; sc:featureList edam:operation_0337, edam:operation_1812 ; sc:name "sonoviewer" ; sc:url "http://www.castlemountain.dk/atlas/index.php?page=mulrecon&mulreconPage=sonoviewer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0659, edam:topic_3168, edam:topic_3397, edam:topic_3697 ; sc:citation , "pmcid:PMC8325813", "pubmed:34332568" ; sc:description "Data analysis workflow for the detection of canine vector-borne pathogens using 16 S rRNA Next-Generation Sequencing." ; sc:featureList edam:operation_0450, edam:operation_3192, edam:operation_3435, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eltonjrv/microbiome.westernu/tree/SOP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC9590096", "pubmed:36265470" ; sc:description "Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework." ; sc:featureList edam:operation_0545, edam:operation_0547, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SOPHIE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/compbel/SOPHIE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC2909219", "pubmed:20576136" ; sc:description "Assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD." ; sc:featureList edam:operation_0310 ; sc:name "SOPRA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.4.6" ; sc:url "http://www.physics.rutgers.edu/~anirvans/SOPRA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_2830, edam:topic_3308 ; sc:citation , "pmcid:PMC10768140", "pubmed:37811897" ; sc:description "SORC : Spatial omics resource of Cancer covering current available spatial transcriptomics datasets for 17 types of cancer, comprising 722,899 spots across 269 slices." ; sc:featureList edam:operation_0314, edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "SORC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/SORC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3053, edam:topic_3489, edam:topic_3810 ; sc:citation , "pmcid:PMC8752523", "pubmed:35015132" ; sc:description "A web-based portal for sorghum genetic information and community advancement." ; sc:featureList edam:operation_0525, edam:operation_2421, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:name "SorghumBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sorghumbase.org/guides" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0622, edam:topic_3293, edam:topic_3500 ; sc:citation "pubmed:20538651" ; sc:description "SoRT2 is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocation, and infer phylogenetic trees of genomes. Input is 2 genomes." ; sc:featureList edam:operation_0323, edam:operation_0546, edam:operation_0555, edam:operation_0557 ; sc:name "SoRT2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genome.cs.nthu.edu.tw/SORT2/" ; biotools:primaryContact "Dr. Chin Lung Lu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3071 ; sc:citation , ; sc:description "Sorts a gff file." ; sc:featureList edam:operation_3802 ; sc:name "sortgff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3941 ; sc:citation ; sc:description "Sequence analysis tool for filtering, mapping and OTU-picking NGS reads." ; sc:featureList edam:operation_0258, edam:operation_0346, edam:operation_2451 ; sc:name "SortMeRNA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bioinfo.cristal.univ-lille.fr/RNA/sortmerna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_0798, edam:topic_3301, edam:topic_3934 ; sc:citation , "pubmed:34349283" ; sc:description "SorTn-seq uses fluorescent reporters, saturation transposon mutagenesis and fluorescence activated cell sorting (FACS) to isolate bacterial mutants with altered gene expression. Sorted cell pools are deep sequenced to identify transposon insertion sites and the enrichment of mutants in high or low fluorescence bins is used to identify putative regulators of gene expression." ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3211, edam:operation_3802, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SorTn-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JacksonLab/SorTn-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0634, edam:topic_0821, edam:topic_3474 ; sc:citation , "pmcid:PMC8703055", "pubmed:34976319" ; sc:description "The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0310 ; sc:isAccessibleForFree true ; sc:name "SortPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://procarb.org/sortpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0736, edam:topic_3168, edam:topic_3325 ; sc:citation , "pmcid:PMC6001062", "pubmed:29898714" ; sc:description """Calculating the statistical significance of rare variants causal for Mendelian and complex disorders.

Background< h4>With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question.

Methods< h4>We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3675, edam:operation_3791 ; sc:name "SORVA" ; sc:url "https://sorva.genome.ucla.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3315, edam:topic_3474 ; sc:citation ; sc:description """Designing, Tuning and Statistically Benchmarking Optimisation Algorithms. The Stochastic Optimisation Software (SOS) is a research-oriented software platform for Metaheuristic Optimisation (Stochastic Optimisation). SOS is a research oriented software platform for Metaheuristic Optimisation (Stochastic Optimisation).""" ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:name "SOS" ; sc:url "https://sites.google.com/site/facaraff/research/sos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3372 ; sc:citation , "pmcid:PMC6198852", "pubmed:29790910" ; sc:description "SoS Notebook is a Jupyter kernel that allows the use of multiple kernels in one Jupyter notebook. It also serves as the IDE for the SoS Workflow engine that allows the development and execution of workflows from Jupyter notebooks. SoS Notebook improving the readability and reproducibility of complex bioinformatic workflows by allowing them to be represented and executed from a Jupyter notebook interface." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SoS Notebook" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.24.1" ; sc:url "https://github.com/vatlab/sos-notebook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_0820, edam:topic_3542 ; sc:citation "pubmed:9632836" ; sc:description "SOSUI is a free online tool that predicts a part of the secondary structure of proteins from a given amino acid sequence (AAS). 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SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads." ; sc:featureList edam:operation_0525 ; sc:license "GPL-2.0" ; sc:name "SPAdes" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cab.spbu.ru/software/spades/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3053, edam:topic_3056, edam:topic_3168 ; sc:citation "pubmed:24215429" ; sc:description "A population genetics software computing several summary statistics from populations or groups of populations, and implementing two clustering algorithms to study the genetic structure of populations. It has been specifically developed for the analysis of DNA sequences. 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Predicting whole-transcriptome expression of spatial transcriptomics data through integration with scRNA-seq data. Python implementation can be found in the 'SpaGE' folder. The SpaGE function takes as input i) two single cell datasets, spatial transcriptomics and scRNA-seq, ii) the number of principal vectors (PVs), and iii) the set of unmeasured genes in the spatial data for which predictions are obtained from the scRNA-seq (optional). The function returns back the predicted expression for these unmeasured genes across all spatial cells.""" ; sc:featureList edam:operation_2454, edam:operation_3463, edam:operation_3891 ; sc:license "MIT" ; sc:name "SpaGE" ; sc:url "https://github.com/tabdelaal/SpaGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3308, edam:topic_3382, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:32976679" ; sc:description """Unsupervised representation of localized spatial gene expression signatures. This repository contains a collection of python notebooks for reproducing analyses and results from the original publication [1]. The notebooks folder contains code for:. Generate spatial gene expression network from in situ transcriptomic data and train an unsupervised graph representation model for producing a node embedding (spage2vec_*.ipynb).""" ; sc:featureList edam:operation_2495, edam:operation_3432, edam:operation_3501 ; sc:license "Apache-2.0" ; sc:name "spage2vec" ; sc:url "https://github.com/wahlby-lab/spage2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3305, edam:topic_3325, edam:topic_3676 ; sc:citation , , "pmcid:PMC6121381", "pubmed:30110963" ; sc:description "The Spanish Undiagnosed Rare Diseases Program." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3454 ; sc:name "SpainUDP" ; sc:url "http://spainudp.isciii.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0607, edam:topic_3071, edam:topic_3077 ; sc:citation , "pmcid:PMC5299738", "pubmed:28178937" ; sc:description "A command-line SPARQL client supporting query generation for distributed RDF databases." ; sc:featureList edam:operation_0224 ; sc:license "MIT" ; sc:name "SPANG" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://spang.dbcls.jp/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Small RNA-seq Portal for Analysis of sequencing expeRiments. interactive processing, analysis, annotation and visualization of small RNA sequencing data. Supports sequencing data generated from various experimental protocols, including smRNA-seq, short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq." ; sc:featureList edam:operation_0314, edam:operation_3680, edam:operation_3792 ; sc:name "SPAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.lisanwanglab.org/SPAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3303, edam:topic_3474 ; sc:citation ; sc:description "An interactive tool to visualize the impact of the SPARC program." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SPARClink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fairdataihub.org/sparclink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0154, edam:topic_3512 ; sc:citation "pubmed:23748952" ; sc:description "Webserver for analysis of analyze structured and unstructured regions in coding RNA sequences. It samples random sequences preserving both the amino acid sequence and the dinucleotide statistics that enable us to calculate accurate z-score values." ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0314, edam:operation_0436, edam:operation_2439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "SPARCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cs.mcgill.ca/sparcs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3343 ; sc:citation ; sc:description "Intelligent virtual screening with confidence based on conformal prediction." ; sc:featureList edam:operation_0478 ; sc:name "spark-cpvs" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/laeeq80/spark-cpvs" ; biotools:primaryContact "Laeeq Ahmed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3512 ; sc:citation ; sc:description """A Publication-quality NGS Visualization Tool. SparK - Publication quality NGS data plotting (Version 2.4.1). SparK will exctract gene and transcript information from column 3 of the gff file.""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "SparK" ; sc:url "https://github.com/harbourlab/SparK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2258, edam:topic_3336, edam:topic_3343 ; sc:citation ; sc:description "Spark-based library for setting up massively parallel Structure-Based Virtual Screening (SBVS) pipelines in Spark." ; sc:featureList edam:operation_0478 ; sc:license "Apache-2.0" ; sc:name "Spark-VS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mcapuccini/spark-vs" ; biotools:primaryContact "Marco Capuccini" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8218388", "pubmed:34154649" ; sc:description "SPARK-X is a plug-in tool for SPARK that provides a non-parametric modeling which enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies" ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPARK-X" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/xzhoulab/SPARK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3372 ; sc:citation , "pmcid:PMC9639292", "pubmed:36344928" ; sc:description "Speeding up alignment-based DNA error correction tools." ; sc:featureList edam:operation_3432, edam:operation_3454, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SparkEC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UDC-GAC/SparkEC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_2815 ; sc:citation , "pmcid:PMC9310413", "pubmed:35879669" ; sc:description "Spark based genome compression for large collections of genomes." ; sc:featureList edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SparkGC" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/haichangyao/SparkGC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3173, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "A scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants." ; sc:featureList edam:operation_3211, edam:operation_3226, edam:operation_3799 ; sc:name "SparkINFERNO" ; sc:url "https://bitbucket.org/wanglab-upenn/SparkINFERNO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC7016739", "pubmed:31947774" ; sc:description """Enabling Big Data Scalability for the GATK RNA-seq Pipeline with Apache Spark. The rapid proliferation of low-cost RNA-seq data has resulted in a growing interest in RNA analysis techniques for various applications, ranging from identifying genotype-phenotype relationships to validating discoveries of other analysis results. However, many practical applications in this field are limited by the available computational resources and associated long computing time needed to perform the analysis. GATK has a popular best practices pipeline specifically designed for variant calling RNA-seq analysis. Some tools in this pipeline are not optimized to scale the analysis to multiple processors or compute nodes efficiently, thereby limiting their ability to process large datasets. In this paper, we present SparkRA, an Apache Spark based pipeline to efficiently scale up the GATK RNA-seq variant calling pipeline on multiple cores in one node or in a large cluster""" ; sc:featureList edam:operation_3227, edam:operation_3432, edam:operation_3680 ; sc:name "SparkRA" ; sc:url "https://github.com/SaiyiW/SparkRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3070, edam:topic_3071 ; sc:citation "pubmed:25127889" ; sc:description "A web-based platform for the visual creation and execution of biological semantic queries." ; sc:featureList edam:operation_0224, edam:operation_0337 ; sc:name "SPARQLGraph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sparqlgraph.i-med.ac.at/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3305 ; sc:citation , "pmcid:PMC7977178", "pubmed:33736677" ; sc:description "sparrpowR is a flexible R package to estimate statistical power to identify spatial clustering of two groups and its application. The sparrpowR package is a suite of R functions to calculate the statistical power to detect clusters using the kernel-based spatial relative risk function that is estimated using the sparr package." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_3432 ; sc:license "Apache-2.0" ; sc:name "sparrpowR" ; sc:url "https://github.com/machiela-lab/sparrpowR" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929, edam:format_2200 ; sc:name "RNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_3466 ; sc:name "RNA structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_1929, edam:format_1982, edam:format_3508 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097 ; sc:author , "Rolf Backofen", "Sebastian Will" ; sc:citation , "pmcid:PMC4514930", "pubmed:25838465" ; sc:contributor "Sebastian Will" ; sc:description "Very efficient structure-based alignment of RNAs." ; sc:featureList edam:operation_0294 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPARSE" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University Freiburg", "rnateam" ; sc:softwareHelp ; sc:softwareVersion "1.8.9" ; sc:url "http://www.bioinf.uni-freiburg.de/Software/SPARSE" ; biotools:primaryContact , "Sebastian Will" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3697 ; sc:description "Sparse Data Observations for Simulating Synthetic Abundance. Provides a model based Bayesian method to characterize and simulate microbiome data. This model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure." ; sc:featureList edam:operation_2238, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sparseDOSSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sparseDOSSA.html" ; biotools:primaryContact "Boyu Ren", "Emma Schwager", "George Weingart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3174, edam:topic_3305, edam:topic_3697 ; sc:citation ; sc:description "SparseDOSSA 2 is an upcoming software for the simulation of null and metadata-associated microbial abundance profiles. It has functionalities for a) fitting to user-provided microbial template datasets, b) synthesizing microbial abundances similar to either user-provided or pre-trained templates, and c) additionally simulating associations with sample metadata or among microbial features." ; sc:featureList edam:operation_3200, edam:operation_3664, edam:operation_3946 ; sc:name "SparseDOSSA 2" ; sc:softwareHelp ; sc:url "http://huttenhower.sph.harvard.edu/sparsedossa2" ; biotools:primaryContact "Curtis Huttenhower" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation ; sc:description "A Bayesian model to identify alternatively splicing isoforms." ; sc:featureList edam:operation_2499 ; sc:name "SparseIso" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/henryxushi/SparseIso" ; biotools:primaryContact "Jianhua Xuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3337, edam:topic_3517 ; sc:citation ; sc:description "An efficient genome-wide fine-mapping method integrating summary statistics and functional annotations." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3557, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SparsePro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhwm/SparsePro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3063 ; sc:description "Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient’s tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient." ; sc:featureList edam:operation_3202 ; sc:license "Other" ; sc:name "SparseSignatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SparseSignatures.html" ; biotools:primaryContact "Daniele Ramazzotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC4743240", "pubmed:26847232", "pubmed:6847232" ; sc:description "Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis. Analyze single-end Illumina RNA-seq data combining several tools: Trimmomatic (read trimming/adapter removal), FastQC (read quality analysis), Bowtie (mapping reads to the reference genome), HTSeq (transcript/gene feature abundance counting), and edgeR (differential gene expression analysis)." ; sc:featureList edam:operation_2495, edam:operation_3192, edam:operation_3223 ; sc:license "CC-BY-4.0" ; sc:name "SPARTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1.0" ; sc:url "http://sparta.readthedocs.io/en/latest/" ; biotools:primaryContact "Benjamin K. Johnson", "Matthew B. Scholz", "Robert B. Abramovitch", "Tracy K. Teal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3512 ; sc:citation ; sc:description "Simulate sequences based on indel parameters inferred using an approximate Bayesian computation algorithm." ; sc:featureList edam:operation_0452, edam:operation_0547, edam:operation_3478 ; sc:license "GPL-2.0" ; sc:name "SpartaABC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://spartaabc.tau.ac.il/webserver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation , "pmcid:PMC3779260" ; sc:description "Simulation Parameter Analysis R Toolkit ApplicatioN. Statistical techniques specifically designed to understand integration of computer simulation with wet-lab research and provide novel biological insight." ; sc:featureList edam:operation_2426, edam:operation_3435, edam:operation_3501 ; sc:license "GPL-2.0" ; sc:name "SPARTAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.0" ; sc:url "https://www.york.ac.uk/computational-immunology/software/spartan/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0204, edam:topic_0749, edam:topic_3308, edam:topic_3934 ; sc:citation , "pmcid:PMC8464045", "pubmed:34500467" ; sc:description "SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network) provides a mechanistically inspired approach for integrating cell-specific transcriptomic and proteomic data with regulatory genomics resources, representing a significant advance in the modeling of cell-specific signaling and gene regulatory programs. The cell surface phenotype is well-known to immunologists through flow cytometry but signaling downstream of cell surface receptors/co-receptors drives transcriptional and chromatin state changes. It is important to connect the “cell surface phenotype” to downstream transcriptional programs and resulting transcriptomic phenotypes. SPaRTAN models this flow of information with single cell resolution." ; sc:featureList edam:operation_0314, edam:operation_0416, edam:operation_1781 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPaRTAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/osmanbeyoglulab/SPaRTAN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2269, edam:topic_3308, edam:topic_3930 ; sc:citation , "pmcid:PMC10232864", "pubmed:37274781" ; sc:description "Bayesian method for the quantification and characterization of cell type interactions in spatial pathology data." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SPARTIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nateosher.github.io/SPARTIN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36243975" ; sc:description "Spatial transcriptomics annotation at single-cell resolution." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_3501, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "SPASCER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ccsm.uth.edu/SPASCER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:26615214" ; sc:description "An R package for spatial continuous assignment from genetic data." ; sc:featureList edam:operation_2403 ; sc:name "SPASIBA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www2.imm.dtu.dk/~gigu/Spasiba/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """SPATA Package for spatial gene expression analysis. Inferring spatially transient gene expression pattern from spatial transcriptomic studies. A Toolbox for Spatial Gene Expression Analysis. Visualize gene expression, pathway enrichment and customized features within a spatial context to highlight areas of interest. Draw spatial trajectories and model gene epression of pathway activtiy within a directional context. Leverage monocle3-pseudotime within SPATA in order to analyse the transcriptional dynamics of your samples in a temporal and a spatial context at once. 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SPDH ├─conf #configuration file ├─datasets #All data │ ├─train_sequence #The sequence files used for the training set │ └─test_sequence #The sequence files used for the test set ├─feature #AAindex feature ├─model #model data file ├─outwhd #output file └─src #code folder.""" ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0420, edam:operation_0477 ; sc:name "SPDH" ; sc:url "https://github.com/xialab-ahu/SPDH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0130, edam:topic_0209, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC9436118", "pubmed:35994486" ; sc:description "Sampling protein ensembles and conformational heterogeneity with Alphafold2." ; sc:featureList edam:operation_0474, edam:operation_3891, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SPEACH_AF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RSvan/SPEACH_AF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_0593, edam:topic_0749, edam:topic_3538 ; sc:citation , "pmcid:PMC10135740", "pubmed:37106781" ; sc:description "Python package for the characterisation of local chemical environment dynamics for Molecular Dynamics trajectories of proteins and other biomolecules." ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "SPEADI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fzj-jsc.github.io/speadi/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:encodingFormat edam:format_3245 ; sc:name "NMR spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3617 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3172, edam:topic_3360 ; sc:citation ; sc:description "A framework for analyzing automatically raw 1D NMR spectra data. It is also compatible with other NMR frameworks or complementary LC-MS workflows." ; sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "speaq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "2.0" ; sc:url "https://cran.r-project.org/web/packages/speaq/index.html" ; biotools:primaryContact "Charlie Beirnaert" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3068, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "SPEAQeasy is a Scalable RNA-seq Pipeline for Expression And Quantification based on the RNAseq-pipeline. 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Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data. Analysis and benchmarking of mass spectra similarity measures using gnps data set.""" ; sc:featureList edam:operation_2421, edam:operation_3801, edam:operation_3803, edam:operation_3860 ; sc:license "Apache-2.0" ; sc:name "Spec2Vec" ; sc:url "https://github.com/iomega/spec2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:16048906" ; sc:description "Aligns multiple LC-MS datasets and much more." ; sc:featureList edam:operation_3628 ; sc:name "SpecArray" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/SpecArray.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3071, edam:topic_3474 ; sc:citation , "pubmed:35930941" ; sc:description "A relational database for archiving biomolecular NMR spectral data." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpecDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.rpi.edu/RPIBioinformatics/SpecDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3173, edam:topic_3574, edam:topic_3673 ; sc:citation ; sc:description "SpecHap is an ultra fast phasing algorithm based on spectral graph analysis. SpecHap currently support general WGS sequencing, Hi-C, 10X linked-reads, PacBio SMRT and Oxford Nanopore ." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SpecHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/deepomicslab/SpecHap" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1868 ; sc:name "Taxon" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3174 ; sc:citation , "pubmed:23892899" ; sc:description "SpecI is a species identification tool using genomic sequences to delineate prokaryotic species. It facilitates fast, accurate and automated taxonomic assignments of newly sequenced genomes based on comparisons of 40 universal, single-copy phylogenetic marker genes extracted from a comprehensive database of sequenced prokaryotic genomes." ; sc:featureList edam:operation_3432, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpecI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "European Molecular Biology Laboratory (EMBL)", "HD-HuB" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://vm-lux.embl.de/~mende/specI/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0601, edam:topic_2814, edam:topic_3520 ; sc:citation "pubmed:24437954" ; sc:description "A novel approach to enable the expedited development of new algorithms for any types of PTM (post-translational modifications) peptide fragmentation." ; sc:featureList edam:operation_3645 ; sc:name "Specialize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.ucsd.edu/software-tools/specialize/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:21429114" ; sc:description "This plugin for the Geneious bioinformatics software is an exploratory tool that allows users to assess putative species in phylogenetic trees." ; sc:featureList edam:operation_0324 ; sc:name "Species Delimitation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.fos.auckland.ac.nz/~howardross/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_0769, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC7034379", "pubmed:32110486" ; sc:description """a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species. The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.""" ; sc:featureList edam:operation_0308, edam:operation_0525, edam:operation_3180, edam:operation_3216, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SpeciesPrimer" ; sc:url "http://primer3.ut.ee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0623 ; sc:citation ; sc:description "SpeciesRax is a tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss." ; sc:featureList edam:operation_0546, edam:operation_0553, edam:operation_3478, edam:operation_3947 ; sc:license "AGPL-3.0" ; sc:name "SpeciesRax" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/BenoitMorel/GeneRax" ; biotools:primaryContact "Benoit Morel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC10290233", "pubmed:37359727" ; sc:description "Unsupervised learning approach for cell surface receptor abundance estimation for single-cell RNA-sequencing data." ; sc:featureList edam:operation_0314, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SPECK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://CRAN.R-project.org/package=SPECK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "The speckle package currently contains functions to analyse differences in cell type proportions in single cell RNA-seq data, and to classify cells as male or female. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions." ; sc:featureList edam:operation_0314, edam:operation_3659, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "speckle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Oshlack/speckle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3444, edam:topic_3954 ; sc:citation ; sc:description "This project implements various filters for Speckle Noise Reduction in Ultrasound Images." ; sc:featureList edam:operation_3443, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "Speckle Noise Reduction in Ultrasound Images" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/41240-speckle-noise-reduction-in-ultrasound-images" ; biotools:primaryContact "Ashish Meshram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:25712692" ; sc:description "Provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software." ; sc:featureList edam:operation_3214, edam:operation_3429 ; sc:license "GPL-3.0" ; sc:name "specL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/specL.html" ; biotools:primaryContact "Christian Panse", "Witold E. Wolski" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2979 ; sc:name "Peptide property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "A web-based application to cluster lists of peptide peak masses, typically extracted from protein mass spectra." ; sc:featureList edam:operation_3432 ; sc:name "SPECLUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://co.bmc.lu.se/speclust/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC8555789", "pubmed:34714871" ; sc:description "Deep cross-modal similarity network for mass spectrometry data based peptide deductions." ; sc:featureList edam:operation_2421, edam:operation_3631, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SpeCollate" ; sc:operatingSystem "Linux" ; sc:url "https://deepspecs.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation , "pmcid:PMC3334612" ; sc:description "This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "SpeCond" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.28.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SpeCond.html" ; biotools:primaryContact "Florence Cavalli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3170, edam:topic_3172, edam:topic_3360 ; sc:citation , , "pmcid:PMC7018003", "pmcid:PMC7026976", "pubmed:32053611", "pubmed:32066370" ; sc:description """a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups. Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models. To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Superposition-based Protein Embedded CA SC score. A non-parameteric method to identify tissue-specific molecular features with unequal sample group sizes.""" ; sc:featureList edam:operation_0479, edam:operation_0480, edam:operation_0481 ; sc:name "SPECS" ; sc:url "http://specs.cmgg.be" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3382, edam:topic_3421 ; sc:citation ; sc:description """cross spectral power-based segmentation of neurons and neurites in chronic calcium imaging datasets. This Github contains 'SpecSeg', an open source calcium imaging processing toolbox to detect regions of interest (ROIs) in calcium imaging datasets. ROI segmentation is based on cross-spectral power over a range of frequencies and has been tested and optimized for a variety of neuronal compartments (cell bodies, dendrites, axons) and (imaging) techniques (chronic glass windows, GRIN lenses, 1P, 2P). The SpecSeg toolbox contains user-friendly graphical interfaces to detect, adjust ROIs and visualize their activity traces. This pipeline includes code adapted from normcorre (Pnevmatikakis & Giovannucci 2016), to apply motion correction to sbx files. To be able to execute the motion correction, download the code from NoRMCorre and add the code into the matlab path below SpectralSegmentation.""" ; sc:featureList edam:operation_3214, edam:operation_3359, edam:operation_3450 ; sc:name "SpecSeg" ; sc:url "https://github.com/Leveltlab/SpectralSegmentation" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7655596", "pubmed:32910939" ; sc:description """An interactive resource for ocular single-cell RNA sequencing data analysis. University of Iowa: Institute for Vision Research. Spectacle and cellcuratoR were developed by an interdisciplinary team within the Institute for Vision Research at the University of Iowa. The Institute of Vision Research is deeply dedicated to treating and curing visual diseases. More information can be found at our website ivr.uiowa.edu.""" ; sc:featureList edam:operation_0571 ; sc:name "Spectacle" ; sc:url "http://OcularGeneExpression.org/singlecell" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:name "Spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_3047 ; sc:citation ; sc:description "An algorithm for the targeted analysis of data-independent acquisition (DIA) mass spectrometry proteomics experiments." ; sc:featureList edam:operation_3214 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Specter" ; sc:softwareHelp ; sc:url "https://github.com/rpeckner-broad/Specter" ; biotools:primaryContact "Ryan Peckner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """Specter: A novel tool for clustering large-scale single cell RNA-seq and multi-modal data. Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data. Specter is a novel computational method for clustering large-scale single cell RNA-seq data. In addition, Specter can combine the data from different measurements such as RNA measurements and the antibody-derived tags (collected on the same set of cells). Specter runs in linear time with respect to number of cells, thus it is very suitable for analyzing very big single cell RNA-seq data. On a data set comprising 2 million cells from mouse embryos, Specter requires only 26 minutes to compute the clusters.""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3891 ; sc:name "Specter" ; sc:url "https://github.com/canzarlab/Specter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3934 ; sc:citation ; sc:description "Spectracular is a computational tool to support selection of fluorochromes for multicolor flow cytometry panels. Specifically, Spectracular finds the optimal (or near-optimal) combination of fluorochromes from a user-defined pool of fluorochromes to choose from." ; sc:name "Spectracular" ; sc:url "https://biosurf.shinyapps.io/spectracular/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_3940 ; sc:citation , "pmcid:PMC7372752", "pubmed:32689928" ; sc:description """an R package for defining a hierarchy of topologically associated domains using spectral clustering. SpectralTAD: Hierarchical TAD detection using spectral clustering. SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.""" ; sc:featureList edam:operation_2436, edam:operation_3359, edam:operation_3432 ; sc:license "MIT" ; sc:name "SpectralTAD" ; sc:url "http://bioconductor.org/packages/SpectralTAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:26556388" ; sc:description "A program for computing the transition density function (TDF) of the diffusion approximation of the Wright-Fisher process with general diploid selection and recurrent mutation." ; sc:featureList edam:operation_0367 ; sc:name "SpectralTDF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/spectraltdf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Matches peptide MS/MS spectra with library spectra." ; sc:featureList edam:operation_3801 ; sc:name "SpectraST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.peptideatlas.org/spectrast/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3512 ; sc:citation , "pmcid:PMC5123373", "pubmed:27884106" ; sc:description "Model the overall tri­nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Examine the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript relative to an idealized reference signal without the matched requirement of mRNA-Seq." ; sc:featureList edam:operation_0314, edam:operation_2990, edam:operation_3501 ; sc:name "SPECtre" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/mills-lab/spectre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data. ||| NAME (Spectre) SIMILAR TO (PUB. DIFFERENT) bio.tools/spectre-phylogeny (SPECTRE), bio.tools/spectre (SPECtre)""" ; sc:featureList edam:operation_1812, edam:operation_2939, edam:operation_3432, edam:operation_3891, edam:operation_3935 ; sc:license "MIT" ; sc:name "Spectre" ; sc:url "https://github.com/immunedynamics/spectre" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3293, edam:topic_3299 ; sc:citation ; sc:description "Readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks." ; sc:featureList edam:operation_0324 ; sc:license "GPL-3.0" ; sc:name "SPECTRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/maplesond/SPECTRE" ; biotools:primaryContact "Sarah Bastkowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3301, edam:topic_3321 ; sc:citation "pubmed:26629978" ; sc:description "A tool for top-down protein identification using unannotated bacterial genome." ; sc:featureList edam:operation_3767 ; sc:name "SpectroGene" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/fenderglass/SpectroGene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:31501851" ; sc:description "Fast density-aware spectral clustering for single and multi-omic data | Fast Adaptive Spectral Clustering for Single and Multi-View Data | A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K" ; sc:featureList edam:operation_3432, edam:operation_3694, edam:operation_3860 ; sc:license "AGPL-3.0" ; sc:name "Spectrum" ; sc:url "https://cran.r-project.org/web/packages/Spectrum/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3467, edam:format_3579, edam:format_3591, edam:format_3592, edam:format_3603 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3382, edam:topic_3520 ; sc:description "Tool for viewing and annotating MS/MS spectra." ; sc:featureList edam:operation_3694 ; sc:name "Spectrum Look" ; sc:operatingSystem "Linux" ; sc:url "http://omics.pnl.gov/software/spectrumlook" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A pipeline for differential proteomics in unsequenced species." ; sc:featureList edam:operation_2479 ; sc:name "Spectrum similarity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Ghent University", "ugent.be" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://github.com/compomics/spectrum_similarity" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3520 ; sc:citation ; sc:description "A Python package for mass spectrometry data processing and visualization | Python package for efficient MS/MS spectrum processing and visualization | spectrum_utils is a Python package for efficient MS/MS spectrum processing and visualization" ; sc:featureList edam:operation_3646, edam:operation_3694, edam:operation_3860 ; sc:license "Apache-2.0" ; sc:name "spectrum_utils" ; sc:url "https://github.com/bittremieux/spectrum_utils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pmcid:PMC9810332", "pubmed:36525361" ; sc:description "Heritability enrichment in context-specific regulatory networks improves phenotype-relevant tissue identification." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_2940, edam:operation_3463, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpecVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AMSSwanglab/SpecVar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_0637, edam:topic_0780, edam:topic_3500 ; sc:citation , "pubmed:35094502" ; sc:description "An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPEDE-sampler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/clarkevansteenderen/spede_sampler_R" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0176, edam:topic_0602, edam:topic_3407 ; sc:citation "pubmed:23742908" ; sc:description "SPEDRE (Systematic Parameter Estimation in Data-Rich Environments) is a web server for estimating rate parameters of cell signalling dynamics in data-rich environments. SPEDRE estimates reaction rates for biochemical networks, taking as input the connectivity of the network and the concentrations of the molecular species at discrete time points." ; sc:featureList edam:operation_2497, edam:operation_3221, edam:operation_3439, edam:operation_3562, edam:operation_3660 ; sc:name "SPEDRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://LTKLab.org/SPEDRE" ; biotools:primaryContact "SPEDRE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:20494976" ; sc:description "Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes." ; sc:featureList edam:operation_0314, edam:operation_0533, edam:operation_2436, edam:operation_3223 ; sc:name "SPEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://speed.sys-bio.net/" ; biotools:primaryContact "Nils Blüthgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0634, edam:topic_2229, edam:topic_3299, edam:topic_3308 ; sc:citation , "pubmed:36305818" ; sc:description "Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "SPEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://speedatlas.net" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0955 ; sc:encodingFormat edam:format_2572 ; sc:name "Data index" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workbench" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation , "pmcid:PMC4589466", "pubmed:26258291" ; sc:description "A flexible framework for rapid genome analysis and interpretation" ; sc:featureList edam:operation_0310, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SpeedSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hall-lab/speedseq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3452 ; sc:description "Faster, mex-based version of Inverse Radon Transform in MATLAB." ; sc:isAccessibleForFree true ; sc:name "Speedy Inverse Radon Transform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/12852-iradon_speedy" ; biotools:primaryContact "Jeff Orchard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3315, edam:topic_3520 ; sc:description "SpeedyGA is a fast simple genetic algorithm in MATLAB. It is a vectorized implementation of a simple genetic algorithm." ; sc:isAccessibleForFree true ; sc:name "SpeedyGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.22.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/15164-speedyga-a-fast-simple-genetic-algorithm" ; biotools:primaryContact "Keki Burjorjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_0749, edam:topic_3299, edam:topic_3895 ; sc:citation , "pubmed:35727444" ; sc:description "An Automated, High-Throughput Platform for the Preparation of Bespoke Ultralarge Variant Libraries for Directed Evolution." ; sc:featureList edam:operation_0310, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SpeedyGenesXL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/neilswainston/SpeedyGenesXL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0623, edam:topic_3534 ; sc:citation "pubmed:22689646" ; sc:description "Web server that encodes the specific conservation pattern of amino acid types in a protein family to identify the specificity determining sites (SDS). The specific conservation pattern is predicted using amino acids_?? physico-chemical properties, relative entropy and the evolutionary rates between the protein subfamilies." ; sc:featureList edam:operation_2575, edam:operation_3092 ; sc:name "SPEER-SERVER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.hpppi.iicb.res.in/ss/" ; biotools:primaryContact "Saikat Chakrabarti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Query-driven search engine for large gene expression microarray compendia. Given a small set of query genes, identifies which datasets are most informative for these genes, then within those datasets additional genes are identified with expression profiles most similar to the query set." ; sc:featureList edam:operation_0224, edam:operation_2421, edam:operation_2495 ; sc:name "SPELL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0.3" ; sc:url "http://spell.princeton.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "This package can optimize the parameter in S-system models given time series data." ; sc:featureList edam:operation_2476, edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "SPEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SPEM.html" ; biotools:primaryContact "Xinyi YANG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3930 ; sc:citation , "pubmed:34570216" ; sc:description "SPENCER is a catalog of small peptides encoded by ncRNAs. The ncRNA encoding peptides were derived from re-annotation of public mass spectrometry data from over 1,700 patient samples spanning diverse cancers. SPENCER enables the users to simply and clearly explore differential expression of ncRNA peptides of interest in different cancer patients. In addition, SPENCER is also a powerful platform for querying the immunogenicity of peptides encoded by ncRNAs." ; sc:featureList edam:operation_0252, edam:operation_2421, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "SPENCER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://spencer.renlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0621 ; sc:citation ; sc:description "Neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes, that identifies the presence of sorting signals and predicts their cleavage sites." ; sc:featureList edam:operation_2479 ; sc:name "SPEPLip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gpcr.biocomp.unibo.it/cgi/predictors/spep/pred_spepcgi.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC8896601", "pubmed:34978568" ; sc:description "Quality Assessment of Peptide Tandem Mass Spectra with Deep Learning." ; sc:featureList edam:operation_3631, edam:operation_3767, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPEQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/sor8sh/SPEQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0099, edam:topic_0203, edam:topic_3053 ; sc:citation "pubmed:20529936" ; sc:description "An automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos." ; sc:featureList edam:operation_2495, edam:operation_3443 ; sc:name "SPEX2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=511" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3518 ; sc:citation , "pmcid:PMC7430270", "pubmed:32864216" ; sc:description """Identifying disease-associated signaling pathways through a novel effector gene analysis. Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received. The signals that the effector genes receive can be quite different in normal vs. disease conditions. However, most of current signaling pathway analysis methods do not take these signal variations into consideration. Methods:In this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that effector genes received between two conditions (normal and disease) in different signaling pathways""" ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3928 ; sc:license "MIT" ; sc:name "SPFA" ; sc:url "https://github.com/ZhenshenBao/SPFA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3411 ; sc:citation , "pmcid:PMC7319179", "pubmed:32595237" ; sc:description """SpGPCW: Spatially Varying Gaussian Process Model for Critical Window Estimation. A spatially varying distributed lag model with application to an air pollution and term low birth weight study. This package implements a hierarchical Bayesian logistic regression analysis to estimate spatially varying critical windows of susceptibility corresponding to exposure from a single time-varying covariate. The method relies on a spatiotemporally structured Gaussian process and is fit using Markov chain Monte Carlo sampling techniques. Please see the "SpGPCW_Example" folder for more specific information regarding package use details.""" ; sc:featureList edam:operation_3659 ; sc:name "SpGPCW" ; sc:url "https://github.com/warrenjl/SpGPCW" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "A script to extract a cell from an uneven background" ; sc:featureList edam:operation_3096, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Sphere assay image size analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/54312-sphere-assay-image-size-analysis" ; biotools:primaryContact "Patrick Granton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0166, edam:topic_0736 ; sc:citation , "pubmed:32154837" ; sc:description """method for precise estimation of residue relative solvent accessible area from limited structural information. This tool calculates an approximate values for relative solvent accessible area for single residues or whole amino acid chains in a PDB file. The method is based on calculating or estimating the number of atoms around a given amino acid residue that are located within a sphere with a cut-out cone. spherecon.py -i /Path/To/Input/File [-o /Path/To/Output/File] [-c chain] [-r residues] [--ca] [--bb] [--dm] -i: Path to an input file in PDB (Protein Data Bank) file format or distance matrix file in case of --dm.""" ; sc:featureList edam:operation_0272, edam:operation_0387, edam:operation_0480, edam:operation_2950 ; sc:license "LGPL-3.0" ; sc:name "SphereCon" ; sc:url "https://github.com/kalininalab/spherecon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:32702486" ; sc:description """Cortical surface registration using unsupervised learning. Non-rigid cortical registration is an important and challenging task due to the geometric complexity of the human cortex and the high degree of inter-subject variability. A conventional solution is to use a spherical representation of surface properties and perform registration by aligning cortical folding patterns in that space. This strategy produces accurate spatial alignment, but often requires high computational cost. Recently, convolutional neural networks (CNNs) have demonstrated the potential to dramatically speed up volumetric registration. However, due to distortions introduced by projecting a sphere to a 2D plane, a direct application of recent learning-based methods to surfaces yields poor results. In this study, we present SphereMorph, a diffeomorphic registration framework for cortical surfaces using deep networks that addresses these issues""" ; sc:name "SphereMorph" ; sc:url "https://github.com/voxelmorph/spheremorph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_3473, edam:topic_3474, edam:topic_3518 ; sc:description "Clustering on the hypersphere with the Spherical K-means algorithm" ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "The Spherical K-means algorithm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32987-the-spherical-k-means-algorithm" ; biotools:primaryContact "Xuan Vinh Nguyen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3300, edam:topic_3336, edam:topic_3382 ; sc:citation , "pmcid:PMC10040300", "pubmed:36992918" ; sc:description "Online platform for analyzing data from 3D spheroids or organoids grown in 96-well plates." ; sc:featureList edam:operation_0490, edam:operation_2943, edam:operation_3436, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "SpheroidAnalyseR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spheroidanalyser.leeds.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "SpheroScan: A user-friendly deep learning tool for analyzing spheroid images. It streamlines spheroid segmentation, area calculation, and downstream analysis, aiding researchers in processing large datasets. The prediction module uses DL models to mask spheroid images and generate CSV files with area and intensity data. The visualization module offers plots and statistical analysis, ready for publication. SpheroScan accelerates and standardizes spheroid assay result analysis." ; sc:featureList edam:operation_3443 ; sc:name "SpheroScan" ; sc:url "https://github.com/FunctionalUrology/SpheroScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3068, edam:topic_3305, edam:topic_3344 ; sc:citation , "pmcid:PMC7069808", "pubmed:32256240" ; sc:description """a gateway to scholarly publishing information. Advances in the health sciences rely on sharing research and data through publication. 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Each record includes 25 metadata fields representing best publishing practices""" ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "SPI-Hub" ; sc:url "https://spi-hub.app.vumc.org/tutorials" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3518 ; sc:citation ; sc:description "This package implements the Signaling Pathway Impact Analysis which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study." ; sc:featureList edam:operation_2497, edam:operation_3223 ; sc:name "SPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.26.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SPIA.html" ; biotools:primaryContact "Adi Laurentiu Tarca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3308, edam:topic_3382 ; sc:citation ; sc:description """An R package for the Spatial Image Analysis of Cells in Tissues. 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R package for the analysis of OPAL multiplex immunohistochemistry images.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3443 ; sc:name "SPIAT" ; sc:url "https://github.com/cancer-evolution/SPIAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8728228", "pubmed:34747477" ; sc:description "The Swiss Portal for Immune Cell Analysis (SPICA) is a web resource dedicated to the exploration and analysis of single-cell RNA-seq data of immune cells." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "SPICA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://spica.unil.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_3473 ; sc:citation "pubmed:21265010" ; sc:description "A data mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically. 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SpiderSeqR accelerates and simplifies genomic research by offering a new framework for searching and filtering metadata from SRA and GEO databases.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3196, edam:operation_3431 ; sc:name "SpiderSeqR" ; sc:url "https://github.com/ss-lab-cancerunit/SpiderSeqR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:37328692" ; sc:description "A feature extraction free approach for protein interactome inference from co-elution data." ; sc:featureList edam:operation_2492, edam:operation_3767, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "SPIFFED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bio-it-station/SPIFFED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0601, edam:topic_3169, edam:topic_3170, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC8315120", "pubmed:34327329" ; sc:description "spikChIP is a computational pipeline to perform multiple alternative normalization corrections on ChIP-seq data with spike-in (Raw, Traditional, ChIP-Rx, Tag removal and spikChIP)" ; sc:featureList edam:operation_3222, edam:operation_3435, edam:operation_3659, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "spikChIP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/eblancoga/spikChIP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0219, edam:topic_0602, edam:topic_2815 ; sc:citation "pubmed:21097778" ; sc:description "Database for highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. Pathways are laid out as maps that reflect the curator's understanding and make the utilization of the pathways easy. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways." ; sc:featureList edam:operation_0533, edam:operation_2422, edam:operation_2429, edam:operation_2497, edam:operation_3562 ; sc:name "SPIKE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.tau.ac.il/~spike/" ; biotools:primaryContact "SPIKE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3304 ; sc:citation ; sc:description """reproducible web-facing ground-truth validation of automated neural spike sorters. Spike sorting is a crucial but time-intensive step in electrophysiological studies of neuronal activity. While there are many popular software packages for spike sorting, there is little consensus about which are the most accurate under different experimental conditions. SpikeForest is an open-source and reproducible software suite that benchmarks the performance of automated spike sorting algorithms across an extensive, curated database of electrophysiological recordings with ground truth, displaying results interactively on a continuously-updating website. With contributions from over a dozen participating laboratories, our database currently comprises 650 recordings (1.3 TB total size) with around 35,000 ground-truth units""" ; sc:featureList edam:operation_2428, edam:operation_3192, edam:operation_3802 ; sc:name "SpikeForest" ; sc:url "https://spikeforest.flatironinstitute.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0736 ; sc:description "A Deep Learning Tool for Identifying Phage Tailspike Proteins. SpikeHunter utilizes a deep learning approach to identify phage tailspike proteins. It achieves this by using a protein language model, ESM-2 transformer, which can detect patterns in protein sequences." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SpikeHunter" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/nlm-irp-jianglab/SpikeHunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "Package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006)." ; sc:featureList edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "spikeLI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.34.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/spikeLI.html" ; biotools:primaryContact "Enrico Carlon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_3305, edam:topic_3306, edam:topic_3945 ; sc:citation ; sc:description "SpikePro algorithm predicts the fitness of a SARS-CoV-2 strain from the sequence of its spike protein. Given the target sequence in fasta format, the algorithm aligns it to the reference SARS-CoV-2 spike protein, list all mutations with respect to the reference and compute the fitness for each mutations as well as for the overal viral strain." ; sc:featureList edam:operation_0303, edam:operation_0331, edam:operation_0477 ; sc:license "MIT" ; sc:name "SpikePro" ; sc:url "http://github.com/3BioCompBio/SpikeProSARS-CoV-2" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1755 ; sc:name "Protein atom" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1756 ; sc:name "Protein residue" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3905 ; sc:name "Histogram" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0611, edam:topic_0736 ; sc:citation , "pmcid:PMC9924081", "pubmed:36758040" ; sc:description "Tool for analyzing structural diversity in experimental structures of the SARS-CoV-2 spike glycoprotein." ; sc:featureList edam:operation_0320, edam:operation_0480, edam:operation_2950 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "SpikeScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spikescape.streamlitapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3306, edam:topic_3674 ; sc:citation ; sc:description "Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls." ; sc:featureList edam:operation_3096, edam:operation_3435, edam:operation_3799 ; sc:name "spiky" ; sc:url "https://github.com/trichelab/spiky" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3299 ; sc:citation , "pmcid:PMC3608327", "pubmed:23190710" ; sc:description "Model selection in phylogenetics based on algebraic invariants." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPIn" ; sc:provider "crg.eu" ; sc:softwareVersion "1" ; sc:url "http://genome.crg.es/cgi-bin/phylo_mod_sel/AlgModelSelection.pl" ; biotools:primaryContact , "Anna Kedzierska" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2269, edam:topic_2828 ; sc:citation , "pmcid:PMC7233013", "pubmed:32356787" ; sc:description """an indexing method for two-color X-ray diffraction data. Two-Color extension of Sparse Pattern INDexing method. 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Feature selection is optimized for human splice sites." ; sc:featureList edam:operation_0253, edam:operation_0264, edam:operation_0433, edam:operation_3092 ; sc:name "SplicePort" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://spliceport.cbcb.umd.edu/" ; biotools:primaryContact "spliceport Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data." ; sc:featureList edam:operation_2995 ; sc:license "GPL-2.0" ; sc:name "spliceR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/spliceR.html" ; biotools:primaryContact "Johannes Waage", "Kristoffer Vitting-Seerup" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "Performs splice centered analysis on RNA-seq data." ; sc:featureList edam:operation_2499, edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "spliceSites" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/spliceSites.html" ; biotools:primaryContact "Wolfgang Kaisers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC10123099", "pubmed:36864749" ; sc:description "Suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing." ; sc:featureList edam:operation_0232, edam:operation_0264, edam:operation_0433, edam:operation_0446, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpliceTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://splicetools.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:21896509" ; sc:description "SpliceTrap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data. Instead of full transcript quantification, SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3’/5’ splice sites or Intron Retention." ; sc:featureList edam:operation_2238 ; sc:name "SpliceTrap" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://rulai.cshl.edu/splicetrap/" ; biotools:primaryContact "SpliceTrap Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3308, edam:topic_3320 ; sc:citation "pubmed:26618088" ; sc:description "A software suite for alternative splicing analysis using next-generation sequencing data." ; sc:featureList edam:operation_2499 ; sc:name "Splicing Express" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics-brazil.org/splicingexpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:23449093" ; sc:description "The tool predicts genes that are differentially spliced between two different conditions using RNA-seq data. The software is based on geometric angles between high dimensional read count vectors and is able to predict genes that undergo differential splicing from next generation RNA sequencing data." ; sc:featureList edam:operation_2499, edam:operation_3680 ; sc:name "SplicingCompass" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.ichip.de/software/SplicingCompass.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:34499147" ; sc:description "The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions." ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_3196, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SplicingFactory" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/SplicingFactory.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_3621 ; sc:name "Gene transcript report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3547 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320 ; sc:citation ; sc:description "This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways." ; sc:featureList edam:operation_2499 ; sc:license "Artistic-2.0" ; sc:name "SplicingGraphs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SplicingGraphs.html" ; biotools:primaryContact "H. Pagès" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:25720307" ; sc:description "Annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level." ; sc:featureList edam:operation_0361, edam:operation_2499 ; sc:name "SplicingTypesAnno" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/splicingtypes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3170 ; sc:citation ; sc:description "SplicingViewer is an integrated tool developed to enable users to detect the splice junctions, annotate alternative splicing events, and visualization of the patterns of alternative splicing events." ; sc:featureList edam:operation_2429 ; sc:license "BSD-3-Clause" ; sc:name "SplicingViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.zj.cn/splicingviewer/" ; biotools:primaryContact "Huabin Hou", "Linglin Zhou", "Qi Liu", "SplicingViewer team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3320, edam:topic_3512, edam:topic_3673 ; sc:citation ; sc:description "Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals." ; sc:featureList edam:operation_0232, edam:operation_0292, edam:operation_2089, edam:operation_3192, edam:operation_3216 ; sc:license "Freeware" ; sc:name "Splign" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi" ; biotools:primaryContact "Yuri Kapustin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602 ; sc:citation ; sc:description "This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks." ; sc:featureList edam:operation_3223, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "splineTimeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/splineTimeR.html" ; biotools:primaryContact "Herbert Braselmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3517 ; sc:citation ; sc:description """A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies. Genome-wide association studies (GWAS) have been widely used to unravel connections between genetic variants and diseases. Larger sample sizes in GWAS can lead to discovering more associations and more accurate genetic predictors. However, sharing and combining distributed genomic data to increase the sample size is often challenging or even impossible due to privacy concerns and privacy protection laws such as the GDPR. While meta-analysis has been established as an effective approach to combine summary statistics of several GWAS, its accuracy can be attenuated in the presence of cross-study heterogeneity. Here, we present sPLINK ( safe PLINK ), a user-friendly tool, which performs federated GWAS on distributed datasets while preserving the privacy of data and the accuracy of the results. sPLINK neither exchanges raw data nor does it rely on summary statistics""" ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3659 ; sc:name "sPLINK" ; sc:url "https://exbio.wzw.tum.de/splink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "This software provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments." ; sc:featureList edam:operation_0337, edam:operation_2419, edam:operation_2499 ; sc:license "GPL-2.0" ; sc:name "SPLINTER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SPLINTER.html" ; biotools:primaryContact "Diana Low" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC6529221", "pubmed:31112130" ; sc:description "Collection of split-GAL4 driver lines providing genetic access to 82 LH cell types." ; sc:featureList edam:operation_3359, edam:operation_3450 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "split-GAL4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.janelia.org/split-gal4" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0621, edam:topic_0632, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:32541852" ; sc:description """Highly specific multiplexed RNA imaging in tissues with split-FISH. A multiplexed FISH image analysis pipeline for multi-FOV datasets using a pixel-vector decoding approach. Will work for any coding scheme. Allows for visualization of correlation to bulk FPKM counts, and stitches images and spots. Scripts and data used for the manuscript figures can be found in the splitFISH_manuscript_figures folder. When running the code, a dialog window will open up asking for the directory containing data. Select the main folder for each figure, e.g for Figure 1, navigate to this folder.""" ; sc:featureList edam:operation_2495, edam:operation_3359, edam:operation_3443 ; sc:name "split-FISH" ; sc:url "https://github.com/khchenLab/split-fish" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3306, edam:topic_3382 ; sc:citation , "pmcid:PMC9931717", "pubmed:36792719" ; sc:description "SPLIT-PIN software enabling confocal and super-resolution imaging with a virtually closed pinhole." ; sc:featureList edam:operation_3359, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPLIT-PIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/llanzano/SPLITPIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:35749336" ; sc:description "A heterogeneity-aware federated deep learning method for medical imaging." ; sc:featureList edam:operation_3359, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SplitAVG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zm17943/SplitAVG" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084 ; sc:description "Calculate the number of splits (edges) that differs for two trees." ; sc:featureList edam:operation_0325 ; sc:name "SplitDist" ; sc:operatingSystem "Linux" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.1.7" ; sc:url "http://www.daimi.au.dk/~mailund/split-dist.html" ; biotools:primaryContact "Thomas Mailund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25398610" ; sc:description "An algorithm that directly constructs the compressed de Bruijn graph in time and space linear to the total number of genomes for a given maximum genome size." ; sc:featureList edam:operation_0524 ; sc:name "SplitMEM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/splitmem/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_2814 ; sc:citation "pubmed:19406922" ; sc:description "SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >,26,000 structures in PDB have been found to have split pockets." ; sc:featureList edam:operation_0245, edam:operation_3351, edam:operation_3359, edam:operation_3767 ; sc:name "SplitPocket" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pocket.med.wayne.edu/patch/" ; biotools:primaryContact "Yan Y. Tseng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3320 ; sc:citation "pubmed:20236510" ; sc:description "De novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts." ; sc:featureList edam:operation_0415, edam:operation_0433 ; sc:license "GPL-3.0" ; sc:name "SplitSeek" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864574/" ; biotools:primaryContact "Adam Ameur" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Split sequence(s) into original source sequences." ; sc:featureList edam:operation_0369 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "splitsource" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/splitsource.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Split sequence(s) into smaller sequences." ; sc:featureList edam:operation_0369 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "splitter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/splitter.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3373 ; sc:citation , "pubmed:36445996" ; sc:description "Improved Computational Drug-Repositioning by Self-Paced Non-Negative Matrix Tri-Factorization." ; sc:featureList edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPLNMTF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/qi0906/SPLNMTF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3518 ; sc:citation ; sc:description "This package provides the plotScreen function for visualising data in microtitre plate or slide format." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "splots" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.40.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/splots.html" ; biotools:primaryContact "Wolfgang Huber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2640, edam:topic_3315 ; sc:citation , "pmcid:PMC6872169", "pubmed:31710622" ; sc:description """Uncovering the subtype-specific temporal order of cancer pathway dysregulation. Subtype-specific Pathway Linear Progression Model. An integer linear program for simultaneous identification of cancer pathways, cancer subtyes and subtype-specific order of pathway dysregulation. The input is the Cancer Cell Fraction (CCF) matrix with rows corresponding to samples and columns indicating somatic genetic variants for which CCF values are measured. The output consists of a partitioning samples into subtypes, a partitioning of variants into pathways, and a linear progression model of the pathways for each subtype. Our software SPM consists of three separate parts: intermediate file generation (matGenerator.cpp), the main algorithm implementation (SPM.""" ; sc:featureList edam:operation_2426, edam:operation_3439 ; sc:name "SPM" ; sc:url "https://github.com/Dalton386/SPM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0781, edam:topic_3324 ; sc:citation "pubmed:26722117" ; sc:description "The tool estimates the infection duration of a single variant or multi-variant HIV infections based on the characteristics of HIV transmission and early evolution." ; sc:featureList edam:operation_2423 ; sc:name "SPMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://p512.usc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3070 ; sc:citation ; sc:description "Automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML) to Graphml format." ; sc:featureList edam:operation_0335, edam:operation_2945 ; sc:name "SPNConverter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.picb.ac.cn/ClinicalGenomicNTW/SPNConverter.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1193 ; sc:encodingFormat edam:format_3987 ; sc:name "Tool name (FASTA)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "SIMD partial order alignment tool/library. Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm" ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Spoa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rvaser/spoa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269 ; sc:citation ; sc:description """Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps. SPOC, short for Statistical Processing of cryo-EM maps, is a software package which contains statistical tools for the analysis and processing of cryo-EM maps. Included are tools for Con dence Map generation, local map processing as well as resolution estimation (global and local) by permutation testing and false discovery rate control.""" ; sc:featureList edam:operation_2429, edam:operation_3431, edam:operation_3435 ; sc:name "SPoC" ; sc:url "https://github.com/MaximilianBeckers/SPOC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_3407, edam:topic_3473, edam:topic_3577 ; sc:citation , "pmcid:PMC9940622", "pubmed:36759942" ; sc:description "The scalable precision medicine open knowledge engine (SPOKE)." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "SPOKE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spoke.rbvi.ucsf.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0625, edam:topic_0637, edam:topic_2885 ; sc:citation , "pmcid:PMC7737520", "pubmed:33320180" ; sc:description """Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families. Rapid and precise prediction of Mycobacterium tuberculosis complex (MTBC) spoligotype families. SpolLineages is a software tool mainly written in Java allowing to predict Mycobacterium tuberculosis complex families from spoligotyping or MIRU-VNTR typing patterns using various methods (SITVIT2 binary rules, RuleTB refined rules, Decision tree and/or Evolutionary algorithm).""" ; sc:featureList edam:operation_3196, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "SpolLineages" ; sc:url "https://github.com/dcouvin/SpolLineages" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_2259, edam:topic_3308 ; sc:description "This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. 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sc:license "GPL-3.0" ; sc:name "spongEffects" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioconductor.org/packages/devel/bioc/html/SPONGE.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099, edam:topic_0659, edam:topic_3170 ; sc:citation "pubmed:27198221" ; sc:description "A web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs." ; sc:featureList edam:operation_3792 ; sc:name "spongeScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://spongescan.rc.ufl.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; 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sc:featureList edam:operation_0484 ; sc:name "SPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://spot.cgsmd.isi.edu" ; biotools:primaryContact "SPOT Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_3474, edam:topic_3542 ; sc:citation , "pubmed:33983382" ; sc:description "SPOT-1D-Single is a tool for improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning." ; sc:featureList edam:operation_0267, edam:operation_0474, edam:operation_2488 ; sc:name "SPOT-1D-Single" ; sc:url "https://sparks-lab.org/server/spot-1d-single" ; biotools:primaryContact , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0102, edam:topic_3474 ; sc:citation ; sc:description "Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks." ; sc:featureList edam:operation_0267, edam:operation_0272, edam:operation_0474, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "SPOT-Contact-Single" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sparks-lab.org/server/spot-contact-single" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3538 ; sc:citation , "pubmed:28011771" ; sc:description "SPOT-Disorder is a method used for predicting disordered regions in proteins. Initial studies indicate that the method is more accurate in predicting functional sites in disordered regions." ; sc:featureList edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "SPOT-Disorder" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "v1.0" ; sc:url "http://sparks-lab.org/server/spot-disorder/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation , "pubmed:30395465" ; sc:description "SPOT-Disorder-Single is a single-sequence method that is more accurate than SPOT-Disorder (a profile-based method) for proteins with few homologous sequences and comparable for proteins in predicting long-disordered regions." ; sc:featureList edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "SPOT-Disorder-Single" ; sc:operatingSystem "Linux", "Windows" ; sc:url "http://sparks-lab.org/server/spot-disorder-single/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0602, edam:topic_3474, edam:topic_3538 ; sc:citation , "pmcid:PMC7212484", "pubmed:32173600" ; sc:description "Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning." ; sc:featureList edam:operation_0272, edam:operation_0470, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "SPOT-Disorder2" ; sc:operatingSystem "Linux" ; sc:url "https://sparks-lab.org/server/spot-disorder2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:33704363" ; sc:description "Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning" ; sc:featureList edam:operation_0278 ; sc:name "SPOT-RNA2" ; sc:softwareHelp ; sc:url "https://sparks-lab.org/server/spot-rna2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_1775, edam:topic_3125, edam:topic_3511 ; sc:citation , "pmcid:PMC3937850", "pubmed:24573478" ; sc:description "Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction." ; sc:featureList edam:operation_1777 ; sc:name "SPOT-Seq-RNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sparks-lab.org/server/SPOT-Seq-RNA/" ; biotools:primaryContact "Yaoqi Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "DNA -binding protein prediction from 3D structure." ; sc:featureList edam:operation_0303, edam:operation_2423, edam:operation_2479 ; sc:name "SPOT-Struct-DNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sparks-lab.org/yueyang/server/SPOT-Struct-DNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation ; sc:description "SPOT-Struct-RNA is a sofware for RNA-binding protein prediction from 3D structure" ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "SPOT-Struct-RNA" ; sc:operatingSystem "Linux" ; sc:url "http://sparks-lab.org/yueyang/server/SPOT-Struct-RNA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC8406885", "pubmed:34289024" ; sc:description "Swift Profiling Of Transcriptomes - a shiny app for gene ranking according to user-defined expression profiles" ; sc:featureList edam:operation_0315, edam:operation_0490, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SPOT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://frischknechtlab.shinyapps.io/SPOT/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3365, edam:topic_3382, edam:topic_3383, edam:topic_3385 ; sc:citation "pubmed:26656569" ; sc:description "A novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size." ; sc:featureList edam:operation_3443, edam:operation_3457 ; sc:name "SpotCaliper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bigwww.epfl.ch/algorithms/spotcaliper/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3512 ; sc:citation , "pmcid:PMC9587566", "pubmed:36271369" ; sc:description "A semi-automated tool for object-based co-localization of fluorescent labels in microscopy images." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SpotitPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/alexiaales/SpotitPy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_1775, edam:topic_2259 ; sc:citation "pubmed:23274651" ; sc:description "The tool is designed to detect community structures in a network. Community, in which vertices are joined tightly together, between which there are only looser edges, exists in many real networks." ; sc:featureList edam:operation_3200 ; sc:name "Spotlight" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hub.iis.sinica.edu.tw/spotlight/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:33544846" ; sc:description """seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. The goal of SPOTlight is to provide a tool that enables the deconvolution of cell types and cell type proportions present within each capture locations comprising mixtures of cells, originally developed for 10X’s Visium - spatial trancsiptomics- technology, it can be used for all technologies returning mixtures of cells. SPOTlight is based on finding topic profile signatures, by means of an NMFreg model, for each cell type and finding which combination fits best the spot we want to deconvolute.""" ; sc:featureList edam:operation_0314, edam:operation_3629, edam:operation_3659 ; sc:name "SPOTlight" ; sc:url "http://mouse.brain-map.org/experiment/siv?id=69672462&imageId=69647545&initImage=ish&coordSystem=pixel&x=4464.5&y=3184.5&z=1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0749, edam:topic_3520 ; sc:citation ; sc:description "SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale." ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SpotLink" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DICP1810/SpotLink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_3520 ; sc:citation "pubmed:25300367" ; sc:description "A user-friendly web application for predicting complex co-membership from affinity purification – mass spectrometry data. This web application employs a logistic regression classifier that integrates existing, proven APMS scoring approaches (SAINT, CompPASS, and HGSCore), gene co-expression patterns, functional annotations, domain-domain binding affinity, and homologous interactions, which we have shown outperforms existing APMS scoring methods." ; sc:featureList edam:operation_2492, edam:operation_3214 ; sc:name "Spotlite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cancer.unc.edu/majorlab/software.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_2350 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:author ; sc:citation , ; sc:description """Determination of Hot-Spots at protein-protein interfaces SpotOn is a robust algorithm developed to identify and classify the interfacial residues as Hot-Spots (HS) and Null-Spots (NS) with a final accuracy of 0.95 and a sensitivity of 0.95 on an independent test set.""" ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "SpotOn" ; sc:provider ; sc:softwareHelp , ; sc:url "https://alcazar.science.uu.nl/cgi/services/SPOTON/spoton/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC7582262", "pubmed:33019775" ; sc:description "SpotONE – Data-Driven Molecular Design. Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features." ; sc:featureList edam:operation_0451, edam:operation_3359, edam:operation_3937 ; sc:name "SPOTONE" ; sc:url "http://moreiralab.com/resources/spotone" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3569 ; sc:citation , "pmcid:PMC4682995", "pubmed:26680783" ; sc:description "SPOTPY (Statistical Parameter Optimization Tool) is an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models." ; sc:featureList edam:operation_2425 ; sc:license "MIT" ; sc:name "SPOTPY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/spotpy/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518, edam:topic_3572 ; sc:citation ; sc:description "Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "spotSegmentation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/spotSegmentation.html" ; biotools:primaryContact "Chris Fraley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0114, edam:topic_0203, edam:topic_3175 ; sc:citation , "pmcid:PMC10516669", "pubmed:37602419" ; sc:description "Single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes." ; sc:featureList edam:operation_0337, edam:operation_0371, edam:operation_0372, edam:operation_2426, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "spotter" ; sc:url "https://github.com/Elcock-Lab/spotter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3344, edam:topic_3372 ; sc:description "Spot identifies the processes in a pipeline that produce different results in different execution conditions." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Spot" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.2" ; sc:url "https://github.com/big-data-lab-team/spot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0199, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC4756441", "pubmed:26883915" ; sc:description "Fast and accurate in silico Mycobacterium spoligotyping from sequence reads." ; sc:featureList edam:operation_3504 ; sc:name "SpoTyping" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "https://github.com/xiaeryu/SpoTyping-v2.0" ; biotools:primaryContact "Rick Twee-Hee Ong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169 ; sc:citation ; sc:description "R-scripts for ChIP-seq analysis." ; sc:featureList edam:operation_3222 ; sc:license "GPL-2.0" ; sc:name "SPP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq" ; biotools:primaryContact "Peter J. Park" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3336, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:34043511" ; sc:description "SPP-CPI is a tool for predicting compound-protein interactions based on neural networks." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3094 ; sc:name "SPP-CPI" ; sc:url "https://github.com/lxlsu/SPP_CPI" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1075 ; sc:name "Protein family identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3299 ; sc:citation ; sc:description "Sequence Platform for the phylogenetic analysis of Plant Genes." ; sc:featureList edam:operation_0553 ; sc:name "SPPG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/cgi-bin/SPPG/index.htpl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_2814 ; sc:citation "pubmed:17152079" ; sc:description "The server can be used to: (1) predict residues to be at the putative protein interface(s) by considering single protein chain with resolved 3D structure; (2) analyse protein-protein complex with given 3D structural information and identify residues that are being in interchain contact." ; sc:featureList edam:operation_0474, edam:operation_2492 ; sc:name "SPPIDER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sppider.cchmc.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3365, edam:topic_3391, edam:topic_3473, edam:topic_3569 ; sc:citation "pubmed:23477384" ; sc:description "The method presented here provides an approach for researchers to perform exploratory data analysis on new -omic datasets containing missing data. 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SPREAD: A fully automated toolkit for single-particle cryo-EM data 3D reconstruction with image network-aided orientation assignment.""" ; sc:featureList edam:operation_3215, edam:operation_3432, edam:operation_3457 ; sc:name "SPREAD" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/SPREAD/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3293, edam:topic_3500 ; sc:citation , "pmcid:PMC9615431", "pubmed:36325034" ; sc:description "Online visualisation of pathogen phylogeographic reconstructions." ; sc:featureList edam:operation_0337, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:name "SPREAD 4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spreadviz.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:19051285" ; sc:description "A computer program for performing regression analysis of secondary phenotype data in case-control association studies. 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Phylogenetic trees based on the rearrangement analysis are also shown as part of the results." ; sc:featureList edam:operation_0289, edam:operation_0546, edam:operation_0557, edam:operation_3478 ; sc:name "SPRING" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://algorithm.cs.nthu.edu.tw/tools/SPRING" ; biotools:primaryContact "Chin Lung Lu", "Chuan Yi Tang", "Ying Chih Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3053, edam:topic_3068 ; sc:citation , "pmcid:PMC10117642", "pubmed:37091810" ; sc:description "An R package for bi-level variable selection of high-dimensional longitudinal data." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "springer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cran.r-project.org/package=springer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3168, edam:topic_3518 ; sc:citation "pubmed:19114001" ; sc:description "A parallel framework for R. It provides an easy access to high performance computing for the analysis of high throughput post genomic data using the statistical programming language R." ; sc:featureList edam:operation_2478, edam:operation_2495 ; sc:name "SPRINT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.r-sprint.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0601, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:35696081" ; sc:description "Computational Prediction of N- and O-Linked Glycosylation Sites for Human and Mouse Proteins." ; sc:featureList edam:operation_0267, edam:operation_0417, edam:operation_0474 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPRINT-Gly" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sparks-lab.org/server/sprint-gly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3321, edam:topic_3511 ; sc:citation ; sc:description "SNP-free toolkit for identifying RNA editing sites." ; sc:featureList edam:operation_0415 ; sc:name "SPRINT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://sprint.tianlab.cn/" ; biotools:primaryContact "Weidong Tian" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_0736 ; sc:citation "pubmed:22573174" ; sc:description "SPRITE is a protein structural motif database searching program. 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It works by identifying split reads from alignments based on soft-clipping information." ; sc:featureList edam:operation_2403, edam:operation_2454, edam:operation_3197 ; sc:name "Sprites" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/zhangzhen/sprites" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_3420, edam:topic_3538 ; sc:citation "pubmed:15585524", "pubmed:16844983" ; sc:description "Spritz is a tool for the prediction of disordered regions of proteins." ; sc:featureList edam:operation_0269, edam:operation_0436, edam:operation_0470, edam:operation_2423, edam:operation_3092 ; sc:name "Spritz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://distill.ucd.ie/spritz/" ; biotools:primaryContact "Gianluca Pollastri" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3170, edam:topic_3308, edam:topic_3520, edam:topic_3922 ; sc:citation , , "pmcid:PMC8024408", "pubmed:32967423" ; sc:description """A Proteogenomic Database Engine. Software for RNA-Seq analysis on Windows, including creating sample-specific proteoform databases from genomic data. Spritz uses snakemake and Docker to install and run commandline tools for Next-Generation Sequencing (NGS) analysis. Monitor progress in the Information textbox. The final database named final/combined.spritz.snpeff.protein.withmods.xml.gz can be used to search MS/MS with MetaMorpheus to find variant peptides and proteoforms, possibly with modifications. We recommend performing 1) Calibration, 2) Global PTM Discovery (G-PTM-D), and 3) Search tasks to get the best results.""" ; sc:featureList edam:operation_0417, edam:operation_3196, edam:operation_3227, edam:operation_3645, edam:operation_3646 ; sc:name "Spritz" ; sc:url "https://smith-chem-wisc.github.io/Spritz/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0154, edam:topic_1775 ; sc:citation , "pubmed:36964722" ; sc:description "Protein function prediction from sequence through pretrained language model and homology-based label diffusion." ; sc:featureList edam:operation_0303, edam:operation_0447, edam:operation_1777 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SPROF-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio-web1.nscc-gz.cn/app/sprof-go" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3067, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9477078", "pubmed:36128423" ; sc:description "spectral sparsification helps restore the spatial structure at single-cell resolution." ; sc:featureList edam:operation_3431, edam:operation_3436, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SPROUT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/deepomicslab/SPROUT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0736, edam:topic_2275 ; sc:citation , "pmcid:PMC7788957", "pubmed:33407073" ; sc:description "Split-statistical Potentials Server (SPServer): split-statistical potentials for the analysis of protein structures and protein-protein interactions." ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_2415, edam:operation_2949, edam:operation_3899 ; sc:name "SPServer" ; sc:url "https://sbi.upf.edu/spserver/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3676 ; sc:citation , "pmcid:PMC7214028", "pubmed:32065619" ; sc:description "SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently, simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size." ; sc:featureList edam:operation_0337, edam:operation_3566 ; sc:name "SPsimSeq" ; sc:url "https://github.com/CenterForStatistics-UGent/SPsimSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "The IBM SPSS software platform offers advanced statistical analysis, a vast library of machine learning algorithms, text analysis, open-source extensibility, integration with big data and seamless deployment into applications." ; sc:featureList edam:operation_2238 ; sc:license "Proprietary" ; sc:name "SPSS" ; sc:softwareHelp ; sc:url "https://www.ibm.com/spss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC7406525", "pubmed:31974805" ; sc:description """A toolkit for the automatic detection of hand movements and gestures in video data. This repository contains the source code of the SPeeding Up the Detection of Non-iconic and Iconic Gestures (SPUDNIG) toolkit for Windows only. A working version of the application can be downloaded here. SPUDNIG is created during my MSc thesis project at the Max Planck Institute Nijmegen. SPUDNIG's purpose is to speed up annotation work of hand gestures in Elan. SPUDNIG takes as input a video file and extracts the gestures and their timing.""" ; sc:featureList edam:operation_0337 ; sc:name "SPUDNIG" ; sc:url "https://github.com/jorrip/SPUDNIG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3168, edam:topic_3174, edam:topic_3520 ; sc:citation ; sc:description "SPUMONI is a fast read classification tool for targeted nanopore sequencing. It uses a compressed r-index together with a streaming matching-statistics algorithm and statsitical test to classify reads." ; sc:featureList edam:operation_0310, edam:operation_1812, edam:operation_3192, edam:operation_3211 ; sc:license "GPL-3.0" ; sc:name "SPUMONI" ; sc:url "https://github.com/oma219/spumoni" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "Method for RNA structure prediction using evolutionary patterns of nucleotide composition." ; sc:featureList edam:operation_0271, edam:operation_2423, edam:operation_2441 ; sc:name "SPuNC" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/spuncwww/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0203, edam:topic_3292 ; sc:citation , "pmcid:PMC5897793", "pubmed:29721311" ; sc:description "Identify spurious protein predictions in prokaryotes. It searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. Features of the matches are used to score the query sequences' likelihood to be a spurious protein prediction using a Gaussian process model." ; sc:featureList edam:operation_3092 ; sc:license "MIT" ; sc:name "Spurio" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/bateman-group/spurio" ; biotools:primaryContact "Alex Bateman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3306, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC6967417", "pubmed:31998687" ; sc:description """A Word2vec-Inspired Feature Representation Method for Drug-Target Interaction Prediction. 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Guigó Lab: Computational Biology of RNA processing @ CRG, Barcelona." ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/guigolab/sqtlseeker2-nf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "This package permits to generate SQUAD simulation matrices, prediction heatmaps and correlation circles from PCA analysis." ; sc:featureList edam:operation_0337, edam:operation_2423, edam:operation_2426, edam:operation_3429 ; sc:license "GPL-2.0" ; sc:name "SQUADD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SQUADD.html" ; biotools:primaryContact "Martial Sankar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3071, edam:topic_3277 ; sc:citation , "pmcid:PMC7125237", "pubmed:32269478" ; sc:description """a natural history database and R package for comparative biology of snake feeding habits. 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With a single RNA sequence as input, SQUARNA annotates and scores potential stems (stretches of consecutive canonical base pairs) and selects them one by one. SQUARNA handles pseudoknots and is able to predict alternative secondary structures. With a multiple sequence alignment input SQUARNA calculates the total matrix of stem scores and derives the most conserved base pairs. 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However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. 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However, finding data of interest can be challenging using current tools. This tool is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "SRAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SRAdb.html" ; biotools:primaryContact "Jack Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3308 ; sc:citation "pubmed:26896799" ; sc:description "A useful tool to predict m6A modification sites on the RNA sequences" ; sc:featureList edam:operation_3204 ; sc:name "SRAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cuilab.cn/sramp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_1775, edam:topic_3170 ; sc:citation , "pmcid:PMC3775632", "pubmed:24058887" ; sc:description "This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). 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Spectrum recognition based on computer vision: A tool for 13C and 1H NMR data extraction from already analyzed spectra. This is the repository of codes for the paper entitled “Machine learning enhanced spectrum recognition system SRCV for intelligent NMR data extraction”. 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Such comparisons are useful for a plethora of purposes such as determination of conserved positions, and explaining different functionalities of proteins that evolved from a common ancestor.""" ; sc:featureList edam:operation_0295, edam:operation_0302, edam:operation_0491 ; sc:license "GPL-3.0" ; sc:name "SS3D" ; sc:url "https://github.com/0x462e41/SS3D/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170 ; sc:citation , "pubmed:31873725" ; sc:description """Causal network perturbations for instance-specific analysis of single cell and disease samples. brca_rnaseq_analysis_111419.html. liver_scrnaseq_analysis_111419.html""" ; sc:featureList edam:operation_3439 ; sc:name "ssNPA" ; sc:url "http://www.benoslab.pitt.edu/Software/ssnpa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation "pubmed:12824379" ; sc:description "SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site (e.g a transcription or translation initiation site)." ; sc:featureList edam:operation_0238, edam:operation_0240, edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "SSA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://epd.expasy.org/ssa/" ; biotools:primaryContact "Prof. Philipp Bucher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:11591649" ; sc:description "Sequence Search and Alignment by Hashing Algorithm is an algorithm for very fast matching and alignment of DNA sequences." ; sc:featureList edam:operation_0292, edam:operation_0495 ; sc:name "SSAHA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/science/tools/ssaha2-0" ; biotools:primaryContact "Adam Spargo", "Hannes Ponstingl", "Zemin Ning" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , , , "pmcid:PMC311141", "pmcid:PMC4051166", "pubmed:11591649", "pubmed:24708189" ; sc:description "Pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences." ; sc:featureList edam:operation_0491, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "SSAHA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.sanger.ac.uk/science/tools/ssaha2-0" ; biotools:primaryContact "Adam Spargo", "Hannes Ponstingl", "Zemin Ning" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "A tool for polymorphism detection. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence." ; sc:featureList edam:operation_0484, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "SsahaSNP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/science/tools/ssahasnp" ; biotools:primaryContact "Dr Zemin Ning" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2546 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3181 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence assembly report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:17158514" ; sc:description "A program for assemblying short DNA sequences. The program cycles through sequence data stored in a hash table and progressively searches through a prefix tree for the longest possible k-mer between any two sequencis." ; sc:featureList edam:operation_0230, edam:operation_0524, edam:operation_0525 ; sc:license "GPL-2.0" ; sc:name "SSAKE" ; sc:operatingSystem "Linux" ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/ssake" ; biotools:primaryContact "Rene Warren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3168, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "A light-weight web app for rapid analysis of spatially resolved transcriptomics data." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3436, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SSAM-lite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ssam-lite.bihealth.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:12116640" ; sc:description "The tool uses a stochastic search algorithm for estimation of maximum likelihood phylogenetic trees for morphological data." ; sc:featureList edam:operation_0324 ; sc:name "SSAMK" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.stat.osu.edu/~lkubatko/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2269, edam:topic_3324 ; sc:citation ; sc:description "Stochastic Simulation Algorithm for effective spreading dynamics on Time-evolving Adaptive NetworX (SSATAN-X)." ; sc:featureList edam:operation_0244, edam:operation_2426, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SSATAN-X" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nmalysheva/SSATAN-X" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3676 ; sc:citation , "pmcid:PMC8120905", "pubmed:33990189" ; sc:description "SSBER is a tool for removing batch effect for single-cell RNA sequencing data." ; sc:featureList edam:operation_0224, edam:operation_3432, edam:operation_3435 ; sc:name "SSBER" ; sc:url "https://github.com/zy456/SSBER" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0622, edam:topic_2259 ; sc:citation ; sc:description "Python framework for structural systems biology." ; sc:featureList edam:operation_2406 ; sc:license "MIT" ; sc:name "ssbio" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/SBRG/ssbio" ; biotools:primaryContact "Nathan Mih" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3518 ; sc:citation ; sc:description "This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002)." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "sscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sscore.html" ; biotools:primaryContact "Richard Kennedy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0769, edam:topic_3168 ; sc:citation , "pubmed:32338512" ; sc:description """Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. There has been a significant improvement in protein residue contact prediction in recent years. Nevertheless, state-of-the-art methods still show deficiencies in the contact prediction of proteins with low-homology information. These top methods depend largely on statistical features that derived from homologous sequences, but previous studies, along with our analyses, show that they are insufficient for inferencing an accurate contact map for nonhomology protein targets. To compensate, we proposed a brand new single-sequence-based contact predictor (SSCpred) that performs prediction through the deep fully convolutional network (Deep FCN) with only the target sequence itself, i.e., without additional homology information. The proposed pipeline makes good use of the target sequence by utilizing the pair-wise encoding technique and Deep FCN""" ; sc:featureList edam:operation_0272, edam:operation_0476, edam:operation_3927 ; sc:name "SSCpred" ; sc:url "http://csbio.njust.edu.cn/bioinf/sscpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053 ; sc:citation ; sc:description "The package can calculate the indexes for selective stength in codon usage in bacteria species. (1) Calculate the strength of selected codon usage bias based on Paul Sharp's method (comparable among different species). (2) Translational accuracy selection can be inferred from Akashi's test. (3) Optimal codon lists can be calculated by either op_highly function, or op_corre_CodonW/op_corre_NCprime function." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "sscu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sscu.html" ; biotools:primaryContact "Yu Sun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3305, edam:topic_3382, edam:topic_3404, edam:topic_3474 ; sc:citation , "pubmed:36462373" ; sc:description "A self-supervised diverse knowledge distillation method for lightweight skin lesion classification using dermoscopic images." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SSD-KD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/enkiwang/Portable-Skin-Lesion-Diagnosis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068, edam:topic_3678 ; sc:citation , "pubmed:32632740" ; sc:description """Sample-size determination for the Bayesian t test and Welch's test using the approximate adjusted fractional Bayes factor. The function SSDttest is used to compute the sample size required per group for the Bayesian t-test and Bayesian Welch's test. The function SSDANOVA and SSDANOVA_robust in the R package SSDbain computes the sample size for the Bayesian ANOVA, Welch's ANOVA, and robust ANOVA. bain is an abbreviation for BAyesian INformative hypothesis evaluation. It uses the Bayes factor to evaluate hypotheses in a wide variety of statistical models. One example are the hypotheses H1: m1 = m2 = m3, H2: m1 > m2 > m3, and Hu: m1, m2, m3 (no constraints) where m1, m2, and m3 denote the means in an ANOVA model. Another example is the hypothesis H1: b1 > 0, b2 > 0, b1 > b2 and its complement Hc: not H1, where b1 and b2 denote standardized regression coefficients.""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "SSDbain" ; sc:url "https://informative-hypotheses.sites.uu.nl/software/bain/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_3474, edam:topic_3542 ; sc:citation , "pmcid:PMC8318245", "pubmed:34320027" ; sc:description "A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction." ; sc:featureList edam:operation_0267, edam:operation_0303, edam:operation_0474, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SSE-PSSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://10.life.nctu.edu.tw/SSE-PSSM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053, edam:topic_3517 ; sc:citation ; sc:description "New SNP-based pathway analysis software for GWAS studies. SSEA consists of two main steps: selecting representative SNPs for each gene, and performing pathway enrichment analysis using all selected SNPs." ; sc:featureList edam:operation_2497, edam:operation_3501 ; sc:name "SSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://cbcl.ics.uci.edu/SSEA/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Pair sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Bill Pearson" ; sc:citation , ; sc:description "Find an optimal local alignment using the Smith-Waterman algorithm." ; sc:featureList edam:operation_0491 ; sc:name "ssearch2seq (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/psa/ssearch2seq" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:12824336", "pubmed:15858275" ; sc:description "Access to information about secondary structural elements present in non-redundant sets of proteins from the PDB." ; sc:featureList edam:operation_0267, edam:operation_0319, edam:operation_2416, edam:operation_2488 ; sc:name "SSEP" ; sc:url "http://cluster.physics.iisc.ernet.in/ssep/options.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation." ; sc:featureList edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "sSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sSeq.html" ; biotools:primaryContact "Danni Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_3299, edam:topic_3474 ; sc:citation , "pubmed:34058749" ; sc:description "SSG-LUGIA is an unsupervised learning based tool to predict genomic islands." ; sc:featureList edam:operation_0464, edam:operation_3435, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SSG-LUGIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://nibtehaz.github.io/SSG-LUGIA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3474 ; sc:citation , "pubmed:33951725" ; sc:description "SSI–DDI is a tool for substructure–substructure interactions for drug–drug interaction prediction." ; sc:featureList edam:operation_3454, edam:operation_3937, edam:operation_4009 ; sc:name "SSI-DDI" ; sc:url "https://github.com/kanz76/SSI-DDI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0154, edam:topic_0602, edam:topic_2229 ; sc:citation , "pmcid:PMC7214018", "pubmed:32065617" ; sc:description "Subsumption-based Sub-term Inference Framework to audit Gene Ontology." ; sc:featureList edam:operation_1812, edam:operation_3625 ; sc:name "SSIF" ; sc:url "https://github.com/rashmie/SSIF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Functions for computing and displaying sample size information for gene expression arrays." ; sc:featureList edam:operation_2238, edam:operation_3223 ; sc:license "GPL-3.0" ; sc:name "ssize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.48.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ssize.html" ; biotools:primaryContact "Gregory R. Warnes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_3277, edam:topic_3500 ; sc:citation , "pubmed:32044343" ; sc:description "Determining the Sample Sufficiency for Comparative Biological Study." ; sc:featureList edam:operation_3435 ; sc:name "SSizer" ; sc:url "https://idrblab.org/ssizer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:26800480" ; sc:description "A scalable implementation of Single Source K Diverse Shortest Paths Algorithm." ; sc:featureList edam:operation_2415 ; sc:name "SSKDSP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://compsci.hunter.cuny.edu/~leixie/sskdsp.html" ; biotools:primaryContact "Lei Xie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_3510 ; sc:citation , "pubmed:32750881" ; sc:description """A novel succinylation sites prediction method incorprating K-means clustering with a new semi-supervised learning algorithm. This package implements the SSKM_Succ algorithm incorporating K-means clustering with a new semi-supervised learning algorithm for predicting of the succinylation sites.""" ; sc:featureList edam:operation_0417, edam:operation_3432, edam:operation_3755 ; sc:name "SSKM Succ" ; sc:url "https://github.com/yangyq505/SSKM_Succ.git" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:encodingFormat edam:format_1929 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC8627024", "pubmed:34838140" ; sc:description "Chemical toxicity prediction based on semi-supervised learning and graph convolutional neural network." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "SSL-GCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://app.cbbio.online/ssl-gcn/home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "A data mining solution to map thousands of viral isolates (influenza, dengue and FMDV virus)." ; sc:featureList edam:operation_0226 ; sc:name "Sequence Similarity Maps (SSM)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ssm.vital-it.ch/" ; biotools:primaryContact "Software Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3303, edam:topic_3452 ; sc:citation , "pmcid:PMC9939022", "pubmed:36811007" ; sc:description "This project provides a freely accessible three-dimensional statistical shape model (SSM) of the tibia, the MATLAB scripts for generating a SSM and the segmented surface models of the cortical and trabecular bone." ; sc:featureList edam:operation_2426, edam:operation_3664, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://simtk.org/projects/ssm_tibia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0632, edam:topic_0654, edam:topic_3518 ; sc:citation , "pmcid:PMC7086184", "pubmed:32256778" ; sc:description "Molecular cytogenetic characterization of small supernumerary marker 15 in infertile male." ; sc:featureList edam:operation_3227 ; sc:name "sSMC" ; sc:url "http://ssmc-tl.com/Start.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_3295, edam:topic_3308, edam:topic_3518 ; sc:citation ; sc:description """SSMD: Semi-Supervised Mouse data Deconvolution. A semi-supervised approach for a robust cell type identification and deconvolution of mouse transcriptomics data. Deconvolution of mouse transcriptomic data is challenged by the fact that mouse models carry various genetic and physiological perturbations, making it questionable to assume fixed cell types and cell type marker genes for different dataset scenarios.""" ; sc:featureList edam:operation_3196, edam:operation_3463, edam:operation_3629 ; sc:name "SSMD" ; sc:url "https://github.com/xiaoyulu95/SSMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3168, edam:topic_3474, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC6805288", "pubmed:31639051" ; sc:description "A semi-supervised machine learning framework for microRNA classification." ; sc:featureList edam:operation_0463, edam:operation_3359, edam:operation_3792 ; sc:name "Semi-supervised miRNA" ; sc:url "https://github.com/GreenCUBIC/SSmiRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3315, edam:topic_3573, edam:topic_3678 ; sc:citation , "pmcid:PMC7508409", "pubmed:32960894" ; sc:description """R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks. Streams and rivers are biodiverse and provide valuable ecosystem services. Maintaining these ecosystems is an important task, so organisations often monitor the status and trends in stream condition and biodiversity using field sampling and, more recently, autonomous in-situ sensors. However, data collection is often costly, so effective and efficient survey designs are crucial to maximise information while minimising costs. Geostatistics and optimal and adaptive design theory can be used to optimise the placement of sampling sites in freshwater studies and aquatic monitoring programs. Geostatistical modelling and experimental design on stream networks pose statistical challenges due to the branching structure of the network, flow connectivity and directionality, and differences in flow volume""" ; sc:featureList edam:operation_3927 ; sc:name "SSNdesign" ; sc:url "https://github.com/apear9/SSNdesign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_0601, edam:topic_2229 ; sc:citation "pubmed:15922331" ; sc:description "A software of SUMO Substrates Prediction. Small Ubiquitin-related MOdifier (SUMO) proteins are ubiquitously expressed in eukaryotic cells , and implicatedly regulate various cellular processes, e.g. stress responsing , cell-cycle progression, and gene expression , etc." ; sc:featureList edam:operation_2423 ; sc:name "SSP" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://ssp.biocuckoo.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0082, edam:topic_0176, edam:topic_3292 ; sc:citation "pubmed:17088319" ; sc:description "An algorithm that combines chemical shifts from different nuclei into a score, which reflects the expected fraction of α- or β-structure." ; sc:featureList edam:operation_0474 ; sc:name "SSP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://abragam.med.utoronto.ca/~JFKlab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2830 ; sc:citation , "pubmed:37356912" ; sc:description "In silico tool for salmonella species serotyping using the sequences of o-antigen biosynthesis proteins and h-antigen filament proteins." ; sc:isAccessibleForFree true ; sc:name "SSP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://project.iith.ac.in/SSP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:23934609" ; sc:description "General Sample size and power analysis for microarray and next-generation sequencing data." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "SSPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SSPA.html" ; biotools:primaryContact "Maarten van Iterson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3172, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC9664704", "pubmed:36376837" ; sc:description "sspa provides a Python interface for metabolomics pathway analysis. In addition to conventional methods over-representation analysis (ORA) and gene/metabolite set enrichment analysis (GSEA), it also provides a wide range of single-sample pathway analysis (ssPA) methods." ; sc:featureList edam:operation_3925, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ssPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://pypi.org/project/sspa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation "pubmed:21149342" ; sc:description "Stand-alone scaffolder of pre-assembled contigs using paired-read data." ; sc:featureList edam:operation_3216 ; sc:name "SSPACE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE" ; biotools:primaryContact "SSPACE Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_0820, edam:topic_2828 ; sc:citation , "pmcid:PMC9503581", "pubmed:36135853" ; sc:description "Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems." ; sc:featureList edam:operation_0320, edam:operation_0337, edam:operation_3215, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "ssPINE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://poky.clas.ucdenver.edu/ssPINE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623, edam:topic_3301 ; sc:citation "pubmed:21904425" ; sc:description "A prediction server for the identification & classification of proteins involved in bacterial secretion systems." ; sc:featureList edam:operation_2995, edam:operation_3767 ; sc:name "SSPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/sspred/html/sspred.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_3542 ; sc:citation "pubmed:24860169" ; sc:description "The first hybrid approach of combining neural network (ab initio) and homology analysis to improve the prediction of secondary structure and solvent accessibility." ; sc:featureList edam:operation_0384, edam:operation_0474 ; sc:name "SSpro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scratch.proteomics.ics.uci.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1520 ; sc:encodingFormat edam:format_2331, edam:format_3468 ; sc:name "Peptide hydrophobic moment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2016 ; sc:encodingFormat edam:format_2331, edam:format_3468 ; sc:name "Amino acid property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:15238601" ; sc:description "Sequence-specific retention time calculator." ; sc:featureList edam:operation_3633 ; sc:name "SSRCalc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hs2.proteome.ca/SSRCalc/SSRCalc.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33647482" ; sc:description "SSRE is a tool for cell type detection based on sparse subspace representation and similarity enhancement. Accurate identification of cell types from single-cell RNA sequencing (scRNA-seq) data plays a critical role in a variety of scRNA-seq analysis studies. This task corresponds to solving an unsupervised clustering problem, in which the similarity measurement between cells affects the result significantly." ; sc:featureList edam:operation_3223, edam:operation_3432 ; sc:name "SSRE" ; sc:url "https://github.com/CSUBioGroup/SSRE" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_2885, edam:topic_3168, edam:topic_3308, edam:topic_3810 ; sc:citation , "pmcid:PMC7335497", "pubmed:32676221" ; sc:description """a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis. This software can automatically enrich polymorphic SSRs with transcripts. You just need to select all of your fasta files from Trinity and run this software.""" ; sc:featureList edam:operation_0237, edam:operation_0292, edam:operation_0308, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "SSREnricher" ; sc:url "https://github.com/byemaxx/SSREnricher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0632, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC7398111", "pubmed:32849772" ; sc:description "A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences." ; sc:featureList edam:operation_0237, edam:operation_0308, edam:operation_0310, edam:operation_3196 ; sc:name "SSRMMD" ; sc:url "https://github.com/GouXiangJian/SSRMMD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3512, edam:topic_3542 ; sc:citation , "pmcid:PMC9136272", "pubmed:35664227" ; sc:description "A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability." ; sc:featureList edam:operation_0278, edam:operation_0474, edam:operation_0502, edam:operation_0570, edam:operation_2441 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SSRTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cobisHSS0.im.nuk.edu.tw/SSRTool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation , "pmcid:PMC3371855", "pubmed:22689785" ; sc:description "Assign secondary structures to protein coordinate data using the Bayesian method of Minimum Message Length (MML) inference." ; sc:featureList edam:operation_2479 ; sc:name "SST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lcb.infotech.monash.edu.au/sstweb/Submission_page.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3304, edam:topic_3474 ; sc:citation , "pmcid:PMC8603828", "pubmed:34803591" ; sc:description "Supervised Spike Timing Dependent Plasticity for Efficient Spiking Neural Network Training." ; sc:featureList edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SSTDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MXHX7199/SNN-SSTDP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0602, edam:topic_3542 ; sc:citation "pubmed:9197551" ; sc:description "RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "SStructView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ctu.edu.vn/~dvxe/Bioinformatic/Software/BIT%20Software/home.html" ; biotools:primaryContact "SStructView Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "Small RNA sequencing viewer." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "ssviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ssviz.html" ; biotools:primaryContact "Diana Low" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0601, edam:topic_0749, edam:topic_0769, edam:topic_3169, edam:topic_3295 ; sc:citation ; sc:description "R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc." ; sc:featureList edam:operation_3218, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "ssvQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/FrietzeLabUVM/ssvQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0622, edam:topic_3277, edam:topic_3571 ; sc:citation "pubmed:24324759" ; sc:description "A fast implementation of the Smith-Waterman algorithm whose API that can be flexibly used by programs written in C, C++ and other languages." ; sc:featureList edam:operation_0292, edam:operation_2409 ; sc:name "SSW" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://blog.gkno.me/post/42508822069/ssw-library" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2640, edam:topic_3517 ; sc:citation ; sc:description "Workflow to perform aggregate rare variant tests for sequencing studies and genetic data. Implements the variant-Set Test for Association using Annotation infoRmation (STAAR) procedure, as well as SKAT, Burden, and ACAT tests for both continuous and dichotomous traits. The STAAR method incorporates qualitative functional categories and quantitative complementary functional annotations (Li and Li et al, 2020). The workflow accounts for population structure and relatedness, and scales for large whole genome sequencing studies." ; sc:featureList edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STAAR workflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sheilagaynor/STAAR_workflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0659, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:36303018" ; sc:description "STAARpipeline is an R package for phenotype-genotype association analyses of biobank-scale WGS WES data, including single variant analysis and variant set analysis." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3436, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STAARpipeline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/xihaoli/STAARpipeline/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3334 ; sc:citation , "pubmed:32976581" ; sc:description """a spatio-temporal cell atlas of the human brain. The human brain is the most complex organ consisting of billions of neuronal and non-neuronal cells that are organized into distinct anatomical and functional regions. Elucidating the cellular and transcriptome architecture underlying the brain is crucial for understanding brain functions and brain disorders. Thanks to the single-cell RNA sequencing technologies, it is becoming possible to dissect the cellular compositions of the brain. Although great effort has been made to explore the transcriptome architecture of the human brain, a comprehensive database with dynamic cellular compositions and molecular characteristics of the human brain during the lifespan is still not available""" ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:name "STAB" ; sc:url "http://stab.comp-sysbio.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:34750606" ; sc:description "A stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides." ; sc:featureList edam:operation_0321, edam:operation_0407, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "StaBle-ABPpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://stable-abppred.anvil.app" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269 ; sc:citation "pubmed:25943565" ; sc:description "An R package for Stability selection. Resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting." ; sc:featureList edam:operation_2238 ; sc:name "stabs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/stabs/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269 ; sc:citation , "pmcid:PMC1557772", "pubmed:16899652" ; sc:description "Method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. It utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach." ; sc:featureList edam:operation_2421, edam:operation_2495 ; sc:name "STAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://www.cbil.upenn.edu/STAC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data. STACAS is a method for anchor identification, designed to be easily incorporated in Seurat pipelines for batch correction and integration of scRNA-seq datasets (Andreatta & Carmona, Bioinformatics 2020). Integrating scRNA-seq data using STACAS and Seurat 3.""" ; sc:featureList edam:operation_3799 ; sc:name "STACAS" ; sc:softwareHelp ; sc:url "https://github.com/carmonalab/STACAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_3168 ; sc:citation "pubmed:16294339" ; sc:description "A structural sequence alignment, correspondence and conservation Analysis tool." ; sc:featureList edam:operation_0295, edam:operation_0492 ; sc:name "STACCATO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/staccato/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC9793644", "pubmed:36575368" ; sc:description "Computational classification of long circRNA from other lncRNA based on stacking strategy.." ; sc:featureList edam:operation_3472, edam:operation_3936, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "StackCirRNAPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/xwang1427/StackCirRNAPred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0202, edam:topic_3474 ; sc:citation , "pubmed:32105326" ; sc:description """a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency. Identifying Cell-Penetrating Peptides and Their Uptake Efficiency.""" ; sc:featureList edam:operation_0272, edam:operation_2489, edam:operation_3901 ; sc:name "StackCPPred" ; sc:url "https://github.com/Excelsior511/StackCPPred" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_3474 ; sc:citation , "pubmed:34883239" ; sc:description "A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides." ; sc:featureList edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "StackDPPIV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/StackDPPIV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2229, edam:topic_3173, edam:topic_3474, edam:topic_3940 ; sc:citation , "pmcid:PMC9277947", "pubmed:35820811" ; sc:description "Identification of cell line-specific enhancer-promoter interactions based on stacking ensemble learning." ; sc:featureList edam:operation_0267, edam:operation_0440, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "StackEPI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/20032303092/StackEPI.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:34622387" ; sc:description "A web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors." ; sc:featureList edam:operation_3454, edam:operation_3899, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "StackHCV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://camt.pythonanywhere.com/StackHCV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3360, edam:topic_3400, edam:topic_3474 ; sc:citation , "pubmed:33963832" ; sc:description "StackIL6 is a stacking ensemble model for improving the prediction of IL-6 inducing peptides." ; sc:featureList edam:operation_0252, edam:operation_3461, edam:operation_3631 ; sc:name "StackIL6" ; sc:url "http://camt.pythonanywhere.com/StackIL6" ; biotools:primaryContact "Balachandran Manavalan", "Watshara Shoombuatong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_3474, edam:topic_3957 ; sc:citation , "pubmed:32768046" ; sc:description """Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier. Protein-protein interactions (PPIs) are involved with most cellular activities at the proteomic level, making the study of PPIs necessary to comprehending any biological process. Machine learning approaches have been explored, leading to more accurate and generalized PPIs predictions. In this paper, we propose a predictive framework called StackPPI. First, we use pseudo amino acid composition, Moreau-Broto, Moran and Geary autocorrelation descriptor, amino acid composition position-specific scoring matrix, Bi-gram position-specific scoring matrix and composition, transition and distribution to encode biologically relevant features. Secondly, we employ XGBoost to reduce feature noise and perform dimensionality reduction through gradient boosting and average gain""" ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3935 ; sc:name "StackPPI" ; sc:url "https://github.com/QUST-AIBBDRC/StackPPI/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2275, edam:topic_2640, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC9525257", "pubmed:36180453" ; sc:description "StackPR is a new computational approach for large-scale identification of progesterone receptor antagonists using the stacking strategy." ; sc:featureList edam:operation_0478, edam:operation_3454, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "StackPR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pmlabstack.pythonanywhere.com/StackPR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3295, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description "a cross-species method for identifying RNA N6-methyladenosine sites based on stacked ensemble." ; sc:featureList edam:operation_0417, edam:operation_3936, edam:operation_3937 ; sc:name "StackRAM" ; sc:url "https://github.com/QUST-AIBBDRC/StackRAM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3056 ; sc:citation ; sc:description "Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis." ; sc:featureList edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "Stacks" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://catchenlab.life.illinois.edu/stacks/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "GUI for displaying image stacks, e.g. time-resolved or z-stacked microscopy images." ; sc:featureList edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "StackSlider" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/32569-stackslider" ; biotools:primaryContact "Otto Manneberg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:citation "pubmed:10547834" ; sc:description "Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_2478 ; sc:license "BSD-3-Clause" ; sc:name "STADEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://staden.sourceforge.net/" ; biotools:primaryContact "Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071, edam:topic_3168 ; sc:citation "pubmed:24930138" ; sc:description "A library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface." ; sc:featureList edam:operation_0335 ; sc:name "Staden io_lib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://staden.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0196, edam:topic_0654, edam:topic_3125 ; sc:citation "pubmed:8837029" ; sc:description "UNIX-based tools for sequence assembly, mutation detection and sequence analysis; free for non-commercial use. Note that Staden development and support have ceased due to lack of funding, despite widespread use." ; sc:featureList edam:operation_0310, edam:operation_2403, edam:operation_2451, edam:operation_2454 ; sc:name "Staden Package" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://staden.sourceforge.net/" ; biotools:primaryContact "Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0605, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC8571400", "pubmed:34786208" ; sc:description "A novel computational approachfor accurate prediction of m5C site." ; sc:featureList edam:operation_0417, edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Staem5" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Cxd-626/Staem5.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0797 ; sc:citation , "pubmed:28602693" ; sc:description "STAG-CNS can identify noncoding regulatory regions of a genome by simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species." ; sc:featureList edam:operation_3194 ; sc:license "MIT" ; sc:name "STAG-CNS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "https://github.com/srbehera11/stag-cns" ; biotools:primaryContact "James C. Schnable" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "The package allows automated stage-wise analysis of high-throughput gene expression data." ; sc:featureList edam:operation_2238, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "stageR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.22" ; sc:url "http://bioconductor.org/packages/release/bioc/html/stageR.html" ; biotools:primaryContact "Koen Van den Berge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3170 ; sc:citation , "pmcid:PMC10153041", "pubmed:37130913" ; sc:description "A web-based tool that integrates data visualization and pathway enrichment analysis for gene expression studies." ; sc:featureList edam:operation_0571, edam:operation_2436, edam:operation_3223, edam:operation_3925, edam:operation_3926 ; sc:isAccessibleForFree true ; sc:name "STAGEs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kuanrongchan-stages-stages-vpgh46.streamlitapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3517, edam:topic_3673, edam:topic_3810 ; sc:citation , "pmcid:PMC10033618", "pubmed:36949348" ; sc:description "Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection." ; sc:featureList edam:operation_3196, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "StageWise" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jendelman/StageWise" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0769, edam:topic_0780 ; sc:citation ; sc:description "This is a repository for making colorful identity heatmaps of genomic sequence." ; sc:featureList edam:operation_0310, edam:operation_0337, edam:operation_0491 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StainedGlass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mrvollger.github.io/StainedGlass/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0601, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:34532736" ; sc:description "A stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction." ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "STALLION" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://thegleelab.org/STALLION" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_3360 ; sc:citation ; sc:description "sTAM: A Tool for Single Sample microRNA Set Enrichment Analysis. An Online Tool for the Discovery of miRNA-set Level Disease Biomarkers." ; sc:featureList edam:operation_0463, edam:operation_3501, edam:operation_3792 ; sc:name "sTAM" ; sc:url "http://mir.rnanut.net/stam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0166, edam:topic_0203, edam:topic_0749 ; sc:citation "pubmed:17397256", "pubmed:17478497" ; sc:description "STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching." ; sc:featureList edam:operation_0239, edam:operation_0253, edam:operation_0496, edam:operation_2404 ; sc:name "STAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.benoslab.pitt.edu/stamp/" ; biotools:primaryContact "Shaun Mahony" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2814, edam:topic_3168 ; sc:citation "pubmed:1409577" ; sc:description "A package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments." ; sc:featureList edam:operation_0295, edam:operation_0492 ; sc:name "STAMP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.compbio.dundee.ac.uk/software.html#3Dstructure" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0654, edam:topic_2269, edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:25061070" ; sc:description "A software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance." ; sc:featureList edam:operation_2238, edam:operation_2403 ; sc:name "STAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kiwi.cs.dal.ca/Software/index.php/STAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "STAMP (Sequence Tag-based Analysis of Microbial Populations) is a tool for the introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters. STAMPR is a successor to STAMP, which accounts for such population expansions." ; sc:featureList edam:operation_0337, edam:operation_3200, edam:operation_3799 ; sc:license "MIT" ; sc:name "STAMPR" ; sc:url "https://github.com/hullahalli/stampr_rtisan" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation , , "pmcid:PMC3106326", "pubmed:20980556", "pubmed:28286147" ; sc:description "a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation." ; sc:featureList edam:operation_0447, edam:operation_2238, edam:operation_3198 ; sc:name "Stampy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.well.ox.ac.uk/project-stampy" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168 ; sc:citation , , ; sc:description "Stampy genome indexer for divergent genomes." ; sc:featureList edam:operation_3211 ; sc:name "stampy_indexer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.20" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/stampy_mapper/stampy_indexer/1.0.20" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1929, edam:format_1931, edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622 ; sc:citation , , ; sc:description "Mapper for divergent genomes." ; sc:featureList edam:operation_3198 ; sc:name "stampy_mapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.20" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/stampy_mapper/stampy_mapper/1.0.20" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3169, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC4300491", "pubmed:25527639" ; sc:contributor ; sc:description "Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. The tool implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data. It de novo learns and annotates the genome into a given number of 'genomic states'. 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sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3298, edam:topic_3336, edam:topic_3373 ; sc:citation , "pmcid:PMC9197487", "pubmed:35711912" ; sc:description "A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit." ; sc:featureList edam:operation_3226, edam:operation_3436, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "StarGazer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AstraZeneca/StarGazer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0611, edam:topic_0769, edam:topic_2275, edam:topic_2828 ; sc:citation , "pubmed:36323866" ; sc:description "A user-friendly workflow for Rosetta-driven molecular structure refinement." ; sc:featureList edam:operation_0321, edam:operation_0322, edam:operation_2429, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "StarMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/wlugmayr/chimerax-starmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3308, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC9976191", "pubmed:36874160" ; sc:description "An interactive and narrative visualisation tool for single-cell and spatial data." ; sc:featureList edam:operation_2939, edam:operation_2940, edam:operation_3890, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StarmapVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://holab-hku.github.io/starmapVis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description """immersive visualisation of single cell spatial omic data. starmap is a web-based VR-enabled tool which combines a 3D scatter plot with star plots (radar chart) to visualise hundreds of thousands of multivariate data points, such as single-cell expression data, imaging single cell data, spatial transcriptomic data and etc.""" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3891 ; sc:license "MIT" ; sc:name "starmapVR" ; sc:url "https://holab-hku.github.io/starmapVR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3125, edam:topic_3511, edam:topic_3512, edam:topic_3794 ; sc:citation , "pmcid:PMC4086099", "pubmed:24803672" ; sc:description "STarMir is a web server for prediction of microRNA binding sites." ; sc:featureList edam:operation_0420, edam:operation_0445, edam:operation_0463, edam:operation_2575 ; sc:name "STarMir" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sfold.wadsworth.org/starmir.html" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:26810894" ; sc:description "A web-server for structural annotation of a protein based on its similarity with known protein structures." ; sc:featureList edam:operation_0226 ; sc:name "StarPDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/starpdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3324, edam:topic_3474 ; sc:citation , "pmcid:PMC10469104", "pubmed:37603724" ; sc:description "StarPep toolbox is a software for studying the antimicrobial peptides' (AMPs) chemical space with molecular network-based representations and similarity searching models. 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It provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles." ; sc:featureList edam:operation_2945 ; sc:license "Artistic-2.0" ; sc:name "Starr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Starr.html" ; biotools:primaryContact "Benedikt Zacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0097, edam:topic_3169, edam:topic_3170, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC7722316", "pubmed:33292397" ; sc:description """uniform processing and accurate identification of STARR-seq active regions. conda create -n starrpeaker python=2.7 pybedtools. statsmodels (v0.10.1, use v0.10.2 or earlier, new function statsmodels/tools/validation/validation.py introduced in v0.11.0 may introduce error in Python 2). Preferably, create a conda environment with Python 2.7. starrpeaker --prefix --chromsize --blacklist --cov --input --output --threshold 0.05.""" ; sc:featureList edam:operation_2409, edam:operation_3222, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "STARRPeaker" ; sc:url "http://github.com/gersteinlab/starrpeaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0625, edam:topic_0780, edam:topic_3452, edam:topic_3474 ; sc:citation ; sc:description "Spatial and Texture Analysis of Root System Architecture with Earth Mover's Distance (STARSEED)." ; sc:featureList edam:operation_3196, edam:operation_3799, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STARSEED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GatorSense/STARSEED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3316, edam:topic_3673, edam:topic_3794 ; sc:citation , "pmcid:PMC7077848", "pubmed:32134915" ; sc:description """Prepare the input directory for 'ASA3P', creating automatically a _config.xls_ file from the reads provided. Requires one or more reference files (.gbk recommended) and a directory with FASTQ files (.fq or .fastq, gzipped). Metadata can be supplied via command line or with a JSON file.""" ; sc:featureList edam:operation_0362, edam:operation_3216, edam:operation_3436, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "start-asap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/quadram-institute-bioscience/start-asap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0593, edam:topic_0736, edam:topic_0749, edam:topic_3068 ; sc:citation , "pmcid:PMC4702845", "pubmed:26582925" ; sc:description """a database of hydrogen/deuterium exchange data on protein folding and stability. There are 57 entries in Start2Fold as of Aug. 30, 2020. We welcome additional data submissions! Please fill in and send the template below to Wim Vranken: XML template. If you have any questions or suggestions regarding the database, the content or the submission procedure, please contact us by sending a message here. The database of hydrogen/deuterium exchange data on protein folding and stability.""" ; sc:featureList edam:operation_0303, edam:operation_0404, edam:operation_2415, edam:operation_2422, edam:operation_3431 ; sc:name "Start2Fold" ; sc:url "http://start2fold.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622, edam:topic_3125, edam:topic_3168 ; sc:citation ; sc:description "Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence." ; sc:featureList edam:operation_0491, edam:operation_3662, edam:operation_3663 ; sc:name "StartLink+" ; sc:url "https://github.gatech.edu/GeneMark/startlink" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation ; sc:description "A tool to detect translation initiation sites in genomic sequences." ; sc:featureList edam:operation_0439 ; sc:name "StartScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/StartScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3068 ; sc:description "Comprehensive general statistics package. It incorporates all the descriptive statistics, parametric and non-parametric statistical tests, graphics and data transforms you will need for processing, analyzing and presenting data." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:name "Stat-200" ; sc:operatingSystem "Windows" ; sc:softwareVersion "2.1" ; sc:url "http://www.biosoft.com/w/stat200.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0749 ; sc:citation ; sc:description "A webserver for the prediction of Stat3 Inhibitor" ; sc:featureList edam:operation_0416, edam:operation_3928, edam:operation_3938, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "STAT3In" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/stat3in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Fast. Accurate. Easy to use. Stata is a complete, integrated software package that provides all your data science needs—data manipulation, visualization, statistics, and automated reporting" ; sc:featureList edam:operation_2238, edam:operation_2409 ; sc:license "Proprietary" ; sc:name "Stata" ; sc:softwareHelp ; sc:softwareVersion "17" ; sc:url "https://www.stata.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC7540394", "pubmed:32275351" ; sc:description """Automatically detect statistical reporting inconsistencies to increase reproducibility of meta-analyses. statcheck is a free, open source R package that can be used to automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies.""" ; sc:featureList edam:operation_2428, edam:operation_3435 ; sc:name "statcheck" ; sc:softwareHelp ; sc:url "http://statcheck.io" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3033, edam:format_3475 ; sc:name "Matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1636 ; sc:encodingFormat edam:format_3547 ; sc:name "Heat map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3366, edam:topic_3391 ; sc:citation ; sc:description "Classes and tools for multi-omics data integration." ; sc:featureList edam:operation_3436 ; sc:license "GPL-2.0" ; sc:name "STATegRa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/STATegRa.html" ; biotools:primaryContact "David Gomez-Cabrero", "Gordon Ball", "Patricia Sebastián-León" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_3169, edam:topic_3173, edam:topic_3305 ; sc:citation ; sc:description """rapid and reproducible chromatin state evaluation for custom genome annotation. StatHub - consistent rules-based chromatin state annotations across Roadmap, ENCODE, Blueprint, CEEHRC, and DEEP.""" ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_3222, edam:operation_3226 ; sc:name "StatePaintR" ; sc:url "http://www.statehub.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0102, edam:topic_3056 ; sc:citation , "pmcid:PMC9665859", "pubmed:36193999" ; sc:description "An R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations." ; sc:featureList edam:operation_0282, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "statgenMPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=statgenMPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:19875854" ; sc:description "Compute the statistical significance of multiple sequence alignments (of either nucleotide or amino acid sequences), much as BLAST’s E-values provide statistical significance for pairwise alignments." ; sc:featureList edam:operation_0492 ; sc:name "StatSigMA" ; sc:operatingSystem "Linux" ; sc:url "http://bio.cs.washington.edu/software/alignment_quality" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0621, edam:topic_3520 ; sc:citation , "pubmed:34600153" ; sc:description "Systematic integration and evaluation of statistical approaches for detecting differential expression in label-free quantitative proteomics." ; sc:featureList edam:operation_3557, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StatsPro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YanglabWCH/StatsPro/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2269, edam:topic_3303 ; sc:citation , "pmcid:PMC7660954", "pubmed:33215069" ; sc:description """Facilitating reproducible research through direct connection of data analysis with manuscript preparation. StatTag is a free plug-in for conducting reproducible research and creating dynamic documents using Microsoft Word with the R, Stata and SAS statistical packages.""" ; sc:featureList edam:operation_1812, edam:operation_3096, edam:operation_3435 ; sc:license "MIT" ; sc:name "StatTag" ; sc:url "https://github.com/StatTag/StatTag" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3520, edam:topic_3572 ; sc:citation ; sc:description "An easy to use tool provide a graphical user interface for quality control based shift signal correction, integration of metabolomic data from multi-batch experiments, and the comprehensive statistic analysis in non-targeted or targeted metabolomics." ; sc:featureList edam:operation_2238, edam:operation_2428, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "statTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.7" ; sc:url "http://bioconductor.org/packages/release/bioc/html/statTarget.html" ; biotools:primaryContact "Hemi Luan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:author ; sc:citation "pubmed:22038510" ; sc:description "Analyses peptide-peptide cross-links for protein-protein interaction or protein structure analysis." ; sc:featureList edam:operation_2406, edam:operation_3092 ; sc:license "Other" ; sc:name "StavroX" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.stavrox.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9055051", "pubmed:35487922" ; sc:description "Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STdeconvolve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/JEFworks-Lab/STdeconvolve" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "A tool for the computation of steady states and exploration of dynamics in intracellular biological networks." ; sc:featureList edam:operation_0244, edam:operation_3890, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SteadyCellPhenotype" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://steadycellphenotype.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0781, edam:topic_3168 ; sc:citation , "pmcid:PMC5597868", "pubmed:28948042" ; sc:description "Specific Transposable Element Aligner (HERV-K)." ; sc:featureList edam:operation_3461 ; sc:name "STEAK" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/applevir/STEAK" ; biotools:primaryContact "Cindy Santander", "Philippe Gambron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2830, edam:topic_3174, edam:topic_3293, edam:topic_3837 ; sc:citation , "pmcid:PMC8785982", "pubmed:35083165" ; sc:description "Clustering and Serotyping of Shigatoxin producing E. coli (STEC) using genomic cluster specific markers" ; sc:featureList edam:operation_0525, edam:operation_0553, edam:operation_2421, edam:operation_3227, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STECFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/LanLab/STECFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC9154219", "pubmed:35435214" ; sc:description "Fast 2D Template Detection with Accurate Orientation Estimation." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Steer nDetect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Biomedical-Imaging-Group/Steer-n-Detect" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3382, edam:topic_3473 ; sc:citation ; sc:description """Offensive Cyber Security Software for Embedding Shellcode in Images. StegArmory is an image-based steganography utility that can be used to embed and extract data from PNG images. StegArmory currently supports least significant bit (LSB) and pixel value differencing (PVD) encoding techniques. StegArmory was meant to embed and extract/execute shellcode payloads from images, though time-constraints didn't allow that feature of the project to be fully developed - this is left as an exercise for the user.""" ; sc:featureList edam:operation_3443 ; sc:name "StegArmory" ; sc:url "https://github.com/MarkoH17/StegArmory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3056, edam:topic_3321, edam:topic_3517 ; sc:citation ; sc:description "Identification of genetic outliers due to sub-structure and cryptic relationships." ; sc:featureList edam:operation_2238 ; sc:name "STEGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/dschlauch/stego" ; biotools:primaryContact "Daniel Schlauch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0749 ; sc:citation "pubmed:22638579" ; sc:description "Webserver for the integration of transcriptional, proteomic and interactome data to reveal regulatory and signalling networks." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2497, edam:operation_3439, edam:operation_3501 ; sc:name "SteinerNet" ; sc:url "http://fraenkel.mit.edu/steinernet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2269 ; sc:citation , "pmcid:PMC7011378", "pubmed:32039704" ; sc:description """a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets. RESULTS:We present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees""" ; sc:featureList edam:operation_0547, edam:operation_3802, edam:operation_3947 ; sc:name "STELAR" ; sc:url "https://islamazhar.github.io/STELAR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3572 ; sc:citation ; sc:description "A local pairwise aligner that has full sensitivity, i.e. guarantees to report all matches of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. For filtering it applies the SWIFT algorithm, for which we have developed a new, exact verification strategy." ; sc:featureList edam:operation_2928, edam:operation_3695 ; sc:name "Stellar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://www.seqan.de/projects/stellar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3170, edam:topic_3173, edam:topic_3308, edam:topic_3500 ; sc:citation , "pmcid:PMC10320151", "pubmed:37224539" ; sc:description "Web server for accurate spatial mapping of single cells based on spatial transcriptomics data." ; sc:featureList edam:operation_0314, edam:operation_2422, edam:operation_2871 ; sc:isAccessibleForFree true ; sc:name "STellaris" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spatial.rhesusbase.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:25344500" ; sc:description "A program for finding the maximum likelihood estimate of the species tree for the given gene trees, which undergo incomplete lineage sorting." ; sc:featureList edam:operation_0324 ; sc:name "STELLS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.engr.uconn.edu/~ywu/STELLS.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3344 ; sc:citation , "pmcid:PMC4086070", "pubmed:24852251" ; sc:description "Web-server that allows users to interactively query, visualize and interrogate molecular networks in the context of stem cell biology. It includes a comprehensive set of physical and regulatory interactions for both human and mouse. Any retrieved network can be readily examined for the presence of genes linked to stemness." ; sc:featureList edam:operation_3083 ; sc:isAccessibleForFree true ; sc:name "StemCellNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://stemcellnet.sysbiolab.eu" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:name "Gene identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3307, edam:topic_3344 ; sc:citation , "pmcid:PMC4489266", "pubmed:26007653" ; sc:description "Web-server that enables researchers to rapidly check whether a given list of genes can be associated with stemness. It compares the genes uploaded by the user with those in curated stemness signatures, and evaluates the statistical significance of the overlap. The results are then displayed in alternative formats showing the overall association of the whole set of input genes with stemness, as well as the occurrence of individual genes in the curated stemness signatures." ; sc:featureList edam:operation_0314, edam:operation_0315 ; sc:isAccessibleForFree true ; sc:name "StemChecker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://193.136.227.168:8080/stemchecker/stemsethome.jsf" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3335, edam:topic_3421, edam:topic_3474 ; sc:citation , , "pmcid:PMC8328310", "pmcid:PMC8387320", "pubmed:34339432", "pubmed:34456567" ; sc:description "Nomogram for the Prediction of Intrahospital Mortality Risk of Patients with ST-Segment Elevation Myocardial Infarction Complicated with Hyperuricemia." ; sc:featureList edam:operation_3503, edam:operation_3659, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "STEMI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bzxzmu.shinyapps.io/STEMI-with-Hyperuricemia-intrahospital-mortality/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_3174, edam:topic_3299, edam:topic_3837 ; sc:citation , "pmcid:PMC10188296", "pubmed:37154701" ; sc:description "Simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data." ; sc:featureList edam:operation_2426, edam:operation_3227, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "STEMSIM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BoyanZhou/STEMSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0769, edam:topic_3070, edam:topic_3170, edam:topic_3382 ; sc:citation ; sc:description "A web templating engine designed to organize, visualize, and en-able sharing of interactive visualization of analyses. STENCIL provides a framework for creating a template to display highly customizable visual frontends, leveraging REST API based backends, that provides programmatic data access and supports easy data dissemination." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3096, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STENCIL" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://pughlab.mbg.cornell.edu/stencil/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3474, edam:topic_3697, edam:topic_3941 ; sc:citation , "pubmed:36047699" ; sc:description "Microbial Source Tracking with ENvironment SeLection." ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "CC-BY-NC-SA-4.0" ; sc:name "STENSL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cozygene/FEAST/tree/STENSL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3299, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:34042467" ; sc:description "STEP3 is a computational tool to use the “evolutionary features” that can be recognized in genome sequences of diverse phages. These features, when integrated into an ensemble framework, achieved a stable and robust prediction performance when benchmarked against other prediction tools using phages from diverse sources." ; sc:featureList edam:operation_3092, edam:operation_3482 ; sc:name "STEP3" ; sc:url "http://step3.erc.monash.edu/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "Detect aberrations in DNA copy number data from aCGH (array-based comparative genomic hybridization) experiments." ; sc:featureList edam:operation_2495 ; sc:name "Stepgram" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.12" ; sc:url "http://bioinfo.cs.technion.ac.il/stepgram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description "Stepwise normalization functions for cDNA microarray data." ; sc:featureList edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "stepNorm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/stepNorm.html" ; biotools:primaryContact "Yuanyuan Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3474 ; sc:citation "pubmed:20568665" ; sc:description "A support vector machine (SVM) model that uses a simple descriptor space based on 35 properties of amino acid content, charge, hydrophilicity and polarity for the quantitative prediction of proteotypic peptides." ; sc:featureList edam:operation_2479 ; sc:name "STEPP" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cbb.pnnl.gov/portal/software/stepp.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9720893", "pubmed:36478706" ; sc:description "Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences." ; sc:featureList edam:operation_2008, edam:operation_2428, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "stepRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.5" ; sc:url "https://github.com/Vicky-Hunt-Lab/stepRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3524 ; sc:citation ; sc:description "Package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries." ; sc:featureList edam:operation_3660 ; sc:license "GPL-3.0" ; sc:name "STEPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://steps.sourceforge.net/STEPS/default.php" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640 ; sc:citation ; sc:description "This package implements a cancer samples classification strategy using multiple data sets. It uses the data type for which full measurements are available at the first stage, and the data type for which only partial measurements are available at the second stage. For incoming new samples, it quantifies how much improvement will be obtained if covariates of new samples for the data types at the second stage are measured." ; sc:featureList edam:operation_2990 ; sc:license "GPL-2.0" ; sc:name "stepwiseCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "https://bioconductor.riken.jp/packages/3.1/bioc/html/stepwiseCM.html" ; biotools:primaryContact "Askar Obulkasim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0130, edam:topic_3382 ; sc:citation , "pmcid:PMC7390991", "pubmed:32415957" ; sc:description """Using stereo images to enrich 3D visualization. Visualization in three-dimensional (3D) space is a standard and critical process for examining the complex structure of high dimensional data. Stereo imaging technology can be adopted to enhance 3D representation of any complex data, especially those consisting mostly of points and lines. We illustrate the simple steps that are involved and strongly encourage others to implement it in their own visualization software. To facilitate its application, we have also created a new software that can convert a regular 3D scatterplot or network figure to a stereo image (Liu, Singh, and Zheng 2020).""" ; sc:featureList edam:operation_0244, edam:operation_0337, edam:operation_3435 ; sc:license "MIT" ; sc:name "Stereo3D" ; sc:url "https://github.com/bioinfoDZ/Stereo3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "Rapid estimation of genome-wide correlation of continuous or interval feature data." ; sc:featureList edam:operation_3194 ; sc:name "StereoGene" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://stereogene.bioinf.fbb.msu.ru/" ; biotools:primaryContact "Elena Stavrovskaya" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "StereoSiTE is a package for the analysis and visualization of spatial transcriptome data. It builds on top of anndata, scanpy and squidpy, from which it inherits modularity and scalability. It provides analysis tools to dissect cellular neighborhood based on cell composition and quantitatively define cell-cell communication in spatial." ; sc:name "stereosite" ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/STOmics/stereosite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Workbench" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3407, edam:topic_3473, edam:topic_3520 ; sc:citation , "pubmed:33784068" ; sc:description "SteroidXtract is a deep-learning based bioinformatics tool for steroid MS2 extraction from untargeted metabolomics data." ; sc:featureList edam:operation_3637, edam:operation_3639, edam:operation_3803, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "SteroidXtract" ; sc:url "https://github.com/HuanLab/SteroidXtract" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_2259, edam:topic_3324, edam:topic_3524 ; sc:citation ; sc:description "Graphical software environment designed to enable easy and efficient simulation of a range of mathematical models of sexually transmitted infections. The software takes existing models from published literature, simulates them using CHASTE (Cancer, Heart and Soft Tissue Environment), and integrates existing open-source plotting software to visualise the results." ; sc:featureList edam:operation_3562 ; sc:license "BSD-3-Clause" ; sc:name "STI-GMaS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sti-gmas.org/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2200 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation ; sc:description "A tool for creating artificial T-cell repertoires and producing simulated sequencing data from them." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STIG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Benjamin-Vincent-Lab/stig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3382 ; sc:citation , "pubmed:33037602" ; sc:description """Psychophysical tests on mobile devices. StimuliApp is a free app designed to create psychophysical tests with precise timing on iOS and iPadOS devices. With a simple system of menus, you can design and run tests to assess perceptual capabilities, right on your iPad or iPhone.""" ; sc:featureList edam:operation_0337 ; sc:name "StimuliApp" ; sc:url "http://www.stimuliapp.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0130, edam:topic_2814, edam:topic_3510 ; sc:citation "pubmed:10775658", "pubmed:12824333", "pubmed:15044232", "pubmed:15044236", "pubmed:15073001", "pubmed:15215458", "pubmed:15301693", "pubmed:15608194", "pubmed:15980473" ; sc:description "STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them." ; sc:featureList edam:operation_2406, edam:operation_2414, edam:operation_2416, edam:operation_2479 ; sc:name "STING Millenium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/" ; biotools:primaryContact "Neshich G." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3053 ; sc:citation , "pmcid:PMC4015962", "pubmed:24606808" ; sc:description "System for integrated genomic resources and analysis." ; sc:featureList edam:operation_0362, edam:operation_2403 ; sc:license "GPL-2.0" ; sc:name "STINGRAY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://stingray.biowebdb.org/" ; biotools:primaryContact "Alberto MR Dávila" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3315, edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:32006678" ; sc:description """PET image reconstruction using physical and mathematical modelling for time of flight PET-MR scanners in the STIR library. This work demonstrates how computational and physical modelling of the positron emission tomography (PET) image acquisition process for a state-of-the-art integrated PET and magnetic resonance imaging (PET-MR) system can produce images comparable to the manufacturer. The GE SIGNA PET MR scanner is manufactured by General Electric and has time-of-flight (TOF) capabilities of about 390 ps. All software development took place in the Software for Tomographic Image Reconstruction (STIR: http: stir.sf.net) library, which is a widely used open source software to reconstruct data as exported from emission tomography scanners. The new software developments will be integrated into STIR, providing the opportunity for researchers worldwide to establish and expand their image reconstruction methods""" ; sc:featureList edam:operation_2426, edam:operation_3443, edam:operation_3660 ; sc:name "STIR" ; sc:url "http://stir.sourceforge.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2546 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196, edam:format_1199, edam:format_3468 ; sc:name "Small molecule structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0990 ; sc:encodingFormat edam:format_2330 ; sc:name "Compound name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2330, edam:format_3547 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2042 ; sc:encodingFormat edam:format_2330 ; sc:name "Evidence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0954 ; sc:encodingFormat edam:format_2330 ; sc:name "Database cross-mapping" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3314, edam:topic_3344 ; sc:author "Michael Kuhn" ; sc:citation , "pmcid:PMC2238848", "pubmed:18084021", "pubmed:19897548", "pubmed:22075997", "pubmed:24293645" ; sc:contributor "BMBF", "CPR", "EC FP6", "EMBL", "EMBO", "SUND-KU", "TUD" ; sc:description "Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature." ; sc:featureList edam:operation_2421, edam:operation_2423, edam:operation_2497, edam:operation_3083 ; sc:funder "BMBF", "CPR", "EC FP6", "EMBL", "EMBO", "SUND-KU", "TUD" ; sc:name "STITCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "HD-HuB" ; sc:softwareHelp ; sc:url "http://stitch.embl.de/" ; biotools:primaryContact "Michael Kuhn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2330 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2958 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid melting curve" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654 ; sc:author "Eivind Hovig", "Eivind Tøstesen", "Geir Ivar Jerstad" ; sc:citation ; sc:contributor "The Research Council of Norway" ; sc:description "Web-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users." ; sc:featureList edam:operation_0262, edam:operation_0456 ; sc:funder "The Research Council of Norway" ; sc:isAccessibleForFree true ; sc:name "Stitchprofiles" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "The Norwegian Radium Hospital", "UiO", "University of Oslo" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://stitchprofiles.uio.no/" ; biotools:primaryContact "Eivind Hovig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_2830, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:35325179" ; sc:description "Stitching coding TCR nucleotide sequences from V/J/CDR3 information." ; sc:featureList edam:operation_0232, edam:operation_3192, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Stitchr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JamieHeather/stitchr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Suite", "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2640, edam:topic_3418, edam:topic_3676 ; sc:citation , "pubmed:33408242" ; sc:description """Pediatric Cancer Genomic Data Sharing Ecosystem. This repository contains all bioinformatics workflows used on the St. Jude Cloud project. Officially, the repository is in beta — the project is adding workflows as they are developed and put into production. St. Jude Cloud is a pediatric catastrophic disease data sharing ecosystem created by St. Jude Children's Research Hospital.""" ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_2871 ; sc:license "MIT" ; sc:name "St Jude Cloud" ; sc:url "https://www.stjude.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0196, edam:topic_0769 ; sc:citation ; sc:description "stk is an extendable Python framework for automated molecular and supramolecular structure assembly and discovery." ; sc:featureList edam:operation_0310, edam:operation_0337 ; sc:name "stk" ; sc:url "http://github.com/lukasturcani/stk" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues. a downstream analysis toolkit for Spatial Transcriptomics data.""" ; sc:featureList edam:operation_0244, edam:operation_2495, edam:operation_3432, edam:operation_3435 ; sc:name "stLearn" ; sc:url "https://stlearn.readthedocs.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3570, edam:topic_3575 ; sc:citation , "pmcid:PMC7908717", "pubmed:33632116" ; sc:description "Sparse Tropical Matrix Factorization (STMF): Sparse data embedding and prediction by tropical matrix factorization." ; sc:featureList edam:operation_3435 ; sc:name "STMF" ; sc:url "https://github.com/Ejmric/STMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0749, edam:topic_2258, edam:topic_3336 ; sc:citation , "pmcid:PMC9538479", "pubmed:36213112" ; sc:description "A component for building interactive molecular visualizations within streamlit web-applications." ; sc:featureList edam:operation_0337, edam:operation_0478, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Stmol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/napoles-uach/stmol" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610 ; sc:citation ; sc:description "Exploratory movement analysis and report building with R package stmove | Abstract Background As GPS tags and data loggers have become lighter, cheaper, and longer-lasting, there has been a growing influx of data on animal movement. Simultaneously, methods of analyses and software to apply such methods to movement data have expanded dramatically. Even so, for many interdisciplinary researchers and managers without familiarity with the field of movement ecology and the open-source tools that have been developed, the analysis of movement data has remained an overwhelming challenge. Description Here we present stmove , an R package designed to take individual relocation data and generate a visually rich report containing a set of preliminary results that ecologists and managers can use to guide further exploration of their data" ; sc:featureList edam:operation_3557 ; sc:name "stmove" ; sc:url "https://github.com/dpseidel/stmove" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3299, edam:topic_3500, edam:topic_3697, edam:topic_3855 ; sc:citation , "pmcid:PMC8629388", "pubmed:34780461" ; sc:description "Welcome to Stoat, the environmental data annotation tool, a data fusion engine design to annotate biodiversity records with environmental remote sensing products. This tutorial provides a step-by-step guide to using the tools to explore, upload, manage, annotate, and download data." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "STOAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mol.org/stoat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2259, edam:topic_2269, edam:topic_3292 ; sc:citation "pubmed:24191070" ; sc:description "A novel, computationally efficient and extendable Matlab package for computational analysis of noise origin in the stochastic models of biochemical reactions." ; sc:featureList edam:operation_2238 ; sc:name "StochDecomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/p/stochdecomp/wiki/Home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2229 ; sc:citation , "pmcid:PMC7958472", "pubmed:33722188" ; sc:description "stochprofML is a tool for sochastic profiling using maximum likelihood estimation in R." ; sc:featureList edam:operation_0314, edam:operation_3435, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "stochprofML" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=stochprofML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0160, edam:topic_2814 ; sc:citation "pubmed:19167704" ; sc:description "A new algorithm to find aligned residues in two proteins with desired rmsd value." ; sc:featureList edam:operation_2487 ; sc:name "STON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bs.ipm.ir/softwares/ston/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0749, edam:topic_3314, edam:topic_3422 ; sc:citation , "pmcid:PMC7493926", "pubmed:32934277" ; sc:description """a database for kidney stone modulatory proteins with experimental evidence. StoneMod is the database of kidney stone (nephrolithiasis or urolithiasis) modulators, which provides the information of calcium oxalate crystal promoter and inhibitor proteins. These protein modulators play key roles in kidney stone formation processes involving crystallization, crystal growth, crystal aggregation, and crystal adhesion to renal tubular cells. Authors: Medical proteomics unit.""" ; sc:featureList edam:operation_3431, edam:operation_3436, edam:operation_3454 ; sc:name "StoneMod" ; sc:url "https://www.stonemod.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_2269, edam:topic_3474 ; sc:citation ; sc:description "STonKGs is a Sophisticated Transformer that can be jointly trained on biomedical text and knowledge graphs. This multimodal Transformer combines structured information from KGs with unstructured text data to learn joint representations." ; sc:featureList edam:operation_0310, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STonKGs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://huggingface.co/stonkgs/stonkgs-150k" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2259, edam:topic_3071 ; sc:citation , "pmcid:PMC10017094", "pubmed:36897014" ; sc:description "Package that allows users to store SBGN maps into a Neo4j database, query the database, and convert query results back to valid SBGN maps." ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_2429 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "StonPy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/adrienrougny/stonpy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2840, edam:topic_3343, edam:topic_3386, edam:topic_3500 ; sc:citation ; sc:description """An In-Silico Alternative to Animal Testing for Acute Systemic and TOPical TOXicity. The STopTox app is a fast, reliable, and user-friendly tool available as an alternative method for assessing the potential of chemicals to cause acute toxicity.""" ; sc:name "STopTox" ; sc:url "https://stoptox.mml.unc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_3050, edam:topic_3293 ; sc:citation , "pmcid:PMC7678788", "pubmed:33216894" ; sc:description """a database on the reproductive strategies of teleost fishes. Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability, nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STOREFISH 2.0, an online database easing the sharing of an original dataset on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2 contains the information for 80 freshwater fish species and 50 traits from the analysis of 1219 references. It is anticipated that this new database could be useful for freshwater biodiversity research, conservation, assessment, and management.""" ; sc:featureList edam:operation_0306, edam:operation_0490, edam:operation_3891 ; sc:name "STOREFISH" ; sc:softwareVersion "2.0" ; sc:url "http://www.storefish.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3168 ; sc:citation "pubmed:15130805" ; sc:description "The tool combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format.More specifically, it extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches as well as Pfam predictions and Protparam calculations of protein physicochemical properties." ; sc:featureList edam:operation_0250, edam:operation_2479 ; sc:name "STORM" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.biw.kuleuven.be/logt/STORM.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3318, edam:topic_3344, edam:topic_3382 ; sc:description "Quantify relative localization of proteins based on STochastic Optical Reconstruction Microscopy (STORM)-based single molecule positional data." ; sc:featureList edam:operation_3432, edam:operation_3443, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "STORM-based Relative Localization Analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/57647-storm-based-relative-localization-analysis" ; biotools:primaryContact "Rengasayee Veeraraghavan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3474 ; sc:citation ; sc:description "Simple and Timely Optode Registration Method for Functional Near-Infrared Spectroscopy (fNIRS)." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "STORM-NET" ; sc:url "https://github.com/yoterel/STORM-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3303, edam:topic_3810, edam:topic_3895 ; sc:citation ; sc:description """Sequence-to-function deep learning frameworks for synthetic biology. While synthetic biology has revolutionized our approaches to medicine, agriculture, and energy, the design of novel circuit components beyond nature-inspired templates can prove itself challenging without well-established design rules. This repository provides code for Valeri, Collins, et al. 2019.""" ; sc:featureList edam:operation_3095, edam:operation_3695, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "STORM" ; sc:url "http://www.github.com/midas-wyss/storm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3360 ; sc:citation , "pmcid:PMC9825731", "pubmed:36632327" ; sc:description "R package and Shiny application designed to visualize real-world data from clinical patient registries." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StoryboardR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/TheMillerLab/StoryboardR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3747 ; sc:name "Protein report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_3747 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pmcid:PMC5891225", "pubmed:29400476" ; sc:description "A tool for analyzing proteomics data acquired by mass spectrometry. Quantifies proteins from shotgun MS/MS data using normalized spectral count or normalized spectral index techniques. Incorporates distributed techniques to account for peptide sequence degeneracy." ; sc:featureList edam:operation_3630, edam:operation_3634, edam:operation_3637, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "StPeter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.0" ; sc:url "http://tppms.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3295, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "stPlus is a reference-based method for the accurate enhancement of spatial transcriptomics. stPlus is a reference-based method for the accurate enhancement of spatial transcriptomics. Based on an auto-encoder with a carefully tailored loss function, stPlus performs joint embedding and predicts spatial gene expression via a weighted k-NN. The spatial transcriptomics enhanced by stPlus can provide better characterization of cell heterogeneity." ; sc:featureList edam:operation_0314, edam:operation_2454, edam:operation_3463 ; sc:license "MIT" ; sc:name "stPlus" ; sc:url "http://health.tsinghua.edu.cn/software/stPlus/" ; biotools:primaryContact "Rui Jiang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3299, edam:topic_3569 ; sc:citation , "pmcid:PMC5324240", "pubmed:28231764" ; sc:description "Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided." ; sc:featureList edam:operation_3664 ; sc:license "GPL-3.0" ; sc:name "stpm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.7.5" ; sc:url "https://cran.r-project.org/web/packages/stpm/index.html" ; biotools:primaryContact "Ilya Y. Zhbannikov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:31449021" ; sc:description "Video Saliency Prediction using Spatiotemporal Residual Attentive Networks | This repository is the implementation of 'Video Saliency Prediction using Spatiotemporal Residual Attentive Networks (TIP2019)'" ; sc:name "Spatiotemporal Residual Attentive Networks" ; sc:url "https://github.com/ashleylqx/STRA-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3068, edam:topic_3382 ; sc:citation , "pmcid:PMC10117057", "pubmed:36939355" ; sc:description "A tool to Simply Track bacterial cells in microscopy time-lapse images." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "STrack" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Helena-todd/STrack" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3382 ; sc:citation , "pubmed:35639941" ; sc:description "STracking is a python framework to develop particles tracking pipeline. This library has been developed to track intra-cellular object in microscopy 2D+t and 3D+t images, but can be use to any spots tracking application in 2D+t and 3D+t images." ; sc:featureList edam:operation_3890 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "STracking" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sylvainprigent/stracking" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3300, edam:topic_3383 ; sc:citation , "pmcid:PMC5577835", "pubmed:28854948" ; sc:description "Experimental, cross-platform tool primarily for freehand 3D ultrasound acquisition, visualisation and elastography. It can also be used with 3D medical data of any sort: its segmentation and surface extraction facilities are particularly powerful. It can load most types of DICOM image files and has unique facilities to measure bone cortical thickness from CT data." ; sc:featureList edam:operation_3443 ; sc:name "Stradwin" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "5.3" ; sc:url "http://mi.eng.cam.ac.uk/~rwp/stradwin/" ; biotools:primaryContact "D. Thurtle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3334, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC8361843", "pubmed:34389037" ; sc:description "Straglr is a tool that can be used for genome-wide scans for tandem repeat(TR) expansions or targeted genotyping using long-read alignments." ; sc:featureList edam:operation_0239, edam:operation_0487, edam:operation_3196, edam:operation_3216, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Straglr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/straglr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_3174 ; sc:citation ; sc:description """Strain-level profiling of metagenomic samples using variation graphs. StrainFLAIR (STRAIN-level proFiLing using vArIation gRaph) is a tool for strain identification and quantification that uses variation graph representation of genes sequences. StrainFLAIR is sub-divided into two main parts: first, an indexing step that stores clusters of reference genes into variation graphs, and then, a query step using mapping of metagenomic reads to infere strain-level abundances in the queried sample. The input for indexation is a collection of complete genomes, draft genomes or metagenome-assembled genomes from which genes will be predicted. The input for query is the so-created graph and any read file.""" ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_2495, edam:operation_3227 ; sc:license "AGPL-3.0" ; sc:name "StrainFLAIR" ; sc:url "http://github.com/kevsilva/StrainFLAIR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3277, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC8900328", "pubmed:35255937" ; sc:description "A toolkit to track and characterize low-abundance strains in complex microbial communities." ; sc:featureList edam:operation_3227, edam:operation_3472, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "StrainGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/strainge" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2912 ; sc:name "Strain accession" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2912 ; sc:name "Strain accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3473 ; sc:citation ; sc:description "The largest integrated microbial knowledge base." ; sc:featureList edam:operation_2421 ; sc:name "StrainInfo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:url "http://www.straininfo.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC8771625", "pubmed:35057847" ; sc:description "Full-length de novo viral haplotype reconstruction from noisy long reads." ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Strainline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HaploKit/Strainline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation ; sc:description "Accurate strain-level microbiome composition analysis from short reads." ; sc:featureList edam:operation_3196, edam:operation_3435, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StrainScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liaoherui/strainScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pmcid:PMC9939595", "pubmed:36814618" ; sc:description "A novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide." ; sc:featureList edam:operation_0362, edam:operation_0523, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:name "StrainSelect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://strainselect.secondgenome.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:35776122" ; sc:description "StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high complexity metagenome sequencing data at strain resolution." ; sc:featureList edam:operation_0310, edam:operation_3219, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "StrainXpress" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HaploKit/StrainXpress" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation , "pubmed:33493821" ; sc:description """An enhanced user interface to facilitate interpretation of MPS data. STRait Razor Online (SRO) serves as the user-interface (UI) for analyzing sequencing data with STRait Razor. Using the SRO, converts STRait Razor* sequence-based allele calls into genotype tables for and/or bar plots for downstream analysis. STRait Razor Online also allows the user to control the genotype calls using several thresholds (e.g., heterozygous balance, strand balance, etc.). Read strands are merged and reported as single strand (Default = Forward) in Genotype Tables.""" ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "STRaitRazor" ; sc:url "https://www.unthsc.edu/straitrazor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3674 ; sc:description "Software platform for alignment, analysis, visualization, and management of data generated by NGS platforms. It supports workflows for RNA-Seq, DNA-Seq, small RNA-Seq, ChIP-seq, and Methyl-Seq data analysis." ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_2403, edam:operation_3218 ; sc:name "Strand NGS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:url "http://www.strand-ngs.com/" ; biotools:primaryContact "Contact Form", "Strand NGS Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_0157, edam:topic_0623 ; sc:citation "pubmed:11301311", "pubmed:14668241" ; sc:description "The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included." ; sc:featureList edam:operation_0295, edam:operation_0492, edam:operation_0504, edam:operation_2488 ; sc:name "STRAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatics.org/strap/" ; biotools:primaryContact "Christoph Gille" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3403, edam:topic_3421, edam:topic_3577 ; sc:citation , "pubmed:36754375" ; sc:description "Multivariable prediction models to predict those at low, medium, and high risk across in-hospital death, 30-day death, and residence change after hip fracture." ; sc:featureList edam:operation_2428, edam:operation_3503, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "stratify-hip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://stratifyhip.co.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0194, edam:topic_0634 ; sc:citation "pubmed:23661681" ; sc:description "STRAW is a web server of workflows for reconstruction of phylogenies of species using 3 species tree methods: MP-EST, STAR, and NJst." ; sc:featureList edam:operation_0544, edam:operation_0546, edam:operation_0557, edam:operation_3221, edam:operation_3478 ; sc:name "STRAW" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/" ; biotools:primaryContact "Liang Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description "Strawberry is a C++ program for fast and accurate ab initio transcript reconstruction and quantification from RNA-seq data." ; sc:featureList edam:operation_2423 ; sc:license "MIT" ; sc:name "Strawberry" ; sc:softwareVersion "1.1.2" ; sc:url "https://github.com/ruolin/strawberry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:18776194" ; sc:description "Bioinformatics application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different situations." ; sc:featureList edam:operation_0438, edam:operation_0445 ; sc:name "STREAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://stream.imb.uq.edu.au/" ; biotools:primaryContact "Denis C. Bauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation ; sc:description "This package encourages a style of programming where data is 'streamed' from disk into R via a 'producer' and through a series of 'consumers' that typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation." ; sc:featureList edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "Streamer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Streamer.html" ; biotools:primaryContact "Martin Morgan" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2534 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence attribute" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3673 ; sc:citation , "pmcid:PMC10112951", "pubmed:37027230" ; sc:description "Fast low-memory duplicate marking using a Bloom filter." ; sc:featureList edam:operation_3695, edam:operation_3963 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "streammd" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/delocalizer/streammd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation "pubmed:22581179" ; sc:description "Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples." ; sc:featureList edam:operation_3227 ; sc:name "Strelka" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/strelkasomaticvariantcaller/" ; biotools:primaryContact "Christopher T. Saunders" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_3169, edam:topic_3295, edam:topic_3794 ; sc:citation , "pubmed:33760053" ; sc:description "STREME is accurate and versatile sequence motif discovery tool. The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). MEME-ChIP performs a comprehensive motif-based analysis of ChIP-seq and other large sequence datasets." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0240, edam:operation_0438 ; sc:name "STREME" ; sc:url "http://meme-suite.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3070, edam:topic_3336, edam:topic_3375 ; sc:citation , "pubmed:33051671" ; sc:description "A compendium of streptomycetes natural products." ; sc:featureList edam:operation_3216, edam:operation_3482, edam:operation_3938 ; sc:name "StreptomeDB" ; sc:url "http://www.pharmbioinf.uni-freiburg.de/streptomedb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3519, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6102892", "pubmed:30129428" ; sc:description """Detecting and discovering pathogenic short tandem repeat expansions. Dashnow, Harriet, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, et al. 2018. “STRetch: Detecting and Discovering Pathogenic Short Tandem Repeat Expansions.” Genome Biology 19 (1): 121. https://doi.org/10.1186/s13059-018-1505-2.""" ; sc:featureList edam:operation_0379, edam:operation_3196, edam:operation_3227 ; sc:license "MIT" ; sc:name "STRetch" ; sc:url "http://github.com/Oshlack/STRetch" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Needleman-Wunsch rapid global alignment of two sequences." ; sc:featureList edam:operation_0491 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "stretcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/stretcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Pairwise sequence alignment of DNA or protein sequences using Myers and Miller global alignment." ; sc:featureList edam:operation_0491 ; sc:name "stretcher-api (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/Tools/webservices/services/psa/emboss_stretcher_rest" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Improved version of the Needleman-Wunsch algorithm that allows rapid global alignment of two larger sequences." ; sc:featureList edam:operation_0491, edam:operation_0496 ; sc:name "stretcher (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/psa/emboss_stretcher" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Calculates a global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space." ; sc:featureList edam:operation_2403 ; sc:name "stretcher WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/stretcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0654, edam:topic_2275, edam:topic_3332, edam:topic_3524 ; sc:citation "pubmed:18974334" ; sc:description "The program explores stretching just a single strand of DNA using optical tweezers or fluid flow. Experiment with the forces involved and measure the relationship between the stretched DNA length and the force required to keep it stretched." ; sc:featureList edam:operation_0279, edam:operation_2426 ; sc:name "Stretching DNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://phet.colorado.edu/en/simulation/stretching-dna" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2305 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3071 ; sc:citation , ; sc:description "Prints the elements which are strictly included in the template." ; sc:featureList edam:operation_3695 ; sc:name "strictlyincludegff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_1317, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:15215436" ; sc:description "Takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map." ; sc:featureList edam:operation_0249, edam:operation_0319, edam:operation_0320 ; sc:name "STRIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webclu.bio.wzw.tum.de/stride/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:26755626" ; sc:description "The program integrates string and de Bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions." ; sc:featureList edam:operation_0310 ; sc:name "StriDe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/ythuang0522/StriDe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Spatial TRanscrIptomics DEconvolution by topic modeling (STRIDE), is a computational method to decompose cell types from spatial mixtures by leveraging topic profiles trained from single-cell transcriptomics. Besides the cell-type composition deconvolution, STRIDE also provides several downstream analysis functions, including signature (i.e., topic) detection and visualization, spatial clustering and domain identification based on neighborhood cell populations and reconstruction of three-dimensional architecture from sequential ST slides of the same tissue." ; sc:featureList edam:operation_3629, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STRIDE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DongqingSun96/STRIDE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0152, edam:topic_0153, edam:topic_0154, edam:topic_0593, edam:topic_2275 ; sc:citation ; sc:description """Steric hindrance estimator. STRIDER, Steric hindrance estimater, is a web server which can estimate and report inter- and intra- molecular steric hindrances based on the atomic van der walls radius of elements, participating in molecule formation. Thus, STRIDER acts as an important tool not only in the modeling of biomacromolecular structures like carbohydrates, lipids, nucleic acids & proteins and their complexes with themselves & small molecules, but also, in the modeling of any chemical structure.""" ; sc:featureList edam:operation_1836, edam:operation_3899, edam:operation_3938 ; sc:name "STRIDER" ; sc:url "http://www.iith.ac.in/strider/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_2814 ; sc:citation "pubmed:22039207" ; sc:description "A program to evaluate protein multiple sequence alignments using a single protein structure." ; sc:featureList edam:operation_0492, edam:operation_2479 ; sc:name "STRIKE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.tcoffee.org/Projects/strike/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation , "pmcid:PMC9805590", "pubmed:36398887" ; sc:description "User-friendly, efficient analysis of structural identifiability and observability." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STRIKE-GOLDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "4.0" ; sc:url "https://github.com/afvillaverde/strike-goldd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128 ; sc:citation ; sc:description "A database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available." ; sc:featureList edam:operation_0276 ; sc:name "STRING" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://string-db.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0128 ; sc:citation , "pmcid:PMC5210637", "pubmed:27924014" ; sc:description "Imports protein-protein and protein-chemical interaction data from STRING and STITCH databases into Cytoscape." ; sc:featureList edam:operation_2422, edam:operation_2497, edam:operation_3083 ; sc:name "stringApp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.0" ; sc:url "http://apps.cytoscape.org/apps/stringapp" ; biotools:primaryContact , "Lars Juhl Jensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128 ; sc:citation , "pmcid:PMC3531103", "pubmed:23203871" ; sc:description "This package provides a R interface to the STRING protein-protein interactions database." ; sc:featureList edam:operation_2421 ; sc:license "GPL-2.0" ; sc:name "STRINGdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/STRINGdb.html" ; biotools:primaryContact "Alexander Roth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26231430" ; sc:description "A toolbox for a construction of protein-protein interaction networks through the ‘STRING’ application programming interface, and an inference of Gaussian networks through ‘SIMoNe’ and ‘WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided to import automatically networks into an active ‘Cytoscape’ session." ; sc:featureList edam:operation_2464 ; sc:name "stringgaussnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/stringgaussnet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3168 ; sc:citation "pubmed:25183486" ; sc:description "A novel, hash based method for constructing the string graph." ; sc:featureList edam:operation_0524 ; sc:name "StringGraph" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cs.tau.ac.il/~bchor/StringGraph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation , "pubmed:27605103" ; sc:description "stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner." ; sc:featureList edam:operation_0310, edam:operation_2928 ; sc:name "stringMLST" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://jordan.biology.gatech.edu/page/software/stringmlst/index.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus." ; sc:featureList edam:operation_3258, edam:operation_3680 ; sc:license "Artistic-2.0" ; sc:name "StringTie" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://ccb.jhu.edu/software/stringtie/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3462 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Database portal", "Desktop application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2533, edam:topic_2885, edam:topic_3071 ; sc:citation , "pubmed:35395114" ; sc:description "A graphical application for detecting known pathogenic short tandem repeats in sequencing data" ; sc:featureList edam:operation_0564, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "STRipy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://stripy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data. It is capable of detecting novel STR expansions, that is expansions where there is no STR in the reference genome at that position (or a different repeat unit from what is in the reference). It can also detect STR expansions that are annotated in the reference genome. STRling uses kmer counting to recover mis-mapped STR reads. It then uses soft-clipped reads to precisely discover the position of the STR expansion in the reference genome." ; sc:featureList edam:operation_0379 ; sc:name "STRling" ; sc:softwareVersion "v0.4.2" ; sc:url "https://github.com/quinlan-lab/STRling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099 ; sc:citation ; sc:description "Structural RNA motif search that takes as input the secondary structure of the query and a target sequence database, and reports all occurrences of the query in the target. The search is based on subtree homeomorphism for ordered, rooted trees (which we use to represent the RNA structures) ." ; sc:featureList edam:operation_0224, edam:operation_0239, edam:operation_2421 ; sc:name "STRMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.2" ; sc:url "http://www.cs.bgu.ac.il/~vaksler/STRMS.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0102, edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC9753264", "pubmed:36522758" ; sc:description "Flexible seed size enables ultra-fast and accurate read alignment." ; sc:featureList edam:operation_0495, edam:operation_3198, edam:operation_3211, edam:operation_3227, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "strobealign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ksahlin/strobealign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3512 ; sc:citation ; sc:description """an alternative to k-mers for sequence comparison. A repository for generating strobemers and evaluation.""" ; sc:featureList edam:operation_0259, edam:operation_2451, edam:operation_3472 ; sc:name "strobemers" ; sc:url "https://github.com/ksahlin/strobemers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3063, edam:topic_3170, edam:topic_3518 ; sc:description "This package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients." ; sc:featureList edam:operation_2990 ; sc:license "GPL-3.0" ; sc:name "STROMA4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/STROMA4.html" ; biotools:primaryContact "Sadiq Saleh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC8311964", "pubmed:34311761" ; sc:description "STRONG resolves strains on assembly graphs by resolving variants on core COGs using co-occurrence across multiple samples." ; sc:featureList edam:operation_0310, edam:operation_0436, edam:operation_0487 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STRONG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/chrisquince/STRONG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0749, edam:topic_2259, edam:topic_3512, edam:topic_3957 ; sc:citation ; sc:description """a Cytoscape application for protein-protein interaction analysis. An application for protein-protein interaction analysis. StrongestPath is a Cytoscape 3 application that enables to look for one or more cascades of interactions connecting two single or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases.""" ; sc:featureList edam:operation_2464, edam:operation_2949, edam:operation_3927 ; sc:name "StrongestPath" ; sc:url "http://github.com/zmousavian/StrongestPath" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3673 ; sc:citation ; sc:description "Targeted profiling of short tandem repeats in whole-genome sequencing data." ; sc:featureList edam:operation_0379 ; sc:name "STRScan" ; sc:operatingSystem "Linux" ; sc:url "http://darwin.informatics.indiana.edu/str/" ; biotools:primaryContact "Haixu Tang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0632, edam:topic_0749, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description "A alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio." ; sc:featureList edam:operation_0484, edam:operation_3185, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "STRspy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/unique379r/strspy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_3172, edam:topic_3474, edam:topic_3520 ; sc:citation , "pubmed:33325493" ; sc:description """an R/bioconductor-based framework for standardised metabolomics data analysis and beyond. Quality Control Report for Mass Spectrometry (QCRMS)-based Metabolomics experiments. Statistics in R Using Class-based Templates. Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. Data processing & analysis tools for Metabolomics and other omics. An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "struct" ; sc:url "http://bioconductor.org/packages/struct" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2269, edam:topic_3056 ; sc:citation , "pmcid:PMC8963280", "pubmed:35080599" ; sc:description "A Rcpp package for ancestry profile and population structure inference from F4 statistics." ; sc:featureList edam:operation_0337, edam:operation_3658 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Struct-f4" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bitbucket.org/plibradosanz/structf4/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0128, edam:topic_0154, edam:topic_3407, edam:topic_3474 ; sc:citation ; sc:description """A graph attention network for structure based predictions of protein-protein interactions. A PyTorch implementation of GCN with mutual attention for protein-protein interaction prediction. Struct2Graph uses two graph convolutional networks (GCNs) with weight sharing, and a mutual attention network to extract relevant geometric features related toquery protein pairs. The details of the GCN architecture is described in our paper (currently under review).""" ; sc:featureList edam:operation_0272, edam:operation_2492, edam:operation_3094, edam:operation_3929 ; sc:name "Struct2Graph" ; sc:url "https://github.com/baranwa2/Struct2Graph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_0130, edam:topic_0602 ; sc:citation "pubmed:20513650" ; sc:description "Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure based approach." ; sc:featureList edam:operation_0272, edam:operation_0302, edam:operation_0474, edam:operation_2492, edam:operation_3439 ; sc:name "Struct2Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://struct2net.csail.mit.edu" ; biotools:primaryContact "Struct2Net Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_3170 ; sc:citation ; sc:description "A complete and robust open-source software solution for index-based search of RNA sequence-structure patterns." ; sc:featureList edam:operation_0224 ; sc:name "Structator" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://www.zbh.uni-hamburg.de/?id=271" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0769 ; sc:citation , "pubmed:33048753" ; sc:description """Flexible Visualization Design through Data-Agnostic and Reusable Graphical Structures. Information visualization research has developed powerful systems that enable users to author custom data visualizations without textual programming. These systems can support graphics-driven practices by bridging lazy data-binding mechanisms with vector-graphics editing tools. Yet, despite their expressive power, visualization authoring systems often assume that users want to generate visual representations that they already have in mind rather than explore designs. They also impose a data-to-graphics workflow, where binding data dimensions to graphical properties is a necessary step for generating visualization layouts. In this paper, we introduce StructGraphics, an approach for creating data-agnostic and fully reusable visualization designs""" ; sc:featureList edam:operation_0337, edam:operation_3096 ; sc:name "StructGraphics" ; sc:url "https://www.lri.fr/~fanis/StructGraphics/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0176, edam:topic_2814 ; sc:citation , "pmcid:PMC4765231", "pubmed:26911476" ; sc:description "Scalable and extensible tool for two-dimensional representation of protein surfaces." ; sc:featureList edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "Structuprint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dgkontopoulos.io/Structuprint/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0166, edam:topic_0736, edam:topic_3308 ; sc:citation , "pmcid:PMC9319604", "pubmed:35881481" ; sc:description "A web server for exploring a database of and generating protein structural features from human cell lines and tissues." ; sc:featureList edam:operation_0303, edam:operation_0570, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "structural signatures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://structural-server.kinametrix.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , , , , , "pmcid:PMC1461096", "pmcid:PMC1462648", "pmcid:PMC1974779", "pmcid:PMC3518025", "pubmed:10835412", "pubmed:12930761", "pubmed:15969739", "pubmed:18784791", "pubmed:21564903" ; sc:description "The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "Structure" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://web.stanford.edu/group/pritchardlab/structure.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0166, edam:topic_0199, edam:topic_2640 ; sc:citation , "pmcid:PMC4495296", "pubmed:25765346" ; sc:description "Module for the annotation of cancer-related single-nucleotide variants at protein–protein interfaces." ; sc:featureList edam:operation_0361 ; sc:name "Structure-PPi" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://structureppi.bioinfo.cnio.es/Structure" ; biotools:primaryContact "Miguel Vazquez", "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0199, edam:topic_0601, edam:topic_2640 ; sc:citation , "pubmed:35751824" ; sc:description "Annotating Cancer-Related Variants at Protein-Protein Interface with Structure-PPi." ; sc:featureList edam:operation_0417, edam:operation_0495, edam:operation_3226, edam:operation_3227, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "Structure-PPi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rbbt.bsc.es/StructurePPI/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317 ; sc:citation ; sc:description "A wrapper program to parallelize and automate runs of \"Structure\", \"fastStructure\" and \"MavericK\"." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Structure_threader" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "https://github.com/StuntsPT/Structure_threader" ; biotools:primaryContact "Francisco Pina Martins" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:encodingFormat edam:format_3752 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3332, edam:topic_3534 ; sc:citation ; sc:description "StructureProfiler was developed as an all-in-one tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods. Test configurations based on either the Astex, the Iridium HT, the Platinum, or the combination of all three criteria catalogs. (Note that RSCC as an electron density validation criteria was replaced by EDIAm scoring)." ; sc:featureList edam:operation_3695 ; sc:name "StructureProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proteinsplus.zbh.uni-hamburg.de/#structureprofiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Novel regularization scheme over multitask regression , which allows shared sparsity patterns for related inputs and outputs to be optimally estimated.  Such patterns capture multiple related single nucleotide polymorphisms (SNPs) that jointly influence multiple-related expression traits." ; sc:featureList edam:operation_2429, edam:operation_3659 ; sc:name "Structured Input-output Lasso" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=483" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099, edam:topic_3168, edam:topic_3170 ; sc:citation "pubmed:9076633" ; sc:description "A computational system which has been developed to permit the use of a broad array of approaches to the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences." ; sc:featureList edam:operation_2478 ; sc:name "StructureLab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://binkley2.ncifcrf.gov/users/bshapiro/structurelab/structureLab.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0128, edam:topic_3318, edam:topic_3382, edam:topic_3892 ; sc:citation , "pmcid:PMC7831659", "pubmed:33505991" ; sc:description """A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions. Studying biomolecular interactions is a crucial but challenging task. Due to their large scales, many biomolecular interactions are difficult to be simulated via all atom models. An effective approach to investigate the biomolecular interactions is highly demanded in many areas. Here we introduce a Structure Manipulation (StructureMan) program to operate the structures when studying the large-scale biomolecular interactions. This novel StructureMan tool provides comprehensive operations which can be utilized to study the interactions in various large biological systems. Combining with electrostatic calculation programs such as DelPhi and DelPhiForce, StructureMan was implemented to reveal the detailed electrostatic features in two large biological examples, the viral capsid and molecular motor-microtubule complexes""" ; sc:featureList edam:operation_0337, edam:operation_2476, edam:operation_3431, edam:operation_3899, edam:operation_4009 ; sc:name "StructureMan" ; sc:url "http://compbio.utep.edu/static/downloads/script-for-munipulation2.zip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC7029954", "pubmed:32074134" ; sc:description """A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis. StructuRly is an R package containing a shiny application to produce detailed and interactive graphs of the results of a Bayesian cluster analysis obtained with the most common population genetic software used to investigate population structure, such as STRUCTURE or ADMIXTURE.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3196, edam:operation_3283, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "StructuRly" ; sc:url "https://nicocriscuolo.shinyapps.io/StructuRly/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3569 ; sc:citation , "pmcid:PMC4404673", "pubmed:25887541" ; sc:description "strum is a structural equation modelling software tool for genetic analysis." ; sc:featureList edam:operation_2478 ; sc:license "GPL-3.0" ; sc:name "strum" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.2" ; sc:url "https://cran.r-project.org/web/packages/strum/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3003, edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3063, edam:topic_3175, edam:topic_3325, edam:topic_3574, edam:topic_3958 ; sc:citation ; sc:description "Method that predicts the pathogenicity of deletions and duplications that affect one or more exons." ; sc:featureList edam:operation_2238, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "StrVCTVRE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://strvctvre.berkeley.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654 ; sc:description "Building and exploring indexes of small or large amounts of DNA data. The indexes are suffix trees, and can be constructed for single or multiple DNA sequences in very flexible ways. The input format is fasta. The output is in the form of tabular results, generally showing longest common substring (LCS) matches among the input sequences. You can also search for exact and inexact occurrences of user specified strings." ; sc:featureList edam:operation_2421 ; sc:name "STS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.4" ; sc:url "http://athena.bioc.uvic.ca/tools/STS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3360, edam:topic_3382 ; sc:citation "pubmed:21527030" ; sc:description "A set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images." ; sc:featureList edam:operation_3443 ; sc:name "STSE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.stse-software.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3318 ; sc:citation , "pmcid:PMC9577246", "pubmed:36277841" ; sc:description "Spatial-Temporal Synchronous Graph Transformer network (STSGT) for COVID-19 forecasting." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "STSGT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/soumbane/STSGT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_2814, edam:topic_2885, edam:topic_3407 ; sc:citation "pubmed:17537826" ; sc:description "StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_2406, edam:operation_2487 ; sc:name "StSNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ilyinlab.org/StSNP/" ; biotools:primaryContact "Alper Uzun", "Valentin Ilyinv" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Search a DNA database for matches with a set of STS primers." ; sc:featureList edam:operation_0338 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "stssearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/stssearch.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_2229, edam:topic_3308, edam:topic_3382 ; sc:citation , "pmcid:PMC9590442", "pubmed:36284674" ; sc:description "A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data." ; sc:featureList edam:operation_0337, edam:operation_2409, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "STtools" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/seqscope/STtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3518 ; sc:citation , "pmcid:PMC9635635", "pubmed:36000885" ; sc:description "An R package for the curation of SNP genotypes from experimental crosses." ; sc:featureList edam:operation_0282, edam:operation_0484, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "stuart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.pasteur.fr/mouselab/stuart/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3397, edam:topic_3421, edam:topic_3444, edam:topic_3452 ; sc:citation , "pmcid:PMC8782222", "pubmed:35064372" ; sc:description "An Open Science Cloud-Based Medical Imaging Analysis Platform." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Studierfenster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://studierfenster.icg.tugraz.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3304, edam:topic_3474 ; sc:citation ; sc:description """Covariate-Profile Similarity Weighting and Bagging Studies with the Study Strap. Prediction settings with multiple studies have become increasingly common. Ensembling models trained on individual studies has been shown to improve replicability in new studies. Motivated by a groundbreaking new technology in human neuroscience, we introduce two generalizations of multi-study ensemble predictions. First, while existing methods weight ensemble elements by cross-study prediction performance, we extend weighting schemes to also incorporate covariate similarity between training data and target validation studies. Second, we introduce a hierarchical resampling scheme to generate pseudo-study replicates (“study straps”) and ensemble classifiers trained on these rather than the original studies themselves. We demonstrate analytically that existing methods are special cases""" ; sc:featureList edam:operation_3435 ; sc:name "studyStrap" ; sc:url "https://github.com/gloewing/studyStrap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3337, edam:topic_3382 ; sc:citation , "pmcid:PMC7386244", "pubmed:32664861" ; sc:description """Seamless integration of image and molecular analysis for spatial transcriptomics workflows. STUtility requires R version >=3.6 and some packages within the Bioconductor suit needs to be installed prior to installing STUtility from github. Welcome to the STUtility web site. STUtility is an R-package with the goal of providing an easy-to-use visualization and analysis tool kit for spatial transcriptomics data.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:name "STUtility" ; sc:url "https://ludvigla.github.io/STUtility_web_site/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0593, edam:topic_2828, edam:topic_3344 ; sc:description "STXM data analysis script collection with stack exploration GUI tool STACKLab" ; sc:featureList edam:operation_0320, edam:operation_0399, edam:operation_3458 ; sc:isAccessibleForFree true ; sc:name "STXM data analysis script collection - STACKLab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/24006-stxm-data-analysis-script-collection-stacklab" ; biotools:primaryContact "Tobias Henn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3277 ; sc:citation ; sc:description "It is developed for gene set enrichment analysis.The primary objective of this program is to measure the enrichment of differentially expressed or phenotype associated genes in given gene sets.The input for the program includes the gene expression data of several samples with corresponding phenotypic data and several given gene sets.The program will assess the significance of the enrichment of genes, whose gene expression profiles are associated with the phenotypic data, in each given gene set." ; sc:featureList edam:operation_3501 ; sc:name "Sub-GSE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www-rcf.usc.edu/~fsun/Programs/SubGSEWebPages/SubGSEMain.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation , "pubmed:26207919" ; sc:description "Signaling-pathway impact analysis (SPIA) is one such method and combines both the classical enrichment analysis and the actual perturbation on a given pathway. Because this method focuses on a single pathway, its resolution generally is not very high because the differentially expressed genes may be enriched in a local region of the pathway. In the present work, to identify cancer-related pathways, we incorporated a recent subpathway analysis method into the SPIA method to form the “sub-SPIA method.”" ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "sub-SPIA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/eshinesimida/subpathway-analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0780 ; sc:citation , ; sc:contributor "Cornelia Hooper", "Harvey Millar", "Ian Castleden", "Sandra Tanz" ; sc:description "A subcellular localisation database for Arabidopsis proteins, with online search interface." ; sc:featureList edam:operation_2422, edam:operation_2489, edam:operation_3646 ; sc:name "SUBA3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ARC Centre of Excellence in Plant Energy Biology", "University of Western Australia", "unimelb.edu.au" ; sc:softwareHelp ; sc:url "http://suba3.plantenergy.uwa.edu.au/" ; biotools:primaryContact "Australia", "Cornelia Hooper", "Sandra Tanz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2269 ; sc:citation "pubmed:25150248" ; sc:description "A naive Bayes classifier that integrates 22 computational prediction algorithms, experimental GFP and MS localizations, protein-protein interaction and co-expression data to derive a consensus call and probability." ; sc:featureList edam:operation_2995 ; sc:name "SUBAcon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://subacon.plantenergy.uwa.edu.au//SUBAcon.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0659 ; sc:citation , "pmcid:PMC9442970", "pubmed:36064320" ; sc:description "A SUbgraph BAsed mulTi-OMIcs Clustering framework to analyze integrated multi-edge networks." ; sc:featureList edam:operation_2436, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SUBATOMIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CBIGR/SUBATOMIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0769, edam:topic_2229, edam:topic_3520 ; sc:citation , "pubmed:35732783" ; sc:description "Integrated workflow for robust spatial proteomics by mass spectrometry." ; sc:featureList edam:operation_0337, edam:operation_2489, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SubCellBarCode" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.subcellbarcode.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0140, edam:topic_0203, edam:topic_2229 ; sc:citation ; sc:description "SubcellulaRVis simplifies visualization of protein enrichment in subcellular compartments." ; sc:featureList edam:operation_0337, edam:operation_2489, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SubcellulaRVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JoWatson2011/subcellularvis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0140, edam:topic_0780 ; sc:citation "pubmed:19679138" ; sc:description "Computational system for predicting protein subchloroplast locations from its primary sequence. It can locate the protein whose subcellular location is chloroplast in one of the four parts: envelope (which consists of outer membrane and inner membrane), thylakoid lumen, stroma and thylakoid membrane." ; sc:featureList edam:operation_2479, edam:operation_2489 ; sc:name "SubChlo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.au.tsinghua.edu.cn/software/subchlo/" ; biotools:primaryContact "Pufeng Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0108, edam:topic_0749, edam:topic_3295, edam:topic_3474 ; sc:citation ; sc:description """SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein/Peptide Sequences. The SubFeat is an extensive Python-based tool for generating various numerical feature representation schemes from DNA, RNA and protein primary structure sequences. It is an extension edition of the PyFeat. We additionally provide the feature overlapping option that user can customize it for own research purposes; we also prove an ensemble classification technique. This After that, it can train model, to evaluate model using various machine learning techniques.""" ; sc:featureList edam:operation_0440, edam:operation_1777, edam:operation_3092, edam:operation_3096 ; sc:name "SubFeat" ; sc:url "https://github.com/fazlulhaquejony/SubFeat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description "Finding ranges of optimal transcript expression quantification in cases of non-identifiability." ; sc:featureList edam:operation_2495, edam:operation_3435, edam:operation_3799 ; sc:name "subgraphquant" ; sc:url "https://github.com/Kingsford-Group/subgraphquant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3168 ; sc:citation , "pubmed:32282873" ; sc:description """A hidden Markov modeling approach for identifying tumor subclones in next-generation sequencing studies. Model for Identifying Tumor Subclones R Package. ||| CORRECT NAME OF TOOL COULD ALSO BE 'subHMM hidden Markov model-based'""" ; sc:featureList edam:operation_0296, edam:operation_0487, edam:operation_3196, edam:operation_3233 ; sc:name "subHMM" ; sc:url "https://dceg.cancer.gov/tools/analysis/subhmm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called \"seed-and-vote\" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data." ; sc:featureList edam:operation_3198 ; sc:name "Subjunc" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://subread.sourceforge.net" ; biotools:primaryContact "Dr Wei Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2259 ; sc:citation "pubmed:22095399" ; sc:description "The software comprises of a number of independent tools that can be used to automate steps in the development of genome-scale metabolic reconstructions." ; sc:featureList edam:operation_3660 ; sc:name "SuBliMinaL Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mcisb.org/resources/subliminal/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description """Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. SubMARine is a polynomial-time algorithm that reconstructs cancer evolutionary histories by building partial clone trees.""" ; sc:featureList edam:operation_0553, edam:operation_0555, edam:operation_3454, edam:operation_3745, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "SubMARine" ; sc:url "https://github.com/morrislab/submarine" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0199, edam:topic_3511 ; sc:citation , "pmcid:PMC4305219", "pubmed:25591662" ; sc:description "Approximate subspace pattern mining for mapping copy-number variations." ; sc:featureList edam:operation_3233 ; sc:name "SubPatCNV" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/subpatcnv/" ; biotools:primaryContact "Johnson N.", "Kuang R." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3295, edam:topic_3299 ; sc:citation , "pubmed:35460274" ; sc:description "A robust allopolyploid subgenome phasing method based on subgenome-specific k-mers." ; sc:featureList edam:operation_3454, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SubPhaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zhangrengang/SubPhaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3510 ; sc:citation "pubmed:25236462" ; sc:description "Web server that could predict phosphosrylation sites in different subcellular compartments (SCs) of homo sapiens, which combines a novel discrete wavelet transform (DWT) strategy with support vector machine (SVM) approach to identify phosphorylation sites for different SCs in human." ; sc:featureList edam:operation_2479, edam:operation_3092 ; sc:name "SubPhosPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.ncu.edu.cn/SubPhosPred.aspx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3168, edam:topic_3170, edam:topic_3673 ; sc:citation , , "pmcid:PMC3664803", "pmcid:PMC5792058", "pubmed:23558742", "pubmed:27941783" ; sc:description "Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called \"seed-and-vote\" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "Subread" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://subread.sourceforge.net/" ; biotools:primaryContact "Dr Wei Shi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:32789660" ; sc:description """Word embeddings from subtitles in 55 languages. Van Paridon & Thompson (2019) introduces pretrained embeddings and precomputed word/bigram/trigram frequencies in 55 languages. The files can be downloaded from the links in this table. Word vectors trained on subtitles are available, as well as vectors trained on Wikipedia, and a combination of subtitles and Wikipedia (for best predictive performance). This repository contains the subs2vec module, a number of Python 3.7 scripts and command line tools to evaluate a set of word vectors on semantic similarity, semantic and syntactic analogy, and lexical norm prediction tasks. In addition, the subs2vec.py script will take an OpenSubtitles archive or Wikipedia and go through all the steps to train a fastText model and produce word vectors as used in the paper associated with this repository.""" ; sc:featureList edam:operation_1812 ; sc:license "MIT" ; sc:name "subs2vec" ; sc:url "https://github.com/jvparidon/subs2vec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "Subsampling of high throughput sequencing count data for use in experiment design and analysis." ; sc:featureList edam:operation_2238 ; sc:license "MIT" ; sc:name "subSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/subSeq.html" ; biotools:primaryContact "Andrew J. Bass", "John D. Storey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0157, edam:topic_0160, edam:topic_3510 ; sc:citation "pubmed:18304932" ; sc:description "Tool to find sequence motifs in low complexity protein sequences. It uses the application of a unique graph based approach." ; sc:featureList edam:operation_0239, edam:operation_0240, edam:operation_2404, edam:operation_2479 ; sc:name "SubSeqer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.compsysbio.org/subseqer/" ; biotools:primaryContact "The Parkinson Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_2269 ; sc:citation , "pmcid:PMC10311335", "pubmed:37387132" ; sc:description "Seeding with minimized subsequence." ; sc:featureList edam:operation_0491, edam:operation_0524, edam:operation_3198, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SubseqHash" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Shao-Group/subseqhash" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "SubspaceEM is a fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction and alignment." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "SubspaceEM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50091-subspaceem-a-fast-maximum-a-posteriori-algorithm-for-cryo-em-single-particle-reconstruction" ; biotools:primaryContact "Nicha Dvornek" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2087 ; sc:name "Molecular property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3314, edam:topic_3316, edam:topic_3391 ; sc:citation , , ; sc:description """Substra is an open source federated learning (FL) software. It provides a flexible Python interface and a web app to run federated learning training at scale. Substra’s main usage is in production environments. It has already been deployed and used by hospitals and biotech companies (see the MELLODDY project for instance). 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Wilson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_3375, edam:topic_3474 ; sc:citation , "pubmed:33769494" ; sc:description "SumGNN is a tool for multi-typed drug interaction prediction via efficient knowledge graph summarization." ; sc:featureList edam:operation_0306, edam:operation_3927, edam:operation_4009 ; sc:name "SumGNN" ; sc:url "https://github.com/yueyu1030/SumGNN" ; biotools:primaryContact "Cao Xiao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. 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Objectives< h4>To develop a computational tool that integrates multiomics data at the level of reactions.

Methods< h4>Changes in metabolic reactions are modeled with input from transcriptomics proteomics measurements of enzymes and metabolomic measurements of metabolites""" ; sc:featureList edam:operation_2495, edam:operation_3660, edam:operation_3891 ; sc:name "SUMMER" ; sc:url "http://summer.salk.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3295, edam:topic_3337, edam:topic_3360, edam:topic_3517 ; sc:citation , "pubmed:35947748" ; sc:description "A Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival" ; sc:featureList edam:operation_0224, edam:operation_3431, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "SUMMER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://njmu-edu.cn:3838/SUMMER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3676 ; sc:citation ; sc:description """A method for detecting and adjusting for population structure in genetic summary data. R scripts and data used for the Summix manuscript analysis. The Python implementation of The Hendricks Team's summix method, which efficiently solves ancestral deconvolution problems, given a (large) genetic database. 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It contains dozens of different summary statistics to be applied on various levels of assumptions, from raw query reads to inferred phylogenies, as well as easy and principled ways to plot and compare repertoires. It currently supports the IgH, IgL, IgK, TRA, and TRB loci." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3695 ; sc:name "sumrep" ; sc:url "https://github.com/matsengrp/sumrep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0622, edam:topic_3053 ; sc:citation "pubmed:23122592" ; sc:description "The tool considers a number of marker loci in the genome. At each marker, genotypes are available for two types of observations." ; sc:featureList edam:operation_0282 ; sc:name "SUMSTAT" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.jurgott.org/linkage/sumstat.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "Suns provides the missing search engine for the Protein Data Bank complete with a PyMOL interface" ; sc:featureList edam:operation_2421 ; sc:name "Suns" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://degradolab.org/suns/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_3053 ; sc:citation "pubmed:16803631" ; sc:description "Extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with a trait locus." ; sc:featureList edam:operation_3232 ; sc:name "SUP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://mlemire.freeshell.org/software.html" ; biotools:primaryContact "Mathieu Lemire" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_2814, edam:topic_3315 ; sc:citation "pubmed:22638586" ; sc:description "Super is a webserver for rapidly screening the PDB to identify all oligopeptide fragments that superpose with a query under a pre-specified threshold of root mean-square deviation." ; sc:featureList edam:operation_0224, edam:operation_0245, edam:operation_0360, edam:operation_0556 ; sc:name "Super" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lcb.infotech.monash.edu.au/super" ; biotools:primaryContact "James Collier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation ; sc:description "Robust gene expression data normalization and differential expression analysis pipeline." ; sc:featureList edam:operation_2495 ; sc:name "Super-delta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fhlsjs/Super-delta" ; biotools:primaryContact "Jinfeng Zhang", "Xing Qiu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3174 ; sc:citation "pubmed:26454280" ; sc:description "An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances." ; sc:featureList edam:operation_0253 ; sc:name "SUPER-FOCUS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://edwards.sdsu.edu/superfocus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0769, edam:topic_3382, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8240683", "pubmed:34189530" ; sc:description "A supervised machine learning pipeline for molecular complex detection in protein-interaction networks." ; sc:featureList edam:operation_0276, edam:operation_2492, edam:operation_3094, edam:operation_3802, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Super Complex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/view/supercomplex/super-complex-v3-0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:35062020" ; sc:description "Out-of-the-box deep learning prediction of quantum-mechanical partial charges by graph representation and transfer learning." ; sc:featureList edam:operation_2476, edam:operation_3891, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SuperAtomicCharge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zjujdj/SuperAtomicCharge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation ; sc:description "This package was designed to help researchers/lab managers wanting to cary out capture sequencing experiments. The R-package supeRbaits, written in R and C++ and implemented in R, can help design your own set of baits from a genome sequence of your species of interest." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "supeRbaits" ; sc:url "https://github.com/BelenJM/supeRbaits" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0602, edam:topic_3375, edam:topic_3407 ; sc:citation "pubmed:19934256" ; sc:description "The database contains about drugs, Cytochrome-Drug interactions and 1,200 alleles. SNPs and mutations are also listed and ordered according to their effect on expression and/or activity. It is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files." ; sc:featureList edam:operation_0306, edam:operation_0331, edam:operation_2422, edam:operation_3436 ; sc:name "SuperCYP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/supercyp" ; biotools:primaryContact "Daniel Kuzmann", "Katharina Kroll", "Mathias Dunkel", "Saskia Preissner", "Stefan Guenther" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0821, edam:topic_3375, edam:topic_3379, edam:topic_3407 ; sc:citation , "pmcid:PMC7319455", "pubmed:32182358" ; sc:description """web server for the prediction of cytochrome activity. SuperCYPsPred - a web server for the prediction of cytochrome activity; AG Preissner; Charité Berlin. Drug metabolism via the cytochrome P450 system has emerged as an important determinant in the occurrence of several drug interactions that can result in drug toxicities, reduced pharmacological effect, and adverse drug reactions. Recognizing whether the drugs involved act as enzyme substrates, inducers, or inhibitors can prevent clinically significant interactions from occurring. The SuperCYPsPred web server is focused on five major CYPs isoforms, including 1A2, 2C9, 2C19, 2D6 and 3A4, that are responsible for more than 90% of the metabolism of clinical drugs. Besides the predictions, the web server provides literature curated details on known cytochrome interaction network of approved drugs.""" ; sc:featureList edam:operation_3660, edam:operation_3929, edam:operation_3938 ; sc:name "SuperCYPsPred" ; sc:url "http://insilico-cyp.charite.de/SuperCYPsPred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:citation ; sc:description "SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SuperDSM" ; sc:softwareHelp ; sc:url "https://github.com/BMCV/SuperDSM" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0623, edam:topic_0625, edam:topic_0736, edam:topic_3174 ; sc:citation "pubmed:21062816" ; sc:description "It provides protein domain assignments at the structural classification of protein superfamily level for completely sequenced genomes, metagenomes and other gene collections such as UniProt. Our scoring component now uses HMMER3. A cloud-based pipeline was implemented and is publicly available. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life." ; sc:featureList edam:operation_0268, edam:operation_0303, edam:operation_0320, edam:operation_2996 ; sc:name "SUPERFAMILY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://supfam.org" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3676 ; sc:citation , "pmcid:PMC7043783", "pubmed:32053599" ; sc:description """Integrated mutation detection and clonal tracking in cancer. SuperFreq is an R package that analyses cancer exomes. Summarised data and code to reproduce figures for the TCGA analysis in the superFreq methods paper. SuperFreq analyses and filters somatic SNVs and short indels, calls copy numbers and tracks clones over multiple samples from the same individual. It identifies the copy number alterations and point mutations in each clone, and highlights potentially causing mutations through variant annotation and COSMIC.""" ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3435 ; sc:license "MIT" ; sc:name "SuperFreq" ; sc:url "https://gitlab.wehi.edu.au/flensburg.c/SuperFreqPaper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_2885, edam:topic_3517, edam:topic_3676 ; sc:citation , "pmcid:PMC8422619", "pubmed:34493297" ; sc:description "SUPERGNOVA (SUPER GeNetic cOVariance Analyzer) is a statistical framework to perform local genetic covariance analysis. SUPERGNOVA only needs GWAS summary data and a reference panel as input data." ; sc:featureList edam:operation_0335, edam:operation_3196, edam:operation_3463, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SUPERGNOVA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/qlu-lab/SUPERGNOVA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "The tool is a novel tool to quantitatively analyze multi dimensional LC-MS data in a label-free approach." ; sc:featureList edam:operation_2945 ; sc:name "SuperHirn" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.03" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:SuperHirn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7855703", "pubmed:33552964" ; sc:description """A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images. High computational cost associated with digital pathology image analysis approaches is a challenge towards their translation in routine pathology clinic. Here, we propose a computationally efficient framework (SuperHistopath), designed to map global context features reflecting the rich tumor morphological heterogeneity. SuperHistopath efficiently combines i) a segmentation approach using the linear iterative clustering (SLIC) superpixels algorithm applied directly on the whole-slide images at low resolution (5x magnification) to adhere to region boundaries and form homogeneous spatial units at tissue-level, followed by ii) classification of superpixels using a convolution neural network (CNN) Code is available by request.""" ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:name "SuperHistopath" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=33552964" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0166, edam:topic_3534 ; sc:citation "pubmed:18492720" ; sc:description "Performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selection of algorithms and databases that best suit their needs." ; sc:featureList edam:operation_0295, edam:operation_0360, edam:operation_0503, edam:operation_0509, edam:operation_0510 ; sc:name "Superimpose" ; sc:url "http://bioinformatics.charite.de/superimpose" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3053 ; sc:citation ; sc:description "Performs exact genetic linkage analysis with input-output relationships. Used for analysis of general pedigrees (many individuals, inbreeding loops, many markers, etc.), analysis of two-locus traits or analysis of autosomal or sex-linked traits." ; sc:featureList edam:operation_0283 ; sc:name "SuperLink" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.cs.technion.ac.il/labs/cbl/superlink/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0153, edam:topic_0736, edam:topic_0820, edam:topic_2275 ; sc:citation "pubmed:19429894" ; sc:description "SuperLooper is a web tool for the modeling of loops in globular and membrane proteins." ; sc:featureList edam:operation_0270, edam:operation_0331, edam:operation_0408, edam:operation_0477, edam:operation_0481 ; sc:name "SuperLooper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinf-applied.charite.de/superlooper/" ; biotools:primaryContact "Peter Hildebrand" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Calculate approximate local pair-wise alignments of larger sequences." ; sc:featureList edam:operation_0491 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "supermatcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/supermatcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Finds a match of a large sequence against one or more sequences." ; sc:featureList edam:operation_2403 ; sc:name "supermatcher WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/supermatcher.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_3511 ; sc:citation ; sc:description "Novel alignment-free approach for representing and comparing RNA secondary structures." ; sc:featureList edam:operation_0278, edam:operation_2483 ; sc:name "supernmotifs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://jpsglouzon.github.io/supernmotifs/" ; biotools:primaryContact "Shengrui Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3673 ; sc:citation ; sc:description "Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances. Almost all other methods instead merge homologous chromosomes into single incorrect 'consensus' sequences. Supernova is the only practical method for creating diploid assemblies of large genomes." ; sc:featureList edam:operation_0227, edam:operation_0524, edam:operation_3192, edam:operation_3933 ; sc:license "Proprietary" ; sc:name "Supernova" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome" ; biotools:primaryContact "David B. Jaffe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3518 ; sc:citation "pubmed:15094809" ; sc:description "This tool does prediction for a censored survival outcome, or a regression outcome, using the “supervised principal component” approach. It is especially useful when the number of features p is >> n, the number of samples, for example in microarray studies." ; sc:featureList edam:operation_2495, edam:operation_3659 ; sc:name "SuperPC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www-stat.stanford.edu/~tibs/superpc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3301, edam:topic_3324 ; sc:citation , "pmcid:PMC4828761", "pubmed:27067409" ; sc:description "Predictive genomics for the bacterial pathogen Escherichia coli." ; sc:featureList edam:operation_3461 ; sc:name "SuperPhy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://lfz.corefacility.ca/superphy/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3678 ; sc:citation ; sc:description "SuperPlotsOfData – a web app for the transparent display and quantitative comparison of continuous data from discrete conditions." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "SuperPlotsOfData" ; sc:url "https://huygens.science.uva.nl/SuperPlotsOfData/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_2814, edam:topic_3382 ; sc:citation "pubmed:15215457" ; sc:description "SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules." ; sc:featureList edam:operation_0292, edam:operation_0295, edam:operation_0510, edam:operation_2488 ; sc:name "SuperPose" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wishart.biology.ualberta.ca/SuperPose/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "A Local Structural Comparison Program That Allows for User-Defined Structure Representations." ; sc:featureList edam:operation_2483 ; sc:name "Superpose3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://cbm.bio.uniroma2.it/superpose3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3336, edam:topic_3375 ; sc:citation "pubmed:18499712" ; sc:description "The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction." ; sc:featureList edam:operation_0360, edam:operation_2436, edam:operation_2489 ; sc:name "SuperPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/superpred" ; biotools:primaryContact "Bjoern-Oliver Gohlke", "Janette Nickel", "Jevgeni Ehreman", "Mathias Dunke", "Priyanka Banerjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:18707533" ; sc:description "A program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees." ; sc:featureList edam:operation_0323 ; sc:name "SuperQ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/superq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:25978296" ; sc:description "Thermo Proteome Discoverer 2.x processing nodes for mixture spectra deconvolution." ; sc:featureList edam:operation_3631, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "SuperQuantNode" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/caetera/SuperQuantNode" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation "pubmed:20410051" ; sc:description "Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of (~)11.4 million reads per hour." ; sc:featureList edam:operation_0310 ; sc:name "Supersplat" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://mocklerlab.org/tools/1" ; biotools:primaryContact "Mockler Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3337, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "superSTR is a ultrafast, alignment-free detection of repeat expansions in next-generation DNA and RNA sequencing data." ; sc:featureList edam:operation_0239, edam:operation_0337, edam:operation_0379, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "superSTR" ; sc:url "https://github.com/bahlolab/superSTR" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0152, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:20952410" ; sc:description "It is a collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Structural information and properties such as number of calories, therapeutic annotations and a sweetness-index are stored in SuperSweet. The database provides a modeled 3D structure of the sweet taste receptor and binding poses of the small sweet molecules. A sweetener classification tree and browsing features allow quick requests to be made to the database." ; sc:featureList edam:operation_0250, edam:operation_0360, edam:operation_0477, edam:operation_0478 ; sc:name "SuperSweet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/sweet/" ; biotools:primaryContact "Franziska Fritz (Web server/ Data related queries)", "Priyanka Banerjee (Data / Toxicity prediction related queries)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0602, edam:topic_3375, edam:topic_3407 ; sc:citation "pubmed:22067455" ; sc:description "Web resource for analyzing drug-target interactions. Integrates drug-related info associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins." ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_2489, edam:operation_3439, edam:operation_3660 ; sc:name "SuperTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.charite.de/supertarget/" ; biotools:primaryContact "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_3292, edam:topic_3373, edam:topic_3407 ; sc:citation , "pubmed:34656056" ; sc:description "A biocultural database combining biological pathways and historical linguistic data of Chinese Materia Medica for drug development." ; sc:featureList edam:operation_2421, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:name "SuperTCM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tcm.charite.de/supertcm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms" ; sc:featureList edam:operation_3478 ; sc:name "SuperTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www2.unil.ch/phylo/bioinformatics/supertree.html" ; biotools:primaryContact "SuperTree Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "Supervised Fuzzy Clustering for the Identification of Fuzzy Classifiers. Each rule can represent more than one classes with different probabilities." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "Supervised Fuzzy Clustering for the Identification of Fuzzy Classifiers" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47203-supervised-fuzzy-clustering-for-the-identification-of-fuzzy-classifiers" ; biotools:primaryContact "Janos Abonyi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3474 ; sc:citation ; sc:description "Supervised-learning is an accurate method for network-based gene classification | Abstract Background Assigning every human gene to specific functions, diseases, and traits is a grand challenge in modern genetics. Key to addressing this challenge are computational methods such as supervised-learning and label-propagation that can leverage molecular interaction networks to predict gene attributes. In spite of being a popular machine learning technique across fields, supervised-learning has been applied only in a few network-based studies for predicting pathway-, phenotype-, or disease-associated genes. It is unknown how supervised-learning broadly performs across different networks and diverse gene classification tasks, and how it compares to label-propagation, the widely-benchmarked canonical approach for this problem" ; sc:featureList edam:operation_2436, edam:operation_3439 ; sc:name "supervised-learning" ; sc:url "https://github.com/krishnanlab/GenePlexus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3308, edam:topic_3320 ; sc:author "Amadí­s Pagès", "Gael P. Alamancos", "JC Entizne", "Miha Skalic" ; sc:citation ; sc:description "This tool generates Alternative Splicing (AS) events from an annotation and calculates the PSI (\"Percentage Spliced In\") value for each event exploiting fast quantification of transcript abundances from multiple samples." ; sc:featureList edam:operation_2499 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SUPPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Pompeu Fabra University", "upf.edu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bitbucket.org/regulatorygenomicsupf/suppa/" ; biotools:primaryContact "SUPPA Users group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0203, edam:topic_3474 ; sc:citation , "pmcid:PMC3905187", "pubmed:24309102" ; sc:description "This tool carries out gene clustering, sample correlation and intuitive visualisations to facilitate exploratory analysis with high-dimensional omics input data. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. Some newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships." ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "supraHex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/supraHex.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082 ; sc:citation "pubmed:21058297" ; sc:description "A threading strucuture prediction algorithm which employs suboptimal alignments." ; sc:featureList edam:operation_0292, edam:operation_0474 ; sc:name "SUPRB" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://kiharalab.org/suprb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3370, edam:topic_3382 ; sc:citation "pubmed:8742734" ; sc:description "A flexible, modular software package intended for the processing of electron microscopy images is presented. The system consists of a set of image processing tools or filters, written in the C programming language, and a command line style user interface based on the UNIX shell. The pipe and filter structure of UNIX and the availability of command files in the form of shell scripts eases the construction of complex image processing procedures from the simpler tools." ; sc:featureList edam:operation_3443 ; sc:name "Suprim" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://itg.beckman.illinois.edu/technology_development/software_development/suprim/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC9741222", "pubmed:36501908" ; sc:description "An Open Source Python Package for Preprocessing Hyperion Radiance Data and Retrieving Surface Reflectance." ; sc:featureList edam:operation_2422, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SUREHYP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tmiraglio/SUREHYP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3474, edam:topic_3516, edam:topic_3518 ; sc:citation ; sc:description "SureTypeSCR is an R package for QC and rapid genotyping of single cell SNP array data. It encapsulates previously developed library SureTypeSC . The core consists of a two layered machine learning method that assigns a quality score to each SNP in an array. On top of that, SureTypeSCR implements various QC strategies to examine the data using packages from the tidyverse collection." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_1812, edam:operation_2428, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SureTypeSCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Meiomap/SureTypeSCR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_3170, edam:topic_3512, edam:topic_3794 ; sc:citation ; sc:description """integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. The Statistical Utility for RBP Functions (SURF) is an integrative analysis framework to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events.""" ; sc:featureList edam:operation_0264, edam:operation_1812, edam:operation_3680, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "SURF" ; sc:url "https://github.com/keleslab/surf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0166, edam:topic_0749, edam:topic_0820 ; sc:citation , "pmcid:PMC10133531", "pubmed:37067488" ; sc:description "Geometry-aware system for protein molecular surface comparison." ; sc:featureList edam:operation_0387, edam:operation_0479, edam:operation_0480, edam:operation_3666, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "Surface ID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Sanofi-Public/LMR-SurfaceID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_2229, edam:topic_3308, edam:topic_3520 ; sc:citation , "pmcid:PMC7267825", "pubmed:32053146" ; sc:description """a web-based application for prioritizing cell-type-specific marker candidates. SurfaceGenie is a web-application for computing the GenieScore , a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type specific surface markers. This prioritization strategy is applicable for analyzing human and rodent data from proteomic and transcriptomic experiments. 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The 2-D maps computed by SURFMAP can be used to analyze and/or compare protein surface properties." ; sc:featureList edam:operation_0387, edam:operation_2429, edam:operation_3666, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SURFMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/i2bc/SURFMAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0166, edam:topic_3382 ; sc:citation ; sc:description "3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!) - yamule/SurfStamp-public." ; sc:featureList edam:operation_0337, edam:operation_0387, edam:operation_3666 ; sc:license "Apache-2.0" ; sc:name "SurfStamp" ; sc:url "https://github.com/yamule/SurfStamp-public/releases" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154 ; sc:citation ; sc:description "Method for finding binding sites in proteins based on the probabilitic analysis of global radial distributions of atoms." ; sc:featureList edam:operation_2423, edam:operation_2479, edam:operation_2575 ; sc:name "SurpResi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "201108" ; sc:url "http://pmbm.ippt.gov.pl/services/surpresi/cgi-bin/prediction.py" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2259, edam:topic_3524 ; sc:citation "pubmed:21148545" ; sc:description "This provides constraint-based simulations and network map visualization. In addition to basic simulation protocols, the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments, but not available in other commonly used programs." ; sc:featureList edam:operation_3660 ; sc:name "SurreyFBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sysbio3.fhms.surrey.ac.uk/sfba/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "R package for the methods described in Bayesian ensemble methods for survival prediction in gene expression data." ; sc:featureList edam:operation_2423, edam:operation_2495 ; sc:name "SurvBART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://works.bepress.com/veera/1/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC9338425", "pubmed:35906887" ; sc:description "Comprehensive benchmarking study of survival analysis methods using both omics data and clinical data." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SurvBenchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SydneyBioX/SurvBenchmark_package" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3379 ; sc:citation , "pmcid:PMC8829729", "pubmed:34870495" ; sc:description "A class of two-sample nonparametric statistics for binary and time-to-event outcomes." ; sc:featureList edam:operation_2238, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SurvBin" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MartaBofillRoig/SurvBin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_2640, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC7716509", "pubmed:33272320" ; sc:description """Pan-cancer identification of clinically relevant genomic subtypes using outcome-weighted integrative clustering. survClust is an outcome weighted supervised clustering algorithm, designed to classify patients according to their molecular as well as time-event or end point of interest. Until now, sub-typing in cancer biology has relied heavily upon clustering/mining of molecular data alone. We present classification of samples on molecular data supervised by time-event data like Overall Survival (OS), Progression Free Survival etc.""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3436 ; sc:name "survClust" ; sc:url "https://github.com/arorarshi/survClust" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3303, edam:topic_3518 ; sc:citation , "pmcid:PMC2553442", "pubmed:18635567" ; sc:description "R package providing functions to assess and to compare the performance of risk prediction (survival) models." ; sc:featureList edam:operation_2424 ; sc:license "Artistic-2.0" ; sc:name "survcomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/survcomp.html" ; biotools:primaryContact , "Catharina Olsen", "Markus Schroeder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "Survival and other incident curves." ; sc:featureList edam:operation_3503 ; sc:name "SurvCurve" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/thornton-srv/databases/SurvCurv/analyse.php" ; biotools:primaryContact "Roman Laskowski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation ; sc:description "A set of six survival analysis models to model high dimensional right-censored survival data by combining kernel ELMs with the Buckley–James estimator, regularized Cox model, random forests and boosting." ; sc:featureList edam:operation_3503 ; sc:license "GPL-3.0" ; sc:name "SurvELM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/whcsu/SurvELM" ; biotools:primaryContact "Hong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3678 ; sc:citation ; sc:description "survGenesInterim is an R package for simulation of survival studies based on simulated gene expression level and patient data. Includes functions to generate such data. Resulting error and power rate can be visualized." ; sc:featureList edam:operation_2495 ; sc:name "survGenesInterim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.ams.med.uni-goettingen.de/software-en.shtml" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3512, edam:topic_3673 ; sc:citation , "pubmed:33444454" ; sc:description "SurVirus a repeat-aware virus integration caller." ; sc:featureList edam:operation_3198, edam:operation_3359, edam:operation_3435 ; sc:name "SurVirus" ; sc:url "https://github.com/kensung-lab/SurVirus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3360 ; sc:citation ; sc:description "A web portal for single-cell data, gene-ratio, and cell composition-based survival analyses." ; sc:featureList edam:operation_0314, edam:operation_3463, edam:operation_3503, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Survival Genie" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bbisr.shinyapps.winship.emory.edu/SurvivalGenie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3055, edam:topic_3056 ; sc:citation ; sc:description "Survival analysis methods were first developed in the biomedical field, which generally involves smaller file sizes and lower levels of effects than agronomic applications. The relative theory of random effects in survival analysis (\"fragile\" models) is not as advanced as with linear models and no freeware is available to use such models. The survival kit analyses large populations with complex models." ; sc:featureList edam:operation_2238 ; sc:license "Not licensed" ; sc:name "Survival kit" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.nas.boku.ac.at/nuwi/the-survival-kit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0208, edam:topic_3056, edam:topic_3569 ; sc:citation , "pmcid:PMC5146816", "pubmed:27931206" ; sc:description "SurvivalGWAS_Power performs power calculations for time to event outcomes over a range of study designs and different analytical approaches. The software calculates the power to detect single nucleotide polymorphism association with a time to event outcome over a range of study design scenarios." ; sc:featureList edam:operation_3480 ; sc:license "GPL-3.0" ; sc:name "SurvivalGWAS_Power" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "v1.5" ; sc:url "https://www.liverpool.ac.uk/translational-medicine/research/statistical-genetics/survival-gwas/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3517 ; sc:citation , "pmcid:PMC5438515", "pubmed:28525968" ; sc:description "Analysis of genome-wide association studies of imputed genotypes with “time-to-event” outcomes." ; sc:featureList edam:operation_2403 ; sc:license "GPL-3.0" ; sc:name "SurvivalGWAS_SV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.liverpool.ac.uk/translational-medicine/research/statistical-genetics/survival-gwas-sv/" ; biotools:primaryContact "Hamzah Syed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3295, edam:topic_3512, edam:topic_3674 ; sc:citation , "pubmed:32778890" ; sc:description """a web server to investigate the effect of DNA methylation-related functional elements on prognosis. The functional elements associated with DNA methylation, for example enhancer region, CpG island, shore, shelf, promoter, gene body, etc., are discovered to be underlying prognostic markers for patients' survival.Here, we built a web server SurvivalMeth (freely available via a user friendly web-server at http://bio-bigdata.hrbmu.edu.cn/survivalmeth/) to investigate the effect of DNA methylation-related functional elements on prognosis, and multiple kinds of commonly used functional elements associated with DNA methylation are considered.""" ; sc:featureList edam:operation_0417, edam:operation_3207, edam:operation_3659, edam:operation_3809 ; sc:name "SurvivalMeth" ; sc:url "http://bio-bigdata.hrbmu.edu.cn/survivalmeth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3305, edam:topic_3421 ; sc:citation , "pmcid:PMC9441606", "pubmed:36072380" ; sc:description "Individualized assessment of risk and overall survival in patients newly diagnosed with primary osseous spinal neoplasms with synchronous distant metastasis." ; sc:featureList edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "SurvivalPOSNs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yxyx.shinyapps.io/SurvivalPOSNs/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC9549197", "pubmed:36225330" ; sc:description "Long Term Survival Prediction of Cancer Patients Based on Somatic RNA-Seq Expression." ; sc:featureList edam:operation_2454, edam:operation_3680, edam:operation_3928, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "surviveAI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tinyurl.com/surviveai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_2640, edam:topic_3168 ; sc:citation "pubmed:24519378" ; sc:description "A free and easy-to-use web tool that assesses miRNA signatures from publicly available miRNA profiles using multivariate survival analysis." ; sc:featureList edam:operation_3792 ; sc:name "SurvMicro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatica.mty.itesm.mx:8080/Biomatec/Survmicro.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3303, edam:topic_3360, edam:topic_3518 ; sc:citation "pubmed:22570412" ; sc:description "SurvNet is a webserver for identifying network-based biomarkers that most correlate with patient survival data. Users provide a biological network file, a molecular profiling file from high-throughput experiment and a patient survival data file. Returned is a list of network biomarkers that best correlate with the observed patient survival data." ; sc:featureList edam:operation_1781, edam:operation_3439, edam:operation_3463, edam:operation_3766 ; sc:name "SurvNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://bioinformatics.mdanderson.org/main/SurvNet" ; biotools:primaryContact "Han Liang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_3053 ; sc:citation ; sc:description "Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures." ; sc:featureList edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "Sushi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Sushi.html" ; biotools:primaryContact "Douglas H Phanstiel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC10245480", "pubmed:37280537" ; sc:description "Pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation." ; sc:featureList edam:operation_0331, edam:operation_0335, edam:operation_0436, edam:operation_3226, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SUsPECT" ; sc:url "https://github.com/cmbi/SUsPECT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_3474, edam:topic_3577 ; sc:citation , "pmcid:PMC8495037", "pubmed:34667533" ; sc:description "Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase." ; sc:featureList edam:operation_0331, edam:operation_0478, edam:operation_2575 ; sc:isAccessibleForFree true ; sc:name "SUSPECT-ABL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biosig.unimelb.edu.au/suspect_abl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_2275, edam:topic_3577 ; sc:citation , "pmcid:PMC7002382", "pubmed:32024884" ; sc:description "Structure guided prediction of Pyrazinamide resistance mutations in pncA." ; sc:featureList edam:operation_0331, edam:operation_0474, edam:operation_3454, edam:operation_3482 ; sc:name "SUSPECT-PZA" ; sc:url "http://biosig.unimelb.edu.au/suspect_pza/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_0654, edam:topic_2640, edam:topic_3168 ; sc:citation "pubmed:26740523" ; sc:description "A computational method to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach." ; sc:featureList edam:operation_3228 ; sc:name "SV-Bay" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/InstitutCurie/SV-Bay" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2012 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence coordinates" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0769, edam:topic_3175 ; sc:author ; sc:citation , , , , "pmcid:PMC6951283", "pubmed:31934500" ; sc:contributor , "Carl Shneider", "Jason Maassen", "Stefan Verhoeven" ; sc:description "Highly portable parallel workflow to detect structural variants in cancer genomes." ; sc:featureList edam:operation_3228 ; sc:license "Apache-2.0" ; sc:name "sv-callers" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.0", "1.1.0", "1.1.1", "1.1.2", "1.1.3", "1.2.0", "1.2.1", "1.2.2" ; sc:url "https://www.research-software.nl/software/sv-callers" ; biotools:primaryContact , . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_2921, edam:format_3003, edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572, edam:format_3327 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0769, edam:topic_3175 ; sc:author ; sc:citation ; sc:contributor , "Jason Maassen", "Lourens Veen", "Stefan Verhoeven" ; sc:description "Highly portable parallel workflow to generate artificial genomes with structural variants." ; sc:featureList edam:operation_0230, edam:operation_3197, edam:operation_3198 ; sc:license "Apache-2.0" ; sc:name "sv-gen" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.0", "1.1.0" ; sc:url "https://www.research-software.nl/software/sv-gen" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3512, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC7522247", "pubmed:32985524" ; sc:description """detection and visualization of hotspots targeted by structural variants associated with gene expression. SV-HotSpot: detection of hotspots targeted by recurrent structural variants associated with gene expression. SV-HotSpot uses bedTools (https://github.com/arq5x/bedtools2) for various overlapping and counting procedures, which should also be installed and made available as command lines.""" ; sc:featureList edam:operation_0337, edam:operation_3222, edam:operation_3436 ; sc:name "SV-HotSpot" ; sc:url "https://github.com/ChrisMaherLab/SV-HotSpot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3063, edam:topic_3382, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6030999", "pubmed:29860504" ; sc:description """A cloud-based framework for manually curating thousands of structural variants. SV-plaudit: A cloud-assisted framework manually curating thousands of structural variants. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. SV-plaudit supports image generation sequencing data from BAM or CRAM files from Illumina paired-end sequencing, PacBio or Oxford Nanopore Technologies long-read sequencing, or 10X Genomics linked-read sequencing. Source code and documentation:https://github.com/jbelyeu/SV-plaudit.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3227 ; sc:license "MIT" ; sc:name "SV-plaudit" ; sc:url "https://www.youtube.com/watch?v=ono8kHMKxDs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3033 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1669 ; sc:encodingFormat edam:format_3547 ; sc:name "P-value" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation ; sc:description "This package contains functions for removing batch effects and other unwanted variation in high-throughput experiments. It contains functions for identifying and building surrogate variables for high-dimensional data sets, which are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise." ; sc:featureList edam:operation_3695 ; sc:license "Artistic-2.0" ; sc:name "sva" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/sva.html" ; biotools:primaryContact "Jeffrey T. Leek", "John D. Storey", "W. Evan Johnson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3056, edam:topic_3335, edam:topic_3574 ; sc:citation , "pmcid:PMC7437891", "pubmed:32813752" ; sc:description """A genetic database curates non-ischemic sudden cardiac death-associated variants. Sudden cardiac death (SCD) is an important cause of mortality worldwide. It accounts for approximately half of all deaths from cardiovascular disease. While coronary artery disease and acute myocardial infarction account for the majority of SCD in the elderly population, inherited cardiac diseases (inherited CDs) comprise a substantial proportion of younger SCD victims with a significant genetic component. Currently, the use of next-generation sequencing enables the rapid analysis to investigate relationships between genetic variants and inherited CDs causing SCD. Genetic contribution to risk has been considered an alternate predictor of SCD. In the past years, large numbers of SCD susceptibility variants were reported, but these results are scattered in numerous publications""" ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:name "SVAD" ; sc:url "http://svad.mbc.nctu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0749, edam:topic_3175, edam:topic_3325, edam:topic_3512 ; sc:citation , "pmcid:PMC9670370", "pubmed:36384437" ; sc:description "Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate." ; sc:featureList edam:operation_1812, edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SVAFotate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fakedrtom/SVAFotate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3175, edam:topic_3293 ; sc:citation , "pmcid:PMC4103593", "pubmed:24700318" ; sc:description "Standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples." ; sc:featureList edam:operation_0323, edam:operation_2478, edam:operation_2939 ; sc:name "SVAMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbrc.kaust.edu.sa/svamp/" ; biotools:primaryContact , "Lailatul Hidayah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3175, edam:topic_3512, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC9047340", "pubmed:35484572" ; sc:description "Efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3461, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SvAnna" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TheJacksonLaboratory/SvAnn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3175, edam:topic_3673 ; sc:citation ; sc:description "Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data." ; sc:featureList edam:operation_0362, edam:operation_0372, edam:operation_0525, edam:operation_1812, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "svaNUMT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PapenfussLab/svaNUMT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3170 ; sc:citation , "pmcid:PMC3733742", "pubmed:23883280" ; sc:description """Accurate identification of genes that are truly differentially expressed over two sample varieties, after adjusting for hidden subject-specific effects of residual heterogeneity.""" ; sc:featureList edam:operation_2495 ; sc:name "svapls" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/svapls/index.html" ; biotools:primaryContact "Sutirtha Chakraborty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "The package contains functions that are intended for the identification of differentially expressed genes between two groups of samples from RNAseq data after adjusting for various hidden biological and technical factors of variability." ; sc:featureList edam:operation_3223, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SVAPLSseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SVAPLSseq.html" ; biotools:primaryContact "Sutirtha Chakraborty" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3175, edam:topic_3512, edam:topic_3673 ; sc:citation ; sc:description "Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data." ; sc:featureList edam:operation_0362, edam:operation_0372, edam:operation_0525, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "svaRetro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PapenfussLab/svaRetro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3168, edam:topic_3263 ; sc:citation ; sc:description "Secure Variant Annotation and Aggregation Tool." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SVAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/harmancilab/SVAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9514969", "pubmed:36208598" ; sc:description "SVD CLAHE Boosting and BWCCE Loss Function Experiments." ; sc:featureList edam:operation_0479, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SVD-CLAHE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/MrinalTyagi/SVD-CLAHE-and-BWCCE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_1775, edam:topic_3293 ; sc:citation "pubmed:26614125" ; sc:description "A phylogenetic profiling algorithm which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions." ; sc:featureList edam:operation_0324 ; sc:name "SVD-Phy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/andrea/svd-phy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:20639544" ; sc:description "Identifies genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions-deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations" ; sc:featureList edam:operation_3197 ; sc:name "SVDetect" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://svdetect.sourceforge.net/Site/Home.html" ; biotools:primaryContact "SVDetect Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2572, edam:format_2573 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence trace" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence trace" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_2533 ; sc:citation , , ; sc:description "BAM preprocessing to get abnormal pairs." ; sc:featureList edam:operation_2403 ; sc:name "svdetect_bam_preprocessing_pairs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://svdetect.sourceforge.net/Site/Home.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; 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sc:featureList edam:operation_0474, edam:operation_0475, edam:operation_2403 ; sc:name "svdetect_run_parallel_step" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://svdetect.sourceforge.net/Site/Home.html" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Singular value decomposition analysis of global gene expression data." ; sc:featureList edam:operation_2495 ; sc:name "SVDMAN" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.9b" ; sc:url "http://public.lanl.gov/mewall/svdman/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637, edam:topic_3053 ; sc:citation "pubmed:25104814" ; sc:description "A program to compute a score based on singular value decomposition of a matrix of site pattern frequencies corresponding to a split on a phylogenetic tree. These quartet scores can be used to select the best-supported topology for quartets of taxa, which in turn can be used to infer the species phylogeny using quartet methods." ; sc:featureList edam:operation_0324 ; sc:name "SVDquartets" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.stat.osu.edu/~lkubatko/software/SVDquartets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0605, edam:topic_2885, edam:topic_3175, edam:topic_3577, edam:topic_3673 ; sc:citation , "pubmed:36550274" ; sc:description "Structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads." ; sc:featureList edam:operation_0524, edam:operation_3196, edam:operation_3199, edam:operation_3227, edam:operation_3228 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SVDSS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Parsoa/SVDSS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3175, edam:topic_3512, edam:topic_3673 ; sc:citation , "pmcid:PMC7981925", "pubmed:33743584" ; sc:description "SVExpress is a suite of computational tools (implemented in Excel VBA and R) that allows one to identify Structural Variant (SV) breakpoint-to-expression associations across a set of cancer samples profiled for both SVs and gene transcription. SVExpress takes as input a table of somatic SV breakpoints and a gene-to-sample expression matrix. SVExpress then constructs a gene-to-sample breakpoint matrix, which the user can then integrate with corresponding expression data by linear regression modeling. Furthermore, using SVExpress, top SV-gene associations identified can be examined in terms of enhancer hijacking or disruption of TADs." ; sc:featureList edam:operation_0314, edam:operation_3463, edam:operation_3659 ; sc:name "SVExpress" ; sc:url "https://github.com/chadcreighton/SVExpress" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC7884742", "pubmed:33589703" ; sc:description "Dimensionality reduction using singular vectors." ; sc:featureList edam:operation_3432, edam:operation_3557, edam:operation_3935 ; sc:name "SVFS" ; sc:url "https://github.com/Majid1292/SVFS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3173, edam:topic_3474 ; sc:citation , "pmcid:PMC7650198", "pubmed:33168059" ; sc:description """SVFX is a machine learning based tool to assign pathogenic scores to large deletions and duplications. a machine learning framework to quantify the pathogenicity of structural variants and using Random Forests to Prioritize Structural Variants.""" ; sc:featureList edam:operation_3226, edam:operation_3359, edam:operation_3461 ; sc:license "MIT" ; sc:name "SVFX" ; sc:url "https://github.com/gersteinlab/SVFX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3175, edam:topic_3299, edam:topic_3676 ; sc:citation ; sc:description "SVhound is a framework to predict regions that harbour so far unidentified genotypes of Structural Variations. It uses a population size VCF file as input and reports the probabilities and regions across the population. SVhound was tested and applied to the 1000genomes VCF file and also other data sets." ; sc:featureList edam:operation_3196, edam:operation_3228, edam:operation_3695 ; sc:name "SVhound" ; sc:url "https://github.com/lfpaulin/SVhound" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0625, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description """Structural variant detection from haploid and diploid genome assemblies. SVIM-asm - Structural variant identification method (Assembly edition). SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments. It analyzes a given sorted BAM file (preferably from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.""" ; sc:featureList edam:operation_0525, edam:operation_3196, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "SVIM-asm" ; sc:url "http://github.com/eldariont/svim-asm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_2885, edam:topic_3175, edam:topic_3676 ; sc:citation , "pmcid:PMC8671832", "pubmed:34925449" ; sc:description "A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SVInterpreter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DGRC-PT/SVInterpreter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "The Swiss Variant Interpretation Platform (SVIP) aims at providing a centralized, joint, and curated knowledge base for the clinical interpretation of somatic variants coming from Swiss hospitals. For characterized variants, annotations are revised by a clinical expert panel. For the uncharacterized variants, manual curation is performed using bioinformatics tools and literature triage. The resulting annotations and their clinical interpretations are validated by a clinical expert panel." ; sc:featureList edam:operation_0227, edam:operation_0361, edam:operation_0570, edam:operation_2995, edam:operation_2996, edam:operation_3778 ; sc:name "SVIP" ; sc:url "https://svip.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3382 ; sc:citation , "pmcid:PMC6404320", "pubmed:30841857" ; sc:description "Simple visualization tool for genomic tracks from sequencing experiments." ; sc:featureList edam:operation_3208, edam:operation_3436, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "WTFPL" ; sc:name "svist4get" ; sc:operatingSystem "Linux" ; sc:url "https://bitbucket.org/artegorov/svist4get/" ; biotools:primaryContact "Artyom Egorov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3175 ; sc:citation , "pubmed:33973820" ; sc:description "SVLR is a tool designed to detect structural variation with long reads sequenced by the third generation sequencing (PacBio or Oxford Nanopore). It detects seven types of SVs (10bp+) which include deletion, insertion, inversion, tandem duplication, interspersed duplication, cut & paste isertion, block replacement, block interchange, and translocation by following four steps: SV signatures marking, SV signatures Clustering, SV clusters combination, SV clusters optimization. The current version of SVLR utilizes the alignments from NGMLR(.sam) or LAST(.maf)." ; sc:featureList edam:operation_3227, edam:operation_3228, edam:operation_3432 ; sc:name "SVLR" ; sc:url "https://github.com/GWYSDU/SVLR" ; biotools:primaryContact "Daming Zhu", "Xuefeng Cui" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3344 ; sc:description "SVM Classification with Hard and Soft margin for cancer cells classification" ; sc:isAccessibleForFree true ; sc:name "SVM Classification for cancer cell" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/74011-svm-classification-with-hard-and-soft-margin-for-cancer-cell" ; biotools:primaryContact "Shakoor Tanoli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0623, edam:topic_1775 ; sc:citation "pubmed:12824396" ; sc:description "Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0303, edam:operation_2454, edam:operation_3092 ; sc:name "SVM-PROT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bidd2.nus.edu.sg/cgi-bin/svm-prot/svmprot.cgi" ; biotools:primaryContact "Chen Yu Zong", "SVM team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3070, edam:topic_3344, edam:topic_3473 ; sc:citation ; sc:description "Support vector machine recursive feature elimination (SVM-RFE) with correlation bias reduction. SVM-RFE is a powerful feature selection algorithm in bioinformatics. It is a good choice to avoid overfitting when the number of features is high." ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:name "SVM-RFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/50701-feature-selection-with-svm-rfe" ; biotools:primaryContact "Ke Yan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Classification and biomarker identification using gene network modules and support vector machines. Uses the Gene Expression Network Analysis Tool (GXNA) as clustering method to identify correlated gene clusters, and Support Vector Machines to identify and (rank) those gene networks (clusters) for accuracy of classification." ; sc:featureList edam:operation_2497, edam:operation_2990, edam:operation_3432 ; sc:name "SVM-RNE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web.macam.ac.il/~myousef/MyTools/SVM-RNE.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation ; sc:description "Detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data." ; sc:featureList edam:operation_2480 ; sc:license "CC-BY-NC-3.0" ; sc:name "SVM2" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareVersion "1.2" ; sc:url "http://159.149.160.53/pub/svm2" ; biotools:primaryContact "David Horner", "Matteo Chiara" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3003 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_3003 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169 ; sc:citation ; sc:description "Detection of cis-regulatory elements using svm implemented in LiblineaR." ; sc:featureList edam:operation_0438 ; sc:license "GPL-3.0" ; sc:name "SVM2CRM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SVM2CRM.html" ; biotools:primaryContact "Guidantonio Malagoli Tagliazucchi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3474, edam:topic_3934, edam:topic_3940 ; sc:citation , "pmcid:PMC8056015", "pubmed:33889181" ; sc:description "svmATAC is a tool for the enhancement and imputation of peak signal enables accurate identification of cell type in scATAC-seq." ; sc:featureList edam:operation_2409, edam:operation_3222, edam:operation_3557 ; sc:license "MIT" ; sc:name "svmATAC" ; sc:url "https://github.com/mrcuizhe/svmATAC" ; biotools:primaryContact "Tianyi Zang", "Yadong Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:21194472" ; sc:description "Pipeline for the detection of structural variants by integrating calls from multiple structural variant callers." ; sc:featureList edam:operation_3197 ; sc:name "SVMerge" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://svmerge.sourceforge.net/" ; biotools:primaryContact "Support Forum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Prediction of MHC class I binding peptides." ; sc:featureList edam:operation_2423 ; sc:name "SVMHC" ; sc:provider "bils.se" ; sc:softwareVersion "1" ; sc:url "http://www.sbc.su.se/%7Epierre/svmhc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_3170, edam:topic_3175, edam:topic_3474 ; sc:citation , "pubmed:33381833" ; sc:description "svMIL2: predicting the pathogenic effect of somatic non-coding structural variants disrupting the 3D genome through Multiple Instance Learning." ; sc:featureList edam:operation_0331, edam:operation_0438, edam:operation_3461 ; sc:license "MIT" ; sc:name "svMIL2" ; sc:url "https://github.com/UMCUGenetics/svMIL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2815, edam:topic_3175 ; sc:citation ; sc:description "mining of SV predictions from multiple tools to improve the performance of SV detection. It refines SV predictions by performing local realignment and assess quality of SV predictions based on likelihoods of the realignments." ; sc:featureList edam:operation_3228 ; sc:name "SVmine" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/xyc0813/SVmine" ; biotools:primaryContact "Ruibin Xi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:citation "pubmed:14978706" ; sc:description "Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format." ; sc:featureList edam:operation_0269, edam:operation_0270, edam:operation_2241 ; sc:name "SVMtm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ccb.imb.uq.edu.au/svmtm/svmtm_predictor.shtml" ; biotools:primaryContact "Dr. Rohan Teasdale", "Dr. Zheng Yuan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0166, edam:topic_0621, edam:topic_2830, edam:topic_3474 ; sc:citation , "pubmed:32162263" ; sc:description """A Method to Predict B-Cell Linear Antigenic Epitopes. a tool to predict linear antigenic epitopes. Realistic prediction of protein surface regions that are preferentially recognized by antibodies (antigenic epitopes) can help the design of vaccine components and immuno-diagnostic reagents. By secreting antibodies against antigens, B-cells play an important role in immune system to fight against the invasive pathogenic organism or substances. Antigenic epitopes are regions of protein surface that are preferentially recognized by B-cell antibodies . Prediction of antigenic epitopes is useful for the investigation to the mechanism in body self-protection systems and help during the design of vaccine components and immuno-diagnostic reagents. In this work, we developed a new method to predict antigenic epitope with lastest sequence input from IEDB database.""" ; sc:featureList edam:operation_0267, edam:operation_0416, edam:operation_2489 ; sc:name "SVMTriP" ; sc:url "http://sysbio.unl.edu/SVMTriP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3475 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0160, edam:topic_0601 ; sc:author ; sc:citation , "pubmed:35662454" ; sc:description "A Web Server Detecting Co- and Post-translational Myristoylation in Proteins." ; sc:featureList edam:operation_0417, edam:operation_0422 ; sc:isAccessibleForFree true ; sc:name "SVMyr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://busca.biocomp.unibo.it/lipipred" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation "pubmed:15852502" ; sc:description "A program for removing systematic variation in microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, this procedure includes background subtraction determined from the distribution of pixel intensity values and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization." ; sc:featureList edam:operation_3435 ; sc:name "SVN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.niehs.nih.gov/research/resources/software/biostatistics/svn/index.cfm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3175, edam:topic_3474 ; sc:citation , "pmcid:PMC8214287", "pubmed:34147063" ; sc:description "SVNN is a fast, and accurate structural variation calling pipeline for long-reads that takes raw reads as the input and detects structural variants of size larger than 50 bp. SVNN utilizes NGMLR, and Minimap2 as long read aligners, and Sniffles, and SVIM as SV callers." ; sc:featureList edam:operation_3227, edam:operation_3228, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SVNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://easy.ce.sharif.edu/svnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_2885, edam:topic_3175, edam:topic_3673 ; sc:citation , "pubmed:33051644" ; sc:description """svpluscnv: R toolkit for the analysis of structural variants and complex genomic rearrangements. svpluscnv is an R package designed for integrative analyses of somatic DNA copy number variations (CNV) and other structural variants (SV).svpluscnv comprises multiple analytical and visualization tools that can be applied to large datasets from cancer patients such as TCGA and PCAWG or cancer cell lines CCLE.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3227 ; sc:name "Svpluscnv" ; sc:url "https://github.com/ccbiolab/svpluscnv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3175, edam:topic_3325, edam:topic_3422, edam:topic_3517, edam:topic_3673 ; sc:citation ; sc:description "SVRare is a tool for discovering disease-causing structural variants in the 100K Genomes Project. Right now SVRare is adapted to be used in the Genomics England (GEL) research environment." ; sc:featureList edam:operation_0224, edam:operation_3227, edam:operation_3436 ; sc:name "SVRare" ; sc:url "https://github.com/Oxford-Eye/SVRare" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3168, edam:topic_3304 ; sc:citation , "pubmed:33871905" ; sc:description "The R package svreg implements the structural varying-coefficient regression (svReg) for the model selection of a varying-coefficient model with structured main predictors or modifying variables. It also provides functions for performing the pliable lasso (plasso)." ; sc:featureList edam:operation_0337, edam:operation_3659, edam:operation_3936 ; sc:name "svreg" ; sc:url "https://github.com/rakheon/svreg" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3175, edam:topic_3299 ; sc:citation , "pubmed:37019014" ; sc:description "A more accurate structural variation detection method in long read data." ; sc:featureList edam:operation_3198, edam:operation_3228, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:name "SVsearcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kensung-lab/SVsearcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2533, edam:topic_3053 ; sc:citation "pubmed:22537045" ; sc:description "An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. It calls both deletions and insertions." ; sc:featureList edam:operation_3197 ; sc:name "SVseq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.engr.uconn.edu/~jiz08001/svseq2.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_2640, edam:topic_3673 ; sc:citation ; sc:description "SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:license "MIT" ; sc:name "SVTyper" ; sc:url "https://github.com/hall-lab/svtyper" ; biotools:primaryContact "Ira Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26286809" ; sc:description "Visualizes high-throughput sequencing data relevant to a structural variant. Only reads supporting the variant or the reference allele will be shown." ; sc:featureList edam:operation_0564 ; sc:name "svviz" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://svviz.github.io/svviz/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC7100977", "pubmed:32182236" ; sc:description """Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures. A structural variant caller that uses discordant read-pairs (PE), split-reads (SR) and read-depth (RD) information. SVXplorer accepts a BAM file of target as input and outputs a BEDPE file (and an equivalent VCF file) containing deletions (DEL), tandem duplications (TD), inversions (INV), non-tandem-duplications, translocations (see below), novel sequence insertions (DN_INS) and undetermined types tagged as "BND." The variant tags listed in parentheses pertain to the BEDPE file, whereas the VCF file follows VCF 4.3 specifications.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3359, edam:operation_3432, edam:operation_3675 ; sc:license "MIT" ; sc:name "SVXplorer" ; sc:url "https://github.com/kunalkathuria/SVXplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3305, edam:topic_3390 ; sc:citation ; sc:description "A generic SAS macro for cross-tabulation between a factor and a by-group variable given a third variable and creating publication-quality tables using data from complex surveys | Abstract Introduction In epidemiological studies, cross-tabulations are a simple but important tool for understanding the distribution of socio-demographic characteristics among study participants. They become more useful when comparisons are presented using a by-group variable such as key demographic characteristic or an outcome status; for instance, sex or the presence or absence of a disease status. Most available statistical analysis software can easily perform cross-tabulations, however, output from these must be processed further to make it readily available for review and use in a publication" ; sc:featureList edam:operation_3659, edam:operation_3891 ; sc:name "svy_freqs" ; sc:url "https://github.com/kmuthusi/generic-sas-macros" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:16845032" ; sc:description "Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure." ; sc:featureList edam:operation_0550, edam:operation_2406, edam:operation_2487, edam:operation_3092 ; sc:name "SWAKK" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://oxytricha.princeton.edu/SWAKK/" ; biotools:primaryContact "Han Liang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3569 ; sc:description "A simple Smith-Waterman alignment implementation in C." ; sc:featureList edam:operation_0258, edam:operation_0491, edam:operation_0495 ; sc:license "MIT" ; sc:name "Swalign" ; sc:url "http://code.google.com/p/swalign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_2269 ; sc:citation , "pmcid:PMC8599790", "pubmed:34417615" ; sc:description "Scaffolding with assembly likelihood optimization" ; sc:featureList edam:operation_0479, edam:operation_0524, edam:operation_0525, edam:operation_2940, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Swalo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://atifrahman.github.io/SWALO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3517 ; sc:citation ; sc:description "SWAM (Smartly weighted averaging across multiple tissues) is an gene expression imputation method which combines information from multiple sources to boost accuracy of imputed gene expression levels. Transcriptome wide association studies (TWAS) can be used as a powerful method to identify and interpret the underlying biological mechanisms behind GWAS by mapping gene expression levels with phenotypes. In TWAS, gene expression is often imputed from individual-level genotypes of regulatory variants identified from external resources, such as Genotype-Tissue Expression (GTEx) Project. In this setting, a straightforward approach to impute expression levels of a specific tissue is to use the model trained from the same tissue type. When multiple tissues are available for the same subjects, it has been demonstrated that training imputation models from multiple tissue types improves the accuracy because of shared eQTLs between the tissues and increase in effective sample size." ; sc:featureList edam:operation_0314, edam:operation_3196, edam:operation_3232, edam:operation_3557 ; sc:license "Apache-2.0" ; sc:name "SWAM" ; sc:url "https://github.com/aeyliu/swam" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0602, edam:topic_0654 ; sc:description "Software to meant for genome-wide prediction of regulatory targets of a motif using a Hidden Markov Model. It differs from Stubb in that instead of asking Does the sequence have more sites than expected from a random (background) model of sequences?, it asks the question Does the sequence have more sites than the average genome-wide frequency of sites?" ; sc:featureList edam:operation_0239 ; sc:name "Swan" ; sc:operatingSystem "Linux" ; sc:softwareVersion "v6" ; sc:url "http://www.sinhalab.net/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """a library for the analysis and visualization of long-read transcriptomes. swan is a tool for visualizing and analyzing transcript isoforms.""" ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_2495 ; sc:license "MIT" ; sc:name "Swan" ; sc:url "https://pypi.org/project/swan-vis/1.0/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:25253533" ; sc:description "A scalable and fully parallelized genome assembler designed for massive sequencing data. Intend of using traditional de Bruijn Graph, it adopts multi-step bi-directed graph (MSG). With MSG, the standard genome assembly (SGA) is equivalent to the edge merging operations in a semi-group." ; sc:featureList edam:operation_0525 ; sc:name "SWAP-Assembler" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/swapassembler/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2546 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1235 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence cluster" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3047, edam:topic_3050, edam:topic_3301 ; sc:citation , ; sc:description "A robust and fast clustering method for amplicon-based studies. The purpose of this tool is to provide a novel clustering algorithm that handles massive sets of amplicons." ; sc:featureList edam:operation_0291 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Swarm" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "UiO" ; sc:softwareHelp , ; sc:softwareVersion "2.1.6" ; sc:url "https://github.com/torognes/swarm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0602, edam:topic_2275, edam:topic_3047 ; sc:citation ; sc:description """Automatic Parametrization of Bonded Terms in Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization. Swarm-CG is designed for automatically optimizing the bonded terms of a MARTINI-based coarse-grained (CG) molecular model, in explicit or implicit solvent, with respect to a reference all-atom (AA) trajectory and starting from a preliminary CG model (topology and non-bonded parameters). The package is designed for usage with Gromacs and contains 3 modules for:.""" ; sc:featureList edam:operation_0394, edam:operation_3891, edam:operation_3893 ; sc:license "MIT" ; sc:name "Swarm-CG" ; sc:url "http://www.github.com/GMPavanLab/SwarmCG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "Generating 3D structures of protein-protein complexes. Allows flexible modelling of protein-protein complexes using the SwarmDock algorithm which incorporates a normal modes approach." ; sc:featureList edam:operation_0478 ; sc:name "SwarmDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bmm.cancerresearchuk.org/~SwarmDock/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3324 ; sc:citation ; sc:description """a computational approach to predict the specificity of T Cell Receptors. SwarmTCR predicts T-cell receptor (TCR) specificity using the 'distance' between TCRs. SwarmTCR is an optimized adaption of TCRdist (Dash et al. 2017) that uses both protein sequence identity of the complementary determining region (CDR) loops and particle swarm optimization. Distance is determined in the same manner as the original TCRdist methodology, where the alignment (BLOSUM62 matrix) values at each CDR loop are multiplied by a weight, the sum of all CDR loop values is the distance. Unlike TCRdist, SwarmTCR optimizes the weight for each CDR loop, making it specific to the repertoire tested. SwarmTCR is functional on both single-cell and deep-sequencing data, input parameters for each will be detailed below.""" ; sc:featureList edam:operation_0491 ; sc:license "GPL-3.0" ; sc:name "SwarmTCR" ; sc:url "https://github.com/thecodingdoc/SwarmTCR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:33662531" ; sc:description "SwarnSeq is an improved statistical approach for differential expression analysis of single-cell RNA-seq data. This R package performs Differential Expression, and Differential Zero Inflation analysis of Single-Cell RNA-seq (scRNA-seq) data." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3680 ; sc:name "SwarnSeq" ; sc:url "https://github.com/sam-uofl/SwarnSeq" ; biotools:primaryContact "Samarendra Das", "Shesh N. Rai" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3110 ; sc:encodingFormat edam:format_2330 ; sc:name "Raw microarray data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3111 ; sc:encodingFormat edam:format_3033, edam:format_3475 ; sc:name "Processed microarray data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation , "pmcid:PMC4824525", "pubmed:27054327" ; sc:description "This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation." ; sc:featureList edam:operation_0335 ; sc:license "GPL-3.0" ; sc:name "SWATH2stats" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SWATH2stats.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "It contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data." ; sc:featureList edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "SwathXtend" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SwathXtend.html" ; biotools:primaryContact "Jemma Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229 ; sc:citation , "pmcid:PMC6977721", "pubmed:31971963" ; sc:description """Module for SWC neuron morphology file validation and correction enabled for high throughput batch processing. Batch validation of directory containing SWC files. Ensures structures are correctly connected. Fix structures with zero size diameter.""" ; sc:featureList edam:operation_1812, edam:operation_2428, edam:operation_3450 ; sc:license "GPL-2.0" ; sc:name "SWC BATCH CHECK" ; sc:url "https://github.com/dohalloran/SWC_BATCH_CHECK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3295, edam:topic_3308, edam:topic_3315 ; sc:citation ; sc:description """swCAM: Unsupervised Sample-wise Deconvolution, a tool for estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution. We report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and subtype-specific expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework (https://github.com/Lululuella/debCAM) to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and l_(2,1)-norm regularized low-rank matrix factorization problem. We determine hyperparameter value using a cross-validation scheme with random entry exclusion and obtain swCAM solution using an efficient alternating direction method of multipliers. The swCAM is implemented in open-source R scripts.""" ; sc:featureList edam:operation_3223, edam:operation_3629, edam:operation_3766 ; sc:name "swCAM" ; sc:url "https://github.com/Lululuella/swCAM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:32554025" ; sc:description """An RPackage for Stepped Wedge Trial Design and Analysis. Stepped wedge trials (SWTs) are a type of cluster-randomized trial that are commonly used to evaluate health care interventions. Most SWT-related software packages have restrictive assumptions about the study design and correlation structure of the data. The objective of this paper is to present a package and corresponding web-based graphical user interface (GUI) that provide researchers with another, more flexible option for SWT design and analysis. METHODS:We developed an Rpackage swCRTdesign ('stepped wedge Cluster Randomized Trial design'), which uses a random effects model to account for correlation in the data induced by a SWT design. Possible sources of correlation include clusters, time within clusters, and treatment within clusters""" ; sc:featureList edam:operation_0337, edam:operation_3432 ; sc:name "swCRTdesign" ; sc:url "https://rdrr.io/cran/swCRTdesign/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_3168 ; sc:citation "pubmed:18387198" ; sc:description "This allows to perform alignments between one or more sequences and a database (all the sequences, even in the DB, are intended to be proteinic). It is implemented in the recently released CUDA programming environment by NVidia." ; sc:featureList edam:operation_0495 ; sc:name "SWCuda" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.cribi.unipd.it/cuda/swcuda.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3295 ; sc:citation ; sc:description "swDMR: a sliding window approach to identify differentially methylated regions based on bisulfite sequencing" ; sc:featureList edam:operation_3204 ; sc:license "GPL-3.0" ; sc:name "SwDMR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://code.google.com/p/swdmr/" ; biotools:primaryContact "BingYu Chen", "Dongsheng Huang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3379 ; sc:citation , "pmcid:PMC8665077", "pubmed:34818620" ; sc:description "A SAS macro and an R package for power calculations in stepped wedge cluster randomized trials." ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "swdpwr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://jiachenchen322.shinyapps.io/swdpwr_shinyapp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3127, edam:topic_3168 ; sc:citation "pubmed:18602951" ; sc:description "A perl program that looks for recombinations in non-aligned sequences using BLAST." ; sc:featureList edam:operation_0451 ; sc:name "SWeBLAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/sweblast/wiki/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC1310644", "pubmed:16251466" ; sc:description "Parallel and checkpointable tool implementing a composite ratio test for detecting selective sweeps. SweeD is based on the SweepFinder algorithm. SweeD can calculate the theoretical SFS of a give demographic model (stepwise changes or with an exponential growth phase + stepwise changes) using the method of Zickovic and Stephan (2011)." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "SweeD" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/alachins/sweed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:description "Allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype (LRH) test to look for alleles of high frequency with long-range linkage disequilibrium (LD), which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers" ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "sweep" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://archive.broadinstitute.org/mpg/sweep/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0610, edam:topic_0625, edam:topic_2885 ; sc:citation ; sc:description "SweepCluster is a python library and toolkit for implementation of SNP clustering and significance estimation based on the anchor-extension method.." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3432, edam:operation_3661 ; sc:license "GPL-3.0" ; sc:name "SweepCluster" ; sc:url "https://github.com/BaoCodeLab/SweepCluster" ; biotools:primaryContact , "Qianjun Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Program implementing the method described in Nielsen et al. 2005. Genomic scans for selective sweeps using SNP data. Genome Research 1566-1575. It can be used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "SweepFinder" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://people.binf.ku.dk/rasmus/webpage/sf.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation ; sc:description "An R package using Hoeffding’s D statistic to visualise the dependence between M and A for large numbers of gene expression samples." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3731 ; sc:name "sweetD" ; sc:url "https://github.com/amberjoybarton/sweetD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275 ; sc:description "Automate work of rendering and animating molecules." ; sc:featureList edam:operation_0337 ; sc:name "SweetMollyGrace" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://rodomontano.altervista.org/engSweetMG.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3474, edam:topic_3678 ; sc:citation , "pubmed:34357537" ; sc:description "SweetPea is a domain-specific programming language built for the declarative specification of randomized experimental designs and the synthesis of trial sequences generated from those design specifications." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SweetPea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://sweetpea-org.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3176, edam:topic_3295 ; sc:description "A peak-calling tool package for functinal genomic and other data sets." ; sc:featureList edam:operation_3215 ; sc:license "Apache-2.0" ; sc:name "SWEMBL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/stevenwilder/SWEMBL" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2906 ; sc:name "Peptide ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2979 ; sc:name "Peptide property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154 ; sc:citation ; sc:description "An endogenous peptide database." ; sc:featureList edam:operation_0224 ; sc:name "SwePep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://www.swepep.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3315 ; sc:description "This package allows users to estimate the science-wise false discovery rate from Jager and Leek, \"Empirical estimates suggest most published medical research is true,\" 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null hypotheses in the presence of covariates, using a regression framework." ; sc:featureList edam:operation_2238, edam:operation_2424 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "swfdr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/swfdr.html" ; biotools:primaryContact "Jeffrey T. Leek", "Simina M. Boca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0769, edam:topic_3168, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC10138271", "pubmed:37068103" ; sc:description "Fast machine-learning-guided primer design pipeline for selective whole genome amplification." ; sc:featureList edam:operation_0308, edam:operation_0458, edam:operation_3237 ; sc:isAccessibleForFree true ; sc:name "swga2_0" ; sc:url "https://anaconda.org/janedwivedi/swga2" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3520 ; sc:author "Ivan Janda", "Jiří­ Vohradský" ; sc:citation , "pubmed:14625849", "pubmed:16400688" ; sc:contributor "Bjorn Grunenfelder", "Czech Science Foundation", "Jan Bobek", "Karel Mikulik", "Marek Basler", "Urs Jenal" ; sc:description "A proteomics web database." ; sc:featureList edam:operation_2421 ; sc:funder "Czech Science Foundation" ; sc:isAccessibleForFree true ; sc:name "SWICZ" ; sc:operatingSystem "Windows" ; sc:provider "Biozentrum, Univ. Basel, Switzerland", "ELIXIR-CZ", "Institute of Microbiology, Prague, Czech Republic" ; sc:softwareHelp , ; sc:url "http://proteom.biomed.cas.cz/" ; biotools:primaryContact "Jiří Vohradský" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Kim R. Rasmussen" ; sc:citation ; sc:description "Program for fast local alignment search, guaranteeing to find epsilon-matches between two sequences. An epsilon-match is a local alignment above a given length with an error rate of at most epsilon." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:name "SWIFT" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "BiBiServ", "Bielefeld University", "CeBiTec" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://bibiserv.cebitec.uni-bielefeld.de/swift" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3444, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:32203803" ; sc:description """Accelerated document screening through active learning and integrated recall estimation. In the screening phase of systematic review, researchers use detailed inclusion exclusion criteria to decide whether each article in a set of candidate articles is relevant to the research question under consideration. A typical review may require screening thousands or tens of thousands of articles in and can utilize hundreds of person-hours of labor. METHODS:Here we introduce SWIFT-Active Screener, a web-based, collaborative systematic review software application, designed to reduce the overall screening burden required during this resource-intensive phase of the review process. To prioritize articles for review, SWIFT-Active Screener uses active learning, a type of machine learning that incorporates user feedback during screening""" ; sc:featureList edam:operation_3454 ; sc:name "SWIFT-Active Screener" ; sc:url "https://www.sciome.com/swift-activescreener/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation "pubmed:19549630" ; sc:description "Primary Data Analysis for the Illumina Solexa Sequencing Platform." ; sc:featureList edam:operation_2403 ; sc:license "LGPL-2.1" ; sc:name "Swift" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/new299/swift" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407, edam:topic_3955 ; sc:citation , "pmcid:PMC7158141", "pubmed:32293238" ; sc:description """a tool for the context-specific reconstruction of genome-scale metabolic networks. swiftcc is a tool for finding the largest flux consistent subnetwork of the original metabolic network. swiftccTest provides a benchmark to compare its performance against fastcc. swiftcore is a tool for the context-specific reconstruction of genome-scale metabolic networks. swiftcoreTest and weightedTest provide a benchmark to compare its performance against fastcore.""" ; sc:featureList edam:operation_3435, edam:operation_3660 ; sc:name "SWIFTCORE" ; sc:url "https://mtefagh.github.io/swiftcore/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3372 ; sc:citation , "pubmed:34524429" ; sc:description "An open-source version of its predecessor SWIM (SWitchMiner) that is a network-based tool for mining key (switch) genes that are associated with intriguing patterns of molecular co-abundance and may play a crucial role in phenotypic transitions in various biological settings." ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SWIMmeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/sportingCode/SWIMmeR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is inputted from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:license "GPL-2.0" ; sc:name "SwimR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/SwimR.html" ; biotools:primaryContact "Randy Blakely" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:name "Sequence alignment (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3047 ; sc:author "Torbjørn Rognes" ; sc:citation ; sc:description "Tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs." ; sc:featureList edam:operation_0292 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "SWIPE" ; sc:operatingSystem "Linux" ; sc:provider "UiO" ; sc:softwareHelp , ; sc:softwareVersion "2.0.5" ; sc:url "http://dna.uio.no/swipe" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2374 ; sc:name "Spot serial number" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2791 ; sc:name "Reference map name (SWISS-2DPAGE)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2791 ; sc:name "Reference map name (SWISS-2DPAGE)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:name "Protein identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2374 ; sc:name "Spot serial number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2330 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:contributor "SIB Swiss Institute of Bioinformatics" ; sc:description "Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps." ; sc:featureList edam:operation_0224 ; sc:name "SWISS-2DPAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.expasy.org/ch2d/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_1317, edam:topic_2275, edam:topic_3306 ; sc:citation ; sc:description "The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for relevant model organisms and experimental structure information for all sequences in UniProtKB. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. It also allows users to assess the quality of the models using the latest QMEAN results. If a sequence has not been modelled, the user can build models interactively via the SWISS-MODEL workspace." ; sc:featureList edam:operation_0474, edam:operation_2414, edam:operation_3431 ; sc:license "CC-BY-SA-4.0" ; sc:name "SWISS-MODEL Repository" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "https://swissmodel.expasy.org/repository/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_2275, edam:topic_3306 ; sc:citation , "pmcid:PMC6030848", "pubmed:29788355" ; sc:description "SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make protein modelling accessible to all life science researchers worldwide." ; sc:featureList edam:operation_0477 ; sc:license "CC-BY-SA-4.0" ; sc:name "SWISS-MODEL Workspace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "https://swissmodel.expasy.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:10470037", "pubmed:9504803" ; sc:description "Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial *Molecular Modeling for Beginners* is a must (listed on this page)." ; sc:featureList edam:operation_0321, edam:operation_0322, edam:operation_0331, edam:operation_0477, edam:operation_0481 ; sc:name "Swiss-PdbViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://spdbv.vital-it.ch/" ; biotools:primaryContact "Feedback Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091 ; sc:citation "pubmed:12824417" ; sc:description "Web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics." ; sc:featureList edam:operation_2479 ; sc:name "Swiss EMBnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ch.embnet.org/" ; biotools:primaryContact "Support form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0122, edam:topic_0601 ; sc:description "Calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations." ; sc:featureList edam:operation_0417 ; sc:name "Swiss Mass Abacus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://glycoproteome.expasy.org/swiss-mass-abacus/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:name "Protein sequence (raw)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476, edam:format_1477 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0602, edam:topic_2275, edam:topic_2814 ; sc:citation , , , , "pmcid:PMC4086089", "pmcid:PMC5210589", "pmcid:PMC6030848", "pubmed:12824332", "pubmed:14681401", "pubmed:16301204", "pubmed:16381875", "pubmed:19517507", "pubmed:24782522", "pubmed:27899672", "pubmed:29788355", "pubmed:9322042", "pubmed:9504803" ; sc:description "SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide." ; sc:featureList edam:operation_0477, edam:operation_0479 ; sc:name "SWISS-MODEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://swissmodel.expasy.org/" ; biotools:primaryContact "Protein Structure Bioinformatics Group" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258 ; sc:citation ; sc:description "Gives free access to a number of parameters and predictive models in order to compute the physicochemistry and estimate the pharmacokinetics, druglikeness and medicinal chemistry friendliness of one or several small molecules." ; sc:featureList edam:operation_2423 ; sc:name "SwissADME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.swissadme.ch/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_2275 ; sc:description "SwissBioisostere is a database containing information on millions of molecular replacements and their performance in biochemical assays. It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, and to give access to the details on particular molecular replacements." ; sc:featureList edam:operation_0482 ; sc:name "SwissBioIsostere" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.swissbioisostere.ch/" ; biotools:primaryContact "SwissBioisostere Contact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0637, edam:topic_2229, edam:topic_3382, edam:topic_3500 ; sc:citation , "pmcid:PMC9216577", "pubmed:35411389" ; sc:description "Interactive library of cell images for the visualization of subcellular location data." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "SwissBioPics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.swissbiopics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121, edam:topic_0209, edam:topic_1317 ; sc:citation ; sc:description "Protein ligand docking server, accessible via the ExPASy web server, and based on EADock DSS. The purpose of this server is to make protein-ligand docking accessible to a wide scientific community worldwide." ; sc:featureList edam:operation_0478, edam:operation_0570, edam:operation_2426 ; sc:name "SwissDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareVersion "1" ; sc:url "http://www.swissdock.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0602 ; sc:description "SwissLipids is a comprehensive reference database that links mass spectrometry-based lipid identifications to curated knowledge of lipid structures, metabolic reactions, enzymes and interacting proteins. It features approximately 500,000 lipid structures from more than 115 lipid classes and over 3,000 enzymatic reactions and 800 proteins." ; sc:featureList edam:operation_3672 ; sc:name "SwissLipids" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.swisslipids.org/#/" ; biotools:primaryContact "SwissLipids Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_3816 ; sc:name "Small molecule structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3872 ; sc:encodingFormat edam:format_3887 ; sc:name "Topology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3871 ; sc:encodingFormat edam:format_3883 ; sc:name "Forcefield parameters" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176 ; sc:citation , "pubmed:21541964" ; sc:description "This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS." ; sc:featureList edam:operation_3893 ; sc:isAccessibleForFree true ; sc:name "SwissParam" ; sc:softwareVersion "1" ; sc:url "http://swissparam.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0749, edam:topic_2259, edam:topic_3512 ; sc:citation ; sc:description "SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form." ; sc:featureList edam:operation_0292, edam:operation_3439 ; sc:name "SwissRegulon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://swissregulon.unibas.ch/sr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0121, edam:topic_0209, edam:topic_3306 ; sc:description "SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins." ; sc:featureList edam:operation_0236 ; sc:name "SwissSidechain" ; sc:url "http://www.swisssidechain.ch/" ; biotools:primaryContact "David Gfeller" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258 ; sc:citation ; sc:description "Allows the rapid screening of small to very large-scale libraries of drugs, bioactive small molecules, commercially available compounds, and an ultra-large library of virtual compounds readily synthesizable from commercially available reagents. The virtual screening can be performed using molecular fingerprints, as well as superpositional or fast non-superpositional 3D shape similarity approaches." ; sc:featureList edam:operation_2423 ; sc:name "SwissSimilarity" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.swisssimilarity.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0621, edam:topic_2275, edam:topic_3336 ; sc:citation , "pmcid:PMC4086140", "pubmed:24792161" ; sc:description "SwissTargetPrediction is a web server for target prediction of bioactive small molecules. This website allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280 000 compounds active on more than 2000 targets of 5 different organisms." ; sc:featureList edam:operation_0478, edam:operation_2489, edam:operation_2492, edam:operation_2575 ; sc:name "SwissTargetPrediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.swisstargetprediction.ch" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Aims to provide a collection of 100 Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service." ; sc:featureList edam:operation_0552 ; sc:name "SwissTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://swisstree.sib.swiss/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1177 ; sc:name "MeSH concept ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1153 ; sc:name "OMIM ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2099 ; sc:name "Name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1150 ; sc:name "Disease ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3475 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3120 ; sc:citation , "pmcid:PMC2832822", "pubmed:20106818" ; sc:description "A portal to search variants (polymorphism) in UniProt Knowledgebase (UniProtKB) entries, and gives direct access to manual annotation on the genotype-phenotype relationship of each specific variant based on literature, as well as pre-computed information (such as conservation scores and a list of structural features when available) to help assess the effect of the variant." ; sc:featureList edam:operation_0349, edam:operation_2422 ; sc:name "SwissVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:softwareHelp ; sc:url "http://swissvar.expasy.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3033 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:encodingFormat edam:format_3033 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3365 ; sc:citation , "pmcid:PMC3662649", "pubmed:23682826" ; sc:description "The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle)." ; sc:featureList edam:operation_3664 ; sc:license "GPL-2.0" ; sc:name "switchBox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/switchBox.html" ; biotools:primaryContact , "Bahman Afsari", "Wikum Dinalankara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories." ; sc:featureList edam:operation_3223, edam:operation_3659 ; sc:license "GPL-2.0" ; sc:name "switchde" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/switchde.html" ; biotools:primaryContact "Kieran Campbell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3511 ; sc:citation "pubmed:22048815" ; sc:description "A software to identify regions of Copy Number Aberrations based on intensity data generated from copy number platforms. 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SYnthetic BAyesian classifier (SYBA) is a Python package for the classification of organic compounds as easy-to-synthesize (ES) or hard-to-synthesize (ES).""" ; sc:featureList edam:operation_0310, edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "SYBA" ; sc:url "https://github.com/lich-uct/syba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_0797 ; sc:citation "pubmed:18314579" ; sc:description "A web-based software package for comparative genomics, whose primary goal is to facilitate the analysis and visualization of comparative genome data, with a particular emphasis on protein and gene cluster data. Herein, a two-phase protein clustering algorithm, used to generate protein clusters suitable for analysis through Sybil and a method for creating graphical displays of protein or gene clusters that span multiple genomes are described." ; sc:featureList edam:operation_0495 ; sc:name "Sybil" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sybil.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis." ; sc:featureList edam:operation_3763 ; sc:license "GPL-3.0" ; sc:name "sybil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/sybil/index.html" ; biotools:primaryContact "Mayo Roettger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3047, edam:topic_3382 ; sc:citation , "pmcid:PMC9704760", "pubmed:36374853" ; sc:description "A web service for laying out, rendering and mining biological maps in SBGN, SBML and more." ; sc:featureList edam:operation_0337, edam:operation_2429, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SyBLaRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://syblars.cs.bilkent.edu.tr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1597 ; sc:name "Codon usage table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1600 ; sc:name "Codon usage bias plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Draw synonymous codon usage statistic plot for a nucleotide sequence." ; sc:featureList edam:operation_0286, edam:operation_0436 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "syco" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/syco.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3334, edam:topic_3473 ; sc:citation ; sc:description "Automated synaptic connectivity inference for volume electron microscopy" ; sc:featureList edam:operation_3443, edam:operation_3562 ; sc:isAccessibleForFree true ; sc:name "SyConn" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://structuralneurobiologylab.github.io/SyConn/" ; biotools:primaryContact "Joergen Kornfeld" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3321 ; sc:citation "pubmed:25910695" ; sc:description "An R package containing the functions exClust, TshrinkPlus and pMim." ; sc:featureList edam:operation_2495 ; sc:name "sydSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ellispatrick.com/r-packages/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3489 ; sc:citation "pubmed:10602881" ; sc:description "Database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. 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Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist." ; sc:featureList edam:operation_3501 ; sc:name "Sylamer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "Retired" ; sc:url "http://www-test.ebi.ac.uk/enright/sylamer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC7565356", "pubmed:32898474" ; sc:description "SYLARAS (SYstemic Lymphoid Architecture Response ASsessment) is a preclinical research platform for the interrogation of systemic immune response to disease and therapy. The approach combines multiplex immunophenotyping with biological computation to transform complex single-cell datasets into a visual compendium of the time and tissue-dependent changes occurring in immune cell frequency and/or function in response to an arbitrary immune stimulus (e.g. tumor model, infectious or autoimmune disease, vaccine, immunotherapy, etc.)." ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3891 ; sc:license "MIT" ; sc:name "SYLARAS" ; sc:url "https://github.com/gjbaker/sylaras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0659 ; sc:citation ; sc:description "Examine influence of small RNAs on expression profiles." ; sc:featureList edam:operation_2495 ; sc:name "Sylarray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/enright-srv/sylarray/" ; biotools:primaryContact "Anton Enright" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0749, edam:topic_3168, edam:topic_3337 ; sc:citation , "pmcid:PMC9805553", "pubmed:36440908" ; sc:description "Syllable-PBWT for space-efficient haplotype long-match query." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Syllable-PBWT" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/ZhiGroup/Syllable-PBWT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174 ; sc:description "fast and precise species-level metagenomic profiling with ANIs" ; sc:featureList edam:operation_3460 ; sc:name "sylph" ; sc:operatingSystem "Linux" ; sc:softwareVersion "v0.4.1" ; sc:url "https://github.com/bluenote-1577/sylph" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:26515823" ; sc:description "A reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations)." ; sc:featureList edam:operation_0324 ; sc:name "SylvX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sylvx.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:citation ; sc:description "Synteny Mapping and Analysis Program is a package for detecting and displaying syntenic relationships between sequenced chromosomes (pseudomolecules) and/or FPC physical maps." ; sc:featureList edam:operation_2429, edam:operation_2945 ; sc:name "SyMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "4.2" ; sc:url "http://www.agcol.arizona.edu/software/symap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3382, edam:topic_3385, edam:topic_3474 ; sc:citation , "pmcid:PMC9710168", "pubmed:36447211" ; sc:description """SyMBac is a tool to generate synthetic phase contrast or fluorescence images of bacteria. Currently the tool supports bacteria growing in the mother machine and in monolayers as microcolonies. This allows easy and rapid creation of training data, matching your experimental images, allowing you to train any model for cell segmentation or tracking.""" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "SyMBac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.3.7" ; sc:url "https://symbac.readthedocs.io/en/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0610, edam:topic_2885 ; sc:citation , "pmcid:PMC3616961", "pubmed:23497177" ; sc:description "Database of all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database." ; sc:featureList edam:operation_2409 ; sc:name "SymbioGBR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.symbiogbr.org" ; biotools:primaryContact "Linda Tonk", "Pim Bongaerts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_2259, edam:topic_3500 ; sc:citation , "pmcid:PMC4659445", "pubmed:26607947" ; sc:description "A database for the integration and access to knowledge on host-symbiont relationships." ; sc:featureList edam:operation_2421 ; sc:name "SymbioGenomesDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://symbiogenomesdb.uv.es/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0769, edam:topic_3168 ; sc:citation ; sc:description """a reference-free filter to automatically separate host sequences and contaminants for long reads or co-barcoded reads by unsupervised clustering. Filter contamination from filial tgs long reads or stlfr co-barcode-reads by parental kmer sets and unsupervised clustering.""" ; sc:featureList edam:operation_0487, edam:operation_3187, edam:operation_3216 ; sc:license "GPL-3.0" ; sc:name "Symbiont-Screener" ; sc:url "https://github.com/BGI-Qingdao/Symbiont-Screener" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3382, edam:topic_3474, edam:topic_3934 ; sc:citation , "pmcid:PMC9160162", "pubmed:35663891" ; sc:description "A Machine Learning Object Detection Tool for Polyploid Independent Estimates of Endosymbiont Population Size." ; sc:featureList edam:operation_3196, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SymbiQuant" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WilsonLabMiami/SymbiQuant" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:author "Christoforos Nikolau", "Sonja Althammer" ; sc:citation , , ; sc:description "SymCurv is a computational ab initio method for nucleosome positioning prediction. It is based on the structural property of natural nucleosome forming sequences, to be symmetrically curved around a local minimum of curvature." ; sc:featureList edam:operation_2478 ; sc:name "SymCurv" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genome.crg.es/cgi-bin/SymCurv/SymCurv.pl" ; biotools:primaryContact "Sonja Althammer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation , "pmcid:PMC4086132", "pubmed:24799435" ; sc:description "SymD webserver is a platform for detecting internally symmetric protein structures. It works through an alignment scan procedure in which a protein structure is aligned to itself after circularly permuting the second copy by all possible number of residues." ; sc:featureList edam:operation_0250, edam:operation_0321, edam:operation_0477, edam:operation_2488 ; sc:name "SymD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ccrod.cancer.gov/confluence/display/CCRLEE/SymD" ; biotools:primaryContact "Byungkook Lee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0602, edam:topic_0625, edam:topic_3303, edam:topic_3325, edam:topic_3336 ; sc:citation , "pmcid:PMC6323958", "pubmed:30380087" ; sc:description """An integrative database of traditional Chinese medicine enhanced by symptom mapping. SymMap integrates traditional Chinese medicine (TCM) with modern medicine (MM) through both internal molecular mechanism and external symptom mapping. It contains 499 herbs registered in the Chinese pharmacopoeia with 19,595 ingredients, and 1,717 corresponding symptoms used in traditional Chinese medicine (TCM symtptom). Those TCM symptoms were rigorously mapped to 961 symptom terms used in modern medicine (MM symptom). Furthermore, SymMap collected associated targets (gene) and diseases for these herbs, either by symptom-disease associations, or by ingredient-target relationships. In total, 4,302 targets and 5,235 diseases were included in SymMap.""" ; sc:featureList edam:operation_2421, edam:operation_2429, edam:operation_3625, edam:operation_3695 ; sc:name "SymMap" ; sc:url "http://www.symmap.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_0154, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:15215437", "pubmed:15980490" ; sc:description "SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking." ; sc:featureList edam:operation_0474, edam:operation_0478, edam:operation_0482, edam:operation_2487 ; sc:name "SymmDock" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo3d.cs.tau.ac.il/SymmDock/" ; biotools:primaryContact "SymmDock Administrator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3318, edam:topic_3384 ; sc:citation , , "pubmed:31820081" ; sc:description """Computer-assisted craniometric evaluation for diagnosis and follow-up of craniofacial asymmetries. The current assessment of patients with craniofacial asymmetries is accomplished by physical examination, anamnesis and radiological imaging. We propose a semi-automated, computer-assisted craniofacial evaluation (SymMetric v 1.0) based on orthogonal photography of the patient's head in 3 positions. The system is simple, low-cost, no-radiation or special resources needed. Although it does not substitute CT in cases of doubt between craniosynostosis and positional plagiocephaly, multiple numeric evaluations indicate regional deformities and severity of the asymmetry, which can help in the clinical decision of indicating or not the orthosis in positional deformities, determining treatment duration or evaluating surgical outcomes after correction.""" ; sc:name "SymMetric" ; sc:softwareVersion "1.0" ; sc:url "https://github.com/ealho/SymMetric_v1.0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_2229 ; sc:citation , "pmcid:PMC8497570", "pubmed:34620862" ; sc:description "Efficient and precise single-cell reference atlas mapping with Symphony." ; sc:featureList edam:operation_0224, edam:operation_2429, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Symphony" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/immunogenomics/symphony" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3063 ; sc:citation ; sc:description """An artificial intelligence-based first-line defence against COVID-19. Digital Health Assistant & Symptom Checker. Symptoma is a Digital Health Assistant & Symptom Checker. Patients and doctors enter symptoms, answer questions, and find a list of matching causes – sorted by probability. Symptoma empowers users to uncover even ultra-rare diseases.""" ; sc:featureList edam:operation_3802 ; sc:name "Symptoma" ; sc:url "https://www.symptoma.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_3293, edam:topic_3373 ; sc:citation , "pmcid:PMC7795190", "pubmed:33396183" ; sc:description "A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance." ; sc:featureList edam:operation_3432, edam:operation_3482, edam:operation_3803 ; sc:name "SYN-view" ; sc:url "https://bitbucket.org/jstahlecker/syn-view/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0611, edam:topic_3382, edam:topic_3385 ; sc:citation ; sc:description "An ImageJ/FIJI macro to identify, count, and measure synaptic puncta from fluorescent images." ; sc:featureList edam:operation_3216, edam:operation_3450, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SynapseJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/GB3Trinity/SynapseJ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation , "pubmed:23514362" ; sc:description "This package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy." ; sc:featureList edam:operation_2428, edam:operation_3630 ; sc:license "GPL-2.0" ; sc:name "synapter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/synapter.html" ; biotools:primaryContact , "Sebastian Gibb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6929295", "pubmed:31870293" ; sc:description """An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach. BACKGROUND:Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having synaptic function to every protein-coding gene in Drosophila melanogaster. This approach resulted in the publication of a catalogue of 893 genes which we postulated to be very enriched in genes with a still undocumented synaptic function. Since then, the scientific community has experimentally identified 79 new synaptic genes. Here we use these new empirical data to evaluate our original prediction. We also implement a series of changes to the training scheme of our model and using the new data we demonstrate that this improves its predictive power""" ; sc:featureList edam:operation_2495, edam:operation_3501 ; sc:name "synaptic genes" ; sc:url "http://synapticgenes.bnd.edu.uy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3954 ; sc:description "A Matlab/Octave toolbox for synthetic aperture ultrasound imaging" ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "Synaptus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/54792-mh-skjelvareid-synaptus" ; biotools:primaryContact "Martin Skjelvareid" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3053, edam:topic_3297 ; sc:citation "pubmed:27402908" ; sc:description "A Matlab-based toolbox for the automatic design of gene circuits with targeted functions from libraries of components." ; sc:featureList edam:operation_2430 ; sc:name "SYNBADm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/synbadm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3895 ; sc:citation , "pmcid:PMC8944294", "pubmed:35350192" ; sc:description "Biologist-friendly tool for batch operations on SBOL designs with Excel inputs." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SynBio2Easy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BioRDM/synbio2easy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3369, edam:topic_3895 ; sc:citation , "pmcid:PMC8063678" ; sc:description "SynBiopython is an open-source software library for Synthetic Biology. SynBiopython provides generic tools for Synthetic Biology." ; sc:featureList edam:operation_0284, edam:operation_0335, edam:operation_3435 ; sc:license "MIT" ; sc:name "SynBiopython" ; sc:url "https://github.com/Global-Biofoundries-Alliance/SynBioPython" ; biotools:primaryContact "Chueh Loo Poh" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3068, edam:topic_3301, edam:topic_3912 ; sc:citation , "pmcid:PMC9107733", "pubmed:35568950" ; sc:description "A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing." ; sc:featureList edam:operation_0224, edam:operation_3096, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "SynBioStrainFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://design.rxnfinder.org/biosynstrain/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3307, edam:topic_3895 ; sc:citation , "pmcid:PMC10111727", "pubmed:37069545" ; sc:description "A catalog of tools for synthetic biology." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "SynBioTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://synbiotools.lifesynther.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0593, edam:topic_2830, edam:topic_3306, edam:topic_3930 ; sc:citation , "pmcid:PMC8728148", "pubmed:34664670" ; sc:description "SYNBIP is a SBP database that UNIQUE in (a) comprehensively describing thousands of SBPs from the perspectives of scaffolds, biophysical & functional properties, etc.; (b) panoramically illustrating the binding targets & the broad application of each SBP; and (c) enabling the sequence-based similarity search against all SBPs and their binding targets." ; sc:featureList edam:operation_0239, edam:operation_0479, edam:operation_2421, edam:operation_3092, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:name "SYNBIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/synbip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0160, edam:topic_3053 ; sc:citation , "pmcid:PMC3961402", "pubmed:24651407" ; sc:description "A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes." ; sc:featureList edam:operation_0283 ; sc:name "SynChr" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/CHROnicle/SynChro.html" ; biotools:primaryContact "Gilles Fischer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:37898050" ; sc:description "SynCLay (Synthesis from Cellular Layouts) can construct realistic and high-quality histology images from user-defined cellular layouts along with annotated cellular boundaries." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "SynCLay" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/Srijay/SynCLay-Framework" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description "Parameterized syncmer schemes improve long-read mapping." ; sc:featureList edam:operation_3198, edam:operation_3216, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "syncmer_mapping" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Shamir-Lab/syncmer_mapping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3382, edam:topic_3393, edam:topic_3500 ; sc:citation , "pmcid:PMC9255576", "pubmed:35787575" ; sc:description "A solution to image-guided synchrotron radiotherapy for quality assurance and pre-clinical trials." ; sc:featureList edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SyncMRT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/stylekilla/syncmrt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3452 ; sc:description "SyncX CT Aligner is a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images." ; sc:featureList edam:operation_2928, edam:operation_3443 ; sc:name "SyncX CT Aligner" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://people.cs.nctu.edu.tw/~chengchc/SCTA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0219, edam:topic_3053 ; sc:citation "pubmed:18697767" ; sc:description "A growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a “namespace”) to another." ; sc:featureList edam:operation_3282 ; sc:name "Synergizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://llama.mshri.on.ca/synergizer/doc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0208, edam:topic_2640, edam:topic_3172, edam:topic_3336, edam:topic_3360 ; sc:citation , "pmcid:PMC7319572", "pubmed:32442307" ; sc:description "an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology." ; sc:featureList edam:operation_2421, edam:operation_2495, edam:operation_2943 ; sc:name "SYNERGxDB" ; sc:softwareHelp ; sc:url "http://SYNERGxDB.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0209, edam:topic_3375 ; sc:citation , "pubmed:32960970" ; sc:description """A Python library for calculating, analyzing, and visualizing drug combination synergy. A python package to calculate, analyze, and visualize drug combination synergy and antagonism.""" ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "synergy" ; sc:url "https://pypi.org/project/synergy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219, edam:topic_0621, edam:topic_0625, edam:topic_3399 ; sc:citation ; sc:description """a curated database for synergistic and antagonistic interactions of longevity-associated genes. Long- and short-lived genetic mutants. SynergyAge database hosts high-quality, manually curated information about the synergistic and antagonistic lifespan effects of genetic interventions in model organisms, also allowing users to explore the longevity relationships between genes in a visual way.""" ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3925 ; sc:name "SynergyAge" ; sc:url "http://www.synergyage.info" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , ; sc:description "Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix. R package available at https://bioconductor.org/packages/release/bioc/html/synergyfinder.html. The web server is available at http://www.synergyfinder.org or http://www.synergyfinderplus.org" ; sc:featureList edam:operation_2238 ; sc:license "Artistic-2.0" ; sc:name "SynergyFinder plus (SynergyFinder+)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://www.synergyfinder.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3374, edam:topic_3577 ; sc:citation , "pmcid:PMC7319457", "pubmed:32246720" ; sc:description """visual analytics of multi-drug combination synergies. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. SynergyFinder front-end web application source code.""" ; sc:featureList edam:operation_0337 ; sc:license "BSD-3-Clause" ; sc:name "SynergyFinder" ; sc:softwareVersion "2.0" ; sc:url "https://synergyfinder.fimm.fi/synergy/202102251238133261/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3373, edam:topic_3379 ; sc:citation ; sc:description "SynergyFinder is an interactive tool for analyzing drug combination dose response data. It enables efficient implementations for all the popular synergy scoring models, including HSA, Loewe, Bliss and ZIP to quantify the degree of drug synergy." ; sc:featureList edam:operation_0337, edam:operation_3935, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "SynergyFinder Plus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.synergyfinderplus.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622 ; sc:citation , "pmcid:PMC4700967", "pubmed:26560340" ; sc:description "Compiling Syntenic Regions across Any Set of Genomes on Demand." ; sc:featureList edam:operation_0253 ; sc:name "SynFind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://genomevolution.org/CoGe/SynFind.pl" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3577, edam:topic_3676 ; sc:citation , "pmcid:PMC9825741", "pubmed:36484701" ; sc:description "Fast and data-driven generation of synthetic heterogeneous NGS cancer data." ; sc:featureList edam:operation_3198, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "synggen" ; sc:operatingSystem "Linux" ; sc:url "https://bitbucket.org/CibioBCG/synggen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0196, edam:topic_0622 ; sc:citation , "pmcid:PMC5697234", "pubmed:29162056" ; sc:description "Synteny imaging tool for annotated genome assemblies." ; sc:featureList edam:operation_3208 ; sc:license "MIT" ; sc:name "Synima" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/rhysf/Synima" ; biotools:primaryContact "Rhys A. Farrer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0128, edam:topic_0203, edam:topic_0622, edam:topic_2640 ; sc:citation , "pubmed:33997893" ; sc:description "SynLeGG (Synthetic Lethality with Gene expression and Genomics) provides a suite of analysis and visualisation tools for polyomics data, including CRISPR screens, with integration of Gene Ontology, protein-protein interactions and evolutionary information. It is a free web-based service open to all users, and there is no login requirement." ; sc:featureList edam:operation_0313, edam:operation_3559, edam:operation_3625, edam:operation_3659 ; sc:name "SynLeGG" ; sc:url "http://www.overton-lab.uk/synlegg" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0659 ; sc:citation ; sc:description "Select hits from synthetic lethal RNAi screen data. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA, implementing quality control and various visualisation tools. Four different algorithms could be used to pick up the interesting hits." ; sc:featureList edam:operation_0337, edam:operation_2428 ; sc:license "GPL-3.0" ; sc:name "synlet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/synlet.html" ; biotools:primaryContact "Chunxuan Shao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0108, edam:topic_0123, edam:topic_3053 ; sc:citation "pubmed:26227144" ; sc:description "An integrated system to provide suitable linker candidates for novel recombinant fusion proteins." ; sc:featureList edam:operation_2479 ; sc:name "SynLinker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://synlinker.syncti.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0659, edam:topic_3512, edam:topic_3523 ; sc:citation ; sc:description "a web tool for designing RNAi-resistant sequences." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_0371 ; sc:name "Synonymous Mutation Generator" ; sc:url "http://jong2.pythonanywhere.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0621, edam:topic_0622, edam:topic_0659, edam:topic_0749 ; sc:citation "pubmed:15980499" ; sc:description "SynoR searches vertebrate genomes for synonymous regulatory elements." ; sc:featureList edam:operation_0438, edam:operation_3439 ; sc:name "SynoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://synor.dcode.org/" ; biotools:primaryContact "Ovcharenko I." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3500, edam:topic_3943 ; sc:citation , "pubmed:36269177" ; sc:description "SYNPHONI detects sets of genes that were located in close proximity to each other in a given ancestor (ancestral microsyntenic blocks) and their descendants that are still syntenic in extant genomes (syntenic blocks)." ; sc:featureList edam:operation_3216, edam:operation_3478, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SYNPHONI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/nsmro/SYNPHONI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_2830, edam:topic_3360, edam:topic_3383 ; sc:citation , "pubmed:37155406" ; sc:description "In silico modeling of the tumor microenvironment from multiplex images." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Synplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/djimenezsanchez/Synplex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3306, edam:topic_3336, edam:topic_3375, edam:topic_3474 ; sc:citation ; sc:description "SynPred (Data-Driven Molecular Design) is a tool for prediction of drug combination effects in cancer using full-agreement synergy metrics and deep learning. SynPred, which leverages state-of-the-art AI advances, specifically designed ensembles of ML and DL algorithms to link in an interdisciplinary approach omics and biophysical traits to predict anticancer drug synergy." ; sc:featureList edam:operation_3891, edam:operation_3935, edam:operation_4009 ; sc:license "GPL-3.0" ; sc:name "SynPred" ; sc:url "http://www.moreiralab.com/resources/synpred/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:36357762" ; sc:description "Explore synesthesia consistency test data, calculate consistency scores, and classify participant data as valid or invalid." ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3283, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "synr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/datalowe/synr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3053 ; sc:citation ; sc:description "> MEDIUM CONFIDENCE! | Ancestral reconstruction of sunflower karyotypes reveals dramatic chromosomal evolution | R package for the reproducible detection of synteny blocks using genetic map data | Detection of synteny blocks via comparison of genetics maps | syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers" ; sc:featureList edam:operation_0282, edam:operation_3211, edam:operation_3745 ; sc:name "syntR" ; sc:url "http://ksamuk.github.io/syntR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0593, edam:topic_3343, edam:topic_3474 ; sc:citation , "pmcid:PMC8163338", "pubmed:34123096" ; sc:description "SyntaLinker is based on a syntactic pattern recognition approach using deep conditional transformer neural networks. It can generate molecular structures based on a given pair of fragments and additional restrictions." ; sc:featureList edam:operation_3927, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "SyntaLinker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/YuYaoYang2333/SyntaLinker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3053, edam:topic_3473 ; sc:citation "pubmed:26915292" ; sc:description "An online tool to test the synergetic effect of genes on survival outcome in cancer." ; sc:featureList edam:operation_2495 ; sc:name "SynTarget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.chemoprofiling.org/cgi-bin/GEO/cancertarget/web_run_CT.EXAMPLES.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0085, edam:topic_0102, edam:topic_0194, edam:topic_0203 ; sc:citation , "pmcid:PMC9825758", "pubmed:36539202" ; sc:description "syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood." ; sc:featureList edam:operation_0323, edam:operation_0337, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Syntenet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/almeidasilvaf/syntenet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC4987893", "pubmed:27154270" ; sc:description "Portal for synteny block analysis." ; sc:featureList edam:operation_3209 ; sc:name "Synteny Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.konkuk.ac.kr/synteny_portal/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_3172, edam:topic_3407, edam:topic_3810 ; sc:citation ; sc:description "synthaser parses the results of a batch NCBI conserved domain search and determines the domain architecture of secondary metabolite synthases." ; sc:featureList edam:operation_0303, edam:operation_1812, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "synthaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gamcil.github.io/synthaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2885, edam:topic_3673, edam:topic_3676 ; sc:citation ; sc:description "Customized de novo mutation detection for any variant calling pipeline." ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3644 ; sc:license "MIT" ; sc:name "SynthDNM" ; sc:url "https://github.com/james-guevara/synthdnm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "Data visualization application extended from the previous software “LD-Plus” which also uses a flexible data display format of multiple data “tracks” that can be viewed. Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference." ; sc:featureList edam:operation_0337, edam:operation_2945 ; sc:name "Synthesis-View" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://visualization.ritchielab.psu.edu/synthesis_views/plot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382, edam:topic_3934 ; sc:citation ; sc:description "This is a synthetic image generation tool that can create realistic Pap-smear images" ; sc:featureList edam:operation_3443, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:name "Synthetic Bright-Field Microscopy Image Generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.8.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/48915-synthetic-bright-field-microscopy-image-generator" ; biotools:primaryContact "Patrik Malm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0209, edam:topic_3303, edam:topic_3343 ; sc:citation , "pubmed:34723532" ; sc:description "Open-source tool for synthons-based library design." ; sc:featureList edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "SynthI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Laboratoire-de-Chemoinformatique/SynthI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:34587005" ; sc:description "SynthMorph is a strategy for learning registration without acquired imaging data, producing powerful networks agnostic to contrast induced by MRI" ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "SynthMorph" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://martinos.org/malte/synthmorph/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3474 ; sc:citation ; sc:description "Hierarchical Machine Learning-Based Protein Quality Assessment." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_3092 ; sc:name "SynthQA" ; sc:url "https://github.com/Cao-Labs/SynthQA.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3067, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:35842095" ; sc:description "The removal of non-brain signal from magnetic resonance imaging (MRI) data, known as skull-stripping, is an integral component of many neuroimage analysis streams. Despite their abundance, popular classical skull-stripping methods are usually tailored to images with specific acquisition properties, namely near-isotropic resolution and T1-weighted (T1w) MRI contrast, which are prevalent in research settings. As a result, existing tools tend to adapt poorly to other image types, such as stacks of thick slices acquired with fast spin-echo (FSE) MRI that are common in the clinic. While learning-based approaches for brain extraction have gained traction in recent years, these methods face a similar burden, as they are only effective for image types seen during the training procedure. To achieve robust skull-stripping across a landscape of imaging protocols, we introduce SynthStrip, a rapid, learning-based brain-extraction tool" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "SynthStrip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://w3id.org/synthstrip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0208, edam:topic_2640, edam:topic_3377, edam:topic_3379 ; sc:citation , "pmcid:PMC7018095", "pubmed:32012154" ; sc:description """SynToxProfiler: an approach for top drug combination selection based on integrated profiling of synergy, toxicity and efficacy. SynToxProfiler: an interactive analysis tool for drug combination prioritization based on integrated synergy, toxicity and efficacy profiling, with interactive visualization of the results. The public version of web application (https://syntoxprofiler.fimm.fi) is hosted by Open Source Shiny Server.""" ; sc:featureList edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "SynToxProfiler" ; sc:url "https://github.com/IanevskiAleksandr/SynToxProfiler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2332 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3474 ; sc:citation ; sc:description "Synthetic transcriptional regulatory networks. A generator of synthetic gene expression data for design and analysis of structure learning algorithms." ; sc:featureList edam:operation_3566 ; sc:name "SynTReN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://bioinformatics.intec.ugent.be/kmarchal/SynTReN/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0637, edam:topic_3053 ; sc:citation , "pmcid:PMC3571937", "pubmed:23323735" ; sc:description "A web server linking synteny to prokaryotic taxonomy." ; sc:featureList edam:operation_3460 ; sc:name "SyntTax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://archaea.u-psud.fr/SyntTax/" ; biotools:primaryContact "Jacques Oberto" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3475 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3168 ; sc:citation , "pmcid:PMC3849071", "pubmed:24053737" ; sc:description "Comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects. The software is characterized by the presentation of syntenic organisations of microbial genomes and the visualization of polymorphism data along these genomes; these features are accessible to the user in an integrated way." ; sc:featureList edam:operation_3197, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "SynTView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genopole.pasteur.fr/SynTView/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2885, edam:topic_3068, edam:topic_3577 ; sc:citation , "pubmed:35612222" ; sc:description "Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service." ; sc:featureList edam:operation_0479, edam:operation_2422, edam:operation_3225, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "SynVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://goldorak.hesge.ch/synvar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0634, edam:topic_3320, edam:topic_3676 ; sc:citation ; sc:description "synVep is a machine learning-based model predicting effect/no-effect for human synonymous single nucleotide variants." ; sc:featureList edam:operation_0331, edam:operation_3225, edam:operation_3226, edam:operation_3227, edam:operation_3431 ; sc:name "synVep" ; sc:softwareHelp , ; sc:url "https://services.bromberglab.org/synvep" ; biotools:primaryContact "Yana Bromberg", "Zishuo Zeng" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0659, edam:topic_2229, edam:topic_3895 ; sc:citation , "pubmed:34515387" ; sc:description "Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "SynWiki" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://synwiki.uni-goettingen.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2885, edam:topic_3174, edam:topic_3673 ; sc:citation ; sc:description "This is a set of command line tools to compute a cover for a set of reference sequences using short bait strings." ; sc:featureList edam:operation_0363, edam:operation_3211, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "syotti" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jnalanko/syotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_0208, edam:topic_2640, edam:topic_3316 ; sc:citation ; sc:description "A model to Decode the Functional Significance of Rare Somatic Mutations in Cancer." ; sc:featureList edam:operation_0314, edam:operation_3227, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "SYS-Mut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/skhalighicase/SYS-Mut" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:author "Damjana Rozman", "Miha Moškon", "Miha Mraz", "Tanja Cvitanović" ; sc:citation ; sc:contributor "Adviti Naik", "Aleš Belič" ; sc:description "Library which implements basic systems biology objects within the modelica environment." ; sc:featureList edam:operation_3660 ; sc:isAccessibleForFree true ; sc:name "SysBio modelica library" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-SI-hackathon", "Faculty of Computer and Information Science, University of Ljubljana" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://lrss.fri.uni-lj.si/bio/sysbio" ; biotools:primaryContact "Miha Moškon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC9825739", "pubmed:36477976" ; sc:description "Simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "SysBiolPGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://spgwas.waslitbre.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2259 ; sc:citation "pubmed:25399028" ; sc:description "A computational tool for model selection and parameter inference using nested sampling." ; sc:featureList edam:operation_2238 ; sc:name "SYSBIONS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.theosysbio.bio.ic.ac.uk/resources/sysbions/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library", "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3324, edam:topic_3474 ; sc:citation ; sc:description "Sysrev is a FAIR platform for data curation and systematic evidence review." ; sc:featureList edam:operation_2422, edam:operation_3280, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Sysrev" ; sc:url "http://Sysrev.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3053, edam:topic_3676 ; sc:citation ; sc:description """Pan-cancer detection of driver genes at the single-patient resolution. sysSMV2 is a computational tool for patient-specific cancer driver gene prioritisation. It is based on the principle that driver genes are characterised by particular molecular properties (e.g. mutations, copy number variants) and systems-level properties (e.g. evolutionary origin, breadth of expression). It works by identifying genes with similar properties to canonical drivers, using a one-class Support Vector Machine framework1. Users may also train their own sysSVM2 models. Models that have been trained on data from TCGA are available to download from the appropriate directory. For smaller TCGA cohorts (N <200 samples), we recommend using the model trained on pan-cancer data. To download sysSVM2, clone this repository. sysSVM2 is implemented in R. In this guide, we assume that the user's working directory corresponds to a clone of this repository.""" ; sc:featureList edam:operation_2454, edam:operation_3435, edam:operation_3928 ; sc:name "sysSVM2" ; sc:url "https://github.com/ciccalab/sysSVM2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3391 ; sc:description "Platform for collaborative research, enabling sharing of workflows and computational tools tailored for lead compound discovery in infectious diseases through four main technical objectives: Access to large shared collections of compounds, assays and knowledge; Access to computational tools that can be tailored for lead compound discovery in infectious diseases; A systems biology approach to infectious diseases drug discovery; Sharing specialised analytical workflows." ; sc:featureList edam:operation_2945 ; sc:name "System Biology Platform" ; sc:provider "unimelb.edu.au" ; sc:softwareVersion "1" ; sc:url "http://sbp.qfab.org/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1930, edam:format_2330, edam:format_2572, edam:format_3020 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1930, edam:format_2573 ; sc:name "Sequence alignment (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC5029110", "pubmed:27650223" ; sc:description "R package for building and running automated end-to-end analysis workflows for a wide range of NGS applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across them, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters." ; sc:featureList edam:operation_0292, edam:operation_3680 ; sc:license "Artistic-2.0" ; sc:name "systemPipeR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/systemPipeR.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3315, edam:topic_3374 ; sc:description "Utility to generate ODEs from and xml file generated by sbiodesktop" ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "Systems Biology Tool Box ODE Generator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/17998-systems-biology-tool-box-ode-generator" ; biotools:primaryContact "Ilya Chorny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3400 ; sc:citation , "pmcid:PMC10015272", "pubmed:36804216" ; sc:description "The SYSVAC resources aim to support National Immunization Technical Advisory Groups (NITAGs) and the World Health Organization Strategic Advisory Group of Experts on Immunization (WHO SAGE) in the development of evidence-based vaccination recommendations by simplifying the identification of relevant systematic reviews and access guidance on how to use existing reviews." ; sc:featureList edam:operation_0560, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "CC-BY-3.0" ; sc:name "SYSVAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.nitag-resource.org/sysvac-systematic-reviews" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation "pubmed:20818383" ; sc:description "Software to identify variants from pooled sequencing data." ; sc:featureList edam:operation_3227 ; sc:name "Syzygy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://software.broadinstitute.org/software/syzygy/" ; biotools:primaryContact "Syzygy Help" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0176, edam:topic_2814 ; sc:citation "pubmed:20689979" ; sc:description "A program for analyzing molecular dynamics trajectories based on internal bond-angle-torsion coordinates. The program computes entropy and rotameric states of dihedrals, clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. It was developed with special focuses on showing changes of protein flexibility between different states, and selecting representative protein conformations for molecular docking studies." ; sc:featureList edam:operation_2406, edam:operation_2476, edam:operation_2479 ; sc:name "T-Analyst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/tanalystprogram/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3373, edam:topic_3378 ; sc:citation , "pmcid:PMC8533369", "pubmed:34679164" ; sc:description "Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "T-ARDIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bioinsilico.org/T-ARDIS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3056, edam:topic_3301 ; sc:citation "pubmed:18052913" ; sc:description "A package for performing clustering analysis using T-RFLP data. T-RFLP is a newly developed molecular fingerprinting technique mainly used to investigate population structures in microbial communities." ; sc:featureList edam:operation_3200 ; sc:name "T-BAPS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.helsinki.fi/bsg/software/T-BAPS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0097, edam:topic_3293 ; sc:citation , "pubmed:28003260" ; sc:description "Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization." ; sc:featureList edam:operation_0567, edam:operation_2421 ; sc:name "T-BAS" ; sc:url "https://vclv99-239.hpc.ncsu.edu:8080/start" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3382, edam:topic_3407, edam:topic_3474 ; sc:citation , "pubmed:31661592" ; sc:description """Classifying T cell activity in autofluorescence intensity images with convolutional neural networks. Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow. This repository contains code and data for the manuscript:. Classifying T cell activity in autofluorescence intensity images with convolutional neural networks. Zijie J Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter. bioRxiv 2019. doi:10.1101/737346.""" ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3704 ; sc:license "BSD-3-Clause-Clear" ; sc:name "T cell classification" ; sc:url "https://github.com/gitter-lab/t-cell-classification" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description """a robust tool for detecting and visualizing copy number variants in targeted sequencing data. T-CNV is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.""" ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3435 ; sc:name "T-CNV" ; sc:url "https://github.com/Top-Gene/T-CNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0199, edam:topic_0625, edam:topic_3047 ; sc:citation , "pmcid:PMC8385993", "pubmed:34396391" ; sc:description "A comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "T-CoV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://t-cov.hse.ru" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0798 ; sc:citation "pubmed:21177644" ; sc:description "Here, we present a computational pipeline (T-lex) that uses NGS data to detect the presence/absence of annotated Transposable Element (TE) copies. T-lex can use data from a large number of strains and returns estimates of population frequencies of individual TE insertions in a reasonable time." ; sc:featureList edam:operation_0427 ; sc:name "T-lex" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://petrov.stanford.edu/cgi-bin/Tlex_manual.html" ; biotools:primaryContact "Anna-Sophie Fiston-Lavier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0749 ; sc:citation , "pmcid:PMC4344482", "pubmed:25510498" ; sc:description "Software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data." ; sc:featureList edam:operation_3196 ; sc:name "T-lex2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://petrov.stanford.edu/cgi-bin/Tlex.html" ; biotools:primaryContact "Anna-Sophie Fiston-Lavier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621 ; sc:citation "pubmed:15980543" ; sc:description "Tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "T-profiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.t-profiler.org/" ; biotools:primaryContact "Harmen J. Bussemaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:15980506" ; sc:description "Tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar)." ; sc:featureList edam:operation_0239, edam:operation_0415, edam:operation_0438, edam:operation_0445 ; sc:name "T-Reg Comparator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://treg.molgen.mpg.de/" ; biotools:primaryContact "roepcke@molgen.mpg.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0602, edam:topic_0621, edam:topic_3293 ; sc:citation "pubmed:22675075" ; sc:description "Tree and Reticulogram REconstruction (T-REX) is a web server for the reconstruction of phylogenetic trees, reticulation networks and the inference of horizontal gene transfer events." ; sc:featureList edam:operation_0323, edam:operation_0540, edam:operation_0546, edam:operation_0555, edam:operation_3478 ; sc:name "T-REX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.trex.uqam.ca" ; biotools:primaryContact "Vladimir Makarenkov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0122, edam:topic_0736 ; sc:citation "pubmed:23716642" ; sc:description "A web server that allows a fine-grained structural classification of proteins using the T-RMSD method (Tree based on Root Mean Square Deviation). Providing a set of proteins sequences, it produces a structural tree with support values for each cluster node, reminiscent to bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology." ; sc:featureList edam:operation_2996 ; sc:name "T-RMSD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.crg.cat/apps/tcoffee/do:trmsd" ; biotools:primaryContact "Cedric Notredame" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0199, edam:topic_0203, edam:topic_0625, edam:topic_3295, edam:topic_3325 ; sc:citation , "pmcid:PMC6648337", "pubmed:31329928" ; sc:description """Data-driven characterization of molecular phenotypes across heterogeneous sample collections. Scripts for t-SNE map generation, evaluation and sample remapping. Detailed User Guide: link. See use case examples for more information on usage in example dataset. Quality control using infoMeasures.R. Evaluation of method and parameter choices. At this step it is wise to verify that the separation of the samples (e.g. clusters in a t-SNE map) reflects biology and not the data provider. We recommend to use established molecular subtypes for the disease in question.""" ; sc:featureList edam:operation_2429, edam:operation_2436, edam:operation_3196, edam:operation_3891, edam:operation_3935 ; sc:name "t-SNE" ; sc:url "https://github.com/systemsgenomics/t-sne.cancermaps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_3172, edam:topic_3569, edam:topic_3570 ; sc:description "Does a t-test and creates box plots for genes/compounds in healthy vs. disease individuals" ; sc:featureList edam:operation_2943 ; sc:isAccessibleForFree true ; sc:name "t-test and box plots for genes compounds etc in healthy vs. disease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47373-t-test-and-box-plots-for-genes-compounds-etc-in-healthy-vs-disease" ; biotools:primaryContact "Dr. Soumya Banerjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3173 ; sc:citation ; sc:description "Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3695 ; sc:name "T-WEoN" ; sc:url "https://weon.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_3053, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:20937630" ; sc:description "Database for type 1 diabetes (T1D). It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "T1DBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.t1dbase.org" ; biotools:primaryContact "Contact Form", "Oliver S. Burren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3179 ; sc:description "Tiling Microarray Analysis Tools 2 analyzes low and high level tiling microarray data using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments for low and high level genomic tiling microarray analysis." ; sc:featureList edam:operation_2409, edam:operation_2495 ; sc:name "T2" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://timat2.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_2269, edam:topic_3517 ; sc:citation , "pmcid:PMC8796375", "pubmed:34755844" ; sc:description "A powerful test for differentially expressed gene pathways via graph-informed structural equation modeling." ; sc:featureList edam:operation_3223, edam:operation_3435, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "T2-DAG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Jin93/T2DAG" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Converts ABI SCIEX 4700/4800 t2d files to mzXML." ; sc:featureList edam:operation_0335 ; sc:name "T2D converter" ; sc:url "http://www.pepchem.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194 ; sc:description "\"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format.\" - Galaxy tool wrapper" ; sc:featureList edam:operation_0567 ; sc:name "Draw phylogeny" ; sc:url "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637 ; sc:description "\"Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks.\" - Galaxy tool wrapper" ; sc:featureList edam:operation_3793 ; sc:name "Summarize taxonomy" ; sc:url "https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3301 ; sc:citation "pubmed:25867189" ; sc:description "Web application for the identification of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) in bacterial genomes." ; sc:featureList edam:operation_3439 ; sc:name "T346Hunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bacterial-virulence-factors.cbgp.upm.es/T346Hunter" ; biotools:primaryContact "Cayo Ramos Rodríguez", "Pablo Rodríguez-Palenzuela", "Pedro M. Martínez García" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3301 ; sc:citation , "pmcid:PMC3589343", "pubmed:23472154" ; sc:description "T3S effector prediction tool based on Markov Model" ; sc:featureList edam:operation_2495 ; sc:name "T3_MM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://biocomputer.bio.cuhk.edu.hk/T3DB/T3_MM.php" ; biotools:primaryContact "Yejun Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_2840, edam:topic_3172 ; sc:citation "pubmed:19897546" ; sc:description "Unique bioinformatics resource that compiles comprehensive information about common or ubiquitous toxins and their toxin-targets. Each record (ToxCard) contains over 80 data fields providing detailed information on chemical properties and descriptors, toxicity values, protein and gene sequences (for both targets and toxins), molecular and cellular interaction data, toxicological data, mechanistic information and references." ; sc:featureList edam:operation_0224, edam:operation_0250, edam:operation_2421, edam:operation_2489 ; sc:name "T3DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.t3db.org" ; biotools:primaryContact "Contact Form", "Wishart Lab's twitter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3474, edam:topic_3510 ; sc:citation ; sc:description """interpretable sequence-based prediction of type IV secreted effectors using eXtreme gradient boosting algorithm. Type IV secreted effectors (T4SEs) can be translocated into the cytosol of host cells via type IV secretion system (T4SS) and cause diseases.""" ; sc:featureList edam:operation_0267, edam:operation_1777, edam:operation_3937 ; sc:name "T4SE-XGB" ; sc:url "https://github.com/CT001002/T4SE-XGB" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0621, edam:topic_0623, edam:topic_3474 ; sc:citation , "pubmed:34657153" ; sc:description "A bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model." ; sc:featureList edam:operation_0474, edam:operation_3092, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "T4SEfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tool2-mml.sjtu.edu.cn/T4SEfinder_TAPE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3375, edam:topic_3524 ; sc:citation "pubmed:16986252" ; sc:description "A simulator for the intracellular infection kinetics of phage T7." ; sc:featureList edam:operation_3660 ; sc:name "T7" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.genome.duke.edu/labs/YouLab/software/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2640, edam:topic_3336 ; sc:citation , "pmcid:PMC6664725", "pubmed:31357929" ; sc:description "Improving prediction of phenotypic drug response on cancer cell lines using deep convolutional network | twin CNN channels on drugs and cancer cell lines" ; sc:featureList edam:operation_3659 ; sc:name "tCNNS" ; sc:url "https://github.com/Lowpassfilter/tCNNS-Project" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0749 ; sc:citation , "pmcid:PMC6500446", "pubmed:31061989" ; sc:description "Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm." ; sc:featureList edam:operation_0441, edam:operation_2492, edam:operation_3439 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "tREMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hansaimlim/REMAP/tree/master/TriFacREMAP" ; biotools:primaryContact "Lei Xie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC6859256", "pubmed:31735953" ; sc:description """Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cell line of NCI-60. The system allows to perform correlation analyses of tRNA-derived ncRNAs expression with all omics data and compound activities available on CellMiner. This provides an important opportunity to investigate their potential biological roles in absence of direct experimental evidences""" ; sc:featureList edam:operation_3463, edam:operation_3792, edam:operation_3800 ; sc:name "tRFexplorer" ; sc:url "https://trfexplorer.cloud/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3474 ; sc:citation , "pubmed:30685762" ; sc:description "Computational approach based on deep neural networks, to predict tRNA gene sequences." ; sc:featureList edam:operation_0267, edam:operation_0464 ; sc:isAccessibleForFree true ; sc:name "tRNA-DL" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://stella-gao.github.io/trna-dl/" ; biotools:primaryContact "Stella Gao" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3382, edam:topic_3512 ; sc:citation , "pmcid:PMC6602477", "pubmed:31127306" ; sc:description "Web application for exploring and visualizing tRNA sequence features." ; sc:featureList edam:operation_0464, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tRNAviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://trna.ucsc.edu/tRNAviz/summary/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452, edam:topic_3474 ; sc:citation , "pubmed:33780873" ; sc:description "TA-Net is a tool for better feature selection, better tumor segmentation." ; sc:featureList edam:operation_0337, edam:operation_3927, edam:operation_3936 ; sc:name "TA-Net" ; sc:url "https://github.com/shuchao1212/TA-Net" ; biotools:primaryContact "Shuchao Pang", "Zhenmei Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "ta-siRNA (trans-acting short interfering RNA): prediction of phased ta-siRNAs in plant sRNA datasets." ; sc:featureList edam:operation_2478 ; sc:name "Ta-si prediction" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://srna-workbench.cmp.uea.ac.uk" ; biotools:primaryContact "Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0820, edam:topic_3379, edam:topic_3407, edam:topic_3419 ; sc:citation , "pubmed:36099402" ; sc:description "Targeting Trace Amine-Associated Receptor 1 (TAAR1) in Schizophrenia." ; sc:featureList edam:operation_0269, edam:operation_3096, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "TAAR1" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.cmesurvey.site/TAAR1" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7359037", "pubmed:32661247" ; sc:description "high-resolution weather radar reflectivity dataset for precipitation nowcasting." ; sc:featureList edam:operation_0337, edam:operation_3891, edam:operation_3935 ; sc:name "TAASRAD19" ; sc:url "https://github.com/MPBA/TAASRAD19" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0219, edam:topic_3518 ; sc:citation "pubmed:17087822" ; sc:description "A software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database. It uses a flexible spreadsheet format for MIAME annotation of microarray experiments. The spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange." ; sc:featureList edam:operation_2495 ; sc:name "Tab2MAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tab2mage.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3295, edam:topic_3360 ; sc:citation , "pmcid:PMC8011137", "pubmed:33789571" ; sc:description "Taba is a R package that calculates the robust Taba linear, Taba rank (monotonic), TabWil, and TabWil rank correlations. Test statistics as well as one sided or two sided p-values are provided for all correlations. Multiple correlations and p-values can be calculated simultaneously across multiple variables. In addition, users will have the option to use the partial, semipartial, and generalized partial correlations; where the partial and semipartial correlations use linear, logistic, or Poisson regression to modify the specified variable." ; sc:featureList edam:operation_3435, edam:operation_3463, edam:operation_3960 ; sc:license "GPL-3.0" ; sc:name "Taba" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/Taba/index.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123 ; sc:citation ; sc:description "Web server for antibody humanisation specifically designed to help researcher in each step of a humanisation experiment. It provides tools to: Select the suitable humane template; Select the grafting region; Predict the non-human and humanised antibody paratope; Select the minimum set of back-mutations to retain the parental binding affinity; Build the three-dimensional humanised antibody model and check its structure." ; sc:featureList edam:operation_0477 ; sc:name "Tabhu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-SAPIENZA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.biocomputing.it/tabhu" ; biotools:primaryContact "Pier Paolo Olimpieri" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1047 ; sc:encodingFormat edam:format_3327, edam:format_3475, edam:format_3615, edam:format_3616 ; sc:name "URI" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:description """Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file (in.tab.bgz.tbi or in.tab.bgz.csi) when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". (Coordinates specified in this region format are 1-based and inclusive.) Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. The tabix (.tbi) and BAI index formats can handle individual chromosomes up to 512 Mbp (2^29 bases) in length. If your input file might contain data lines with begin or end positions greater than that, you will need to use a CSI index.""" ; sc:featureList edam:operation_2409, edam:operation_2422, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "tabix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.htslib.org/doc/tabix.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "Take the output from MLINK or LINKMAP and tabulate it in a more easily digestible form. It can also produce files suitable for graphing lod scores and for input to HOMOG, BTEST and FASTMAP." ; sc:featureList edam:operation_0283, edam:operation_0335 ; sc:name "TABLE" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.9" ; sc:url "http://www.davecurtis.net/dcurtis/software.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2332 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2066 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3336, edam:topic_3379 ; sc:author "Nikola Milosevic" ; sc:citation ; sc:description "Tool for annotating tables written in Java. It uses specific annotation schema we proposed that is able to capture information about functions of a cell and inter-cell relationships. It is a tool for extracting annotations from tables in PMC and DailyMed in XML format." ; sc:featureList edam:operation_0226, edam:operation_0306, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TableAnnotator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "manchester.ac.uk" ; sc:softwareHelp , ; sc:softwareVersion "0.3" ; sc:url "https://github.com/nikolamilosevic86/TableAnnotator" ; biotools:primaryContact "Nikola Milosevic" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Tableau is a visual analytics platform transforming the way we use data to solve problems—empowering people and organizations to make the most of their data. As the market-leading choice for modern business intelligence, our analytics platform makes it easier for people to explore and manage data, and faster to discover and share insights that can change businesses and the world. Everything we do is driven by our mission to help people see and understand data, which is why our products are designed to put the user first—whether they’re an analyst, data scientist, student, teacher, executive, or business user. From connection through collaboration, Tableau is the most powerful, secure, and flexible end-to-end analytics platform.""" ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:license "Proprietary" ; sc:name "Tableau" ; sc:softwareHelp ; sc:softwareVersion "2022.4" ; sc:url "https://www.tableau.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3379 ; sc:citation , "pubmed:32665250" ; sc:description "An R package that provides an easy way of exporting the descriptive table 1 that is commonly used in articles to a Word document for easy editing and copying to the article." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3435 ; sc:name "TableOne" ; sc:url "https://esm.uoi.gr/shiny/tableone/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196 ; sc:description "Extract sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parse out contigs, singletons, and assembled reads into separate files." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_2928 ; sc:name "TableParser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.personal.psu.edu/jhm10/Vera/SoftwareC.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0797 ; sc:citation "pubmed:19965881" ; sc:description "Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments." ; sc:featureList edam:operation_3184 ; sc:license "BSD-3-Clause" ; sc:name "Tablet" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://ics.hutton.ac.uk/tablet/" ; biotools:primaryContact "June Johnston" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_2815, edam:topic_3520 ; sc:citation , "pmcid:PMC5753264", "pubmed:29040688" ; sc:description """an annotated database of protein associations. Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE.These associations represent a broad scala of biological associations between pairs of proteins that goes well beyond mere binary protein interactions. More info. Select species: Homo sapiens (Human) Mus musculus (Mouse).""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3767 ; sc:name "Tabloid Proteome" ; sc:url "http://iomics.ugent.be/tabloidproteome" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:14871640" ; sc:description "A sofrware for DNA sequencing by hybridization with isothermic libraries." ; sc:featureList edam:operation_2478 ; sc:name "Tabusearch" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bio.cs.put.poznan.pl/programs/5191f1e39dfb89a857000001" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2326 ; sc:name "DrugBank ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1904 ; sc:name "Locus ID (EntrezGene)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2899 ; sc:name "Drug name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0602, edam:topic_0634, edam:topic_3308 ; sc:citation , "pmcid:PMC9558163", "pubmed:36254161" ; sc:description "A single-cell molecular map for translational therapeutics accelerator in Alzheimer's disease." ; sc:featureList edam:operation_2436, edam:operation_2492, edam:operation_3223, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "TACA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://taca.lerner.ccf.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0659, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9294414", "pubmed:35753698" ; sc:description "A novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization." ; sc:featureList edam:operation_2489, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "TACOS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://balalab-skku.org/TACOS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description """Time Course Analysis of Control strength toward nodes/gene expression on directed graph based on Information Criterion.""" ; sc:featureList edam:operation_1781 ; sc:license "MIT" ; sc:name "tacs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1" ; sc:url "https://github.com/takenakayoichi/tacs" ; biotools:primaryContact "Yoichi Takenaka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0203, edam:topic_2815, edam:topic_2885, edam:topic_3512 ; sc:citation "pubmed:15103394", "pubmed:16185827", "pubmed:16845023" ; sc:description "Automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. It was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project." ; sc:featureList edam:operation_0303, edam:operation_0331, edam:operation_0346, edam:operation_2404, edam:operation_2454 ; sc:name "TACT" ; sc:url "http://jbirc.jbic.or.jp/tact/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3382, edam:topic_3383 ; sc:citation "pubmed:23341500" ; sc:description "A versatile MATLAB toolbox for High Content Analysis (HCA) of microscopy data. TATICS has been developed for image cytometry of non-adherent cells such as hematopoietic cells." ; sc:featureList edam:operation_3443 ; sc:name "TACTICS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tactics-toolbox.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_2275, edam:topic_3336, edam:topic_3534 ; sc:citation ; sc:description """Finding Druggable Sites in Proteins using TACTICS. This code finds the locations of possible cryptic pockets within MD trajectories.""" ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_2575, edam:operation_4009 ; sc:license "GPL-3.0" ; sc:name "TACTICS" ; sc:url "https://github.com/Albert-Lau-Lab/tactics_protein_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3382, edam:topic_3421 ; sc:citation , "pubmed:32401082" ; sc:description """an open-source platform for planning, simulating and validating stereotactic surgery. Tactics is a prototype application for assigning target coordinates to locations within the brain, so that neurosurgeons can easily and precisely target those locations with electrodes that stimulate the brain in order to provide therapy for certain brain disorders.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "Tactics" ; sc:url "https://github.com/atamai/tactics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3383 ; sc:description "TACTICS is an interactive platform for customized high content bioimaging analysis." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "TACTICS Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/39920-tactics-toolbox" ; biotools:primaryContact "Raz Shimoni" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3518 ; sc:citation ; sc:description "Tissue Array Database consists of an Active Server Page web interface to a relational SQL database that automates recording scores and linking them with clinical data for future interpretation." ; sc:featureList edam:operation_2495 ; sc:name "TAD" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/TAD:Overview" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1240 ; sc:encodingFormat edam:format_1957 ; sc:name "PCR primers" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1930 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3707 ; sc:name "Biodiversity data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3917 ; sc:encodingFormat edam:format_3475 ; sc:name "Count matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3697 ; sc:author "Gerrit Botha", "Jessica Holmes", "Katie Lennard", "Lindsay Clark" ; sc:contributor "Gerrit Botha", "Jessica Holmes", "Katie Lennard", "Lindsay Clark" ; sc:description "Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region. Microbiome, amplicon analysis, 16S, 18S, ITS, COI, PacBio, Shoreline, Loop" ; sc:featureList edam:operation_3192, edam:operation_3237, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TADA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/h3abionet/TADA" ; biotools:primaryContact "Christopher Fields" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3474, edam:topic_3512, edam:topic_3673, edam:topic_3958 ; sc:citation , "pmcid:PMC8886976", "pubmed:35232478" ; sc:description "Machine learning tool for functional annotation-based prioritisation of pathogenic CNVs." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TADA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jakob-he/TADA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0154, edam:topic_3293 ; sc:citation "pubmed:20929871" ; sc:description "TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity search, sequence alignment, genome context browser and phylogenetic tools are readily accessible via TADB." ; sc:featureList edam:operation_0346, edam:operation_2421, edam:operation_3208 ; sc:name "TADB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo-mml.sjtu.edu.cn/TADB/" ; biotools:primaryContact "Hong-Yu OU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pubmed:32252545" ; sc:description """a sensitive and fast method for detection of typologically associated domain boundaries. A topologically associated domain (TAD) is a self-interacting genomic block. Detection of TAD boundaries on Hi-C contact matrix is one of the most important issues in the analysis of 3D genome architecture at TAD level. Here, we present TAD boundary detection (TADBD), a sensitive and fast computational method for detection of TAD boundaries on Hi-C contact matrix. This method implements a Haar-based algorithm by considering Haar diagonal template, acceleration via a compact integrogram, multi-scale aggregation at template size and statistical filtering. In most cases, comparison results from simulated and experimental data show that TADBD outperforms the other five methods. In addition, a new R package for TADBD is freely available online""" ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3799 ; sc:name "TADBD" ; sc:url "http://github.com/bioinfo-lab/TADBD" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_1930 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3033, edam:format_3617 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_3176 ; sc:citation ; sc:description "Computational framework to analyze and model 3C-based experiments." ; sc:featureList edam:operation_0279, edam:operation_2403, edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TADbit" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://3dgenomes.github.io/TADbit/" ; biotools:primaryContact "Marc A. Marti-Renom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0654, edam:topic_3170, edam:topic_3295, edam:topic_3940 ; sc:citation , "pmcid:PMC7076128", "pubmed:32211023" ; sc:description """An R Package for Differential and Temporal Analysis of Topologically Associated Domains. TADCompare is an R package for differential Topologically Associated Domain (TAD) detection between two Hi-C contact matrices and across a time course, and TAD boundary calling across multiple Hi-C replicates. It has three main functions, TADCompare for differential TAD analysis, TimeCompare for time course analysis, and ConsensusTADs for consensus boundary identification. The DiffPlot function allows for visualizing the differences between two contact matrices.""" ; sc:featureList edam:operation_2436, edam:operation_3359, edam:operation_3799 ; sc:name "TADCompare" ; sc:url "https://github.com/dozmorovlab/TADCompare" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3169, edam:topic_3175, edam:topic_3676 ; sc:citation , "pmcid:PMC9252839", "pubmed:35524567" ; sc:description "A web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TADeus2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tadeus2.mimuw.edu.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3382, edam:topic_3940 ; sc:citation , "pmcid:PMC9636664", "pubmed:36333787" ; sc:description "A comprehensive web-based tool for the analysis of topologically associated domains." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TADMaster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://tadmaster.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0654, edam:topic_3169, edam:topic_3940 ; sc:citation , "pmcid:PMC7144900", "pubmed:32083658" ; sc:description """Hierarchical chromatin organization detected by TADpole. TADpole is a computational tool designed to identify and analyze the entire hierarchy of topologically associated domains (TADs) in intra-chromosomal interaction matrices.""" ; sc:featureList edam:operation_2429, edam:operation_3216, edam:operation_3435, edam:operation_3891 ; sc:license "LGPL-3.0" ; sc:name "TADpole" ; sc:url "https://github.com/3DGenomes/TADpole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC8892791", "pubmed:35236295" ; sc:description "A versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction." ; sc:featureList edam:operation_3435, edam:operation_3501, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TADreg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/raphaelmourad/TADreg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2269, edam:topic_3569 ; sc:citation "pubmed:26315910" ; sc:description "An algorithm the identification of hierarchical topological domains in Hi-C data." ; sc:featureList edam:operation_2495 ; sc:name "TADtree" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.brown.edu/projects/tadtree/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0637, edam:topic_0654, edam:topic_3299 ; sc:citation "pubmed:25027647" ; sc:description "A new homology-based approach for taxonomic analysis, utilizes the similarity in the genomic sequence in addition to the result of an alignment tool." ; sc:featureList edam:operation_3460 ; sc:name "TAEC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://cals.arizona.edu/~anling/software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3174, edam:topic_3308 ; sc:citation "pubmed:26319390" ; sc:description "A tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference." ; sc:featureList edam:operation_3258 ; sc:name "TAG" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://omics.informatics.indiana.edu/TAG/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:description "Provides a user-friendly, lightweight and open-source graphical user interface for running the de novo sequencing algorithm PepNovo+ and also holds the possibiliy to search derived short amino acid sequences (so-called tags) against a protein database in order to retrieve peptide and protein identifications." ; sc:featureList edam:operation_2479 ; sc:name "Tag-DB" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.4.0" ; sc:url "https://code.google.com/p/tag-db/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0654, edam:topic_0798, edam:topic_3168, edam:topic_3912 ; sc:citation , "pmcid:PMC8253812", "pubmed:34215845" ; sc:description "A convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases." ; sc:featureList edam:operation_0308, edam:operation_0495, edam:operation_3096, edam:operation_3200, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tag-seq" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/zhoujj2013/Tag-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0659, edam:topic_3512 ; sc:citation , "pmcid:PMC10578202", "pubmed:37850035" ; sc:description "TAGADA is an RNA-seq data analysis pipeline for Transcript And Gene Assembly, Deconvolution, and Analysis." ; sc:featureList edam:operation_0264, edam:operation_0314, edam:operation_0362, edam:operation_3629, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TAGADA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/FAANG/analysis-TAGADA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3308 ; sc:citation "pubmed:20573248" ; sc:description "TagCleaner can be used to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based versions." ; sc:featureList edam:operation_3192 ; sc:license "GPL-3.0" ; sc:name "TagCleaner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tagcleaner.sourceforge.net/index.html" ; biotools:primaryContact "Schmieder R." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_2640 ; sc:citation "pubmed:22815924" ; sc:description "The tool is designed to identify significant consensus events from copy number alterations in cancer genome." ; sc:featureList edam:operation_3233 ; sc:name "TAGCNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/tagcna/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:19737799" ; sc:description "TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate (FDR), TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation." ; sc:featureList edam:operation_3218 ; sc:license "GPL-3.0" ; sc:name "TagDust" ; sc:operatingSystem "Linux" ; sc:url "http://genome.gsc.riken.jp/osc/english/software/" ; biotools:primaryContact "TagDust Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3168 ; sc:citation , "pmcid:PMC4384298", "pubmed:25627334" ; sc:description "A generic method to extract reads from sequencing data." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "TagDust2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tagdust.sourceforge.net/" ; biotools:primaryContact "Timo Lassmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:23469199" ; sc:description "A fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy." ; sc:featureList edam:operation_3200 ; sc:name "TagGD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/pelinakan/UBD.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121 ; sc:description "Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw." ; sc:featureList edam:operation_2479 ; sc:name "TagIdent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/tagident/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0654, edam:topic_2885 ; sc:citation "pubmed:21104886" ; sc:description "A command-line program for the imputation of untyped SNPs. It is based on a few flanking SNPs that can optimally predict the SNP under imputation." ; sc:featureList edam:operation_0367 ; sc:name "tagIMPUTE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://dlin.web.unc.edu/software/tagimpute-2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0637, edam:topic_2814, edam:topic_3366 ; sc:citation , "pmcid:PMC8541804", "pubmed:34688246" ; sc:description "Data(base) integration using the data warehousing approach." ; sc:featureList edam:operation_0478, edam:operation_2406, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TAGOPSIN" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ebundhoo/TAGOPSIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053 ; sc:description "Time-series Analysis for Gene Set analyses gene set enrichment for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations." ; sc:featureList edam:operation_3501 ; sc:name "TAGS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.au.tsinghua.edu.cn/software/TAGS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation ; sc:description """a flexible and comprehensive analysis pipeline for NAD tagSeq data. 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Therefore, TagSeqTools provides a convenient and comprehensive workflow for researchers to study data produced by NAD tagSeq or similar method using Nanopore sequencing.""" ; sc:featureList edam:operation_0337, edam:operation_3431, edam:operation_3799 ; sc:license "Apache-2.0" ; sc:name "TagSeqTools" ; sc:url "https://github.com/dorothyzh/TagSeqTools" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2330, edam:format_3508 ; sc:name "Text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2332, edam:format_3464 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3671 ; sc:encodingFormat edam:format_2330, edam:format_3508 ; sc:name "Text" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_2332, edam:format_3464 ; sc:name "Text data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3464, edam:format_3475 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3464, edam:format_3475 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0218 ; sc:author "Jorge Campos", "Juan Miguel Cejuela" ; sc:citation ; sc:description "Automatic, manual, and search annotation tool." ; sc:featureList edam:operation_0306 ; sc:isAccessibleForFree true ; sc:name "tagtog" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "tagtog.net" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://www.tagtog.net" ; biotools:primaryContact "tagtog" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_2640, edam:topic_3068, edam:topic_3336 ; sc:citation , "pmcid:PMC9465370", "pubmed:36105222" ; sc:description "A small-molecule target identification and annotation web server." ; sc:featureList edam:operation_0276, edam:operation_3899, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "TAIGET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.taiget.cn/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9014879", "pubmed:35181644" ; sc:description "A Pipeline for Sequencing-Based Analysis of Non-Polyadenylated RNA 3’ End Processing." ; sc:featureList edam:operation_0363, edam:operation_0496, edam:operation_3192, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tailer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TimNicholsonShaw/tailer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "tailfindr is a R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tailfindr" ; sc:url "https://github.com/adnaniazi/tailfindr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_0625, edam:topic_3934 ; sc:citation , "pubmed:33476090" ; sc:description """Targeting heavy tails in flow cytometry data with fast, interpretable mixture modeling. An R package for clustering via Gaussian Mixture Modeling, optimized for heavy-tailed distributions in flow cytometry data. It's easiest to install Tailor with the help of the devtools package.""" ; sc:featureList edam:operation_3432, edam:operation_3435 ; sc:name "Tailor" ; sc:url "http://www.github.com/matei-ionita/Tailor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0082, edam:topic_3047, edam:topic_3520 ; sc:citation , "pmcid:PMC8047770", "pubmed:33797237" ; sc:description "TAILOR-MS is a Python tool that helps users to identify fatty acyl moieties of triacylglycerol species with input LC/MS data." ; sc:featureList edam:operation_0337, edam:operation_3215, edam:operation_3633 ; sc:name "TAILOR-MS" ; sc:softwareHelp ; sc:url "https://github.com/kangyup/TAILOR-MS" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3386, edam:topic_3500 ; sc:citation ; sc:description """TailTimer: Automating the tail immersion assay. An open-source device for automating the rodent tail immersion assay. The tail immersion assay is a widely used method for measuring acute thermal pain in rodents. TailTimer uses the Raspberry Pi computer to automatically record both tail withdrawal latency and water temperature. The device has a radio frequency identification (RFID) system that can record the ID of animals. The software recognizes several specific RFID keys as user interface commands, which allows TailTimer to be operated via RFID fobs. We also programmed the device to only allow tests to be conducted when the water is within ± 0.25 °C of the target temperature.""" ; sc:featureList edam:operation_0387, edam:operation_3659, edam:operation_3799 ; sc:name "TailTimer" ; sc:url "https://github.com/chen42/openbehavior/tree/master/tailTimer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:19535537" ; sc:description "Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources." ; sc:featureList edam:operation_0310 ; sc:name "Taipan" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/taipan/" ; biotools:primaryContact "Schmidt B" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0621, edam:topic_0780, edam:topic_3512 ; sc:citation "pubmed:22140109" ; sc:description "The Arabidopsis Information Resource (TAIR): genome database for Arabidopsis thaliana. 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TALC: Transcription-Aware Long Read Correction.""" ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3472 ; sc:name "TALC" ; sc:url "https://gitlab.igh.cnrs.fr/lbroseus/TALC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0089, edam:topic_0621, edam:topic_3168, edam:topic_3474 ; sc:citation ; sc:description """Transformer-based protein function Annotation with joint sequence–Label Embedding. For TALE+ (TALE+Diamond), please download Diamond and put the executable file into TALE/diamond/. Input feature: sequence data (using transformer). Output label: hierarchical nodes on directed graphs.""" ; sc:featureList edam:operation_0303, edam:operation_3672, edam:operation_3695 ; sc:license "MIT" ; sc:name "TALE" ; sc:url "https://github.com/Shen-Lab/TALE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0203, edam:topic_0749, edam:topic_3125 ; sc:citation "pubmed:22693217" ; sc:description "Transcription activator-like (TAL) Effector-Nucleotide Targeter 2.0 (TALE-NT) is a suite of web-based tools that allows for custom design of TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites." ; sc:featureList edam:operation_0445, edam:operation_2489, edam:operation_2575 ; sc:name "TALE-NT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://boglab.plp.iastate.edu/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """Talend Open Studio for Data Integration is free-to-download software to kickstart your first data integration and ETL projects. Features: Free open source Apache license RDBMS connectors: Oracle, Teradata, Microsoft SQL server SaaS connectors: Marketo, Salesforce, NetSuite Packaged apps: SAP, Microsoft Dynamics, Sugar CRM""" ; sc:featureList edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "Talend Open Studio" ; sc:softwareHelp ; sc:url "https://www.talend.com/products/talend-open-studio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0749, edam:topic_3308 ; sc:citation , "pubmed:23995255" ; sc:description "Genome-wide TALEN off-target prediction." ; sc:featureList edam:operation_0438 ; sc:license "GPL-3.0" ; sc:name "TALENoffer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.jstacs.de/index.php/TALENoffer" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description """talklr uncovers ligand-receptor mediated intercellular crosstalk. talklr (intercellular crossTALK using Ligand-Receptor)uses Kullback-Leibler divergence, a concept from inforamtion theory, to uncover interesting ligand-receptor interactions among multiple cell types in single cell RNA-seq data.""" ; sc:featureList edam:operation_3435, edam:operation_3501, edam:operation_3680 ; sc:name "talklr" ; sc:url "https://yuliangwang.shinyapps.io/talklr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3071 ; sc:citation , "pubmed:35703577" ; sc:description "A global tree allometry and crown architecture database." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Tallo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/selva-lab-repo/TALLO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation ; sc:description "Tally is a program for deduplicating sequence fragments for both single and paired end input. Single reads, paired-end reads." ; sc:featureList edam:operation_0290, edam:operation_3187, edam:operation_3219 ; sc:license "GPL-3.0" ; sc:name "Tally" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://bioinfo.montp.cnrs.fr/?r=Tally" ; biotools:primaryContact "Andrey V. KAJAVA", "Christian LE PEUCH", "Julien JORDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation "pubmed:18976482" ; sc:description "A collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets." ; sc:featureList edam:operation_3211, edam:operation_3472 ; sc:name "Tallymer" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.zbh.uni-hamburg.de/tallymer/" ; biotools:primaryContact "Doreen Ware" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0637, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC7218625", "pubmed:32397982" ; sc:description """improved metagenomic sequence classification through meta-analysis. Taxonomy Analysis pipeline for metagenome using Meta-Analysis. When you run TAMA based on the species rank analysis using the included example dataset.""" ; sc:featureList edam:operation_3192, edam:operation_3211, edam:operation_3219, edam:operation_3460 ; sc:name "TAMA" ; sc:url "https://github.com/jkimlab/TAMA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "No-code platform for structural biology tools" ; sc:featureList edam:operation_0474, edam:operation_0478, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:name "Tamarind" ; sc:url "https://www.tamarind.bio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC8088724", "pubmed:33932979" ; sc:description "Tamock simulates habitat-specific benchmark data for metagenomic samples. Tamock facilitates the simulation of metagenomic reads according to a microbial community, derived from real metagenomic data. Thus, Tamock simulations enable an assessment of computational methods, workflows and parameters specific for a microbial habitat. Tamock automatically determines taxonomic profiles from shotgun metagenomic data, selects reference genomes accordingly and uses them to simulate metagenomic reads." ; sc:featureList edam:operation_0310, edam:operation_3460, edam:operation_3731 ; sc:license "GPL-3.0" ; sc:name "Tamock" ; sc:url "https://github.com/gerners/tamock" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3172, edam:topic_3174, edam:topic_3673 ; sc:citation , "pmcid:PMC9972184", "pubmed:36852763" ; sc:description "TAMPA (Taxonomic metagenome profiling evaluation) , is a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community." ; sc:featureList edam:operation_0337, edam:operation_3200, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TAMPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dkoslicki/TAMPA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_3518, edam:topic_3520 ; sc:citation , "pmcid:PMC10137904", "pubmed:37122388" ; sc:description "Batch correction and harmonization of -omics datasets with a tunable median polish of ratio." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TAMPOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.github.com/edammer/TAMPOR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3053, edam:topic_3056 ; sc:citation "pubmed:19420055" ; sc:description "All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. This tool fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units." ; sc:featureList edam:operation_3227 ; sc:name "Tandem2" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:url "http://www.evoinformatics.eu/tandem2.htm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3711 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3655 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pmcid:PMC4506239", "pubmed:25631240" ; sc:description "Convertor between file format from peptide database search. Converts tandem xml output into pepXML format" ; sc:featureList edam:operation_3267 ; sc:name "Tandem2XML" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "5.0.0" ; sc:url "http://tools.proteomecenter.org/wiki/index.php?title=Software:Tandem2XML" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621 ; sc:citation , "pmcid:PMC7355294", "pubmed:32657355" ; sc:description "TandemTools package includes TandemQUAST tool for evaluating and improving assemblies of extra-long tandem repeats (ETR) and TandemMapper tool for mapping long error-prone reads to ETRs." ; sc:featureList edam:operation_0310, edam:operation_2429, edam:operation_3180 ; sc:name "TandemTools" ; sc:url "https://github.com/ablab/TandemTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_2885, edam:topic_3518, edam:topic_3676 ; sc:citation , "pubmed:36040167" ; sc:description "Tangent normalization for somatic copy-number inference in cancer genome analysis." ; sc:featureList edam:operation_0484, edam:operation_3435, edam:operation_3918 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tangent" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/broadinstitute/tangent" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659, edam:topic_2815 ; sc:citation ; sc:description "This Pipeline process data from raw fastq data to circular RNA related results." ; sc:featureList edam:operation_2495 ; sc:license "CC-BY-4.0" ; sc:name "TanglabCircularRNAPipeline" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/huboqiang/TanglabCircularRNAPipeline" ; biotools:primaryContact "Fuchou Tang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0634, edam:topic_3474 ; sc:citation , "pmcid:PMC6799900", "pubmed:31626666" ; sc:description """TANGLE is a timespan-guided neural attention mechanism that can be used to integrate sequences of Medicare services and the time span between them to provide interpretable patients representations, which can be further used for some target prediction task. Predictive capabilities of TANGLE are demonstrated here with an application on the 10% publicly available sample of deidentified, individual level, linked Medicare Benefits Schedule (MBS) and Pharmaceutical Benefits Scheme (PBS) electronic databases of Australia. Starting from sequences of MBS-items and timespans, TANGLE can predict which diabetic patient, currently on metformin only, is likely to be prescribed with a different type of diabetes controlling drug in the near future.""" ; sc:featureList edam:operation_0337, edam:operation_3439 ; sc:name "Tangle" ; sc:url "https://github.com/samuelefiorini/tangle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_3510 ; sc:citation "pubmed:15361882" ; sc:description "A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. The model used here, is designed to predict cross-beta aggregation in peptides and denatured proteins and consists of a phase-space encompassing the random coil and 4 possible structural states: beta-turn, alpha-helix, beta-sheet aggregation and alpha-helical aggregation." ; sc:featureList edam:operation_0474, edam:operation_2479 ; sc:name "Tango" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://tango.crg.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2229, edam:topic_3383 ; sc:citation , "pmcid:PMC3702251", "pubmed:23681123" ; sc:description "Generic tool for high-throughput 3D image analysis for studying nuclear organization." ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "TANGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biophysique.mnhn.fr/tango/HomePage" ; biotools:primaryContact "Jean Ollion", "Julien Cochennec", "Thomas Boudier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0654, edam:topic_3174 ; sc:citation "pubmed:23645816" ; sc:description "A tool for the optimal taxonomic assignment of ambiguous pyrosequencing reads." ; sc:featureList edam:operation_3460 ; sc:name "TANGO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.lsi.upc.edu/~valiente/tango/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3175 ; sc:citation "pubmed:25931804" ; sc:description "A command line toolbox for structural variation(SV) detection based on MOSAIK alignments." ; sc:featureList edam:operation_3228 ; sc:name "Tangram" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/jiantao/Tangram#readme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3170 ; sc:citation , "pmcid:PMC4573884", "pubmed:26208906" ; sc:description "An interactive open platform to explore the function of lncRNAs in cancer." ; sc:featureList edam:operation_3680 ; sc:name "TANRIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.mdanderson.org/main/TANRIC:Overview" ; biotools:primaryContact "Dr. Han Liang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3512, edam:topic_3966 ; sc:citation , "pmcid:PMC8045306", "pubmed:33849445" ; sc:description "TANTIGEN 2.0 (Tumor T-cell Antigen Database) is a knowledge base of tumor T cell antigens and epitopes." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480, edam:operation_2421 ; sc:name "TANTIGEN 2.0" ; sc:url "http://projects.met-hilab.org/tadb" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "Validate the local torsion angles of a protein structure." ; sc:featureList edam:operation_2423 ; sc:name "TAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://old.protein.bio.unipd.it/tap/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3304, edam:topic_3444 ; sc:citation ; sc:description "TAP is a TMS targeting and analysis pipeline for fMRI. It is a custom MATLAB code to determine" ; sc:featureList edam:operation_0337 ; sc:license "MIT" ; sc:name "TAP" ; sc:url "https://github.com/moritzdannhauer/TAP" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474, edam:topic_3794 ; sc:citation , "pmcid:PMC6860437", "pubmed:31738786" ; sc:description """A static analysis model for PHP vulnerabilities based on token and deep learning technology. With the widespread usage of Web applications, the security issues of source code are increasing. The exposed vulnerabilities seriously endanger the interests of service providers and customers. There are some models for solving this problem. However, most of them rely on complex graphs generated from source code or regex patterns based on expert experience. In this paper, TAP, which is based on token mechanism and deep learning technology, was proposed as an analysis model to discover the vulnerabilities of PHP: Hypertext Preprocessor (PHP) Web programs conveniently and easily. Based on the token mechanism of PHP language, a custom tokenizer was designed, and it unifies tokens, supports some features of PHP and optimizes the parsing.""" ; sc:featureList edam:operation_1812, edam:operation_3802 ; sc:name "TAP" ; sc:url "https://github.com/das-lab/TAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Suite" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3300, edam:topic_3304, edam:topic_3384, edam:topic_3419 ; sc:citation ; sc:description """TAPAS (Translational Algorithms for Psychiatry-Advancing Science) is an open-source software package for Translational Neuromodeling and Computational Psychiatry. TAPAS is a collection of algorithms and software tools that are developed by the Translational Neuromodeling Unit (TNU, Zurich) and collaborators. These tools have been developed to support translational neuroscience, particularly concerning the application of neuroimaging and computational modeling to research questions in psychiatry, neurology and psychosomatics. Problems that can be addressed by tools in TAPAS presently include:.""" ; sc:featureList edam:operation_3658, edam:operation_3659, edam:operation_3907 ; sc:license "GPL-3.0" ; sc:name "TAPAS" ; sc:url "https://www.translationalneuromodeling.org/tapas" ; biotools:primaryContact "Klaas E. Stephan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_2885, edam:topic_3912 ; sc:citation ; sc:description """validate and edit small eukaryotic genome assemblies with long reads. Tapestry is a tool to validate and edit small eukaryotic genome assemblies using long sequence reads. It is designed to help identify complete chromosomes, symbionts, haplotypes, complex features and errors in close-to-complete genome assemblies.""" ; sc:featureList edam:operation_0337, edam:operation_0525, edam:operation_3096, edam:operation_3198 ; sc:license "MIT" ; sc:name "Tapestry" ; sc:url "https://anaconda.org/bioconda/tapestry" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0166, edam:topic_3295, edam:topic_3474, edam:topic_3940 ; sc:citation ; sc:description "TAPIOCA (Topological Attention and Predictive Inference of Chromatin Arrangement Using Epigenetic Features) is a tool for prediction of Topologically associated domains using epigenetic data as inputs." ; sc:featureList edam:operation_0303, edam:operation_3927 ; sc:name "TAPIOCA" ; sc:url "https://github.com/Max-Highsmith/TAPIOCA" ; biotools:primaryContact "Max Highsmith" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "A web server for the prediction of plant microRNA targets, including target mimics." ; sc:featureList edam:operation_3439 ; sc:name "TAPIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/tapir/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1212 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Laurent Gautier" ; sc:citation ; sc:description "This service is like a DNA search engine." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "Tapir" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.9" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/tapir/" ; biotools:primaryContact "Ole Lund" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7236505", "pubmed:32423416" ; sc:description """tappAS is a comprehensive computational framework for the analysis of the functional impact of differential splicing. tappAS: a user-friendly application to analyze the functional implications of alternative splicing. tappAS is a Java GUI application for the analysis of RNA-Seq data down to the isoform level. TappAS is a bioinformatics application containing a wide range of analyses to evaluate the functional impact of Alternative Transcript Expression Mechanisms (AltTEM), in the form of a GUI application developed in Java and R.""" ; sc:featureList edam:operation_0264, edam:operation_2436, edam:operation_2939, edam:operation_3197, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "tappAS" ; sc:url "https://app.tappas.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3534 ; sc:citation "pubmed:14978300" ; sc:description "On-line service for predicting binding affinity of peptides toward the TAP transporter. The Prediction is based on cascade SVM, using sequence and properties of the the amino acids." ; sc:featureList edam:operation_0478, edam:operation_2479 ; sc:name "TAPPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/tappred/" ; biotools:primaryContact "Dr G P S Raghava" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3400, edam:topic_3474, edam:topic_3948 ; sc:citation , "pubmed:33592504" ; sc:description """A robust immunoinformatic tool for the prediction of tumor T-cell antigens based on AAindex properties. Paste a single sequence or several sequences in FASTA format to use the predictor.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0418 ; sc:name "TAP" ; sc:url "https://tapredictor.herokuapp.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2830, edam:topic_3047 ; sc:citation , "pubmed:37258918" ; sc:description "Prediction of tap transport of peptides with variable length using Tapreg." ; sc:featureList edam:operation_0252, edam:operation_0416 ; sc:isAccessibleForFree true ; sc:name "TAPREG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://imed.med.ucm.es/Tools/tapreg/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3673 ; sc:citation "pubmed:21672185" ; sc:description "Efficient BWT-based read aligner supporting multiple sequencing platforms." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "TAPyR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tapyr.net" ; biotools:primaryContact "TAPyR Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0128, edam:topic_0621, edam:topic_3474 ; sc:citation , "pmcid:PMC7331999", "pubmed:32614833" ; sc:description """Data-driven network alignment. Network alignment (NA) aims to find a node mapping between compared networks that uncovers regions of high topological similarity, thus allowing for the transfer of functional knowledge between aligned nodes.""" ; sc:featureList edam:operation_0292, edam:operation_0303, edam:operation_3927 ; sc:name "TARA" ; sc:url "http://www.nd.edu/~cone/TARA/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:encodingFormat edam:format_3475 ; sc:name "Matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2855 ; sc:encodingFormat edam:format_3475 ; sc:name "Distance matrix" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_3475, edam:format_3603 ; sc:name "Nucleic acid report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3914 ; sc:encodingFormat edam:format_3475, edam:format_3603 ; sc:name "Quality control report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3301, edam:topic_3339 ; sc:author , "Esperanza López", "Luis Chapado" ; sc:description "cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch." ; sc:featureList edam:operation_0289, edam:operation_0495, edam:operation_2478, edam:operation_3209, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Taranis" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0.1" ; sc:url "https://github.com/BU-ISCIII/taranis" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0602, edam:topic_0659, edam:topic_3518 ; sc:citation , , "pmcid:PMC3245116", "pmcid:PMC5753203", "pubmed:22135297", "pubmed:29156006" ; sc:description "Reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Comprehensive cataloging of the miRNA interactome that enables the browsing of interactions through different filtering combinations." ; sc:featureList edam:operation_0463, edam:operation_2423, edam:operation_2428, edam:operation_2436, edam:operation_3431 ; sc:name "TarBase v8" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "8" ; sc:url "http://www.microrna.gr/tarbase" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_0769, edam:topic_0780, edam:topic_3170 ; sc:citation , "pmcid:PMC8120726", "pubmed:33985427" ; sc:description "TarDB is a database for conserved miRNA targets, degradome supported miRNA targets and miRNA-triggered phasiRNAs in plants. TarDB is a plant miRNA target repository, which is based on cross-species conservation filter, degradome PARE-seq, and small RNA-seq data analysis." ; sc:featureList edam:operation_0463, edam:operation_3431, edam:operation_3454, edam:operation_3792 ; sc:name "TarDB" ; sc:softwareHelp ; sc:url "http://www.biosequencing.cn/TarDB" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_0769, edam:topic_3673 ; sc:citation , "pmcid:PMC5499541", "pubmed:28402514" ; sc:description "TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TAREAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://repeatexplorer.org/?page_id=826" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0209, edam:topic_2275, edam:topic_3336 ; sc:citation "pubmed:16844997" ; sc:description "Web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets." ; sc:featureList edam:operation_0478, edam:operation_0482, edam:operation_2489 ; sc:name "TarFisDock" ; sc:url "http://www.dddc.ac.cn/tarfisdock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0769 ; sc:citation ; sc:description """a novel programmatic tool for deep learning based de novo drug design for a target of interest. The on-going data-science and AI revolution offers researchers with fresh set of tools to approach structure-based drug design problems in the computer aided drug design space. A novel programmatic tool that can be used in aid of in silico-deep learning based de novo drug design for any target of interest has been reported. Once the user specifies the target of interest, the programmatic workflow of the tool generates novel SMILES of compounds that are likely to be active against the target. The tool also performs a computationally efficient In-Silico modeling of the target and the newly generated compounds and stores the results in the working folder of the user. A demonstrated use of the tool has been shown with the target signatures of Tumor Necrosis Factor-Alpha, an important therapeutic target in the case of anti-inflammatory treatment""" ; sc:featureList edam:operation_3938 ; sc:name "Target2DeNovoDrug" ; sc:url "https://github.com/bengeof/Target2DeNovoDrug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3512 ; sc:citation "pubmed:12824372" ; sc:description "The tool can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required." ; sc:featureList edam:operation_0438, edam:operation_0445 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Target Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://luna.bioc.columbia.edu/Target_Explorer/" ; biotools:primaryContact "Alona Sosinsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_3534 ; sc:citation "pubmed:23288787" ; sc:description "Full-featured GUI application for targeting protein-ATP binding residues in protein sequences, consisting of two parts of local client and remote server." ; sc:featureList edam:operation_2575 ; sc:name "TargetATPsite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/targetATP/" ; biotools:primaryContact "Dong-Jun Yu", "Jun Hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2269, edam:topic_3125, edam:topic_3179 ; sc:citation , "pubmed:33410688" ; sc:description """Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. A DNA-binding protein identification method via using sequence-driven features.""" ; sc:featureList edam:operation_0267, edam:operation_3900, edam:operation_3903 ; sc:name "TargetDBP+" ; sc:url "http://csbio.njust.edu.cn/bioinf/targetdbpplus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , "pubmed:22743225" ; sc:description "targetedRetrieval is a model for the regulation of specific genes from a data repository and exploit it to construct a similarity metric for an information retrieval task." ; sc:featureList edam:operation_2422, edam:operation_2495 ; sc:name "targetedRetrieval" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "120705" ; sc:url "http://research.ics.aalto.fi/mi/software/rex12/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3173, edam:topic_3517, edam:topic_3574 ; sc:citation , "pmcid:PMC10767789", "pubmed:37870478" ; sc:description "Comprehensive database of cell-type-specific target genes for genetic variants." ; sc:featureList edam:operation_0282, edam:operation_3791, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "TargetGene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ngdc.cncb.ac.cn/targetgene/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_2229 ; sc:citation , "pmcid:PMC8946727", "pubmed:35350773" ; sc:description "A comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2437 ; sc:isAccessibleForFree true ; sc:name "TargetGeneReg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "2.0" ; sc:url "http://www.TargetGeneReg.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097 ; sc:citation ; sc:description "CouchDB database of miRNA-gene interactions." ; sc:featureList edam:operation_2403 ; sc:name "targetHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://app1.bioinformatics.mdanderson.org/tarhub/_design/basic/docs.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation "pubmed:15980559" ; sc:description "TargetIdentifier is designed for identifying full-length EST cDNAs and functionally annotating EST cDNAs." ; sc:featureList edam:operation_0526, edam:operation_3672 ; sc:name "TargetIdentifier" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ysu.edu/tools/TargetIdentifier.html" ; biotools:primaryContact "Dr. X. (Jack) Min" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3336 ; sc:citation ; sc:description "Integrated data warehouse for retrieval of target genes and proteins for experimental characterisation and drug discovery. Provides integration of custom annotations and in-house experimental data, as well as it facilitates the analysis of query gene/protein sets for enriched biological themes and associations." ; sc:featureList edam:operation_0224, edam:operation_2422, edam:operation_2945 ; sc:name "TargetMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "20150831" ; sc:url "http://targetmine.mizuguchilab.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_0209, edam:topic_0634, edam:topic_3542 ; sc:citation , "pubmed:33280588" ; sc:description """accurate missense mutation prediction by utilizing local and global sequence information with classifier ensemble. TargetMM: Missense mutation is one kind of Single Nucleotide Variations, which might likely cause diseade or even cancer.TargetMM utilize evaluationary information, such as PSSM and predicted Secondary Structure information, and Disorder region of proteins. In addition, we also consider protein global features, such as APAAC and PAAC. On the training data, we trained and validated SVM, RF,and GPC models. Then,intergate them together to form an ensemble classifier model. We compare TargetMM with four existing prediction methods,such as, SIFT, PROVEAN, FATHMM, and PolyPhen-2. The comparision results showed that TargetMM has much higher MCC than that of all these four methods.""" ; sc:featureList edam:operation_0267, edam:operation_3904, edam:operation_3937 ; sc:name "TargetMM" ; sc:url "https://github.com/sera616/TargetMM.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3452, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:34677573" ; sc:description "Functional microRNA Target Prediction with Deep Neural Networks." ; sc:featureList edam:operation_0463, edam:operation_3359, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TargetNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mswzeus/TargetNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation , "pubmed:10891285" ; sc:description "Prediction of the subcellular location of eukaryotic proteins." ; sc:featureList edam:operation_0422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TargetP" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "http://cbs.dtu.dk/services/TargetP/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:22954617" ; sc:description "A novel miRNA target prediction tool that utilizes a probabilistic learning algorithm in the form of a hidden Markov model trained on experimentally verified miRNA targets." ; sc:featureList edam:operation_3792 ; sc:name "TargetProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mirna.imbb.forth.gr/Targetprofiler.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0820, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC10320068", "pubmed:37166966" ; sc:description "Processed gene and protein expression levels across cells and tissues for target discovery." ; sc:featureList edam:operation_0314, edam:operation_2940, edam:operation_3431, edam:operation_3938 ; sc:name "TargetRanger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://targetranger.maayanlab.cloud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0154, edam:topic_0621, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:18477632" ; sc:description "TargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species." ; sc:featureList edam:operation_0314, edam:operation_0443, edam:operation_2423, edam:operation_2489 ; sc:name "TargetRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cs.wellesley.edu/~btjaden/TargetRNA2/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0128, edam:topic_3534 ; sc:citation "pubmed:24334392" ; sc:description "Nnew ligand-specific template-free predictor for targeting protein-ligand binding sites from primary sequences." ; sc:featureList edam:operation_2575 ; sc:name "TargetS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.csbio.sjtu.edu.cn:8080/TargetS/" ; biotools:primaryContact "Dong-Jun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3511 ; sc:citation "pubmed:25077573" ; sc:description "A novel computational approach for predicting miRNA targets with the target sites located along entire gene sequences, which permits finding additional targets that are not located in the 3′ un-translated regions." ; sc:featureList edam:operation_3792 ; sc:name "TargetS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://liubioinfolab.org/targetS/mirna.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0659 ; sc:citation ; sc:description "Infers the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variational Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final score is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features." ; sc:featureList edam:operation_3658 ; sc:license "GPL-2.0" ; sc:name "TargetScore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TargetScore.html" ; biotools:primaryContact "Yue Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3172 ; sc:citation , "pmcid:PMC3087348", "pubmed:20015393" ; sc:description "This packages provides a targeted pre-processing method for GC-MS data." ; sc:featureList edam:operation_2945 ; sc:license "GPL-2.0" ; sc:name "TargetSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.30.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TargetSearch.html" ; biotools:primaryContact "Alvaro Cuadros-Inostroza" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:24501098" ; sc:description "A probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts." ; sc:featureList edam:operation_3228 ; sc:name "targetSeqView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Eitan177/targetSeqView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2640, edam:topic_3336, edam:topic_3337, edam:topic_3418 ; sc:citation , "pmcid:PMC6941971", "pubmed:31900415" ; sc:description """Integrative discovery of treatments for high-risk neuroblastoma. You have reached the TargetTranslator, an interactive tool that enables the creation of gene signatures and exploration of their connections to different compounds.""" ; sc:featureList edam:operation_2436, edam:operation_3557, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "TargetTranslator" ; sc:url "http://targettranslator.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Vitamin-specific predictor for targeting protein-vitamin binding residues." ; sc:featureList edam:operation_2479 ; sc:name "TargetVita" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.csbio.sjtu.edu.cn:8080/TargetVita/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0154, edam:topic_0601, edam:topic_0736 ; sc:citation "pubmed:18385152" ; sc:description "Collection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple sequence alignments and presentation of integrated results." ; sc:featureList edam:operation_0303, edam:operation_0492, edam:operation_2479 ; sc:name "TarO" ; sc:url "http://www.compbio.dundee.ac.uk/taro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3168, edam:topic_3577 ; sc:citation , "pmcid:PMC7158102", "pubmed:32293247" ; sc:description "TarPan Viewer is a tool used to visually inspect targeted panel sequencing data. an easily adaptable targeted sequencing panel viewer for research and clinical use." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "TarPan" ; sc:url "https://github.com/tcashby/tarpan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3500, edam:topic_3512 ; sc:citation , "pubmed:37427797" ; sc:description "Database of putative and validated targets of piRNAs." ; sc:featureList edam:operation_0443, edam:operation_2421, edam:operation_2428 ; sc:isAccessibleForFree true ; sc:name "TarpiD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tarpid.nitrkl.ac.in/tarpid_db/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659 ; sc:citation "pubmed:27207945" ; sc:description "A miRNA-mRNA binding sites prediction tool, which can utilize miRNA-mRNA binding experiment data such as CLASH (cross-linking ligation and sequencing of hybrids) ." ; sc:featureList edam:operation_3792 ; sc:name "TarPmiR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_1929, edam:format_2572, edam:format_3003 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929, edam:format_2572, edam:format_3003 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3620 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3620 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3303 ; sc:citation , "pubmed:28236343" ; sc:description "The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output." ; sc:featureList edam:operation_2403, edam:operation_2428 ; sc:license "GPL-2.0" ; sc:name "TarSeqQC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TarSeqQC.html" ; biotools:primaryContact "Gabriela Merino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC4902911", "pubmed:27287006" ; sc:description "This increases the accuracy of variant calling when using microfluidic PCR based targeted sequencing approaches." ; sc:featureList edam:operation_3227 ; sc:name "tarSVM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/christopher-gillies/TargetSpecificGATKSequencingPipeline" ; biotools:primaryContact "Sampson MG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:25041903" ; sc:description "A tree-based method to explore the association between rare variants and complex diseases, and find potential genetic and environmental factors and their interactions." ; sc:featureList edam:operation_3225 ; sc:name "TARV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://c2s2.yale.edu/software/TARV/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:2059814" ; sc:description "Rapid tag-counting and annotation software tool specifically designed for Illumina CASAVA sequencing datasets." ; sc:featureList edam:operation_3800 ; sc:name "TASE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/tase/" ; biotools:primaryContact "Author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2269, edam:topic_3360, edam:topic_3382 ; sc:citation ; sc:description "Temporal Analysis of Spheroid Imaging." ; sc:featureList edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "TASI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/cooperlab/TASI" ; biotools:primaryContact "Contact Form (Lee A. D. Cooper)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3676 ; sc:citation "pubmed:21589938" ; sc:description "Exome capture of short read data to identify the presence of variants" ; sc:featureList edam:operation_0310 ; sc:license "GPL-2.0" ; sc:name "TASR" ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/tasr" ; biotools:primaryContact "Rene Warren" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1276 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3511 ; sc:citation , "pmcid:PMC1669710", "pubmed:17142241" ; sc:description "This tool stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors." ; sc:featureList edam:operation_0224 ; sc:name "Tandem splice site database (TassDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tassdb.info/" ; biotools:primaryContact "Placeholder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3517 ; sc:citation ; sc:description "Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium." ; sc:featureList edam:operation_0283, edam:operation_0488 ; sc:license "LGPL-2.1" ; sc:name "TASSEL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.maizegenetics.net/tassel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC7750361", "pubmed:33365037" ; sc:description "A Fast Implementation for High-Throughput Plant Counting From High-Resolution RGB Imagery." ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "TasselNetV2plus" ; sc:url "https://tinyurl.com/TasselNetV2plus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3943 ; sc:citation , "pmcid:PMC7061232", "pubmed:32022857" ; sc:description """TASTI: Taxa with Ancestral structure Species Tree Inference. Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure. This R package uses maximum likelihood methods to construct species trees from gene trees, with or without ancestral population structure.""" ; sc:featureList edam:operation_0544, edam:operation_0553, edam:operation_0556 ; sc:license "Artistic-2.0" ; sc:name "TASTI" ; sc:url "https://github.com/hillarykoch/TASTI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_2885 ; sc:citation , "pmcid:PMC3702261", "pubmed:23749962" ; sc:description "Web-based genome browser that visualizes large-scale resequencing data generated by next-generation sequencing technologies. The variation and read depth of multiple genomes, as well as annotations, can be shown simultaneously at various scales. The frequency of variants and depth of coverage are shown by gradational colors in a block whose size is variable from 1bp to 100kb." ; sc:featureList edam:operation_3208, edam:operation_3227 ; sc:name "TASUKE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://tasuke.dna.affrc.go.jp/" ; biotools:primaryContact "Takeshi Itoh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2885 ; sc:citation ; sc:description "Identification and classification of homopolymeric tracts from reads." ; sc:featureList edam:operation_3198, edam:operation_3431, edam:operation_3435, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tatajuba" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/quadram-institute-bioscience/tatajuba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9825446", "pubmed:36350638" ; sc:description "A database of Ago1-mediated targets of transfer RNA fragments." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "tatDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://grigoriev-lab.camden.rutgers.edu/tatdb" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation , "pmcid:PMC1182353", "pubmed:15992409" ; sc:description "Prediction of the presence and location of Twin-arginine signal peptide cleavage sites in bacteria." ; sc:featureList edam:operation_0418, edam:operation_0422 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TatP" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/TatP/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3293, edam:topic_3673 ; sc:citation , "pmcid:PMC10336021", "pubmed:37417952" ; sc:description "Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species." ; sc:featureList edam:operation_0324, edam:operation_0525, edam:operation_3840 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tau-typing" ; sc:url "https://github.com/hseabolt/tautyping" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3452 ; sc:citation ; sc:description "App for analysis of image based geometry data in terms of tortuosity factors, volume fractions, surface areas and triple phase boundaries." ; sc:featureList edam:operation_3443, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "TauFactor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.422" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/57956-taufactor" ; biotools:primaryContact "Samuel Cooper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3068, edam:topic_3071 ; sc:citation , "pubmed:32027495" ; sc:description """A Comprehensive Resource for Tautomerism Analyses. Tautomer Structures Extracted from Experimental Literature. A spreadsheet (Tautomer_database_release_3a.xlsx file) with 5,977 structures extracted from experimental literature representing 2,819 cases of tautomeric tuples (mostly tautomer pairs but also a few triples and higher-order tuples). All structures have been annotated with experimental conditions, structure identifiers, bibliographic references and types of tautomerism involved. The structures and experiment-related data were extracted from a total of 171 publications, including reviews reporting on multiple primary studies. Minor correction of references uploaded on 2020-01-29 as version 3a. No scientific data were changed. 2,819 Tautomeric Tuples Comprising 5,977 Structures.""" ; sc:featureList edam:operation_2421, edam:operation_3454, edam:operation_3799 ; sc:name "Tautomer Database" ; sc:url "https://cactus.nci.nih.gov/download/tautomer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_3068 ; sc:citation ; sc:description """Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. 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An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea." ; sc:featureList edam:operation_0323 ; sc:name "tax2tree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://knightlab.ucsd.edu/wordpress/?p=194" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_1775, edam:topic_3301 ; sc:citation "pubmed:25957349" ; sc:description "An open-source R package that predicts the functional capabilities of microbial communities based on 16S datasets." ; sc:featureList edam:operation_3200 ; sc:name "Tax4Fun" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tax4fun.gobics.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0659, edam:topic_3050, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC8067651", "pubmed:33902725" ; sc:description "Tax4Fun2 is a prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences." ; sc:featureList edam:operation_0314, edam:operation_3200, edam:operation_3460 ; sc:license "GPL-3.0" ; sc:name "Tax4Fun2" ; sc:url "https://github.com/bwemheu/Tax4Fun2" ; biotools:primaryContact "Bernd Wemheuer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation ; sc:description "Define and manipulate taxonomic data. Robust and flexible solution to storing and manipulating taxonomic data and any application-specific information associated with it. It provides parsers that can read common sources of taxonomic information from nearly any format while preserving associated data. It takes into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync." ; sc:featureList edam:operation_1812, edam:operation_2409, edam:operation_3460 ; sc:license "MIT" ; sc:name "Taxa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "0.3.1" ; sc:url "https://github.com/ropensci/taxa" ; biotools:primaryContact "Zachary Foster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC10689668", "pubmed:38046097" ; sc:description "A machine learning approach to collapse microbiome datasets using taxonomic structure." ; sc:featureList edam:operation_1812, edam:operation_3695, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TaxaHFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aoliver44/taxaHFE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3293, edam:topic_3500, edam:topic_3944 ; sc:citation ; sc:description """Closing gaps in the NCBI Taxonomy. Taxallnomy is a taxonomic database that provides taxonomic lineages according to the ranks used on Linnean classification system (e.g. Kingdom, Phylum, Class etc.). Taxallnomy is based on the NCBI Taxonomy, thus you will find along the taxonomic lineage either taxa originally ranked in NCBI Taxonomy or some unique nodes created by the Taxallnomy algorithm, since some taxonomic ranks are missing in the original taxonomic lineage (for example, the Superclass rank is missing on the Homo sapiens lineage). Taxallnomy is a taxonomic database based on NCBI Taxonomy that provides taxonomic lineages according to the ranks used on Linnean classification system (e.g. Kingdom, Phylum, Class etc.). Taxallnomy is an extension of NCBI Taxonomy in which all taxa comprising it are organized in a balanced hierarchy, i.e all leaf (end) nodes are in the same hierarchical level.""" ; sc:featureList edam:operation_0224, edam:operation_0558, edam:operation_3431, edam:operation_3460, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "taxallnomy" ; sc:url "http://bioinfo.icb.ufmg.br/taxallnomy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3050, edam:topic_3697 ; sc:citation , "pubmed:32491285" ; sc:description """Automated biodiversity data management tool. Taxamat is avialable either as a single executable file or as an installable package. In addition you can also download example test data together with a manual that contains a step-by-step user'guide.""" ; sc:featureList edam:operation_1812, edam:operation_3460, edam:operation_3695 ; sc:name "Taxamat" ; sc:url "http://www.taxamat.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3293 ; sc:citation "pubmed:25388150" ; sc:description "Algorithm and the accompanying software, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities." ; sc:featureList edam:operation_2403, edam:operation_3460 ; sc:name "taxator-tk" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://github.com/fungs/taxator-tk" ; biotools:primaryContact "Johannes Droege" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0637, edam:topic_0736 ; sc:citation ; sc:description "A new taxonomy-based protein fold recognition method. It extensively exploits the sequence evolution information from PSI-BLAST profiles and the secondary structure information from PSIPRED profiles. A comprehensive set of 137 features is constructed, which allows for the depiction of both global and local characteristics of PSI-BLAST and PSIPRED profiles." ; sc:featureList edam:operation_0303 ; sc:name "TAXFOLD" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://www1.spms.ntu.edu.sg/~chenxin/TAXFOLD/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get taxon(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "taxget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/taxget.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get descendants of taxon(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "taxgetdown" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/taxgetdown.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get parents of taxon(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "taxgetrank" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/taxgetrank.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get all species under taxon(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "taxgetspecies" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/taxgetspecies.html" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2858 ; sc:name "Ontology concept" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get parents of taxon(s)." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "taxgetup" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/taxgetup.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3314, edam:topic_3318, edam:topic_3344 ; sc:description "Friendly user-interface simulating the chemo-taxis movement of biological systems" ; sc:isAccessibleForFree true ; sc:name "Taxi - movement of bacteria to the food" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/9732-taxi-movement-of-bacteria-to-the-food" ; biotools:primaryContact "Shmuel Ben-Ezra" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1930 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3419, edam:topic_3697 ; sc:citation ; sc:description "TaxiBGC (Taxonomy-guided Identification of Biosynthetic Gene Clusters): A computational strategy for identifying experimentally verified Biosynthetic Gene Clusters (BGCs) and inferring their annotated secondary metabolites (SMs) from metagenomic shotgun sequencing data." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TaxiBGC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.1101/2021.07.30.454505" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637 ; sc:citation , "pmcid:PMC3901538", "pubmed:24555091" ; sc:description "Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3460 ; sc:license "MIT" ; sc:name "taxize" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.9.4" ; sc:url "https://github.com/ropensci/taxize" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602, edam:topic_0632, edam:topic_3168 ; sc:citation "pubmed:22618877" ; sc:description "Trims rRNA reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa." ; sc:featureList edam:operation_0308, edam:operation_2419, edam:operation_3192, edam:operation_3237, edam:operation_3460 ; sc:name "TaxMan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/taxmanwww/" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0637, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC5644092", "pubmed:29037173" ; sc:description "Analysis tool for a reliable mapping to a provided microeukaryotic reference database and part of a comprehensive Snakemake workflow. It is used to assign taxonomic information to each NGS read by mapping to the database and filtering low quality assignments." ; sc:featureList edam:operation_0282 ; sc:name "TaxMapper" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/dbeisser/taxmapper" ; biotools:primaryContact "Daniela Beisser" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0637 ; sc:citation ; sc:description "R package to merge the NCBI taxonomy and the GBIF backbone taxonomy" ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "Taxonbridge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://CRAN.R-project.org/package=taxonbridge" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_3293 ; sc:citation , "pmcid:PMC9704803", "pubmed:36377483" ; sc:description "A web-based tool for exploring large phylogenetic trees." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:name "Taxonium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://taxonium.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0637, edam:topic_3297 ; sc:citation , "pubmed:34001434" ; sc:description "TaxonKit is a practical and efficient NCBI taxonomy toolkit." ; sc:featureList edam:operation_0335, edam:operation_2422 ; sc:license "MIT" ; sc:name "TaxonKit" ; sc:softwareHelp ; sc:url "https://github.com/shenwei356/taxonkit" ; biotools:primaryContact , "Hong Ren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3474, edam:topic_3697 ; sc:citation , "pmcid:PMC7750934", "pubmed:32449747" ; sc:description """ensemble of neural networks on stratified microbiome data for disease prediction. An ensemble learning based method for training Convolutional Neural Networks on OTU data after stratification based on phyla. This is a deep learning methodology to arrange OTU data for CNN modelling based on similarity between OTUs in phylum level of the taxonomy tree.""" ; sc:featureList edam:operation_3432, edam:operation_3435, edam:operation_3927 ; sc:name "TaxoNN" ; sc:url "https://github.com/divya031090/TaxoNN_OTU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0637 ; sc:description "Annotate BLAST reports with taxonomic information" ; sc:isAccessibleForFree true ; sc:name "Taxonomic Annotation of BLAST Reports" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/15970-taxonomic-annotation-of-blast-reports" ; biotools:primaryContact "Paola Favaretto" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_1932 ; sc:name "DNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:encodingFormat edam:format_2330 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3174 ; sc:citation ; sc:description "Taxonomic classification of shotgun metagenomic sequences." ; sc:featureList edam:operation_3460 ; sc:name "Taxonomic metagenome tool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-NO" ; sc:softwareVersion "1" ; sc:url "https://galaxy-uit.bioinfo.no/root/index" ; biotools:primaryContact "Erik Hjerde" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2331 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3299 ; sc:citation , , ; sc:description "Krona pie chart from taxonomic profile." ; sc:featureList edam:operation_0337 ; sc:name "taxonomy_krona_chart" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/kronatools/taxonomy_krona_chart/2.0.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2330 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3168 ; sc:citation , ; sc:description "Count the redundancy from a taxonomy file." ; sc:featureList edam:operation_3460 ; sc:name "taxonomy_summary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.1 beta" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/Taxonomy_summary/0.1%20beta" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0654, edam:topic_3050 ; sc:citation ; sc:description """A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data. TaxonTableTools (TTT) aims to provide easy-to-use tools for biologists and non-bioinformaticians to analyse and visualize their metabarcoding data quickly and reproducible via a graphical user interface.""" ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_3192, edam:operation_3431, edam:operation_3797 ; sc:license "MIT" ; sc:name "TaxonTableTools" ; sc:url "https://github.com/TillMacher/TaxonTableTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_0637, edam:topic_0769, edam:topic_3293 ; sc:citation ; sc:description """TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query.""" ; sc:featureList edam:operation_0326, edam:operation_0544, edam:operation_0558, edam:operation_0567, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "TaxOnTree" ; sc:url "http://bioinfo.icb.ufmg.br/taxontree" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_3299 ; sc:citation , ; sc:description "Retrieves taxonomy using tabulated BLAST results." ; sc:featureList edam:operation_3460 ; sc:name "taxoptimizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.0.2" ; sc:url "https://github.com/C3BI-pasteur-fr/taxo_pack" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2182 ; sc:name "DNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:citation , "pmcid:PMC6591855", "pubmed:31234910" ; sc:description "A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants)." ; sc:featureList edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tb-profiler" ; sc:operatingSystem "Linux" ; sc:softwareVersion "4.1.1-1", "4.2.0" ; sc:url "https://github.com/jodyphelan/TBProfiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC10074023", "pubmed:37033466" ; sc:description "Framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TB-ML" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tb-ml.github.io/tb-ml-containers/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_0736, edam:topic_0820, edam:topic_3474 ; sc:citation "pubmed:15162482" ; sc:description "Predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be done based only on neural networks or based on statistical learning technique - SVM or combination of two methods." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0270, edam:operation_0492, edam:operation_2241 ; sc:name "TBBpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/tbbpred/" ; biotools:primaryContact "Dr G.P.S.Raghava", "Ms. Navjyot Kaur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3384, edam:topic_3398, edam:topic_3444 ; sc:citation , "pubmed:32058000" ; sc:description """A toolbox for co-activation pattern analysis. Functional magnetic resonance imaging provides rich spatio-temporal data of human brain activity during task and rest. Many recent efforts have focussed on characterising dynamics of brain activity. One notable instance is co-activation pattern (CAP) analysis, a frame-wise analytical approach that disentangles the different functional brain networks interacting with a user-defined seed region. While promising applications in various clinical settings have been demonstrated, there is not yet any centralised, publicly accessible resource to facilitate the deployment of the technique""" ; sc:featureList edam:operation_3431, edam:operation_3891 ; sc:name "TbCAPs" ; sc:url "https://miplab.epfl.ch/index.php/software/tbcaps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0749, edam:topic_3071, edam:topic_3168 ; sc:citation ; sc:description """TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs. T-box riboswitch annotation database. This database contains T-box riboswitch fold prediction, tRNA pairs from host organisms, information regarding T-box riboswitch genetic context, and thermodynamic calculations of putative T-box riboswitch sequences found in nature. Click on individual T-box riboswitch IDs to access more information. To find a list of searchable parameters, look at our faq page. For advanced search, please use the advanced search feature. The complete database is available to download as a single flat file.""" ; sc:featureList edam:operation_0303, edam:operation_0441, edam:operation_0464, edam:operation_0476, edam:operation_2421 ; sc:name "TBDB" ; sc:url "https://tbdb.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_2885 ; sc:citation ; sc:description "tbg-tools is a program to quickly look up positions on scaffolds and get some further informations about these positions." ; sc:featureList edam:operation_0335, edam:operation_3216, edam:operation_3227 ; sc:license "MIT" ; sc:name "tbg-tools" ; sc:url "https://github.com/Croxa/tbg-tools" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0203, edam:topic_0632, edam:topic_0780 ; sc:citation , "pubmed:35670735" ; sc:description "A comprehensive genome platform for Brassicaceae plants." ; sc:featureList edam:operation_0308, edam:operation_0525, edam:operation_0544, edam:operation_0553 ; sc:isAccessibleForFree true ; sc:name "TBGR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.tbgr.org.cn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099 ; sc:citation "pubmed:25798933" ; sc:description "TBI (Tightly Bound Ion Model ) predicts the electrostatic free energy, the different free energy components, the average binding fraction of ions, and the most probable ion binding modes for a given RNA structure (provided in the PDB format) in a salt solution of given ion concentrations." ; sc:featureList edam:operation_2481 ; sc:name "TBI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.physics.missouri.edu/MCTBI/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_2333 ; sc:name "Feature table" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_2333 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0219 ; sc:description "Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Genome Workbench but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "tbl2asn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Convert a table into GFF3. 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It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment." ; sc:featureList edam:operation_0492, edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "T-Coffee" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "1" ; sc:url "http://www.tcoffee.org/Projects/tcoffee/" ; biotools:primaryContact "Cedric Notredame" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3372, edam:topic_3892 ; sc:citation , "pubmed:36725506" ; sc:description "Accelerating QM and QM/MM simulations with a client-server model." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TCPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/mtzgroup/tcpb-client" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3168 ; sc:citation , "pmcid:PMC4445501", "pubmed:26017500" ; sc:description "TCR repertoire data analysis after preprocessing data with CDR3 extraction and gene alignment software tools such as MiTCR, ImmunoSEQ and MiGEC." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3797 ; sc:license "Apache-2.0" ; sc:name "tcR" ; sc:softwareHelp ; sc:softwareVersion "2.2.1.7" ; sc:url "http://imminfo.github.io/tcr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0632, edam:topic_2275, edam:topic_2830 ; sc:citation , "pubmed:31589793" ; sc:description """Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Geometrical approach to characterise the pMHC/TCR binding modes. TCR CoM : TCR complex geometrical parameters. T cell receptor structural repertoire database. tcr_mhci_pos selection [,mhc_a=None [,tcr_a = None [,tcr_b = None [,mhc_a_init=1 [,mhc_a_final=180 [,tcr_a_init=1 [,tcr_a_final=109 [, tcr_b_init=1 [,tcr_b_final=116 [,state=None ]]]]]]]]]].""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3899 ; sc:license "LGPL-3.0" ; sc:name "TCR" ; sc:url "https://tcr3d.ibbr.umd.edu/tcr_com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3474, edam:topic_3930 ; sc:citation , "pmcid:PMC8275323", "pubmed:34252922" ; sc:description "T-cell receptor specificity prediction with bimodal attention networks." ; sc:featureList edam:operation_0416, edam:operation_3359, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TITAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/PaccMann/TITAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3063 ; sc:citation , "pmcid:PMC9939424", "pubmed:36814721" ; sc:description "A novel webtool for T cell receptor repertoire analysis." ; sc:featureList edam:operation_3218 ; sc:isAccessibleForFree true ; sc:name "TCR_Explore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tcr-explore.erc.monash.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0605, edam:topic_2830 ; sc:citation , "pubmed:32181809" ; sc:description "multi-state T-cell receptor structure prediction." ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_2575 ; sc:name "TCRBuilder" ; sc:url "http://opig.stats.ox.ac.uk/webapps/stcrpred/TCRBuilder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0625, edam:topic_2229, edam:topic_2830, edam:topic_3324 ; sc:citation , "pmcid:PMC9825763", "pubmed:36477794" ; sc:description "Predicting recognition between T cell receptors and epitopes using contextualized motifs." ; sc:featureList edam:operation_0239, edam:operation_0252, edam:operation_0416, edam:operation_3891, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TCRconv" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/emmijokinen/tcrconv" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0625, edam:topic_3047, edam:topic_3474 ; sc:citation , "pubmed:33156327" ; sc:description """Target Central Resource Database mining the human proteome for disease biology. This page contains information related to the implementation and current status of the Target Central Resource Database (TCRD) at UNM. TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiative: GPCRs, kinases, ion channels and nuclear receptors. Olfactory GPCRs (oGPCRs) are treated as a separate family. A key aim of the KMC is to classify the development/druggability level of targets. We currently categorize targets into four development/druggability levels (TDLs) defined as follows:.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3436 ; sc:name "TCRD" ; sc:url "http://juniper.health.unm.edu/tcrd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:32990749" ; sc:description """TCRdb: A comprehensive database of T-cell receptor sequences in various conditions. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical conditions/cell types. The unique features of TCRdb include:.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422 ; sc:name "TCRdb" ; sc:url "http://bioinfo.life.hust.edu.cn/TCRdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0160, edam:topic_2229, edam:topic_2830 ; sc:citation , "pubmed:36087210" ; sc:description "Flexible Distance-Based TCR Analysis in Python with tcrdist3." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "tcrdist3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/kmayerb/tcrdist3" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_2830, edam:topic_3308, edam:topic_3400 ; sc:citation , "pmcid:PMC8023491", "pubmed:33764977" ; sc:description "TCRGP is a novel Gaussian process method that can predict if TCRs recognize certain epitopes. This method can utilize different CDR sequences from both TCRα and TCRβ chains from single-cell data and learn which CDRs are important in recognizing the different epitopes." ; sc:featureList edam:operation_0303, edam:operation_0416, edam:operation_3891 ; sc:license "MIT" ; sc:name "TCRGP" ; sc:url "http://github.com/emmijokinen/TCRGP" ; biotools:primaryContact , "Harri Lähdesmäki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2830, edam:topic_3324, edam:topic_3930, edam:topic_3948 ; sc:citation ; sc:description "Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors." ; sc:featureList edam:operation_0416, edam:operation_3192, edam:operation_3695 ; sc:license "AGPL-3.0" ; sc:name "TCRMatch" ; sc:url "http://tools.iedb.org/tcrmatch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2830 ; sc:citation ; sc:description "Automated high resolution modeling of T cell receptors" ; sc:featureList edam:operation_0477, edam:operation_3431 ; sc:name "TCRmodel" ; sc:url "https://tcrmodel.ibbr.umd.edu" ; biotools:primaryContact "Ragul Gowthaman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0203, edam:topic_2830, edam:topic_3512 ; sc:citation , "pubmed:34487137" ; sc:description "Prediction of functional pairing between HLA-A*02:01-restricted T cell receptor α and β chains." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TCRpair" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.github.com/amoesch/TCRpair" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:11050560" ; sc:description "A program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented is also known as Statistical Parsimony. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data." ; sc:featureList edam:operation_0324 ; sc:name "TCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://darwin.uvigo.es/software/tcs.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25855806" ; sc:description "Web server is a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index." ; sc:featureList edam:operation_0447 ; sc:name "TCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tcoffee.crg.cat/apps/tcoffee/do:core" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3307 ; sc:citation "pubmed:26515821" ; sc:description "A web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network." ; sc:featureList edam:operation_2990 ; sc:name "tcsBU" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cibio.up.pt/software/tcsBU/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3169, edam:topic_3170, edam:topic_3295 ; sc:description "Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "TCseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TCseq.html" ; biotools:primaryContact "Mengjun Wu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602 ; sc:citation ; sc:description "To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data." ; sc:featureList edam:operation_2497 ; sc:license "GPL-2.0" ; sc:name "TDARACNE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TDARACNE.html" ; biotools:primaryContact "Zoppoli Pietro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_3382 ; sc:citation , "pubmed:32614445" ; sc:description """an online visualization tool for topological data analysis. a TDA analysis and visualization tool, by importing the data and metadata, and choosing the Mapper parameters. For this option, TDAview implements the TDAmapper algorithm in JavaScript.""" ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3695 ; sc:license "MIT" ; sc:name "TDAview" ; sc:url "https://voineagulab.github.io/TDAview/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3295, edam:topic_3360 ; sc:citation , "pmcid:PMC10503044", "pubmed:37719083" ; sc:description "Bioconductor packages to perform tensor decomposition based unsupervised feature extraction." ; sc:featureList edam:operation_3223, edam:operation_3501, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TDbasedUFE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioconductor.org/packages/TDbasedUFE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3334, edam:topic_3360, edam:topic_3419, edam:topic_3474 ; sc:citation , "pmcid:PMC9198070", "pubmed:35701407" ; sc:description "The two decades brainclinics research archive for insights in neurophysiology (TDBRAIN) database." ; sc:featureList edam:operation_2428 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TDBRAIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BCD-gitprojects/TDBRAIN/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3342 ; sc:description "Lists the large variety of clinical and translational medicine datasets that will become available, from academic and industry research projects as well as from clinical cohorts and genome consortia." ; sc:name "Translational Medicine Data Catalog (TMDC)" ; sc:url "https://datacatalog.elixir-luxembourg.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0621, edam:topic_0634, edam:topic_3336 ; sc:citation "pubmed:22116064" ; sc:description "Tropical Disease Research (TDR) Database: Designed and developed to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data for genes collected from various sources, including literature curation. Information can be browsed and queried." ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_2489 ; sc:name "TDR Targets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tdrtargets.org/" ; biotools:primaryContact "TDR-Target Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:11443734" ; sc:description "A software for Power Calculation for the TDT (Transmission disequilibrium test)." ; sc:featureList edam:operation_2238 ; sc:name "TDT Power Calculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://people.virginia.edu/~wc9c/TDTPC/Download.htm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_0780 ; sc:citation , "pubmed:35713985" ; sc:description "Web server tool for the analysis of transcription factor binding sites in plants." ; sc:featureList edam:operation_0372, edam:operation_0445 ; sc:isAccessibleForFree true ; sc:name "TDTHub" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://acrab.cnb.csic.es/TDTHub/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3304, edam:topic_3384, edam:topic_3419, edam:topic_3474 ; sc:citation , "pubmed:34761367" ; sc:description "An Ensemble of Transfer Hierarchical Graph Convolutional Networks for Disorder Diagnosis." ; sc:featureList edam:operation_3435, edam:operation_3927, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TE-HI-GCN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/llt1836/TE-HI-GCN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_0798, edam:topic_3295, edam:topic_3299 ; sc:citation , "pmcid:PMC9004194", "pubmed:35413944" ; sc:description "Calculate TE density for every gene in a genome, along sliding windows, upstream, intragenically, and downstream of genes, and correctly allocate TE density values to a gene along TE Order and Superfamily identities. Our main goal in writing this tool was to provide a clear and concise pipeline/metric to aid in the study of TE presence relative to genes." ; sc:featureList edam:operation_0314, edam:operation_0335, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TE Density" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/sjteresi/TE_Density" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:name "Sequence search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0780, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3810 ; sc:citation , "pmcid:PMC8215737", "pubmed:34154536" ; sc:description "A comprehensive database for alternative splicing in tea plants (Camellia sinensis)." ; sc:featureList edam:operation_0264, edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TeaAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.teaas.cn/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0622 ; sc:citation ; sc:description "Teaching Engine for Genomics. It provides educational games to help students and researchers understand key bioinformatics concepts. The current version includes interactive modules for sequence alignment and phylogenetic tree reconstruction algorithms, with accompanying video tutorials." ; sc:featureList edam:operation_2426 ; sc:name "TeachEnG" ; sc:url "http://teacheng.illinois.edu/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3170, edam:topic_3172, edam:topic_3810 ; sc:citation , "pmcid:PMC7333269", "pubmed:32620074" ; sc:description """a database of gene co-expression network for tea plant (Camellia sinensis). Tea plant (Camellia sinensis) is one of the world’s most important beverage crops with essential economic and health benefits. However, the functional exploration of tea genes related to important agronomic traits, such as secondary metabolism, leaf yield, and stress resistance, is now significantly lagging, which puts an obstacle for applied genetic improvement and molecular breeding in tea plant. Here, a database of gene co-expression network for tea plant (TeaCoN) was developed to serve as a solid platform for candidate gene screening and functional exploration of important agronomical traits in tea plant.""" ; sc:featureList edam:operation_2421, edam:operation_2436, edam:operation_3463 ; sc:name "TeaCoN" ; sc:url "http://teacon.wchoda.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:23268448" ; sc:description "An open source GUI software consisting of two modules: Topology Enrichment Analysis frameworK and Query Structure Enrichment Analysis. TEAK is used to find biologically activated KEGG subpathways given molecular profiling data whereas QSEA is used to perform hierarchical querying of the KEGG pathways." ; sc:featureList edam:operation_3660 ; sc:name "TEAK" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/teak/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3300, edam:topic_3315, edam:topic_3318 ; sc:citation , "pmcid:PMC6899345", "pubmed:31844509" ; sc:description """an R package for modelling leaf temperature using energy budgets. Solve for leaf temperature using energy balance. tealeaves: an R package for modeling leaf temperature using energy budgets. Accepted in AoB PLANTS. {tealeaves} is a lightweight R package to model leaf temperature using leaf energy balance. It uses the R package units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately. It’s straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind, or trait gradients such as leaf size or stomatal conductance. Implements models of leaf temperature using energy balance""" ; sc:featureList edam:operation_0460, edam:operation_2426, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "tealeaves" ; sc:url "https://github.com/cdmuir/tealeaves-ms" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0634, edam:topic_3168 ; sc:citation , "pmcid:PMC4086136", "pubmed:24861626" ; sc:description "TEAM is a web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications." ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3197 ; sc:name "TEAM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://team.babelomics.org" ; biotools:primaryContact "Joaquín Dopazo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_2229, edam:topic_2885, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7065459", "pubmed:32159215" ; sc:description """A comprehensive database of simple sequence repeat markers of tea. Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs""" ; sc:featureList edam:operation_0308, edam:operation_2421, edam:operation_3196 ; sc:name "TeaMiD" ; sc:url "http://indianteagenome.in:8080/teamid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3068, edam:topic_3303, edam:topic_3473, edam:topic_3489 ; sc:citation , "pmcid:PMC7319445", "pubmed:32383756" ; sc:description "A Text Annotation Tool for Team Collaboration." ; sc:featureList edam:operation_2422, edam:operation_3283, edam:operation_3553, edam:operation_3778 ; sc:license "MIT" ; sc:name "TeamTat" ; sc:url "https://www.teamtat.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:35759515" ; sc:description "Upstream and Downstream Proteomics Analysis." ; sc:featureList edam:operation_0417, edam:operation_2436, edam:operation_3645 ; sc:isAccessibleForFree true ; sc:name "TeaProt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tea.coffeeprot.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218 ; sc:author "Andrés Cañada" ; sc:description "A tool designed to facilitate the retrieval, extraction and annotation of bacterial enzymatic reactions and pathways from the literature." ; sc:featureList edam:operation_0305 ; sc:name "TeBactEn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "cnio.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://tebacten.bioinfo.cnio.es/" ; biotools:primaryContact "Andrés Cañada", "Martin Krallinger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0634, edam:topic_3940 ; sc:citation , "pmcid:PMC9825605", "pubmed:36350663" ; sc:description "A database of temporal gene expression patterns during multiple developmental periods in human and model organisms." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3232, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "TEDD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://TEDD.obg.cuhk.edu.hk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0654 ; sc:citation "pubmed:24894500" ; sc:description "A lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads." ; sc:featureList edam:operation_0310 ; sc:name "Tedna" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://urgi.versailles.inra.fr/Tools/Tedna" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "TedSim or single cell Temporal dynamics Simulator simulates the cell division events from the root cell to present-day cells, simultaneously generating the CRISPR/Cas9 genome editing lineage barcodes and scRNA-seq data. In particular, TedSim generates cells from multiple cell types through cell division events. TedSim can be used to benchmark and investigate computational methods which use either or both of the two types of data, scRNA-seq and lineage barcodes, to study cell lineages or trajectories." ; sc:featureList edam:operation_0314, edam:operation_3478, edam:operation_3745, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TedSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Galaxeee/TedSim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3299 ; sc:citation , "pmcid:PMC8636989", "pubmed:34870190" ; sc:description "Task-based Extensible Evolutionary algorithm Platform for Optimization and Real-time Testing." ; sc:featureList edam:operation_0479 ; sc:isAccessibleForFree true ; sc:name "Teeport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://teeport.ml/tasks" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3577 ; sc:citation , "pubmed:35426914" ; sc:description "Estimation of Treatment EFFects on transcriptomic data using causal random forest." ; sc:featureList edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "teff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://teff-package.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0769, edam:topic_0798, edam:topic_3168, edam:topic_3299 ; sc:citation ; sc:description """A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data. A bioinformatics tool for detecting novel transposable element insertions. TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.""" ; sc:featureList edam:operation_0308, edam:operation_3211, edam:operation_3227 ; sc:name "TEfinder" ; sc:url "https://github.com/VistaSohrab/TEfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0621, edam:topic_0625, edam:topic_3056, edam:topic_3071 ; sc:citation , "pmcid:PMC7263200", "pubmed:32478790" ; sc:description "TEGA is a WEB-based standalone software (WEB-based platform) designed for the management of biological data, with emphasis on population genetics studies. This platform is free and any research group can install it in their institute, and modify it." ; sc:featureList edam:operation_0554, edam:operation_3197, edam:operation_3283 ; sc:license "AGPL-3.0" ; sc:name "TEGA" ; sc:url "https://github.com/darioelias/TEGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_3512 ; sc:citation ; sc:description "Robust and powerful framework for discovering post-transcriptional regulatory elemenets." ; sc:featureList edam:operation_0438 ; sc:name "TEISER" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://tavazoielab.c2b2.columbia.edu/TEISER/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_0659, edam:topic_2885, edam:topic_3173 ; sc:citation ; sc:description """Reverse regression increases power for detecting trans-eQTLs. Tejaas is a command line tool to find trans-eQTLs from eQTL data. It is released under the GNU General Public License version 3. Tejaas is based on the hypothesis that a trans-eQTL should regulate the expression levels of multiple genes. In brief, it implements two statistical methods to find trans-eQTLs.""" ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3436, edam:operation_3463, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Tejaas" ; sc:url "https://github.com/soedinglab/tejaas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3263, edam:topic_3300 ; sc:citation , "pubmed:32989722" ; sc:description """Using a Telegram chatbot as cost-effective software infrastructure for ambulatory assessment studies with iOS and Android devices. A Telegram bot to conduct your ambulatory assessment study by sending surveys to participants' smartphones. The bot script is written in Python, can be simply configured by a single JSON-file and runs under Windows, MacOS and Linux. Telegram Survey Bot is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.""" ; sc:featureList edam:operation_2422, edam:operation_3096 ; sc:license "GPL-3.0" ; sc:name "Telegram" ; sc:url "https://github.com/Raze97/Telegram-Survey-Bot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2259 ; sc:description "Read/write functions for Telemac hydrodynamic model files (both Selafin and Leonard formats)" ; sc:isAccessibleForFree true ; sc:name "Telemac Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.6.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/25021-telemac-tools" ; biotools:primaryContact "Thomas Benson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_3168 ; sc:citation "pubmed:22962446" ; sc:description "A local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert." ; sc:featureList edam:operation_0310 ; sc:name "Telescoper" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/p/telescoper/wiki/Home/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_0621, edam:topic_3175, edam:topic_3673 ; sc:citation , "pmcid:PMC10100673", "pubmed:36847562" ; sc:description "TelFinder: a program for de novo detection of telomeric motif sequences." ; sc:featureList edam:operation_0239, edam:operation_0240, edam:operation_3472, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "TelFinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bio-tombow/TelFinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3412 ; sc:citation , "pmcid:PMC7893465", "pubmed:33609383" ; sc:description "TELLAPRIALBI is a calculator for Aspartate aminotransferase/platelet ratio index (APRI) and albumin–bilirubin grade (ALBI), which can be used as validated prognostic predictors of postoperative liver dysfunction after hepatic resection." ; sc:featureList edam:operation_2428, edam:operation_3503 ; sc:name "TELLAPRIALBI" ; sc:url "https://tellaprialbi.37binary.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0780, edam:topic_3168, edam:topic_3944 ; sc:citation , "pmcid:PMC10767889", "pubmed:37602392" ; sc:description "TeloBase is a curated database containing computationally predicted and experimentally confirmed telomere sequences of species across the whole tree of life." ; sc:featureList edam:operation_0238, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "TeloBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cfb.ceitec.muni.cz/telobase/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2182 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2572 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0798 ; sc:description "TElocal is a tool that utilizes both uniquely and ambiguously mapped reads to quantify transposable element expression at the locus level. TElocal takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements." ; sc:featureList edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TElocal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hammelllab.labsites.cshl.edu/software/#TElocal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_3360 ; sc:citation , "pmcid:PMC8963315", "pubmed:35022670" ; sc:description "A method for reporting chromosome-specific telomere lengths from long reads." ; sc:featureList edam:operation_0310, edam:operation_3182, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Telogator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/zstephens/telogator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3383, edam:topic_3511 ; sc:citation "pubmed:11768660" ; sc:description "A software package that enables users to assess the sizes and distribution of telomeric fragments represented in autoradiograph images of agarose gels. The hybridization from multiple matching telomeric probes is corrected for and simple statistics and plots are generated for each selected lane." ; sc:featureList edam:operation_2478, edam:operation_3443 ; sc:name "Telometric" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.fccc.edu/software/OpenSource/telometric/telometric.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0632, edam:topic_0749, edam:topic_3520 ; sc:citation ; sc:description "TeloTool is a tool for telomere length measurement from Terminal Restriction Fragment Analysis." ; sc:isAccessibleForFree true ; sc:name "TeloTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/44573-telotool-terminal-restriction-fragment-analysis" ; biotools:primaryContact "Janett Göhring" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0196, edam:topic_0621, edam:topic_2229, edam:topic_3500 ; sc:citation ; sc:description "Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line." ; sc:featureList edam:operation_0310, edam:operation_3180, edam:operation_3192, edam:operation_3198, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "TELR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/bergmanlab/telr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_0798, edam:topic_3810 ; sc:citation , "pubmed:37646936" ; sc:description "Curated data resource for transposon element-based molecular markers in plants." ; sc:featureList edam:operation_0346, edam:operation_0427, edam:operation_3194 ; sc:isAccessibleForFree true ; sc:name "TEMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinformatics.um6p.ma/TEMM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:24753423" ; sc:description "A software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data." ; sc:featureList edam:operation_0427 ; sc:name "TEMP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/JialiUMassWengLab/TEMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0659, edam:topic_0798, edam:topic_3673, edam:topic_3958 ; sc:citation , "pubmed:33511407" ; sc:description """A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. TEMP2 is an algorithm for detecting transposon insertions using short-read whole-genome sequencing data. It can not only precisely detect germline transposon insertions, but also estimate the number of uninherited/somatic transposon insertions by removing artificial insertion introduced by chimeric reads.""" ; sc:featureList edam:operation_0337, edam:operation_0427, edam:operation_0452, edam:operation_3644 ; sc:name "TEMP2" ; sc:url "https://github.com/weng-lab/TEMP2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3299, edam:topic_3474 ; sc:citation , "pubmed:31999330" ; sc:description "time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks." ; sc:featureList edam:operation_0267, edam:operation_0331, edam:operation_3927 ; sc:name "Tempel" ; sc:url "https://drive.google.com/drive/folders/15WULR5__6k47iRotRPl3H7ghi3RpeNXH" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3304, edam:topic_3334, edam:topic_3384, edam:topic_3418 ; sc:citation , ; sc:description "TemplateFlow a community archive of imaging templates and atlases for improved consistency in neuroimaging." ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3553 ; sc:name "TemplateFlow" ; sc:url "http://www.templateflow.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0218, edam:topic_3293, edam:topic_3305, edam:topic_3382 ; sc:citation , "pmcid:PMC9747230", "pubmed:36535209" ; sc:description "A transformer-based mutation prediction framework for SARS-CoV-2 evolution." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0331 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TEMPO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZJUDataIntelligence/TEMPO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3295, edam:topic_3474, edam:topic_3940 ; sc:citation , "pubmed:34255822" ; sc:description "A deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets." ; sc:featureList edam:operation_3222, edam:operation_3907 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TempoMAGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/pkhoueiry/TempoMAGE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0621, edam:topic_0637, edam:topic_3297, edam:topic_3300 ; sc:citation , "pmcid:PMC7511790", "pubmed:32727974" ; sc:description "Database of Growth TEMPeratures of Usual and RAre Prokaryotes." ; sc:featureList edam:operation_3431 ; sc:name "TEMPURA" ; sc:url "http://togodb.org/db/tempura" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3474 ; sc:citation "pubmed:26079348" ; sc:description "The tool first computes a set of topological features and then leverages a SVM-based approach to identify predictive topological features that characterizes known targets." ; sc:featureList edam:operation_3562 ; sc:name "TENET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/cosbyntu/softwares/tenet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:33170214" ; sc:description """gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data. A tool for reconstructing Transfer Entropy-based causal gene NETwork from pseudo-time ordered single cell transcriptomic data.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3192 ; sc:name "TENET" ; sc:url "https://github.com/neocaleb/TENET" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32960209" ; sc:description """an R package based tool for tissue enrichment and gene expression analysis. Tissue-Enrichment Analysis of any Number of Genes and Tissues. While working on transcripts such as CDS, alternative splicing, circular RNAs or lncRNAs, one can annotate them to assign some biological process or functions to relate with some specific pathway or network analysis. While working on transcripts such as CDS, alternative splicing, circular RNAs or lncRNAs, one can annotate them to assign some biological process or functions to relate with some specific pathway or network analysis.""" ; sc:featureList edam:operation_0264, edam:operation_2495, edam:operation_3501 ; sc:name "TEnGExA" ; sc:url "http://webtom.cabgrid.res.in/tissue_enrich/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:citation ; sc:description "This repository contains code for classifying tensors using different tensor projection and classification methods. Currently the implementations only support matrix observations, There will also be code for simulating data to allow comparisons between the methods." ; sc:featureList edam:operation_2990 ; sc:license "MIT" ; sc:name "tensor_classification" ; sc:softwareHelp ; sc:url "https://github.com/laurafroelich/tensor_classification" ; biotools:primaryContact "Laura Frølich" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3360, edam:topic_3474 ; sc:citation , "pmcid:PMC6873409", "pubmed:31752864" ; sc:description """Prediction of cognitive impairment via deep learning trained with multi-center neuropsychological test data. An end-to-end open source machine learning platform. Announcing the TensorFlow Dev Summit 2020 Learn more. TensorFlow is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML powered applications""" ; sc:featureList edam:operation_3435 ; sc:name "TensorFlow" ; sc:url "https://www.tensorflow.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2269, edam:topic_3304 ; sc:citation ; sc:description "Tensorpac is an Python open-source toolbox for computing Phase-Amplitude Coupling (PAC) using tensors and parallel computing for an efficient, and highly flexible modular implementation of PAC metrics both known and novel. 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They also are known as flat mites and false spider mites.""" ; sc:featureList edam:operation_2421 ; sc:name "Tenuipalpidae" ; sc:url "https://www.tenuipalpidae.ibilce.unesp.br/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:description "Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "tenXplore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tenXplore.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3068, edam:topic_3071 ; sc:citation , "pmcid:PMC7775117", "pubmed:33383578" ; sc:description """Documenting contributions to scholarly articles using CRediT and tenzing. Tenzing, an easy-to-use web-based app, allows researchers to generate reports about the contribution of each team member on a project using CRediT, for insertion into their manuscripts and for publishers to potentially incorporate into article metadata. Documenting Contributions to Scientific Scholarly Output with CRediT.""" ; sc:featureList edam:operation_3435 ; sc:name "tenzing" ; sc:url "https://martonbalazskovacs.shinyapps.io/tenzing/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:27479659" ; sc:description "The tool provides prediction of peptides binding to MHC class I and class II molecules." ; sc:featureList edam:operation_2575 ; sc:name "TepiTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.iedb.org/tepitool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3518 ; sc:citation ; sc:description "Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. 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It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. 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Terminology is the most basic information that researchers and literature analysis systems need to understand. Mining terms and revealing the semantic relationships between terms can help biomedical researchers find solutions to some major health problems and motivate researchers to explore innovative biomedical research issues. However, how to mine terms from biomedical literature remains a challenge. At present, the research on text segmentation in natural language processing (NLP) technology has not been well applied in the biomedical field. Named entity recognition models usually require a large amount of training corpus, and the types of entities that the model can recognize are limited. Besides, dictionary-based methods mainly use pre-established vocabularies to match the text. However, this method can only match terms in a specific field, and the process of collecting terms is time-consuming and labour-intensive""" ; sc:featureList edam:operation_0306, edam:operation_3435, edam:operation_3891 ; sc:name "TermInformer" ; sc:url "https://github.com/prayagtiwari/TermInformer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3063, edam:topic_3068, edam:topic_3315 ; sc:citation , "pubmed:35612097" ; sc:description "Detecting Semantic Differences in HL7 FHIR CodeSystems." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TerminoDiff" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/itcr-uni-luebeck/TerminoDiff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_3510 ; sc:citation ; sc:description "N-Terminal Acetylation and initial methionine predictor based on patterns discovery and decision trees. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high-performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and Nα-terminal acetylation (N-Ac), two of the most common PTMs." ; sc:featureList edam:operation_0417 ; sc:name "Terminus" ; sc:url "http://terminus.unige.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0625, edam:topic_3063 ; sc:citation , "pubmed:36328766" ; sc:description "A Web Application for Streamlined Human Phenotype Ontology (HPO) Tagging and Document Annotation." ; sc:featureList edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TermViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/WGLab/TermViewer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330, edam:format_3033 ; sc:name "Experimental measurement" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2330, edam:format_3033 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_3033 ; sc:name "Statistical estimate score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2229, edam:topic_2269 ; sc:citation , "pmcid:PMC3215431", "pubmed:23089817" ; sc:description "A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments." ; sc:featureList edam:operation_3439 ; sc:license "GPL-2.0" ; sc:name "ternarynet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ternarynet.html" ; biotools:primaryContact "Matthew N. McCall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3047, edam:topic_3303, edam:topic_3336 ; sc:citation , "pubmed:32286817" ; sc:description """A Database-Driven Web Server for Terpenome Research. Terpenome defines as all terpenoid-like and terpenoid-derived compounds, including the terpenoids, steroids and their derivatives. Terpenoids represent the most chemically and structurally diverse family of natural products. There is a growing concern about terpenome by the Pharmaceutical Chemist because of their huge medicinal value, with artemisinin and paclitaxel for representative. By utilizing the tenet of enzyme catalysis in all living organisms, all the natural terpenome are derived from the two essential C5 isoprene units, IPP and DAMPP (see left figures). TeroKit is a webserver-based multi-scale kit conducive to the research of terpenome. It contains a database with annotated data of more than 120,000 terpenome compounds. TeroKit provides the online retrieval and analysis of chemical space, target identification and biosynthetic pathway (under construction) for terpenome.""" ; sc:featureList edam:operation_2422, edam:operation_3216, edam:operation_3803 ; sc:name "TeroKit" ; sc:url "http://terokit.qmclab.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3174, edam:topic_3697, edam:topic_3837 ; sc:citation , "pubmed:31728526" ; sc:description """a public repository of curated and standardized metadata for terrestrial metagenomes. Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials""" ; sc:featureList edam:operation_0306, edam:operation_0310, edam:operation_0362, edam:operation_3431 ; sc:name "TerrestrialMetagenomeDB" ; sc:url "https://webapp.ufz.de/tmdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_2269, edam:topic_3524 ; sc:citation "pubmed:19570995" ; sc:description "A software for estimating time-varying network from time-series of nodal attributes. It stems from the acronym TESLLOR, which stands for TEmporally Smoothed 11-regularized Logistic Regression. It represents a novel extension of the well-known lasso-style sparse structure recovery technique." ; sc:featureList edam:operation_2238 ; sc:name "TESLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=444" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:35876845" ; sc:description "Consensus-specific quantification of transposable element expression preventing biases from exonized fragments." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3223, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TEspeX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/fansalon/TEspeX/tree/fansalon/TEspeX" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:26543171" ; sc:description "An R-package for simulation of reconstructed phylogenetic trees under global, time-dependent birth-death processes. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference." ; sc:featureList edam:operation_0324, edam:operation_2426 ; sc:name "TESS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/TESS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pubmed:32873432" ; sc:description "A Novel MATLAB Program for Automated Tessitura Analysis." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_1812 ; sc:license "GPL-3.0" ; sc:name "Tessa" ; sc:url "https://github.com/Allerseelen/Tessa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3384, edam:topic_3452 ; sc:citation , "pubmed:26632045" ; sc:description "Nuclear medicine software based on Monte Carlo modeling for generating gamma camera acquisitions and dosimetry." ; sc:featureList edam:operation_3443 ; sc:name "TestDose" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dositest.com/" ; biotools:primaryContact "D. Villoing", "L. Ferrer", "M. Bardies" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3385, edam:topic_3524 ; sc:citation ; sc:description "Simulator written in Mathworks Matlab for modelling the whole imaging procedure in an optical fluorescence localization microscope." ; sc:featureList edam:operation_2426 ; sc:license "CC-BY-SA-4.0" ; sc:name "TestSTORM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://titan.physx.u-szeged.hu/~adoptim/?page_id=183" ; biotools:primaryContact "Miklos Erdelyi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0140 ; sc:citation "pubmed:23475502" ; sc:description "Sequence-based predictor for identifying submitochondria location of proteins." ; sc:featureList edam:operation_2489 ; sc:name "TetraMito" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/TetraMito" ; biotools:primaryContact "Hao Lin", "Lin Ding Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_3173, edam:topic_3400 ; sc:citation , "pmcid:PMC9264601", "pubmed:35799269" ; sc:description "Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "tex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://liwzlab.cn/tex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0621, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC9518666", "pubmed:36170113" ; sc:description "TEx-MST is a novel bioinformatic database for providing the valuable expression information of MANE-select transcripts in normal human tissues." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "TEx-MST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://texmst.ibms.sinica.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3068 ; sc:description "Query PubMed and store references in BibTeX format." ; sc:featureList edam:operation_0224 ; sc:name "TeXMed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0.7" ; sc:url "http://www.bioinformatics.org/texmed/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0218, edam:topic_3474 ; sc:author , , ; sc:citation ; sc:description "text id an R-package for analyzing and visualizing human language using natural language processing and deep learning. The language that individuals use contains a wealth of psychological information interesting for research." ; sc:featureList edam:operation_0337, edam:operation_3436 ; sc:license "GPL-3.0" ; sc:name "text" ; sc:softwareHelp ; sc:url "https://cloud.r-project.org/package=text" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_3068, edam:topic_3384, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:35914394" ; sc:description "A transformer-Based neural language model that synthesizes brain activation maps from free-form text queries." ; sc:featureList edam:operation_0224, edam:operation_3908, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Text2Brain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://braininterpreter.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; 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sc:description "Get text data entries." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "textget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/textget.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3756 ; sc:name "Localisation score" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Search the textual description of sequence(s)." ; sc:featureList edam:operation_0224 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "textsearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/textsearch.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_2229, edam:topic_2640, edam:topic_3068 ; sc:citation , "pmcid:PMC8728118", "pubmed:34986601" ; sc:description "A comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human." ; sc:featureList edam:operation_0224, edam:operation_0415, edam:operation_3778 ; sc:isAccessibleForFree true ; sc:name "TF-Marker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio.liclab.net/TF-Marker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC9156873", "pubmed:35636345" ; sc:description "A practical introduction to EEG Time-Frequency Principal Components Analysis (TF-PCA)." ; sc:featureList edam:operation_2939, edam:operation_3891, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "TF-PCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NDCLab/tfpca-tutorial" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0602 ; sc:description "This pipeline gives you a full analysis of nfcore chromatine accessibility data (ChIP-Seq, DNAse-Seq or ATAC-Seq and nfcore RNA-seq count data. It performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform the data. It also gives you plots for deep analysis of the data." ; sc:license "GPL-3.0" ; sc:name "TF-Prioritizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/biomedbigdata/TF-Prioritizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0204, edam:topic_0749, edam:topic_0780, edam:topic_3512 ; sc:citation , "pmcid:PMC5888541", "pubmed:29272447" ; sc:description """predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. This tool predicts potential regulators for a set of co-expressed or functionally related genes in Arabidopsis thaliana. It uses TF binding site information (1793 PWMs corresponding to TFBS for 916 TFs) and integrates co-expression data and experimental Protein-DNA and Protein-Protein Interactions in an interactive visualization. Paste input genes below or upload a gene set file to get started. Clicking the demo button will start TF2Network with a demo gene set containing genes annotated with circadian rhythm.""" ; sc:featureList edam:operation_0445, edam:operation_1781, edam:operation_2436, edam:operation_2437, edam:operation_2575 ; sc:name "TF2Network" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/TF2Network/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3047, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:32392062" ; sc:description "Three-Dimensional Force Fields Fingerprint Learned by Deep Capsular Network." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:name "TF3P" ; sc:url "https://github.com/canisw/tf3p" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC10155229", "pubmed:37132521" ; sc:description "Java pipeline to prioritize condition-specific transcription factors." ; sc:featureList edam:operation_0445, edam:operation_3222, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TF-Prioritizer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/biomedbigdata/TF-Prioritizer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0659 ; sc:citation "pubmed:16473847", "pubmed:17591612" ; sc:description "System to classify the function of tRNAs that is based on tRNA structural alignments." ; sc:featureList edam:operation_0295, edam:operation_0503, edam:operation_0509, edam:operation_0510 ; sc:name "TFAM" ; sc:url "http://tfam.lcb.uu.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3474 ; sc:citation ; sc:description "Predicting transcription factor binding using ensemble random forest models | processing and analysis of transcription factor binding sites" ; sc:featureList edam:operation_0335, edam:operation_0445, edam:operation_3903 ; sc:license "MIT" ; sc:name "TFAnalysis" ; sc:url "https://github.com/SchulzLab/TFAnalysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation , "pubmed:31504203" ; sc:description "It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules." ; sc:featureList edam:operation_2428 ; sc:license "Artistic-2.0" ; sc:name "TFARM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TFARM.html" ; biotools:primaryContact "Liuba Nausicaa Martino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:10487870" ; sc:description "A software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS))." ; sc:featureList edam:operation_0445 ; sc:name "TFBIND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tfbind.hgc.jp/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2605 ; sc:name "Compound ID (KEGG)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1077 ; sc:name "Transcription factor identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0749, edam:topic_3360, edam:topic_3398 ; sc:citation , "pmcid:PMC10204090", "pubmed:37053505" ; sc:description "User-friendly command line tool for the rapid mining of transcription factor-based biosensors." ; sc:featureList edam:operation_0435, edam:operation_2437, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TFBMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UoMMIB/TFBMiner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0749, edam:topic_3308 ; sc:citation "pubmed:12176838" ; sc:description "A set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces." ; sc:featureList edam:operation_0445 ; sc:name "TFBS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tfbs.genereg.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:15855248", "pubmed:16845063" ; sc:description "TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized." ; sc:featureList edam:operation_0445, edam:operation_2422, edam:operation_3432 ; sc:name "TFBScluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html" ; biotools:primaryContact "TFBScluster Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0621, edam:topic_0654, edam:topic_0749, edam:topic_3179 ; sc:citation ; sc:description "It is an identification method that utilizes several data sources. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods." ; sc:featureList edam:operation_3432 ; sc:name "TFBSfinder" ; sc:operatingSystem "Linux" ; sc:url "http://bits.iis.sinica.edu.tw/~TFBSfinder/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_2330 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pmcid:PMC4866524", "pubmed:26794315" ; sc:description "Package for the analysis and manipulation of transcription factor binding sites. It includes a matrix conversion system between Position Frequency Matrix (PFM), Position Weight Matrix (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query the JASPAR database and provide a wrapper of de novo motif discovery software." ; sc:featureList edam:operation_0239, edam:operation_0438, edam:operation_0445 ; sc:license "GPL-2.0" ; sc:name "TFBSTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TFBSTools.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0602, edam:topic_0749, edam:topic_2640, edam:topic_3068 ; sc:citation , "pubmed:34037703" ; sc:description "TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimensions in cancer: dysexpression, molecular alteration, regulatory relationships between TFs and other genes, last but not least, cancer process and signaling pathways. Users can retrieve results by searching specific TF names or cancer types." ; sc:featureList edam:operation_2421, edam:operation_2422 ; sc:name "TFcancer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://lcbb.swjtu.edu.cn/tfcancer/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2815, edam:topic_3500 ; sc:citation , "pubmed:23933972" ; sc:description "Curated compendium of specific DNA-binding RNA polymerase II transcription factors." ; sc:featureList edam:operation_2421 ; sc:name "TFcheckpoint" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tfcheckpoint.org/" ; biotools:primaryContact "Astrid Lægreid" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Process TRANSFAC transcription factor database for use by tfscan." ; sc:featureList edam:operation_1812 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tfextract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/tfextract.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:20965973" ; sc:description "Tomato Functional Genomics Database provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database. It is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_2422, edam:operation_2495 ; sc:name "Tomato Functional Genomics Database (TFGD)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ted.bti.cornell.edu" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3169 ; sc:citation ; sc:description "It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Two different methods for the search of TF high accumulation DNA zones, called \"binding regions\" and \"overlaps\", are available." ; sc:featureList edam:operation_0445 ; sc:license "Artistic-2.0" ; sc:name "TFHAZ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TFHAZ.html" ; biotools:primaryContact "Alberto Marchesi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation ; sc:description "Transcription Factor Inference from microarray data." ; sc:featureList edam:operation_2495 ; sc:name "TFInfer" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://homepages.inf.ed.ac.uk/s0976841/TFInfer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_3169, edam:topic_3179 ; sc:citation , "pubmed:31899481" ; sc:description "Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules." ; sc:name "tfLDA" ; sc:url "https://github.com/lichen-lab/tfLDA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC9480832", "pubmed:36124642" ; sc:description "An integrated gateway to access transcription factor-target gene interactions for multiple species." ; sc:featureList edam:operation_0445, edam:operation_2436, edam:operation_2575, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "TFLink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tflink.net/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0958 ; sc:name "Tool metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Display full documentation for an application." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tfm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/tfm.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3500, edam:topic_3512 ; sc:citation "pubmed:20522509" ; sc:description "Toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575 ; sc:name "TFM-Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinfo.lifl.fr/TFM" ; biotools:primaryContact "TFM-explorer team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3068, edam:topic_3318, edam:topic_3382 ; sc:citation ; sc:description """a MATLAB toolbox for 4D traction force microscopy. PIV(Particle Image Velocimetry), Traction force microscopy, Template matching (OpenCV), Export movie files using ffmpeg, Align slices in stack and autofocus plugins for imageJ.""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3552 ; sc:name "TFMLAB" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/qingzongtseng/tfm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "The program scans a protein sequence P against a library of protein-DNA complexes and builds comparative models of P if good templates are found." ; sc:featureList edam:operation_2479 ; sc:name "TFmodellerServiceService" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://maya.ccg.unam.mx/~tfmodell/tutorial.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0204, edam:topic_0621, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC7319436", "pubmed:32324215" ; sc:description """a webserver for the visualization of transcription factor motifs in genomic regions. TFmotifView is a web server that allows to study the distribution of known transcription factor (TF) motifs in genomic regions. Based on genomic regions of interest and selected TF motifs (settings), TFmotifView performs an overlap of the genomic regions with TF motif occurrences from the JASPAR database to generate three different outputs: (1) an enrichment table and scatterplot calculating the significance of motif occurrences in genomic regions compared to control regions, (2) a genomic view of the organisation of TF motifs in each genomic region including an option to export the motif positions into the UCSC genome browser, and (3) a metaplot summarising the position of TF motifs relative to the center of the regions.""" ; sc:featureList edam:operation_0239, edam:operation_3208, edam:operation_3222 ; sc:name "TFmotifView" ; sc:url "http://bardet.u-strasbg.fr/tfmotifview/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0099, edam:topic_0659 ; sc:citation ; sc:description "An algorithm for predicting non-coding RNA secondary structures." ; sc:featureList edam:operation_0278 ; sc:name "TFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://evryrna.ibisc.univ-evry.fr/evryrna/tfold" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3292, edam:topic_3295, edam:topic_3474, edam:topic_3674 ; sc:citation , "pmcid:PMC7691157", "pubmed:33294291" ; sc:description """Predicting Preference of Transcription Factors for Methylated DNA Using Sequence Information. The role of this page is a brief introduction to TFPred. TFPred is a webserver for the identification of transcription factors and transcription factors that prefer bind to methylated DNA. In the predictors, sequence-based methods were used to represent proteins. The support vector machine (SVM) and XGBoost were applied for model construction. For the differentiation of transcription factors and non-transcription factors, the accuracy of the 5-fold cross validation test and independent dataset test was 86.66% and 83.02%, respectively. For the classification of transcription factors that prefer methylated DNA and transcription factors that prefer non-methylated DNA, the accuracy of the 5-fold cross-validation test and independent dataset test was 71.58% and 68.87%, respectively. We hope the webserver could provide convenience for Biochemistry scholars.""" ; sc:featureList edam:operation_0372, edam:operation_0417, edam:operation_0445, edam:operation_3935 ; sc:name "TFPred" ; sc:url "http://lin-group.cn/server/TFPred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_0654, edam:topic_0749 ; sc:citation ; sc:description "Transcription Factor predict. Combines sequence similarity searching with supervised machine learning methods for the identification of TFs and the prediction of their structural superclass." ; sc:featureList edam:operation_2479, edam:operation_2990 ; sc:name "TFpredict" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.ra.cs.uni-tuebingen.de/software/TFpredict/welcome_e.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:name "Protein report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3512 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Identify transcription factor binding sites in DNA sequences." ; sc:featureList edam:operation_0445 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tfscan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/tfscan.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2755 ; sc:name "Transcription factor name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:36200824" ; sc:description "A database of transcription factors binding syntax in mammalian genomes." ; sc:featureList edam:operation_0327, edam:operation_0445, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "TFSyntax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tfsyntax.zhaopage.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3053, edam:topic_3307 ; sc:citation , "pmcid:PMC5175166", "pubmed:28000771" ; sc:description "Transcription Factor Target Enrichment Analysis" ; sc:name "TFTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/babelomics/TFTEA" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC8444601", "pubmed:34530727" ; sc:description "A python toolbox for annotation enrichment analysis of transcription factor target genes." ; sc:featureList edam:operation_3223, edam:operation_3463, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TFTenricher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/rasma774/Tftenricher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3308 ; sc:description "Package to work with TF data." ; sc:featureList edam:operation_0445 ; sc:license "Artistic-2.0" ; sc:name "TFutils" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TFutils.html" ; biotools:primaryContact "Shweta Gopaulakrishnan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0208, edam:topic_2640, edam:topic_3474, edam:topic_3518 ; sc:citation , "pmcid:PMC6975549", "pubmed:31967990" ; sc:description """Tissue-guided LASSO for prediction of clinical drug response using preclinical samples. Then, we developed a new algorithm called TG-LASSO (Tissue-Guided LASSO) that explicitly integrates information on samples’ tissue of origin with samples gene expression profiles to improve prediction performance (see figure below). Cancer is one of the leading causes of death globally and is expected to be the most important obstacle in increasing the life expectancy in the 21st century.""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3659, edam:operation_3891 ; sc:name "TG-LASSO" ; sc:url "https://github.com/emad2/TG-LASSO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308, edam:topic_3315, edam:topic_3318 ; sc:citation , "pmcid:PMC9041782", "pubmed:35706920" ; sc:description "Temporal gene coexpression network analysis using a low-rank plus sparse framework." ; sc:featureList edam:operation_2426, edam:operation_3463, edam:operation_3766 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TGCnA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/QiZhangStat/TGCnA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC6937949", "pubmed:31888639" ; sc:description """Genome analysis and knowledge-driven variant interpretation with TGex. · Rapid and accurate phenotype-driven variant prioritization. · Automated ACMG/ClinGen variant classification. · Comprehensive evidence collection & reporting. 整合超过120个关键数据来源,GeneCards® Suite信息数据库通过突出基因和表型之间的关联、提供即时评估的支持证据以及自动生成案例报告的方式进行您的新一代测序分析。. 如果您需要在防火墙内安装,只需要将TGex集成到您的商业数据库和内部及外部数据源即可。根据您的自有测序数据创建属于自己的内部专属数据库。. 通过简单易且配有灵活的交互式过滤工具和注释的强大用户界面浏览和发现关键基因体变异体。.""" ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:name "TGex" ; sc:url "http://tgex.genecards.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0199, edam:topic_0632, edam:topic_3168, edam:topic_3511 ; sc:citation "pubmed:11848399" ; sc:description "TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping." ; sc:featureList edam:operation_0308, edam:operation_0460, edam:operation_2419, edam:operation_3237 ; sc:name "TGGE-STAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.charite.de/bioinf/tgge/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2200 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3477 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0196 ; sc:author "WurmLab" ; sc:citation ; sc:description "Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly." ; sc:featureList edam:operation_3083 ; sc:name "TGNet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/ksanao/TGNet" ; biotools:primaryContact "Yannick Wurm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3168 ; sc:citation "pubmed:26565975" ; sc:description "An all-in-one web-based tool for genotyping Mtb to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface." ; sc:featureList edam:operation_3196 ; sc:name "TGS-TB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://gph.niid.go.jp/tgs-tb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:34559177" ; sc:description "Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation." ; sc:featureList edam:operation_3659, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/violet-sto/TGSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3325 ; sc:citation , "pmcid:PMC6678717", "pubmed:31295871" ; sc:description """A Bioinformatics Suit to Facilitate Transcriptome Analysis of Long Reads from Third Generation Sequencing Platform. TGStools is a bioinformatics suit to facilitate transcriptome analysis of long reads from third generation sequencing platform. Third generation sequencing can de novo detect long reads of several thousand base pairs, thus provides a global view of the full length transcriptome.""" ; sc:featureList edam:operation_0264, edam:operation_3501, edam:operation_3644 ; sc:name "TGStools" ; sc:url "https://github.com/BioinformaticsSTU/TGStools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3170, edam:topic_3308, edam:topic_3360, edam:topic_3518 ; sc:citation , "pmcid:PMC7931968", "pubmed:33693359" ; sc:description "TGx-DDI is a transcriptomic biomarker for genotoxicity hazard assessment of pharmaceuticals and environmental chemicals." ; sc:featureList edam:operation_0309, edam:operation_0314, edam:operation_3891 ; sc:name "TGx-DDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://manticore.niehs.nih.gov/tgxddi/tool" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3056, edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC7359849", "pubmed:32684973" ; sc:description """Detecting drivers of pathogen transmission from genomic signatures using density measures. Time-scaled haplotypic density (THD) for R. THD is an R package for estimating and comparing the evolutionary success of individuals in a population based on genetic distances. The primary application of THD is the quantitative analysis and identification of factors that influence the epidemic success of pathogens. The approach assigns a index of epidemic success to each individual in a population. This index is then typically used as the response variable in multivariate models including potential predictors of success. See the publication list below for applications.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3659 ; sc:license "MIT" ; sc:name "THD" ; sc:url "https://github.com/rasigadelab/thd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0081 ; sc:citation "pubmed:20972215" ; sc:description "Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs. From the database, the user can search for proteins by keywords or sequences to obtain a wealth of data including functional and structural information and find possible functional homologs of proteins whose functions have been demonstrated in other species." ; sc:featureList edam:operation_0477, edam:operation_2414, edam:operation_2421, edam:operation_3092 ; sc:name "The Autophagy Database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tanpaku.org/autophagy/" ; biotools:primaryContact "Hideaki Sugawara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation , ; sc:description "A collaborative chickpea genomics program comprising advanced pre-breeding tools for the discovery and validation of novel genes and traits leading to development of abiotic stress tolerant chickpea. This is a project for an abiotic stress tolerant chickpea, and contains: Chickpea GBrowse Viewer; Sequence Similarity Search Tools; Raw data download." ; sc:featureList edam:operation_0224 ; sc:name "The Chickpea Portal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:url "http://www.cicer.info/databases.php" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0781, edam:topic_3324 ; sc:description "Track the spread of the Wuhan Coronavirus Covid-19 outbreak, browse an interactive map, view stats and charts, check affected regions in real-time and more." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "The Coronavirus App" ; sc:softwareHelp , ; sc:url "https://coronavirus.app" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2306, edam:format_2572 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077 ; sc:author "Micha Sammeth" ; sc:citation ; sc:description "Predict abundances for transcript molecules and alternative splicing events from RNAseq experiments." ; sc:featureList edam:operation_0361 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "The Flux Capacitor" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1.6.1" ; sc:url "http://sammeth.net/confluence/display/FLUX/Home" ; biotools:primaryContact "Micha Sammeth" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_2306 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Micha Sammeth" ; sc:citation ; sc:description "Model RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts." ; sc:featureList edam:operation_3566 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "The Flux Simulator" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Lab Roderic Guigo Group", "crg.eu" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "http://sammeth.net/confluence/display/SIM/Home" ; biotools:primaryContact "Micha Sammeth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0797, edam:topic_3053 ; sc:citation ; sc:description "A user-friendly application to display and compare genetic maps." ; sc:featureList edam:operation_2451 ; sc:name "The Genetic Map Comparator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioweb.supagro.inra.fr/geneticMapComparator/" ; biotools:primaryContact "Vincent Ranwez", "Yan Holtz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003, edam:format_3005, edam:format_3164, edam:format_3475 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_3003, edam:format_3005, edam:format_3164, edam:format_3475 ; sc:name "Experimental measurement" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_2269, edam:topic_3173, edam:topic_3308 ; sc:citation , , , ; sc:contributor "EMBIO", "Helse Sør-Øst", "Oslo University Hospital", "Statistics for Innovation", "University Of Oslo" ; sc:description "A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets." ; sc:featureList edam:operation_0531, edam:operation_2238, edam:operation_3194, edam:operation_3463 ; sc:funder "EMBIO", "Helse Sør-Øst", "Oslo University Hospital", "Statistics for Innovation", "University Of Oslo" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "The Genomic HyperBrowser" ; sc:operatingSystem "Linux" ; sc:provider "UiO", "University Of Oslo" ; sc:softwareHelp , ; sc:softwareVersion "1.6" ; sc:url "https://hyperbrowser.uio.no" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_3053, edam:topic_3318 ; sc:citation "pubmed:12620108", "pubmed:16381927" ; sc:description "Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically." ; sc:featureList edam:operation_0276, edam:operation_2949, edam:operation_3439 ; sc:name "The GRID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.thebiogrid.org/" ; biotools:primaryContact "BioGRID Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3752 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3752 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3383, edam:topic_3474 ; sc:citation ; sc:description "The Image Data Explorer (IDE) is a web application that integrates interactive linked visualization of images and derived data points with exploratory data analysis methods, annotation, classification and feature selection functionalities. A cloud deployment is accessible at https://shiny-portal.embl.de/shinyapps/app/01_image-data-explorer." ; sc:featureList edam:operation_0226, edam:operation_2939, edam:operation_2940, edam:operation_2943, edam:operation_2945, edam:operation_3432, edam:operation_3552, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "The Image Data Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "v1.3.2" ; sc:url "https://git.embl.de/heriche/image-data-explorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "Platform built to visualise very large interactome datasets. It functions as an atlas of known protein-protein interactions." ; sc:featureList edam:operation_0337 ; sc:name "The Interactorium" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.systemsbiology.org.au/the-interactorium/" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_0625, edam:topic_3047, edam:topic_3053, edam:topic_3056, edam:topic_3305, edam:topic_3307, edam:topic_3321, edam:topic_3325, edam:topic_3360, edam:topic_3408, edam:topic_3489, edam:topic_3574 ; sc:citation , , "pmcid:PMC4109966", "pubmed:19657830", "pubmed:25058394" ; sc:contributor ; sc:description "The portal integrates information on news, events, clinical trials and thalassaemia-related organisations, research projects and other scientific networks, wiki-based content of protocols, clinical guidelines and educational articles. Most importantly, disease-specific databases are developed and maintained on the portal, such as databases of haemoglobin variations (IthaGenes), epidemiology (IthaMaps) and HbF inducers (IthaDrugs)." ; sc:featureList edam:operation_2421, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "ITHANET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "cing.ac.cy" ; sc:softwareHelp ; sc:url "http://www.ithanet.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0153, edam:topic_0601, edam:topic_3510 ; sc:citation "pubmed:12824382" ; sc:description "Collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences." ; sc:featureList edam:operation_0417, edam:operation_0418, edam:operation_2479, edam:operation_3092 ; sc:name "The Mendel Site" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://mendel.imp.ac.at/" ; biotools:primaryContact "IMP Bioinformatics Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_3068, edam:topic_3474, edam:topic_3489 ; sc:citation , "pmcid:PMC8288053", "pubmed:34279596" ; sc:description "Automatization and self-maintenance of the O-GlcNAcome catalog." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_3092, edam:operation_3435, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "The O-GlcNAc Database" ; sc:softwareHelp , , , ; sc:url "http://www.oglcnac.mcw.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0140, edam:topic_0621, edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation , "pmcid:PMC7642925", "pubmed:32934016" ; sc:description """A Database for Visualizing and Mining High-Content Cell Imaging Projects. Automated analysis of protein localization and abundance for the yeast ORF-GFP collection following treatment with different chemicals and in mutant backgrounds. Cell cycle-specific analysis of protein localization and abundance, with gene expression and translational efficiency.""" ; sc:featureList edam:operation_2421, edam:operation_2489, edam:operation_3431, edam:operation_3443 ; sc:name "TheCellVision" ; sc:url "http://TheCellVision.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3336, edam:topic_3360, edam:topic_3375, edam:topic_3377 ; sc:citation , "pmcid:PMC10767989", "pubmed:37850638" ; sc:description "Comprehensive database of therapeutic biomarkers." ; sc:featureList edam:operation_3760, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "TheMarker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/themarker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_3518 ; sc:citation "pubmed:22188791" ; sc:description "The tool is designed for biologists to identify Differentially Expressed Genes (DEG) from loop-design microarray experiments." ; sc:featureList edam:operation_3223 ; sc:name "THEME" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://metadb.bmes.nthu.edu.tw/theme/home.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0637, edam:topic_0659, edam:topic_3174, edam:topic_3697 ; sc:citation , "pmcid:PMC6905537", "pubmed:31825995" ; sc:description """Exploring thematic structure and predicted functionality of 16S rRNA amplicon data. themetagenomics provides functions to explore topics generated from 16S rRNA sequencing information on both the abundance and functional levels. It also provides an R implementation of PICRUSt and wraps Tax4fun, giving users a choice for their functional prediction strategy""" ; sc:featureList edam:operation_2454, edam:operation_2495, edam:operation_3659 ; sc:name "themetagenomics" ; sc:url "https://cran.r-project.org/package=themetagenomics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3370 ; sc:citation "pubmed:17105170" ; sc:description "An online tool for peptide and protein retention time prediction in liquid chromatography. It implements the BioLCCC model for the most popular case of linear gradient chromatography." ; sc:featureList edam:operation_3203 ; sc:name "TheorChromo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.theorchromo.ru/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2330 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3475 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15166022" ; sc:description "Command line tool for predicting MS/MS spectra." ; sc:featureList edam:operation_3438 ; sc:name "theospec" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/protms/files/theospec/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "A webserver for the prediction of T-helper cell Epitopes." ; sc:featureList edam:operation_2945 ; sc:name "thepred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/thepred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3336, edam:topic_3373, edam:topic_3375, edam:topic_3379 ; sc:citation , "pmcid:PMC8728281", "pubmed:34718717" ; sc:description "Facilitating drug discovery with enriched comparative data of targeted agents." ; sc:featureList edam:operation_2421, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "Therapeutic target database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://idrblab.org/ttd/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_3702 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Parser and viewer for thermo msf files." ; sc:featureList edam:operation_2479 ; sc:name "Thermo MSF Parser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "2.0.5" ; sc:url "https://github.com/compomics/thermo-msf-parser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_2885 ; sc:citation ; sc:description "Genome-aware oligonucleotide design algorithm embedded within a distributable tool designed for targeted resequencing." ; sc:featureList edam:operation_2419 ; sc:name "ThermoAlign" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/drmaize/ThermoAlign" ; biotools:primaryContact "Randall J. Wisser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3068, edam:topic_3297, edam:topic_3300, edam:topic_3407 ; sc:citation , "pmcid:PMC9089862", "pubmed:35536846" ; sc:description "A database of the phylogeny and physiology of thermophilic and hyperthermophilic organisms." ; sc:featureList edam:operation_0335, edam:operation_2421, edam:operation_2422, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "ThermoBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://togodb.org/db/thermobase" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0123, edam:topic_0128, edam:topic_0130 ; sc:citation , "pmcid:PMC8963285", "pubmed:35020787" ; sc:description "A webserver to predict protein thermal stability." ; sc:featureList edam:operation_0248, edam:operation_0276 ; sc:isAccessibleForFree true ; sc:name "Thermometer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://service.tartaglialab.com/new_submission/thermometer_file" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0219, edam:topic_0736 ; sc:citation , "pubmed:33095862" ; sc:description "Protein Mutation Thermodynamics Database." ; sc:featureList edam:operation_0331, edam:operation_0455, edam:operation_0475, edam:operation_2421 ; sc:name "ThermoMutDB" ; sc:url "http://biosig.unimelb.edu.au/thermomutdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0199, edam:topic_0736, edam:topic_3306, edam:topic_3474 ; sc:citation , "pmcid:PMC7728386", "pubmed:33253214" ; sc:description """Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. ThermoNet is a computational framework for quantitative prediction of the changes in protein thermodynamic stability () caused by single-point amino acid substitutions. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks. ThermoNet was compared with a large set of predictors and was shown to perform equally well as the best methods in the field while effectively addressing prediction bias.""" ; sc:featureList edam:operation_0272, edam:operation_0331, edam:operation_0474, edam:operation_0475, edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "ThermoNet" ; sc:url "https://github.com/gersteinlab/ThermoNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_1775 ; sc:citation "pubmed:21044646" ; sc:description "Sequence-based predictor for identifying thermophilic proteins." ; sc:featureList edam:operation_0250 ; sc:name "ThermoPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lin.uestc.edu.cn/server/ThermoPredv1" ; biotools:primaryContact "Hao Lin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0218, edam:topic_3120 ; sc:citation , "pmcid:PMC8027235", "pubmed:33842537" ; sc:description "ThermoScan is a tool for semi-automatic identification of protein stability data from PubMed." ; sc:featureList edam:operation_0306, edam:operation_0331, edam:operation_3196, edam:operation_3431 ; sc:name "ThermoScan" ; sc:url "https://github.com/biofold/ThermoScan" ; biotools:primaryContact "Emidio Capriotti", "Piero Fariselli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0780, edam:topic_0820, edam:topic_2229 ; sc:citation , "pubmed:37460312" ; sc:description """Toward the cell simulation platform for Thermus thermophilus. Knowledgebase and simulator of Thermus thermophilus.""" ; sc:featureList edam:operation_0533, edam:operation_2422, edam:operation_3660 ; sc:isAccessibleForFree true ; sc:name "ThermusQ" ; sc:url "https://www.thermusq.net/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2737 ; sc:name "FIG ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2737 ; sc:name "FIG ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2737 ; sc:name "FIG ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2711 ; sc:encodingFormat edam:format_2331 ; sc:name "Genome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0797 ; sc:citation , "pmcid:PMC2265698", "pubmed:18261238" ; sc:description "Environment for comparative genome analysis." ; sc:featureList edam:operation_0224 ; sc:name "The SEED genome comparison environment" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.theseed.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_3336 ; sc:citation , "pmcid:PMC7390989", "pubmed:32437556" ; sc:description """transcriptome-driven efficacy estimates for gene-based TArget discovery. Estimating efficacy of gene-target-disease associations is a fundamental step in drug discovery. An important data source for this laborious task is RNA expression, which can provide gene-disease associations on the basis of expression fold change and statistical significance. However, the simply use of the log-fold change can lead to numerous false-positive associations. On the other hand, more sophisticated methods that utilize gene co-expression networks do not consider tissue specificity. Here, we introduce Transcriptome-driven Efficacy estimates for gene-based TArget discovery (ThETA), an R package that enables non-expert users to use novel efficacy scoring methods for drug-target discovery. In particular, ThETA allows users to search for gene perturbation (therapeutics) that reverse disease-gene expression and genes that are closely related to disease-genes in tissue-specific networks""" ; sc:featureList edam:operation_2421 ; sc:license "GPL-3.0" ; sc:name "ThETA" ; sc:url "https://github.com/vittoriofortino84/ThETA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0621, edam:topic_0769, edam:topic_3315 ; sc:citation ; sc:description "Tree House Explorer (THEx) is a novel genome browser for exploring phylogenetic and genomic data in one succinct place." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0567, edam:operation_3208, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "THEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/harris-2374/THEx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3316, edam:topic_3382 ; sc:citation , "pmcid:PMC7595229", "pubmed:33116161" ; sc:description """automated ImageJ retinal layer thickness and profile in digital images. To develop an automated retina layer thickness measurement tool for the ImageJ platform, to quantitate nuclear layers following the retina contour. We developed the ThicknessTool (TT), an automated thickness measurement plugin for the ImageJ platform. To calibrate TT, we created a calibration dataset of mock binary skeletonized mask images with increasing thickness masks and different rotations. Following, we created a training dataset and performed an agreement analysis of thickness measurements between TT and two masked manual observers. Finally, we tested the performance of TT measurements in a validation dataset of retinal detachment images. In the calibration dataset, there were no differences in layer thickness between measured and known thickness masks, with an overall coefficient of variation of 0.00%""" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "ThicknessTool" ; sc:url "https://github.com/DanielMaidana/ThicknessTool" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3295, edam:topic_3512 ; sc:citation , "pmcid:PMC9429961", "pubmed:35950764" ; sc:description "A Suite of Tools for Investigating HPV-Dependent Human Carcinogenesis." ; sc:featureList edam:operation_0314, edam:operation_3207, edam:operation_3435, edam:operation_3463 ; sc:isAccessibleForFree true ; sc:name "THInCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://thincr.ca/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3473 ; sc:citation , "pmcid:PMC10038662", "pubmed:36847339" ; sc:description "THINGS-data is a collection of large-scale datasets for the study of natural object representations in brain and behavior. It includes functional magnetic resonance imaging (fMRI) data, magnetoencephalographic (MEG) recordings, and 4.70 million similarity judgments in response to thousands of images from the THINGS object concept and image database." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "THINGS-data" ; sc:url "https://github.com/ViCCo-Group/THINGS-data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3444, edam:topic_3474, edam:topic_3794 ; sc:citation ; sc:description "THINGSvision is a Python toolbox for streamlining the extraction of activations from deep neural networks." ; sc:featureList edam:operation_3625, edam:operation_3891, edam:operation_3927, edam:operation_3937 ; sc:license "MIT" ; sc:name "THINGSvision" ; sc:url "https://github.com/ViCCo-Group/THINGSvision" ; biotools:primaryContact , "Martin N. Hebart" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_3174, edam:topic_3301, edam:topic_3339 ; sc:citation ; sc:description "Taxonomy-free reduction of massive genome collections using embeddings of protein content." ; sc:featureList edam:operation_3359, edam:operation_3432, edam:operation_3460 ; sc:license "BSD-3-Clause" ; sc:name "thinspace" ; sc:url "http://github.com/phiweger/thinspace" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3068, edam:topic_3335, edam:topic_3421 ; sc:citation , "pmcid:PMC9575923", "pubmed:36262735" ; sc:description "Thoracoscore (The Thoracic Surgery Scoring System)." ; sc:featureList edam:operation_3435, edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "Thoracoscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://sfar.org/scores2/thoracoscore2.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3303, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description "Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs." ; sc:featureList edam:operation_0264, edam:operation_0496, edam:operation_3478 ; sc:license "MIT" ; sc:name "ThorAxe" ; sc:url "http://www.lcqb.upmc.fr/ThorAxe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC5536290", "pubmed:28759605" ; sc:description "THPdb is a comprehensive database based on approved and approved/investigational therapeutic peptides compiling important information about these peptides, like their description, sequence, indication, mechanism of action, pharmacodynamics, toxicity, metabolism, absorption, half life, volume of distribution, clearance rate, patent information, interaction with other drugs, targets, physicochemical properties, etc." ; sc:featureList edam:operation_2945 ; sc:name "thpdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/thpdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0654, edam:topic_3053, edam:topic_3500 ; sc:citation "pubmed:20494977" ; sc:description "THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers." ; sc:featureList edam:operation_0282, edam:operation_0283, edam:operation_0302, edam:operation_2429, edam:operation_2944 ; sc:name "THREaD Mapper Studio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cbr.jic.ac.uk/threadmapper" ; biotools:primaryContact "THREaD Mapper support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:8710831" ; sc:description "A software of threading which is an approach to fold recognition which used a detailed 3-D representation of protein structure. The idea was to physically “thread” a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential." ; sc:featureList edam:operation_0303 ; sc:name "THREADER" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinf.cs.ucl.ac.uk/?id=747" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_2814, edam:topic_3474 ; sc:citation ; sc:description """Template-based prediction of protein structure with deep learning. We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. ThreaderAI formulates the task of aligning query sequence with template as the classical pixel classification problem in computer vision and naturally applies deep residual neural network in prediction. ThreaderAI first employs deep learning to predict residue-residue aligning probability matrix by integrating sequence profile, predicted sequential structural features, and predicted residue-residue contacts, and then builds template-query alignment by applying a dynamic programming algorithm on the probability matrix.""" ; sc:featureList edam:operation_0267, edam:operation_0302, edam:operation_0476, edam:operation_0477, edam:operation_3927 ; sc:license "BSD-3-Clause" ; sc:name "ThreaderAI" ; sc:url "https://github.com/ShenLab/ThreaderAI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_0654 ; sc:citation ; sc:description "Predicting DNA mechanics’ contribution to sequence selectivity of proteins along whole genomes." ; sc:featureList edam:operation_0239 ; sc:name "ThreaDNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.insa-lyon.fr/prod.php" ; biotools:primaryContact "Sam Meyer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:23812990" ; sc:description "A template-based algorithm for protein domain boundary prediction. Given a protein sequence, ThreaDom first threads the target through the PDB library to identify protein template that have similar structure fold. A domain conservation score (DCS) will be calculated for each residue which combines information from template domain structure, terminal and internal gaps and insertions. Finally, the domain boundary information is derived from the DCS profile distributions." ; sc:featureList edam:operation_0303 ; sc:name "ThreaDom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zhanglab.ccmb.med.umich.edu/ThreaDom/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0196, edam:topic_0736 ; sc:citation , "pmcid:PMC5793814", "pubmed:28498994" ; sc:description "Takes the amino acid sequence of the query protein as input. It first creates multiple threading alignments to recognize homologous and analogous template structures, from which a domain conservation score is then calculated for deducing the domain boundaries. Next, a boundary clustering method is used to optimize the domain model selections. For discontinuous domain structures, a symmetric alignment algorithm is applied to further integrate and refine the domain assignments." ; sc:featureList edam:operation_0246, edam:operation_0267, edam:operation_2479 ; sc:name "ThreaDomEx" ; sc:softwareHelp , ; sc:url "http://zhanglab.ccmb.med.umich.edu/ThreaDomEx" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:10868275" ; sc:description "Three to One converts three letter translations to single letter translations" ; sc:featureList edam:operation_3434 ; sc:name "Three to One" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/sms2/three_to_one.html" ; biotools:primaryContact "Paul Stothard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "This tool can convert 3-letter amino acid codes to 1-letter amino acid codes and inversely." ; sc:featureList edam:operation_3434 ; sc:name "Three to one letter code" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://molbiol.ru/eng/scripts/01_17.html" ; biotools:primaryContact "Three to One support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3055 ; sc:description "Computes likelihood of a phylogenetic tree under the Threshold model of Wright and Fisher." ; sc:featureList edam:operation_0282, edam:operation_0324, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "thresholdLikelihood" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/55002-thresholdlikelihood-m" ; biotools:primaryContact "David Bryant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2640, edam:topic_3382 ; sc:citation , "pubmed:33360986" ; sc:description """ThresholdNet with Confidence-Guided Manifold Mixup for Polyp Segmentation. The automatic segmentation of polyp in endoscopy images is crucial for early diagnosis and cure of colorectal cancer. Existing deep learning-based methods for polyp segmentation, however, are inadequate due to the limited annotated dataset and the class imbalance problems. Moreover, these methods obtained the final polyp segmentation results by simply thresholding the likelihood maps at an eclectic and equivalent value (often set to 0.5). In this paper, we propose a novel ThresholdNet with a confidence-guided manifold mixup (CGMMix) data augmentation method, mainly for addressing the aforementioned issues in polyp segmentation. The CGMMix conducts manifold mixup at the image and feature levels, and adaptively lures the decision boundary away from the under-represented polyp class with the confidence guidance to alleviate the limited training dataset and the class imbalance problems""" ; sc:featureList edam:operation_2429 ; sc:license "MIT" ; sc:name "ThresholdNet" ; sc:url "https://github.com/Guo-Xiaoqing/ThresholdNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3495 ; sc:encodingFormat edam:format_1929 ; sc:name "RNA sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:35662472" ; sc:description "A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "THRONE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://thegleelab.org/THRONE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0219, edam:topic_0780 ; sc:citation , "pmcid:PMC7706180", "pubmed:33258964" ; sc:description "Thai Rice Starch Database (ThRSDB) is the first-of-its-kind database with a large collection of data on Thai rice starch composition, molecular structure, and functionality for research and industrial uses." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3196, edam:operation_3431, edam:operation_3891 ; sc:name "ThRSDB" ; sc:url "http://thairicestarch.kku.ac.th" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0621, edam:topic_0769, edam:topic_3382, edam:topic_3500 ; sc:citation ; sc:description "ThruTracker iis a high-throughput software for 2-D and 3-D tracking. ThruTracker is a powerful and free software platform for automated 2-D and 3-D video-based animal tracking." ; sc:featureList edam:operation_3436 ; sc:name "ThruTracker" ; sc:url "http://www.sonarjamming.com/thrutracker" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3295 ; sc:citation ; sc:description """A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. THUNDER is a deconvolution method specifically tailored to address unique challenges of estimating cell type proportions in Hi-C data. Our algorithm is a two-step deconvolution approach based off of NMF, which first performs feature selection specific to the type of Hi-C readout (intra or intercrhomosomal contacts), then provides estimated cell type proportions using only informative bin-pairs.""" ; sc:featureList edam:operation_2495, edam:operation_3629, edam:operation_3659 ; sc:name "THUNDER" ; sc:url "https://github.com/brycerowland/thundeR.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3383, edam:topic_3384 ; sc:citation "pubmed:24771516" ; sc:description "An open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy." ; sc:featureList edam:operation_3443 ; sc:name "ThunderSTORM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://zitmen.github.io/thunderstorm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_2229, edam:topic_3336, edam:topic_3382 ; sc:citation , "pubmed:34038546" ; sc:description "Thunor is free software for high throughput cell proliferation data management, analysis and visualization." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "Thunor" ; sc:softwareHelp , ; sc:url "http://www.thunor.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC6713979", "pubmed:31488915" ; sc:description "> MEDIUM CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'Thurstonian IRT' | On the Statistical and Practical Limitations of Thurstonian IRT Models | Fit Thurstonian IRT models in R using Stan, lavaan, or Mplus | The thurstonianIRT package allows to fit various models from Item Response Theory (IRT) for forced-choice questionnaires, most notably the Thurstonian IRT model originally proposed by (Brown & Maydeu-Olivares, 2011)" ; sc:featureList edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "thurstonianIRT" ; sc:url "https://github.com/paul-buerkner/thurstonianIRT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This web server allows browsing, searching and fetching of the Biomarkers data related to ThyCanBio database." ; sc:featureList edam:operation_2945 ; sc:name "thycanbio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/thycanbio/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0623, edam:topic_0736, edam:topic_0821, edam:topic_3534 ; sc:citation "pubmed:21045059" ; sc:description "This database has amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles." ; sc:featureList edam:operation_0320, edam:operation_0339, edam:operation_0346, edam:operation_2487, edam:operation_2518 ; sc:name "ThYme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.enzyme.cbirc.iastate.edu" ; biotools:primaryContact "David Cantu", "Peter Reilly" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0654, edam:topic_3524 ; sc:citation "pubmed:20563611" ; sc:description "The tool allows the calculation of the spectral moments derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation using such sequence/structure numerical indices." ; sc:featureList edam:operation_3637 ; sc:name "TI2BioP" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/ti2biop/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0605 ; sc:author , ; sc:citation , ; sc:contributor , , , , , , ; sc:description """Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community we have created "Training Infrastructure-as-a-Service" (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organisers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress. Training Infrastructure as a Service (TIaaS) has been in development since 21 June 2018, and three days later became a production service at Galaxy Europe on 24 June. As of June 7th, 2023 is has supported 504 training events with over 24000 learners have used this infrastructure for Galaxy training.""" ; sc:featureList edam:operation_3760 ; sc:funder "Bundesministerium für Bildung und Forschung", "Erasmus+ Programme", "National Human Genome Research Institute" ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "Training Infrastructure as a Service (TIaaS)" ; sc:operatingSystem "Linux" ; sc:provider , , , , ; sc:softwareHelp , , , ; sc:softwareVersion "2.1.0" ; sc:url "https://github.com/galaxyproject/tiaas2" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885, edam:topic_3168, edam:topic_3175 ; sc:citation "pubmed:21051338" ; sc:description "Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs)." ; sc:featureList edam:operation_2422, edam:operation_3208, edam:operation_3209, edam:operation_3227, edam:operation_3228 ; sc:name "TIARA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tiara.gmi.ac.kr" ; biotools:primaryContact "D. Hong" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0637, edam:topic_2229, edam:topic_3174, edam:topic_3512 ; sc:citation ; sc:description """Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch. tiara – a tool for DNA sequence classification. The sequences are classified in two stages:. In the first stage, the sequences are classified to classes: archaea, bacteria, prokarya, eukarya, organelle and unknown. In addition to creating the files above, it creates, in the folder where tiara is run, three files containing sequences from sample_input.fasta classified as mitochondria, plastid and prokarya (--tf mit pla pro option). In the Polish translation of the Harry Potter book series, the Sorting Hat (which assigned wizards to different houses) was called Tiara Przydziału.""" ; sc:featureList edam:operation_0310, edam:operation_2995, edam:operation_3802 ; sc:license "MIT" ; sc:name "Tiara" ; sc:url "https://ibe-uw.github.io/tiara" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0621, edam:topic_3125 ; sc:citation "pubmed:15994191", "pubmed:16526950", "pubmed:16845076" ; sc:description "TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER." ; sc:featureList edam:operation_0436, edam:operation_0439, edam:operation_2454 ; sc:name "TiCo" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://tico.gobics.de/" ; biotools:primaryContact "TiCo Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3423 ; sc:citation ; sc:description "Tic suppression training meant to help you build your ability to fight tics. 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The Tumor IsomiR Encyclopedia (TIE) is a dynamic tool that allows researchers to query and compare isomiR expression across more than 11,000 adult and pediatric tumor samples from The Cancer Genome Atlas (TCGA) and the Therapeutically Applicable Research to Generate Effective Treatment (TARGET) datasets.""" ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3792 ; sc:name "TIE" ; sc:url "https://github.com/Gu-Lab-RBL-NCI/TIE-database/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3170, edam:topic_3512, edam:topic_3676 ; sc:citation , "pubmed:33964128" ; sc:description "TieBrush is an efficient method for aggregating and summarizing mapped reads across large datasets. TieBrush is a simple yet efficient method for merging redundant information from multiple alignment files, designed to enable rapid manipulation of extremely large sequencing datasets. The method is specifically designed to optimize investigations of RNA, whole-genome, exome and other types of sequencing experiments. 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TiFoSi (Tissues: Forces & Signalling) is a computational tool to simulate the cellular dynamics of planar epithelia. TiFoSi allows to model feedbacks between cellular mechanics and gene expression (either in a deterministic or a stochastic way), the interaction between different cell populations, the custom design of the cell cycle and cleavage properties, the protein number partitioning upon cell division, and the modeling of cell communication (juxtacrine and paracrine signalling).""" ; sc:featureList edam:operation_2476, edam:operation_3927 ; sc:name "TiFoSi" ; sc:url "http://tifosi.thesimbiosys.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_0769, edam:topic_3336, edam:topic_3517 ; sc:citation ; sc:description """Target illumination GWAS analytics. Genome-wide association studies (GWAS) generate large volumes of associations between genomic variations and phenotypic traits. However, assessing strength, specificity and relevance of associations, and semantically valid aggregation of associations, for applications such as drug target prioritization, is challenging. This project addresses this challenge. Beta coefficients require units and thus are not comparable between non-convertible units (e.g. mg vs mm). Nor are beta coefficients comparable with OR, so it is questionable that these values are combined in one field OR_or_BETA. Current TIGA workaround is to use simple count of beta values supporting gene-trait association.""" ; sc:featureList edam:operation_3196, edam:operation_3436, edam:operation_3791 ; sc:license "BSD-2-Clause" ; sc:name "TIGA" ; sc:url "https://unmtid-shinyapps.net/tiga/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_3016 ; sc:name "Genotype/phenotype report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3273 ; sc:name "Sample ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_0634, edam:topic_2640, edam:topic_3517 ; sc:citation ; sc:description "Efficient TWAS Tool with Nonparametric Bayesian eQTL Weights of 49 Tissue Types from GTEx V8." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TIGAR-V2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.synapse.org/TIGAR_V2_Resource_GTExV8" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622, edam:topic_2259, edam:topic_3308 ; sc:citation "pubmed:21943338" ; sc:description "A software platform for building and analyzing genome-scale models of metabolism. 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It provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software." ; sc:featureList edam:operation_3443 ; sc:name "TIKAL" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://ibios.dkfz.de/tbi/index.php/software/further-software/99-tikal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_2640, edam:topic_3360, edam:topic_3382 ; sc:citation , "pmcid:PMC8889499", "pubmed:35251953" ; sc:description "Deep Learning-Based Mapping of Tumor Infiltrating Lymphocytes in Whole Slide Images of 23 Types of Cancer." ; sc:featureList edam:operation_2429, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "TIL classification" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ShahiraAbousamra/til_classification" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3366 ; sc:description "Open source python package that uses serverless TileDB multidimensional arrays indexed on chromosome, position, and sample to enable variant warehousing scalable to thousands of samples. Offers lossless import VCF or gVCF files, the latter in an N+1 compliant manner. Can be combined with TileDB-Cloud powers real-time queries for variant browsers as well as large notebook-based analyses that use task graphs in conjunction with user-defined functions." ; sc:featureList edam:operation_2422 ; sc:license "MIT" ; sc:name "tiledb-vcf" ; sc:softwareHelp , ; sc:softwareVersion "0.26.5" ; sc:url "https://github.com/TileDB-Inc/TileDB-VCF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3179 ; sc:citation ; sc:description "Hidden Markov Models for ChIP-on-Chip Analysis. It provides methods and classes to build HMMs that are suitable for the analysis of ChIP-on-chip data. The provided parameter estimation methods include the Baum-Welch algorithm and Viterbi training as well as a combination of both." ; sc:featureList edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "TileHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.0-6" ; sc:url "http://www.bioinformatics.csiro.au/tilehmm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3572 ; sc:citation "pubmed:18507856" ; sc:description "System for tile-based quality control of Solexa data." ; sc:featureList edam:operation_3218 ; sc:name "TileQC" ; sc:url "http://denverlab.science.oregonstate.edu/tileqc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation , "pubmed:16787969" ; sc:description "The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:license "Artistic-2.0" ; sc:name "tilingArray" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.52.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tilingArray.html" ; biotools:primaryContact "Zhenyu Xu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_3518 ; sc:citation "pubmed:26040457" ; sc:description "An application for the identification of differentially expressed DNA regions in Tiling Microarray data." ; sc:featureList edam:operation_3223 ; sc:name "TilingScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tilingscan.uv.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9293566", "pubmed:35859930" ; sc:description "Transformer in M-Net for Retinal Vessel Segmentation." ; sc:featureList edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TiM-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZX-ECJTU/TiM-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3518 ; sc:description "TiMAT2 contains tools for genomic tiling microarray analysis" ; sc:featureList edam:operation_2495 ; sc:license "BSD-3-Clause" ; sc:name "TiMat2" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://timat2.sourceforge.net/" ; biotools:primaryContact "TiMAT2 Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3344 ; sc:description "Time resolved image analyzer designed for non-thermal plasma imaging and spectroscopy." ; sc:featureList edam:operation_0320, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Time resolved image analyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/68653-time-resolved-image-analyzer" ; biotools:primaryContact "ryan muddiman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC4095003", "pubmed:25077979" ; sc:description "Topology based pathway analysis specifically tailored to long time series without replicates. It combines dimension reduction techniques and graph decomposition theory to explore and identify the portion of pathways that is most time-dependent. In the first step, it selects the time-dependent pathways; in the second step, the most time dependent portions of these pathways are highlighted." ; sc:featureList edam:operation_2497 ; sc:license "AGPL-3.0" ; sc:name "timeClip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.6.2" ; sc:url "http://romualdi.bio.unipd.it/software/pathway-based-methods" ; biotools:primaryContact "Chiara Romualdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654 ; sc:citation ; sc:description "TimeClust is a user-friendly software package to cluster genes according to their temporal expression profiles. It can be conveniently used to analyze data obtained from DNA microarray time-course experiments. It implements two original algorithms specifically designed for clustering short time series together with hierarchical clustering and self-organizing maps." ; sc:featureList edam:operation_3432 ; sc:name "TimeClust" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://aimed11.unipv.it/TimeClust/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:citation ; sc:description "Functions for data analysis and graphical displays for developmental microarray time course data." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "timecourse" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/timecourse.html" ; biotools:primaryContact "Yu Chuan Tai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3315, edam:topic_3518 ; sc:citation , "pubmed:34175927" ; sc:description "TimeCycle is designed to detect rhythmic genes in circadian transcriptomic time-series data. Based on topological data analysis, TimeCycle provides a reliable and efficent reference-free framework for cycle detection — handling custom sampling schemes, replicates, and missing data." ; sc:featureList edam:operation_0314, edam:operation_3463, edam:operation_3565, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TimeCycle" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/nesscoder/TimeCycle-data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3400, edam:topic_3518 ; sc:citation , "pmcid:PMC9825442", "pubmed:36399488" ; sc:description "Tumor immune micro-environment cell composition database with automatic analysis and interactive visualization." ; sc:featureList edam:operation_0314, edam:operation_0337, edam:operation_3463, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "TIMEDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://timedb.deepomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3383, edam:topic_3385 ; sc:citation "pubmed:21705106" ; sc:description "A free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging." ; sc:featureList edam:operation_3443 ; sc:name "TimeLapseAnalyzer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/tla/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3169, edam:topic_3179, edam:topic_3295 ; sc:citation , "pmcid:PMC7841892", "pubmed:33509077" ; sc:description """TimelessFlex - A flexible framework for investigating chromatin state trajectories. Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. TimelessFlex is a flexible framework for investigating chromatin state trajectories during linear and branched tissue differentiation. This framework adapts and extends Timeless, a Bayesian network for co-clustering of multiple histone modifications at promoter and enhancer feature regions. TimelessFlex is flexible depending on the available genomic data. The basic required data is ChIP-seq for histone modifications with at least three time points and a set of regions of interest.""" ; sc:featureList edam:operation_0440, edam:operation_3222, edam:operation_3431, edam:operation_3432, edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "TimelessFlex" ; sc:url "https://github.com/henriettemiko/TimelessFlex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3170, edam:topic_3518 ; sc:citation ; sc:description """A Novel Cytoscape App to Analyze Time-Series Data Using Temporal MultiLayer Networks (tMLNs). Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.""" ; sc:featureList edam:operation_1781, edam:operation_3094, edam:operation_3925 ; sc:name "TimeNexus" ; sc:url "https://apps.cytoscape.org/apps/TimeNexus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3172, edam:topic_3512, edam:topic_3697 ; sc:citation , "pubmed:34554215" ; sc:description "timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "timeOmics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/abodein/timeOmics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3169, edam:topic_3170 ; sc:citation ; sc:description """a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. Trajectory Inference and Mechanism Exploration with Omics in R. It's about time! Click here for a quick video demonstration of the TIMEOR application, and click here for a video guide through the tutorial below. Analyzing time series differential gene expression and other multi-omics data is computationally laborious and full of complex choices for the various types of time series experiment analyses. The TIMEOR web-application offers a solution as an interactive and adaptive R-Shiny web interface to support reproducibility and the best tools for a given experimental design.""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_2939, edam:operation_3435, edam:operation_3891 ; sc:name "TIMEOR" ; sc:url "https://github.com/ashleymaeconard/TIMEOR.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7319575", "pubmed:32442275" ; sc:description """TIMER2.0 for analysis of tumor-infiltrating immune cells. Tumor progression and the efficacy of immunotherapy are strongly influenced by the composition and abundance of immune cells in the tumor microenvironment. Due to the limitations of direct measurement methods, computational algorithms are often used to infer immune cell composition from bulk tumor transcriptome profiles. These estimated tumor immune infiltrate populations have been associated with genomic and transcriptomic changes in the tumors, providing insight into tumor-immune interactions. However, such investigations on large-scale public data remain challenging. To lower the barriers for the analysis of complex tumor-immune interactions, we significantly improved our previous web platform TIMER""" ; sc:featureList edam:operation_0531, edam:operation_3223, edam:operation_3233 ; sc:name "TIMER" ; sc:softwareVersion "2.0" ; sc:url "http://timer.cistrome.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:name "Genotype/phenotype report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2523 ; sc:name "Phylogenetic data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Plug-in" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2229, edam:topic_2640 ; sc:citation ; sc:description "a tool from E-scape suite for visualizing clonal dynamics over time." ; sc:featureList edam:operation_0567, edam:operation_2426, edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TimeScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "https://bioconductor.org/packages/release/bioc/html/timescape.html" ; biotools:primaryContact "Maia Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3382 ; sc:citation , "pmcid:PMC6612850", "pubmed:31510686" ; sc:description "Inferring signalling dynamics by integrating interventional with observational data | Please make sure that you have the package devtools installed. Then run: devtools::install_github(\"cbg-ethz/timeseriesNEM\") | A method for mapping a non-interventional time series onto a static nested effects model, as inferred using the Bioconductor package nem | In order to install the vignette, add the option build_vignettes = TRUE to the above command. If the vignette is still not created, the following command should do the trick: remotes::install_github(\"cbg-ethz/timeseriesNEM\", build_opts = c(\"--no-resave-data\", \"--no-manual\"), force = TRUE)" ; sc:license "GPL-3.0" ; sc:name "timeseriesNEM" ; sc:url "https://github.com/cbg-ethz/timeseriesNEM" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0621, edam:topic_3382 ; sc:citation , "pubmed:32356730" ; sc:description "Temporal Sensemaking in Intelligence Analysis." ; sc:featureList edam:operation_0337 ; sc:name "TimeSets" ; sc:url "http://vis4sense.github.io/timesets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3344, edam:topic_3474 ; sc:citation , "pmcid:PMC8260877", "pubmed:34258599" ; sc:description "A machine learning pipeline for predicting outcomes from time-series clinical records." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Timesias" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/GuanLab/timesias.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pmcid:PMC8775016", "pubmed:35052413" ; sc:description "A Web Service for Analysing Time Course Transcriptome Data with Multiple Conditions." ; sc:featureList edam:operation_0315, edam:operation_2436, edam:operation_3223, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "TimesVector-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cobi.knu.ac.kr/webserv/TimesVector-web" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3056, edam:topic_3299, edam:topic_3474, edam:topic_3796 ; sc:citation , "pmcid:PMC10324941", "pubmed:37157914" ; sc:description "Accurately identifying selective sweeps using population genomic time series." ; sc:featureList edam:operation_0484, edam:operation_0487, edam:operation_1812, edam:operation_3196, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Timesweeper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SchriderLab/Timesweeper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0637, edam:topic_3293 ; sc:citation , "pubmed:21622662", "pubmed:28387841" ; sc:description "A public resource for knowledge on the timescale and evolutionary history of life.A search utility allows exploration of the thousands of divergence times among organisms in the published literature. A tree-based (hierarchical) system is used to identify all published molecular time estimates bearing on the divergence of two chosen taxa, such as species, compute summary statistics, and present the results." ; sc:featureList edam:operation_0324, edam:operation_2421 ; sc:name "TimeTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.timetree.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3170, edam:topic_3300, edam:topic_3308, edam:topic_3678 ; sc:citation ; sc:description """An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Times-Series Data in Circadian Biology Research. TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. Elan Ness-Cohn, Marta Iwanaszko, William Kath, Ravi Allada, and Rosemary Braun. TimeTrial is an interactive application for the design and optimization of omic time-series experiments to aid researchers in developing their experiment design. Consisting of two interactive applications using both synthetic and biological data, TimeTrial allows researchers to explore the effects of experimental design on signal shape, examine cycling detection reproducibility across biological datasets, and optimize experimental design for cycle detection. TimeTrial is currently in beta.""" ; sc:featureList edam:operation_3565, edam:operation_3799 ; sc:name "TimeTrial" ; sc:url "https://nesscoder.shinyapps.io/TimeTrial_Synthetic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3518 ; sc:citation , "pubmed:33901274" ; sc:description "TIMEx is a tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures." ; sc:featureList edam:operation_0314, edam:operation_3629 ; sc:name "TIMEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://timex.moffitt.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_3053 ; sc:citation ; sc:description "Identifying cellular response networks from diverse omics time-course data." ; sc:featureList edam:operation_3439 ; sc:name "TimeXNet Web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://txnet.hgc.jp/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3168, edam:topic_3400 ; sc:citation ; sc:description "NGS data mining pipeline for cancer immunology and immunotherapy" ; sc:featureList edam:operation_0253, edam:operation_3092 ; sc:name "TIminer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://icbi.i-med.ac.at/software/timiner/timiner.shtml" ; biotools:primaryContact "Zlatko Trajanoski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3170 ; sc:author ; sc:citation , "pubmed:33993215" ; sc:description "TimiRGeN is a R/Bioconductor package for time series microRNA-mRNA integration and analysis. TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds of thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions effecting a signalling pathway, across a time course." ; sc:featureList edam:operation_0463, edam:operation_1781, edam:operation_3223, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "TimiRGeN" ; sc:url "https://bioconductor.org/packages/TimiRGeN" ; biotools:primaryContact , "Daryl Shanley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3869 ; sc:name "Simulation" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3315 ; sc:citation ; sc:description """Timothy is a novel large scale parallel computational model allowing 3-D simulations of cell colonies growing and interacting with variable environment in previously unavailable tissue scale. The cells are modeled as individuals located in the lattice-free 3-D space. The model incorporates cellular environment modelled in a continuous manner, mathematical description based on partial differential equations is formulated for selected important components of the environment. Discrete and continuous formulations are efficiently coupled in one model and allow considerations on different scales: sub-cellular, cellular and tissue scale. High parallel scalability achieved allows simulation of up to 109 individual cells. 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The TA are distributed relatively evenly along genome. The Mariner-based transposons can be inserted to impact statistically every gene, with in average more than 30 insertions site per kb. With the low insertion bias, it is easy to build saturated libraries. 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TISCH provides detailed cell-type annotation at the single-cell level, enabling the exploration of TME across different cancer types.""" ; sc:featureList edam:operation_0313, edam:operation_0337, edam:operation_2436, edam:operation_3431 ; sc:name "TISCH" ; sc:url "http://tisch.comp-genomics.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0749, edam:topic_3510, edam:topic_3512 ; sc:citation , "pubmed:33744969" ; sc:description "TIsigner is web services for improving recombinant protein production, which includes TIsigner, SoDoPE and Razor, the protein expression optimisation, solubility optimisation and signal peptides prediction tools, respectively." ; sc:featureList edam:operation_0363, edam:operation_0409, edam:operation_0418, edam:operation_0479 ; sc:name "TIsigner" ; sc:url "http://tisigner.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2640, edam:topic_3170, edam:topic_3421 ; sc:citation , "pubmed:34534350" ; sc:description "syngeneic mouse tumor database to model tumor immunity and immunotherapy response." ; sc:featureList edam:operation_0314, edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TISMO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/zexian/TISMO_data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_2640, edam:topic_3299, edam:topic_3396 ; sc:citation ; sc:description "TISON (Theatre for In Silico Systems Oncology) is a next-generation multi-scale modeling theatre for in silico systems oncology." ; sc:featureList edam:operation_2426, edam:operation_3927, edam:operation_4009 ; sc:license "MIT" ; sc:name "TISON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tison.lums.edu.pk" ; biotools:primaryContact "Safee U Chaudhary" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168 ; sc:description "This package is used to calculate enrichment of tissue-specific genes in a set of input genes. 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TissUUmaps is a lightweight viewer that uses basic web tools to visualize gene expression data or any kind of point data on top of whole slide images. TissUUmaps tries to keep it minimal so the setup doesn't become complicated. You can use more advanced libraries if you want but we try to make it simple, just HTML, JavaScript and CSS. TissUUmaps allows the display of tissue slide images and uses an overlay to display any sort of marker data on top. Be it spatially resolved gene expression, per cell data, or regions of interest.""" ; sc:featureList edam:operation_0571, edam:operation_3443, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TissUUmaps" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tissuumaps.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2269, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:36549467" ; sc:description "Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics." ; sc:featureList edam:operation_0313, edam:operation_2238, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TIST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lifeome.net/software/tist/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2640, edam:topic_3175, edam:topic_3473, edam:topic_3673 ; sc:citation , "pmcid:PMC4216928", "pubmed:25060187" ; sc:description "Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data." ; sc:featureList edam:operation_2403, edam:operation_3202, edam:operation_3228 ; sc:license "GPL-3.0" ; sc:name "TitanCNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TitanCNA.html" ; biotools:primaryContact , "Sohrab P Shah" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3375, edam:topic_3379 ; sc:citation ; sc:description "A Bayesian Time-to-event Pharmacokinetic Model for Sequential Phase I Dose-escalation Trials with Multiple Schedules." ; sc:featureList edam:operation_3435, edam:operation_3454, edam:operation_3659 ; sc:name "TITE-PK" ; sc:url "https://github.com/gunhanb/TITEPK_sequential" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361, edam:topic_3489 ; sc:citation , "pmcid:PMC7575480", "pubmed:32128697" ; sc:description """A toolbox for creating PsychToolbox and Psychopy experiments with Tobii eye trackers. The current repository furthermore offers a C++ wrapper around the Tobii SDK, which is in turn used as a basis for the MATLAB MEX file TittaMex providing MATLAB Titta with connectivity to the Tobii eye trackers. This C++ wrapper can be consumed by your own C++ projects as well, or be wrapped for other programming languages (a wrapper to Python is also provided). Titta is a toolbox for using eye trackers from Tobii Pro AB with Python, specifically offering integration with PsychoPy.""" ; sc:featureList edam:operation_0337, edam:operation_2428, edam:operation_3216 ; sc:name "Titta" ; sc:url "https://github.com/dcnieho/Titta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """Sampling and Summarizing Transmission Trees with Multi-strain Infections. TiTUS is a code that takes as input a timed pathogen phylogeny with leaves labelled by the host along with epidemiological data such as entry-removal times for the hosts and a contact map. It counts and uniformly samples from the set of feasbile interval vertex labelings of the timed phylogeny that satisfy the direct transmission constraint while supporting a weak transmission bottleneck.""" ; sc:featureList edam:operation_0337, edam:operation_3478 ; sc:name "TiTUS" ; sc:url "https://github.com/elkebir-group/TiTUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0625, edam:topic_3173, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC9900211", "pubmed:36707993" ; sc:description "A computational framework for annotating and predicting noncoding regulatory small insertion and deletion." ; sc:featureList edam:operation_0417, edam:operation_2437, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "TIVAN-indel" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/lichen-lab/TIVAN-indel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3382, edam:topic_3520 ; sc:citation , "pubmed:33141669" ; sc:description "A Diverse High-Resolution Dataset for Object Detection." ; sc:featureList edam:operation_2428, edam:operation_3436, edam:operation_3443 ; sc:license "MIT" ; sc:name "TJU-DHD" ; sc:url "https://github.com/tjubiit/TJU-DHD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3071 ; sc:citation ; sc:description "The R package contains widgets to provide user interfaces. The package uses tcltk or widgetTools, which should be for the widgets to run." ; sc:featureList edam:operation_0337, edam:operation_2409 ; sc:license "Artistic-2.0" ; sc:name "tkWidgets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tkWidgets.html" ; biotools:primaryContact "J. Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Used to perform clustering on fasta formatted sequences." ; sc:featureList edam:operation_3432 ; sc:name "tlcluster" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://genome.uiowa.edu/home.old/pubsoft/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_3053 ; sc:citation "pubmed:8213836" ; sc:description "The programs described here are an extension of the general LINKAGE programs for genetic linkage analysis. The extension consists of allowing for a disease phenotype to be under the control of two loci." ; sc:featureList edam:operation_0283 ; sc:name "TLINKAGE" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.jurgott.org/linkage/tlinkage.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Prediction of inhibitors against human tlr4" ; sc:featureList edam:operation_2945 ; sc:name "tlr4hi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/tlr4hi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments." ; sc:featureList edam:operation_2480 ; sc:name "TLS Motion Determination" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://skuld.bmsc.washington.edu/~tlsmd/index.html" ; biotools:primaryContact "Ethan Merritt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_0659, edam:topic_2640 ; sc:citation , "pmcid:PMC10185877", "pubmed:37205123" ; sc:description "Tool for lncRNA set enrichment analysis based on multi-source heterogeneous information fusion." ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "TLSEA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lirmed.com:5003/tlsea" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0820, edam:topic_3168 ; sc:citation ; sc:description "Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy." ; sc:featureList edam:operation_0492 ; sc:name "TM-Aligner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://lms.snu.edu.in/TM-Aligner/" ; biotools:primaryContact "Ashutosh Singh", "Basharat Ahmad Bhat", "Garima Singh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814 ; sc:citation ; sc:description "Is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)." ; sc:featureList edam:operation_2479 ; sc:name "TM-score" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "20130511" ; sc:url "http://zhanglab.ccmb.med.umich.edu/TM-score/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3360, edam:topic_3365, edam:topic_3518 ; sc:citation "pubmed:23761446" ; sc:description "TMA Navigator is a suite of tools developed specifically for tissue microarray data. It allows network inference, patient stratification and survival analysis from tissue microarray data." ; sc:featureList edam:operation_0276, edam:operation_0314, edam:operation_2495, edam:operation_2497 ; sc:name "TMA Navigator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.tmanavigator.org" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3518 ; sc:description "It is for Tissue MicroArrays (TMA’s). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program." ; sc:featureList edam:operation_3443 ; sc:name "TMAJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.7.1" ; sc:url "http://tmaj.pathology.jhmi.edu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:name "Organism name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3021 ; sc:name "UniProt accession" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0153, edam:topic_0820, edam:topic_2814 ; sc:citation , "pmcid:PMC9825488", "pubmed:36318239" ; sc:description "Membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures." ; sc:featureList edam:operation_0269, edam:operation_0474, edam:operation_2241, edam:operation_2421, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "TmAlphaFold database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tmalphafold.ttk.hu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102 ; sc:citation , "pmcid:PMC4051166", "pubmed:24708189" ; sc:description "A short read aligner specifically tuned for data from the Ion Torrent PGM." ; sc:featureList edam:operation_3198 ; sc:name "TMAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://github.com/iontorrent/TS/tree/master/Analysis/TMAP" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2258, edam:topic_2640, edam:topic_3369 ; sc:citation ; sc:description "Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees | Visualize big high-dimensional data | tmap is a very fast visualization library for large, high-dimensional data sets | We suggest using faerun to plot the data layed out by tmap. But you can of course also use matplotlib (which might be to slow for large data sets and doesn't provide interactive features). Following, an example plot produced with tmap and matplotlib" ; sc:featureList edam:operation_2422, edam:operation_2942, edam:operation_3891 ; sc:name "TMAP" ; sc:url "http://tmap.gdb.tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0634, edam:topic_2885, edam:topic_3053 ; sc:citation ; sc:description "It is a program that takes SNP population haplotypes and case/control phenotypes to identify disease associated sites. It takes the approach of inferring genealogical history (in the form of ancestral recombination graph or ARG) and then using the ARGs to map the trait." ; sc:featureList edam:operation_2429 ; sc:name "TMARG" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.engr.uconn.edu/~ywu/TMARG.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "TMatch is a tool for comparing two rooted ordered labeled trees, which are represented in a preorder parenthesized form. The tool calculates the editing distance of the two trees and displays the edit operations (insertions, deletions and substitutions) needed to transform one tree to the other." ; sc:featureList edam:operation_3096 ; sc:name "TMatch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://web.njit.edu/~wangj/tmatch.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:15637715" ; sc:description "A program for performing association analysis on a set of linked loci within a targeted region." ; sc:featureList edam:operation_0283 ; sc:name "tmax" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wpicr.wpic.pitt.edu/WPICCompGen/tmax.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0157, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:15980452" ; sc:description "Classifies protein sequences as transmembrane B-barrel (TMB) or non-TMB based on amino acid composition." ; sc:featureList edam:operation_0236, edam:operation_0269, edam:operation_0270, edam:operation_0418, edam:operation_2241 ; sc:name "TMB-Hunt" ; sc:url "http://bmbpcu36.leeds.ac.uk/~andy/betaBarrel/AACompPred/aaTMB_Hunt.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3360 ; sc:citation , "pmcid:PMC9523486", "pubmed:36189291" ; sc:description "Multi-endpoint assessment on immunotherapy benefits suggests multi-stratification thresholds for tumor mutation burden" ; sc:featureList edam:operation_0310, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TMBcat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YixuanWang1120/JM_TMBcat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_3510 ; sc:citation , "pmcid:PMC9358067", "pubmed:35941534" ; sc:description "Transmembrane proteins predicted through Language Model embeddings." ; sc:featureList edam:operation_0269, edam:operation_0408, edam:operation_0474, edam:operation_2241 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TMbed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BernhoferM/TMbed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:14978719", "pubmed:15980447" ; sc:description "Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0270, edam:operation_2489 ; sc:name "TMBETA-NET" ; sc:url "http://psfs.cbrc.jp/tmbeta-net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3360, edam:topic_3673, edam:topic_3676 ; sc:citation , "pubmed:34927668" ; sc:description "Bioinformatic tool to optimize TMB estimation and predictive power." ; sc:featureList edam:operation_3435, edam:operation_3675, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TMBleR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://acc-bioinfo.github.io/TMBleR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0610, edam:topic_2269, edam:topic_3474 ; sc:citation ; sc:description "Enabled 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects." ; sc:featureList edam:operation_2426 ; sc:name "tmbstan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/tmbstan/index.html" ; biotools:primaryContact "Kasper Kristensen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3379, edam:topic_3673 ; sc:citation , "pmcid:PMC9450342", "pubmed:36071521" ; sc:description "A distributable tumor mutation burden approach for whole genome sequencing." ; sc:featureList edam:operation_3227, edam:operation_3359, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TMBur" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/bcgsc/TMBur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0122, edam:topic_0820, edam:topic_2828 ; sc:citation ; sc:description "Predict propensity of success for transmembrane protein crystallization." ; sc:featureList edam:operation_0410 ; sc:license "GPL-3.0" ; sc:name "TMCrys" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/brgenzim/tmcrys" ; biotools:primaryContact "Gábor E Tusnády" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC10198730", "pubmed:37213253" ; sc:description "Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis." ; sc:featureList edam:operation_3223, edam:operation_3557, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:name "TMECircDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.maherlab.com/tmecircdb-overview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0769, edam:topic_3295, edam:topic_3315 ; sc:citation , , "pubmed:37310837" ; sc:description "An end-to-end pipeline for quantification and visualization of waddington's epigenetic landscape based on gene regulatory network." ; sc:featureList edam:operation_1781, edam:operation_1812, edam:operation_2426, edam:operation_3799, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TMELand" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/JieZheng-ShanghaiTech/TMELand" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2640, edam:topic_2885, edam:topic_3295, edam:topic_3400 ; sc:citation , "pmcid:PMC8356190", "pubmed:34376552" ; sc:description "TMEscore is an R package to estimate tumor microenvironment score. Provides functionality to calculate Tumor microenvironment (TME) score using PCA or z-score." ; sc:featureList edam:operation_0252, edam:operation_3454, edam:operation_3891, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TMEscore" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/DongqiangZeng0808/TMEscore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2640, edam:topic_3170 ; sc:citation ; sc:description """A Tumour Microenvironment Single-cell RNAseq Database and Search Tool. TMExplorer (Tumour Microenvironment Explorer) is a curated collection of scRNAseq datasets sequenced from tumours. It aims to provide a single point of entry for users looking to study the tumour microenvironment gene expressions at the single-cell level.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_2495 ; sc:name "TMExplorer" ; sc:url "https://github.com/shooshtarilab/TMExplorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:12441377", "pubmed:12824384" ; sc:description "The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods." ; sc:featureList edam:operation_0269, edam:operation_0270 ; sc:name "TMH Benchmark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rostlab.org/owiki/index.php/TMHBenchmark" ; biotools:primaryContact "Andrew Kernytsky" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_0820 ; sc:citation ; sc:description "It predicts helix-helix contacts specifically within the transmembrane parts of membrane proteins. It includes predictions by two different neural networks, one developed for helix-helix contacts on all transmembrane helix pairs and one specifically tailored for the prediction of helix-helix contacts lying on non-neighboring transmembrane helices." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "TMHcon" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20101215" ; sc:url "http://webclu.bio.wzw.tum.de/tmhcon/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "The server will predict MHC Class I and II binding peptides. The prediction based on the virtual and quantitative matrices." ; sc:featureList edam:operation_2945 ; sc:name "tmhcpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/tmhcpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0602, edam:topic_0820 ; sc:citation ; sc:description "It is developed to predict residue-residue contacts in alpha-helix transmembrane proteins. The predicted contacts could be further used to predict helix-helix interactions between helices." ; sc:featureList edam:operation_2479 ; sc:name "TMhhcp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://systbio.cau.edu.cn/tmhhcp/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2305 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_0736, edam:topic_0820, edam:topic_3542 ; sc:citation , "pubmed:11152613" ; sc:description "Prediction of transmembrane helices in proteins." ; sc:featureList edam:operation_0269 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "TMHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "CBS" ; sc:softwareVersion "2.0" ; sc:url "http://cbs.dtu.dk/services/TMHMM/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Topology prediction of membrane proteins with optional fixing and reliability score calculation." ; sc:featureList edam:operation_0270 ; sc:name "TMHMMfix" ; sc:provider "bils.se" ; sc:softwareVersion "1" ; sc:url "http://www.sbc.su.se/%7Emelen/TMHMMfix/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0820, edam:topic_3318 ; sc:citation , "pmcid:PMC6736313", "pubmed:31461441" ; sc:description "A lipophilicity-based energy function for membrane-protein modelling and design | Valid academic email address to send the reports to | I am from an academic institute*" ; sc:featureList edam:operation_0409, edam:operation_0476, edam:operation_0478 ; sc:name "tmhop" ; sc:url "http://tmhop.weizmann.ac.il" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:description "Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets." ; sc:featureList edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "TMixClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TMixClust.html" ; biotools:primaryContact "Monica Golumbeanu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:21563225" ; sc:description "A method to predict transmembrane helix kinks." ; sc:featureList edam:operation_0474 ; sc:name "TMKink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tmkinkpredictor.mbi.ucla.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0130, edam:topic_0736, edam:topic_0820, edam:topic_0821 ; sc:citation , "pmcid:PMC10516361", "pubmed:37594311" ; sc:description "Python interface for computational analysis of transmembrane proteins." ; sc:featureList edam:operation_0269, edam:operation_0272, edam:operation_0303, edam:operation_0564, edam:operation_2241 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TMKit" ; sc:softwareHelp ; sc:url "https://github.com/2003100127/tmkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0199, edam:topic_3120 ; sc:citation ; sc:description "Predictor for protein folding free energy change upon single point mutation for soluble proteins." ; sc:featureList edam:operation_2415 ; sc:name "TML-MP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://weilab.math.msu.edu/TML/TML-MP/" ; biotools:primaryContact "Guo-Wei Wei" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_3303, edam:topic_3308 ; sc:citation , "pubmed:34933331" ; sc:description "A transcriptome-based multi-scale network pharmacology platform for herbal medicine." ; sc:featureList edam:operation_0314 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TMNP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bcxnfz.top/TMNP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0659, edam:topic_0749, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC9825477", "pubmed:36408909" ; sc:description "Deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data." ; sc:featureList edam:operation_0337, edam:operation_0464, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "tModBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.tmodbase.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_0820, edam:topic_3474 ; sc:citation , "pmcid:PMC8006303", "pubmed:33790952" ; sc:description "TMP-SSurface 2.0 is a deep learning-based predictor for surface accessibility of transmembrane protein residues." ; sc:featureList edam:operation_0269, edam:operation_0387, edam:operation_2241, edam:operation_3891 ; sc:name "TMP-SSurface2" ; sc:url "https://github.com/NENUBioCompute/TMP-SSurface-2.0" ; biotools:primaryContact "Li Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0153, edam:topic_0166, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:21177659" ; sc:description "Integrates experimentally observed helix-helix interactions and related structural information of membrane proteins. It offers pre-calculated geometric descriptors at the helix-packing interface. It also includes the corresponding sequence, topology, lipid accessibility, ligand-binding information and supports structural classification, schematic diagrams and visualization of the above structural features of TM helix-packing." ; sc:featureList edam:operation_0270, edam:operation_0303, edam:operation_2415, edam:operation_2950 ; sc:name "TMPad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bio-cluster.iis.sinica.edu.tw/TMPad" ; biotools:primaryContact "Ting-Yi Sung" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_0780 ; sc:citation , "pmcid:PMC6020451", "pubmed:29945549" ; sc:description "The Tobacco Markers & Primers Database." ; sc:featureList edam:operation_2422 ; sc:name "TMPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://biodb.sdau.edu.cn/tmpd/index.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0736, edam:topic_3542 ; sc:description "The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins" ; sc:featureList edam:operation_2423, edam:operation_2489 ; sc:name "TMPred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://embnet.vital-it.ch/software/TMPRED_form.html" ; biotools:primaryContact "TMPred Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0196, edam:topic_0203, edam:topic_0749, edam:topic_2815 ; sc:citation "pubmed:19515937" ; sc:description "Allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-pool assembly and codon optimization for expression." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_3198 ; sc:name "TmPrime" ; sc:url "http://prime.ibn.a-star.edu.sg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3314, edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description "Quantum Geometries and Properties of 86k Transition Metal Complexes." ; sc:featureList edam:operation_0386, edam:operation_2476, edam:operation_3938 ; sc:name "tmQM" ; sc:url "https://github.com/bbskjelstad/tmqm" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1192 ; sc:encodingFormat edam:format_2064 ; sc:name "Tool name (BLAST)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0820 ; sc:author "Michael Bernhofer" ; sc:citation ; sc:description "Predict transmembrane proteins (TMP) and transmembrane helices (TMH) using position-specific scoring matrices (PSSM) generated by PSI-BLAST and the physico-chemical properties of the amino acids." ; sc:featureList edam:operation_0474 ; sc:name "TMSEG" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "tum.de" ; sc:softwareHelp ; sc:softwareVersion "2.1.0" ; sc:url "https://github.com/Rostlab/TMSEG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0736, edam:topic_0820, edam:topic_2885, edam:topic_3676 ; sc:citation ; sc:description "a web server to predict pathogenesis of missense mutations in transmembrane region of membrane proteins." ; sc:featureList edam:operation_0269, edam:operation_0331, edam:operation_3196, edam:operation_3226, edam:operation_3461 ; sc:name "TMSNP" ; sc:url "http://lmc.uab.es/tmsnp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0157, edam:topic_0736, edam:topic_0820 ; sc:citation "pubmed:22564899" ; sc:description "The Transmembrane helix: Simple Or Complex (TMSOC) webserver identifies the simple and complex transmembrane helices in a protein sequence. Simple TM helices are then masked prior to sequence similarity searches to decrease the false discovery rate of similarity searches." ; sc:featureList edam:operation_0269, edam:operation_0270, edam:operation_0346, edam:operation_0360, edam:operation_0368 ; sc:name "TMSOC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tmsoc.bii.a-star.edu.sg" ; biotools:primaryContact "TMSOC Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0203, edam:topic_0218 ; sc:citation , "pmcid:PMC5860583", "pubmed:28968638" ; sc:description "Text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS)." ; sc:featureList edam:operation_0306 ; sc:name "tmVar" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/tmvar/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3407 ; sc:citation , "pubmed:33180303" ; sc:description """Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis. Tn-Core is Matlab toolbox for generation of gene-centric, context-specific core metabolic network reconstructions through integration of experimental Tn-seq and RNA-seq datasets. The last named version is version 2.3. As the toolbox will continue to be updated, and to avoid countless version numbers, each change will no longer be associated with a new version number. Instead, changes will be made in Tn-Core Toolbox version stored in the directory entitled Most-Recent-Version. When using this version of the toolbox, the commit number can be used to document the version of the toolbox used. Transposon-sequencing (TnSeq) and genome-scale constraint-based metabolic modelling are highly complementary experimental and in silico approaches.""" ; sc:featureList edam:operation_1781, edam:operation_3283, edam:operation_3660 ; sc:license "MIT" ; sc:name "Tn-Core" ; sc:url "http://combo.dbe.unifi.it/tncore" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622, edam:topic_2640, edam:topic_3474 ; sc:citation , "pmcid:PMC8484710", "pubmed:34603338" ; sc:description "A Machine Learning Model to Predict the Triple Negative Breast Cancer Immune Subtype." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3463, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "TNBCIS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://immunotypes.shinyapps.io/TNBCIS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0749, edam:topic_0780, edam:topic_0798, edam:topic_3810 ; sc:citation ; sc:description "TnCentral is a prokaryotic transposable element database and web portal for transposon analysis." ; sc:featureList edam:operation_0427, edam:operation_2421, edam:operation_2422 ; sc:name "TnCentral" ; sc:url "https://tncentral.proteininformationresource.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC8482286", "pubmed:34630945" ; sc:description "tncRNA Toolkit is a pipeline, designed for convenient identification of tncRNAs. It identifies the tncRNAs using small RNA sequencing datasets. It also provides detailed information related to each tncRNA entry viz. tncRNA type, tRNA information, position on tRNA, strand, sequence, length, read count, RPM and modification site." ; sc:featureList edam:operation_0464, edam:operation_2929, edam:operation_3792 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tncRNAs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nipgr.ac.in/tncRNA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3305, edam:topic_3324 ; sc:citation , "pubmed:34255632" ; sc:description "Phylogeny-Based Inference of Disease Transmission Networks UsingWithin-Host Strain Diversity" ; sc:featureList edam:operation_0539, edam:operation_3478, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://compbio.engr.uconn.edu/software/TNet/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "A webserver for prediction of TNF inducing epitopes." ; sc:featureList edam:operation_2945 ; sc:name "tnfepitope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/tnfepitope/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0176, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:20867208" ; sc:description "An elastic network model whose degrees of freedom are the torsion angles of the protein backbone. Normal modes of the program displace backbone atoms including C β maintaining their covalent geometry." ; sc:featureList edam:operation_0249 ; sc:name "TNM" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://ub.cbm.uam.es/software/tnm.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3295, edam:topic_3360, edam:topic_3512 ; sc:citation , "pmcid:PMC7961455", "pubmed:33807717" ; sc:description """a web tool for the comparison of gene expression in normal, tumor and metastatic tissues. differential gene expression analysis in Tumor, Normal and Metastatic tissues.""" ; sc:featureList edam:operation_0315, edam:operation_3223, edam:operation_3435 ; sc:name "TNMplot" ; sc:url "http://www.tnmplot.com" ; biotools:primaryContact "Balázs Győrffy", "Áron Bartha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Online application for automated and user-supervised standardization of plant scientific names." ; sc:featureList edam:operation_2422 ; sc:name "Taxonomic Name Resolution Service (TNRS)" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://tnrs.iplantcollaborative.org/about.html#api" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data." ; sc:featureList edam:operation_0337 ; sc:license "AGPL-3.0" ; sc:name "TnT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TnT.html" ; biotools:primaryContact "Jialin Ma" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC10562672", "pubmed:37822562" ; sc:description "A novel method for identifying topologically associated domains based on graph auto-encoders and clustering." ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "TOAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ghaiyan/TOAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_0780, edam:topic_3308, edam:topic_3316 ; sc:citation , "pubmed:33070442" ; sc:description """A software package for automated functional annotation in non-model plant species. TOA (Taxonomy-oriented Annotation). TOA aims to establish workflows geared towards plant species that automate the extraction of information from genomic databases and the annotation of sequences. TOA uses the following databases: Dicots PLAZA 4.0, Monocots PLAZA 4.0, Gymno PLAZA 1.0, NCBI RefSeq Plant and NCBI Nucleotide Database (NT) and NCBI Non-Redundant Protein Sequence Database (NR). Although TOA was primarily designed to work with woody plant species, it can also be used in the analysis of experiments on any type of plant organism. Additionally, NCBI Gene, InterPro and Gene Ontology databases are also used to complete the information.""" ; sc:featureList edam:operation_0362, edam:operation_0524, edam:operation_2422, edam:operation_3431, edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "TOA" ; sc:url "https://github.com/GGFHF/TOA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0194, edam:topic_0780, edam:topic_3170, edam:topic_3308 ; sc:citation , , "pmcid:PMC7076552", "pmcid:PMC7106827", "pubmed:32228442", "pubmed:32265943" ; sc:description """Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. We introduce TOAST, open source software designed to help you use BUSCO to effectively harness public data, visualize missing data patterns, and assemble multiple sequence alignments. With over 30,000 species, it is an understatement to say that there is much to discover about the diversity of fishes.""" ; sc:featureList edam:operation_0292, edam:operation_0337, edam:operation_3196, edam:operation_3258, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "TOAST" ; sc:url "https://carolinafishes.github.io/software/TOAST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_3170, edam:topic_3305, edam:topic_3810 ; sc:citation , "pmcid:PMC7544112", "pubmed:33031371" ; sc:description "Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_3196 ; sc:name "ToBRFV" ; sc:url "https://nextstrain.nrcnvwa.nl/ToBRFV/20191231" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0632, edam:topic_0749, edam:topic_3512 ; sc:citation ; sc:description "Web tool for designing toehold switches." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "toehold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yiplab.cse.cuhk.edu.hk/toehold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0780, edam:topic_3125, edam:topic_3512, edam:topic_3895 ; sc:citation ; sc:description "Toeholder is a tool that can efficiently design toehold riboswitches for the detection of a target gene." ; sc:featureList edam:operation_0479, edam:operation_2428, edam:operation_2476 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Toeholder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/igem-ulaval/toeholder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3068, edam:topic_3520 ; sc:citation ; sc:description "Toffee – A highly efficient, lossless file format for DIA-MS | A library for fast access to Time of Flight SWATH-MS data — toffee latest documentation | Free document hosting provided by Read the Docs" ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "toffee" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/cmriprocan/toffee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3520 ; sc:description "TOFistAC toolbox is a collection of scripts for automated ionization state assignment and calibration of time-of-flight mass spectrometry data over the broad m/z range (1-100 kDa). The scripts include automated correction of acquisition time delay, assignment of ionization sates in corrected TOF, and quadratic calibration from TOF to M/Z domain based on known +1 standards and their auto-detected ionization states." ; sc:featureList edam:operation_3627, edam:operation_3755, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "TOFistAC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/26642-tofistac" ; biotools:primaryContact "Dariya Malyarenko" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3306, edam:topic_3382 ; sc:citation ; sc:description "This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF)." ; sc:featureList edam:operation_3351, edam:operation_3443, edam:operation_3694 ; sc:license "GPL-3.0" ; sc:name "tofsims" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tofsims.html" ; biotools:primaryContact "Lorenz Gerber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3385, edam:topic_3452 ; sc:citation , "pmcid:PMC9070706", "pubmed:35511025" ; sc:description "A fast, versatile and user-friendly image processing toolkit for computed tomography." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3443, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "tofu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ufo-kit/tofu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , "pmcid:PMC4640241", "pubmed:26552596" ; sc:description "Toolbox for generic NGS analyses." ; sc:featureList edam:operation_2403 ; sc:name "TOGGLE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/SouthGreenPlatform/TOGGLE" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2610 ; sc:name "Ensembl ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0736, edam:topic_3068, edam:topic_3277 ; sc:citation , "pubmed:35801937" ; sc:description "An exploratory ID converter to bridge biological datasets." ; sc:featureList edam:operation_0250, edam:operation_1777, edam:operation_3197, edam:operation_3282 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TogoID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://togoid.dbcls.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0602, edam:topic_2259, edam:topic_3489 ; sc:citation , "pmcid:PMC4086138", "pubmed:24829452" ; sc:description "TogoTable TogoTable is a web tool to add user-specified annotations from several biological databases to a user-uploaded table that contains identifiers of a biological database." ; sc:featureList edam:operation_0224, edam:operation_2409, edam:operation_2422, edam:operation_3282 ; sc:name "TogoTable" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://togotable.dbcls.jp/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3056, edam:topic_3673 ; sc:citation , "pmcid:PMC9744889", "pubmed:36509753" ; sc:description "A comprehensive Japanese genetic variation database." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3431, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "TogoVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://togovar.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0781 ; sc:description "Service which retrieves and searches data from the Genome Information Broker for Viruses database; a complete virus genome database." ; sc:featureList edam:operation_2422 ; sc:name "TogowsDdbjGibvService" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://togows.dbcls.jp/site/en/soap.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0611, edam:topic_1317 ; sc:description "This toolbox supports a wide range of functions for tomography." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "TOM" ; sc:operatingSystem "Linux", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.biochem.mpg.de/tom" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_3752 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pubmed:30501201" ; sc:description "Desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data." ; sc:featureList edam:operation_2430 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TomahaqCompanion" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.2" ; sc:url "https://github.com/CMRose3355/TomahaqCompanionProgram" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_2275 ; sc:citation "pubmed:19443448" ; sc:description "A web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_0478, edam:operation_0482, edam:operation_2487 ; sc:name "aTOME-2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://abcis.cbs.cnrs.fr/AT2/" ; biotools:primaryContact "@TOME team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2269, edam:topic_2640 ; sc:citation , "pmcid:PMC9754607", "pubmed:36469540" ; sc:description "A probabilistic tree-structured model for cancer progression." ; sc:featureList edam:operation_0547, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ToMExO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mrmohaghegh/tomexo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3452 ; sc:description "Tomobox is a collection of a few tools for tomographic reconstruction experiments." ; sc:isAccessibleForFree true ; sc:name "tomobox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28496-tomobox" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3382, edam:topic_3452 ; sc:citation , "pmcid:PMC1976622", "pubmed:17683598" ; sc:description "A plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ." ; sc:featureList edam:operation_3443 ; sc:name "TOMOJ" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.30" ; sc:url "https://sourceforge.net/projects/tomoj/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3452 ; sc:citation , "pmcid:PMC5567730", "pubmed:28552576" ; sc:description "Large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Also provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features." ; sc:featureList edam:operation_0503 ; sc:license "Unlicense" ; sc:name "TomoMiner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://web.cmb.usc.edu/people/alber/Software/tomominer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3393, edam:topic_3452, edam:topic_3500 ; sc:citation , "pmcid:PMC7324692", "pubmed:32268003" ; sc:description """Automated analysis program for MVCT quality assurance of helical tomotherapy. TomoMQA is written in MATLAB and contains three steps for analysis: (a) open the DICOM dataset folder generated via helical tomotherapy (i.e., TomoTherapy® and Radixact™), (b) call the baseline data for the consistency test and click the "Analysis" button (or click the "Analysis" button without the baseline data and export the results as the baseline data), and (c) print an analyzed report. The overall procedure for the QA analysis included in TomoMQA is referred from the TG-148 recommendation. Here, the tolerances for MVCT QA were implemented from TG-148 recommended values as default; however, it can be modified by a user manually""" ; sc:name "TomoMQA" ; sc:url "http://www.tomomqa.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3452 ; sc:citation ; sc:description "TomoPhantom is a software package used to generate 2D–4D analytical phantoms for CT image reconstruction algorithm benchmarks." ; sc:featureList edam:operation_3443 ; sc:license "Apache-2.0" ; sc:name "TomoPhantom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX_2018_19" ; biotools:primaryContact "Daniil Kazantsev" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3452, edam:topic_3473 ; sc:citation , "pmcid:PMC10250198", "pubmed:37188953" ; sc:description "Generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining." ; sc:featureList edam:operation_0337, edam:operation_3443, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "MPL-2.0" ; sc:name "TomoTwin" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/MPI-Dortmund/tomotwin-cryoet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0659, edam:topic_2269 ; sc:citation ; sc:description "Tool for statistical modeling of enrichment from RNA-seq data comprising enriched and unenriched control libraries." ; sc:featureList edam:operation_3501, edam:operation_3680 ; sc:name "ToNER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www4a.biotec.or.th/GI/tools/toner" ; biotools:primaryContact "Jittima Piriyapongsa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769 ; sc:description "CLI tool to verify workflow reproducibility." ; sc:license "Apache-2.0" ; sc:name "Tonkaz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.2.3" ; sc:url "https://github.com/sapporo-wes/tonkaz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3316, edam:topic_3474 ; sc:description "Workflows in Galaxy can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a system is developed to recommend tools which can facilitate further data analysis. The recommendation model is accessed by a Galaxy API to provide researchers with recommended tools in an interactive manner using multiple user interface (UI) integrations on the European Galaxy server. Good quality and highly-used tools are shown at the top of the recommended tools. The system developed is available as open-source software." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Tool recommender system in Galaxy using deeplearning" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/anuprulez/galaxy_tool_recommendation" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3424 ; sc:encodingFormat edam:format_3547 ; sc:name "Raw image" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3547, edam:format_3617 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3334, edam:topic_3382 ; sc:citation ; sc:description "A computational data processing pipeline for the analysis of neuronal population calcium dynamics from fluorescence imaging." ; sc:featureList edam:operation_2497, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Toolbox-Romano-et-al" ; sc:softwareHelp ; sc:url "https://github.com/zebrain-lab/Toolbox-Romano-et-al" ; biotools:primaryContact "Sebastián A. Romano" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """For life science research infrastructures, sensitive data generate an additional layer of complexity. Cross-domain categorisation and discovery of digital resources related to sensitive data presents major interoperability challenges. To support the FAIRification process, a toolbox demonstrator aiming at improving the discovery of digital objects related to sensitive data (e.g., regulations, guidelines, best practice, tools) has been developed. The toolbox is based upon a categorisation system developed and harmonised across a cluster of 6 life science research infrastructures (ECRIN, EATRIS, BBMRI, ERINHA, EMBRC, Euro-BioImaging). 3 different versions were built, tested by subsequent pilot studies, finally leading to a system with 7 main categories (sensitive data type, resource type, research field, data type, stage in data sharing life cycle, geographical scope, specific topics).""" ; sc:name "Toolbox for Sensitive Data Objects (TSDO)" ; sc:url "https://tsdo.ecrin-rms.org/" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_2332, edam:format_3750 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091 ; sc:citation ; sc:description "This tool aims to generate XML template for Galaxy or CWL from the description of tools from the bio.tools registry." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ToolDog" ; sc:operatingSystem "Linux" ; sc:provider "Bioinformatics and Biostatistics Hub", "Institut Pasteur" ; sc:softwareHelp ; sc:softwareVersion "0.3.5" ; sc:url "https://github.com/bio-tools/ToolDog" ; biotools:primaryContact "Hervé Ménager", "Kenzo-Hugo Hillion" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3303, edam:topic_3372 ; sc:citation ; sc:description "ToolJig is an web application that enables researchers to create Common Workflow Language (CWL) tool and workflow descriptions in an interactive manner. 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This is a very simple way to create locus-specific fusion primers that can be used in conjunction with iTru primers of Glenn et al. 2016 [https://www.biorxiv.org/content/early/2016/06/15/049114] to create dual or quadruple indexed amplicons ready for sequencing on Illumina instruments. You need to have Google Chrome or Safari browser only.""" ; sc:featureList edam:operation_0308, edam:operation_3192, edam:operation_3237 ; sc:name "tools-taggi" ; sc:url "http://baddna.uga.edu/tools-taggi.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0769, edam:topic_2269 ; sc:citation , "pmcid:PMC7924506", "pubmed:33816818" ; sc:description "Tools4MSP is a python-based Free and Open Source Software (FOSS) for geospatial analysis in support of Maritime Spatial Planning (MSP) and marine environmental management. Tools4MSP implements models for Cumulative Effects Assessment (CEA), Maritime Use Conflict (MUC) Analysis and Marine Ecosystem Services Threat (MES-Threat) analysis. The package can be used as stand-alone library or as integrated GeoNode Plugin providing additional functionalities to geospatial CMS and enhancing usability through a graphical user interface (GUI)." ; sc:featureList edam:operation_3436, edam:operation_3891, edam:operation_3946 ; sc:license "GPL-3.0" ; sc:name "Tools4MSP" ; sc:url "http://data.tools4msp.eu" ; biotools:primaryContact "Stefano Menegon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308, edam:topic_3382, edam:topic_3934 ; sc:citation , "pmcid:PMC7439807", "pubmed:32123397" ; sc:description """TooManyCells identifies and visualizes relationships of single-cell clades. An R wrapper for using 'TooManyCells', a command line program for clustering, visualizing, and quantifying cell clade relationships. See for more details. .""" ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3797, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "TooManyCells" ; sc:url "https://github.com/faryabib/too-many-cells" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_3468, edam:format_3475, edam:format_3620, edam:format_3752 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0749, edam:topic_3518 ; sc:citation , "pmcid:PMC9665867", "pubmed:36179084" ; sc:description "A method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics." ; sc:featureList edam:operation_0292, edam:operation_2575, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Top-Down Crawl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://topdowncrawl.usc.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_3337, edam:topic_3577, edam:topic_3673 ; sc:citation , "pmcid:PMC9247832", "pubmed:35504290" ; sc:description "A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data." ; sc:featureList edam:operation_0487, edam:operation_0488, edam:operation_3196, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:name "TOP-LD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://topld.genetics.unc.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3383, edam:topic_3385 ; sc:citation "pubmed:19607690" ; sc:description "This program implements an integer linear programming approach for topologically aligning two segmented images as the linking step in cell tracking." ; sc:featureList edam:operation_3443 ; sc:name "topaln" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinf.rub.de/software/topaln.html.en" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013, edam:format_2058 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2013, edam:format_2058 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0951 ; sc:encodingFormat edam:format_2330 ; sc:name "Statistical estimate score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2330 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC4625615", "pubmed:26514335" ; sc:description "Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a single pathway." ; sc:featureList edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "ToPASeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/ToPASeq.html" ; biotools:primaryContact "Ivana Ihnatova" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Consensus prediction of membrane protein topology." ; sc:featureList edam:operation_0270 ; sc:name "TOPCONS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://topcons.cbr.su.se/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2789 ; sc:name "Protein ID (TopDB)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2789 ; sc:name "Protein ID (TopDB)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2789 ; sc:name "Protein ID (TopDB)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2789 ; sc:name "Protein ID (TopDB)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2332 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0820 ; sc:citation ; sc:description "Transmembrane protein datasets containing experimentally derived topology information." ; sc:featureList edam:operation_0224 ; sc:name "Topology Data Bank of Transmembrane Proteins" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://toPDB.enzim.hu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "This package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "topdownr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/topdownr.html" ; biotools:primaryContact "Sebastian Gibb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0736, edam:topic_0821, edam:topic_2275, edam:topic_3534 ; sc:citation , "pmcid:PMC10023222", "pubmed:36883717" ; sc:description "Framework and database for structural coverage of the functional enzyme space. Created with TopModel and linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database." ; sc:featureList edam:operation_0321, edam:operation_0477, edam:operation_2480, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "TopEnzyme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cpclab.uni-duesseldorf.de/topenzyme/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0634, edam:topic_3473, edam:topic_3474 ; sc:citation , "pmcid:PMC9369716", "pubmed:35951425" ; sc:description "TopEx is a natural language processing application developed to facilitate the exploration of topics and key words in a set of texts through a user interface that requires no programming or natural language processing knowledge, thus enhancing the ability of nontechnical researchers to explore and analyze textual data." ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "TopEx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://topex.cctr.vcu.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0160, edam:topic_3474, edam:topic_3520 ; sc:citation , "pmcid:PMC10233584", "pubmed:37196155" ; sc:description "Proteoform feature detection tool for top-down proteomics." ; sc:featureList edam:operation_3092, edam:operation_3215, edam:operation_3629, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TopFD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.toppic.org/software/toppic/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121, edam:topic_0601, edam:topic_0736, edam:topic_3534 ; sc:citation "pubmed:22102574" ; sc:description "First public knowledgebase for protein termini and protease processing." ; sc:featureList edam:operation_0417, edam:operation_2409, edam:operation_2414, edam:operation_2436 ; sc:name "TopFIND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://clipserve.clip.ubc.ca/topfind" ; biotools:primaryContact "TopFIND team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0622, edam:topic_2269, edam:topic_3473 ; sc:citation ; sc:description "Package that provides tools for enrichment analysis for Gene Ontology (GO) terms. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied." ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3672 ; sc:license "GPL-3.0" ; sc:name "topGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.30.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/topGO.html" ; biotools:primaryContact "Adrian Alexa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0196, edam:topic_0199, edam:topic_3168, edam:topic_3943 ; sc:citation , "pmcid:PMC8687460", "pubmed:34931186" ; sc:description "Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity." ; sc:featureList edam:operation_0323, edam:operation_0487, edam:operation_3227, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TopHap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SayakaMiura/TopHap" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2749 ; sc:name "Genome identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2573 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3170, edam:topic_3325 ; sc:citation , , "pubmed:19289445" ; sc:description "Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program." ; sc:featureList edam:operation_0433, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:name "TopHat" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "2.1.1" ; sc:url "http://ccb.jhu.edu/software/tophat/index.shtml" ; biotools:primaryContact "Daehwan Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:21835007" ; sc:description "A tool that enables fusion genes detection and read alignment across fusion points." ; sc:featureList edam:operation_2451, edam:operation_3198, edam:operation_3228, edam:operation_3680 ; sc:name "TopHat-Fusion" ; sc:softwareHelp ; sc:url "http://ccb.jhu.edu/software/tophat/fusion_index.shtml" ; biotools:primaryContact "Daehwan Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "A post-processor for TopHat/TopHat2 data that corrects several issues in the original data." ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "TopHat-Recondition" ; sc:url "https://github.com/cbrueffer/tophat-recondition" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1932 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation , , , ; sc:contributor "Cole Trapnell", "Daehwan Kim", "Geo Pertea", "Harold Pimentel", "Lior Pachter", "Ryan Kelley", "Steven Salzberg" ; sc:description "Gapped-read mapper for RNA-seq data." ; sc:featureList edam:operation_3198 ; sc:name "tophat2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.0.10" ; sc:url "http://ccb.jhu.edu/software/tophat/index.shtml" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0623, edam:topic_0769, edam:topic_3293, edam:topic_3944 ; sc:citation , "pubmed:36565302" ; sc:description "Pruning the manual labor from ancestral sequence reconstruction." ; sc:featureList edam:operation_0544, edam:operation_0553, edam:operation_3478, edam:operation_3745, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "topiary" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/harmslab/topiary" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC5809007", "pubmed:29432422" ; sc:description "TopicalPdb: Database of Topically Administered Peptide." ; sc:featureList edam:operation_2945 ; sc:name "topicalpdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/topicalpdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0749, edam:topic_3173, edam:topic_3656 ; sc:citation , "pmcid:PMC7355251", "pubmed:32657410" ; sc:description """a framework for measuring transcriptional regulatory network change. Topicnet uses a method called TopicNet that applies latent Dirichlet allocation to extract functional topics for a collection of genes regulated by a given TF""" ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3196 ; sc:name "TopicNet" ; sc:url "https://github.com/gersteinlab/topicnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2258, edam:topic_3382 ; sc:citation ; sc:description "Topino is a graphical tool for quantitative assessment of molecular stream separations. In molecular-stream separation (MSS), a stream of a multi-component mixture is separated into multiple streams of individual components. Quantitative evaluation of MSS data has been a bottleneck in MSS for decades as there was no conventional way to present the data in a reproducible and uniform fashion. The roots of the problem were in the multi-dimensional nature of MSS data; even in the ideal case of steady-state separation, the data is three-dimensional: intensity and two spatial coordinates." ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:license "BSD-3-Clause" ; sc:name "Topino" ; sc:softwareHelp ; sc:url "https://github.com/Schallaven/topino" ; biotools:primaryContact "Sergey N. Krylov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0082, edam:topic_0121, edam:topic_0623, edam:topic_2814 ; sc:citation "pubmed:18174182" ; sc:description "Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins." ; sc:featureList edam:operation_0295, edam:operation_0510, edam:operation_2480, edam:operation_2488 ; sc:name "TopMatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://topmatch.services.came.sbg.ac.at/" ; biotools:primaryContact "TopMatch Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0209, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:31967823" ; sc:description """Template-Based Protein Structure Prediction at Low Sequence Identity Using Top-Down Consensus and Deep Neural Networks. Knowledge of protein structures is essential to understand proteins' functions, evolution, dynamics, stabilities, and interactions and for data-driven protein- or drug design. Yet, experimental structure determination rates are far exceeded by that of next-generation sequencing, resulting in less than 1 1000th of proteins having an experimentally known 3D structure. Computational structure prediction seeks to alleviate this problem, and the Critical Assessment of Protein Structure Prediction (CASP) has shown the value of consensus and meta-methods that utilize complementary algorithms. However, traditionally, such methods employ majority voting during template selection and model averaging during refinement, which can drive the model away from the native fold if it is underrepresented in the ensemble""" ; sc:featureList edam:operation_0303, edam:operation_0320, edam:operation_0474, edam:operation_2476 ; sc:name "TopModel" ; sc:url "https://cpclab.uni-duesseldorf.de/topsuite/standalone_download.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0820 ; sc:description "It is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired." ; sc:featureList edam:operation_2479 ; sc:name "TOPO2" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.sacs.ucsf.edu/TOPO2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3303, edam:topic_3386, edam:topic_3489, edam:topic_3500 ; sc:citation , "pmcid:PMC7673335", "pubmed:33206961" ; sc:description """a novel multifunctional management system for laboratory animal colonies. TopoDB requires Ruby version >= 2.5.2, Ruby on Rails version >= 5.2.0, and bundler version 2.0 . We recommend using rbenv to install and manage Ruby gems. Log in as the admin user that was created as part of the sample data set: email: admin@topodb.topo, password: admin123 . Once logged in as the administrator it is strongly recommended that you create new users to handle day-to-day activities in the application and that you change the Administrator account password (failure to do so can put your data at risk). Both of these activities can be done either directly in the users database table, or through the included rails admin feature, available in the main navigation bar.""" ; sc:featureList edam:operation_3096, edam:operation_3196 ; sc:license "MIT" ; sc:name "TopoDB" ; sc:url "https://github.com/UCSF-MS-DCC/TopoDB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2259, edam:topic_2269 ; sc:citation , "pmcid:PMC6990465", "pubmed:31996136" ; sc:description """a MATLAB package for mechanistic model identification in systems biology. Topological filtering method: model space exploration for ODE models based on approximate parameter space exploration.""" ; sc:featureList edam:operation_2426, edam:operation_3695, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "TopoFilter" ; sc:url "https://gitlab.com/csb.ethz/TopoFilter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3068, edam:topic_3360, edam:topic_3379, edam:topic_3577 ; sc:citation ; sc:description """Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology. TOPOGRAPH precision oncology compendium. An oncologist-led effort in cataloguing literature evidence for streamlining the recommendation of drug treatments in precision cancer medicine, based on diagnostic molecular profiling. TOPOGRAPH is intended to be a resource to help oncologists find evidence for decision-making in patients with advanced cancers based on contemporary genomic profiling results and other assays.""" ; sc:featureList edam:operation_2422 ; sc:name "TOPOGRAPH" ; sc:url "https://topograph.info/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0602, edam:topic_2229 ; sc:citation "pubmed:20335277" ; sc:contributor "Natalio Krasnogor" ; sc:description "Web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, can be computed and compared with those of known cellular pathways and processes (Gene Ontology, BioCarta, KEGG, among others)." ; sc:featureList edam:operation_0276, edam:operation_0277, edam:operation_1781, edam:operation_2497, edam:operation_3562 ; sc:name "TopoGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.topogsa.net" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation ; sc:description "Compute topological distances between atoms on the surface of proteins and validate structural models from cross-linking experimental data." ; sc:featureList edam:operation_3351 ; sc:license "GPL-3.0" ; sc:name "TopoLink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://leandro.iqm.unicamp.br/topolink/home.shtml" ; biotools:primaryContact "Leandro Martinez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085 ; sc:citation , "pmcid:PMC2945950", "pubmed:20809931" ; sc:description "Novel approach to perform pathway analysis using gene expression data. Given the structure of a graph (a pathway) it introduces two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques)." ; sc:featureList edam:operation_2497 ; sc:license "AGPL-3.0" ; sc:name "TopologyGSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.4.4" ; sc:url "http://cran.r-project.org/web/packages/topologyGSA/index.html" ; biotools:primaryContact "Chiara Romualdi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0736, edam:topic_3306 ; sc:citation , "pubmed:32935829" ; sc:description "Topoly is a Python package that collects programs useful for polymer topology analysis." ; sc:featureList edam:operation_0278, edam:operation_0570, edam:operation_2929 ; sc:name "Topoly" ; sc:softwareHelp ; sc:url "https://topoly.cent.uw.edu.pl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3047, edam:topic_3382 ; sc:citation ; sc:description """An AFM image analysis program to batch process data and obtain statistics from images. Image progessing is performed using the 'pygwytracing' script. The algorithm searches recursively for files within a user-defined directory. This search also excludes any files of the format ‘_cs’ which are cropped files exported by the Nanoscope Analysis software. AFM images are loaded using gwyddion functions and topography data is automatically selected using the choosechannels function. The pixel size and dimensions of each image are determined using the imagedetails function, which allows all inputs to be specified in real, i.e. nanometre values, in place of pixel values. This is especially important for datasets with changing resolution.""" ; sc:featureList edam:operation_0310, edam:operation_3096, edam:operation_3443 ; sc:license "LGPL-3.0" ; sc:name "TopoStats" ; sc:url "https://github.com/afmstats/TopoStats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3512, edam:topic_3577, edam:topic_3697 ; sc:citation , "pmcid:PMC9035726", "pubmed:35479398" ; sc:description "Tumor online prognostic analysis platform for prognostic feature selection and clinical patient subgroup selection." ; sc:featureList edam:operation_1781, edam:operation_3223, edam:operation_3503 ; sc:isAccessibleForFree true ; sc:name "ToPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.biostatistics.online/topp/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0602, edam:topic_0625, edam:topic_0659, edam:topic_0749 ; sc:citation "pubmed:20484371" ; sc:description "ToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-associated mammalian phenotypes, promoter cis-elements, miR binding sites, etc. that are differentially represented in the gene lists can be clustered or transformed into high dimensional Cytoscape or Gephi -compatible networks." ; sc:featureList edam:operation_1781, edam:operation_2436, edam:operation_3766 ; sc:name "ToppCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://toppcluster.cchmc.org" ; biotools:primaryContact "Anil Jegga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3422 ; sc:citation "pubmed:19465376" ; sc:description "ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome." ; sc:featureList edam:operation_2436, edam:operation_2495, edam:operation_3223, edam:operation_3463, edam:operation_3672 ; sc:name "ToppGene Suite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://toppgene.cchmc.org" ; biotools:primaryContact "Anil Jegga" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3245 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_2331 ; sc:name "Protein sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_2330 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation "pubmed:22027200", "pubmed:22543365", "pubmed:24564718" ; sc:description "Proteoform identification/characterizaion at the proteome level using database search." ; sc:featureList edam:operation_3631, edam:operation_3645, edam:operation_3646, edam:operation_3648, edam:operation_3695, edam:operation_3755, edam:operation_3767 ; sc:license "Apache-2.0" ; sc:name "TopPIC" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://proteomics.informatics.iupui.edu/software/toppic/" ; biotools:primaryContact "Xiaowen Liu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation , "pubmed:36631391" ; sc:description "A companion R package for top-down proteomics data analysis." ; sc:featureList edam:operation_0417, edam:operation_3634, edam:operation_3635 ; sc:isAccessibleForFree true ; sc:name "TopPICR" ; sc:url "https://github.com/PNNL-Comp-Mass-Spec/TopPICR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0659, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC4086116", "pubmed:24829448" ; sc:description "ToppMiR web server ranks microRNAs and their mRNA targets based on biological functions and context." ; sc:featureList edam:operation_0314, edam:operation_0463, edam:operation_2436, edam:operation_3224 ; sc:name "ToppMiR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://toppmir.cchmc.org" ; biotools:primaryContact "Anil Jegga" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:name "Sequence accession (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1238 ; sc:name "Proteolytic digest" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "Online Protein Processing Resource" ; sc:featureList edam:operation_2479 ; sc:name "TOPPR" ; sc:provider "ugent.be" ; sc:softwareVersion "1" ; sc:url "http://iomics.ugent.be/toppr/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736, edam:topic_0820, edam:topic_3474, edam:topic_3542 ; sc:citation , "pubmed:34663069" ; sc:description "TopProperty is a meta-predictor that combines outputs of 27 primary predictors using two ensembles of deep neural networks to predict secondary structure, solvent accessibility, transmembrane topology and membrane exposure for both transmembrane and globular proteins. TopProperty is trained on datasets without bias towards a high number of sequence homologs and the predictions are significantly better than all primary predictors on all quality metrics. TopProperty eliminates the need for protein type- or property-tailored tools, especifically for transmembrane proteins." ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_0408, edam:operation_0477, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TopProperty" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cpclab.uni-duesseldorf.de/topsuite/topproperty.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2814 ; sc:citation ; sc:description "They are source code of TPOS dadabase (an enhanced database of protein structural topology)." ; sc:featureList edam:operation_2479 ; sc:name "TOPS" ; sc:operatingSystem "Linux" ; sc:url "http://www.bioinformatics.leeds.ac.uk/TOPS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0122, edam:topic_1317, edam:topic_2814 ; sc:citation "pubmed:20961957" ; sc:description "Platform for exploring and annotating structures determined by structural genomics efforts. The platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich the database’s content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages." ; sc:featureList edam:operation_0224, edam:operation_0474, edam:operation_2406, edam:operation_3501 ; sc:name "TOPSAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.topsan.org" ; biotools:primaryContact "Adam Godzik" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units." ; sc:featureList edam:operation_2480 ; sc:name "TopSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://topsearch.services.came.sbg.ac.at/" ; biotools:primaryContact "TopSearch Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_2814, edam:topic_3382 ; sc:citation "pubmed:8982602" ; sc:description "A software which has been developed for the purpose of analysing 2-dimensional electrophoretic imaging (2DE) of gels. It enables the user to obtain qualitative and quantitative gel data from gel images available in a BMP format or obtained using a scanner." ; sc:featureList edam:operation_2406, edam:operation_3431, edam:operation_3443 ; sc:name "TopSpot" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://web.mpiib-berlin.mpg.de/pdbs/2d-page/downloads.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite", "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0593, edam:topic_0611, edam:topic_2828, edam:topic_3474 ; sc:citation , "pubmed:33464891" ; sc:description "A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0474, edam:operation_4009 ; sc:name "TopSuite" ; sc:url "https://cpclab.uni-duesseldorf.de/topsuite/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0621, edam:topic_3957 ; sc:citation , "pmcid:PMC9235477", "pubmed:35758793" ; sc:description "Integrating a global view into sequence-based PPI prediction." ; sc:featureList edam:operation_2464, edam:operation_2492, edam:operation_3094, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Topsy-Turvy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://topsyturvy.csail.mit.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_0602, edam:topic_3318, edam:topic_3474 ; sc:citation ; sc:description "TorchANI is a pytorch implementation of ANI. 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Networks of up to 25 proteins may be input." ; sc:featureList edam:operation_0224, edam:operation_0276, edam:operation_0277, edam:operation_3083, edam:operation_3439 ; sc:name "Torque" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.tau.ac.il/~bnet/torque.html" ; biotools:primaryContact "Sharon Bruckner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621 ; sc:citation ; sc:description """Tool for Retrieving Queried Eubacteria, Metadata and Dereplicating Assemblies. TQMD is a tool which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods ( k -mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). 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Application to the twenty proteinogenic amino acids. TorsiFlex is an user-friendly program written in Python 3. It was designed to seek the conformers of a given molecule by using a combined low-level/high-level (LL/HL) methodology." ; sc:featureList edam:operation_0479, edam:operation_0480, edam:operation_1844 ; sc:name "TorsiFlex" ; sc:url "https://github.com/cathedralpkg/TorsiFlex" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3047, edam:topic_3474, edam:topic_3892 ; sc:citation ; sc:description "A Deep Neural Network to Rapidly Predict Small Molecule Torsion Energy Profiles with the Accuracy of Quantum Mechanics." ; sc:featureList edam:operation_0249, edam:operation_0337, edam:operation_3454, edam:operation_3927, edam:operation_3938 ; sc:name "TorsionNet" ; sc:url "https://github.com/PfizerRD/TorsionNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3304, edam:topic_3520 ; sc:citation ; sc:description "Toolkit for Oscillatory Real-time Tracking and Estimation (TORTE)." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TORTE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tne-lab/TORTE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0166, edam:topic_2229, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , , "pmcid:PMC7954949", "pubmed:33589839" ; sc:description "A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3435, edam:operation_3630, edam:operation_3935 ; sc:name "Total Variational Inference" ; sc:url "https://scvi-tools.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3316 ; sc:author "Perforce Software, Inc." ; sc:description "TotalView is a debugger for High Performance Computing applications." ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "TotalView" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , , ; sc:url "https://totalview.io/" ; biotools:primaryContact "Perforce Software, Inc." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053 ; sc:citation , "pmcid:PMC6020218", "pubmed:29940847" ; sc:description "Variant calling pipeline optimization." ; sc:featureList edam:operation_3762 ; sc:isAccessibleForFree true ; sc:name "ToTem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://totem.software/login/?backlink=iplpf&_fid=t22e" ; biotools:primaryContact "Nikola Tom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10474950", "pubmed:37624916" ; sc:description """Cell-connectivity-guided trajectory inference from single-cell data. Totem package is a tool designed to facilitate inference of tree-shaped trajectories from single-cell data. These include linear, bifurcating, multifurcating, and other tree-shaped trajectories. Totem uses Slingshot to find linear curves through the lineages of the tree. ||| NAME (Totem) SIMILAR TO (PUB. DIFFERENT) bio.tools/totem (ToTem)""" ; sc:featureList edam:operation_2939, edam:operation_3890, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Totem" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/elolab/Totem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3407 ; sc:citation , "pmcid:PMC8905348", "pubmed:35281848" ; sc:description "Identifying Active Reactions During the Transient State for Metabolic Perturbations." ; sc:featureList edam:operation_3660, edam:operation_3799, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Totoro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.inria.fr/erable/totoro" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_0749 ; sc:citation "pubmed:12626717", "pubmed:15980497" ; sc:description "Regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms." ; sc:featureList edam:operation_0239, edam:operation_0253, edam:operation_0451, edam:operation_0452, edam:operation_2404 ; sc:name "TOUCAN 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php" ; biotools:primaryContact "Aerts S." . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0769 ; sc:description "Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software packages it wraps. Tourmaline manages commands, inputs, and outputs using the Snakemake workflow management system." ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Tourmaline" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/aomlomics/tourmaline" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2840, edam:topic_3360, edam:topic_3474, edam:topic_3500, edam:topic_3679 ; sc:citation , "pubmed:34971401" ; sc:description "An Artificial Intelligence Approach Alternative to Animal Studies." ; sc:featureList edam:operation_0314, edam:operation_0315, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Tox-GAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/XC-NCTR/Tox-GAN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0621, edam:topic_2840, edam:topic_3343 ; sc:citation , "pmcid:PMC7319561", "pubmed:32491175" ; sc:description "Tox21BodyMap provides a visualization of mapping 971 Tox21 ToxCast assay targets to regions of the human body, and allows users to identify target tissues where a specific chemical is more likely to produce effects." ; sc:featureList edam:operation_2429, edam:operation_3463, edam:operation_3925 ; sc:name "Tox21BodyMap" ; sc:url "https://sandbox.ntp.niehs.nih.gov/bodymap/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2258, edam:topic_2840, edam:topic_3343, edam:topic_3489 ; sc:citation , "pmcid:PMC10333489", "pubmed:37441091" ; sc:description "Shiny application for toxicity functional annotation analysis." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "Tox21Enricher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://hurlab.med.und.edu/Tox21Enricher/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:33866357" ; sc:description "ToxCodAn is a computational tool designed to detect and annotate toxin genes in transcriptome assembly." ; sc:featureList edam:operation_0524, edam:operation_3192, edam:operation_3216, edam:operation_3258, edam:operation_3891 ; sc:license "GPL-3.0" ; sc:name "ToxCodAn" ; sc:url "https://github.com/pedronachtigall/ToxCodAn" ; biotools:primaryContact "Pedro G Nachtigall" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_2306 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:description "ToxCodAn-Genome is a computational tool designed to annotate toxin genes in genomes of venomous lineages." ; sc:featureList edam:operation_0362 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ToxCodAn-Genome" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/pedronachtigall/ToxCodAn-Genome" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1463 ; sc:encodingFormat edam:format_1196, edam:format_3814 ; sc:name "Small molecule structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3047, edam:topic_3336, edam:topic_3379, edam:topic_3474 ; sc:citation , "pubmed:35998885" ; sc:description "Comprehensive prediction of small molecule toxicity profiles." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "toxCSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biosig.lab.uq.edu.au/toxcsm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_0736, edam:topic_3474, edam:topic_3500 ; sc:citation , "pubmed:32692832" ; sc:description "Deep learning using primary structure and domain embeddings for assessing protein toxicity." ; sc:featureList edam:operation_0303, edam:operation_1777, edam:operation_3925 ; sc:license "Apache-2.0" ; sc:name "ToxDL" ; sc:url "http://www.csbio.sjtu.edu.cn/bioinf/ToxDL/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0121, edam:topic_0154, edam:topic_0634, edam:topic_3474 ; sc:citation , "pubmed:34999757" ; sc:description "A generic webserver for peptide toxicity prediction" ; sc:featureList edam:operation_0267, edam:operation_0278, edam:operation_0303 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ToxIBTL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://server.wei-group.net/ToxIBTL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0203, edam:topic_0602, edam:topic_2840, edam:topic_3407 ; sc:citation , "pmcid:PMC7319553", "pubmed:32421831" ; sc:description """ToxicoDB is a database of curated toxicogenomics datasets that provides convenient data summar and visualization to mine these complex data. A statistical analysis package for use exploring the relationship between toxicity and gene expression in specific cell types. The package includes a specialized object, the ToxicoSet, which allows unified storage of all data related to a specific toxico-genomic study. Methods accepting this object are inlcuded for summarize results and annotaiton, conduct various analyses as well as to visualize the results thereof.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2495 ; sc:name "ToxicoDB" ; sc:softwareHelp ; sc:url "http://toxicodb.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2269, edam:topic_2840, edam:topic_3336 ; sc:citation , "pmcid:PMC9997717", "pubmed:36909352" ; sc:description "ToxicR is an R package that utilizes the core functionality of the US EPA’s Benchmark Dose Software and the NTP’s BMDexpress. It was developed in unison with researchers from the National Institute of Environmental Health. ToxicR is fully interactive and can be used to create custom analysis pipelines within the R programming environment." ; sc:featureList edam:operation_3928 ; sc:isAccessibleForFree true ; sc:name "ToxicR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.ncbi.nlm.nih.gov/pubmed/?term=36909352" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_2258, edam:topic_2259, edam:topic_3172 ; sc:citation , "pubmed:33360695" ; sc:description """A data-driven integrative platform for computational prediction of toxin biotransformation with a case study. A Data-driven Integrative Platform for Computational Prediction of Toxin Biotransformation. ToxinDB is offered to the public as a freely available resource. The service is completely free and just requires a quick registration. Login/Register. Toxins can be retrieved by the following fields: common name, CAS number, InChI, InChI key. In recent years, biogenic toxins have received increasing attention because of their high contamination levels in feeds, foods, and environments. Example: Common name: Aflatoxin : CAS number: 65195-55-3: InChI key: JLWQFKMKUKQXMW-IYSWYEEDSA-N.""" ; sc:featureList edam:operation_2422 ; sc:name "ToxinDB" ; sc:url "http://www.rxnfinder.org/toxindb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:25555724" ; sc:description "ToxinPred is an in silico method, which is developed to predict and design toxic/non-toxic peptides. This server is specifically developed for predicting toxicity of peptides or for designing peptides with desired toxicity." ; sc:featureList edam:operation_2945 ; sc:name "toxinpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/toxinpred/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0160, edam:topic_2840, edam:topic_3379, edam:topic_3474 ; sc:citation , "pubmed:35595541" ; sc:description "A webserver for designing and predicting toxic and non-toxic proteins." ; sc:featureList edam:operation_0239, edam:operation_3092, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ToxinPred2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://webs.iiitd.edu.in/raghava/toxinpred2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:description "ToxiPred: A server for prediction of aqueous toxicity of small chemical molecules in T. pyriformis" ; sc:featureList edam:operation_2945 ; sc:name "toxipred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/toxipred/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma." ; sc:featureList edam:operation_0224 ; sc:name "Toxoplasma genome resources (ToxoDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://toxodb.org/toxo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2840, edam:topic_3170, edam:topic_3300 ; sc:citation , "pmcid:PMC7900624", "pubmed:33633572" ; sc:description """A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. ToxPanel is a web-based platform to calculate activation scores for liver and kidney injury gene sets for genome-wide analysis by using aggregated gene set fold-change values. Users can either apply our predefined gene sets to identify liver and kidney injury phenotypes or upload their own gene sets.""" ; sc:featureList edam:operation_2436, edam:operation_3435, edam:operation_3436 ; sc:name "ToxPanel" ; sc:url "https://toxpanel.bhsai.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_2840 ; sc:citation ; sc:description "The ToxPi framework provides a method for transparently integrating and visualizing data across disparate information domains and is often used to determine risk values for the data being analyzed." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ToxPiGIS Toolkit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Jonathon-Fleming/ToxPi-GIS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1001 ; sc:name "Chemical name (synonymous)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0610, edam:topic_2840, edam:topic_3336, edam:topic_3375 ; sc:citation , "pmcid:PMC9825425", "pubmed:36400569" ; sc:description "A comprehensive database of toxicological data and benchmarks." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "TOXRIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://toxric.bioinforai.tech/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_2840 ; sc:citation ; sc:description "The TOXicogenomic sIgNature (TOXsIgN) is a cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data. TOXsIgN thus allows users to upload lists of genes positively (overexpressed for transcriptomic assays) affected and negatively (underexpressed) affected from distinct –omics experiments (e.g., transcriptomics, proteomics, or epigenomics). It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable cross-species and cross-technology signature comparisons or enrichment analyses. TOXsIgN is thus intended to serve as a warehouse for toxicogenomics and predictive toxicology tools simultaneously based on and able to analyze the overall set of signatures deposited by the community." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "TOXsIgN" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://toxsign.genouest.org" ; biotools:primaryContact "Chalmel Frédéric" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2301 ; sc:name "SMILES string" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0634, edam:topic_2840, edam:topic_3172, edam:topic_3297 ; sc:citation , "pubmed:35900148" ; sc:description "ToxSTAR is a platform to predict human toxicity caused by drugs and chemicals through integration of biotechnology (BT) and information technology (IT)." ; sc:featureList edam:operation_2423 ; sc:isAccessibleForFree true ; sc:name "ToxSTAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://toxstar.kitox.re.kr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_3063, edam:topic_3068, edam:topic_3474 ; sc:citation ; sc:description """Deep Language Model-Based Representation Learning for Venom Peptide Classification. Venom is a mixture of substances produced by a venomous organism aiming at preying, defending, or intraspecific competing resulting in certain unwanted conditions for the target organism.""" ; sc:name "ToxVec" ; sc:url "https://github.com/meahmadi/ToxVec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0202, edam:topic_3172 ; sc:citation ; sc:description """an Integrated Software Package for the Analysis of 1D and 2D Thermal Profiling Data. Thermal Profiling Meltome Analysis Program.""" ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "TP-MAP" ; sc:url "https://www.gitlab.com/ChemBioHub/tpmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3303, edam:topic_3315, edam:topic_3360 ; sc:citation , "pubmed:36088546" ; sc:description "A web tool for tipping-point detection based on dynamic network biomarker." ; sc:featureList edam:operation_0337, edam:operation_3223, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "TPD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.rpcomputationalbiology.cn/TPD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Tree Pattern Matching Suite. It can manage phylogenetic tree collections, root them, query some peculiar pattern, and detect horizontal transfer." ; sc:featureList edam:operation_0224 ; sc:name "TPMS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://pbil.univ-lyon1.fr/software/tpms/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3336, edam:topic_3520 ; sc:author "Nils Kurzawa" ; sc:description "Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR)." ; sc:featureList edam:operation_2406 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "TPP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "3.4.2" ; sc:url "https://bioconductor.org/packages/TPP/" ; biotools:primaryContact "Dorothee Childs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0082, edam:topic_0154, edam:topic_3373, edam:topic_3474 ; sc:citation , "pubmed:35389426" ; sc:description "Therapeutic peptides prediction by adaptive multi-view tensor learning model." ; sc:featureList edam:operation_0475, edam:operation_3092, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "TPpred-ATMV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cokeyk/TPpred-ATMV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269 ; sc:citation ; sc:description "A tool for prior elicitation and obtaining posterior distributions of true disease prevalence." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tPRiors" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.21203/RS.3.RS-1019762/V1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0601 ; sc:citation , "pmcid:PMC6295338", "pubmed:30257219" ; sc:description "TPS is a tool for combining time series global phosphoproteomic data and protein-protein interaction networks to reconstruct the vast signaling pathways that control post-translational modifications." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TPS" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/koksal/tps" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0203, edam:topic_3474 ; sc:citation , "pubmed:36719781" ; sc:description "Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm." ; sc:featureList edam:operation_3092, edam:operation_3900, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:name "TPSO-DBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://jun-csbio.github.io/TPSO-DBP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_2640, edam:topic_3336, edam:topic_3375 ; sc:citation , "pubmed:34450618" ; sc:description "An interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs." ; sc:featureList edam:operation_0224, edam:operation_2940, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TPWshiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://brpnci.shinyapps.io/TPWshiny/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269 ; sc:description "tpWY (t-statistics, p-values, and Westfall and Young step-down method) consists of software to implement the methods illustrated by Dudoit et al. (2000) to compute unadjusted and adjusted p-values for the t-statistics derived from a collection of two-channel microarray experiments" ; sc:featureList edam:operation_2495 ; sc:name "tpWY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbil.upenn.edu/tpWY/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Computation of the triplet- and Quartet-distance between evolutionary trees." ; sc:featureList edam:operation_0325 ; sc:name "tqDist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://users-cs.au.dk/cstorm/software/tqdist/" ; biotools:primaryContact "Christian N. S. Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3372, edam:topic_3489 ; sc:citation , "pmcid:PMC9454887", "pubmed:36091995" ; sc:description "Ephemeral data handling in microservices with Tquery." ; sc:featureList edam:operation_0224, edam:operation_3436, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "Tquery" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jolie/tquery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0091, edam:topic_2885, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description """Transfer learning improves antibiotic resistance class prediction. TRansfer Learning for Antibiotic Resistance Gene Classification (TRAC) is a neural network based method to predict antibiotic resistance genes. Unlike traditional alignment based approaches such as BLAST or HMMER, TRAC uses an alignment free approach. We show in our upcoming paper that performance of TRAC is better than the alignment based approaches.""" ; sc:featureList edam:operation_0303, edam:operation_3482, edam:operation_3927 ; sc:name "TRAC" ; sc:url "https://github.com/nafizh/TRAC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3173, edam:topic_3325, edam:topic_3474, edam:topic_3676 ; sc:citation ; sc:description "TRACE (Tissue Risk Assesment of Casuality by Expression) is a tissue-aware machine learning framework enhances the mechanistic understanding and genetic diagnosis of Mendelian and rare diseases." ; sc:featureList edam:operation_3226, edam:operation_3227, edam:operation_3799 ; sc:name "trace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://netbio.bgu.ac.il/trace/" ; biotools:primaryContact "Esti Yeger-Lotem" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:26922377" ; sc:description "A full pipeline for mapping bisulfite se-quencing data using bowtie2 and then generating CpG level data." ; sc:featureList edam:operation_2429 ; sc:name "TRACE-RRBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformaticstools.mayo.edu/research/trace-rrbs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:description "Harmonize numerical values extracted from medical images (e.g. acquired with different models of image-acquisition system)" ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Trace4Harmonization" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareVersion "v1.0.00" ; sc:url "http://deeptracetech.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3168 ; sc:citation "pubmed:17490482" ; sc:description "Streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads." ; sc:featureList edam:operation_0310 ; sc:name "Tracembler" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.plantgdb.org/tool/tracembler/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2229, edam:topic_3170 ; sc:citation ; sc:description "TraceQC is a R package for quality control (QC) of CRISPR Lineage Tracing Sequence Data. With simple programming, users can create an HTML QC report page and plots for the QC." ; sc:featureList edam:operation_3218, edam:operation_3227, edam:operation_3695 ; sc:name "TraceQC" ; sc:url "https://github.com/LiuzLab/TraceQC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3293 ; sc:citation ; sc:description "Graphical tool for visualization and diagnostics of MCMC (Markov chain Monte Carlo) output. It can read output files from MrBayesand BEAST." ; sc:featureList edam:operation_0337, edam:operation_2238 ; sc:name "Tracer" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tree.bio.ed.ac.uk/software/tracer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3304, edam:topic_3421, edam:topic_3444 ; sc:citation ; sc:description "TRACER-3D is a useful toolbox for visualizing the trajectories of recording electrodes(e.g Neuropixels) through different sub-regions of the rat brain." ; sc:featureList edam:operation_3890 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TRACER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Whitlock-Group/TRACER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769 ; sc:description "A hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TRACESPipe" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/viromelab/tracespipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0749, edam:topic_3168 ; sc:citation , "pmcid:PMC10348866", "pubmed:37456510" ; sc:description "The TraceTrack application serves for automatic batch analysis of Sanger sequencing trace files. 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It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs). Moreover, it can do tracking on the TOMs creating bundle-specific tractogram and do Tractometry analysis on those | The tool works very well for data similar to the Human Connectome Project. 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Annotated output will include exon/intron regions and tract information." ; sc:featureList edam:operation_0361 ; sc:name "TRACTS" ; sc:url "http://bioportal.weizmann.ac.il/tracts/tracts.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0625, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description """TraCurate – explore its functionality to curate your tracks from time-lapse image data. A tool for curating object tracks. The tracking view is where you will spend most of your time. It provides means for inspecting cells and autotracklets as well as modifying tracklets. Hovered/Selected cell Many of TraCurate’s functions require the user to select cells. The tracking view contains general information (A) about the cell that is currently selected and the cell that the mouse pointer hovers over. Navigation To navigate through the movie you can either click the navigation buttons (C) on the right side, use the frame slider at the bottom, or use a number of shortcuts:.""" ; sc:featureList edam:operation_2422, edam:operation_3359, edam:operation_3501 ; sc:name "TraCurate" ; sc:url "https://tracurate.gitlab.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7058077", "pubmed:32139671" ; sc:description """Trajectory-based differential expression analysis for single-cell sequencing data. TRAjectory Differential Expression analysis for SEQuencing data. trajectory-based differential expression analysis for sequencing data. tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Scripts to reproduce analyses of tradeSeq paper. tradeSeq provides a flexible method for discovering genes that are differentially expressed along one or multiple lineages, using a variety of tests suited to answer many questions of interest.""" ; sc:featureList edam:operation_2495 ; sc:license "MIT" ; sc:name "tradeSeq" ; sc:softwareVersion "1.2.01", "1.3.15" ; sc:url "https://github.com/statOmics/tradeSeq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511, edam:topic_3512 ; sc:citation "pubmed:12213778" ; sc:description "TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach." ; sc:featureList edam:operation_0438, edam:operation_0445 ; sc:name "TraFaC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://trafac.cchmc.org/trafac/index.jsp" ; biotools:primaryContact "Anil Jegga" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3474, edam:topic_3810 ; sc:citation , "pmcid:PMC8138169", "pubmed:34025720" ; sc:description "TrainSel is an R package for selection of training populations." ; sc:name "TrainSel" ; sc:url "https://github.com/TheRocinante-lab/TrainSel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0769, edam:topic_3068 ; sc:citation ; sc:description "TRAIT2D is a software for quantitative analysis of single particle diffusion data. It is a cross-platform Python software package with compilable graphical user interfaces (GUIs) to support Single Particle Tracking experiments. The software can be divided, in three main sections: the tracker, the simulator and the data analyzer." ; sc:featureList edam:operation_0244, edam:operation_3457, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "TRAIT2D" ; sc:softwareHelp ; sc:url "https://github.com/Eggeling-Lab-Microscope-Software/TRAIT2D" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3293, edam:topic_3301 ; sc:citation , "pmcid:PMC5192078", "pubmed:28066816" ; sc:description "Traitar is a fully automated software package for deriving phenotypes from a genome sequence." ; sc:featureList edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "Traitar" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/hzi-bifo/traitar" ; biotools:primaryContact "Alice McHardy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_0780, edam:topic_3299 ; sc:citation , "pmcid:PMC5570260", "pubmed:28453644" ; sc:contributor ; sc:description "Detection of associations between sequence evolution rate and whole-organism phenotypes. 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It includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions." ; sc:featureList edam:operation_0361 ; sc:name "TRAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/acg-team/tral" ; biotools:primaryContact "Lorenzo Gatti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0154, edam:topic_0736, edam:topic_3510, edam:topic_3542 ; sc:citation "pubmed:11274469", "pubmed:12169530", "pubmed:15980454", "pubmed:8670618", "pubmed:8844859" ; sc:description "Tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides." ; sc:featureList edam:operation_0267, edam:operation_0269, edam:operation_0278, edam:operation_0468, edam:operation_2488 ; sc:name "TRAMPLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gpcr.biocomp.unibo.it/biodec/" ; biotools:primaryContact "BDM Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:name "Sequence alignment (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Generate an alignment of nucleic coding regions from aligned proteins." ; sc:featureList edam:operation_0260, edam:operation_0371 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tranalign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/tranalign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Align nucleic coding regions given the aligned proteins." ; sc:featureList edam:operation_2403 ; sc:name "tranalign WS (husar)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/tranalign.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:citation ; sc:description "TRAnsforming Nested Collections Efficiently (TraNCE) is a compilation framework that auto- mates the difficulties of designing distributed analyses with complex, biomedical data types." ; sc:featureList edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TraNCE" ; sc:url "https://github.com/jacmarjorie/trance" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2546 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_2055 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation "pubmed:20935650" ; sc:description "A pipeline for de novo short-read transcriptome assembly and analyses." ; sc:featureList edam:operation_0292, edam:operation_0524, edam:operation_3258 ; sc:name "Trans-ABySS" ; sc:operatingSystem "Linux" ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss" ; biotools:primaryContact "Readman Chiu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1870 ; sc:name "Genus name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1045 ; sc:name "Species name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1046 ; sc:name "Strain name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3297, edam:topic_3301, edam:topic_3390 ; sc:citation , "pmcid:PMC9973855", "pubmed:36748555" ; sc:description "an automated annotation pipeline for membrane transporter prediction in bacterial genomes." ; sc:featureList edam:operation_0337, edam:operation_0362, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "TransAAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.membranetransport.org/transportDB2/TransAAP_login.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3047 ; sc:author "Ketil Malde" ; sc:citation ; sc:description "Calculate more accurate pairwise alignments by making use of a (large) database of uncurated sequences to aid matching against a (small) database of curated target sequences." ; sc:featureList edam:operation_0292 ; sc:name "transalign" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "imr.no" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "http://malde.org/~ketil/biohaskell/transalign/" ; biotools:primaryContact "Ketil Malde" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3752 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2725 ; sc:name "Ensembl transcript ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0622, edam:topic_2885, edam:topic_3512 ; sc:citation , "pmcid:PMC8240296", "pubmed:34182919" ; sc:description "TransAT is a package within the R programming language for converting RefSeq ID to Ensembl ID and mapping the genomic position, followed by providing variant allele frequencies and gene annotations." ; sc:featureList edam:operation_2422, edam:operation_3196, edam:operation_3227, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TransAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ShihChingYu/TransAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7462071", "pubmed:32817072" ; sc:description """genome-guided transcriptome assembly by borrowing assemblies from different assemblers. RNA-seq technology is widely used in various transcriptomic studies and provides great opportunities to reveal the complex structures of transcriptomes. To effectively analyze RNA-seq data, we introduce a novel transcriptome assembler, TransBorrow, which borrows the assemblies from different assemblers to search for reliable subsequences by building a colored graph from those borrowed assemblies. Then, by seeding reliable subsequences, a newly designed path extension strategy accurately searches for a transcript-representing path cover over each splicing graph. TransBorrow was tested on both simulated and real data sets and showed great superiority over all the compared leading assemblers""" ; sc:featureList edam:operation_0523, edam:operation_0524, edam:operation_0525, edam:operation_3258, edam:operation_3472 ; sc:name "TransBorrow" ; sc:url "https://sourceforge.net/projects/transcriptomeassembly/files/TransBorrow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0659, edam:topic_3320, edam:topic_3512 ; sc:citation , "pubmed:33074314" ; sc:description "an interactive database for translatable circular RNAs based on multi-omics evidence." ; sc:featureList edam:operation_0439, edam:operation_2421, edam:operation_2422 ; sc:name "TransCirc" ; sc:url "https://www.biosino.org/transcirc/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2730 ; sc:encodingFormat edam:format_1929 ; sc:name "COGEME unisequence ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2161 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence similarity plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_2330 ; sc:name "Alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Jan Baumbach" ; sc:citation , "pubmed:20508635" ; sc:description "Comprehensive clustering tool that incorporates the hidden transitive nature occuring e.g. within biomedical data sets. It is based on Weighted Transitive Graph Projection problem." ; sc:featureList edam:operation_0291 ; sc:name "TransClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bmb.sdu.dk" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://transclust.compbio.sdu.dk/main_page/index.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0625, edam:topic_2229, edam:topic_2640, edam:topic_3934 ; sc:citation , "pubmed:31971581" ; sc:description "TRANSCOMPP is a tool that allows users to quantify phenotypic plasticity starting from single-cell or bulk measurements of phenotype. TRANSCOMPP uses Markov modeling and optimization to estimate best-fit values for stochastic transition rates, transition rate intervals, and phenotype-specific proliferation parameters." ; sc:featureList edam:operation_3435, edam:operation_3629 ; sc:license "GPL-3.0" ; sc:name "Transcompp" ; sc:url "http://github.com/nsuhasj/Transcompp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099, edam:topic_0219, edam:topic_0749, edam:topic_3170 ; sc:citation "pubmed:26581084" ; sc:description "A computational pipeline to functionally annotate differentially expressed transcripts and carry out GO enrichment analysis of expression profiles, under the different treatment condition for organisms, which lacks the referenced genome." ; sc:featureList edam:operation_0361, edam:operation_2436, edam:operation_2495 ; sc:name "Transcriptator" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www-labgtp.na.icar.cnr.it/Transcriptator/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2259, edam:topic_3308 ; sc:description "R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering." ; sc:featureList edam:operation_0337, edam:operation_2436 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "transcriptogramer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/transcriptogramer.html" ; biotools:primaryContact "Diego Morais" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , ; sc:description """Data-Driven Annotation of Complex Transcriptomes. TranscriptomeReconstructoR is an R package for data-driven annotation of transcriptomes.""" ; sc:featureList edam:operation_0527, edam:operation_3258, edam:operation_3644 ; sc:license "GPL-3.0" ; sc:name "TranscriptomeReconstructoR" ; sc:url "https://github.com/Maxim-Ivanov/TranscriptomeReconstructoR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3473, edam:topic_3512 ; sc:citation ; sc:description "An R package for identifying and quantifying de novo continuous regions of transcription across the genome. The package uses ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs) to divide closely spaced transcripts into individually transcriped units." ; sc:featureList edam:operation_0524, edam:operation_3258, edam:operation_3680 ; sc:license "GPL-3.0" ; sc:name "transcriptR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.6.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/transcriptR.html" ; biotools:primaryContact "Armen R. Karapetyan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0654, edam:topic_0659, edam:topic_3168 ; sc:citation , "pmcid:PMC10320084", "pubmed:37158253" ; sc:description "TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs." ; sc:featureList edam:operation_0239, edam:operation_0240, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "transCRISPR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://transcrispr.igcz.poznan.pl/transcrispr/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0736, edam:topic_3474, edam:topic_3538 ; sc:citation , "pubmed:36272675" ; sc:description "Identification of Disordered Flexible Linkers in Proteins by Transfer Learning." ; sc:featureList edam:operation_0470, edam:operation_3767, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:name "TransDFL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bliulab.net/TransDFL/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Translate nucleic acid sequences." ; sc:featureList edam:operation_0371 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "transeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/transeq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web API", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Transeq translates nucleic acid sequences to their corresponding peptide sequences. It can translate to the three forward and three reverse frames, and output multiple frame translations at once." ; sc:featureList edam:operation_0371 ; sc:name "transeq (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/st/emboss_transeq" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:name "Protein sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0157 ; sc:author "EMBOSS" ; sc:citation , ; sc:description "Translate nucleic acid sequences to the corresponding peptide sequences." ; sc:featureList edam:operation_0371 ; sc:name "transeq (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "https://www.ebi.ac.uk/jdispatcher/st/emboss_transeq" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_0749, edam:topic_3125 ; sc:citation "pubmed:10592259", "pubmed:11125113", "pubmed:12520026", "pubmed:16381825", "pubmed:18436575", "pubmed:8594589", "pubmed:9847216" ; sc:description "Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use." ; sc:featureList edam:operation_0314, edam:operation_0438, edam:operation_0445 ; sc:name "TRANSFAC" ; sc:softwareHelp ; sc:url "http://www.gene-regulation.com/pub/databases.html#transfac" ; biotools:primaryContact "Webmaster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "Tool for prediction of transcription factor given a protein sequence" ; sc:featureList edam:operation_2945 ; sc:name "transfacpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/transfacpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3337, edam:topic_3384, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description "Repository for transferGWAS, a deep learning method for performing genome-wide association studies on full medical imaging data." ; sc:featureList edam:operation_3791, edam:operation_3920, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "transferGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mkirchler/transferGWAS/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0749, edam:topic_3125, edam:topic_3512 ; sc:citation "pubmed:20511592" ; sc:description "TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets." ; sc:featureList edam:operation_0438, edam:operation_0440, edam:operation_0441, edam:operation_0445 ; sc:name "TransFind" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://transfind.sys-bio.net/" ; biotools:primaryContact "Nils Bluethgen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3305, edam:topic_3324, edam:topic_3673 ; sc:citation , "pmcid:PMC9825751", "pubmed:36469333" ; sc:description "A Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data." ; sc:featureList edam:operation_0337, edam:operation_3192, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TransFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cvn001/transflow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_0820, edam:topic_3542 ; sc:citation "pubmed:16844989" ; sc:description "transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments." ; sc:featureList edam:operation_0267, edam:operation_0268, edam:operation_0269, edam:operation_0270, edam:operation_0474 ; sc:name "transFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.bc.edu/clotelab/transFold" ; biotools:primaryContact "Jérôme Waldispühl" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0176, edam:topic_0749, edam:topic_3318 ; sc:citation , "pmcid:PMC9485484", "pubmed:36148009" ; sc:description "Transformato is a package that helps to set up relative alchemical free energy calculations of small molecules with a common core scaffold, either for solvation free energy1 or binding free energy2 estimates. The package is designed to be used with output generated by CHARMM-GUI." ; sc:featureList edam:operation_2476, edam:operation_3216, edam:operation_3893, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "transformato" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/wiederm/transformato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_3336, edam:topic_3474, edam:topic_3957 ; sc:citation , "pubmed:32428219" ; sc:description "TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments." ; sc:featureList edam:operation_2492, edam:operation_3359, edam:operation_3938 ; sc:license "Apache-2.0" ; sc:name "TransformerCPI" ; sc:url "https://github.com/lifanchen-simm/transformerCPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC8323195", "pubmed:34330244" ; sc:description "A Fitting, Scoring and Predicting Toolkit for Transformer Series Models." ; sc:featureList edam:operation_3280, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "transformers-sklearn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/trueto/transformers_sklearn" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1936 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC9048660", "pubmed:35244144" ; sc:description "A web application for the design of mammalian transgenes." ; sc:featureList edam:operation_0446, edam:operation_2428, edam:operation_2962 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Transgene-design" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://transgene-design.bath.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3308 ; sc:citation , ; sc:description "Software tool for finding genes in assembled transcripts from metatranscriptomic sequences." ; sc:featureList edam:operation_2454 ; sc:name "TransGeneScan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.2.1" ; sc:url "https://github.com/COL-IU/TransGeneScan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_0798, edam:topic_3168 ; sc:citation "pubmed:26447887" ; sc:description "A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions." ; sc:featureList edam:operation_0427 ; sc:name "TRANSIT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://saclab.tamu.edu/essentiality/transit/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0622, edam:topic_3308 ; sc:description "Translation of a nucleotide (DNA/RNA) sequence to a protein sequence." ; sc:featureList edam:operation_2479, edam:operation_3434 ; sc:name "Translate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://web.expasy.org/translate/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_3473 ; sc:citation ; sc:description "This tool detects differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression using several statistical methods." ; sc:featureList edam:operation_0315, edam:operation_0571, edam:operation_2436 ; sc:license "GPL-3.0" ; sc:name "tRanslatome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tRanslatome.html" ; biotools:primaryContact "Erik Dassi", "Toma Tebaldi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0108, edam:topic_0154, edam:topic_3168 ; sc:citation "pubmed:20435676" ; sc:description "TranslatorX is a web-server designed to align protein coding nucleotide sequences based on their corresponding amino acid translations rather than nucleotide alignments." ; sc:featureList edam:operation_0260, edam:operation_0292, edam:operation_2479 ; sc:name "TranslatorX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://translatorx.co.uk" ; biotools:primaryContact "TranslatorX Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0659, edam:topic_2640, edam:topic_3512 ; sc:citation , "pubmed:34570220" ; sc:description "A comprehensive database for translatable lncRNAs ( TransLnc) extends immunopeptidome. TransLnc provides both computationally predicted and experimentally supported lncRNA peptides in multiple species." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_2422, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "TransLnc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bio-bigdata.hrbmu.edu.cn/TransLnc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3303 ; sc:citation "pmcid:PMC4333702", "pubmed:25717408" ; sc:description "Its knowledge management and high-content analysis platform is a flexible software framework featuring novel research capabilities. It enables analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_2403, edam:operation_2479, edam:operation_2495 ; sc:name "tranSMART" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "16.1" ; sc:url "http://transmartfoundation.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_3170 ; sc:citation , "pubmed:35858749" ; sc:description "TransMeta is an assembler that can simultaneously assemble RNA-seq reads of multiple samples. TransMeta can output a unified set of meta-annotations(GTF format) for all samples in an RNA-seq experiment and use the information from all the samples to generate a set of transcripts for each individual sample. TransMeta constructs the novel vector-weighted splicing graph model, in which the edges and nodes are weighted by vectors rather than single numbers with the element in kth position of the vectors being the corresponding weight in sample k. And TransMeta employs a cosine-similarity based combing strategy and label setting algorithm to recover the transcripts. TransMeta takes a file that lists the alignment files(Bam format) of multiple RNA-seq samples as input, and outputs all assembled candidate transcripts in GTF format." ; sc:featureList edam:operation_0310, edam:operation_3563, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TransMeta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yutingsdu/TransMeta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0634, edam:topic_0659, edam:topic_0749 ; sc:citation "pubmed:19786497" ; sc:description "Contains transcription factors and miRNAs along with regulatory pairs. References to the published literature (PubMed ID) information about the organism in which the relationship was found, whether the TFs and miRNAs are involved with tumors, miRNA function annotation and miRNA-associated disease annotation are also included. 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sc:name "TraSig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/doraadong/TraSig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_3170 ; sc:citation , ; sc:description "Template-based RNA secondary structure visualization." ; sc:featureList edam:operation_0570 ; sc:license "GPL-3.0" ; sc:name "TRAVeLer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/davidhoksza/traveler" ; biotools:primaryContact "David Hoksza", "Richard Elias" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3172 ; sc:author "Sam De Craemer" ; sc:citation , "pmcid:PMC9321460", "pubmed:35888717" ; sc:description "Tracer metabolomics is a powerful technology for the biomedical community to study and understand disease-inflicted metabolic mechanisms. However, the interpretation of tracer metabolomics results is highly technical, as the metabolites' abundances, tracer incorporation and positions on the metabolic map all must be jointly interpreted. The field is currently lacking a structured approach to help less experienced researchers start the interpretation of tracer metabolomics datasets. We propose an approach using an intuitive visualization concept aided by a novel open-source tool, and provide guidelines on how researchers can apply the approach and the visualization tool to their own datasets. Using a showcase experiment, we demonstrate that the visualization approach leads to an intuitive interpretation that can ease researchers into understanding their tracer metabolomics data." ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TraVis Pies" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://mec-shiny.vib.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3511 ; sc:citation , "pmcid:PMC5887194", "pubmed:29621972" ; sc:description "De novo motif discovery tool for next-generation sequencing datasets." ; sc:featureList edam:operation_0238 ; sc:license "GPL-3.0" ; sc:name "TrawlerWeb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://trawler.erc.monash.edu.au/" ; biotools:primaryContact "Louis Dang", "Mirana Ramialison" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0157, edam:topic_2885 ; sc:citation "pubmed:24681324" ; sc:description "A rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs." ; sc:featureList edam:operation_0237, edam:operation_2479 ; sc:name "TRDistiller" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinfo.montp.cnrs.fr/?r=TRDistiller" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_0769, edam:topic_3170 ; sc:citation , "pmcid:PMC9063265", "pubmed:35501677" ; sc:description "R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data." ; sc:featureList edam:operation_0314, edam:operation_0464, edam:operation_3192, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tReasure" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://treasure.pmrc.re.kr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:24794927" ; sc:description "An R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome." ; sc:featureList edam:operation_2238 ; sc:name "TREAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.hanzhang.name/softwares/treat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0659, edam:topic_3474, edam:topic_3512, edam:topic_3930 ; sc:citation , "pmcid:PMC9589171", "pubmed:36320935" ; sc:description "Therapeutic RNAs exploration inspired by artificial intelligence technology." ; sc:featureList edam:operation_0252, edam:operation_0314, edam:operation_0479, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "TREAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://rna.org.cn/treat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3325, edam:topic_3404, edam:topic_3407 ; sc:citation , , "pmcid:PMC3458980", "pmcid:PMC8042729", "pubmed:22824307", "pubmed:33845862" ; sc:description "treatable-ID is an interactive tool for the clinician and scientist presenting identified 81 inborn errors of metabolism which are causally related to Intellectual Disability and amenable to therapy." ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "treatable-ID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://treatable-id.org" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3063, edam:topic_3303 ; sc:citation ; sc:description "An R package to analyze treatment patterns of a study population of interest." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "TreatmentPatterns" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://github.com/mi-erasmusmc/TreatmentPatterns" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3293, edam:topic_3299 ; sc:description "An extension of the popular ChromHMM for doing clustering of epigenetic markers. Given a complete set of epigenetic markers for several cell types, and the phylogeny describing their relationship, Tree-HMM will perform approximate inference on the graphical model induced by connecting genomic positions of a certain cell type in a chain while also connecting different species according to the tree." ; sc:featureList edam:operation_3432 ; sc:name "Tree-HMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.0" ; sc:url "https://cbcl.ics.uci.edu//doku.php/software#tree-hmm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0654, edam:topic_3293 ; sc:citation "pubmed:11934758" ; sc:description "Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method." ; sc:featureList edam:operation_0323, edam:operation_0499, edam:operation_0545, edam:operation_0547, edam:operation_0548 ; sc:name "TREE-PUZZLE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tree-puzzle.de/" ; biotools:primaryContact "Arndt von Haeseler", "Heiko A. Schmidt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0194, edam:topic_0621, edam:topic_3050, edam:topic_3299 ; sc:citation , "pubmed:36218394" ; sc:description "Tree2GD provides an integrated pipeline to identify WGD events, with friendful commands in one-step or multiple steps, with smart quality control in custom dataset, with multithreading design costing low time, with well performance in detect WGD signals, and with advanced visualization of GDs and Ks peaks." ; sc:featureList edam:operation_0553, edam:operation_3478, edam:operation_3947, edam:operation_3963 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Tree2GD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Dee-chen/Tree2gd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:description "simple GUI tool for clusterization of data" ; sc:featureList edam:operation_3432, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:name "tree_network" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/24862-tree_network-v-1-0-example" ; biotools:primaryContact "W.M. Saj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3305 ; sc:citation , "pmcid:PMC6874070", "pubmed:31751352" ; sc:description "A new resolution function to evaluate tree shape statistics." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:name "tree shape statistics" ; sc:url "https://github.com/WGS-TB/TreeShapeStats" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3305 ; sc:citation , "pubmed:34864914" ; sc:description "The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves." ; sc:featureList edam:operation_2938, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "TreeAndLeaf" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioconductor.org/packages/TreeAndLeaf/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0621, edam:topic_0769, edam:topic_3293, edam:topic_3944 ; sc:citation , "pubmed:32073732" ; sc:description """An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data. This python script can be used to infer species trees and phylogenetic networks from sequences.""" ; sc:featureList edam:operation_0326, edam:operation_0327, edam:operation_0335, edam:operation_0544, edam:operation_3478 ; sc:license "GPL-3.0" ; sc:name "TREEasy" ; sc:url "https://github.com/MaoYafei/TREEasy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3293 ; sc:description """TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate. TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.""" ; sc:featureList edam:operation_0324, edam:operation_0540, edam:operation_0567 ; sc:name "TreeBeST" ; sc:softwareVersion "1.9.2.post0" ; sc:url "https://treesoft.sourceforge.net/treebest.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3299 ; sc:citation "pubmed:7828077" ; sc:description "Construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences." ; sc:featureList edam:operation_0323 ; sc:name "TREECON" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/TREECON" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_1775, edam:topic_3168, edam:topic_3510 ; sc:citation "pubmed:12589769", "pubmed:14764569", "pubmed:16844971", "pubmed:7749921" ; sc:description "Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments." ; sc:featureList edam:operation_0272, edam:operation_0292, edam:operation_1777, edam:operation_2479 ; sc:name "TreeDet" ; sc:url "http://treedetv2.bioinfo.cnio.es/treedet/index.html" ; biotools:primaryContact "TreeDet Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0084, edam:topic_0736, edam:topic_3293 ; sc:citation "pubmed:16844970" ; sc:description "Tool for the visualization of phylogeny and protein domain structure. It constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment." ; sc:featureList edam:operation_0246, edam:operation_0303, edam:operation_0492, edam:operation_0499 ; sc:name "TreeDomViewer" ; sc:url "http://www.bioinformatics.nl/tools/treedom" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910, edam:format_1912 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:encodingFormat edam:format_3603 ; sc:name "Phylogenetic tree image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_0084 ; sc:citation ; sc:description "Dynamic graphics and annotations for tree investigations." ; sc:featureList edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "TreeDyn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "198.3" ; sc:url "http://www.treedyn.org/" ; biotools:primaryContact "François Chevenet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0858 ; sc:name "Sequence signature matches" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0084, edam:topic_0623 ; sc:author "Fabian Schreiber", "Mateus Patricio" ; sc:citation ; sc:description "Search of TreeFam's HMM collection, allows query sequence to be aligned (MAFFT) and inserted into tree (RAxML) to significantly matching models." ; sc:featureList edam:operation_0239, edam:operation_0323 ; sc:name "TreeFam" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://www.treefam.org/search" ; biotools:primaryContact "Fabian Schreiber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654, edam:topic_3511 ; sc:citation "pubmed:17540681" ; sc:description "Software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction of regulatory elements in multiple genomes of both closely related and distant species." ; sc:featureList edam:operation_0239 ; sc:name "TreeGibbsSampler" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://hulab.ucf.edu/software" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3053, edam:topic_3293 ; sc:citation "pubmed:21685070" ; sc:description "Software which builds on the l1 plus total variation penalized logistic regression to effectively estimate multiple gene networks corresponding to cell types related by a tree-genealogy, based on only a few samples from each cell type." ; sc:featureList edam:operation_1781 ; sc:name "Treegl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sailing.cs.cmu.edu/main/?page_id=495" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050, edam:topic_3382 ; sc:citation , "pubmed:37602408" ; sc:description "A database with globally observed environmental ranges for 48,129 tree species." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "TreeGOER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.5281/zenodo.7922928" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3751 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910, edam:format_1912, edam:format_2332, edam:format_3159, edam:format_3160 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1707 ; sc:encodingFormat edam:format_3508, edam:format_3579, edam:format_3591, edam:format_3603, edam:format_3604 ; sc:name "Phylogenetic tree image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3751 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910, edam:format_1912, edam:format_2332 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3050, edam:topic_3070, edam:topic_3293, edam:topic_3299 ; sc:author "Ben C. Stöver", "Sarah Wiechers" ; sc:citation ; sc:contributor "Kai F. Müller" ; sc:description "A feature rich editor for phylogenetic trees that offers a variety of editing and formatting options. Tree nodes and branches can carry an unlimited number of annotations that can also be calculated from each other. Features for visualizing and interactively analyzing differences between alternative tree topologies are provided. Reconstructed ancestral character states can be imported and visualized." ; sc:featureList edam:operation_0325, edam:operation_0326, edam:operation_0558, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TreeGraph 2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , , ; sc:softwareVersion "2.15.0" ; sc:url "http://treegraph.bioinfweb.info/" ; biotools:primaryContact "Ben Stöver" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0749, edam:topic_3474 ; sc:citation , , "pubmed:32702108" ; sc:description """Heatmap-Integrated Decision Tree Visualizations. an R package for interpretable decision tree visualizations. Your decision tree may be cool, but what if I tell you you can make it hot?. Creates interpretable decision tree visualizations with the data represented as a heatmap at the tree's leaf nodes. 'treeheatr' utilizes the customizable 'ggparty' package for drawing decision trees. You can install the released version of treeheatr from CRAN with:. The first argument of heat_tree(), data is now replaced with x, which can be a dataframe (or tibble), a party (or constparty) object specifying the precomputed tree, or partynode object specifying the customized tree. custom_tree argument is no longer needed. treeheatr incorporates a heatmap at the terminal node of your decision tree. The basic building blocks to a treeheatr plot are (yes, you guessed it!) a decision tree and a heatmap.""" ; sc:featureList edam:operation_0567, edam:operation_2938, edam:operation_3478 ; sc:license "MIT" ; sc:name "treeheatr" ; sc:url "https://trang1618.github.io/treeheatr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0780 ; sc:citation , "pmcid:PMC6712805", "pubmed:31455362" ; sc:description "a user-friendly application to obtain subtrees from large phylogenies | Phylogenies are rapidly becoming larger due to the rising number of available genomes. Beyond broad patterns, large phylogenies often become uninterpretable as tip labels are so small or excluded altogether. As a result, large phylogenies can be difficult to use for other researchers especially for groups interested in the relationships among a subset of taxa. Here, we introduce treehouse, a user friendly shiny app that allows researchers to obtain subtrees from large-scale phylogenies. Treehouse is populated with a handful of large-scale phylogenies available through treehouseDB. Additionally, treehouse features an additional function, userTree, which allows a user to upload and parse their own phylogeny | Our aim is to make phylogenies more accessible to all and facilitate researchers exploration in their own phylogenies" ; sc:featureList edam:operation_0325, edam:operation_0552, edam:operation_3478 ; sc:name "treehouse" ; sc:url "https://github.com/JLSteenwyk/treehouse" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Base classes and functions for parsing and exporting phylogenetic trees. This package supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file." ; sc:featureList edam:operation_0226, edam:operation_2409, edam:operation_2928, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "treeio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/treeio.html" ; biotools:primaryContact "Guangchuang Yu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0637 ; sc:citation ; sc:description "TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences." ; sc:featureList edam:operation_0325 ; sc:name "TreeJuxtaposer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://olduvai.sourceforge.net/" ; biotools:primaryContact "Bug report", "Mailing list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2815, edam:topic_3943 ; sc:citation , "pmcid:PMC9447925", "pubmed:35984845" ; sc:description "TreeKnit is a Julia package that performs the inference of Ancestral Reassortment Graph for segmented genomes (typically, human influenza)." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TreeKnit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/PierreBarrat/TreeKnit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3293 ; sc:citation "pubmed:21335609" ; sc:description "A python package that allows the comparison of any two phylogenetic tree topologies, even those with missing leaves and duplications" ; sc:featureList edam:operation_0325 ; sc:name "TreeKO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://treeko.cgenomics.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3055 ; sc:citation ; sc:description "Performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location." ; sc:featureList edam:operation_2429 ; sc:license "Not licensed" ; sc:name "TreeLD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sph.umich.edu/csg/software_pages/treeld.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0081, edam:topic_2269, edam:topic_3293 ; sc:citation ; sc:description """A test statistic to quantify treelikeness in phylogenetics. This repository contains code to simulate a series of sequence alignments and estimate a series of treelikeness and introgression metrics, including a new test for treelikeness called tree proportion. Tree proportion represents the proportion of information from an alignment that is included in the phylogenetic tree estimated from that alignment.""" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0552, edam:operation_3192 ; sc:name "treelikeness" ; sc:url "https://github.com/caitlinch/treelikeness" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation , "pmcid:PMC5219798", "pubmed:28061884" ; sc:description "An R package for manipulating phylogentic trees." ; sc:featureList edam:operation_0324 ; sc:license "GPL-2.0" ; sc:name "treeman" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/DomBennett/TreeMan" ; biotools:primaryContact "Dominic J. Bennett" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """A Structured Approach to Fine Mapping of eQTL Variants. TreeMap prioritizes putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus.""" ; sc:featureList edam:operation_2942, edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3232 ; sc:name "TreeMap" ; sc:url "https://github.com/liliulab/treemap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. The allele frequencies in the modern populations are used to infer the structure of this graph." ; sc:featureList edam:operation_0323, edam:operation_3197 ; sc:license "GPL-3.0" ; sc:name "TreeMix" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://bitbucket.org/nygcresearch/treemix/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0154, edam:topic_0622 ; sc:citation , "pmcid:PMC9805588", "pubmed:36453872" ; sc:description "Treenome Browser is a web browser tool to interactively visualize millions of genomes alongside huge phylogenetic trees." ; sc:featureList edam:operation_0323, edam:operation_0325, edam:operation_0326, edam:operation_0551, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:name "Treenome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cov2tree.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0622, edam:topic_3293 ; sc:citation "pubmed:16447969" ; sc:description "Aan efficient program for refining multiple alignment of genomic sequences based on a phylogenetic tree. It has demonstrated significant improvements in the accuracy of alignments generated by several popular aligners." ; sc:featureList edam:operation_0292, edam:operation_0324, edam:operation_2403 ; sc:name "TreeRefiner" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://treerefiner.stanford.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0084, edam:topic_0123, edam:topic_0154, edam:topic_2269 ; sc:citation "pubmed:12651734" ; sc:description "The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests." ; sc:featureList edam:operation_0250, edam:operation_0262, edam:operation_0455, edam:operation_2238, edam:operation_3197 ; sc:name "TreeSAAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dna.cs.byu.edu/treesaap/" ; biotools:primaryContact "S. Woolley" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:20547782" ; sc:description "A program for simulating phylogenetic trees with a fixed number of species." ; sc:featureList edam:operation_0324, edam:operation_2426 ; sc:name "TreeSample" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/treesample/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0602, edam:topic_3174, edam:topic_3293, edam:topic_3944 ; sc:citation , "pmcid:PMC7695126", "pubmed:32637989" ; sc:description """the Tree-based Sensitive and Accurate Phylogenetic Profiler. If you are working with a particularly complex reference package, from an orthologous group for example, or have extra phylogenetic information you'd like to include in your classifications, try annotating extra features with treesapp layer.""" ; sc:featureList edam:operation_0224, edam:operation_3460, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "TreeSAPP" ; sc:url "https://github.com/hallamlab/TreeSAPP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3293 ; sc:citation ; sc:description "R package for phylogenetic tree search under custom optimality criteria" ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TreeSearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ms609.github.io/TreeSearch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_2269, edam:topic_3293, edam:topic_3524 ; sc:citation "pubmed:21482552" ; sc:description "An R package for simulating phylogenetic trees." ; sc:featureList edam:operation_0323, edam:operation_0324 ; sc:name "TreeSim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cran.r-project.org/web/packages/TreeSim/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3336, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC8753810", "pubmed:35016609" ; sc:description "A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Treesist-TB" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/WDee/Treesist-TB" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0092, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:8902363" ; sc:description "Simple program for displaying phylogenies on Apple Macintosh and Windows PCs. It provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from." ; sc:featureList edam:operation_0567 ; sc:name "TreeView" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://taxonomy.zoology.gla.ac.uk/rod/treeview.html" ; biotools:primaryContact "Rod Page" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3293, edam:topic_3299 ; sc:citation "pubmed:23036855" ; sc:description "New visualization algorithm to generate clear two-dimensional layouts of complex tree structures." ; sc:featureList edam:operation_0567 ; sc:name "TreeVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://pengqiu.gatech.edu/software/TreeVis/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3293, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description "A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes" ; sc:featureList edam:operation_0323 ; sc:name "treeWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/caitiecollins/treeWAS" ; biotools:primaryContact "Xavier Didelot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0611, edam:topic_3344, edam:topic_3452 ; sc:description "True equilibrium bolus estimation (TREMBLE) and transient equilibrium bolus estimation (TEM) are two kinetic models that offer quantification of PET ligand binding at transient equilibrium." ; sc:featureList edam:operation_0337, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "TREMBLE and TEM analysis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70208-tremble-and-tem-analysis" ; biotools:primaryContact "Jenny" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2084 ; sc:encodingFormat edam:format_2331 ; sc:name "Nucleic acid report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0798, edam:topic_3168, edam:topic_3175 ; sc:citation , "pmcid:PMC10069131", "pubmed:37013657" ; sc:description "Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches." ; sc:featureList edam:operation_0427, edam:operation_0523, edam:operation_0525, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TrEMOLO" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/DrosophilaGenomeEvolution/TrEMOLO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation , "pmcid:PMC6961062", "pubmed:31956739" ; sc:description """An online platform for tremor analysis. The electrophysiological classification of tremors can be a key element in the diagnosis and can facilitate treatment of a patient with tremor; however, the ability to conduct electrophysiological studies of tremor is not widely available.""" ; sc:featureList edam:operation_2428, edam:operation_2940 ; sc:name "Tremoroton" ; sc:url "https://electrophysiology.shinyapps.io/Tremoroton/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_2259 ; sc:description "Methods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available." ; sc:featureList edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "trena" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/trena.html" ; biotools:primaryContact "Paul Shannon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_3365, edam:topic_3444 ; sc:citation , "pmcid:PMC5266145", "pubmed:28122211" ; sc:contributor ; sc:description "A multiplatform software that can track equilibrium and nonequilibrium population shifts among two-dimensional Data frames." ; sc:featureList edam:operation_2939 ; sc:license "Proprietary" ; sc:name "TREND" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://biochem.missouri.edu/trend/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3295, edam:topic_3308, edam:topic_3320, edam:topic_3512 ; sc:citation ; sc:description """TREND-DB – A Transcriptome-wide Atlas of the Dynamic Landscape of Alternative Polyadenylation. The diversity and dynamics of the transcriptome are important means for development and adaptation. This work contains a number of TREND-seq datasets investigating transcriptome-wide APA, covering >170 RNAis conditions.""" ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_3501 ; sc:license "MIT" ; sc:name "TREND-DB" ; sc:url "https://github.com/federicomarini/trend-db" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2385 ; sc:name "RefSeq accession (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1900 ; sc:encodingFormat edam:format_2330 ; sc:name "NCBI locus tag" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3604 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1384 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3464 ; sc:name "Protein features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_1910 ; sc:name "Phylogenetic tree" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1245 ; sc:encodingFormat edam:format_3464 ; sc:name "Sequence cluster (protein)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0085, edam:topic_0091, edam:topic_0194, edam:topic_3299, edam:topic_3301, edam:topic_3510 ; sc:citation , , "pmcid:PMC7319448", "pubmed:32282909" ; sc:description "TREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis." ; sc:featureList edam:operation_0246, edam:operation_0291, edam:operation_0323, edam:operation_0492, edam:operation_2945, edam:operation_3092 ; sc:name "TREND Protein Evolution Function" ; sc:softwareHelp ; sc:url "http://trend.evobionet.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0769, edam:topic_3575 ; sc:citation ; sc:description "trendbreaker is an R package with which implement the ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics) method for detecting sudden changes in COVID-19 incidence." ; sc:featureList edam:operation_3435, edam:operation_3926, edam:operation_3929 ; sc:name "trendbreaker" ; sc:url "https://github.com/reconhub/trendbreaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3315, edam:topic_3512 ; sc:citation ; sc:description "TrendCatcher is a versatile R package for identifying dynamic differentially expressed genes (DDEGs) in RNA-seq longitudinal studies. A time course experiment is a widely used design in the study of cellular processes such as cell differentiation or response to external stimuli. Temporal changes to the gene expression, such as mRNA, is the key to characterizing such biological processes. Here, we present a versatile R package named TrendCatcher to identify the dynamic differentially expressed genes along the biological process time course. TrendCatcher uses a framework that combines the smoothing spline ANOVA model and break point searching strategy." ; sc:featureList edam:operation_0244, edam:operation_3223, edam:operation_3890 ; sc:name "TrendCatcher" ; sc:url "https://github.com/jaleesr/TrendCatcher" ; biotools:primaryContact "Jalees Rehman" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2032 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0607, edam:topic_2229 ; sc:citation ; sc:description "A method based on marked point processes that identifies genes with statistically significant spatial expression trends. IT finds these genes in spatial transcriptomic and sequential fluorescence in situ hybridization data, and also reveals significant gene expression gradients and hot spots in low-dimensional projections of dissociated single-cell RNA-seq data." ; sc:featureList edam:operation_2495, edam:operation_3438, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "trendsceek" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/edsgard/trendsceek" ; biotools:primaryContact "Daniel Edsgärd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions." ; sc:featureList edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "Trendy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Trendy.html" ; biotools:primaryContact "Rhonda Bacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:22962448" ; sc:description "Read mapper for high-throughput DNA sequencing reads, in particular reads from 100 nt to hundreds of nucleotides, and for large edit distance between sequencing read and match in the reference genome." ; sc:featureList edam:operation_3198 ; sc:name "TreQ 0.1 beta" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/p/treq/home/Home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:description "Method that accelerates and improves read mapping. 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Find tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. It uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori knowledge of the pattern, pattern size or number of copies. There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat." ; sc:featureList edam:operation_0379 ; sc:license "Other" ; sc:name "TRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tandem.bu.edu/trf/trf.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0659, edam:topic_3300, edam:topic_3512 ; sc:citation , "pubmed:33035346" ; sc:description """A relational database of Transfer RNA related Fragments. tRFs are 14-32 base long single-stranded RNA derived from mature or precursor tRNA and are distinct from the stress-induced tRNA fragments created by cleavage in the anti-codon loop. tRFs have been shown to be important for cell-cycle progression and for regulating the dynamics of RISC.""" ; sc:featureList edam:operation_0278, edam:operation_0463, edam:operation_2575 ; sc:name "tRFdb" ; sc:url "http://genome.bioch.virginia.edu/trfdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation , ; sc:description "Telomerase RNA (TR) specific structure prediction. 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Simulating Triad Genomewide Genotypes. Simulate genotypes for case-parent triads, case-control, and quantitative trait samples with realistic linkage diequilibrium structure and allele frequency distribution. For studies of epistasis one can simulate models that involve specific SNPs at specific sets of loci, which we will refer to as "pathways". TriadSim generates genotype data by resampling triad genotypes from existing data. The details of the method is described in the manuscript under preparation "Simulating Autosomal Genotypes with Realistic Linkage Disequilibrium and a Spiked in Genetic Effect" Shi, M., Umbach, D.M., Wise A.S., Weinberg, C.R.""" ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196, edam:operation_3928 ; sc:license "GPL-3.0" ; sc:name "TriadSim" ; sc:url "https://cran.r-project.org/web/packages/TriadSim/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0622, edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description """TRIAGE - T hroughput R anking by I terative A nalysis of G enomic E nrichment. A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from high-throughput assays. 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The database tRNA in Cancer (TRIC) show the dynamic landscape of tRNAs expression across 31 cancer types and more than 10000 samples from The Cancer Genome Atlas (TCGA). Here we systematically analyzed tRNA expression profiles at gene, codon and amino acid levels and the functional consequence (e.g. patient tumor stage, subtype, and survival). 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Goff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3295, edam:topic_3518 ; sc:citation ; sc:description """Analysis of gene expression and connectivity on hippocampus of Alzheimer’s disease by a new comprehensive approach. Calculation of gene TRID weights from a gene expression matrix.""" ; sc:featureList edam:operation_0313, edam:operation_3223, edam:operation_3463, edam:operation_3766 ; sc:name "TRID" ; sc:url "https://github.com/shannjiang/TRID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0154, edam:topic_3391 ; sc:citation "pubmed:17335588" ; sc:description "A MathDAMP extension for the visualization of three-way comparisons between metabolite profiles. 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This is an EU-funded collaborative project on establishing an integrative and innovative pipeline for the exploitation of plant triterpenes." ; sc:featureList edam:operation_2422, edam:operation_2483 ; sc:isAccessibleForFree true ; sc:name "TriForC Database" ; sc:operatingSystem "Linux" ; sc:provider "VIB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/triforc/#/home" ; biotools:primaryContact "Alain Goossens" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169 ; sc:citation , "pmcid:PMC3480842", "pubmed:22827163" ; sc:description "IT is an R package to find enriched regions in trancription factor ChIP-seq data. The algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics." ; sc:featureList edam:operation_0445, edam:operation_2238, edam:operation_3222, edam:operation_3501 ; sc:license "GPL-2.0" ; sc:name "triform" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/triform.html" ; biotools:primaryContact "Thomas Carroll" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929, edam:format_1949, edam:format_1961, edam:format_2924 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1912, edam:format_1929, edam:format_1961, edam:format_1997, edam:format_2924 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0194, edam:topic_3056, edam:topic_3293 ; sc:author "Diogo Silva" ; sc:contributor "Fernando Alves" ; sc:description "Modern GUI and command line application designed to make the life of anyone with proteome and/or alignment sequence data easier and more pleasurable. It allows user to process their data through three independent modules: (i) Search and explore orthologs across multiple proteomes; (ii) Convert, concatenate, collapse, filter and perform many other manipulations of thousands sequence alignments files. (iii) Visually explore your sequence alignment data." ; sc:featureList edam:operation_0258, edam:operation_0259, edam:operation_0260, edam:operation_0337, edam:operation_0346, edam:operation_2409 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TriFusion" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.5.0" ; sc:url "http://odiogosilva.github.io/TriFusion/" ; biotools:primaryContact "Diogo Silva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_0625 ; sc:citation ; sc:description "This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of genotypes and traits. They allow to construct global linkage maps between genetic markers and gene expression, analyze multiple-locus linkage for gene expression, quantify the proportion of GW variation explained by each locus and identify eQTL hotspots, estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks." ; sc:featureList edam:operation_0314, edam:operation_1781, edam:operation_2238, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "trigger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/trigger.html" ; biotools:primaryContact "John D. Storey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """A feature selection method based on nearest neighbors for single-cell data. Feature selection is a relevant step in the analysis of single-cell RNA sequencing datasets. Triku is a feature selection method that favours genes defining the main cell populations. It does so by selecting genes expressed by groups of cells that are close in the nearest neighbor graph. Triku efficiently recovers cell populations present in artificial and biological benchmarking datasets, based on mutual information and silhouette coefficient measurements. Additionally, gene sets selected by triku are more likely to be related to relevant Gene Ontology terms, and contain fewer ribosomal and mitochondrial genes. Triku is available at https: gitlab.com alexmascension triku""" ; sc:featureList edam:operation_0314, edam:operation_3501, edam:operation_3936 ; sc:name "triku" ; sc:url "https://gitlab.com/alexmascension/triku" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0602, edam:topic_0654, edam:topic_3293 ; sc:citation "pubmed:27189565" ; sc:description "Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data." ; sc:featureList edam:operation_3429 ; sc:name "TriLoNet" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://www.uea.ac.uk/computing/TriLoNet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries." ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3237 ; sc:name "Trim Galore" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/" ; biotools:primaryContact "F. Krueger" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3365 ; sc:citation , ; sc:description "Remove the 3' adaptor of a list of reads." ; sc:featureList edam:operation_3192, edam:operation_3219 ; sc:name "trimadaptor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1916 ; sc:encodingFormat edam:format_1929, edam:format_1982, edam:format_1997, edam:format_1998 ; sc:name "Alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3168 ; sc:citation "pubmed:19505945" ; sc:description "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment." ; sc:featureList edam:operation_0492 ; sc:isAccessibleForFree true ; sc:name "trimAl" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.4", "2.0-RC" ; sc:url "http://trimal.cgenomics.org" ; biotools:primaryContact "Salvador Capella-Gutierrez" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3511 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove poly-A tails from nucleotide sequences." ; sc:featureList edam:operation_0363, edam:operation_0369, edam:operation_0428 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "trimest" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/trimest.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930, edam:format_1931, edam:format_1932, edam:format_1933, edam:format_2333 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3475 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3572 ; sc:citation , "pubmed:22684630" ; sc:description "A flexible read trimming tool for Illumina NGS data" ; sc:featureList edam:operation_3192 ; sc:isAccessibleForFree true ; sc:name "Trimmomatic" ; sc:softwareHelp ; sc:softwareVersion "0.36" ; sc:url "http://www.usadellab.org/cms/index.php?page=trimmomatic" ; biotools:primaryContact "Anthony Bolger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3300, edam:topic_3336, edam:topic_3379, edam:topic_3474 ; sc:citation , "pubmed:33147620" ; sc:description """TrimNet is a lightweight message passing neural network for multiple molecular property predictions. TrimNet can accurately complete multiple molecular properties prediction tasks with significant parameter reduction, including the quantum properties, bioactivity, physiology, and compound-protein interaction (CPI) prediction tasks.""" ; sc:featureList edam:operation_0250, edam:operation_0337, edam:operation_3938 ; sc:license "MIT" ; sc:name "TrimNet" ; sc:url "http://moleculenet.ai" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove unwanted characters from start and end of sequence(s)." ; sc:featureList edam:operation_0235, edam:operation_0369 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "trimseq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/trimseq.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , ; sc:description "Remove the 5' and/or 3' adaptors of a list of reads." ; sc:featureList edam:operation_3192 ; sc:name "trimsequences" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://urgi.versailles.inra.fr/Tools/REPET" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove extra whitespace from an ASCII text file." ; sc:featureList edam:operation_0335 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "trimspace" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/trimspace.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:26873930" ; sc:description "Program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software." ; sc:featureList edam:operation_3197 ; sc:name "Trinculo" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/trinculo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_3474 ; sc:citation , "pmcid:PMC10028424", "pubmed:36960450" ; sc:description "A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides." ; sc:featureList edam:operation_0267, edam:operation_3631, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "TriNet" ; sc:operatingSystem "Mac", "Windows" ; sc:url "http://liulab.top/TriNet/server" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Welcome to the world’s largest, living ecosystem of real-world data and evidence for the life sciences and healthcare industries. Global data, for global health." ; sc:featureList edam:operation_2409 ; sc:license "Other" ; sc:name "TriNetX" ; sc:softwareHelp ; sc:url "https://trinetx.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308, edam:topic_3512 ; sc:citation , , "pmcid:PMC3571712", "pmcid:PMC3875132", "pubmed:21572440", "pubmed:23845962" ; sc:description "Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads." ; sc:featureList edam:operation_3258 ; sc:name "Trinity" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/trinityrnaseq/trinityrnaseq/wiki" ; biotools:primaryContact "Aviv Regev", "Nir Friedman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3308 ; sc:citation , "pmcid:PMC5419050", "pubmed:28099853" ; sc:description "Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms." ; sc:featureList edam:operation_3672 ; sc:name "Trinotate" ; sc:softwareHelp ; sc:url "https://github.com/Trinotate/Trinotate.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3063, edam:topic_3516, edam:topic_3569 ; sc:citation ; sc:description "The package contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data." ; sc:featureList edam:operation_0283, edam:operation_3197, edam:operation_3557 ; sc:license "GPL-2.0" ; sc:name "trio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/trio.html" ; biotools:primaryContact "Holger Schwender" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3168, edam:topic_3516 ; sc:citation "pubmed:26772743" ; sc:description "This is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals)." ; sc:featureList edam:operation_3196 ; sc:name "TrioCaller" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://genome.sph.umich.edu/wiki/TrioCaller" ; biotools:primaryContact "Goncalo Abecasis", "Wei Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3673 ; sc:citation "pubmed:26644415" ; sc:description "A tool designed to jointly detect CNVs from WGS data in parent-offspring trios. It models read depth signal with the negative binomial regression to accommodate over-dispersion and considered GC content and mappability bias." ; sc:featureList edam:operation_3228 ; sc:name "TrioCNV" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/yongzhuang/TrioCNV" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673, edam:topic_3676, edam:topic_3958 ; sc:citation , "pubmed:34151932" ; sc:description "TrioCNV2 is a tool designed to jointly detecting copy number variations from WGS data of the parent-offspring trio. TrioCNV2 first makes use of the read depth and discordant read pairs to infer approximate locations of copy number variations, and then employs the split read and local de novo assembly approach to refine the breakpoints." ; sc:featureList edam:operation_0452, edam:operation_0524, edam:operation_3359, edam:operation_3961 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "TrioCNV2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/yongzhuang/TrioCNV2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2533, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25535243" ; sc:description "The program implements a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data." ; sc:featureList edam:operation_3202 ; sc:name "Triodenovo" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/Triodenovo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3055, edam:topic_3168 ; sc:citation , "pmcid:PMC8607709", "pubmed:34809557" ; sc:description "Using Mendelian inheritance logic to improve genomic phasing of trios" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3435, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "trioPhaser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dmiller903/trioPhaser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3676 ; sc:description "It is a visualisation tool developed to assist filtering on coverage and variant frequency for genomic variants from exome sequencing of parent-child trios. It organises the variant data by grouping each variant based on the laws of Mendelian inheritance. Taking three Variant Call Format files as input, the tool provides a user interface to test different coverage thresholds, to find the optimal threshold values, and to gain insights into the global effects of filtering." ; sc:featureList edam:operation_0337, edam:operation_3695 ; sc:name "TrioVis" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130409" ; sc:url "http://www.bytebucket.org/vda-lab/triovis/wiki/Home" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0219, edam:topic_0602 ; sc:citation "pubmed:20851834" ; sc:description "TRansient receptor potential channel-Interacting Protein Database is a manually curated database that aims to offer comprehensive information on protein-protein interactions (PPIs) of mammalian transient receptor protein (TRP) channels. The database provides a detailed summary of PPI data that fit into four categories: screening, validation, characterization and functional consequence." ; sc:featureList edam:operation_2421, edam:operation_2428, edam:operation_2429, edam:operation_2464 ; sc:name "TRIP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.trpchannel.org" ; biotools:primaryContact "Dongseop Kwon", "Ju-Hong Jeon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3512, edam:topic_3523, edam:topic_3912 ; sc:citation ; sc:description "TRiP is a large-scale transgenic Drosophila resource collections for loss- and gain-of-function studies." ; sc:featureList edam:operation_0308 ; sc:name "TRiP" ; sc:url "https://fgr.hms.harvard.edu/trip-in-vivo-fly-rnai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053 ; sc:citation , "pmcid:PMC3808541", "pubmed:21959868", "pubmed:24163125" ; sc:description "Tripal is a collection of open-source, freely-available Drupal modules that serves as a web interface for a GMOD Chado database. It is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools. Tripal is part of the open-source tool collection available through the Generic Model Organism Database (GMOD) project." ; sc:featureList edam:operation_0337 ; sc:name "Tripal" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://tripal.sourceforge.net/" ; biotools:primaryContact "Support Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0621, edam:topic_0780, edam:topic_3277 ; sc:citation , "pmcid:PMC6989756", "pubmed:31960040" ; sc:description """a Tripal module to increase exchange and reuse of genome assembly metadata. This module connects to the NCBI EUtils API to load in accessions for the Assembly, BioProject, and BioSample databases. Primary, as well as linked, records are loaded into Chado. Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database, and is a member of the GMOD family of tools. This record is maintained by: bcondon ORCID , spficklin , mestato.""" ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3096, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "Tripal EUtils" ; sc:softwareHelp , ; sc:url "https://github.com/NAL-i5K/tripal_eutils" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3489, edam:topic_3810 ; sc:citation , "pmcid:PMC7334887", "pubmed:32621602" ; sc:description "The Tripal Galaxy module is designed to support integration of Tripal with Galaxy. It uses the blend4php library. In the past, community databases have often provided analytical tools that come prepared with site-specific data. Examples include BLAST, CAP3, and InterProScan servers, for example. By integrating Tripal with Galaxy, the Tripal-based community database can offer more complicated analytical tools that support larger data sets using Galaxy as a backend." ; sc:featureList edam:operation_2422, edam:operation_3431 ; sc:license "GPL-2.0" ; sc:name "Tripal Galaxy" ; sc:softwareHelp , , ; sc:url "https://github.com/tripal/tripal_galaxy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0625, edam:topic_3489 ; sc:citation , "pmcid:PMC8074878", "pubmed:33900378" ; sc:description "Tripal MegaSearch is a tool for downloading biological data stored in a Tripal/Chado database. Site administrators may choose from two different data sources to serve data, i.e. Tripal MegaSearch materialized views (MViews) or Chado base tables. If neither data source is desired, administrators may also create their own MViews and serve them through Tripal MegaSearch. Site administrators can also set download limits according to their server's capability." ; sc:featureList edam:operation_0282, edam:operation_2421, edam:operation_2422, edam:operation_3196 ; sc:license "Not licensed" ; sc:name "Tripal MegaSearch" ; sc:softwareHelp ; sc:url "https://gitlab.com/mainlabwsu/tripal_megasearch" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3489 ; sc:citation , "pmcid:PMC5532966", "pubmed:29220446" ; sc:description "The module allows you to easily manage the indexing and display of Elasticsearch on your Tripal website. It also easily enables Cross-Site Querying, allowing you to connect to other Tripal sites and provide additional search results to your users." ; sc:featureList edam:operation_3762 ; sc:license "GPL-3.0" ; sc:name "Tripal Elasticsearch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tripal/tripal_elasticsearch" ; biotools:primaryContact "Margaret Staton" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0659, edam:topic_3071 ; sc:citation , "pmcid:PMC10202427", "pubmed:37223317" ; sc:description "Database for identifying the human genomic DNA and lncRNA triplexes." ; sc:featureList edam:operation_0335, edam:operation_0441, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:name "TRIPBASE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://tripbase.iis.sinica.edu.tw/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1772 ; sc:name "Score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128 ; sc:description "Predict RNA binding proteins from sequences using string kernel SVMs." ; sc:featureList edam:operation_1777 ; sc:isAccessibleForFree true ; sc:name "TriPepSVM" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/marsicoLab/TriPepSVM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0621, edam:topic_3512, edam:topic_3518 ; sc:citation ; sc:description "TripletGO is an algorithm for predicting Gene Ontology (GO) of genes. It consists of four pipelines to detect GO terms through (1) expression profile similarity based on triplet network, (2) genetic sequence alignment, (3) protein sequence alignment, and (4) naïve probability. The final function insights are a combination of the four pipelines through neural network" ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "TripletGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanglab.ccmb.med.umich.edu/TripletGO/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description """Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. A contact map prediction based on a triplet of coevolutionary features and deep residual neural networks. TripletRes is a method for protein inter-residue contact prediction. For a query sequence, TripletRes starts with the collection of deep multiple sequence alignments (MSAs) through whole-genome and metagenome sequence databases. Next, three complimentary coevolutionay feature matrices (covariance martrix, precision matrix and the pseudolikelihood maximization) extracted from the MSAs are used to create contact-map models through deep residual convolutional neural network training.""" ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0392, edam:operation_0476, edam:operation_2415 ; sc:name "TripletRes" ; sc:url "https://zhanglab.ccmb.med.umich.edu/TripletRes/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0097, edam:topic_0602, edam:topic_3332 ; sc:citation , "pubmed:23709494" ; sc:description "This package provides functions for the identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D." ; sc:featureList edam:operation_0262, edam:operation_0570, edam:operation_2481 ; sc:license "BSD-4-Clause" ; sc:name "triplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.14.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/triplex.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_0659, edam:topic_3315, edam:topic_3474 ; sc:citation , "pmcid:PMC7663897", "pubmed:33183242" ; sc:description """TriplexFPP: A deep learning program for DNA:RNA triplex potential prediction. TriplexFPP is an integrated program for DNA:RNA triplex prediction. It contains two models: 1) triplex lncRNA prediction model, to predict the most likely triplex forming lncRNA in practical, and 2) triplex DNA site prediction model, to predict if a DNA site can form triplex in practical. It will give researchers useful guidelines to study the DNA:RNA triplex formation. Fig. 1.An overview of the architechture and model parameters for TriplexFPP.""" ; sc:featureList edam:operation_0475, edam:operation_3435, edam:operation_3902, edam:operation_3903 ; sc:license "GPL-3.0" ; sc:name "TriplexFPP" ; sc:url "https://github.com/yuuuuzhang/TriplexFPP" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2909 ; sc:encodingFormat edam:format_2330 ; sc:name "Organism name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2342 ; sc:encodingFormat edam:format_2330 ; sc:name "Pathway or network name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2355 ; sc:encodingFormat edam:format_2330 ; sc:name "RNA family identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3603 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:encodingFormat edam:format_1457, edam:format_3603, edam:format_3604 ; sc:name "Sequence composition plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2140 ; sc:encodingFormat edam:format_3603 ; sc:name "Concentration" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2331, edam:format_3464, edam:format_3752 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_0749 ; sc:citation ; sc:description "Database of cooperating miRNAs and their mutual targets which enables researchers explore novel patterns in gene regulation." ; sc:featureList edam:operation_2422, edam:operation_3083, edam:operation_3184, edam:operation_3436, edam:operation_3695 ; sc:name "TriplexRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://triplexrna.org" ; biotools:primaryContact "Andrea Bagnacani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2830 ; sc:citation , "pmcid:PMC7525938", "pubmed:32993478" ; sc:description "T-cell Receptor/Immunoglobulin Profiler (TRIP)" ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "tripr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/TRIP" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0194, edam:topic_3053, edam:topic_3293 ; sc:citation , "pubmed:34978565" ; sc:description "Completing Gene Trees Without Species Trees in Sub-quadratic Time." ; sc:featureList edam:operation_0544, edam:operation_0553, edam:operation_3478, edam:operation_3942 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "tripVote" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/uym2/tripVote" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Workflow" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_0797, edam:topic_3810 ; sc:description """Triti-Map is a Snakemake-based pipeline for gene mapping in Triticeae, which contains a suite of user-friendly computational packages and web-interface integrating multi-omics data from Triticeae species including genomic, epigenomic, evolutionary and homologous information. Triti-Map could efficiently explore trait-related genes or functional elements not present in the reference genome and reduce the time and labor required for gene mapping in large genome species.""" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Triti-Map" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "v0.9.0" ; sc:url "https://github.com/fei0810/Triti-Map" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3055, edam:topic_3298, edam:topic_3518, edam:topic_3810 ; sc:citation ; sc:description "Combining heterogeneous data sets via relationships matrices." ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3557, edam:operation_3659 ; sc:name "triticeaetoolbox" ; sc:url "https://breedbase.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1759 ; sc:name "PDB model number" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3332 ; sc:citation ; sc:description "In silico construction of protein mutants, modelling enzymatic reactions, analysis of essential interactions between the enzyme and its substrate and docking ligand molecules into protein receptors." ; sc:featureList edam:operation_0331, edam:operation_0570, edam:operation_2426, edam:operation_2492 ; sc:isAccessibleForFree true ; sc:name "TRITON" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-CZ" ; sc:softwareHelp , , ; sc:softwareVersion "4.0" ; sc:url "http://ncbr.chemi.muni.cz/triton/triton.html" ; biotools:primaryContact "Martin Prokop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3500 ; sc:citation "pubmed:19843604" ; sc:description "Integrated database providing access to genome-scale datasets for kinetoplastid parasites. Integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data can be interrogated utilizing a search strategy system that enables a user to construct complex queries combining multiple data types." ; sc:featureList edam:operation_0224, edam:operation_0226, edam:operation_2422, edam:operation_3429 ; sc:name "Kinetoplastid genome resources (TritryPDB)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.TriTrypDB.org" ; biotools:primaryContact "TriTrypDB Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3940 ; sc:citation , "pubmed:32047897" ; sc:description """TRInc is a comprehensive database for human transcriptional regulatory information of lncRNAs. Long noncoding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and biological functions. With the increasing study of human diseases and biological processes, information in human H3K27ac ChIP-seq, ATAC-seq and DNase-seq datasets is accumulating rapidly, resulting in an urgent need to collect and process data to identify transcriptional regulatory regions of lncRNAs. We therefore developed a comprehensive database for human regulatory information of lncRNAs (TRlnc, http: bio.licpathway.net TRlnc), which aimed to collect available resources of transcriptional regulatory regions of lncRNAs and to annotate and illustrate their potential roles in the regulation of lncRNAs in a cell type-specific manner""" ; sc:featureList edam:operation_0440, edam:operation_0443, edam:operation_3222 ; sc:name "TRlnc" ; sc:url "http://bio.licpathway.net/TRlnc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0219, edam:topic_0623, edam:topic_3174 ; sc:citation "pubmed:21071414" ; sc:description "The tRNA Gene DataBase Curated by Experts \"\"tRNADB-CE\"\" contains tRNA sequences." ; sc:featureList edam:operation_0464 ; sc:name "tRNADB-CE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://trna.nagahama-i-bio.ac.jp" ; biotools:primaryContact "tRNADB-CE Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC4287530", "pubmed:25272949" ; sc:description "The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications. Post-transcriptional modifications of tRNA plays a major role in their functionality." ; sc:featureList edam:operation_2945 ; sc:name "trnamod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/trnamod/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0099, edam:topic_0602 ; sc:citation "pubmed:27016142" ; sc:description "A method for predicting modifications in tRNA using the MODOMICS database of RNA modification pathways as a reference." ; sc:featureList edam:operation_0464 ; sc:name "tRNAmodpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://genesilico.pl/trnamodpred/" ; biotools:primaryContact "Janusz Bujnicki", "Magdalena Machnicka" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0622 ; sc:citation , "pmcid:PMC146525", "pubmed:27174935", "pubmed:9023104" ; sc:description "A program for improved detection of transfer RNA genes in genomic sequence." ; sc:featureList edam:operation_0253, edam:operation_0464 ; sc:name "Trnascan-SE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://trna.ucsc.edu/tRNAscan-SE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070 ; sc:description "The package imports the result of tRNAscan-SE as a GRanges object." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tRNAscanImport" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/tRNAscanImport.html" ; biotools:primaryContact "Felix GM Ernst" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:35389452" ; sc:description "tRNAstudio is a tool designed to analyze small RNA-seq datasets (single-end or paired-end data) in order to characterize tRNAs. It includes a specific mapping workflow and extracts information on tRNA gene expression (DESeq2 and Iso-tRNA-CP), classification of sequencing reads likely derived from precursor tRNAs (pre-tRNAs) or mature tRNAs (processed tRNAs), tRNA gene sequence coverage, and post-transcriptional tRNA modification levels." ; sc:featureList edam:operation_0464, edam:operation_2939, edam:operation_3185, edam:operation_3192, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "tRNAstudio" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/GeneTranslationLab-IRB/tRNAstudio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0654, edam:topic_0659, edam:topic_3512 ; sc:citation "pubmed:12000851", "pubmed:15215363" ; sc:description "T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering." ; sc:featureList edam:operation_0560, edam:operation_3198 ; sc:name "TROD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cellbio.unige.ch/RNAi.html" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3752 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2830, edam:topic_3474, edam:topic_3966 ; sc:citation , "pmcid:PMC10456195", "pubmed:37624802" ; sc:description "A novel sequence-based stacked approach for the accelerated discovery of linear T-cell epitopes of hepatitis C virus." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3196, edam:operation_3968 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "TROLLOPE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabqsar.pythonanywhere.com/TROLLOPE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3293, edam:topic_3308 ; sc:citation , "pmcid:PMC5542419", "pubmed:28781712" ; sc:description "TROM (Transcriptome Overlap Measure) is an R package for comparing transcriptomes within or between different species, and provide a different perspective, in contrast to traditional correlation analyses, about capturing transcriptomic similarity." ; sc:featureList edam:operation_3258 ; sc:license "GPL-2.0" ; sc:name "TROM" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.3" ; sc:url "http://www.stat.ucla.edu/~jingyi.li/software-and-data/trom.html" ; biotools:primaryContact "Jingyi Jessica Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3308 ; sc:description "The transcriptome analyser project aims to provide tools to determine and document all the transcribed parts of a genome. The transcribed parts are defined by analysing experimental evidence, like expressed sequence tags (EST) and other mRNA sequences." ; sc:featureList edam:operation_0226 ; sc:name "tromer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://epd.expasy.org/tromer/" ; biotools:primaryContact "TromER Helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3168 ; sc:citation , , , "pmcid:PMC6280783", "pubmed:26861821" ; sc:description "An R suite for state-of-the-art algorithms for the reconstruction of causal models of cancer progressions from genomic cross-sectional data." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TRONCO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BICOCCA" ; sc:softwareHelp ; sc:softwareVersion "2" ; sc:url "https://sites.google.com/site/troncopackage/" ; biotools:primaryContact "Marco Antoniotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3572 ; sc:citation "pubmed:25075116" ; sc:description "An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. 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The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments." ; sc:featureList edam:operation_0379 ; sc:name "TRUST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ibi.vu.nl/programs/trustwww/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0804, edam:topic_3170 ; sc:citation , "pubmed:33986545" ; sc:description "TRUST4 is a tool for immune repertoire reconstruction from bulk and single-cell RNA-seq data." ; sc:featureList edam:operation_0310, edam:operation_0335, edam:operation_3800 ; sc:license "GPL-3.0" ; sc:name "TRUST4" ; sc:url "https://github.com/liulab-dfci/TRUST4" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3382, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:33381839" ; sc:description """Conditional out-of-distribution generation for unpaired data using transfer VAE. 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TrypInDB is a searchable online resource of small molecule inhibitors having a varying degree of activity towards Trypanosoma sp. Information of about >14,000 small molecules from >700 published research articles were collected and made as an easy-to-search database. Four major sets of information were made available for each collected inhibitors viz., General information (activity values; source of the inhibitors; enzyme targets; etc.,), Structural information, Toxicity information, and Literature information. More than 40 different information about each inhibitor were collected or predicted and made accessible for searching.""" ; sc:featureList edam:operation_2421, edam:operation_3695 ; sc:name "TrypInDB" ; sc:url "http://trypindb.biomedinformri.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC7199321", "pubmed:32366212" ; sc:description """TS is a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data. 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TSMiner provides a network map with extensive interactive visualization operations to help users explore the time-specific regulatory networks""" ; sc:featureList edam:operation_0314, edam:operation_3660, edam:operation_3929 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "TSMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/free1234hm/tsminer-tool.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3673, edam:topic_3676, edam:topic_3930 ; sc:citation , , "pmcid:PMC5414268", "pmcid:PMC8385119", "pubmed:28484631", "pubmed:34471496" ; sc:description "A one-stop software solution for tumor-specific neoantigen detection. 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Grey Monroe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33481705" ; sc:description "Part-Object Relational Visual Saliency." ; sc:featureList edam:operation_0337, edam:operation_3625 ; sc:name "TSPORTNet" ; sc:url "https://github.com/liuyi1989/TSPORTNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "This server allows you to predict the 3D structure of proteins from its amino acid sequence. 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Taylor Raborn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0634, edam:topic_0749, edam:topic_3407, edam:topic_3512 ; sc:citation , "pmcid:PMC8265037", "pubmed:34250478" ; sc:description "TSRexploreR facilitates processing and exploration of data generated by global transcription start site (TSS) mapping technologies such as CAGE and STRIPE-seq. TSSs can be extracted and aggregated from mapped reads in BAM/SAM format or pre-aggregated TSSs in GRanges, bigWig, bedGraph, or CTSS format can be imported. 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It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers." ; sc:featureList edam:operation_2480 ; sc:name "TSSV" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://git.lumc.nl/j.f.j.laros/tssv/blob/master/README.md" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "A new variance ratio metric to detect the timescale of compensatory dynamics | Abstract Understanding the mechanisms governing ecological stability why a property such as primary productivity is stable in some communities and variable in others has long been a focus of ecology. 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TTD includes information about successful, clinical trial and research targets, approved, clinical trial and experimental drugs linked to their primary targets, new ways to access data by drug mode of action, recursive search of related targets or drugs, similarity target and drug searching, customized and whole data download, and standardized target ID." ; sc:featureList edam:operation_0346, edam:operation_0360, edam:operation_0429, edam:operation_2421, edam:operation_2489 ; sc:name "TTD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bidd.nus.edu.sg/group/cjttd/" ; biotools:primaryContact "Feng Zhu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0659, edam:topic_3336, edam:topic_3379 ; sc:citation , "pubmed:31691823" ; sc:description "Therapeutic Target Database (TTD) s an enriched resource for facilitating research and early development of targeted therapeutics." ; sc:featureList edam:operation_0463, edam:operation_2421, edam:operation_2422 ; sc:name "TTD" ; sc:url "http://db.idrblab.net/ttd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3518 ; sc:description "It is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free." ; sc:featureList edam:operation_2424, edam:operation_2990, edam:operation_3223, edam:operation_3432 ; sc:license "GPL-2.0" ; sc:name "TTMap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/TTMap.html" ; biotools:primaryContact "Rachel Jeitziner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_0749 ; sc:citation "pubmed:19958507" ; sc:description "Web-based search engine to find and annotate pTTSs within human genome region of interest. 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Its main focus is on the analysis of high-throughput sequencing data.""" ; sc:featureList edam:operation_3197, edam:operation_3199, edam:operation_3258 ; sc:license "GPL-3.0" ; sc:name "uap" ; sc:softwareHelp ; sc:url "https://github.com/yigbt/uap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0780, edam:topic_3810 ; sc:citation ; sc:description "Create Multi-Polygon Shapefiles for Extraction of Research Plot Scale Agriculture Remote Sensing Data." ; sc:featureList edam:operation_0337 ; sc:license "GPL-2.0" ; sc:name "UAStools" ; sc:url "https://github.com/andersst91/UAStools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0781, edam:topic_3168, edam:topic_3511, edam:topic_3577 ; sc:citation , "pmcid:PMC5474025", "pubmed:28623888" ; sc:description "UNIX-based vector integration site analysis pipeline that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads." ; sc:featureList edam:operation_3461 ; sc:name "Ub-ISAP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/ub-isap/" ; biotools:primaryContact "Atul Kamboj" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0194, edam:topic_0769, edam:topic_3293 ; sc:citation , "pubmed:34052993" ; sc:description "UBCG is a pipeline tool to infer a highly resolved phylogenetic tree using core gene set." ; sc:featureList edam:operation_0326, edam:operation_0567, edam:operation_3478 ; sc:name "UBCG2" ; sc:softwareHelp , ; sc:url "http://leb.snu.ac.kr/ubcg2" ; biotools:primaryContact "Jongsik Chun" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0602, edam:topic_2229, edam:topic_3520 ; sc:citation , "pmcid:PMC9004656", "pubmed:35139152" ; sc:description "A Bioinformatic Strategy to Elucidate Ubiquitin E3 Ligase Activities in Quantitative Proteomics Study." ; sc:featureList edam:operation_0417, edam:operation_3435, edam:operation_3501, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "UbE3-APA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Chenlab-UMN/Ub-E3-ligase-Activity-Profiling-Analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0637, edam:topic_0749, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "uBin – a manual refining tool for metagenomic bins designed for educational purposes." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216, edam:operation_3478 ; sc:license "MIT" ; sc:name "uBin" ; sc:url "https://github.com/ProbstLab/uBin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2814 ; sc:citation , "pmcid:PMC4843525", "pubmed:27114492" ; sc:description "Knowledge-based system that could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities." ; sc:featureList edam:operation_2414 ; sc:name "UbiNe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://140.138.144.145/~ubinet/index.php" ; biotools:primaryContact "Lee TY" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0601, edam:topic_3511 ; sc:citation , "pmcid:PMC4895383", "pubmed:26818456" ; sc:description "Incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines." ; sc:featureList edam:operation_0253 ; sc:name "UbiSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/UbiSite/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510 ; sc:citation ; sc:description "Software package and web tool that probabilistically determines whether a lysine residue in a protein is ubiquitinated. It is a random forest-based predictor of potential ubiquitination sites in proteins." ; sc:featureList edam:operation_0250 ; sc:name "UbPred" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ubpred.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3379, edam:topic_3382 ; sc:citation , "pubmed:36058054" ; sc:description "Deep learning-enabled assessment of ulcerative colitis from colonoscopy images." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UC-NfNet" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/DeepMIALab/UC-NfNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "UC2 – A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging." ; sc:featureList edam:operation_0310, edam:operation_3431, edam:operation_3443 ; sc:name "UC2" ; sc:url "https://github.com/bionanoimaging/UC2-GIT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_3336, edam:topic_3374 ; sc:citation , "pmcid:PMC8278538", "pubmed:34291144" ; sc:description "This suite of packages is developed to predicts resistome for unknown chemical compounds. 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UCell scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands relatively less computing time and memory than other available methods, enabling the processing of large datasets. UCell can be applied to any cell vs. gene data matrix, and includes functions to directly interact with Seurat objects." ; sc:featureList edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "UCell" ; sc:url "https://github.com/carmonalab/UCell" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:15980489", "pubmed:20507913" ; sc:description "A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. 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Bryson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "This tool has multiple functions, including: Protein Structure Prediction, Protein Sequence Analysis, Genome Analysis, Protein Structure Classification, Transmembrane Protein Modelling." ; sc:featureList edam:operation_2479 ; sc:name "UCL Web Services" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinf.cs.ucl.ac.uk/web_servers/web_services/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0781, edam:topic_2269, edam:topic_3324 ; sc:author "Copenhagen Causality Lab (CoCaLa)", "Martin Emil Jakobsen", "Nikolaj Theodor Thams", "Phillip Bredahl Mogensen" ; sc:description "The dashboard provides tools for visualizing the COVID-19 spread in individual countries over time, as well as comparing different countries on a similar time scale. 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All tables in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories.""" ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_0525, edam:operation_3208 ; sc:name "UCSC Genome Browser database" ; sc:url "https://hgdownload.soe.ucsc.edu/downloads.html#gbdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0622, edam:topic_2640, edam:topic_3382 ; sc:citation "pubmed:21059681" ; sc:description "The UCSC Cancer Genomics Browser comprises to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3208, edam:operation_3436, edam:operation_3695 ; sc:name "UCSC Cancer Genomics Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://genome-cancer.ucsc.edu" ; biotools:primaryContact "Cancer Genomics Browser Support", "Genomics Browser Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0621, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3366 ; sc:citation , , , , , , , , , , , , , , , "pmcid:PMC186604", "pmcid:PMC2808870", "pmcid:PMC3245018", "pmcid:PMC3245183", "pubmed:12045153", "pubmed:12519945", "pubmed:16381938", "pubmed:18086701", "pubmed:18996895", "pubmed:19906737", "pubmed:20959295", "pubmed:22075998", "pubmed:22086951", "pubmed:23155063", "pubmed:24270787", "pubmed:25428374", "pubmed:26590259", "pubmed:27899642", "pubmed:30407534" ; sc:description "Large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users own annotation data." ; sc:featureList edam:operation_0292, edam:operation_0308, edam:operation_2421, edam:operation_3197, edam:operation_3208 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "UCSC Genome Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://genome.ucsc.edu/" ; biotools:primaryContact "Brooke Rhead" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_0602, edam:topic_3391, edam:topic_3557 ; sc:citation "pubmed:23748957" ; sc:description "Online tool fo biologists to view high-throughput data sets simultaenously for the analysis of functional relationships between biological entities. Users can access several public interaction networks and functional genomics datasets through the portal as well as upload their own data for analysis. Using CircleMap, multiple genomic datasets can be viewed simultaneously." ; sc:featureList edam:operation_0276, edam:operation_2495, edam:operation_3463 ; sc:name "UCSC Interaction Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sysbio.soe.ucsc.edu/nets" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2640, edam:topic_3071 ; sc:citation ; sc:description """An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser. The goal of UCSCXenaShiny is to provide a web app for downloading, analyzing and visualizing datasets from UCSC Xena, which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded. A Shiny App for UCSC Xena Database. Provides a web app for downloading, analyzing and visualizing datasets from UCSC Xena (), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.""" ; sc:featureList edam:operation_0337, edam:operation_2422 ; sc:license "MIT" ; sc:name "UCSCXenaShiny" ; sc:url "https://github.com/openbiox/UCSCXenaShiny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640 ; sc:author ; sc:citation ; sc:description "UCSCXenaTools is an R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq. Public omics data from UCSC Xena are supported through multiple turn-key Xena Hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "UCSCXenaTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ropensci/UCSCXenaTools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2229, edam:topic_2830, edam:topic_3473, edam:topic_3500 ; sc:citation , "pmcid:PMC10040587", "pubmed:36993970" ; sc:description "T cell receptor sequence database with online analysis functions." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "UcTCRdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://uctcrdb.cn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0166, edam:topic_2275, edam:topic_3336 ; sc:citation , "pubmed:37792496" ; sc:description "Interactive real-time multi-body protein-protein docking software." ; sc:featureList edam:operation_0337, edam:operation_2492, edam:operation_3899 ; sc:isAccessibleForFree true ; sc:name "UDock2" ; sc:url "http://udock.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0154, edam:topic_0218, edam:topic_0623, edam:topic_0821 ; sc:citation , "pmcid:PMC7178389", "pubmed:31913448" ; sc:description "UDSMProt is an algorithm for the classification of proteins based on the sequence of amino acids alone. Its key component is a self-supervised pretraining step based on a language modeling task. The model is then subsequently finetuned to specific classification tasks. In our paper we considered enzyme class classification, gene ontology prediction and remote homology detection showcasing the excellent performance of UDSMProt." ; sc:featureList edam:operation_0303, edam:operation_0477, edam:operation_2995 ; sc:name "UDSMProt" ; sc:url "https://github.com/nstrodt/UDSMProt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0632, edam:topic_3318 ; sc:citation ; sc:description """A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs. Automation framework for conducting ultrafast electron microscopy experiments. This project is best understood while using Visual Studio (2019).""" ; sc:name "UEMtomaton" ; sc:url "https://github.com/CEMSFlannigan/UEMtomaton/releases/tag/v1.0" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2877 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2856 ; sc:encodingFormat edam:format_3752 ; sc:name "Structural distance matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_2814 ; sc:author "Pep Amengual" ; sc:citation , "pubmed:32761082" ; sc:description "An open-source and fast classifier for predicting the impact of mutations in protein–protein complexes" ; sc:featureList edam:operation_2423, edam:operation_2492 ; sc:name "UEP" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "V. Guallar Lab: Electronic and Atomic Protein Modelling @ Barcelona Supercomputer Center" ; sc:url "https://github.com/pepamengual/UEP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293, edam:topic_3299 ; sc:citation , , "pmcid:PMC3670741", "pmcid:PMC5850222", "pubmed:23418397", "pubmed:29077904" ; sc:description "Improving the Ultrafast Bootstrap Approximation." ; sc:featureList edam:operation_0324 ; sc:name "UFBoot2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.iqtree.org/" ; biotools:primaryContact "Le Sy Vinh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0194, edam:topic_0621, edam:topic_0769, edam:topic_3293 ; sc:citation , "pmcid:PMC9825530", "pubmed:36271795" ; sc:description "Database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi." ; sc:featureList edam:operation_0300, edam:operation_0544, edam:operation_0553, edam:operation_3460, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "UFCG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ufcg.steineggerlab.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3444, edam:topic_3474 ; sc:citation , "pubmed:35373388" ; sc:description "High fidelity deep learning-based MRI reconstruction with instance-wise discriminative feature matching loss." ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UFLoss" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mikgroup/UFLoss" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0128, edam:topic_0625, edam:topic_0634, edam:topic_3360 ; sc:citation , "pmcid:PMC7347127", "pubmed:32645039" ; sc:description "A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization." ; sc:featureList edam:operation_3501, edam:operation_3559, edam:operation_3925 ; sc:name "UFO" ; sc:url "http://apps.cytoscape.org/apps/ufo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0659, edam:topic_3474, edam:topic_3512 ; sc:citation ; sc:description """Fast and Accurate RNA Secondary Structure Prediction with Deep Learning. Abstract For many RNA molecules, the secondary structure is essential for the correction function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time. Traditional RNA secondary structure prediction algorithms are primarily based on thermodynamic models through free energy minimization. Here we propose a deep learning-based method, called UFold, for RNA secondary structure prediction, trained directly on annotated data without any thermodynamic assumptions""" ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2441 ; sc:name "UFold" ; sc:url "https://ufold.ics.uci.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3053, edam:topic_3071 ; sc:citation "pubmed:26921280" ; sc:description "An algorithm designed to provide a distributed method for assigning accession numbers to genomic features. The website is designed to introduce the utility of the tool by providing resources for mapping human genomic features among various bioinformatic databases and versions of databases with a focus on lncRNAs." ; sc:featureList edam:operation_3282 ; sc:name "UGAHash" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ugahash.uni-frankfurt.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2885, edam:topic_3127, edam:topic_3168 ; sc:citation , "pmcid:PMC9773435", "pubmed:36544090" ; sc:description "A generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes." ; sc:featureList edam:operation_0451, edam:operation_0484, edam:operation_3196, edam:operation_3211 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "UGDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AnimaTardeb/Meiogenix-UGDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_2814, edam:topic_3293 ; sc:citation ; sc:description "UGENE is a free cross-platform genome analysis suite that combines popular bioinformatics tools within a single user friendly interface." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "UGENE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ugene.unipro.ru" ; biotools:primaryContact "UGENE Tech Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0114 ; sc:description "Updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered." ; sc:featureList edam:operation_2423, edam:operation_3432 ; sc:name "UIcluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.5" ; sc:url "https://genome.uiowa.edu/home.old/pubsoft/clustering/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3070, edam:topic_3344 ; sc:description "Interactive dendrogram viewer." ; sc:featureList edam:operation_0283, edam:operation_3432 ; sc:isAccessibleForFree true ; sc:name "uidendrogram" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/28530-uidendrogram" ; biotools:primaryContact "Malcolm McLean" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_3053 ; sc:description "Used for the creation of fixed-length pooled library tags for EST-Based Gene Discovery." ; sc:featureList edam:operation_0335 ; sc:name "UITagCreator" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.9" ; sc:url "https://genome.uiowa.edu/home.old/pubsoft/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_3179, edam:topic_3325, edam:topic_3337, edam:topic_3676 ; sc:citation , "pmcid:PMC6987107", "pubmed:31992710" ; sc:description """Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts. Helix UK Biobank browser.""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3791 ; sc:name "UK Biobank" ; sc:url "https://ukb.research.helix.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3324, edam:topic_3337, edam:topic_3379, edam:topic_3419 ; sc:citation ; sc:description "The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH)." ; sc:featureList edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "UK-REACH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.uk-reach.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_3337, edam:topic_3517 ; sc:citation , "pubmed:34737426" ; sc:description "A generalized linear mixed model association tool for biobank-scale data." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:name "UKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://fastgwa.info/ukbimpbin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3305, edam:topic_3337, edam:topic_3400 ; sc:citation , "pmcid:PMC10132819", "pubmed:37114803" ; sc:description "The landscape of health disparities in the UK Biobank." ; sc:featureList edam:operation_2421, edam:operation_3436, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:name "UKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://ukbatlas.health-disparities.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3063, edam:topic_3303, edam:topic_3337 ; sc:citation ; sc:description """Categorising UK Biobank Self-Reported Medication Data using Text Matching. UK Biobank self reported medications are represented in UK Biobank as a list of codes per participant captured at the time of the Baseline Assessment Interview.""" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3196 ; sc:license "LGPL-3.0" ; sc:name "UKBB self-reported medications" ; sc:url "https://github.com/PhilAppleby/ukbb-srmed/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3337, edam:topic_3452 ; sc:citation ; sc:description "Tool for curation of UK Biobank data to generate cohorts. The tool can filter the main and associated datasets (e.g general practioner clinical data) based on search terms provided by the user. It can be used interactively through a web-based interface, a command line interface, or imported as a module and integrated into a broader pipeline. Additional functionality, such as automatically downloading large data files (bulk data) is also supported." ; sc:featureList edam:operation_2421, edam:operation_3359 ; sc:license "Apache-2.0" ; sc:name "UKBCC" ; sc:url "https://pypi.org/project/ukbcc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3335, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC9234069", "pubmed:35769930" ; sc:description "An R package for phenotyping health-related outcomes in the UK Biobank." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ukbpheno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/niekverw/ukbpheno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3337 ; sc:citation , "pmcid:PMC6544205", "pubmed:31150407" ; sc:description "R package to manage and query UK Biobank data." ; sc:featureList edam:operation_2422, edam:operation_2428, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "ukbtools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://cran.r-project.org/package=ukbtools" ; biotools:primaryContact "Ken Hanscombe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0634, edam:topic_2640, edam:topic_3053, edam:topic_3676 ; sc:citation , "pubmed:32684276" ; sc:description "uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes." ; sc:featureList edam:operation_3196 ; sc:name "uKIN" ; sc:url "https://github.com/Singh-Lab/uKIN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0749, edam:topic_3068, edam:topic_3303 ; sc:citation "pubmed:21062818" ; sc:description "UK PubMed Central is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as Agricola, Patents and recent biomedical theses. Furthermore, UKPMC contains 'Cited By' information as an alternative way to navigate the literature and has incorporated text-mining approaches to semantically enrich content and integrate it with related database resources." ; sc:featureList edam:operation_0305, edam:operation_0306, edam:operation_2436, edam:operation_3431 ; sc:name "UKPMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ukpmc.ac.uk" ; biotools:primaryContact "Help desk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3067, edam:topic_3304, edam:topic_3315, edam:topic_3382 ; sc:citation , "pubmed:36434788" ; sc:description "A framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience." ; sc:featureList edam:operation_2426, edam:operation_3799, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Ultraliser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BlueBrain/Ultraliser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Network Phylogeny" ; sc:featureList edam:operation_0324, edam:operation_2497 ; sc:license "GPL-3.0" ; sc:name "UltraNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html" ; biotools:primaryContact "Matteo Comin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_2545 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3168, edam:topic_3170 ; sc:citation , "pmcid:PMC8287537", "pubmed:34286104" ; sc:description "Ultraplex is a rapid, flexible all-in-one software package for processing and demultiplexing fastq files." ; sc:featureList edam:operation_3192, edam:operation_3359, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Ultraplex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ulelab/ultraplex" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0092 ; sc:citation , "pmcid:PMC5713368", "pubmed:29135934" ; sc:description "A universal and extensible software platform for biological sequence representations." ; sc:featureList edam:operation_0564 ; sc:license "GPL-3.0" ; sc:name "UltraPse" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/pufengdu/UltraPse" ; biotools:primaryContact "Pu-Feng Du" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3070, edam:topic_3344, edam:topic_3384, edam:topic_3954 ; sc:description "Ultrasound field simulation for transducer geometries for medical ultrasound and sonar applications." ; sc:featureList edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "Ultrasim" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/1335-ultrasim" ; biotools:primaryContact "Sverre Holm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3954 ; sc:description "Finds the optimal frame rate of an ultrasound acquisition including electrical stimulation." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Ultrasound framerate finder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/59006-ultrasound_find_best_framerate" ; biotools:primaryContact "Diego Miguez" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25380961" ; sc:description "Chimeric python/R tool that is designed to provide an accurate detection of low-frequency structural variations in large insert-size sequencing libraries." ; sc:featureList edam:operation_2480 ; sc:name "Ulysses" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.lcqb.upmc.fr/ulysses/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0821, edam:topic_3301 ; sc:citation "pubmed:19767608" ; sc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on compounds, enzymes, reactions and microorganism entries. It includes a Biochemical Periodic Table (UM-BPT) and a rule-based Pathway Prediction System (UM-PPS) that predicts plausible pathways for microbial degradation of organic compounds. UM-BBD compound data are contributed to PubChem and ChemSpider, the public chemical databases." ; sc:featureList edam:operation_0224, edam:operation_3431, edam:operation_3439 ; sc:name "UM-BBD" ; sc:softwareHelp ; sc:url "http://eawag-bbd.ethz.ch/aboutBBD.html" ; biotools:primaryContact "Kathrin Fenner, EAWAG-BBD Director" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_0621 ; sc:citation "pubmed:18524801" ; sc:description "The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made." ; sc:featureList edam:operation_2489, edam:operation_3439 ; sc:name "UM-PPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://eawag-bbd.ethz.ch/predict/aboutPPS.html" ; biotools:primaryContact "Kathrin Fenner, EAWAG-BBD Director" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_2830, edam:topic_3324, edam:topic_3379 ; sc:citation , "pmcid:PMC9535261", "pubmed:36213257" ; sc:description "UmabsDB is a comprehensive antibody therapeutics database serving the industry and academic community. It covers information on sequence, indication, target patent and clinical trial of antibody therapies." ; sc:featureList edam:operation_0252, edam:operation_0480 ; sc:isAccessibleForFree false ; sc:name "Umabs-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://umabs.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_2229, edam:topic_3474 ; sc:citation , "pubmed:34176069" ; sc:description "An Improved DNA-Binding Proteins Prediction Method Based on Uniform Manifold Approximation and Projection." ; sc:featureList edam:operation_0303, edam:operation_3900, edam:operation_3903, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "UMAP-DBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Wang-Jinyue/UMAP-DBP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3305, edam:topic_3325 ; sc:citation "pubmed:10612827", "pubmed:16086365" ; sc:description "Universal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3202 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "UMD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.umd.be/" ; biotools:primaryContact "Christophe Béroud" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3063, edam:topic_3325, edam:topic_3512, edam:topic_3574 ; sc:citation ; sc:description "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA." ; sc:featureList edam:operation_3197, edam:operation_3225 ; sc:name "UMD-Predictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://umd-predictor.eu" ; biotools:primaryContact "Christophe Beroud", "David Salgado" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC10176759", "pubmed:37173725" ; sc:description "Untargeted metabolomics workflow for high-throughput data processing and analysis." ; sc:featureList edam:operation_2409, edam:operation_3557, edam:operation_3629 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "UmetaFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/biosustain/snakemake_UmetaFlow" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3050, edam:topic_3174, edam:topic_3837 ; sc:citation , "pmcid:PMC9188040", "pubmed:35689184" ; sc:description "A taxonomic classifier for shotgun metagenomics reads" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UMGAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://unipept.ugent.be/umgap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0632, edam:topic_0749, edam:topic_0769, edam:topic_3940 ; sc:citation ; sc:description """ATAC-seq with unique molecular identifiers improves quantification and footprinting. This pipeline is used for UMI-ATAC-seq raw data processing, including removing the sequencing adapters, extracting UMIs from the original FASTQ read1 file, removing ME sequences and using the UMIs to remove PCR duplicates.""" ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3237, edam:operation_3799 ; sc:name "UMI-ATAC-seq" ; sc:url "https://github.com/tzhu-bio/UMI-ATAC-seq" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description """a UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries. Abstract Motivation With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. A lot of different variant callers are publicly available and usually do a good job at calling out variants. However, when frequencies begin to drop under 1%, the specificity of these tools suffers greatly as true variants at very low frequencies can be easily confused with sequencing or PCR artifacts. The recent use of Unique Molecular Identifiers (UMI) in NGS experiments offered a way to accurately separate true variants from artifacts.""" ; sc:featureList edam:operation_3198, edam:operation_3227, edam:operation_3675 ; sc:license "MIT" ; sc:name "UMI-Gen" ; sc:url "https://gitlab.com/vincent-sater/umigen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_3168, edam:topic_3393 ; sc:citation , "pmcid:PMC5340976", "pubmed:28100584" ; sc:description "Tools for handling Unique Molecular Identifiers in NGS data sets." ; sc:featureList edam:operation_3218 ; sc:license "MIT" ; sc:name "UMI-tools" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/CGATOxford/UMI-tools" ; biotools:primaryContact "Ian Sudbery" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3520, edam:topic_3940 ; sc:author ; sc:citation , "pubmed:34009302" ; sc:description "UMI4Cats is an R package to analyze processing, analysis and visualization of UMI-4C chromatin contact data. UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3799 ; sc:license "Artistic-2.0" ; sc:name "UMI4Cats" ; sc:url "https://www.bioconductor.org/packages/release/bioc/html/UMI4Cats.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2269, edam:topic_3474, edam:topic_3697 ; sc:citation ; sc:description "Umibato is a method for estimating time-varying microbial interactions using time-series quantitative data based on the Lotka-Volterra equation. Details for this method are described in this paper. Umibato is implemented as a python Class. Variational inference for CTRHMM, the second step of Umibato, is written in C++. You can also perform Umibato on UNIX shells using run_umibato.py." ; sc:featureList edam:operation_0276, edam:operation_3659, edam:operation_3799 ; sc:name "Umibato" ; sc:url "http://github.com/shion-h/Umibato" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0091, edam:topic_0632, edam:topic_3168, edam:topic_3519 ; sc:citation , "pmcid:PMC8193862", "pubmed:34122513" ; sc:description "UMIc is an alignment free framework serving as a pre-processing step of FASTQ files for deduplication and correction of reads building consensus sequences from each UMI. The tool takes into account the frequency and the Phred quality of nucleotides and the distances between the UMIs and the actual sequences, and produces FASTQ files that contain the corrected sequences (without the UMI) and their quality." ; sc:featureList edam:operation_3192, edam:operation_3219, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UMIc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/BiodataAnalysisGroup/UMIc" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0654, edam:topic_0769 ; sc:citation , "pubmed:36031761" ; sc:description "Software for Consensus Read Generation, Error Correction, and Visualization Using Unique Molecular Identifiers." ; sc:featureList edam:operation_0337, edam:operation_3227, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UMIErrorCorrect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tobbeost/umierrorcorrect" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_1930 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "A package that provides tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias." ; sc:featureList edam:operation_3680, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "umis" ; sc:url "https://github.com/vals/umis/" ; biotools:primaryContact "Valentine Svensson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0218, edam:topic_3303, edam:topic_3474 ; sc:citation , "pubmed:31730202" ; sc:description "Cross-lingual Semantic Annotation of Biomedical Literature." ; sc:featureList edam:operation_2422, edam:operation_3778 ; sc:name "UMLSmapper" ; sc:url "https://snlt.vicomtech.org/umlsmapper" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3063, edam:topic_3379, edam:topic_3474 ; sc:citation ; sc:description "The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is an R package to facilitate the simulation of realistic microarray data sets with links to associated outcomes." ; sc:featureList edam:operation_2428, edam:operation_3432, edam:operation_3566 ; sc:license "Apache-2.0" ; sc:name "Umpire 2.0" ; sc:url "https://cran.r-project.org/package=Umpire" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC8658322", "pubmed:34884927" ; sc:description "A New Approach for Accurate Prediction of Umami Peptides Using Feature Representation Learning." ; sc:featureList edam:operation_0418, edam:operation_0477, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:name "UMPred-FRL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pmlabstack.pythonanywhere.com/UMPred-FRL" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0611 ; sc:citation , "pubmed:30944056" ; sc:description "Twin and path-based structural equation modeling in R." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "umx" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.10.0" ; sc:url "https://cran.r-project.org/package=umx" ; biotools:primaryContact "Timothy C. Bates" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0082, edam:topic_0099, edam:topic_0602, edam:topic_0654 ; sc:citation ; sc:description "Unified Nucleic Acid Folding. Simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, entire melting profiles are computed , not just melting temperatures." ; sc:featureList edam:operation_0279, edam:operation_2423 ; sc:name "UNAFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "3.9-1" ; sc:url "http://www.unafold.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0634, edam:topic_3396, edam:topic_3423, edam:topic_3577 ; sc:citation , "pmcid:PMC7243028", "pubmed:32454857" ; sc:description "A Universal Natural Product Database for Materia Medica of Iranian Traditional Medicine." ; sc:featureList edam:operation_0306, edam:operation_3096 ; sc:name "UNaProd" ; sc:url "http://jafarilab.com/unaprod/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3174, edam:topic_3512, edam:topic_3673 ; sc:citation ; sc:description "Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED." ; sc:featureList edam:operation_0452, edam:operation_0484, edam:operation_3185, edam:operation_3919 ; sc:license "MIT" ; sc:name "UNCALLED" ; sc:url "http://github.com/skovaka/UNCALLED" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3517 ; sc:citation , "pmcid:PMC4668777", "pubmed:25979475" ; sc:description "Perform single marker association testing on raw next generation sequencing data. It allows for flexible covariates adjustment and does not require genotype calling. Provides a likelihood ratio test (LRT), score test and a combination of the two." ; sc:featureList edam:operation_2238, edam:operation_2429 ; sc:license "Not licensed" ; sc:name "UNCcombo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yunliweb.its.unc.edu/UNCcombo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3300, edam:topic_3318, edam:topic_3398 ; sc:citation , "pmcid:PMC9812870", "pubmed:36521358" ; sc:description "Uncertainty quantification for computational models in biomedicine and bioengineering." ; sc:featureList edam:operation_2426, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UncertainSCI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SCIInstitute/UncertainSCI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3305, edam:topic_3452, edam:topic_3474 ; sc:citation , "pmcid:PMC9534540", "pubmed:36217534" ; sc:description "Robust uncertainty-aware hierarchical feature fusion model with Ensemble Monte Carlo Dropout for COVID-19 detection." ; sc:featureList edam:operation_3799, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "UncertaintyFuseNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/moloud1987/UncertaintyFuseNet-for-COVID-19-Classification" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_2275 ; sc:citation "pubmed:15713458" ; sc:description "Software analysis of coupled folding and binding equilibria by global analysis of temperature dependence isothermal titration calorimetry and CD data." ; sc:featureList edam:operation_2415, edam:operation_2949 ; sc:name "Uncoupler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://people.cryst.bbk.ac.uk/~ubcg66a/uncoupler_summary.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Characterising single circulating tumor cell transcriptomes." ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3432, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "unCTC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/SaritaPoonia/unCTC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0749, edam:topic_2229, edam:topic_3067, edam:topic_3170 ; sc:citation ; sc:description """Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data. UNCURL-App is a unified framework for interactively analyzing single-cell RNA-seq data. It is based on UNCURL for data preprocessing and clustering. It can be used to perform a variety of tasks such as:. This exposes the given port, and then the uncurl-app website can be visited in the browser at http://your-ip-address:port. To stop the server, run sudo killall gunicorn in another terminal.""" ; sc:featureList edam:operation_2938, edam:operation_3432, edam:operation_3935 ; sc:license "MIT" ; sc:name "UNCURL-App" ; sc:url "https://uncurl.cs.washington.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , ; sc:description "Parameter-free Alignment-free comparison of regulatory sequences (cis-regulatory modules). Assembly-free Genome Comparison based on Next-Generation Sequencing Reads and Variable Length Patterns." ; sc:featureList edam:operation_2403, edam:operation_2478 ; sc:license "Other" ; sc:name "UnderIICRMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.dei.unipd.it/~ciompin/main/UnderIICRMS.html" ; biotools:primaryContact "Matteo Comin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation ; sc:description "Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords." ; sc:featureList edam:operation_0258 ; sc:license "Other" ; sc:name "UnderlyingApproach" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.dei.unipd.it/~ciompin/main/underlying.html" ; biotools:primaryContact "Matteo Comin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Filtering Degenerate Motifs with Application to Protein Sequence Analysis" ; sc:featureList edam:operation_2478 ; sc:license "Other" ; sc:name "UnderlyingFilter" ; sc:operatingSystem "Linux" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.dei.unipd.it/~ciompin/main/filtering.html" ; biotools:primaryContact "Matteo Comin" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_2056 ; sc:name "Gene expression profile" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2056 ; sc:name "Gene expression matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3360, edam:topic_3518 ; sc:citation ; sc:description "R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge." ; sc:featureList edam:operation_0313, edam:operation_3232 ; sc:license "GPL-2.0" ; sc:name "UNDO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/UNDO.html" ; biotools:primaryContact "Niya Wang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation ; sc:description """Unfazed is a parent-of-origin detection for large and small de novo variants. Unfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30,000 de novo variants in under 60 hours.""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3454, edam:operation_3644 ; sc:name "Unfazed" ; sc:url "https://github.com/jbelyeu/unfazed" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3712 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:description "Reading Thermo .raw files without MsFileReader." ; sc:featureList edam:operation_0335 ; sc:name "unfinnigan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://code.google.com/p/unfinnigan/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0602 ; sc:citation ; sc:description "Predict the sequence of protein (un)folding events by recursive min-cut on a weighted secondary structure element graph." ; sc:featureList edam:operation_2479 ; sc:name "UNFOLD" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.cs.rpi.edu/~zaki/www-new/pmwiki.php/Software/Software#toc34" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3300, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC6815663", "pubmed:31660265" ; sc:description """an integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis. A matlab EEG toolbox to perform overlap correction and non-linear & linear regression. EEG Deconvolution Toolbox — Unfold EEG Toolbox. Unfold - EEG Deconvolution Toolbox. A toolbox for deconvolution of overlapping EEG (Pupil, LFP etc.) signals and (non)-linear modeling. A toolbox for deconvolution of overlapping EEG signals and (non)-linear modeling. git clone https://github.com/unfoldtoolbox/unfold. If you use the toolbox, please cite us as: Ehinger BV & Dimigen O, Unfold: An integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis, bioRxiv, https://doi.org/10.1101/360156. Model specification using R-style formulas (EEG~1+face+age).""" ; sc:featureList edam:operation_0408, edam:operation_3629, edam:operation_3659 ; sc:license "GPL-3.0" ; sc:name "unfold" ; sc:url "http://www.unfoldtoolbox.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3572 ; sc:description "Unfold and show the content of the given structure. UNFOLD_STRUCTURE(STRUCT) shows recursively the content of the given structure STRUCT. Clean and generic implementation which can be easily extended, e.g. for structures containing cells." ; sc:featureList edam:operation_0408 ; sc:isAccessibleForFree true ; sc:name "Unfold structures" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/31808-unfold-structures" ; biotools:primaryContact "Thomas Schaffter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_3292, edam:topic_3306 ; sc:description "Applicable for thermal as well as chemical denaturation of protein" ; sc:featureList edam:operation_0408, edam:operation_0430, edam:operation_3755 ; sc:isAccessibleForFree true ; sc:name "Unfolding protein in two states" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42849-unfolding-protein-in-two-states" ; biotools:primaryContact "Rohan Dandage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0097, edam:topic_3070 ; sc:description "Calculates protein melting point, Tm, from unfolding data in three different ways." ; sc:featureList edam:operation_0250, edam:operation_0408 ; sc:isAccessibleForFree true ; sc:name "unfoldprotein" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.3.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/26091-unfoldprotein-m" ; biotools:primaryContact "Kristopher White" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_3308 ; sc:citation , "pubmed:31631213" ; sc:description "uniConSig is a genome-wide quantification of new biological and pathological functions of genes and pathways." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3799 ; sc:name "uniConSig" ; sc:url "https://github.com/wangxlab/uniConSig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3343 ; sc:citation , "pubmed:37125970" ; sc:description "GPU-accelerated docking." ; sc:featureList edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "Uni-Dock" ; sc:operatingSystem "Linux" ; sc:url "https://app.bohrium.dp.tech/uni-dock/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2830, edam:topic_3336 ; sc:citation , "pubmed:37328705" ; sc:description "Open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening." ; sc:featureList edam:operation_0387, edam:operation_2476, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Uni-GBSA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://labs.dp.tech/projects/uni-gbsa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_3510 ; sc:citation "pubmed:26059715" ; sc:description "Protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation." ; sc:featureList edam:operation_0503 ; sc:name "UniAlign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://sacan.biomed.drexel.edu/unialign" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3169, edam:topic_3295, edam:topic_3512 ; sc:citation ; sc:description """A map of direct TF-DNA interactions across species. UniBind is a comprehensive map of direct interactions between transcription factor (TFs) and DNA. High confidence TF binding site predictions were obtained from uniform processing of thousands of ChIP-seq data sets using the ChIP-eat software. A RESTful API to access the latest version of UniBind database programmatically. This API provides an easy-to-use REST web interface to query/retrieve data from the UniBind database. The API comes with a human browsable interface and also a programmatic interface which return the results in different formats, including json, jsonp, yaml, bed, and also api for a browsable interface.""" ; sc:featureList edam:operation_0441, edam:operation_2422, edam:operation_2575, edam:operation_3501 ; sc:name "UniBind" ; sc:softwareHelp ; sc:url "https://unibind.uio.no/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3425 ; sc:name "Carbohydrate property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0152 ; sc:citation ; sc:description "A database of LC-MS structural data for oligosaccharides." ; sc:featureList edam:operation_0224 ; sc:name "UniCarb-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "bils.se" ; sc:softwareHelp ; sc:url "http://unicarb-db.biomedicine.gu.se/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0122, edam:topic_0152, edam:topic_0601 ; sc:citation , "pmcid:PMC3964942", "pubmed:24234447" ; sc:contributor "CCRC, USA", "Macquarie University, Australia", "Max Planck Institute of Colloids and Interfaces, Germany", "National Institute for Bioprocessing Research and Training (NIBRT), Ireland", "SIB Swiss Institute of Bioinformatics", "Soka University, Japan", "UNSW, Australia", "University of Gothenburg, Sweden" ; sc:description "Curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures." ; sc:featureList edam:operation_0416, edam:operation_0417 ; sc:isAccessibleForFree true ; sc:name "UniCarbKB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://unicarb-db.expasy.org/" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:name "Map data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3736 ; sc:name "Ecological data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2019 ; sc:name "Map data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0610 ; sc:contributor "František Mastil", "Jakub Geyer", "Jiří Hauser", "Miloš Prokýšek", "Ondřej Doktor", "Rudolf Vohnout" ; sc:description "Universal Catalog Database for biological findings" ; sc:featureList edam:operation_3436 ; sc:license "Other" ; sc:name "UniCatDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Institute of Applied Informatics, Faculty of Science, University of South Bohemia" ; sc:softwareHelp ; sc:url "https://www.unicatdb.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_2275 ; sc:citation "pubmed:27259540" ; sc:description "Software for de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling." ; sc:featureList edam:operation_0474 ; sc:name "UniCon3D" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sysbio.rnet.missouri.edu/UniCon3D/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_2571 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929, edam:format_3617 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_3168, edam:topic_3301 ; sc:citation , "pmcid:PMC5481147", "pubmed:28594827" ; sc:description "A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads." ; sc:featureList edam:operation_0525, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Unicycler" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/rrwick/Unicycler" ; biotools:primaryContact "Ryan R. Wick" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3374, edam:topic_3520 ; sc:citation , "pubmed:37478487" ; sc:description "UniDec processing pipeline for rapid analysis of biotherapeutic mass spectrometry data." ; sc:featureList edam:operation_1812, edam:operation_3215, edam:operation_3629, edam:operation_3860 ; sc:isAccessibleForFree true ; sc:name "UniDec" ; sc:softwareHelp ; sc:url "https://github.com/michaelmarty/UniDec" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0128, edam:topic_0130, edam:topic_0154, edam:topic_0821 ; sc:citation , "pmcid:PMC10199764", "pubmed:37078688" ; sc:description "Computational framework for protein design, targeting a diversity of protein design and engineering tasks, and it can also be used for protein structure modeling and scoring." ; sc:featureList edam:operation_0394, edam:operation_0477, edam:operation_2476, edam:operation_4008 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UniDesign" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/tommyhuangthu/UniDesign" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0897 ; sc:name "Protein property" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0623, edam:topic_3474 ; sc:citation , "pubmed:37020337" ; sc:description "Universal deep learning architecture for binary classification in peptide bioactivity." ; sc:featureList edam:operation_2995, edam:operation_3631, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UniDL4BioPep" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nepc2pvmzy.us-east-1.awsapprunner.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1476, edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0108, edam:topic_0736, edam:topic_3318 ; sc:citation , "pmcid:PMC9919455", "pubmed:36734597" ; sc:description "A unified approach to protein domain parsing with inter-residue distance matrix." ; sc:featureList edam:operation_0272, edam:operation_0303, edam:operation_0474, edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "UniDoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yanglab.nankai.edu.cn/UniDoc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3474 ; sc:citation ; sc:description "UNIFAN (Unsupervised Single-cell Functional Annotation) simultaneously clusters and annotates cells with known biological processes (including pathways)." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "UNIFAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/doraadong/UNIFAN" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3475 ; sc:name "Gene expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_2331, edam:format_3033, edam:format_3475 ; sc:name "Gene expression data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3519 ; sc:citation , "pubmed:24794933" ; sc:description "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data." ; sc:featureList edam:operation_3223 ; sc:license "GPL-2.0" ; sc:name "unifiedWMWqPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/unifiedWMWqPCR.html" ; biotools:primaryContact "Joris Meys" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2594 ; sc:name "UniGene taxon" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1104 ; sc:name "Sequence cluster ID (UniGene)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3134 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene transcript report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0623, edam:topic_3512 ; sc:description "Each entry is a set of transcript (expressed sequence tag) sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location." ; sc:featureList edam:operation_0224 ; sc:name "UniGene gene-oriented nucleotide sequence clusters" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0152, edam:topic_0154, edam:topic_0637 ; sc:citation , "pubmed:33174598" ; sc:description """Update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. UniLectin platform is a dedicated portal of databases and tools to study the lectins. Lectins are carbohydrate (glycan) binding proteins, macromolecules that are highly specific for sugars. Lectins perform biological recognition mechanisms involving cells, carbohydrates, and proteins. Lectins also bind bacteria and viruses to their targets. The LectomeXplore database provides predicted lectin domains (reversible carbohydrate binding site) in all species proteomes (de novo translated genomes).""" ; sc:featureList edam:operation_0253, edam:operation_0303, edam:operation_2575 ; sc:name "UniLectin" ; sc:softwareHelp ; sc:url "https://www.unilectin.eu/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2618 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein modification ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0844 ; sc:encodingFormat edam:format_2330 ; sc:name "Molecular mass" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:citation ; sc:description "Database of simple protein modifications." ; sc:featureList edam:operation_2421 ; sc:name "UniMod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.unimod.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:22815356" ; sc:description "Software tool unifying five genome rearrangement distance models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these five distances between pairs of genomes represented as sequences of oriented common blocks." ; sc:featureList edam:operation_0236 ; sc:name "UniMoG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bibiserv.techfak.uni-bielefeld.de/dcj/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation , "pmcid:PMC3722526", "pubmed:23766417" ; sc:description "A universal tool for de novo peptide sequencing." ; sc:featureList edam:operation_3631 ; sc:name "UniNovo" ; sc:url "http://proteomics.ucsd.edu/Software/UniNovo/" ; biotools:primaryContact "K. Jeong" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Concatenate multiple sequences into a single sequence." ; sc:featureList edam:operation_0232 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "union" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/union.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_2229, edam:topic_3315, edam:topic_3474 ; sc:citation ; sc:description """Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration. UnionCom software is available on the Python package index (PyPI), latest version 0.2.1.""" ; sc:featureList edam:operation_0496, edam:operation_0510, edam:operation_3435 ; sc:license "MIT" ; sc:name "UnionCom" ; sc:url "https://github.com/caokai1073/UnionCom" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_2331 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0623 ; sc:citation ; sc:description "UniParc is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. Proteins may exist in different source databases and in multiple copies in the same database. UniParc avoids such redundancy by storing each unique sequence only once and giving it a stable and unique identifier (UPI)." ; sc:featureList edam:operation_0224 ; sc:name "UniParc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "UniProt Consortium" ; sc:softwareHelp ; sc:url "http://www.uniprot.org/uniparc/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_3170, edam:topic_3173, edam:topic_3308 ; sc:citation , "pubmed:33275158" ; sc:description """a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles. UniPath provides robust statistical methods to represent every single cell using pathway and gene-set enrichment scores. It can be used with both single cell RNA-seq and single cell ATAC-seq profile with scalability for atlas scale data-sets. 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sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3572 ; sc:citation ; sc:description "UNITE is a database and sequence management environment centered on the eukaryotic nuclear ribosomal ITS region. 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The program can report exactly the number of all repeat (freq>1) and unique(freq = 1) mers , and the number of all possible substrings of the sequence without cutting off any low frequency mers." ; sc:featureList edam:operation_0379 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "Universal-mer" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://ugrammer.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0659, edam:topic_3125, edam:topic_3512 ; sc:citation , "pmcid:PMC6518440", "pubmed:31131080" ; sc:description "The code to identify the universal Triplex Target Sites (TTSs) DNA regions" ; sc:featureList edam:operation_2495, edam:operation_3222, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "universal TTSs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/vanya-antonov/universal_tts" ; biotools:primaryContact "Yulia A. Medvedeva" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3314 ; sc:citation ; sc:description """UniverSC: Single-cell processing across technologies and a flexible cross-platform single-cell data processing pipeline. Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. UniverSC is a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms. Here we provide a guide to install and use this tool to process single-cell RNA-Seq data from FASTQ format.""" ; sc:featureList edam:operation_0335, edam:operation_3192, edam:operation_3200 ; sc:license "GPL-3.0" ; sc:name "UniverSC" ; sc:url "https://github.com/minoda-lab/universc" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3174 ; sc:citation , "pmcid:PMC10516365", "pubmed:37478378" ; sc:description "moltenNMF is an R package for Nonnegative Matrix Factorization for tidy data format." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3557, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:name "UNMF" ; sc:url "https://github.com/abikoushi/moltenNMF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0632, edam:topic_3077, edam:topic_3382 ; sc:citation , "pmcid:PMC7510912", "pubmed:33014571" ; sc:description """UNMIX-ME (Unmix Multiple Emissions) spectral and lifetime fluorescence unmixing via deep learning. Deep Learning for Hyperspectral Fluorescence Lifetime Image (HFLI) Unmixing.""" ; sc:featureList edam:operation_3443, edam:operation_3797, edam:operation_3799 ; sc:name "UNMIX-ME" ; sc:url "https://github.com/jasontsmith2718/UNMIX-ME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3315, edam:topic_3318, edam:topic_3344 ; sc:description "This toolbox contains various scripts for nonlinear analysis." ; sc:featureList edam:operation_0455, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "UNO Biomechanics Nonlinear Analysis Toolbox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.2" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71907-uno-biomechanics-nonlinear-analysis-toolbox" ; biotools:primaryContact "UNO Biomechanics" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3170 ; sc:citation ; sc:description "Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists." ; sc:featureList edam:operation_0361, edam:operation_0525 ; sc:name "UnoSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://sourceforge.net/projects/unoseq/" ; biotools:primaryContact "Fabian Birzele" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_2229, edam:topic_3170, edam:topic_3940 ; sc:citation , "pmcid:PMC9295346", "pubmed:35854350" ; sc:description "Integration of single-cell multi-omics data by regression analysis on unpaired observations." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_0441, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "UnpairReg" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Durenlab/UnpairReg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:18382088" ; sc:description "Application for performing genetic association analysis in nuclear families and unrelated subjects. It implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes." ; sc:featureList edam:operation_2478 ; sc:name "UNPHASED" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/fdudbridge/software/unphased-3-1" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1537 ; sc:name "Protein structure report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_0736 ; sc:citation ; sc:description "A server implementation of the UNRES package for coarse-grained simulations of protein structures with the physics-based UNRES model. It can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run" ; sc:featureList edam:operation_0476, edam:operation_2476 ; sc:name "UNRES server" ; sc:softwareHelp ; sc:url "http://unres-server.chem.ug.edu.pl/" ; biotools:primaryContact "Adam Liwo", "Cezary Czaplewski" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168 ; sc:citation ; sc:description "An efficient software for computing shortest strings which do not occur in a given set of DNA sequences. It is more efficient than previous algorithms and easier to use. It uses bit vector encoding of strings and therefore we called it unwords-bits. It directly computes unwords without the need to specify a length estimate. Moreover, it avoids the space requirements of index structures such as suffix trees and suffix arrays." ; sc:featureList edam:operation_3211 ; sc:name "UNWORDS" ; sc:operatingSystem "Linux" ; sc:url "http://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/unwords.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0621, edam:topic_0749, edam:topic_3512 ; sc:citation , "pmcid:PMC10219788", "pubmed:37184890" ; sc:description "Tool for annotation of conserved upstream open reading frames." ; sc:featureList edam:operation_0310, edam:operation_0436, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "CC0-1.0" ; sc:name "uORF4u" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://server.atkinson-lab.com/uorf4u" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3360, edam:topic_3678 ; sc:citation ; sc:description "UPB is an Urinary Protein Biomarker database to collect existing studies of urinary protein biomarkers from published literature." ; sc:featureList edam:operation_2479 ; sc:name "UPB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20130710" ; sc:url "http://59.108.16.249/biomarker/web/indexdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3516, edam:topic_3518 ; sc:citation ; sc:description "Priors for Genotyping Polyploids | Flexible Genotyping for Polyploids | Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allelic bias, overdispersion, and sequencing error. The main function is flexdog(), which allows the specification of many different genotype distributions. An experimental function that takes into account varying levels of relatedness is implemented in mupdog(). Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = \"updog\") in R for example usage. See Gerard et al. (2018) and Gerard and Ferrao (2019) for details on the implemented methods" ; sc:featureList edam:operation_3196, edam:operation_3658 ; sc:license "GPL-3.0" ; sc:name "updog" ; sc:url "https://cran.r-project.org/package=updog" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3293 ; sc:citation "pmcid:PMC2658875", "pubmed:19325851" ; sc:description "Evaluate closeness of tree matches. The method computes the Updown distance between two phylogenetic trees, the query tree and the data tree." ; sc:featureList edam:operation_0224 ; sc:name "UpdownDistance" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web.njit.edu/~wangj/updown.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0203, edam:topic_0634, edam:topic_3170 ; sc:citation , "pubmed:33155801" ; sc:description """A Bioinformatic Tool for the Study of Uncharacterized Proteins Based on Gene Expression Correlation and the PageRank Algorithm. The Human Proteome Project (HPP) is leading the international effort to characterize the human proteome. neXtProt Ensemble Id Gene Name GO Term GO Id MSIG Term Disease Chromosome.""" ; sc:featureList edam:operation_0224, edam:operation_2436, edam:operation_3463, edam:operation_3767 ; sc:license "MIT" ; sc:name "UPEFinder" ; sc:url "https://upefinder.proteored.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2974 ; sc:encodingFormat edam:format_2200 ; sc:name "Protein sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1270 ; sc:encodingFormat edam:format_3475 ; sc:name "Feature table" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121 ; sc:author "Dr. Michael Kohl" ; sc:citation ; sc:description "The standalone tool UPF offers the possibility for a highly efficient and simple detection of unique peptides. In a first step a SQL-based database of theoretically digested peptides from a given FASTA formatted protein database is generated by choosing a protease. In a second step, in silico generated peptides from a pre-defined protein sequence are compared to this peptide database in order to identify unique peptides." ; sc:featureList edam:operation_3092 ; sc:isAccessibleForFree true ; sc:name "Unique Peptide Finder (UPF)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.912" ; sc:url "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.en#UPF" ; biotools:primaryContact "PD Dr. Martin Eisenacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0780, edam:topic_3474 ; sc:citation , "pubmed:34903012" ; sc:description "A ubiquitylation predictor for plant through combining sequence information and random forest." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "UPFPSR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ysw-sunshine/UPFPSR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3293, edam:topic_3958 ; sc:citation , "pmcid:PMC8180062", "pubmed:34090344" ; sc:description "Visualizing phylogenetic trees from single-cell RNA-seq data." ; sc:featureList edam:operation_0323, edam:operation_0326, edam:operation_0567 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Uphyloplot2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/harbourlab/UPhyloplot2/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_0654 ; sc:citation "pubmed:19707300" ; sc:description "A decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers." ; sc:featureList edam:operation_2419 ; sc:name "UPIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ars.usda.gov/Main/docs.htm?docid=18376" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2886 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0857 ; sc:encodingFormat edam:format_3475 ; sc:name "Sequence search results" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0907 ; sc:name "Protein family report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0085 ; sc:author ; sc:citation ; sc:description "UniProt Id Mapping through API" ; sc:featureList edam:operation_3282, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "UPIMAPI" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1.7.4" ; sc:url "https://github.com/iquasere/UPIMAPI" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2229, edam:topic_2269, edam:topic_3299, edam:topic_3382 ; sc:citation ; sc:description """a novel framework for dynamic cell population modeling. Docker image to simulate UPMaBoSS models. Markovian Boolean Stochastic Simulator. UPMaBoSS computes the evolution and the dynamics of a population of cells taking into account both their intracellular and intercellular regulations. Simulations with UPMaBoSS are based on a logical model describing the intracellular regulations (logical regulatory graph complemented with logical rules), taking into account cell death, cell division, and intercellular communications. MaBoSS is a C++ software for simulating continuous/discrete time Markov processes, applied on a Boolean network.""" ; sc:featureList edam:operation_0335, edam:operation_2426, edam:operation_3927 ; sc:name "UPMaBoSS" ; sc:url "https://maboss.curie.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0123, edam:topic_0623 ; sc:citation "pubmed:25540185" ; sc:description "The toolbox implements a novel algorithm (“Mosaic Matching”) for large-scale sequence analysis and is now available in terms of an open source C library. It is up to three orders of magnitude faster than profile-based methods and achieved up to 80% higher sensitivity on unassembled short reads (100 bp) from simulated metagenomes." ; sc:featureList edam:operation_2479, edam:operation_2995 ; sc:name "UProC" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://uproc.gobics.de/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269 ; sc:citation ; sc:description "Employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties." ; sc:featureList edam:operation_3744 ; sc:name "UpSetR" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/hms-dbmi/UpSetR/" ; biotools:primaryContact "Nils Gehlenborg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0099, edam:topic_0623, edam:topic_3314 ; sc:citation , "pmcid:PMC5198500", "pubmed:28031034" ; sc:description "Combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data." ; sc:featureList edam:operation_0291 ; sc:name "uQlust" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/uQlust" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3390, edam:topic_3399, edam:topic_3419 ; sc:citation , "pubmed:31583779" ; sc:description """Differences by County-Level Urban-Rural and Economic Distress Classifications. Urban Rural Classification Scheme for Counties. Centers for Disease Control and Prevention. CDC twenty four seven. Saving Lives, Protecting People. NCHS Urban-Rural Classification Scheme for Counties. National Center for Health Statistics. National Center for Health Statistics (NCHS) data systems are often used to study the associations between urbanization level of residence and health and to monitor the health of urban and rural residents. NCHS has developed a six-level urban-rural classification scheme for U.S. counties and county-equivalent entities. The most urban category consists of “central” counties of large metropolitan areas and the most rural category consists of nonmetropolitan “noncore” counties. Three versions of the NCHS scheme are available:""" ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "urban-rural" ; sc:url "https://www.cdc.gov/nchs/data_access/urban_rural.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_2259, edam:topic_3047 ; sc:citation ; sc:description "General software framework for modeling and simulation of stochastic reaction-diffusion processes on arbitrary meshes. URDME emphasizes modularity in order to be useful both as a simulation tool and as a framework for development of stochastic simulation algorithms." ; sc:featureList edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "URDME" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://urdme.github.io/urdme/" ; biotools:primaryContact "Andreas HellanderEmail author" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0108, edam:topic_0780, edam:topic_3175, edam:topic_3943 ; sc:citation , "pmcid:PMC10167986", "pubmed:37159239" ; sc:description "Comparative genomics-driven translational research tool." ; sc:featureList edam:operation_2421, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "urgi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://urgi.versailles.inrae.fr/synteny" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Get URLs of data resources." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "urlget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/urlget.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "The Ultra-fast Read Mapper (URMAP) is ~10x faster than BWA with comparable accuracy on benchmark tests. URMAP offers faster options when when very high accuracy is not essential. In such applications, speeds ~20x faster than BWA can be achieved (up to ~1M reads per second on a 24-core server)." ; sc:featureList edam:operation_3198, edam:operation_3211, edam:operation_3227 ; sc:name "URMAP" ; sc:url "https://drive5.com/urmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:15725731" ; sc:description "Protein structure comparison program that compares two structures (in PDB format)." ; sc:featureList edam:operation_2487 ; sc:name "urms" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://biozon.org/ftp/software/urms/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3168, edam:topic_3169 ; sc:citation ; sc:description "Intended for universal genomic range (e.g. peaks) annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries." ; sc:featureList edam:operation_3222 ; sc:name "UROPA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://uropa-manual.readthedocs.io/introduction.html" ; biotools:primaryContact "Mario Looso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3572 ; sc:citation ; sc:description "New quality control method for Unsupervised Quality trimming of Next Generation Sequencing reads." ; sc:featureList edam:operation_3192, edam:operation_3218 ; sc:name "UrQt" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.0.17" ; sc:url "https://lbbe.univ-lyon1.fr/-UrQt-.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3325, edam:topic_3407, edam:topic_3474 ; sc:citation , "pmcid:PMC7374759", "pubmed:30685436" ; sc:description """A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. A data-driven perspective to your gene expression profile for human tissues and diseases. Leveraging gene expression profiles of thousands of tissue and disease samples by comparing them all to each other, URSA and URSA(HD) identify distinct molecular signatures of individual tissues and diseases. To ascertain the tissue and disease signals in your data, submit your gene expression profiles one at a time. A link to a single list of all your results is sent by email.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3799 ; sc:name "URSAHD" ; sc:url "http://ursahd.princeton.edu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3244, edam:format_3712 ; sc:name "Spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3752 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0601, edam:topic_3520 ; sc:citation , , "pubmed:26709623", "pubmed:33514075" ; sc:description "Ursgal - Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis" ; sc:featureList edam:operation_3631, edam:operation_3634, edam:operation_3644, edam:operation_3645, edam:operation_3647, edam:operation_3649, edam:operation_3767 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Ursgal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.6.8" ; sc:url "https://github.com/ursgal/ursgal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1465 ; sc:encodingFormat edam:format_1476 ; sc:name "RNA structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0099, edam:topic_0654, edam:topic_2275 ; sc:citation , "pubmed:36038728" ; sc:description "Universal structure alignments of proteins, nucleic acids, and macromolecular complexes." ; sc:featureList edam:operation_0491, edam:operation_0502, edam:operation_0503, edam:operation_0504, edam:operation_0510 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "US-align" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://zhanggroup.org/US-align/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Usagi is a software tool used to help in the process of mapping codes from a source system into terminologies, preferably standard ones, stored in the Observational Medical Outcomes Partnership (OMOP) Vocabulary (http://www.ohdsi.org/data-standardization/vocabulary-resources/). The word Usagi is Japanese for rabbit and was named after the first mapping exercise it was used for; mapping source codes used in a Japanese dataset into OMOP Vocabulary concepts." ; sc:featureList edam:operation_2409, edam:operation_2429 ; sc:license "Apache-2.0" ; sc:name "Usagi" ; sc:softwareHelp ; sc:url "https://www.ohdsi.org/analytic-tools/usagi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC9675219", "pubmed:36402991" ; sc:description "A Bioinformatic Toolkit to Facilitate Interpretation and Comparative Visualization of Tandem Repeat Sequences." ; sc:featureList edam:operation_0337, edam:operation_0487, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "USAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/XuewenWangUGA/USAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3474, edam:topic_3577 ; sc:citation , "pubmed:33866367" ; sc:description "Undersampling scheme based method for deleterious synonymous mutation (usDSM) is a novel method for deleterious synonymous mutation prediction using undersampling scheme." ; sc:featureList edam:operation_0331, edam:operation_3227, edam:operation_3461 ; sc:name "usDSM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://usdsm.xialab.info/" ; biotools:primaryContact "Junfeng Xia", "Tiejun Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154 ; sc:citation ; sc:description """USE (Universal Spectrum Explorer) A standalone (web-)application for cross-resource spectrum comparison. The Universal Spectrum Explorer (USE) is a web-based tool based for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/).""" ; sc:featureList edam:operation_2422, edam:operation_3644, edam:operation_3645, edam:operation_3694, edam:operation_3801 ; sc:license "MIT" ; sc:name "Universal Spectrum Explorer" ; sc:softwareHelp ; sc:url "https://github.com/kusterlab/universal_spectrum_explorer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3315, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9060239", "pubmed:35506043" ; sc:description "Extending U-Net Network for Improved Nuclei Instance Segmentation Accuracy in Histopathology Images." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "USE-Net" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/CIVA-Lab/USE-Net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation , , "pmcid:PMC5013910", "pubmed:26139637", "pubmed:27256311" ; sc:description "Algorithm designed to enable high-throughput, sensitive search of very large sequence databases." ; sc:featureList edam:operation_2403 ; sc:name "USEARCH" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.drive5.com/usearch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3169, edam:topic_3170, edam:topic_3572 ; sc:citation "pubmed:19061503" ; sc:description "Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. 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While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods." ; sc:featureList edam:operation_0540, edam:operation_0567, edam:operation_2990 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "usher" ; sc:softwareVersion "0.2.1" ; sc:url "https://github.com/yatisht/usher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0781, edam:topic_3315, edam:topic_3324, edam:topic_3379 ; sc:citation , "pmcid:PMC7014720", "pubmed:32046642" ; sc:description """Understanding suppression of HIV in R. Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) ; and Wu and Ding (1999) ). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results. ushr is an open-source R package that models the decline of HIV during ART using a popular mathematical framework.""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3454 ; sc:license "MIT" ; sc:name "ushr" ; sc:url "https://github.com/SineadMorris/ushr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC6841694", "pubmed:31704962" ; sc:description "Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data. Quantitation of gene expression from read alignments." ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3223, edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "uslcount" ; sc:url "https://github.com/mikpom/uslcount" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2830, edam:topic_3474 ; sc:citation , "pmcid:PMC7330990", "pubmed:32615972" ; sc:description """USMPep: Universal Sequence Models for Major Histocompatibility Complex Binding Affinity Prediction. USMPep is a simple recurrent neural network for MHC binding affinity prediction. It is competitive with state-of-the-art tools for a single model trained from scratch, while ensembling multiple regressors and language model pretraining can slightly improve its performance. In our paper we report the excellent predictive performance of USMPep on several benchmark datasets.""" ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0445, edam:operation_3927 ; sc:name "USMPep" ; sc:url "https://github.com/nstrodt/USMPep" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3170 ; sc:citation ; sc:description "This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization." ; sc:featureList edam:operation_0337, edam:operation_3680 ; sc:license "Artistic-2.0" ; sc:name "uSORT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/uSORT.html" ; biotools:primaryContact "Hao Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3077, edam:topic_3304, edam:topic_3382 ; sc:citation , "pmcid:PMC7762823", "pubmed:33017646" ; sc:description """A software platform for selective plane illumination microscopy. Selective Plane Illumination Microscopy (SPIM) is a fluorescence imaging technique that allows volumetric imaging at high spatio-temporal resolution to monitor neural activity in live organisms such as larval zebrafish. A major challenge in the construction of a custom SPIM microscope using a scanned laser beam is the control and synchronization of the various hardware components.

New method< h4>We present an open-source software, μSPIM Toolset, built around the widely adopted MicroManager platform, that provides control and acquisition functionality for a SPIM""" ; sc:featureList edam:operation_3443 ; sc:name "uSPIM Toolset" ; sc:url "https://uspim.org/#/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2275 ; sc:citation "pubmed:27106057" ; sc:description "Webserver for large-scale prospective virtual screening using USR and USRCAT, two ultrafast ligand-based 3D molecular similarity methods that have been retrospectively validated." ; sc:featureList edam:operation_0482 ; sc:name "USR-VS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://usr.marseille.inserm.fr/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0781, edam:topic_2885, edam:topic_3305, edam:topic_3489 ; sc:citation ; sc:description "United States Swine Pathogen Database is integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_3196 ; sc:name "United States Swine Pathogen Database" ; sc:url "https://swinepathogendb.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3361 ; sc:citation ; sc:description """Representation of k-mer sets using spectrum-preserving string sets. UST is a bioinformatics tool for constructing a spectrum-preserving string set (SPSS) representation from sets of k-mers.""" ; sc:featureList edam:operation_0524, edam:operation_3472, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "UST" ; sc:url "https://github.com/medvedevgroup/UST/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3676 ; sc:citation , "pmcid:PMC6936141", "pubmed:31888480" ; sc:description "An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data." ; sc:featureList edam:operation_0488, edam:operation_3192, edam:operation_3196, edam:operation_3891 ; sc:name "UT-AIM250" ; sc:url "https://github.com/chenlabgccri/UT-AIM250" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3303, edam:topic_3422 ; sc:citation ; sc:description "Tool to predict acute kidney injury in patients with ST-elevation myocardial infarction." ; sc:featureList edam:operation_2423 ; sc:name "UT-AKI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.uthsc.edu/cardiology/research/utaki.php" ; biotools:primaryContact "Guy L. Reed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "University of Tokyo Genome Browser Toolkit. Develop personalized genome browsers that work in web browsers." ; sc:featureList edam:operation_3208 ; sc:license "Apache-2.0" ; sc:name "UTGB Toolkit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.5.8" ; sc:url "http://utgenome.org/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC8210516", "pubmed:34155422" ; sc:description "An agent-based framework for modeling infectious diseases and public interventions" ; sc:featureList edam:operation_0479, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "UTLDR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KDDComplexNetworkAnalysis/UTLDR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0605 ; sc:citation , ; sc:description "User-friendly Tools for Operating Informatics Applications visualizes and analyzes bioinformatics data in a user-friendly way. Based on an ontology-driven data model, it allows to view and align protein sequences, to render complex molecular structures in 3D, and to find and use resources such as web services and data objects." ; sc:featureList edam:operation_0337, edam:operation_2479, edam:operation_2502 ; sc:name "Utopia" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareVersion "1.4.5" ; sc:url "http://utopia.cs.man.ac.uk/utopia/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_1929 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC10118999", "pubmed:37039842" ; sc:description "Decomposing mosaic tandem repeats accurately from long reads." ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "uTR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/morisUtokyo/uTR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3384, edam:topic_3444, edam:topic_3452 ; sc:citation , "pubmed:34973607" ; sc:description "Anomaly detection and localization with U-Transformer." ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "UTRAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/gordon-chenmo/UTRAD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_0621, edam:topic_3120 ; sc:citation , "pubmed:32926138" ; sc:description """Annotating high-impact 5'untranslated region variants with the UTRannotator. A VEP Plugin to annotate high-impact five prime UTR variants either creating new upstream ORFs or disrupting existing upstream ORFs.""" ; sc:featureList edam:operation_0331, edam:operation_3226 ; sc:license "MIT" ; sc:name "UTRannotator" ; sc:url "https://github.com/ImperialCardioGenetics/UTRannotator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3308 ; sc:citation ; sc:description "Database of Untranslated regions (UTRs)." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "UTRdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-CNR" ; sc:softwareHelp ; sc:url "http://utrdb.ba.itb.cnr.it/" ; biotools:primaryContact "Graziano Pesole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3047, edam:topic_3308 ; sc:citation ; sc:description "A collection of functional sequence patterns located in UTR sequences." ; sc:featureList edam:operation_0224 ; sc:isAccessibleForFree true ; sc:name "UTRSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-CNR" ; sc:softwareHelp ; sc:url "http://utrsite.ba.itb.cnr.it/" ; biotools:primaryContact "Graziano Pesole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "V-Phaser is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity." ; sc:featureList edam:operation_3227, edam:operation_3454 ; sc:name "V-Phaser" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2975 ; sc:name "Nucleic acid sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0920 ; sc:encodingFormat edam:format_1929, edam:format_3016 ; sc:name "Genotype/phenotype report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_0781, edam:topic_3056, edam:topic_3168 ; sc:author , ; sc:citation , , , , , , , , , , , , "pmcid:PMC5977249", "pmcid:PMC7427299", "pmcid:PMC8002591", "pmcid:PMC8289377", "pmcid:PMC8452947", "pubmed:27693290", "pubmed:29757994", "pubmed:30835266", "pubmed:32794443", "pubmed:33471068", "pubmed:33802899", "pubmed:34153841", "pubmed:34488035" ; sc:contributor ; sc:description "Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations." ; sc:featureList edam:operation_0292, edam:operation_3197, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "V-pipe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , , , , , , , ; sc:softwareVersion "v1.0", "v2.0", "v2.99.0", "v2.99.1", "v2.99.2" ; sc:url "https://cbg-ethz.github.io/V-pipe/" ; biotools:primaryContact "V-pipe Dev Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pmcid:PMC7267827", "pubmed:32119082" ; sc:description """Visual Surrogate Variable Analysis (V-SVA). is an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data. To facilitate the interpretation of surrogate variables detected by algorithms including IA-SVA, SVA, or ZINB-WaVE, we developed an R Shiny application (Visual Surrogate Variable Analysis (V-SVA)) that provides a web-browser interface for the identification and annotation of hidden sources of variation in scRNA-seq data.""" ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3935 ; sc:license "GPL-3.0" ; sc:name "V-SVA" ; sc:url "https://vsva.jax.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174 ; sc:citation "pubmed:20804791" ; sc:description "This program uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences." ; sc:featureList edam:operation_2238 ; sc:license "GPL-3.0" ; sc:name "V-Xtractor" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.microbiome.ch/software" ; biotools:primaryContact "Martin Hartmann" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:31061483" ; sc:description "Network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions." ; sc:featureList edam:operation_0362, edam:operation_3431, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "vConTACT" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/MAVERICLab/vcontact2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:19079253" ; sc:description "Variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants." ; sc:featureList edam:operation_0292 ; sc:name "VAAL" ; sc:url "http://archive.broadinstitute.org/crd/vaal-manual" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:21700266" ; sc:description "Variant Annotation, Analysis and Search Tool" ; sc:featureList edam:operation_3226 ; sc:name "VAAST" ; sc:softwareHelp ; sc:url "http://www.yandell-lab.org/software/vaast.html" ; biotools:primaryContact "Mark Yandell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3301, edam:topic_3336, edam:topic_3343 ; sc:citation "pubmed:24790156" ; sc:description "Highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens." ; sc:featureList edam:operation_0560 ; sc:name "Vacceed" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/sgoodswe/vacceed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0804, edam:topic_2640, edam:topic_3524 ; sc:citation , "pmcid:PMC3651379", "pubmed:23586423" ; sc:description "Simulating peptide vaccination in cancer therapy." ; sc:featureList edam:operation_3660 ; sc:name "VaccImm" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.charite.de/vaccimm/" ; biotools:primaryContact "Joachim von Eichborn", "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC4515643", "pubmed:26212482" ; sc:description "‘VaccineDA’ has been made available to the scientific community as a webserver in order to assist the experimentalists in designing better IMODN based adjuvants using sequence information of the oligonucleotides." ; sc:featureList edam:operation_2945 ; sc:name "vaccineda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/vaccineda/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0780, edam:topic_3474, edam:topic_3577 ; sc:citation "pubmed:32975233" ; sc:description """VacPred software is a machine-learning based package for prediction of Plant Vacuolar proteins. User have to provide the single or multiple protein sequence in fasta format and the software based on our model will predict the plant vacuole protein. DSL provide the help to new learner of bioinformatics, genomics and personalized medicine, job in india and abroad along with learning tool and software to motivate the researchers all over the world.""" ; sc:featureList edam:operation_2489 ; sc:name "VacPred" ; sc:url "http://www.deepaklab.com/vacpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC5307925", "pubmed:28193166" ; sc:description "Automate the high throughput in silico vaccine candidate prediction process for the identification of putative vaccine candidates against the proteome of bacterial pathogens." ; sc:featureList edam:operation_0416, edam:operation_0560, edam:operation_3461 ; sc:name "VacSol" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/vacsol/" ; biotools:primaryContact "Muhammad Rizwan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC6190870", "pubmed:30356876" ; sc:description "VacTarBac is a platform which stores vaccine candidate against several pathogenic bacteria." ; sc:featureList edam:operation_2945 ; sc:name "vactarbac" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/vactarbac/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0176, edam:topic_0209, edam:topic_3318, edam:topic_3474 ; sc:citation , "pubmed:34014672" ; sc:description "VAD-MM/GBSA is a variable atomic dielectric MM/GBSA model for improved accuracy in protein-ligand binding free energy calculations. In VAD-MM/GBSA, simuled annealing was used for dielectric optimization." ; sc:featureList edam:operation_0409, edam:operation_2476, edam:operation_3938 ; sc:name "VAD-MM-GBSA" ; sc:softwareHelp ; sc:url "http://cadd.zju.edu.cn/vdgb" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:12824316" ; sc:description "Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data." ; sc:featureList edam:operation_0320, edam:operation_0321, edam:operation_0474, edam:operation_2406, edam:operation_2487 ; sc:name "VADAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://redpoll.pharmacy.ualberta.ca/vadar/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3170, edam:topic_3321 ; sc:citation ; sc:description "Integrated approach to Variant Detection in RNA." ; sc:featureList edam:operation_3227 ; sc:license "MIT" ; sc:name "VaDiR" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://gigadb.org/dataset/100360" ; biotools:primaryContact "Dr. Andrea Mariani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2885, edam:topic_3170, edam:topic_3295, edam:topic_3810 ; sc:citation , "pmcid:PMC7889858", "pubmed:33597613" ; sc:description """Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. Currently the program is in beta-phase and a manuscript drafted for submission. Please feel free to use, but please cite the github for the time period until it is published. VADT performs various filtering steps of a VCF file before testing for ASE. The first filter performed is removing all variants that have been flagged as failing (FILTER column). Specifically the program looks for a "PASS" in the filter column to include that variant in further analysis. VADT removes all variants within a certain distance of an indel defined by the user. VADT also removes all variants with multiple reference and alternative alleles and variants with less than the minimum quality score defined by user.""" ; sc:featureList edam:operation_0484, edam:operation_1812, edam:operation_3196, edam:operation_3436, edam:operation_3695 ; sc:license "MIT" ; sc:name "VADT" ; sc:url "https://github.com/mjtiv/VADT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308, edam:topic_3474 ; sc:citation , "pmcid:PMC7355236", "pubmed:32657401" ; sc:description """Improved survival analysis by learning shared genomic information from pan-cancer data. Recent advances in deep learning have offered solutions to many biomedical tasks. However, there remains a challenge in applying deep learning to survival analysis using human cancer transcriptome data. Since the number of genes, the input variables of survival model, is larger than the amount of available cancer patient samples, deep learning models are prone to overfitting. To address the issue, we introduce a new deep learning architecture called VAECox. VAECox employs transfer learning and fine tuning.""" ; sc:featureList edam:operation_2426, edam:operation_3659, edam:operation_3935 ; sc:name "VAECox" ; sc:url "https://github.com/dmis-lab/VAECox" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_3170, edam:topic_3303, edam:topic_3474 ; sc:citation , "pmcid:PMC9805559", "pubmed:36342203" ; sc:description "Vaeda computationally annotates doublets in single-cell RNA sequencing data." ; sc:featureList edam:operation_0314, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "vaeda" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kostkalab/vaeda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3168, edam:topic_3174, edam:topic_3305, edam:topic_3697 ; sc:citation ; sc:description "VALENCIA is a nearest-centroid based algorithm for the classification of human vaginal microbial community into state types based on their taxonomic composition." ; sc:featureList edam:operation_3435, edam:operation_3460, edam:operation_3891 ; sc:name "VALENCIA" ; sc:url "http://github.com/ravel-lab/VALENCIA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3500, edam:topic_3512 ; sc:citation , "pmcid:PMC7500686", "pubmed:32898151" ; sc:description """Visual-based inspection of alternative splicing events at single-cell resolution. Visualising Splicing at Single-Cell Resolution. Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events.""" ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_0446 ; sc:license "GPL-3.0" ; sc:name "VALERIE" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/VALERIE/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174 ; sc:contributor "Christopher Hill" ; sc:description "VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies." ; sc:featureList edam:operation_0310, edam:operation_3184 ; sc:license "MIT" ; sc:name "VALET" ; sc:url "https://github.com/marbl/VALET" ; biotools:primaryContact "Maryland Bioinformatics Labs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0654 ; sc:citation "pubmed:21904437" ; sc:description "The program is capable of predicting secondary structures with improved accuracy based on unique aptamer characteristics. It predicts not only the canonical Watson-Crick pairs but also G-G pairs derived from G-quadruplex (known structure for many aptamers) using the stem candidate selection algorithm." ; sc:featureList edam:operation_2481 ; sc:name "ValFold" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://code.google.com/p/valfold/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Library" ; sc:applicationSubCategory edam:topic_0804, edam:topic_3336, edam:topic_3379, edam:topic_3967 ; sc:citation ; sc:description "provides validated GPCR antibodies and detailed information concerning the validation" ; sc:name "Validated GPCR Antibodies" ; sc:url "https://leod.shinyapps.io/gpcr_abval_2022/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3572 ; sc:description "This tool validates a FASTQ file. When data is paired it can also validate a pair of FASTQ files. ValidateFastq will check if the FASTQ is in valid FASTQ format. This includes checking for duplicate reads and checking whether a pair of FASTQ files contains the same amount of reads and headers match. It also check whether the quality encodings are correct and outputs the most likely encoding format (Sanger, Solexa etc.)." ; sc:featureList edam:operation_0336 ; sc:license "MIT" ; sc:name "validatefastq" ; sc:softwareHelp ; sc:softwareVersion "0.1.1" ; sc:url "https://biopet.github.io/validatefastq/0.1.1/index.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:encodingFormat edam:format_1476 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1539 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein structural quality report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0154 ; sc:author "David Sehnal" ; sc:citation ; sc:contributor "Crina-Maria Ionescu", "Deepti Jaiswal", "Lukáš Pravda", "Radka Svobodová Vařeková" ; sc:description "Database of validation results for ligands and non-standard residues in the Protein Data Bank." ; sc:featureList edam:operation_0336 ; sc:isAccessibleForFree true ; sc:name "ValidatorDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-CZ", "Masaryk University, Brno, Czech Republic" ; sc:softwareHelp , ; sc:url "http://webchem.ncbr.muni.cz/Platform/ValidatorDB" ; biotools:primaryContact "David Sehnal", "Lukáš Pravda", "Primacy Contact" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0593, edam:topic_0736, edam:topic_1317 ; sc:citation "pubmed:23625965" ; sc:description "Web server for validating and quality control of protein circular dichromism spectra." ; sc:featureList edam:operation_0319, edam:operation_0321, edam:operation_2409, edam:operation_2428, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "ValiDichro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3170, edam:topic_3320, edam:topic_3512, edam:topic_3518 ; sc:citation , "pmcid:PMC7066660", "pubmed:32211018" ; sc:description """Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. Information Theory is proven to accurately predict the impact a mutation has on mRNA splicing, and has been used to interpret coding and non-coding mutations that alter mRNA splicing in both common and rare diseases (Caminsky et al., 2014; Burke et al., 2018; Dos Santos et al., 2018; Yang et al., 2017; Caminsky et al., 2016; Mucaki et al., 2016; Peterlongo et al., 2014; Mucaki et al., 2013; Mucaki et al., 2011; Rogan et al., 2003; Rogan et al., 1998; Rogan and Schneider, 1995).""" ; sc:featureList edam:operation_0264, edam:operation_0308, edam:operation_0331, edam:operation_0433, edam:operation_3196 ; sc:name "ValidSpliceMut" ; sc:url "http://validsplicemut.cytognomix.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3003, edam:format_3016, edam:format_3583 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0749, edam:topic_2885, edam:topic_3512 ; sc:citation ; sc:description "Read and manipulate genome intervals and signals. Provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data." ; sc:featureList edam:operation_0282, edam:operation_2409, edam:operation_2436 ; sc:license "MIT" ; sc:name "valr" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "http://valr.hesselberthlab.org" ; biotools:primaryContact "Jay Hesselberth" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1127 ; sc:name "PDB ID" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0092 ; sc:author "Vladimír Horský" ; sc:citation ; sc:description "A web database of biomacromolecular structure validation trends." ; sc:featureList edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "ValTrendsDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webchem.ncbr.muni.cz/ValTrendsDB/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0203, edam:topic_2269 ; sc:citation "pubmed:25582071" ; sc:description "The tool consists of a collection of measures for validation of clustering solutions and algorithms. It has external measures, as the Adjusted Rand index, and internal measures as Figure of Merit, Gap Statistics, Within Cluster Sum Square, Consensus Clustering and more." ; sc:featureList edam:operation_0313 ; sc:name "ValWorkBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.math.unipa.it/~raffaele/valworkbench/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0602, edam:topic_0625, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7498348", "pubmed:32633778" ; sc:description """Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring Distribution of squared modified Mahalanobis distances computed using the VAM method on simulated null scRNA-seq data. The densities of the non-central chi-squared approximation and estimated gamma distribution are also plotted. a) Density estimates for data with a simulated sparsity of 0.5. b) Density estimates for data with a simulated sparsity of 0.8.""" ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3436, edam:operation_3891 ; sc:name "VAM" ; sc:url "http://www.dartmouth.edu/~hrfrost/VAM" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:33398153" ; sc:description """Improved metagenome binning and assembly using deep variational autoencoders. Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation.""" ; sc:featureList edam:operation_3432 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VAMB" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/RasmussenLab/vamb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_2885, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC10373352", "pubmed:37501141" ; sc:description "Variable-number tandem repeats annotation using efficient motif sets." ; sc:featureList edam:operation_0238, edam:operation_0310, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "vamos" ; sc:url "https://github.com/chaissonlab/vamos" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3365 ; sc:citation "pubmed:15217816", "pubmed:15980550" ; sc:description "Collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data." ; sc:featureList edam:operation_0314, edam:operation_2238, edam:operation_2495, edam:operation_3223, edam:operation_3232 ; sc:name "VAMPIRE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://genome.ucsd.edu/microarray/" ; biotools:primaryContact "Carol Kling" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0625, edam:topic_2640, edam:topic_3173, edam:topic_3517 ; sc:citation ; sc:description """A model blood cell trait focused annotation tool for interpretation and prioritization of complex trait genome-wide association study results. Variant Annotation Method Pointing to Interesting Regulatory Effects.""" ; sc:featureList edam:operation_3226, edam:operation_3501, edam:operation_3791 ; sc:name "VAMPIRE" ; sc:url "http://shiny.bios.unc.edu/vampire/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_3474, edam:topic_3673 ; sc:citation , "pmcid:PMC7015433", "pubmed:31929521" ; sc:description "VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning." ; sc:featureList edam:operation_3227, edam:operation_3482, edam:operation_3840 ; sc:name "VAMPr" ; sc:url "https://github.com/jiwoongbio/VAMPr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3056, edam:topic_3697 ; sc:citation , "pmcid:PMC3922339", "pubmed:24499292" ; sc:description "A website for visualization and analysis of microbial population structures." ; sc:featureList edam:operation_3200 ; sc:name "VAMPS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://vamps.mbl.edu/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3375 ; sc:citation , "pmcid:PMC6572512", "pubmed:31075931" ; sc:description "Open-Source Software for Vancomycin Therapeutic Drug Management." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "vancomycin TDM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://pipet.shinyapps.io/vancomycin" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259, edam:topic_3344 ; sc:citation "pubmed:24953454" ; sc:description "Software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior." ; sc:featureList edam:operation_2497 ; sc:name "VANESA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://agbi.techfak.uni-bielefeld.de/vanesa/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3175, edam:topic_3518, edam:topic_3569 ; sc:citation , "pmcid:PMC2710854", "pubmed:19609370" ; sc:description "An R package that uses Hidden Markov Model for characterizing chromosomal alterations in high throughput SNP arrays." ; sc:featureList edam:operation_2238, edam:operation_3196, edam:operation_3228 ; sc:license "GPL-2.0" ; sc:name "VanillaICE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.36.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/VanillaICE.html" ; biotools:primaryContact "Robert Scharpf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_3673 ; sc:citation , "pubmed:25196204" ; sc:description "Visualization-aided variant annotation tool." ; sc:featureList edam:operation_3227 ; sc:name "Vanno" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cgts.cgu.edu.tw/vanno/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0634, edam:topic_3173 ; sc:citation , "pubmed:34570217" ; sc:description "VannoPortal is a variant annotation database that comprehensively collects and integrates genome-wide variant annotations and prediction scores from various biological domains, including allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, pathogenesis, allele imbalance, base-wise functional prediction and tissue/cell type-specific functional profile. It greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps across human tissues/cell types, and compiles many genome-scale base-wise prediction scores for pathogenic/regulatory variant classification beyond protein-coding region. VannoPortal focuses more on interpretability of variant annotations using many intuitive visualizations and interactive web components." ; sc:featureList edam:operation_0331, edam:operation_2495, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "VannoPortal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://mulinlab.org/vportal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3391 ; sc:citation ; sc:description "Open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation." ; sc:featureList edam:operation_0337, edam:operation_2238, edam:operation_2409, edam:operation_2429 ; sc:name "VANTED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.5.3" ; sc:url "https://www.cls.uni-konstanz.de/software/vanted/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0622, edam:topic_3169, edam:topic_3512 ; sc:citation , "pmcid:PMC4086060", "pubmed:24753414" ; sc:description "VAP is a versatile aggregate profiler for efficient genome-wide data representation and discovery. VAP was designed to be used by biologists and bioinformaticians to analyze genomic datasets to generate aggregate or individual profiles of groups of genes / annotations / regions of interest from their genome of interest." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3436 ; sc:name "VAP" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://lab-jacques.recherche.usherbrooke.ca/vap/" ; biotools:primaryContact "VAP Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3673 ; sc:citation , "pmcid:PMC6756534", "pubmed:31545812" ; sc:description "Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data | VAP : For Reference mapping and Variant detection | Thank you for your interest in using the Variant Analysis Pipeline. VAP is a comprehensive workflow for reference mapping and variant detection of genomic and transcriptomic reads using a suite of bioinformatics tools" ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:name "VAP" ; sc:url "https://modupeore.github.io/VAP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3297, edam:topic_3305, edam:topic_3324 ; sc:citation , "pmcid:PMC10471898", "pubmed:37624923" ; sc:description "Interactive web server for the deep exploration of natural virus and phage genomes." ; sc:featureList edam:operation_0224, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "VAPEX" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://archaea.i2bc.paris-saclay.fr/vapex/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_3673 ; sc:citation , "pmcid:PMC7703727", "pubmed:31693070" ; sc:description "VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain." ; sc:featureList edam:operation_0524, edam:operation_2422, edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "VAPOR" ; sc:url "https://github.com/connor-lab/vapor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3056 ; sc:citation ; sc:description "Efficient population-scale variant analysis and prioritization." ; sc:featureList edam:operation_3197, edam:operation_3226 ; sc:name "VAPr" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ucsd-ccbb/VAPr" ; biotools:primaryContact "Adam Mark", "Amanda Birmingham", "Kathleen Fisch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0199, edam:topic_1775, edam:topic_2814 ; sc:citation , "pmcid:PMC5274651", "pubmed:28012137" ; sc:description "A database-integration approach for protein/genome information retrieval." ; sc:featureList edam:operation_1778 ; sc:name "VaProS" ; sc:softwareHelp ; sc:url "http://pford.info/vapros/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0218, edam:topic_0634, edam:topic_0821 ; sc:citation ; sc:description """A Search Engine to Find Related Protein. Vapur is an online entity-oriented search engine for the COVID-19 anthology. Vapur is empowered with a semantic inverted index that is created through named entity recognition and relation extraction on CORD-19 abstracts. In order to run scripts from scratch, please follow these:. Enter a chemical or protein/gene and let Vapur find related bio-molecules in 150,000 COVID-19 publications!.""" ; sc:featureList edam:operation_0305, edam:operation_2422, edam:operation_3280, edam:operation_3625 ; sc:name "Vapur" ; sc:url "https://tabilab.cmpe.boun.edu.tr/vapur/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_2885, edam:topic_3173, edam:topic_3940 ; sc:citation , "pubmed:33095866" ; sc:description "A comprehensive variation annotation database for human." ; sc:featureList edam:operation_0224, edam:operation_3196, edam:operation_3226 ; sc:name "VARAdb" ; sc:url "http://www.licpathway.net/VARAdb/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_3053, edam:topic_3063, edam:topic_3325 ; sc:citation ; sc:description "VarAFT (Variant Analysis and Filtration Tool) is a standalone and multiplatform tool for annotation and prioritization of potential disease causing genes. With this tool users can annotate variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionally, users can perform a coverage analysis and quality check from any BAM file." ; sc:featureList edam:operation_3218, edam:operation_3225, edam:operation_3436, edam:operation_3661, edam:operation_3695, edam:operation_3763 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "VarAFT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.x" ; sc:url "http://varaft.eu" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_3015 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:author "Ketil Malde" ; sc:citation ; sc:description "Read processed sequence data in samtools' mpileup format and calculate various statistics for variant sites. In addition to some standard values, it also gives the expected information value (ESIV) which attempts to combine uncertainity (like p-values) with effect size (e.g. Fst) in a single value. Since the tool can read mpileup from a pipe, this eliminates the need to generate a huge temporary file containing mpileup output." ; sc:featureList edam:operation_3197 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "varan" ; sc:operatingSystem "Linux" ; sc:provider "imr.no" ; sc:softwareHelp , ; sc:softwareVersion "0.5.2" ; sc:url "http://hackage.haskell.org/package/varan" ; biotools:primaryContact "Ketil Malde" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_2640, edam:topic_3168 ; sc:citation , "pubmed:33346148" ; sc:description """Generating in silico Reference Datasets for Clinical Next-Generation Sequencing Bioinformatics Pipeline Evaluation. Next-generation sequencing (NGS) is increasingly being adopted as a valuable method for the detection of somatic variants in clinical oncology. However, it is still challenging to reach a satisfactory level of robustness and standardization in clinical practice when using the currently available bioinformatics pipelines to detect variants from raw sequencing data. Moreover, appropriate reference datasets are lacking for clinical bioinformatics pipeline development, validation and proficiency testing. Here, we developed VarBen, an open-source software for variant simulation to generate customized reference datasets by directly editing the original sequencing reads""" ; sc:featureList edam:operation_2428, edam:operation_3096, edam:operation_3227 ; sc:name "VarBen" ; sc:url "https://github.com/nccl-jmli/VarBen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3169, edam:topic_3170, edam:topic_3673 ; sc:citation , "pmcid:PMC8373110", "pubmed:34313779" ; sc:description "A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads." ; sc:featureList edam:operation_3196, edam:operation_3225, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VarCA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/aryarm/varCA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0196, edam:topic_2885, edam:topic_3320, edam:topic_3512 ; sc:citation , "pmcid:PMC7691889", "pubmed:33281441" ; sc:description """An R Package for Retrieving Neighboring Nucleotides of an SNV. Reporting of a single nucleotide variant (SNV) follows the Sequence Variant Nomenclature (http: varnomen.hgvs.org ), using an unambiguous numbering scheme specific for coding and noncoding DNA. However, the corresponding sequence neighborhood of a given SNV, which is required to assess its impact on splicing regulation, is not easily accessible from this nomenclature. Providing fast and easy access to this neighborhood just from a given SNV reference, the novel tool VarCon combines information of the Ensembl human reference genome and the corresponding transcript table for accurate retrieval. VarCon also displays splice site scores (HBond and MaxEnt scores) and HEXplorer profiles of an SNV neighborhood, reflecting position-dependent splice enhancing and silencing properties""" ; sc:featureList edam:operation_0232, edam:operation_0433, edam:operation_2422 ; sc:name "VarCon" ; sc:url "https://github.com/caggtaagtat/VarConTables" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0602, edam:topic_0634, edam:topic_3175, edam:topic_3676 ; sc:citation , "pmcid:PMC10265870", "pubmed:37312221" ; sc:description "Novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "VarDecrypt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vardecrypt.com/app/vardecrypt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0654, edam:topic_3053 ; sc:citation "pubmed:19091032" ; sc:description "A stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces." ; sc:featureList edam:operation_3197 ; sc:name "VarDetect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www4a.biotec.or.th/GI/tools/vardetect" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description "VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads and better scalability than many Java based variant callers." ; sc:featureList edam:operation_3227 ; sc:name "vardict" ; sc:url "https://github.com/AstraZeneca-NGS/VarDict" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Composition and classification analysis of the malaria antigen family PfEMP1." ; sc:featureList edam:operation_2421, edam:operation_2995 ; sc:license "Other" ; sc:name "VarDom" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/VarDom/" ; biotools:primaryContact "Anders Gorm Pedersen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2534 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence attribute" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Plug-in" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3325, edam:topic_3676, edam:topic_3958 ; sc:citation ; sc:description "VarGenius-HZD allows accurate detection of rare homozygous or hemizygous deletions in targeted sequencing leveraging breadth of coverage." ; sc:featureList edam:operation_0452, edam:operation_3226, edam:operation_3962 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VarGenius-HZD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/frankMusacchia/VarGenius-HZD" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0097, edam:topic_0654, edam:topic_3332 ; sc:citation "pubmed:25391397" ; sc:description "The tool implements a new optimization method which calculates nearest-neighbour entropies and enthalpies from melting temperatures." ; sc:featureList edam:operation_0455 ; sc:name "VarGibbs" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://sites.google.com/site/geraldweberufmg/vargibbs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3337, edam:topic_3360, edam:topic_3517 ; sc:citation ; sc:description "Hypothesis-free detection of gene-interaction effects on biomarker concentration in UK Biobank using variance prioritisation." ; sc:featureList edam:operation_0282, edam:operation_0337, edam:operation_3659, edam:operation_3791 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "varGWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/MRCIEU/varGWAS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3168, edam:topic_3512 ; sc:citation , "pmcid:PMC10032633", "pubmed:36916756" ; sc:description "R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines." ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "vaRHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/emunte/vaRHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_0623, edam:topic_3512 ; sc:citation ; sc:description """Prediction, analysis and visualisation of variable genes. Varia is a tool to predict var genes based on short 150-200 base pair sequences (like PCR fragments). It is composed of two module Varia VIP and Varia GEM.""" ; sc:featureList edam:operation_0303, edam:operation_2454, edam:operation_2495 ; sc:license "GPL-3.0" ; sc:name "Varia" ; sc:url "https://github.com/GCJMackenzie/Varia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_3055, edam:topic_3298, edam:topic_3305, edam:topic_3390 ; sc:citation ; sc:description "Inference and visualization of phenome-wide causal relationships using genetic data." ; sc:featureList edam:operation_0282, edam:operation_3196, edam:operation_3625 ; sc:name "variable LCV" ; sc:url "https://vl.genoma.io" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3112 ; sc:encodingFormat edam:format_2058 ; sc:name "Gene expression matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , "pmcid:PMC5123296", "pubmed:27884101" ; sc:description "Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables." ; sc:featureList edam:operation_0315, edam:operation_3565 ; sc:license "GPL-2.0" ; sc:name "variancePartition" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.4.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/variancePartition.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "Command line, web service, and web interface for fast and accurate functional characterization of variants found by Next Generation Sequencing." ; sc:featureList edam:operation_0226 ; sc:name "VARIANT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "cipf.es", "http://bioinfo.cipf.es" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://variant.bioinfo.cipf.es/" ; biotools:primaryContact "babelomics@cipf.es (Francisco García)" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "A scalable, parallel and efficient implementation of pre-processing and variant calling workflows on cluster environments for next generation sequencing data." ; sc:featureList edam:operation_2945 ; sc:name "VariantCalling-at-Scale" ; sc:softwareVersion "0.01" ; sc:url "https://github.com/abs-tudelft/variant-calling-at-scale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622, edam:topic_3517 ; sc:citation , "pmcid:PMC5514526", "pubmed:28716001" ; sc:description "Performs ranking and annotation of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information." ; sc:featureList edam:operation_3197 ; sc:name "Variant Ranker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://paschou-lab.mbg.duth.gr/html5up/index.html" ; biotools:primaryContact "John Alexander" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0919 ; sc:encodingFormat edam:format_3016, edam:format_3752 ; sc:name "Chromosome report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325 ; sc:citation , "pubmed:36300680" ; sc:description "A web-based tool to notify updates in genetic variant annotations." ; sc:featureList edam:operation_0224, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VariantAlert" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://variant-alert.crs4.it/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3673 ; sc:citation , "pmcid:PMC4080743", "pubmed:24681907" ; sc:description "Annotate variants, compute amino acid coding changes, predict coding outcomes." ; sc:featureList edam:operation_3202, edam:operation_3225, edam:operation_3661 ; sc:license "Artistic-2.0" ; sc:name "VariantAnnotation" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.20.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html" ; biotools:primaryContact "Valerie Obenchain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3168 ; sc:citation "pubmed:27153727" ; sc:description "Tool to extract/count specific sets of sequencing reads from next-generational sequencing files." ; sc:featureList edam:operation_2403, edam:operation_3695 ; sc:name "VariantBam" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/jwalabroad/VariantBam" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation "pubmed:20626889" ; sc:description "Software tool for hierarchically classifying variants based on the genome annotation that is provided. Instead of looking at a region of the genome and seeing all the features relative to each other on the genomic axis, the tool inverts the process so that novel variants can be tested for interest, based on the known features on the genomic axis. Furthermore, our hierarchical classification provides a prioritisation of the variants that should be considered for more intensive study." ; sc:featureList edam:operation_3661 ; sc:name "VariantClassifier" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.jcvi.org/cms/research/projects/variantclassifier" ; biotools:primaryContact "Contact" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc." ; sc:featureList edam:operation_3202, edam:operation_3208, edam:operation_3225, edam:operation_3661 ; sc:license "Artistic-2.0" ; sc:name "VariantFiltering" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.10.1" ; sc:url "http://bioconductor.org/packages/release/bioc/html/VariantFiltering.html" ; biotools:primaryContact "Robert Castelo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3293, edam:topic_3945 ; sc:author "Luca Minotti" ; sc:citation ; sc:contributor , "Erika Ferrandi" ; sc:description "VariantHunter is an application that monitors the evolution of mutations and indicates possible emerging variants." ; sc:name "VariantHunter" ; sc:url "http://gmql.eu/variant_hunter" ; biotools:primaryContact , , , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3053 ; sc:citation , "pmcid:PMC4625715", "pubmed:26510841" ; sc:description "Automated fusion of variant calling pipelines for quantitative, precision-based filtering." ; sc:featureList edam:operation_3227 ; sc:name "VariantMetaCaller" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://bioinformatics.mit.bme.hu/VariantMetaCaller/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3295, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC7407261", "pubmed:32761098" ; sc:description "VariantSpark is a tailored Apache Spark-based machine learning framework that creates insights from high-dimensional data, including genomics and clinical data. VariantSpark’s machine learning method overcomes the limitation of traditional approaches that requires data to be eliminated or identifying only independent markers. Especially complex events are triggered by multiple contributing factors. VariantSpark is able to detect such sets of interacting features thereby identifying more accurate predictive markers. VariantSpark builds on the Random Forest Machine Learning method, which allows to interrogate the tree-based models and identify which features contributed in what proportion to the overall prediction outcome. We also provide a visualization engine that shows the interplay between features and their label association." ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VariantSpark" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformatics.csiro.au/variantspark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_3474, edam:topic_3517 ; sc:citation , "pmcid:PMC7407261", "pubmed:32761098" ; sc:description """Cloud-based machine learning for association study of complex phenotype and large-scale genomic data. variant-spark is a scalable toolkit for genome-wide association studies optimized for GWAS like datasets.""" ; sc:featureList edam:operation_3196, edam:operation_3226, edam:operation_3227, edam:operation_3557 ; sc:name "VariantSpark" ; sc:url "https://bioinformatics.csiro.au/variantspark/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:citation ; sc:description "Tools for detecting, filtering, calling, comparing and plotting variants." ; sc:featureList edam:operation_0240, edam:operation_3227, edam:operation_3695 ; sc:license "Artistic-2.0" ; sc:name "VariantTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.16.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/VariantTools.html" ; biotools:primaryContact "Michael Lawrence" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885 ; sc:description "A set of C++ tools for the interpretation of VCF data." ; sc:featureList edam:operation_3227, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Variation toolkit" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "http://code.google.com/p/variationtoolkit/" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_0622, edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "An Emboss tool that reads sequence variation data and writes the data in one of the EMBOSS variation output formats" ; sc:featureList edam:operation_0335, edam:operation_2403, edam:operation_2422, edam:operation_3197 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "variationget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://www.bioinformatics.nl/cgi-bin/emboss/variationget" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3175 ; sc:citation "pubmed:19447966" ; sc:description "Detection of structural rearrangements." ; sc:featureList edam:operation_3198, edam:operation_3227 ; sc:name "VariationHunter" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://variationhunter.sourceforge.net/Home" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2885, edam:topic_3168, edam:topic_3678 ; sc:citation "pubmed:20529926" ; sc:description "VARiD is a Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads. VARiD combines both types of data in a single framework which allows for accurate predictions." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3227 ; sc:name "VARID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.cs.utoronto.ca/varid/" ; biotools:primaryContact "VARID support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2229, edam:topic_3170 ; sc:citation , "pubmed:31740822" ; sc:description "VarID analysis of murine hematopoietic progenitors and intestinal epithelial cells. VarID is part of RaceID v0.1.4." ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3659, edam:operation_3799, edam:operation_3891 ; sc:name "VarID" ; sc:url "https://github.com/dgrun/VarID_analysis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0622, edam:topic_0634, edam:topic_3325, edam:topic_3337 ; sc:citation , "pmcid:PMC6637258", "pubmed:31317185" ; sc:description """The first integrated database of gene annotation and expression profiles for variants related to human diseases. An integrated database of variants and gene expression profiles for genetic diseases.""" ; sc:featureList edam:operation_0224, edam:operation_2495, edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:name "VariED" ; sc:url "http://varied.cgm.ntu.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0622, edam:topic_3474, edam:topic_3676 ; sc:citation , "pmcid:PMC6936113", "pubmed:31888441" ; sc:description """a variant filter by automated scoring based on tagged-signatures. A tool for variant filtering.""" ; sc:featureList edam:operation_3227, edam:operation_3675, edam:operation_3695 ; sc:name "VariFAST" ; sc:url "https://github.com/bioxsjtu/VariFAST" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3053 ; sc:citation "pubmed:24186831" ; sc:description "Desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases." ; sc:featureList edam:operation_0361, edam:operation_2403, edam:operation_2451 ; sc:name "VarioBox" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.ua.pt/software/variobox/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0634, edam:topic_2640, edam:topic_3068, edam:topic_3325 ; sc:citation , "pmcid:PMC9048643", "pubmed:35274687" ; sc:description "A high recall search engine to support the curation of genomic variants." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3226, edam:operation_3435, edam:operation_3504 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Variomes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://candy.hesge.ch/Variomes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_2885, edam:topic_3517, edam:topic_3678 ; sc:citation "pubmed:18440974", "pubmed:22618869" ; sc:description "Disease gene mining browser for association study. It annotates both known SNPs and novel variants using information from public domain websites such as NCBI, UniProt, KEGG and GO." ; sc:featureList edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "VarioWatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://grch38.genepipe.ncgm.sinica.edu.tw/variowatch/main.do" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0749, edam:topic_2640 ; sc:citation ; sc:description "Enhancing sensitivity and controlling false discovery rate in somatic indel discovery | Varlociraptor is a flexible, uncertainty-aware variant calling framework with parameter free filtration via FDR control" ; sc:featureList edam:operation_0452, edam:operation_3227, edam:operation_3675 ; sc:name "varlociraptor" ; sc:url "https://varlociraptor.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0602, edam:topic_0625, edam:topic_3510, edam:topic_3534 ; sc:citation , "pmcid:PMC4086131", "pubmed:24906884" ; sc:description "VarMod is a web server for modelling the functional effects of non-synonymous variants." ; sc:featureList edam:operation_3197, edam:operation_3225 ; sc:name "VarMod" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.wasslab.org/varmod" ; biotools:primaryContact "Mark Wass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_0625, edam:topic_3474, edam:topic_3517 ; sc:citation ; sc:description """A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. Population studies such as GWAS have identified a variety of genomic variants associated with human diseases. To further understand potential mechanisms of disease variants, recent statistical methods associate functional omic data (e.g., gene expression) with genotype and phenotype and link variants to individual genes. However, how to interpret molecular mechanisms from such associations, especially across omics is still challenging. To address this, we develop an interpretable deep learning method, Varmole to simultaneously reveal genomic functions and mechanisms while predicting phenotype from genotype. In particular, Varmole embeds multi-omic networks into a deep neural network architecture and prioritizes variants, genes and regulatory linkages via drop-connect without needing prior feature selections.""" ; sc:featureList edam:operation_1781, edam:operation_3196, edam:operation_3226 ; sc:name "Varmole" ; sc:url "https://github.com/daifengwanglab/Varmole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3053, edam:topic_3321 ; sc:citation , "pmcid:PMC4997702", "pubmed:27562213" ; sc:description "Incorporating variant prioritization in tests of de novo mutation association." ; sc:featureList edam:operation_3226 ; sc:license "GPL-3.0" ; sc:name "VARPRISM" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.hufflab.org/software/VARPRISM/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_2640, edam:topic_2885, edam:topic_3517 ; sc:citation , "pmcid:PMC8421213", "pubmed:34313777" ; sc:description "Associating pathways with a set of genomic variants using network analysis." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_3196, edam:operation_3227, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VarSAn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/UIUCSinhaLab/VarSAn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3168 ; sc:citation , , "pmcid:PMC2734323", "pmcid:PMC3290792", "pubmed:19542151", "pubmed:22300766" ; sc:description "VarScan, an open source tool for variant detection that is compatible with several short read align-ers." ; sc:featureList edam:operation_3227 ; sc:name "VarScan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://dkoboldt.github.io/varscan/" ; biotools:primaryContact "Support Forum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0622, edam:topic_2885, edam:topic_3676, edam:topic_3958 ; sc:citation , "pmcid:PMC10446208", "pubmed:37566612" ; sc:description "A computational tool for sequence context annotations of genomic variants." ; sc:featureList edam:operation_0362, edam:operation_1812, edam:operation_3192, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VarSCAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/elolab/VarSCAT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0199, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:22210868" ; sc:description "Graphical java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments.It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file (see User Guide for details.) These files should be pre-generated with desired annotation information one would like to view." ; sc:featureList edam:operation_3197 ; sc:name "VarSifter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://research.nhgri.nih.gov/software/VarSifter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3325, edam:topic_3574 ; sc:citation ; sc:description "A search engine for human genomic variants." ; sc:featureList edam:operation_2421, edam:operation_3197, edam:operation_3436, edam:operation_3761 ; sc:isAccessibleForFree true ; sc:name "VarSome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://varsome.com/" ; biotools:primaryContact "Saphetor SA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_2640 ; sc:citation ; sc:description """a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer. Please enter your mutation's gene name, peptide change, and coding strand change.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3227 ; sc:name "VarStack" ; sc:url "https://varstack.brown.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2885, edam:topic_3473, edam:topic_3796 ; sc:author ; sc:citation ; sc:description "VarSum is an API that returns summary statistics on user-defined populations and their variants, using the genomic data repository maintained by the genomic computing group (GeCo) at Politecnico di Milano." ; sc:name "VarSum" ; sc:url "https://github.com/DEIB-GECO/VarSum" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781 ; sc:description "variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences." ; sc:featureList edam:operation_0308 ; sc:license "GPL-3.0" ; sc:name "varVAMP" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/jonas-fuchs/varVAMP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0625, edam:topic_3325, edam:topic_3676 ; sc:citation , "pmcid:PMC6483337", "pubmed:31022234" ; sc:description """Stand-alone software tool for variant matching. VarWatch is a tool for professional human geneticists, genetic counselors and researchers working with genetic data from patients. High-throughput sequencing is uncovering an increasing number of genomic variants with a suspected link to an observed clinical phenotype. However, substantiating the clinical relevance of these variants-of-unknown-significance (VUS) typically requires one or more independent observations. VarWatch offers a non-commercial platform where such VUS can be registered to be continuously monitored for similar findings in external databases or the VarWatch register itself. Potential matches to other case descriptions will be forwarded to the variant owners to aid in the finding of a diagnosis for the affected patient(s).""" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3431 ; sc:name "VarWatch" ; sc:url "https://github.com/broderF/varwatch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3511 ; sc:citation , "pmcid:PMC4210471", "pubmed:25306238" ; sc:description "A convenient web portal for efficient integration of genomic features with millions of genetic variants." ; sc:featureList edam:operation_3661 ; sc:name "VAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://yiplab.cse.cuhk.edu.hk/vas/" ; biotools:primaryContact "Kevin Y Yip" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0601, edam:topic_0634 ; sc:citation , "pubmed:36111625" ; sc:description "Accurate prediction of variant effects for amino acid substitutions in multidrug resistance protein 3." ; sc:featureList edam:operation_0331, edam:operation_0417, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "Vasor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cpclab.uni-duesseldorf.de/mdr3_predictor/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0166, edam:topic_0736 ; sc:citation , "pmcid:PMC2930297", "pubmed:20814581" ; sc:description "Vienna Ab initio Simulation Package. Tool for comparison of binding sites in aligned protein structures. Uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods." ; sc:featureList edam:operation_0387, edam:operation_0482, edam:operation_3216 ; sc:name "VASP" ; sc:operatingSystem "Windows" ; sc:softwareHelp , ; sc:softwareVersion "5.4.4" ; sc:url "https://www.vasp.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:8804824" ; sc:description "Tool for viewing protein structure neighbours." ; sc:featureList edam:operation_2483, edam:operation_2487, edam:operation_2488 ; sc:name "VAST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml" ; biotools:primaryContact "Stephen HBryant" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation ; sc:description "VaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications." ; sc:featureList edam:operation_0484, edam:operation_2430 ; sc:license "MIT" ; sc:name "VaST" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/FofanovLab/VaST" ; biotools:primaryContact "Viacheslav Y. Fofanov" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1025 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2080 ; sc:encodingFormat edam:format_2060 ; sc:name "Database search results" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3320 ; sc:citation ; sc:description "An atlas of alternative splicing profiles in vertebrate cell and tissue types" ; sc:featureList edam:operation_0226, edam:operation_0315, edam:operation_3680 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "VastDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://vastdb.crg.eu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3168, edam:topic_3325 ; sc:citation , "pmcid:PMC3995020", "pubmed:24033266" ; sc:description "Variant Assessment Tool (VAT) for assessing the clinical significance of genetic variants." ; sc:featureList edam:operation_3197, edam:operation_3225, edam:operation_3226 ; sc:isAccessibleForFree true ; sc:name "VAT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://opengenetics.ca/2015/02/25/variant-assessment-tool-vat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3168 ; sc:author "Colby Chiang" ; sc:description "vawk is an awk-like VCF parser." ; sc:featureList edam:operation_1812 ; sc:license "MIT" ; sc:name "vawk" ; sc:url "https://github.com/cc2qe/vawk" ; biotools:primaryContact "Colby Chiang" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2291 ; sc:name "UniProt ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3324, edam:topic_3379, edam:topic_3474, edam:topic_3966 ; sc:citation , "pubmed:35381451" ; sc:description "A web-based deep learning server to identify potential vaccine candidates." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "Vaxi-DL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vac.kamalrawal.in/vaxidl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2830, edam:topic_3324, edam:topic_3379, edam:topic_3474 ; sc:citation , "pmcid:PMC7214037", "pubmed:32096826" ; sc:description """Vaxign-ML is a supervised machine learning classification to predict protective antigens. This tool is a supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Vaxign-ML (Vaxign - Machine Learning) is a machine learning-based vaccine candidate prediction and analysis system based on the principle of reverse vaccinology.""" ; sc:featureList edam:operation_0224, edam:operation_0252, edam:operation_0416, edam:operation_3461 ; sc:name "Vaxign-ML" ; sc:url "http://www.violinet.org/vaxign/vaxign-ml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_0804, edam:topic_3324, edam:topic_3966 ; sc:citation , "pmcid:PMC7994782", "pubmed:33777032" ; sc:description "VaximmutorDB is database for vaccine immune factors. A \"vaximmutor\" is coined here to represent an immune factors that is triggered by a vaccination and plays a role in vaccine-induced host immunity. Vaximmuntors are specifically targeted by the innate or acquired immune system of the host and are able to induce acquired immunity and protection in the host against infectious and non-infectious diseases. Vaximmutors play important roles in development of vaccines and biological markers for disease diagnosis and analysis of fundamental host immunity against diseases. VaximmutorDB is a web-based central database and analysis system that curates, stores, and analyzes various vaccine-induced immune factors (i.e., Vaximmutors)." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0560 ; sc:name "VaximmutorDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.violinet.org/vaximmutordb" ; biotools:primaryContact "Guanming Wu", "Yongqun He" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pmcid:PMC6029051", "pubmed:29970096" ; sc:description "A website for designing peptide based vaccine adjuvants." ; sc:featureList edam:operation_2945 ; sc:name "vaxinpad" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/vaxinpad/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Workflow" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_0203, edam:topic_0659, edam:topic_3697 ; sc:citation , "pmcid:PMC10631056", "pubmed:37936197" ; sc:description "20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution." ; sc:featureList edam:operation_0553, edam:operation_2428, edam:operation_3478 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "VBCG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/tianrenmaogithub/vbcg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3473 ; sc:citation ; sc:description """The package implements multinomial probit regression with Gaussian Process priors and estimates class membership posterior probability employing variational and sparse approximation to the full posterior.""" ; sc:featureList edam:operation_2409, edam:operation_3659, edam:operation_3664 ; sc:license "GPL-2.0" ; sc:name "vbmp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/vbmp.html" ; biotools:primaryContact "Nicola Lama" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0625, edam:topic_0769 ; sc:citation , "pmcid:PMC6289131", "pubmed:29868720" ; sc:description """Comparing complex variants in family trios. VARIANT BENCHMARKING TOOLS (VBT). Author: Berke Cagkan Toptas (berke.toptas@sbgdinc.com). VBT provides a set of tools that is used for aligner/variant calling benchmarking. VBT uses vcfeval as its core variant comparison library and htslib to read/write VCF and FASTA files.""" ; sc:featureList edam:operation_3196, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "VBT" ; sc:url "https://github.com/sbg/VBT-TrioAnalysis.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation "pubmed:17893086" ; sc:description "De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE." ; sc:featureList edam:operation_0310, edam:operation_3472 ; sc:license "GPL-3.0" ; sc:name "VCAKE" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/vcake/files/" ; biotools:primaryContact "William Jeck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3316, edam:topic_3673 ; sc:citation , "pmcid:PMC8424057", "pubmed:34494101" ; sc:description "Variant Calling at Scale is a scalable, parallel and efficient implementation of next generation sequencing data pre-processing and variant calling workflows. Our design tightly integrates most pre-processing workflow stages, using Spark built-in functions to sort reads by coordinates, and mark duplicates efficiently. A cluster scaled DeepVariant for both CPU-only and CPU+GPU clusters is also integrated in this workflow." ; sc:featureList edam:operation_3211, edam:operation_3227, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "VCaScale" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/abs-tudelft/variant-calling-at-scale" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation ; sc:description "Estimate dispersion parameters under a general linear model. The statistical models cover a variety of possibilities like heterogeneous covariance components for residuals as well as other random effects, models with longitudinal data, random regression, and multi-environment analyzes. Additive and dominance relationships are implemented." ; sc:featureList edam:operation_2238, edam:operation_3659 ; sc:license "Unlicense" ; sc:name "VCE" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.tzv.fal.de/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:description "Python tool to convert vcf files to Arlequin format." ; sc:featureList edam:operation_2409 ; sc:license "Not licensed" ; sc:name "VCF2Arlequin" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.dropbox.com/s/otui4ea6finnecs/VCF2Arlequin_Sept%202016.7z?dl=0" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0780, edam:topic_2885, edam:topic_3168, edam:topic_3519 ; sc:citation , "pubmed:34014924" ; sc:description "VCF2CAPS is a VCF file analysis tool for CAPS marker development. The software facilitates the conversion of a large number of single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs) and insertion/deletion (indel) polymorphisms detected by SNP calling tools, e.g. SAMtools, Platypus or FreeBayes, into CAPS markers." ; sc:featureList edam:operation_0282, edam:operation_0308, edam:operation_0452, edam:operation_0484, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "VCF2CAPS" ; sc:url "https://github.com/Aviatore/vcf2caps" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0654, edam:topic_3524 ; sc:citation "pubmed:21811232" ; sc:description "A personal genome constructor, it can be used to construct a personal diploid genome sequence by including personal variants into reference genome." ; sc:featureList edam:operation_0296 ; sc:name "vcf2diploid" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://alleleseq.gersteinlab.org/tools.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2640, edam:topic_2885, edam:topic_3168, edam:topic_3400 ; sc:citation , "pmcid:PMC7923512", "pubmed:33653260" ; sc:description "vcf2fhir is a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. VCF-formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of clinical genomics applications are emerging, based on the HL7 FHIR Genomics standard. Here, we provide an open source utility for converting variants from VCF format into HL7 FHIR Genomics format. Details of the translation logic are on the manual page." ; sc:featureList edam:operation_0335, edam:operation_3227, edam:operation_3454 ; sc:license "Apache-2.0" ; sc:name "vcf2fhir" ; sc:url "https://github.com/elimuinformatics/vcf2fhir" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_2885, edam:topic_3517 ; sc:citation ; sc:description "vcf2gwas is a Python-built API for GEMMA, PLINK and bcftools performing GWAS directly from a VCF file as well as multiple post-analysis operations." ; sc:featureList edam:operation_3096, edam:operation_3196, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "vcf2gwas" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/frankvogt/vcf2gwas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Script" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:25282646" ; sc:description "Calculate Genotype Networks from Variant Call Format (VCF) files." ; sc:featureList edam:operation_0277, edam:operation_3196, edam:operation_3439 ; sc:license "GPL-3.0" ; sc:name "VCF2Networks" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:url "https://bitbucket.org/dalloliogm/vcf2networks" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_3016 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3577, edam:topic_3676, edam:topic_3922 ; sc:citation ; sc:description "Generating sample-specific FASTA files from a consequence called VCF-file and a reference proteome." ; sc:featureList edam:operation_3227, edam:operation_3359, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VCF2Prot" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ikmb/vcf2prot" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:encodingFormat edam:format_3475 ; sc:name "Text data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:description "A Python script that converts genomic variant data encoded in VCF format into a tab-separated values file." ; sc:featureList edam:operation_3434 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "vcf2tsv" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.3.7.1" ; sc:url "https://github.com/sigven/vcf2tsv" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Set of tools for vcf file manipulation." ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "vcfPytools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/AlistairNWard/vcfPytools" ; biotools:primaryContact "Alistair Ward" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0080 ; sc:citation , , ; sc:description "Apply VCF variants to a fasta file to create a new consensus sequence." ; sc:featureList edam:operation_2409 ; sc:name "vcf_consensus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1" ; sc:url "https://bio.tools/vcftools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3002 ; sc:encodingFormat edam:format_3003 ; sc:name "Annotation track" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3071 ; sc:citation , , ; sc:description "Generate the intersection of two VCF files." ; sc:featureList edam:operation_2409 ; sc:name "vcf_intersect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=vcf_intersect" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3056 ; sc:citation , , ; sc:description "Remove filtered lines from vcf files." ; sc:featureList edam:operation_3695 ; sc:name "vcf_remove_filtered" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://bio.tools/vcftools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0199, edam:topic_3056, edam:topic_3071 ; sc:citation , , ; sc:description "Substract one or more VCF file(s) from an initial one." ; sc:featureList edam:operation_3359 ; sc:name "vcf_substract" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://bio.tools/vcftools" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0219 ; sc:citation ; sc:description "Fast, flexible annotation of genetic variants." ; sc:featureList edam:operation_3661 ; sc:license "MIT" ; sc:name "vcfanno" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/brentp/vcfanno" ; biotools:primaryContact "Brent Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0625, edam:topic_0769, edam:topic_3512, edam:topic_3676 ; sc:citation ; sc:description """A method for expressing biobank-scale Variant Call Format data in a SQLite database using R. This processing pipeline converts a VCF into an SQLite representation, using R. This readme only covers the practical matters of executing the pipeline. Please see the wiki or FAQ for more detailed discussions and tutorials covering how to use a VCFdb once it is created. VCFdbR was designed with Linux-based high performance computing clusters in mind, but it should work on any distro. It has not been tested on Windows or Mac operating systems, and changes to specifically support them are not planned.""" ; sc:featureList edam:operation_0335, edam:operation_1812, edam:operation_3196, edam:operation_3227, edam:operation_3675 ; sc:license "MIT" ; sc:name "VCFdbR" ; sc:url "https://github.com/tkoomar/VCFdbR" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_3016 ; sc:name "File name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_3016 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Filtering VCF with javascript (java rhino)." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VCFFilterJS" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/VCFFilterJS" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_3016 ; sc:name "File name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1050 ; sc:encodingFormat edam:format_3016 ; sc:name "File name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Pierre Lindenbaum" ; sc:citation ; sc:description "Print the first variants of a VCF." ; sc:featureList edam:operation_0335 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VcfHead" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Institut du Thorax, Nantes, France", "univ-nantes.fr" ; sc:softwareHelp , , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/lindenb/jvarkit/wiki/VcfHead" ; biotools:primaryContact "Pierre Lindenbaum" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_3071 ; sc:citation ; sc:description "API and command line utilities for the manipulation of VCF files." ; sc:featureList edam:operation_2409 ; sc:license "MIT" ; sc:name "Vcflib" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/vcflib/vcflib" ; biotools:primaryContact "GitHub Issues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0610, edam:topic_0780, edam:topic_3056, edam:topic_3168, edam:topic_3810 ; sc:citation , "pubmed:36458971" ; sc:description "Performing population genetics analyses for polyploids and anisoploids based on next-generation sequencing variant calling dataset." ; sc:featureList edam:operation_3227, edam:operation_3432, edam:operation_3946 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VCFPOP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/huangkang1987/vcfpop" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3071 ; sc:citation , "pmcid:PMC5909048", "pubmed:29706990" ; sc:description "Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes." ; sc:featureList edam:operation_0335 ; sc:license "GPL-3.0" ; sc:name "vcfR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.8.0" ; sc:url "https://cran.r-project.org/web/packages/vcfR/index.html" ; biotools:primaryContact "Brian J. Knaus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:citation ; sc:description """how to squeeze a VCF file. VCFShark is a tool to compress any VCF file. It achieves compression ratios up to an order of magnitude better than the de facto standards (gzipped VCF and BCF).""" ; sc:featureList edam:operation_3227, edam:operation_3359 ; sc:license "GPL-3.0" ; sc:name "VCFShark" ; sc:url "https://github.com/refresh-bio/vcfshark" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3170, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC10493178", "pubmed:37701675" ; sc:description "An R/Shiny application for interactively analyzing and visualizing genetic variants." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VCFshiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://123xiaochen.github.io/VCFshiny" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199 ; sc:citation , "pmcid:PMC3137218", "pubmed:21653522" ; sc:description "Provide easily accessible methods for working with complex genetic variation data in the form of VCF files." ; sc:featureList edam:operation_2409, edam:operation_3197, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "VCFtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp , ; sc:url "https://vcftools.github.io/index.html" ; biotools:primaryContact "Mailing list" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3056, edam:topic_3293 ; sc:citation , "pmcid:PMC5615795", "pubmed:28950836" ; sc:description "User-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences." ; sc:featureList edam:operation_0323 ; sc:name "VCFtoTree" ; sc:operatingSystem "Mac" ; sc:softwareHelp ; sc:softwareVersion "3.0.0" ; sc:url "https://github.com/duoduoo/VCFtoTree_3.0.0" ; biotools:primaryContact "Duo Xu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_3016, edam:format_3020 ; sc:name "Data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1930 ; sc:name "Data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3071, edam:topic_3168 ; sc:citation , ; sc:description "Program from SAMtools/BCFtools package (only vcf2fq command is implemented)." ; sc:featureList edam:operation_2409 ; sc:name "vcfutils" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.1.18" ; sc:url "http://www.htslib.org/" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_2640, edam:topic_3168, edam:topic_3393 ; sc:citation , "pmcid:PMC7672756", "pubmed:33239857" ; sc:description """An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis. An interactive Rshiny tool designed to support the evaluation of somatic mutation calls from cancer sequencing data. The tool takes as input a single variant call format (VCF) file and enables researchers to explore the impacts of analytical choices on the mutant allele frequency spectrum, on mutational signatures and on annotated somatic variants in genes of interest. It allows variants that have failed caller filters to be re-examined in order to improve sensitivity or guide strategies for optimal sample / sequencing preparation. It is extensible allowing other algorithms to take advantage of its VCF preprocessing capabilities.""" ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3227, edam:operation_3675 ; sc:license "GPL-3.0" ; sc:name "vcfView" ; sc:url "https://github.com/BrianOSullivanGit/vcfView" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170 ; sc:citation ; sc:description "Vector-based gene co-expression network construction and its application to RNA-seq data." ; sc:featureList edam:operation_3463 ; sc:license "GPL-3.0" ; sc:name "VCNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/wangzengmiao/VCNet" ; biotools:primaryContact "Minghua Deng", "Nelson Leung-Sang Tang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3068, edam:topic_3315, edam:topic_3342, edam:topic_3375 ; sc:citation ; sc:description """a Novel Tool to Create and Visualize a COmputational Model of Bacterial Antibiotic Target-binding. Computational Model of Bacterial Antibiotic Target-binding. Simulate and visualize predictions of bacterial killing based on the kinetics of drug-target binding.""" ; sc:featureList edam:operation_0337, edam:operation_2426, edam:operation_3454 ; sc:name "vCOMBAT" ; sc:url "https://combat-bacteria.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275 ; sc:description "Independently developed extension for Vina, a program for flexible ligand docking. Carry out high-throughput screening of compound libraries with Vina and cluster resulting PDB files of ligands by binding energies and by binding positions. Results processing functions do not require Vina installed. Screening scale is unlimited." ; sc:featureList edam:operation_2409 ; sc:name "VcPpt" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://biochemlabsolutions.com/Molecule%20Docking/Molecule_Docking.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pubmed:35081029" ; sc:description "Visual Compensation Restoration Network for No-Reference Image Quality Assessment." ; sc:featureList edam:operation_3443, edam:operation_3925, edam:operation_3928 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VCRNet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/NUIST-Videocoding/VCRNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3335, edam:topic_3421, edam:topic_3422, edam:topic_3474 ; sc:citation , "pubmed:36567255" ; sc:description "Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire." ; sc:featureList edam:operation_0252 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VDJMiner" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gene.ai.tencent.com/VDJMiner/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3170 ; sc:citation ; sc:description "Pipelined tool for pre-processing immune repertoire sequencing data." ; sc:featureList edam:operation_3680 ; sc:name "VDJPipe" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://vdjserver.org/vdjpipe/index.html" ; biotools:primaryContact "Lindsay G. Cowell" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2830, edam:topic_3170 ; sc:citation ; sc:description "B-cell receptor reconstruction from single-cell RNA-seq." ; sc:featureList edam:operation_0252 ; sc:name "VDJPuzzle" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://bitbucket.org/kirbyvisp/vdjpuzzle2" ; biotools:primaryContact "Fabio Luciani" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170 ; sc:citation ; sc:description "In silico detection of the main clone V(D)J recombination sequence characterizing neoplastic tissues, using RNA-Seq paired-end reads." ; sc:featureList edam:operation_0451, edam:operation_2423 ; sc:name "VDJSeq-Solver" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://eda.polito.it/VDJSeq-Solver/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:17005006" ; sc:description "Tool for analysing human immunoglobulin VDJ recombination." ; sc:featureList edam:operation_2403 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "VDJsolver" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://cbs.dtu.dk/services/VDJsolver/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2229, edam:topic_2640, edam:topic_2830, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC7029546", "pubmed:32070336" ; sc:description "Exploring and analysing single cell multi-omics data with VDJView." ; sc:featureList edam:operation_0337, edam:operation_2495, edam:operation_3802, edam:operation_3891 ; sc:name "VDJView" ; sc:url "https://bitbucket.org/kirbyvisp/vdjview" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0804, edam:topic_3168 ; sc:citation , "pmcid:PMC4907000", "pubmed:27297497" ; sc:description "Versatile browser for immunogenomics data." ; sc:featureList edam:operation_2421 ; sc:name "VDJviz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/antigenomics/vdjviz" ; biotools:primaryContact "Mikhail Shugay" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_2885, edam:topic_3810 ; sc:citation , "pmcid:PMC8014032", "pubmed:33815430" ; sc:description "Variety discrimination power (VDP) is an Appraisal Index for Loci Combinations Screening Applied in Plant Variety Discrimination. VDP refers to the overall capability of a certain loci combination to distinguish all given varieties calculated by certain statistic method, based on the fact that the genotype of a loci combination can be used to identify a certain variety of plant." ; sc:featureList edam:operation_0337, edam:operation_3196, edam:operation_3454 ; sc:license "MIT" ; sc:name "VDPtools" ; sc:url "https://github.com/caurwx1/VDPtools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Suite" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3050, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC9554839", "pubmed:36224545" ; sc:description "A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VEBA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/jolespin/veba" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885, edam:topic_3168 ; sc:citation , "pmcid:PMC9636371", "pubmed:36333324" ; sc:description "Correcting errors in long reads using variation graphs." ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3195 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VeChat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/HaploKit/vechat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3077, edam:topic_3168, edam:topic_3572 ; sc:citation ; sc:description "Run vecscreen and interpret and annotate output matches taking taxonomy into account." ; sc:featureList edam:operation_3218 ; sc:name "VecScreen_plus_taxonomy" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/aaschaffer/vecscreen_plus_taxonomy" ; biotools:primaryContact "Alejandro A Schäffer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3307, edam:topic_3372, edam:topic_3391 ; sc:citation "pubmed:15884679" ; sc:description "Visual extraction conversion program that provides biomedical researches with minimal computer programming background a way to generate data extraction and conversion programs. It provides a convenient graphical user interface that allows using common point and click methods to extract and arrange data in the way that is useful to their purposes and then provides the computer program to generate such results on other documents with the same formatting." ; sc:featureList edam:operation_3762 ; sc:name "Vect" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.complex.iastate.edu/download/Vect/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0749, edam:topic_2640, edam:topic_3169, edam:topic_3512 ; sc:citation , "pmcid:PMC8305227", "pubmed:34210067" ; sc:description "An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma." ; sc:featureList edam:operation_0463, edam:operation_2422, edam:operation_3463, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VECTOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://vectordb.it/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2759 ; sc:name "Gene ID (VectorBase)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2749 ; sc:encodingFormat edam:format_2331 ; sc:name "Genome identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0114, edam:topic_0622 ; sc:citation , "pmcid:PMC2686483", "pubmed:19028744" ; sc:description "Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. It annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, it contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis." ; sc:featureList edam:operation_2422 ; sc:name "VectorBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Identifiers.org" ; sc:softwareHelp ; sc:url "http://www.vectorbase.org/" ; biotools:primaryContact "Dan Lawson", "VectorBase contact email" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3071 ; sc:description "Advanced, integrated, and user-friendly sequence analysis software for molecular biologists. It combines various types of in-silico cloning, sequence analysis and data management into a single application." ; sc:featureList edam:operation_0564, edam:operation_2403, edam:operation_2409, edam:operation_3760 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Vectorfriends" ; sc:operatingSystem "Windows" ; sc:softwareVersion "1.2.0" ; sc:url "http://www.vectorfriends.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0602, edam:topic_0634, edam:topic_3308, edam:topic_3489 ; sc:citation , "pubmed:32598921" ; sc:description """A web resource for medically important Indian arthropod disease vectors. VectorInfo is a freely accessible web resource, emphasised on medically important Indian arthropods funded by Indian Council of Medical Research (ICMR) and maintained by one of its premier institute, Vector Control Research Centre (VCRC). VectorInfo elucidates and curates medically important Indian arthropod's biological, omics technologies to adopt a holistic view of the molecules that make up an organism, aimed at the detection of genomics, transcriptomics, proteomics, enzymes & pathways and immune specific genes. The nitty-gritty of VectorInfo is aimed at scrutinizing all the possible information on Indian disease vectors in a single window for the scientific community. The database affords 53 medically important Indian arthropod's biological and omics information well-structured and provided with downloadable facilities""" ; sc:name "VectorInfo" ; sc:url "http://vectorinfo.icmr.org.in/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0610, edam:topic_3305, edam:topic_3500, edam:topic_3810 ; sc:citation , "pmcid:PMC8906066", "pubmed:35284881" ; sc:description "A local scale operational management tool for entomological monitoring, to support vector control activities in Greece and the Mediterranean Basin." ; sc:featureList edam:operation_0224, edam:operation_2428, edam:operation_3454 ; sc:isAccessibleForFree true ; sc:name "VectorMap-GR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://vectormap.si.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0632, edam:topic_3168 ; sc:citation "pubmed:15606974" ; sc:description "Application for integrated for molecular sequence analysis including primer design, virtual cloning, alignments, and sequence assembly. The free license needs to be renewed every year." ; sc:featureList edam:operation_0308, edam:operation_0310, edam:operation_2403, edam:operation_3184 ; sc:name "VectorNTI" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.thermofisher.com/dk/en/home/life-science/cloning/vector-nti-software.html" ; biotools:primaryContact "Vector NTI support" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3071 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Remove vectors from the ends of nucleotide sequence(s)." ; sc:featureList edam:operation_0266, edam:operation_0369 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "vectorstrip" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/vectorstrip.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3512 ; sc:citation , "pubmed:27334474" ; sc:description "Identifies vector-originated reads by inspecting the clipping patterns at exon junctions and False variant calls are further detected based on the biased distribution of mutant alleles to vector-originated reads." ; sc:featureList edam:operation_0451, edam:operation_3196, edam:operation_3227 ; sc:name "Vecuum" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "https://sourceforge.net/projects/vecuum/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_2056 ; sc:name "Microarray hybridisation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3518 ; sc:citation ; sc:description "The Variational Estimator for Genomic Aberrations is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected." ; sc:featureList edam:operation_2495, edam:operation_3202, edam:operation_3209 ; sc:license "GPL-2.0" ; sc:name "Vega" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.22.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/Vega.html" ; biotools:primaryContact "Sandro Morganella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3343 ; sc:citation , "pubmed:31757721" ; sc:description """New in silico models to predict in vitro micronucleus induction as marker of genotoxicity. VEGA HUB – Virtual models for property Evaluation of chemicals within a Global Architecture. We use cookies to personalise content and ads, to provide social media features and to analyse our traffic. We also share information about your use of our site with our social media, advertising and analytics partners who may combine it with other information that you’ve provided to them or that they’ve collected from your use of their services. Use necessary cookies only Allow all cookies Show details. Offering a family of tools to evaluate chemical hazard: VEGA, ToxRead, ToxWeight, ToxDelta, and JANUS. Necessary (2) Preferences (0) Statistics (4) Marketing (0) Unclassified (0).""" ; sc:featureList edam:operation_3664 ; sc:name "VEGA HUB" ; sc:url "https://www.vegahub.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_2275 ; sc:citation , "pubmed:33289523" ; sc:description "VEGA ZZ is a complete molecular modelling suite that includes several features to make your research jobs very easy. This software is FREE for non-profit academic uses." ; sc:featureList edam:operation_0337, edam:operation_3938 ; sc:name "VEGA ZZ" ; sc:url "http://www.vegazz.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0621, edam:topic_0622, edam:topic_2815, edam:topic_3168 ; sc:citation "pubmed:15975227" ; sc:description "In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence." ; sc:featureList edam:operation_0362, edam:operation_3208, edam:operation_3435 ; sc:name "Vega Annotation Browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vega.sanger.ac.uk" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3117 ; sc:encodingFormat edam:format_3475 ; sc:name "Microarray hybridisation data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2533, edam:topic_3518 ; sc:citation ; sc:description "This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutations. It also has been implemented so that it can be integrated with the output produced by PennCNV tool." ; sc:featureList edam:operation_2495, edam:operation_3202, edam:operation_3209 ; sc:license "GPL-2.0" ; sc:name "VegaMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/VegaMC.html" ; biotools:primaryContact "Sandro Morganella" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3293, edam:topic_3855 ; sc:description "Ordination methods, diversity analysis and other functions for community and vegetation ecologists" ; sc:featureList edam:operation_2945, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "vegan" ; sc:softwareVersion "2.4-3", "2.6-4" ; sc:url "https://cran.r-project.org/web/packages/vegan/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0769, edam:topic_3304, edam:topic_3384, edam:topic_3444 ; sc:citation , "pubmed:32852588" ; sc:description """Automated age- and sex-specific volumetric estimation of regional brain atrophy. Brain Imaging Accessoires: Volumetric estimation of gross atrophy and brain age longitudinally (veganbagel). Estimating regional deviations of brain volume from a patient’s normative age cohort is challenging and entails immense inter-reader variation. We propose an automated workflow for sex- and age-dependent estimation of brain volume changes relative to a normative population. The veganbagel script takes a directory with DICOM files of a non-enhanced 3D T1-weighted structural MR brain scan as input and then generates a map of regional volume changes in relation to an age- and sex-matched cohort of pre-processed normal scans.""" ; sc:featureList edam:operation_3435 ; sc:name "veganbagel" ; sc:url "https://github.com/BrainImAccs/veganbagel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0623, edam:topic_3053 ; sc:citation , "pubmed:25518859" ; sc:description "An extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. It allows greater flexibility when defining gene boundaries." ; sc:featureList edam:operation_3224 ; sc:name "VEGAS2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://vegas2.qimrberghofer.edu.au/" ; biotools:primaryContact "A. Mishra", "S. MacGregor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_3382, edam:topic_3810 ; sc:citation , "pmcid:PMC9352751", "pubmed:35927555" ; sc:description "Near-real-time MODIS-derived vegetation index data products and online services for CONUS based on NASA LANCE." ; sc:featureList edam:operation_3431, edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "VegScape" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://nassgeodata.gmu.edu/VegScape/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0203, edam:topic_0769, edam:topic_3170, edam:topic_3474 ; sc:citation , "pmcid:PMC8414693", "pubmed:34479487" ; sc:description "An ensemble learning pipeline for RNA velocity prediction." ; sc:featureList edam:operation_0314, edam:operation_2499, edam:operation_3557, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Velo-Predictor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/clay001/Velo-Predictor" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3325, edam:topic_3676 ; sc:description "High-performance variant analysis pipeline contained in a single app. It consumes raw read data (fa, fq) and returns annotated, prioritized variants in one step. 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RNA-velocity informed 2D embeddings for visualizing cellular trajectories." ; sc:featureList edam:operation_2939, edam:operation_3890, edam:operation_3891 ; sc:name "VeloViz" ; sc:url "https://github.com/JEFworks-Lab/veloviz" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929, edam:format_1930, edam:format_2572, edam:format_2573 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2337 ; sc:name "Resource metadata" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196 ; sc:citation , "pmcid:PMC2336801", "pubmed:18349386" ; sc:description "A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD." ; sc:featureList edam:operation_0335, edam:operation_0524 ; sc:license "GPL-3.0" ; sc:name "Velvet" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dzerbino/velvet" ; biotools:primaryContact "Daniel Zerbino" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "Estimate the best k-mer size to use for your Velvet de novo assembly. It needs two inputs: the estimated genome size, and all your sequence read files. 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When filtering based on ANN, annotation entries are filtered first. If no annotation entry remains, the entire variant is deleted." ; sc:featureList edam:operation_3675 ; sc:name "vembrane" ; sc:softwareVersion "v0.6.1" ; sc:url "https://github.com/vembrane/vembrane" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0820, edam:topic_3407, edam:topic_3421 ; sc:citation , "pmcid:PMC10176784", "pubmed:37170313" ; sc:description "Cervical and ocular vestibular evoked myogenic potentials in patients with diabetic peripheral neuropathy." ; sc:isAccessibleForFree true ; sc:name "VEMP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fyey.shinyapps.io/VEMP_Model/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:16335983" ; sc:description "Platform for protein identification and characterization." ; sc:featureList edam:operation_3647 ; sc:name "VEMS" ; sc:url "http://portugene.com/vems.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3170, edam:topic_3308, edam:topic_3390 ; sc:citation ; sc:description """Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas. A collection of 1298 publicly available soybean RNAseq samples. © Copyright 2019 Venancio Research Group""" ; sc:featureList edam:operation_0313, edam:operation_3196, edam:operation_3680 ; sc:name "venanciogroup" ; sc:url "http://venanciogroup.uenf.br/resources/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1033 ; sc:name "Ensembl gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1027 ; sc:name "Gene ID (NCBI)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3517 ; sc:citation , "pmcid:PMC9082955", "pubmed:35534820" ; sc:description "Genome-wide identification of associations between enhancer and alternative splicing in human and mouse." ; sc:featureList edam:operation_0264, edam:operation_0446, edam:operation_3800 ; sc:isAccessibleForFree true ; sc:name "VEnAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://venas.iis.sinica.edu.tw/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3366 ; sc:description "With this tool you can calculate the intersection(s) of list of elements. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. If the number of lists is lower than 6 it will also produce a graphical output in the form of a venn diagram. You have the choice between symmetric (default) or non symmetric venn diagrams. Currently you are able to calculate the intersections of at maximum 30 lists." ; sc:featureList edam:operation_3224 ; sc:name "Venn Diagrams" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "PSB" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/webtools/Venn/" ; biotools:primaryContact "Lieven Sterck" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0797, edam:topic_3053 ; sc:citation , "pmcid:PMC4847855", "pubmed:27120465" ; sc:description "VennPainter is a program for depicting unique and shared sets of genes lists and generating Venn diagrams." ; sc:featureList edam:operation_3209 ; sc:license "Other" ; sc:name "VennPainter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/linguoliang/VennPainter/" ; biotools:primaryContact "Wei Zhou" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0769, edam:topic_3170, edam:topic_3308 ; sc:citation , "pubmed:35727542" ; sc:description "An Automated Bioinformatic Pipeline for Identification of Disulfide-Rich Peptides from Venom Arsenals." ; sc:featureList edam:operation_0418, edam:operation_3192, edam:operation_3631 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VenomFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://venomflow.github.io/Venom_Flow/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0637, edam:topic_3068, edam:topic_3172, edam:topic_3520 ; sc:citation , "pmcid:PMC7464580", "pubmed:32796671" ; sc:description """Website for the Low Molecular Mass Compounds in Spider Venoms. venoMS is a free database for low molecular mass compounds found in spider venoms (< 1000 Da) and provides fast access to ESI-MS/MS spectra, fragment ion annotation and literature references about the structure elucidation, synthesis and biological activity of the metabolites. The spider taxonomy is based on the latest version of the World Spider Catalog.""" ; sc:featureList edam:operation_3644, edam:operation_3646, edam:operation_3803 ; sc:name "venoms" ; sc:url "http://www.venoms.ch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:description "VenomZone is a free web resource that provides information on venoms from six animal taxa (snakes, scorpions, spiders, cone snails, sea anemones and insects), as well as on their targets. Information can be browsed through pages on taxonomy, activity and venom protein families and all these pages link to related venom/toxin protein information from the manually curated UniProtKB/Swiss-Prot database." ; sc:featureList edam:operation_2479 ; sc:name "VenomZone" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://venomzone.expasy.org/" ; biotools:primaryContact "ExPASy helpdesk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3305, edam:topic_3418, edam:topic_3421 ; sc:citation , "pmcid:PMC7720788", "pubmed:33288876" ; sc:description """Computational analysis of neonatal ventilator waveforms and loops. Ventiliser is a tool for segmenting pressure and flow waveforms from ventilators into breaths. It also attempts to find the position of breath sub-phases. Ventiliser was developed on data from neonates ventialted on Draeger ventilators.""" ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3454 ; sc:license "MIT" ; sc:name "Ventiliser" ; sc:url "https://github.com/barrinalo/Ventiliser" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0199, edam:topic_0601, edam:topic_0736 ; sc:citation , "pubmed:35662467" ; sc:description "Elucidating the Impact of Amino Acid Variants on Protein Function Beyond Structure Destabilisation." ; sc:featureList edam:operation_0321, edam:operation_0331, edam:operation_0417, edam:operation_3096 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Venus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://venus.cmd.ox.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script", "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622 ; sc:author "Ensembl" ; sc:citation ; sc:description "Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology" ; sc:featureList edam:operation_3197, edam:operation_3661 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "Variant Effect Predictor (VEP)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://www.ensembl.org/vep" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3360, edam:topic_3474, edam:topic_3517 ; sc:citation , "pubmed:32828070" ; sc:description """Predicting the effect of variants associated with Alzheimer's disease using machine learning. VEPAD is a tool for scoring the effect of Single Nucleotide Variants with respect to Alzheimer's Disease in the human genome. VEPAD makes use of 7 histone marks from multiple brain tissues, combined with 2 conservation scores, GC content and CpG site features at and around the point of mutation to assign scores to the variants.""" ; sc:featureList edam:operation_0331, edam:operation_3225 ; sc:name "VEPAD" ; sc:url "http://web.iitm.ac.in/bioinfo2/vepad/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0625 ; sc:citation ; sc:description "Variance association mapping for molecular phenotypes." ; sc:featureList edam:operation_3227 ; sc:name "veqtl-mapper" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://funpopgen.github.io/veqtl-mapper/" ; biotools:primaryContact "Andrew Brown" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2269, edam:topic_3393, edam:topic_3518 ; sc:citation "pubmed:11382363" ; sc:description "Estimates error model parameters from replicated, preprocessed experiments, and  uses error model to improve the accuracy of the expression ratio and to assign a value ‘lambda’ to each gene, indicating the likelihood that the gene is differentially expressed." ; sc:featureList edam:operation_2495 ; sc:name "VERA SAM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp , ; sc:url "http://db.systemsbiology.net/software/VERAandSAM/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3314 ; sc:citation ; sc:description "Virtual Excited State Reference for the Discovery of Electronic Materials Database (VERDE Materials DB) | VERDE materials DB < b>is open-access and searchable via http: www.verdedb.org. It is focused on light-responsive π-conjugated organic molecules with applications in green chemistry, organic solar cells, and organic redox flow batteries. It includes results of our active and past virtual screening studies; to date, more than 11,000 density functional theory (DFT) calculations have been performed on at least 1,282 molecules to obtain ground- and excited-state structures and photophysical properties" ; sc:name "verdedb" ; sc:url "http://www.verdedb.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:encodingFormat edam:format_2572 ; sc:name "Sequence alignment (nucleic acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3498 ; sc:encodingFormat edam:format_3016 ; sc:name "Sequence variations" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3572 ; sc:citation ; sc:description "Software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. It can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, it still robustly detects sample swaps." ; sc:featureList edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "verifyBamID" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "University of Michigan", "sanger.ac.uk" ; sc:softwareHelp ; sc:softwareVersion "1.1.2" ; sc:url "http://genome.sph.umich.edu/wiki/VerifyBamID" ; biotools:primaryContact "Hyun Min Kang", "verifyBamID Google Group" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2533, edam:topic_2814 ; sc:citation ; sc:description "Multi-perspective visual interactive platform for mutational analysis." ; sc:featureList edam:operation_0564, edam:operation_3083 ; sc:name "Vermont" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.dcc.ufmg.br/vermont/" ; biotools:primaryContact "Alexandre V. Fassio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0160, edam:topic_0166 ; sc:citation , "pubmed:34791045" ; sc:description "A Tool for Mining Fuzzy Network Motifs in RNA." ; sc:featureList edam:operation_0239, edam:operation_0245, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Vernal" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://vernal.cs.mcgill.ca" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0625, edam:topic_2814, edam:topic_3474 ; sc:citation , "pmcid:PMC9800725", "pubmed:36593954" ; sc:description "Artificial intelligence-based recognition for variant pathogenicity of BRCA1 using AlphaFold2-predicted structures." ; sc:featureList edam:operation_0331, edam:operation_3092, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "vERnet-B" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ai-lab.bjrz.org.cn/vERnet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3382, edam:topic_3520 ; sc:citation , "pmcid:PMC7085520", "pubmed:32155749" ; sc:description "VersaVIS provides a complete, open-source hardware, firmware and software bundle to perform time synchronization of multiple cameras with an IMU featuring exposure compensation, host clock translation and independent and stereo camera triggering." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "VersaVIS" ; sc:url "http://www.github.com/ethz-asl/versavis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0659, edam:topic_3295, edam:topic_3512 ; sc:citation , "pubmed:31721105" ; sc:description "Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii." ; sc:featureList edam:operation_0308, edam:operation_0463, edam:operation_3792 ; sc:name "vert_71" ; sc:url "http://www.targetscan.org/vert_71/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1912, edam:format_1929, edam:format_1930, edam:format_1997 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3293 ; sc:citation ; sc:description """VeryFastTree is a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments. It is important to highlight that VeryFastTree keeps unchanged the phases, methods and heuristics used by FastTree-2 to estimate the phylogenetic tree. In this way, it produces trees with the same topological accuracy than FastTree-2. In addition, unlike the parallel version of FastTree-2, VeryFastTree is deterministic. To facilitate the adoption from the research community, VeryFastTree keeps exactly the same command line arguments than FastTree-2. 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In runtime, each worker gets a small chunk of reactions to process and once finished, gets another one and so on (right figure). 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sc:citation , "pmcid:PMC8428259", "pubmed:34567846" ; sc:description "VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data." ; sc:featureList edam:operation_0310, edam:operation_3192, edam:operation_3211, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VGEA" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/pauloluniyi/VGEA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0108, edam:topic_0130, edam:topic_0736, edam:topic_3474 ; sc:citation , "pubmed:33537753" ; sc:description """Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. As an essential task in protein structure and function prediction, protein fold recognition has attracted increasing attention. The majority of the existing machine learning-based protein fold recognition approaches strongly rely on handcrafted features, which depict the characteristics of different protein folds; however, effective feature extraction methods still represent the bottleneck for further performance improvement of protein fold recognition. 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It can also be used to perform a regular expression search, a fuzzy motif search and a masslist search, as well as compare genomes with VOCs genome sequence database." ; sc:featureList edam:operation_0239, edam:operation_2421, edam:operation_3208 ; sc:name "VGO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.1" ; sc:url "http://athena.bioc.uvic.ca/virology-ca-tools/vgo/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_3071, edam:topic_3373, edam:topic_3379 ; sc:citation , "pmcid:PMC9628066", "pubmed:36320030" ; sc:description "An online database of voltage-gated sodium channels." ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "VGSC-DB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://cadd.zju.edu.cn/vgsc/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3305, edam:topic_3974 ; sc:citation ; sc:description "VGsim is a scalable viral genealogy simulator for global pandemic" ; sc:featureList edam:operation_0487, edam:operation_2426, edam:operation_3211, edam:operation_3359, edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "VGsim" ; sc:softwareHelp ; sc:url "https://github.com/Genomics-HSE/VGsim" ; biotools:primaryContact "Vladimir Shchur" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0654, edam:topic_2269 ; sc:citation ; sc:description """Virus-host codon usage co-adaptation analysis. Analyze the co-adaptation of codon usage between a virus and its host, calculate various codon usage bias measurements as: effective number of codons (ENc) Novembre (2002) , codon adaptation index (CAI) Sharp and Li (1987) , relative codon deoptimization index (RCDI) Puigbò et al (2010) , similarity index (SiD) Zhou et al (2013) , synonymous codon usage orderliness (SCUO) Wan et al (2004) and, relative synonymous codon usage (RSCU) Sharp et al (1986) . vhcub is an R package to analyze the co-adaptation of codon usage between a virus and its host. Furthermore, vhcub uses ggplot to visualize two important plots named ENc-GC3 plot and PR2plot, which help to explain what are the factors influence a virus's evolution concerning its CUB""" ; sc:featureList edam:operation_0284, edam:operation_0285, edam:operation_0335, edam:operation_2962, edam:operation_2964 ; sc:license "GPL-3.0" ; sc:name "vhcub" ; sc:url "https://cran.r-project.org/web/packages/vhcub/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2538 ; sc:encodingFormat edam:format_2206 ; sc:name "Mutation identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0896 ; sc:encodingFormat edam:format_2331, edam:format_2332, edam:format_3464, edam:format_3475, edam:format_3752 ; sc:name "Protein report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2814, edam:topic_3325 ; sc:citation , "pmcid:PMC4980628", "pubmed:27511743" ; sc:description "A database of interactors and mutations of the human von Hippel-Lindau tumor suppressor protein (pVHL)." ; sc:featureList edam:operation_0224, edam:operation_2414 ; sc:isAccessibleForFree true ; sc:name "VHLdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "University of Padua, Department of Biomedical Sciences, BioComputing UP lab" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://vhldb.bio.unipd.it/" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0623, edam:topic_3174, edam:topic_3474 ; sc:citation ; sc:description "Viral Host UnveiLing Kit - A tool-kit for phage host prediction. This tool is for bacteriophage host prediction based on annotated genomic features and deep neural networks." ; sc:featureList edam:operation_3092, edam:operation_3461, edam:operation_3927 ; sc:license "GPL-3.0" ; sc:name "vHULK" ; sc:url "https://github.com/LaboratorioBioinformatica/vHULK" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3168 ; sc:citation , "pubmed:32926162" ; sc:description """Inference of viral quasispecies with a paired de Bruijn graph. RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available. Current methods for assembling viral quasispecies are either based on overlap graphs or on de Bruijn graphs. Overlap graph based methods tend to be accurate but slow, whereas de Bruijn graph based methods are fast but less accurate.""" ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_3216, edam:operation_3644 ; sc:name "viaDBG" ; sc:url "https://bitbucket.org/bfreirec1/viadbg" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "Volume Integration and Alignment System integrates tiled optical sections obtained from Laser Scanning Microscopy into a single volumetric dataset." ; sc:featureList edam:operation_2928, edam:operation_3443 ; sc:name "VIAS" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.4" ; sc:url "http://research.mssm.edu/cnic/tools-vias.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3337, edam:topic_3379 ; sc:citation , "pubmed:34051621" ; sc:description "Virtual BioBanking (ViBiBa) for the DETECT multicenter trial program." ; sc:license "MIT" ; sc:name "ViBiBa" ; sc:url "https://vibiba.com" ; biotools:primaryContact "Hans Neubauer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174 ; sc:citation ; sc:description "Software to train models and detect highly divergent DNA and RNA viruses in microbiome data" ; sc:featureList edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "Vica" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "v0.1.6" ; sc:url "https://github.com/USDA-ARS-GBRU/vica" ; biotools:primaryContact "Adam Rivers" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_0769, edam:topic_3299, edam:topic_3382 ; sc:citation , "pmcid:PMC10304752", "pubmed:37388820" ; sc:description "Interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_1812, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:name "ViCloD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lcqb.upmc.fr/viclod/Format" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0623, edam:topic_3301, edam:topic_3407 ; sc:citation "pubmed:16689701" ; sc:description "Classification of bacterial proteins into virulence factors, information molecule, cellular process and metabolism molecule." ; sc:featureList edam:operation_3225 ; sc:name "VICMpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://webs.iiitd.edu.in/raghava/vicmpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0081 ; sc:citation ; sc:description "Open-source project dedicated to providing tools for analyzing and manipulating protein structures." ; sc:featureList edam:operation_0250, edam:operation_0477, edam:operation_3092 ; sc:name "Victor" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-PADOVA" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://protein.bio.unipd.it/victor/index.php/Main_Page" ; biotools:primaryContact "Silvio C.E. Tosatto" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0622, edam:topic_0781 ; sc:citation ; sc:description "Genome-based phylogeny and classification of prokaryotic viruses." ; sc:featureList edam:operation_3460 ; sc:name "VICTOR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ggdc.dsmz.de/victor.php" ; biotools:primaryContact "Jan Meier-Kolthoff" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0219, edam:topic_0637, edam:topic_0781 ; sc:citation ; sc:description "Automated framework for taxonomic classification from protein sequences." ; sc:featureList edam:operation_2995 ; sc:license "GPL-3.0" ; sc:name "ViCTree" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioinformatics.cvr.ac.uk/victree_web/" ; biotools:primaryContact "Sejal Modha" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_0622, edam:topic_0781 ; sc:citation "pubmed:22974120" ; sc:description "A software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations." ; sc:featureList edam:operation_0524, edam:operation_3197, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:name "Vicuna" ; sc:softwareHelp ; sc:url "http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation , "pmcid:PMC29831", "pubmed:11125070" ; sc:description "Complete collection of homologous protein families derived from open reading frames from complete and partial virus genomes." ; sc:featureList edam:operation_0349 ; sc:name "Virus Database (VIDA)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "rki.de" ; sc:softwareHelp ; sc:url "http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:description "The aim of this package is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR." ; sc:featureList edam:operation_0337, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "vidger" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/vidger.html" ; biotools:primaryContact "Brandon Monier" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0804 ; sc:citation , "pmcid:PMC5106020", "pubmed:27835690" ; sc:description "Open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time." ; sc:featureList edam:operation_2403 ; sc:name "Vidjil" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.vidjil.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2840, edam:topic_3047, edam:topic_3375, edam:topic_3474 ; sc:citation , "pmcid:PMC6966498", "pubmed:31998690" ; sc:description "Set of Machine Learning Models for Prediction of Interactions Profiles of Small Molecules With Transporters Relevant for Regulatory Agencies." ; sc:featureList edam:operation_0303, edam:operation_2428, edam:operation_3454 ; sc:name "Vienna LiverTox Workspace" ; sc:url "https://livertox.univie.ac.at" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0166, edam:topic_0176, edam:topic_0601 ; sc:citation "pubmed:23703210" ; sc:description "Vienna-PTM web server is a platform for automated introduction of post-translational modifications (PTMs) of choice to protein 3D structures." ; sc:featureList edam:operation_0321, edam:operation_0417, edam:operation_2476, edam:operation_3645, edam:operation_3755 ; sc:name "Vienna-PTM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vienna-ptm.univie.ac.at" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_3512, edam:topic_3542 ; sc:citation "pubmed:12824340" ; sc:description "Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures." ; sc:featureList edam:operation_0278, edam:operation_0502, edam:operation_0570, edam:operation_2439 ; sc:name "Vienna RNA Package" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.tbi.univie.ac.at/~ivo/RNA/" ; biotools:primaryContact "Vienna RNA Package Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099, edam:topic_0130, edam:topic_0736 ; sc:citation "pubmed:18424795" ; sc:description "Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. Tools include folding of single and aligned sequences, prediction of RNA-RNA interactions, design of sequences with a given structure, analysis of folding landscapes and structural RNA alignments using LocARNA." ; sc:featureList edam:operation_0278, edam:operation_0483, edam:operation_0502, edam:operation_2441 ; sc:name "Vienna RNA Websuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://rna.tbi.univie.ac.at/" ; biotools:primaryContact "Judith Ivansits" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0097, edam:topic_0099 ; sc:citation ; sc:description "The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures." ; sc:featureList edam:operation_0278, edam:operation_0279, edam:operation_0502, edam:operation_2518, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "Freeware" ; sc:name "ViennaRNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.tbi.univie.ac.at/RNA/" ; biotools:primaryContact "Ivo L Hofacker", "Ronny Lorenz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3169, edam:topic_3170 ; sc:citation , "pmcid:PMC4513691", "pubmed:26236465" ; sc:description "Build efficient pipelines for NGS data processing. Extracts and converts features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, It allows identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools." ; sc:featureList edam:operation_2495, edam:operation_3198, edam:operation_3435, edam:operation_3800 ; sc:name "ViennNGS" ; sc:softwareHelp ; sc:softwareVersion "0.19" ; sc:url "https://metacpan.org/release/Bio-ViennaNGS" ; biotools:primaryContact , , , "Fabian Amman" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3168, edam:topic_3674 ; sc:citation ; sc:description "Powerful toolkit for visualization of high-throughput bisulfite sequencing data." ; sc:featureList edam:operation_0564, edam:operation_3186 ; sc:license "GPL-3.0" ; sc:name "ViewBS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/xie186/ViewBS" ; biotools:primaryContact "Shaojun Xie" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3444 ; sc:citation ; sc:description "Multidimensional image processing tool developed to handle data from magnetic resonance imaging. Some features include: Projection reconstruction algorithms for MRI data, Multidimensional Fourier transforms ,Convolution operators for image smoothing and enhancement or Simple volume rendering functionality." ; sc:featureList edam:operation_2409, edam:operation_3443 ; sc:name "ViewIt" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "4.23" ; sc:url "http://itg.beckman.illinois.edu/technology_development/software_development/viewit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3168, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC10753531", "pubmed:38048079" ; sc:description "One-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data." ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:name "VIGA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/viralInformatics/VIGA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0203, edam:topic_0781, edam:topic_3512 ; sc:citation "pubmed:22669909" ; sc:description "Gene prediction program for small viral genomes in support of high throughput feature prediction and annotation. Identified genome-specific features include frame shifts, ribosomal slippage, RNA editing, stop codon read-through, overlapping genes, embedded genes, and mature peptide cleavage sites." ; sc:featureList edam:operation_0436, edam:operation_2454, edam:operation_3092, edam:operation_3663 ; sc:name "VIGOR" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.jcvi.org/vigor" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269, edam:topic_2885, edam:topic_3474 ; sc:citation , "pmcid:PMC9191213", "pubmed:35575313" ; sc:description "An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference." ; sc:featureList edam:operation_3196, edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VIGoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/Onogi/VIGoR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0634, edam:topic_3170, edam:topic_3577 ; sc:citation , "pubmed:36395816" ; sc:description "Multi-layer network approach to data integration demonstrated for patient stratification." ; sc:featureList edam:operation_0313, edam:operation_0314, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ViLoN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/data-int/vilon/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0749, edam:topic_3068, edam:topic_3295 ; sc:citation ; sc:description """A Database of Human Disease-related Virus Mutations, Integration Sites and Cis-effects. Molecular mechanisms of virus-related diseases involve multiple factors, including viral mutation accumulation and integration of a viral genome into the host DNA. With increasing attention being paid to virus-mediated pathogenesis and the development of many useful technologies to identify virus mutations (VMs) and viral integration sites (VISs), abundant literatures on these topics are available in PubMed. However, knowledge of VMs and VISs is widely scattered in numerous published papers, and the association of VMs with VISs in the viral genome or the functional annotation of VISs still lacks integration and curation. To address these challenges, we built a database of human disease-related Vi rus M utations, I ntegration sites and C is-effects (ViMIC), which specialize in three features: virus mutation sites, viral integration sites and target genes""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3208 ; sc:name "ViMIC" ; sc:url "http://bmtongji.cn/ViMIC/index.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2913 ; sc:name "Virus identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3668 ; sc:name "Disease name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0218, edam:topic_3303, edam:topic_3473, edam:topic_3966 ; sc:citation , "pmcid:PMC9805560", "pubmed:36342236" ; sc:description "A text-mining tool and search engine for automated virus mutation recognition." ; sc:featureList edam:operation_0306, edam:operation_2421, edam:operation_4009 ; sc:isAccessibleForFree true ; sc:name "ViMRT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bmtongji.cn:1225/mutation/index" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_3168 ; sc:citation , "pmcid:PMC4562374", "pubmed:26346985" ; sc:description "Visualization of deep sequencing signals." ; sc:featureList edam:operation_3208 ; sc:license "GPL-3.0" ; sc:name "VING" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vm-gb.curie.fr/ving/" ; biotools:primaryContact "Marc Descrimes" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2640, edam:topic_3175 ; sc:citation ; sc:description "Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures. We provide following tools for SV signature analysis: Custom SV classification tool, Feature matrix generator, and SV signature extractor (NMF) with stability evaluation system." ; sc:featureList edam:operation_2996, edam:operation_3225, edam:operation_3227 ; sc:license "Apache-2.0" ; sc:name "Viola" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/dermasugita/Viola-SV/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2885 ; sc:citation "pubmed:20487544" ; sc:description "A complete package designed for next-generation diagnostics using 454 sequencing." ; sc:featureList edam:operation_0484, edam:operation_2429, edam:operation_3661 ; sc:license "LGPL-2.1" ; sc:name "VIP" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/keylabivdc/VIP" ; biotools:primaryContact "Yang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0634, edam:topic_3053, edam:topic_3168 ; sc:citation ; sc:description """Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss. The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG AMP framework for genetic hearing loss. This study aimed to semi-automate the HL ACMG AMP rules. Methods VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. Results We benchmarked VIP-HL using 50 variants where 83 rules were activated by the HL expert panel. VIP-HL concordantly activated 96% (80 83) rules, significantly higher than that of by InterVar (47%; 39 83)""" ; sc:featureList edam:operation_3225, edam:operation_3227, edam:operation_3436 ; sc:name "VIP-HL" ; sc:url "http://hearing.genetics.bgi.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0749, edam:topic_3308, edam:topic_3473, edam:topic_3510 ; sc:citation , "pmcid:PMC5040167", "pubmed:27322546" ; sc:description "The package uses gene expression data to Infer protein activity. The package uses VIPER and msVIPER algorithms." ; sc:featureList edam:operation_0314, edam:operation_3562, edam:operation_3630 ; sc:name "viper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.12.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/viper.html" ; biotools:primaryContact "Mariano J Alvarez" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1461 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein-ligand complex" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0781, edam:topic_2814 ; sc:description "VIPER is a framework and tool for the automated design of inhibitory decoy peptides based on structural binding data of two proteins." ; sc:featureList edam:operation_4008 ; sc:license "MIT" ; sc:name "VIPER" ; sc:operatingSystem "Linux" ; sc:softwareVersion "1.0.1" ; sc:url "https://github.com/A-Klingenberg/VIPER/tree/main" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation , "pmcid:PMC2686430", "pubmed:16205712", "pubmed:18981051" ; sc:contributor ; sc:description "Web-based catalogue of structural information that describes the icosahedral virus particles. In addition to high-resolution crystal structures, it has expanded to include virus structures obtained by cryo-electron microscopy (EM) techniques. This database is a powerful resource for virologists, microbiologists, virus crystallographers and EM researchers." ; sc:featureList edam:operation_0570 ; sc:name "VIPERdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "rki.de" ; sc:softwareHelp ; sc:url "http://viperdb.scripps.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0634, edam:topic_3474, edam:topic_3577, edam:topic_3930 ; sc:citation , "pubmed:35598327" ; sc:description "A gene-specific single nucleotide variant pathogenicity prediction tool for primary immunodeficiency diseases." ; sc:featureList edam:operation_0331, edam:operation_3461, edam:operation_3920 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "VIPPID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://mylab.shinyapps.io/VIPPID/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application", "Workbench" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation , "pmcid:PMC3245011", "pubmed:22006842", "pubmed:23202522" ; sc:description "This database supports the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank, etc.), direct submissions, and internal curation and analysis pipelines, and provides a suite of bioinformatics analysis and visualization tools to expedite virology research." ; sc:featureList edam:operation_0292, edam:operation_0323, edam:operation_0570, edam:operation_2421 ; sc:name "Virus Pathogen Resource (ViPR)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "rki.de" ; sc:softwareHelp ; sc:url "http://www.viprbrc.org/brc/home.spg?decorator=vipr" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0820, edam:topic_2885, edam:topic_3337, edam:topic_3517 ; sc:citation , "pmcid:PMC10183379", "pubmed:37030289" ; sc:description "Fast and accurate Bayesian polygenic risk modeling with variational inference." ; sc:featureList edam:operation_3196, edam:operation_3557, edam:operation_3658, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VIPRS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/shz9/viprs" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1233 ; sc:encodingFormat edam:format_1929, edam:format_2330 ; sc:name "Sequence set (protein)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_2330, edam:format_3752 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3752 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_2331, edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script", "Web service" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0108, edam:topic_0121, edam:topic_0601, edam:topic_3520 ; sc:author "Vasileios Tsiamis" ; sc:citation ; sc:contributor "Veit Schwämmle" ; sc:description "VIQoR, is a user-friendly web service for Visually supervised protein Inference and protein Quantification implemented in R. The Shiny web interface integrates the post-identification processes involved in protein inference and relative protein abundance summarization, along with smart and novel interactive visualization modules to support the common researchers with a straight-forward tool for protein quantification, data browsing and data inspection." ; sc:featureList edam:operation_0531, edam:operation_0571, edam:operation_1812, edam:operation_2429, edam:operation_2938, edam:operation_3184, edam:operation_3435, edam:operation_3463, edam:operation_3630, edam:operation_3695, edam:operation_3767, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "VIQoR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Veit Schwämmle" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://computproteomics.bmb.sdu.dk:443/app_direct/VIQoR/" ; biotools:primaryContact "Vasileios Tsiamis", "Veit Schwämmle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:25398613" ; sc:description "This is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used." ; sc:featureList edam:operation_0310 ; sc:name "ViQuaS" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/viquas/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168, edam:topic_3299 ; sc:citation , "pubmed:35853050" ; sc:description "De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks." ; sc:featureList edam:operation_0487, edam:operation_0524, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ViQUF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/borjaf696/ViQUF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140, edam:topic_0154, edam:topic_0202, edam:topic_3379 ; sc:citation , "pmcid:PMC9851336", "pubmed:36513376" ; sc:description "A drug repurposing framework based on protein similarities between pathogens." ; sc:isAccessibleForFree true ; sc:name "Vir2Drug" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://bioinformatics.cing.ac.cy/vir2drug" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0102, edam:topic_0634, edam:topic_0781, edam:topic_3168 ; sc:citation "pubmed:10871272", "pubmed:11074125", "pubmed:12424130", "pubmed:12805459", "pubmed:14734323", "pubmed:15253776", "pubmed:15701178", "pubmed:16013958", "pubmed:16227218", "pubmed:16503070", "pubmed:16772042" ; sc:description "Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses." ; sc:featureList edam:operation_0308, edam:operation_0346, edam:operation_2454, edam:operation_3431 ; sc:name "Viral Bioinformatics" ; sc:url "http://athena.bioc.uvic.ca/" ; biotools:primaryContact "Viral Bioinformatics Resource Center" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621, edam:topic_0769, edam:topic_3174, edam:topic_3940 ; sc:citation , "pmcid:PMC9889337", "pubmed:36720887" ; sc:description "ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data." ; sc:featureList edam:operation_0310, edam:operation_2422, edam:operation_3192 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ViralCC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/dyxstat/ViralCC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0154, edam:topic_0637, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC8757699", "pubmed:35047951" ; sc:description "A centralized datasource for all data relevant for the understanding of viral fusion peptides." ; sc:featureList edam:operation_0416, edam:operation_2575, edam:operation_3935 ; sc:isAccessibleForFree true ; sc:name "ViralFP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://viralfp.bio.di.uminho.pt/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0114, edam:topic_0196, edam:topic_0622 ; sc:citation "pubmed:23314323" ; sc:description "Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly" ; sc:featureList edam:operation_0292, edam:operation_0310, edam:operation_3198, edam:operation_3219 ; sc:license "GPL-3.0" ; sc:name "ViralFusionSeq" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/viralfusionseq/" ; biotools:primaryContact "Marco Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0154, edam:topic_0602, edam:topic_0769, edam:topic_3308 ; sc:citation ; sc:description """An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. ViralLink is a systems biology workflow which reconstructs and analyses networks representing the effect of viral infection on specific human cell types.""" ; sc:featureList edam:operation_0276, edam:operation_0335, edam:operation_3501, edam:operation_3925 ; sc:name "ViralLink" ; sc:url "https://github.com/korcsmarosgroup/ViralLink" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3497 ; sc:encodingFormat edam:format_2545 ; sc:name "DNA sequence (raw)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "Viral fragment detection in MBD-seq data." ; sc:featureList edam:operation_0415 ; sc:name "ViralMBD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.biobix.be/viralmbd/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_0622, edam:topic_0659 ; sc:citation "pubmed:25708359" ; sc:description "First public resource dedicated to identify the microRNA precursor in virus." ; sc:featureList edam:operation_0463 ; sc:name "ViralMir" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/viralmir/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3305 ; sc:citation , "pubmed:32814953" ; sc:description """Massively scalable reference-guided multiple sequence alignment of viral genomes. ViralMSA is a tool to perform reference-guided multiple sequence alignment of viral genomes. Importantly, ViralMSA differs significantly from VIRULIGN, a codon-correct reference-guided alignment tool designed for viruses, in three key ways:.""" ; sc:featureList edam:operation_0491, edam:operation_0492, edam:operation_3182, edam:operation_3196 ; sc:license "GPL-3.0" ; sc:name "ViralMSA" ; sc:url "https://github.com/niemasd/ViralMSA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0632, edam:topic_0749, edam:topic_0781 ; sc:citation "pubmed:20007148" ; sc:description "Database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. It provides an interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. It has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain." ; sc:featureList edam:operation_0308, edam:operation_0436, edam:operation_2428 ; sc:name "ViralORFeome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://doi.org/10.1093/nar/gkp1000" ; biotools:primaryContact "C. Rabourdin-Combe", "P. O. Vidalain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:description "ViralPhos is a web server for identifying potential virus phosphorylation sites with substrate motifs." ; sc:featureList edam:operation_2479 ; sc:name "ViralPhos" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://csb.cse.yzu.edu.tw/ViralPhos/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:26733451" ; sc:description "Predictor capable of identifying capsid and tail protein sequences using support vector machines (SVM) with an accuracy estimated to be between 90% and 97%." ; sc:featureList edam:operation_3092 ; sc:name "VIRALpro" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://scratch.proteomics.ics.uci.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0621, edam:topic_3174, edam:topic_3299, edam:topic_3512 ; sc:citation ; sc:description """A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in Omic Data. ViralRecall is a flexible command-line tool for detecting signatures of giant viruses (NCLDV) in genomic data. Version 2 has been updated to focus more on NCLDV compared to version 1, but the original options are still available.""" ; sc:featureList edam:operation_0310, edam:operation_0436, edam:operation_3192 ; sc:name "ViralRecall" ; sc:softwareVersion "2.0" ; sc:url "https://github.com/faylward/viralrecall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "ViraVacDB is a repository of human vaccines developed against viral diseases." ; sc:featureList edam:operation_2945 ; sc:name "viralvacdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/viralvacdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0199, edam:topic_3299 ; sc:citation , "pmcid:PMC9781208", "pubmed:36560718" ; sc:description "A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes." ; sc:featureList edam:operation_0331, edam:operation_0337, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "ViralVar" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://viralvar.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Script" ; sc:applicationSubCategory edam:topic_0622 ; sc:description """viralVerify classifies contigs (output of metaviralSPAdes or other assemblers) as viral, non-viral or uncertain, based on gene content. Also for non-viral contigs it can optionally provide plasmid/non-plasmid classification. viralVerify predicts genes in the contig using Prodigal in the metagenomic mode, runs hmmsearch on the predicted proteins and classifies the contig as vrial or non-viral by applying the Naive Bayes classifier (NBC). For the set of predicted HMMs, viralVerify uses trained NBC to classify this set to be viral or chromosomal.""" ; sc:name "viralverify" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "1.1" ; sc:url "https://github.com/ablab/viralVerify" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0121, edam:topic_0781 ; sc:citation , "pmcid:PMC3013774", "pubmed:20947564" ; sc:description "A web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "ViralZone" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "SIB Swiss Institute of Bioinformatics" ; sc:url "http://viralzone.expasy.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0781, edam:topic_3168 ; sc:citation "pubmed:25918639" ; sc:description "Web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. It is a collection of existing tools, combined into a single Galaxy interface. Users without further computational knowledge can easily operate the pipeline." ; sc:featureList edam:operation_0524, edam:operation_0525 ; sc:name "VirAmp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://docs.viramp.com/en/latest/introduction.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_3752 ; sc:name "Nucleic acid sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0872 ; sc:encodingFormat edam:format_2331 ; sc:name "Phylogenetic tree" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174, edam:topic_3697 ; sc:author , ; sc:citation ; sc:description """VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more. It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.""" ; sc:featureList edam:operation_0291, edam:operation_0361, edam:operation_0566 ; sc:name "virAnnot" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "https://github.com/marieBvr/virAnnot" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3174 ; sc:citation ; sc:description "Apache Spark based scalable pipeline for metagenome analysis from NGS read data." ; sc:featureList edam:operation_0291, edam:operation_2403, edam:operation_3461 ; sc:license "MIT" ; sc:name "ViraPipe" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/NGSeq/ViraPipe" ; biotools:primaryContact "Altti Ilari Maarala" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0622, edam:topic_0637, edam:topic_3293 ; sc:citation ; sc:description "A tool for hierarchical clustering, core gene detection and annotation of (prokaryotic) viruses." ; sc:featureList edam:operation_0553, edam:operation_3359, edam:operation_3432, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VirClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://virclust.icbm.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0140, edam:topic_0154, edam:topic_0203, edam:topic_2275 ; sc:citation , "pmcid:PMC7246032", "pubmed:32509450" ; sc:description """a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo. A comprehensive resource for Vitiligo. Vitiligo Information resource (VIRdb) is a comprehensive database which systematically mounts all the information relating to vitiligo in terms of Potential protein targets and differentially expressed genes in a user-friendly database.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3431, edam:operation_3925, edam:operation_3938 ; sc:name "VIRdb" ; sc:url "http://www.vitiligoinfores.com/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2913 ; sc:encodingFormat edam:format_1929 ; sc:name "Virus identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0091, edam:topic_0199, edam:topic_0622, edam:topic_3168 ; sc:citation , "pmcid:PMC10025937", "pubmed:36939008" ; sc:description "Virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids." ; sc:featureList edam:operation_0451, edam:operation_0452, edam:operation_3192, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ViReMa" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://sourceforge.net/projects/virema/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_3003 ; sc:name "Sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0219, edam:topic_3168, edam:topic_3299 ; sc:citation , "pubmed:35904541" ; sc:description "An Interactive Application for Analysis of Viral Recombination Data." ; sc:featureList edam:operation_0451, edam:operation_3431, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ViReMaShiny" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://routhlab.shinyapps.io/ViReMaShiny/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description """An Analysis of SARS-CoV-2 Using ViReport. This repository contains a report on SARS-CoV-2 generated by ViReport using data from the NCBI Virus database.""" ; sc:featureList edam:operation_0567, edam:operation_3478, edam:operation_3942 ; sc:name "ViReport" ; sc:url "https://github.com/mirandajsong/ViReport-SARS-CoV-2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:description "VirFacPred is developed for predicting virulent proteins. It utilizes wide range of information and techniques for prediction that includes machine learning techniques, BLAST, and MERCI." ; sc:featureList edam:operation_2945 ; sc:name "virfacpred" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/virfacpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_2815 ; sc:citation "pubmed:14981259", "pubmed:16845022" ; sc:description "Provides gene function predictions for yeast and human by constructing a functional linkage network (FLN) from gene expression and molecular interaction data. It then labels genes in the FLN with their annotations from Gene Ontology, and systematically propagates these labels across the FLN in order to predict the functions of unlabelled genes." ; sc:featureList edam:operation_0314, edam:operation_2454, edam:operation_2495, edam:operation_3463, edam:operation_3672 ; sc:name "VIRGO" ; sc:url "http://whipple.cs.vt.edu/virgoperl/welcome.cgi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3420, edam:topic_3697, edam:topic_3837, edam:topic_3941 ; sc:citation , "pmcid:PMC7044274", "pubmed:32103005" ; sc:description """A comprehensive non-redundant gene catalogue reveals extensive within-community intraspecies diversity in the human vagina. Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources.""" ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_2495, edam:operation_3192, edam:operation_3672 ; sc:name "VIRGO" ; sc:url "http://virgo.igs.umaryland.edu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_0659, edam:topic_3175, edam:topic_3512 ; sc:citation , "pubmed:37572440" ; sc:description "A comprehensive database to explore lncRNAs and their targets in viral infections." ; sc:featureList edam:operation_0310, edam:operation_0443, edam:operation_3223 ; sc:isAccessibleForFree true ; sc:name "VirhostlncR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://ciods.in/VirhostlncR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal", "Database portal", "Web service" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0781, edam:topic_3324, edam:topic_3957 ; sc:citation "pubmed:18984613", "pubmed:25392406", "pubmed:33147627" ; sc:description "Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases." ; sc:featureList edam:operation_0277, edam:operation_2949, edam:operation_3083, edam:operation_3439, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VirHostnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://virhostnet.prabi.fr/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781 ; sc:description "VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination)." ; sc:featureList edam:operation_2995 ; sc:name "VirHunter" ; sc:softwareVersion "1.0.0" ; sc:url "https://github.com/cbib/virhunter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3174, edam:topic_3301, edam:topic_3512 ; sc:citation , "pmcid:PMC7094006", "pubmed:32182365" ; sc:description "Comprehensive metagenomic analysis of blastic plasmacytoid dendritic cell neoplasm." ; sc:featureList edam:operation_2421, edam:operation_3435, edam:operation_3461 ; sc:license "MIT" ; sc:name "virID" ; sc:url "https://github.com/jnoms/virID" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0622, edam:topic_0769 ; sc:citation ; sc:description """VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Comparative phage genome analysis tool.""" ; sc:featureList edam:operation_0496, edam:operation_3182, edam:operation_3435 ; sc:name "VIRIDIC" ; sc:url "http://viridic.icbm.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_0637, edam:topic_3174, edam:topic_3941 ; sc:citation , "pmcid:PMC10491390", "pubmed:37639475" ; sc:description "An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models." ; sc:featureList edam:operation_0310, edam:operation_0362, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "VIRify" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/EBI-Metagenomics/emg-viral-pipeline" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1234 ; sc:name "Sequence set (nucleic acid)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3028 ; sc:name "Taxonomy" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174 ; sc:citation , "pmcid:PMC6086868", "pubmed:30097567" ; sc:description "VirMAP a tool that merge nucleotide and protein information to taxonomically classify viral reconstructions independent of genome coverage or read overlap" ; sc:featureList edam:operation_0232, edam:operation_3435, edam:operation_3460 ; sc:isAccessibleForFree true ; sc:license "AGPL-3.0" ; sc:name "VirMAP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cmmr/VirMAP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_2885, edam:topic_3053, edam:topic_3277 ; sc:citation ; sc:description "Virtual Microdissection for SNP calling. Variant caller designed for disease-control matched samples. It is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. It can uncover SNPs with low allele frequency by considering the level of contamination (alpha)." ; sc:featureList edam:operation_0484 ; sc:name "Virmid" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "http://sourceforge.net/p/virmid/wiki/Home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0199, edam:topic_0622, edam:topic_2259, edam:topic_3170 ; sc:citation , "pmcid:PMC9680118" ; sc:description "Discovery and assignment of viral mutational signatures from sequencing data." ; sc:featureList edam:operation_2422, edam:operation_3192, edam:operation_3227, edam:operation_3644 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "VirMutSig" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/BIMIB-DISCo/VirMutSig" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC9922274", "pubmed:36774364" ; sc:description "Characterizing the landscape of viral expression in cancer by deep learning." ; sc:featureList edam:operation_0239, edam:operation_0310, edam:operation_3198 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "viRNAtrap" ; sc:operatingSystem "Linux", "Mac" ; sc:url "https://github.com/AuslanderLab/virnatrap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0622, edam:topic_0769, edam:topic_0781, edam:topic_2640 ; sc:citation , "pubmed:35612221" ; sc:description "A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_3196, edam:operation_3218 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "viroCapt" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://shiny.maximewack.com/viroCapt_MIE" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_0780, edam:topic_2814, edam:topic_3170 ; sc:citation , "pmcid:PMC8728161", "pubmed:34751403" ; sc:description "ViroidDB is the most comprehensive collection of viroid, satellite RNA, retrozyme, and deltavirus genome sequences available on the internet." ; sc:featureList edam:operation_0278, edam:operation_0292, edam:operation_0337, edam:operation_0502, edam:operation_2422 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ViroidDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://viroids.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0781, edam:topic_3174, edam:topic_3301 ; sc:citation , "pmcid:PMC4774116", "pubmed:26932765" ; sc:description "ViromeScan is a metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing." ; sc:featureList edam:operation_3436 ; sc:license "BSD-2-Clause-FreeBSD" ; sc:name "ViromeScan" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/viromescan/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3174, edam:topic_3316, edam:topic_3697 ; sc:citation , "pmcid:PMC10072060", "pubmed:36998174" ; sc:description "A containerized bioinformatics pipeline for viral metagenomic data analysis." ; sc:featureList edam:operation_3219, edam:operation_3731 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "ViroProfiler" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/deng-lab/viroprofiler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0780, edam:topic_0781, edam:topic_3168 ; sc:citation , "pmcid:PMC9634423", "pubmed:36338106" ; sc:description "Plant viral diagnosis from NGS data using biologically-informed genome assembly coverage." ; sc:featureList edam:operation_0523, edam:operation_0525, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "Viroscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://Viroscope.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0769, edam:topic_3168 ; sc:citation , "pmcid:PMC10191607", "pubmed:37129547" ; sc:description "An easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing." ; sc:featureList edam:operation_0310 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VirPipe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/KijinKims/VirPipe" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3299, edam:topic_3324, edam:topic_3474 ; sc:citation ; sc:description """A weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all 8 segments. Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. The goal of this work is to predict the virulence of influenza viruses using sequence data.""" ; sc:featureList edam:operation_0267, edam:operation_3461, edam:operation_3927 ; sc:name "VirPreNet" ; sc:url "https://github.com/Rayin-saber/VirPreNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3174, edam:topic_3474, edam:topic_3837 ; sc:citation , "pubmed:35316191" ; sc:description "Identifying Bacteriophages from Metagenomes by Combining Convolutional Neural Network and Gene Information." ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "virSearcher" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://github.com/DrJackson18/virSearcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0219, edam:topic_0659, edam:topic_0781 ; sc:citation "pubmed:22139916" ; sc:description "VIRsiRNAdb is a curated database of experimentally validated viral siRNA/shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences." ; sc:featureList edam:operation_0465, edam:operation_2008, edam:operation_2428, edam:operation_3431 ; sc:name "VIRsiRNAdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crdd.osdd.net/servers/virsirnadb/" ; biotools:primaryContact "Dr. Manoj Kumar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168, edam:topic_3174, edam:topic_3305, edam:topic_3324 ; sc:citation ; sc:description """An RNA virus strain-level identification tool for short reads. The output of VirStrain contains two files. The first is a report file in text format. This file contains all identified strains and their depth and site coverage, etc. The other file is an interactive HTML page to display the depth and uniqueness of sites.""" ; sc:featureList edam:operation_0487, edam:operation_3196, edam:operation_3472 ; sc:name "VirStrain" ; sc:url "https://github.com/liaoherui/VirStrain" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_3318, edam:topic_3474 ; sc:citation , "pubmed:33639808" ; sc:description "Virtual Acoustics (VA) is a real-time auralization framework for scientific research providing modules and interfaces for experiments and demonstrations. It is open source and fully controllable enabling reproducible research." ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:license "Apache-2.0" ; sc:name "Virtual Acoustics" ; sc:softwareHelp , , ; sc:url "http://www.virtualacoustics.org/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3108 ; sc:encodingFormat edam:format_2330 ; sc:name "Experimental measurement" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_2330 ; sc:name "Report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation ; sc:description "Software to perform human in silico drug trials in populations of human cardiac cell models, based on ion channel information." ; sc:featureList edam:operation_2426 ; sc:isAccessibleForFree false ; sc:license "Proprietary" ; sc:name "Virtual Assay" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.2" ; sc:url "https://www.cs.ox.ac.uk/ccs/virtual-assay/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3940 ; sc:citation , "pmcid:PMC9185870", "pubmed:35681170" ; sc:description "Predicting transcription factor binding by learning from the transcriptome." ; sc:featureList edam:operation_0445, edam:operation_2575, edam:operation_3222, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Virtual ChIP-seq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://virchip.hoffmanlab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_3068, edam:topic_3304, edam:topic_3308, edam:topic_3382 ; sc:citation , "pmcid:PMC9908962", "pubmed:36776967" ; sc:description "Interactive atlas of the Drosophila nervous system." ; sc:featureList edam:operation_2421, edam:operation_3450, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:name "Virtual Fly Brain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://virtualflybrain.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3070 ; sc:author "Tomas Kulhanek" ; sc:contributor "West-Life Horizon 2020" ; sc:description "It provides internal file repository with limited scratch disc space available within virtual machine and accessible via WEBDAV protocol. The internal file repository can be used by installed application to execute processing tasks etc. It provides integration of external file repositories specific to user/group. Currently user specific EUDAT (B2DROP) can be mounted and data processed." ; sc:featureList edam:operation_2409 ; sc:funder "West-Life Horizon 2020" ; sc:isAccessibleForFree true ; sc:name "Virtual Folder for Structural Biology Projects" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "STFC" ; sc:softwareHelp , ; sc:softwareVersion "16.06.2" ; sc:url "https://appdb.egi.eu/store/vappliance/d6.1.virtualfoldervm/" ; biotools:primaryContact "Tomas Kulhanek" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0780, edam:topic_3050, edam:topic_3277, edam:topic_3810 ; sc:citation , "pmcid:PMC8292289", "pubmed:34316271" ; sc:description "The Virtual Herbarium ALTB (Russian interface ) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country" ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "Virtual Herbarium ALTB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://altb.asu.ru" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_2333 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:citation "pubmed:23014715" ; sc:description "VIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide." ; sc:featureList edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "CECILL-B" ; sc:name "Virtual Imaging Platform" ; sc:url "https://vip.creatis.insa-lyon.fr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0208, edam:topic_2885, edam:topic_3168, edam:topic_3516 ; sc:citation "pubmed:26496198" ; sc:description "Web tool that interprets personal genome for the impact of genetic variation on drug response. It can take variants data (VCF format), microarray SNP genotyping data and high-throughput sequencing data as input, and report to the users how the variants in their personal genomes impact their drug response, including drug efficacy, dosage and toxicity." ; sc:featureList edam:operation_3197 ; sc:name "Virtual Pharmacist" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sustc-genome.org.cn/vp/" ; biotools:primaryContact "Jiankui He", "Ross Ka-Kit Leung", "Zhoufang Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0637, edam:topic_0654, edam:topic_3125, edam:topic_3512 ; sc:citation "pubmed:16845033" ; sc:description "The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results." ; sc:featureList edam:operation_0256, edam:operation_0307, edam:operation_0371 ; sc:license "Other" ; sc:name "Virtual Ribosome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cbs.dtu.dk/services/VirtualRibosome/" ; biotools:primaryContact "Rasmus Wernersson" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0077, edam:topic_3374, edam:topic_3519 ; sc:description "This little program generates real-time PCR plots based all important real-time PCR parameters." ; sc:featureList edam:operation_0307, edam:operation_0308, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "virtualPCR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "0.6" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/13655-virtualpcr-v0-6" ; biotools:primaryContact "Gie Spaepen" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0883 ; sc:encodingFormat edam:format_3816 ; sc:name "Structure" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1460 ; sc:encodingFormat edam:format_1476 ; sc:name "Protein structure" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_3307, edam:topic_3314, edam:topic_3344 ; sc:citation ; sc:description "VirtualScreening is a Python package inheriting from pymdsetup to perform virtual screening on a set of predefined targets." ; sc:featureList edam:operation_2423, edam:operation_2425, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "BioExcel Virtual Screening pipeline" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "Alpha" ; sc:url "https://github.com/bioexcel/virtualscreening" ; biotools:primaryContact "Pau Andrio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0820, edam:topic_3336, edam:topic_3474 ; sc:citation , "pubmed:33905509" ; sc:description "VirtualTaste is a web server for the prediction of organoleptic properties of chemical compounds. The taste of a chemical compound present in food stimulates us to take in nutrients and avoid poisons. Many active ingredients present in drugs taste bitter and thus are aversive to children as well as many adults. Bitterness of medicines presents compliance problems and early flagging of potential bitterness of a drug candidate may help its further development. Taste prediction of a compound is of large interest for the food industry." ; sc:featureList edam:operation_0269, edam:operation_0303, edam:operation_3938 ; sc:name "VirtualTaste" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://virtualtaste.charite.de/VirtualTaste" ; biotools:primaryContact , "Robert Preissner" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_0769, edam:topic_3170, edam:topic_3512 ; sc:citation ; sc:description """VIRTUS : VIRal Transcript Usage Sensor v1.2.1. A pipeline for comprehensive virus analysis from conventional RNA-seq data. Virus transcript detection and quantification using normal human RNAseq. VIRTUS is the first tool to detect viral transcripts considering their splicing event rather than the viral genome copy number. VIRTUS can be applied to both bulk RNAseq and single-cell RNAseq. The virus reference covers 762 viruses including SARS-CoV-2 (cause of COVID-19). The workflow is implemented by Common Workflow Language and Rabix. You can specify each parameter individually or give yaml or json file which describes all the parameter information. In detail, check the CWL User Guide out.""" ; sc:featureList edam:operation_3435, edam:operation_3680, edam:operation_3800 ; sc:license "CC-BY-4.0" ; sc:name "VIRTUS" ; sc:url "https://github.com/yyoshiaki/VIRTUS" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_3299, edam:topic_3305 ; sc:citation , "pubmed:35040923" ; sc:description "Direct comparison of SARS-CoV-2 genomes and genetic variants in space and time." ; sc:featureList edam:operation_2422, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "ViruClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://gmql.eu/viruclust/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0625, edam:topic_0632, edam:topic_3673 ; sc:citation , "pmcid:PMC7512150", "pubmed:32669379" ; sc:description """In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. Only data from one single isolate should be uploaded. If raw sequencing reads are uploaded KMA will be used for mapping. KMA supports the following sequencing platforms: Illumina, Ion Torrent, Roche 454, SOLiD, Oxford Nanopore, and PacBio.""" ; sc:featureList edam:operation_0308, edam:operation_2421, edam:operation_3431, edam:operation_3840 ; sc:name "VirulenceFinder" ; sc:url "http://cge.cbs.dtu.dk/services/VirulenceFinder/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0634, edam:topic_3322, edam:topic_3379 ; sc:citation , "pmcid:PMC7454273", "pubmed:32715315" ; sc:description """an integrated bioinformatics platform and analysis resource for COVID-19 research. A generic knowledgebase computation platform integrated with our established chemogenomics tools as well as our algorithms for data visualization and analyses. Virus-CKB is a knowledgebase for COVID-19 and similar viral infection research that implemented with our established chemogenomics tools as well as our algorithms for data visualization and analyses. This tool predicts the BioActivities on 92 viral related targets for a query compound and provides a handy user interface for viewing, downloading and plotting the output results.""" ; sc:featureList edam:operation_0337, edam:operation_2489, edam:operation_3938 ; sc:name "Virus-CKB" ; sc:url "https://www.cbligand.org/g/virus-ckb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0625, edam:topic_0781, edam:topic_3168, edam:topic_3293 ; sc:citation "pubmed:19483099" ; sc:description "This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis." ; sc:featureList edam:operation_0224, edam:operation_0258, edam:operation_0550, edam:operation_3196 ; sc:name "Virus Genotyping Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioafrica.mrc.ac.za/rega-genotype/html/" ; biotools:primaryContact "Tulio de Oliveira" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_0219, edam:topic_0781 ; sc:citation "pubmed:18251994" ; sc:description "MySQL database of virus sequences and alignments that is accessed via a Java program." ; sc:featureList edam:operation_0338 ; sc:name "Virusbanker" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinformatics.org/virusbanker/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0781, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32349124" ; sc:description """VirusCircBase Database for viral circRNA. VirusCircBase(1.1), is a comprehensive database of circular RNA molecules encoded by viruses. All the viral circRNAs were identified by computational tools such as CIRI2 based on the viral infection-related RNA-seq data downloaded from NCBI SRA. The latest version of the database contains 46,440 viral circRNAs from 26 viruses. VirusCircBase is freely available for non-commercial use and would be a valuable resource for further research on viral circRNAs.""" ; sc:featureList edam:operation_0463, edam:operation_2436, edam:operation_3192 ; sc:name "VirusCircBase" ; sc:softwareVersion "1.1" ; sc:url "http://www.computationalbiology.cn/ViruscircBase/home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3068, edam:topic_3263, edam:topic_3293, edam:topic_3305 ; sc:citation ; sc:description """Virus Data Integration Platform. The Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created. Results To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI)""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3431 ; sc:name "VirusDIP" ; sc:url "https://db.cngb.org/virus/virus" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0781 ; sc:citation ; sc:description "This is a tool for the identification of viruses and their integration sites in host genomes using any type of NGS data. Its unique features include the characterization of insertion loci of any type of virus in the host genome and high accuracy and computational efficiency because of its well-designed pipeline." ; sc:featureList edam:operation_2403 ; sc:name "VirusHunter" ; sc:url "http://pathology.wustl.edu/VirusHunter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0199, edam:topic_0769, edam:topic_0781, edam:topic_3305 ; sc:citation , "pmcid:PMC9245481", "pubmed:35822801" ; sc:description "A Tool for Customized SARS-CoV-2 Data Analysis. Comparative analysis and effective visualization of viral nucleotide and amino acid variants." ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_2422, edam:operation_3197 ; sc:isAccessibleForFree true ; sc:name "VirusLab" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://viruslab.quantiaconsulting.com/viruslab/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0621, edam:topic_0749, edam:topic_2830, edam:topic_3534 ; sc:citation , "pmcid:PMC8479994", "pubmed:34614039" ; sc:description "Metal binding sites, antigen epitopes, and drug binding sites are viral protein hotspots that control how viruses interact with their hosts. Like Google maps organizes and annotates points of interest on the planet, virus-M-E-D (Metal binding sites, antigenic Epitopes, and Drug binding sites) recognizes the relative locations of individual hotspots of viral proteins, and depicts a collection of maps upon which newly-characterized functional sites can be marked as they are being discovered. While we define drug as small molecule compounds collected by the DrugBank database, other small molecules binders observed in complex viral protein structures were also cataloged." ; sc:featureList edam:operation_0252, edam:operation_0416, edam:operation_0480, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "virusMED" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://virusmed.biocloud.top" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0781 ; sc:author "Alberto Calderone" ; sc:citation , "pmcid:PMC4384001", "pubmed:25217587" ; sc:contributor "Gianni Cesareni" ; sc:description "This tool archives evidence about viral interactions collected from different manually curated protein-protein interaction databases that have adhered to the IMEx consortium." ; sc:featureList edam:operation_2421, edam:operation_3083 ; sc:name "VirusMentha" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-TORVERGATA", "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://virusmentha.uniroma2.it/" ; biotools:primaryContact "Alberto Calderone", "Luana Licata" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2526 ; sc:name "Text data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:name "Protein interaction data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0906 ; sc:encodingFormat edam:format_3158 ; sc:name "Protein interaction data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0781 ; sc:author ; sc:citation , "pmcid:PMC2686573", "pubmed:18974184", "pubmed:23900247" ; sc:contributor "Andrew Chatr-aryamontri", "Daniele Peluso" ; sc:description "This database aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network." ; sc:featureList edam:operation_3083, edam:operation_3431 ; sc:name "VirusMINT" ; sc:provider "ELIXIR-ITA-TORVERGATA", "Molecular Genetic Group, University of Rome \"Tor Vergata\", Rome, Italy" ; sc:url "http://mint.bio.uniroma2.it/virusmint/" ; biotools:primaryContact "Luana Licata" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0154, edam:topic_0804, edam:topic_3520 ; sc:citation , "pubmed:33811468" ; sc:description "virusMS is a database for synthetic peptides of viruses with mass spectrometry. It is a tool for resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies." ; sc:featureList edam:operation_0252, edam:operation_3431, edam:operation_3643, edam:operation_3646 ; sc:name "virusMS" ; sc:softwareHelp ; sc:url "https://virusms.erc.monash.edu/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3127, edam:topic_3299 ; sc:citation , "pubmed:36567622" ; sc:description "An information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2." ; sc:featureList edam:operation_0224, edam:operation_0451, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "LGPL-2.1" ; sc:name "VirusRecom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZhijianZhou01/virusrecom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622 ; sc:citation ; sc:description "We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on RNA-Seq data of 256 TCGA human cancer samples. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole genome sequencing data of human tissue." ; sc:featureList edam:operation_3198 ; sc:name "VirusSeq" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html" ; biotools:primaryContact "Xiaoping Su" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0196, edam:topic_0637, edam:topic_3474, edam:topic_3673 ; sc:citation ; sc:description "VirusTaxo is a tool for taxonomic classification of virus genome using multi-class hierarchical classification by k-mer enrichment. VirusTaxo classifies DNA and RNA viruses to their taxonomic ranks using genome sequence. To assign taxonomic ranks, VirusTaxo extracts k-mers from genome sequence and creates bag-of-k-mers for each class in a rank. VirusTaxo uses a top-down hierarchical classification approach by enriching k-mers and accurately assigns the order, family and genus of a virus from the genome sequence." ; sc:featureList edam:operation_0475, edam:operation_2996, edam:operation_3208, edam:operation_3460, edam:operation_3472 ; sc:name "VirusTaxo" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://virustaxo.omics-lab.com/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0219, edam:topic_0781, edam:topic_3168 ; sc:citation , , "pmcid:PMC7778888", "pubmed:33045721" ; sc:contributor , , "Pietro Pinoli" ; sc:description """ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK, and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences.""" ; sc:featureList edam:operation_0224, edam:operation_0292, edam:operation_2403, edam:operation_2409, edam:operation_2422, edam:operation_3227 ; sc:name "ViruSurf" ; sc:softwareHelp ; sc:url "http://gmql.eu/virusurf/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0154, edam:topic_0199, edam:topic_0749 ; sc:citation , , "pmcid:PMC8344854", "pubmed:34107016" ; sc:description "VirusViz is a Web Server for analyzing viral sequences and visualizing their variants and characteristics." ; sc:featureList edam:operation_0331, edam:operation_0337, edam:operation_3197, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VirusViz" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/DEIB-GECO/VirusViz/wiki" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3494 ; sc:encodingFormat edam:format_2545 ; sc:name "DNA sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:name "Sequence set" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "A low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering." ; sc:featureList edam:operation_3227 ; sc:name "VirVarSeq" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://sourceforge.net/projects/virtools/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0637, edam:topic_0781, edam:topic_3168, edam:topic_3512 ; sc:citation , "pubmed:33367605" ; sc:description "A Lexicon Of Viral Sequences." ; sc:featureList edam:operation_2421, edam:operation_3431, edam:operation_3460 ; sc:name "Virxicon" ; sc:url "http://virxicon.cs.put.poznan.pl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0202, edam:topic_0602, edam:topic_0634, edam:topic_3407 ; sc:citation "pubmed:15028117", "pubmed:15980487", "pubmed:17483841", "pubmed:17586824", "pubmed:19465394", "pubmed:23716640" ; sc:description "VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions allow determination of over-representation and expression enrichment, integrated search and navigation of disease and drug hierarchies, drug/disease annotation, etc." ; sc:featureList edam:operation_0533, edam:operation_2436, edam:operation_2497, edam:operation_3463, edam:operation_3766 ; sc:name "VisANT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://visant.bu.edu/" ; biotools:primaryContact "VisANT Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_0769, edam:topic_3474 ; sc:citation , "pubmed:32170933" ; sc:description """an interactive tool for dissecting chemical features learned by deep neural network QSAR models. Here we took a step forward to interpret the learned features from deep neural network QSAR models, and present VISAR, an interactive tool for visualizing structure-activity relationship and the chemical activity landscape based on the learned features, thus providing deeper insights of the neural network 'black-box'. For a learning task, VISAR firstly provided users with useful functions to build, train and test the deep neural network models.""" ; sc:featureList edam:operation_3659, edam:operation_3799, edam:operation_3925 ; sc:name "VISAR" ; sc:url "https://github.com/qid12/visar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3518 ; sc:citation , "pubmed:32031874" ; sc:description """A Matrix-Based Bicluster Visualization of Expression Data. VisBicluster is an interactive, web based visualization technique designed to analyze biclusters generated from gene expression data. VisBicluster visualizes both, bicluster intersections and their properties, and the elements (genes and conditions as a heatmap )of each intersection or each bicluster.""" ; sc:featureList edam:operation_0337, edam:operation_2421, edam:operation_3802 ; sc:name "VisBicluster" ; sc:url "http://vis.usal.es/~visusal/visbicluster" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3295, edam:topic_3382, edam:topic_3697, edam:topic_3934 ; sc:citation , "pmcid:PMC8557071", "pubmed:34715773" ; sc:description "ViSCAR is a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. It can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view." ; sc:featureList edam:operation_0337, edam:operation_3435, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ViSCAR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://gitlab.com/ManolakosLab/viscar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0154, edam:topic_0797, edam:topic_3168 ; sc:citation "pubmed:14960475" ; sc:description "Web based tool that takes a set of sequences (aligned or unaligned) and calculates a consensus sequence and the conservation rates for the sequence alignment, producing an easy to interpret visualization as output. One can also compare and visualize a set of consensus sequences generated from several sequence sets." ; sc:featureList edam:operation_0259, edam:operation_0448, edam:operation_2451 ; sc:name "VisCoSe" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bio.math-inf.uni-greifswald.de/viscose/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3810 ; sc:citation , "pubmed:32725804" ; sc:description """Empirical Bayes small area prediction under a zero-inflated lognormal model with correlated random area effects. Many variables of interest in agricultural or economical surveys have skewed distributions and can equal zero. Our data are measures of sheet and rill erosion called Revised Universal Soil Loss Equation - 2 (RUSLE2). Small area estimates of mean RUSLE2 erosion are of interest. We use a zero-inflated lognormal mixed effects model for small area estimation. The model combines a unit-level lognormal model for the positive RUSLE2 responses with a unit-level logistic mixed effects model for the binary indicator that the response is nonzero. In the Conservation Effects Assessment Project (CEAP) data, counties with a higher probability of nonzero responses also tend to have a higher mean among the positive RUSLE2 values. We capture this property of the data through an assumption that the pair of random effects for a county are correlated""" ; sc:featureList edam:operation_3658, edam:operation_3659, edam:operation_3936 ; sc:name "viscover" ; sc:url "https://lyux.shinyapps.io/viscover/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622 ; sc:citation "pubmed:18801195" ; sc:description "Software for cluster modeling, visualization, and discovery in genomic data. It performs progressive, coarse-to-fine (divisive) hierarchical clustering and visualization, supported by hierarchical mixture modeling, supervised/unsupervised informative gene selection, supervised/unsupervised data visualization, and user/prior knowledge guidance, to discover hidden clusters within complex, high-dimensional genomic data." ; sc:featureList edam:operation_0564, edam:operation_2403 ; sc:name "VISDA" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.cbil.ece.vt.edu/caBIG-VISDA.htm" ; biotools:primaryContact "Computational Bioinformatics and Bioimaging Laboratory" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2259, edam:topic_2269 ; sc:citation "pubmed:23468157" ; sc:description "It provides a graphical visualization for statistical epistasis.  Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks." ; sc:featureList edam:operation_3083 ; sc:name "ViSEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sourceforge.net/projects/visen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0160, edam:topic_0593, edam:topic_3047 ; sc:citation , "pmcid:PMC7068867", "pubmed:32164574" ; sc:description """A graph mining based detection and visualization of conserved motifs in 3D protein-ligand interface at the atomic level. Interactions between proteins and non-proteic small molecule ligands play important roles in biological processes of living systems.""" ; sc:featureList edam:operation_0239, edam:operation_0337, edam:operation_2575 ; sc:name "visGReMLIN" ; sc:url "http://vagner.dti.ufv.br/visgremlin4" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0166, edam:topic_2275 ; sc:citation "pubmed:17975834" ; sc:description "The algorithm identifies geometric features of protein surfaces using an intuitive concept of the visibility. It correctly identified 95.0% of ligand binding sites as one of the three largest pockets in 5616 benchmark proteins." ; sc:featureList edam:operation_0474 ; sc:name "VisGrid" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://kiharalab.org/VisGrid/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_1775, edam:topic_3335 ; sc:citation "pubmed:19483095" ; sc:description "Web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters." ; sc:featureList edam:operation_0313, edam:operation_2436, edam:operation_2495, edam:operation_3432, edam:operation_3501 ; sc:name "VisHiC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://biit.cs.ut.ee/vishic" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3301 ; sc:citation ; sc:description "Microbiome search and visualization tool." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "Visibiome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/syaffers/visibiome.git" ; biotools:primaryContact "Andreas Henschel" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_2229, edam:topic_2259 ; sc:citation "pubmed:20460470" ; sc:description "Web-based pathway visualization and layout service for pathway models in BioPAX format. Models are based on the Systems Biology Graphical Notation and pathway object properties such as external database references, may be inspected interactively." ; sc:featureList edam:operation_0335, edam:operation_2409, edam:operation_2497, edam:operation_3083, edam:operation_3562 ; sc:name "VISIBIOweb" ; sc:url "http://visibioweb.patika.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3407 ; sc:citation , "pmcid:PMC4447416", "pubmed:26020230" ; sc:description "Visinets is a graphically oriented method for pathway modeling and a software package that allows for both modeling and visualization of biological networks in a user-friendly format." ; sc:featureList edam:operation_3083 ; sc:license "MIT" ; sc:name "Visinets" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.visinets.com/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3063, edam:topic_3304 ; sc:citation , "pubmed:36621552" ; sc:description "An open-source platform for building rodent touchscreen-based behavioral assays." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Visiomode" ; sc:operatingSystem "Linux", "Mac" ; sc:url "http://www.visiomode.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:35077359" ; sc:description "A Permutable MLP-Like Architecture for Visual Recognition." ; sc:featureList edam:operation_0337, edam:operation_2475, edam:operation_3436 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Vision Permutator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Andrew-Qibin/VisionPermutator" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_2259 ; sc:citation ; sc:description "Streamlined visualization to transform large and dense overlapping transcription factor networks into sparse human-readable graphs via numerically filtering." ; sc:featureList edam:operation_0337, edam:operation_3695 ; sc:name "VISIONET" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://visionet.erc.monash.edu.au/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC9279291", "pubmed:35831385" ; sc:description "VisionTool is a python toolbox for pose estimation on videos containing actions. It is powered with a simple and intuititive Graphical User Interface (GUI) to allow a complete analysis from annotation to semantic features detection (e.g., joint position estimation)." ; sc:featureList edam:operation_1812, edam:operation_3443, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VisionTool" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/Malga-Vision/VisionTool.git" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_3053 ; sc:citation ; sc:description "Tool to bring the interactivity of networks created with vis.js into jupyter notebook cells." ; sc:featureList edam:operation_3083 ; sc:license "MIT" ; sc:name "visJS2jupyter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/ucsd-ccbb/visJS2jupyter" ; biotools:primaryContact "Sara Brin Rosenthal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0102, edam:topic_0781, edam:topic_3303 ; sc:citation ; sc:description "Ultra-fast exhaustive cartography of viral insertion sites for gene therapy." ; sc:featureList edam:operation_0564 ; sc:name "VISMapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vismapper.babelomics.org/" ; biotools:primaryContact "Joaquín Dopazo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0749, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC7962676", "pubmed:33828749" ; sc:description "VisME (Visual Microsaccades Explorer) is a visual analytics system to explore high frequency eye tracking data with a special focus on microsaccades. The exploration can take place on different levels, for fixations, participants, trials, and test conditions using data of individuals as well as groups of participants. The system provides multiple views, eye movement filters, visibility filters and further options to support users in their exploration." ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3695 ; sc:name "VisME" ; sc:url "https://github.com/MunzT/VisME" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Desktop application" ; sc:applicationSubCategory edam:topic_3170, edam:topic_3308, edam:topic_3320, edam:topic_3388, edam:topic_3512 ; sc:citation , "pmcid:PMC10060319", "pubmed:36881176" ; sc:description "Interactive tool for the detection, quantification and fine-tuning of isoforms in selected genes using long-read sequencing." ; sc:featureList edam:operation_0264, edam:operation_0337, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "VIsoQLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TBLabFJD/VIsoQLR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0196, edam:topic_0781 ; sc:citation "pubmed:21989211" ; sc:description "It implements a novel viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via Expectation Maximization on all reads." ; sc:featureList edam:operation_0310 ; sc:name "ViSpA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://alan.cs.gsu.edu/NGS/?q=content/vispa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description "A computer-vision-based representation system for individual images and concept prototypes, with large-scale evaluation." ; sc:featureList edam:operation_0337, edam:operation_3443 ; sc:isAccessibleForFree true ; sc:name "ViSpa" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://vispa.fritzguenther.de" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3053 ; sc:citation , "pmcid:PMC4160258", "pubmed:25208325" ; sc:description "A web application to produce multi-track, multi-scale, multi-region plots of genetic data." ; sc:featureList edam:operation_0571 ; sc:license "GPL-3.0" ; sc:name "visPIG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vispig.icr.ac.uk/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0099 ; sc:citation , "pmcid:PMC8223366", "pubmed:34167459" ; sc:description "VISPR-online is a web-based interactive framework for CRISPR screens visualization, exploration and sharing." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "VISPR-online" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vispr-online.weililab.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0736, edam:topic_0780, edam:topic_3512, edam:topic_3945 ; sc:citation , "pmcid:PMC9235191", "pubmed:35761171" ; sc:description "An interactive Shiny/R application for displaying protein domains with transcriptional features." ; sc:featureList edam:operation_0224, edam:operation_0303, edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VisProDom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://whweve.shinyapps.io/VisProDom" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3293 ; sc:citation "pubmed:19397803" ; sc:description "Software package allowing graphical inspection of the phylogenetic content of a sequence alignment, that is primarily intended for detection of recombination and recombination breakpoints." ; sc:featureList edam:operation_0258, edam:operation_0567 ; sc:name "VisRD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/phylogenetics-software-visrd" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0625, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC10320187", "pubmed:37158226" ; sc:description "Webserver to visualise higher order molecular phenotypes from enrichment analysis." ; sc:featureList edam:operation_0337, edam:operation_2436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "vissE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; 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Vitiligo is a complex skin depigmentation disorder characterized by the patchy loss of skin pigmentation. 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Manual: | VIVA: A VCF File Visualization Tool and VariantVisualization.jl | VIVA Command Line Tool and Jupyter Notebook | VIVA is a user-friendly command line tool for creating publication quality graphics from Variant Call Format (VCF) files | VIVA is a user-friendly command line tool built with our VariantVisualization.jl package for exploratory analysis and generation of publication quality graphics for variant analysis projects using Variant Call Format (VCF) files | Then, follow add Julia to the path variable to run VIVA" ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3675 ; sc:name "VIVA" ; sc:softwareHelp ; sc:url "https://compbiocore.github.io/VariantVisualization.jl/latest/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3360, edam:topic_3372 ; sc:citation , "pmcid:PMC7191767", "pubmed:32349651" ; sc:description """a survival data set generator for software testing. An amendment to this paper has been published and can be accessed via the original article""" ; sc:featureList edam:operation_3503 ; sc:license "GPL-2.0" ; sc:name "vivaGen" ; sc:url "https://sourceforge.net/projects/vivagen/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0593, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:23180575" ; sc:description "Web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). It provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information." ; sc:featureList edam:operation_0321, edam:operation_0570, edam:operation_2406 ; sc:name "Vivaldi" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.ebi.ac.uk/pdbe/vivaldi/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0781, edam:topic_3053 ; sc:citation "pubmed:25701575" ; sc:description "Complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations." ; sc:featureList edam:operation_2403 ; sc:name "ViVan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vivan.tau.ac.il/index.php" ; biotools:primaryContact "The ViVan team at Dr. Noam Shomron Lab" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3307, edam:topic_3318 ; sc:citation ; sc:description "The Vivarium Collective is a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism." ; sc:featureList edam:operation_1781, edam:operation_2426, edam:operation_3660 ; sc:license "MIT" ; sc:name "Vivarium Collective" ; sc:softwareHelp ; sc:url "https://vivarium-collective.github.io/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0202, edam:topic_0749, edam:topic_3068 ; sc:citation , "pubmed:31596400" ; sc:description "vivasemtabaco is a tool for comparing gain- and loss-framed ads for the purposes of an Internet-based smoking cessation intervention." ; sc:name "vivasemtabaco" ; sc:softwareHelp ; sc:url "https://github.com/crepeia/wati" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_2885, edam:topic_3302 ; sc:citation ; sc:description "A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax | Abstract Imported cases present a considerable challenge to the elimination of malaria. Traditionally, patient travel history has been used to identify imported cases, but the long-latency liver stages confound this approach in Plasmodium vivax. Molecular tools to identify and map imported cases offer a more robust approach, that can be combined with drug resistance and other surveillance markers in high-throughput, population-based genotyping frameworks. Using a machine learning approach incorporating hierarchical FST (HFST) and decision tree (DT) analysis applied to 831 P. vivax genomes from 20 countries, we identified a 28-Single Nucleotide Polymorphism (SNP) barcode with high capacity to predict the country of origin" ; sc:featureList edam:operation_3196, edam:operation_3891 ; sc:name "vivaxGEN-geo" ; sc:url "http://vivaxgen.menzies.edu.au/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0157, edam:topic_3302, edam:topic_3516 ; sc:citation , "pmcid:PMC5389845", "pubmed:28362818" ; sc:description "Open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations." ; sc:featureList edam:operation_0379, edam:operation_3196 ; sc:name "VivaxGEN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vivaxgen.menzies.edu.au/" ; biotools:primaryContact "Sarah Auburn" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_2229, edam:topic_3383 ; sc:citation "pubmed:26261223" ; sc:description "Software for the evaluation of single-cell experiments. While its core functionality is the visualization of time-resolved, single-cell but also population data, it can be used for the automated/scripted analysis of data as well." ; sc:featureList edam:operation_3457 ; sc:name "Vizardous" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/modsim/vizardous" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_2885 ; sc:citation , "pmcid:PMC2607484", "pubmed:14693813", "pubmed:16613906" ; sc:description "Exploratory visualisation for gene expression profiling." ; sc:featureList edam:operation_0337 ; sc:license "Not licensed" ; sc:name "VizStruct" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://www.cse.buffalo.edu/DBGROUP/bioinformatics/supplementary/vizstruct/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0084, edam:topic_0621, edam:topic_3293 ; sc:citation "pubmed:20972209" ; sc:description "The Voltage-gated K(+) Channel DataBase contains full-length or nearly full-length unique channel sequences from Bacteria, Archaea and Eukaryotes. Corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses." ; sc:featureList edam:operation_0224, edam:operation_2422, edam:operation_2479 ; sc:name "VKCDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://vkcdb.biology.ualberta.ca" ; biotools:primaryContact "W. Gallin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0623, edam:topic_0625, edam:topic_3053 ; sc:citation , "pmcid:PMC4602057", "pubmed:26047590" ; sc:description "Visual annotation display- finding functional themes in lists of genes." ; sc:featureList edam:operation_0362 ; sc:name "VLAD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://proto.informatics.jax.org/prototypes/vlad/" ; biotools:primaryContact "Carol J. Bult" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3307 ; sc:citation , "pubmed:33465550" ; sc:description "A Web Resource For Designing Subunit Vaccine Candidates Against Lung Cancer Associated Viruses" ; sc:featureList edam:operation_2945 ; sc:name "vlcvirus" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://webs.iiitd.edu.in/raghava/vlcvirus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0166, edam:topic_2828 ; sc:citation "pubmed:23761450" ; sc:description "Web server designed to determine protein contacts, accessibility and residue volume using Laguerre diagram." ; sc:featureList edam:operation_0321, edam:operation_0384, edam:operation_0387, edam:operation_2406, edam:operation_2950 ; sc:name "VLDP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.dsimb.inserm.fr/dsimb_tools/vldp" ; biotools:primaryContact "Alexandre G. de Brevern", "Jeremy Esque", "Sylvain Leonard" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3277, edam:topic_3306, edam:topic_3382 ; sc:citation , "pubmed:33046895" ; sc:description """3D virtual reality for single-molecule localization microscopy. An important feature of vLUME the ability to perform local analysis on a subregion of point-cloud data (RoI).""" ; sc:featureList edam:operation_0337, edam:operation_3435 ; sc:name "vLUME" ; sc:url "https://github.com/lumevr/vLume_OpenSourcePlugins" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_3168 ; sc:citation ; sc:description "A versatile software tool for efficiently solving large scale sequence matching tasks" ; sc:featureList edam:operation_0258, edam:operation_0292, edam:operation_2409 ; sc:name "Vmatch" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.vmatch.de/" ; biotools:primaryContact "Prof. Dr. Stefan Kurtz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2269, edam:topic_3293, edam:topic_3474 ; sc:citation , "pmcid:PMC5301390", "pubmed:28187712" ; sc:description "Statistical graphical software that takes as input Markov Chain Monte Carlo (MCMC) traces from various softwares, visualize it, and calculates and displays the statistical properties such as burnin and convergence tests." ; sc:featureList edam:operation_3744 ; sc:name "VMCMC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bitbucket.org/rhali/visualmcmc/" ; biotools:primaryContact "Raja H. 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In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation." ; sc:featureList edam:operation_0379 ; sc:name "VNTRfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://sites.google.com/a/codushlaine.com/colm-o-dushlaine/Data" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3053, edam:topic_3071 ; sc:citation "pubmed:12424130" ; sc:description "An easy-to-use Java GUI used to access the VBRC genome databases." ; sc:featureList edam:operation_0338 ; sc:name "VOCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://virology.uvic.ca/virology-ca-tools/vocs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0634, edam:topic_3300, edam:topic_3360, edam:topic_3407 ; sc:citation , "pmcid:PMC10339195", "pubmed:37336362" ; sc:description "Breath volatile organic compounds (VOCs) as biomarkers for the diagnosis of pathological conditions." ; sc:featureList edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "VOCs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://neomeditec.com/VOCdatabase/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0622, edam:topic_3056 ; sc:citation , "pubmed:27153572" ; sc:description "A cross-platform portal for interactive data visualization." ; sc:featureList edam:operation_3208, edam:operation_3209 ; sc:name "Visual Omics Explorer (VOE)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bcil.github.io/VOE/" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0781, edam:topic_2259 ; sc:description "Virus Orthologous Groups." ; sc:featureList edam:operation_3672 ; sc:name "VOGDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vogdb.org/" ; biotools:primaryContact "CUBE-AT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0202, edam:topic_2258 ; sc:description "VoID dataset description tool." ; sc:featureList edam:operation_0336 ; sc:name "VoID Editor" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "manchester.ac.uk" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "http://voideditor.cs.man.ac.uk/" ; biotools:primaryContact "Lefteris Tatakis" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3384, edam:topic_3444 ; sc:citation , "pmcid:PMC9171328", "pubmed:35685943" ; sc:description "A New Online Pipeline for Whole Brain MRI Analysis." ; sc:featureList edam:operation_3435, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:name "vol2Brain" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://volbrain.upv.es" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_0176, edam:topic_2275 ; sc:citation "pubmed:24164915" ; sc:description "Plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure." ; sc:featureList edam:operation_0250, edam:operation_3351 ; sc:name "Volarea" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.fc.up.pt/PortoBioComp/Software/Volarea/Home.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0622 ; sc:citation ; sc:description """VolcaNoseR – a web app for creating, exploring, labeling and sharing volcano plots. A Shiny App for making Volcano plots.""" ; sc:featureList edam:operation_2422, edam:operation_2940, edam:operation_3431 ; sc:license "GPL-3.0" ; sc:name "VolcaNoseR" ; sc:url "http://goedhart.shinyapps.io/VolcaNoseR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "It is the universal solution for 3D analysis of fluorescence microscopy images.  A collection of high performance 3D imaging software products, Volocity lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication." ; sc:featureList edam:operation_3443 ; sc:name "Volocity Demo" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareVersion "6.3" ; sc:url "http://www.perkinelmer.co.uk/lab-solutions/resources/docs/BRO_VolocityBrochure_PerkinElmer.pdf" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3308 ; sc:citation , "pubmed:34498028" ; sc:description "VOLTA is a Python network analysis package, suited for different types of networks but with a focus on co-expression network analysis. The goal of VOLTA is to provide all functionalities needed for a comprehensive network analysis and comparison in a single package. Its aim is to expose all functionalities in order to allow users to build their own analysis pipelines and adjust functionalities as needed. Additional complete analysis pipelines are provided in the form of Jupyter Notebooks." ; sc:featureList edam:operation_3463, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VOLTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/fhaive/VOLTA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382 ; sc:description "Volume Browser created at the Pittsburgh Supercomputing Center (PSC) enables you to view large three dimensional images (datasets) over the internet. You can interact with with the image to view from any angle, or slice through it to see inside. You can also trace and label sections of the image. The PSC Volume Browser is a breathrough in 3D imaging because it allows you to view uncompressed datasets from a desktop computer that wouldn’t have the capability view such data on its own." ; sc:featureList edam:operation_3443 ; sc:name "Volume Browser" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareVersion "2.0.393" ; sc:url "http://www.nrbsc.org/vb/index.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3304, edam:topic_3444, edam:topic_3452 ; sc:citation ; sc:contributor "James Ryland" ; sc:description "3D Volumetric fMRI visualization" ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:name "Volumetric 3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.05" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/59161-volumetric-3" ; biotools:primaryContact "Alice J. O'Toole" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:15797905", "pubmed:16845064" ; sc:description "Predict transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order Bayesian Trees." ; sc:featureList edam:operation_0438, edam:operation_0445, edam:operation_2575 ; sc:name "VOMBAT" ; sc:url "https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3168, edam:topic_3520 ; sc:citation ; sc:description "New de novo sequencing algorithm which has been developed specifically for analysis of such high-resolution tandem mass spectra." ; sc:featureList edam:operation_3644 ; sc:name "Vonode" ; sc:operatingSystem "Windows" ; sc:url "http://www.omicsbio.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0804, edam:topic_3421, edam:topic_3474, edam:topic_3934 ; sc:citation , "pmcid:PMC7385162", "pubmed:32719375" ; sc:description "VoPo leverages cellular heterogeneity for predictive modeling of single-cell data." ; sc:featureList edam:operation_0337, edam:operation_3432, edam:operation_3935 ; sc:name "VoPo" ; sc:url "https://github.com/stanleyn/VoPo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0130, edam:topic_0736, edam:topic_3474 ; sc:citation ; sc:description """Deep convolutional neural network built on 3D Voronoi tessellation of protein structures. VoroCNN is a novel method for local residue-level quality assessment of protein folds. The method is based on a deep convolutional neural network (CNN) constructed on a Voronoi tessellation of 3D molecular structures.""" ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_2415 ; sc:name "VoroCNN" ; sc:url "https://team.inria.fr/nano-d/software/vorocnn/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0097, edam:topic_0166, edam:topic_0593 ; sc:citation , "pubmed:34132767" ; sc:description "Voronota is a software tool for analyzing three-dimensional structures of biological macromolecules using the Voronoi diagram of atomic balls.." ; sc:featureList edam:operation_0384, edam:operation_0387, edam:operation_1839 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VoroContacts" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bioinformatics.lt/wtsam/vorocontacts" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0128, edam:topic_2275, edam:topic_3474 ; sc:citation , "pubmed:37482904" ; sc:description "Voronoi tessellation-derived protein-protein interface assessment using a graph neural network." ; sc:featureList edam:operation_0477, edam:operation_3899, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VoroIF-GNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://kliment-olechnovic.github.io/voronota/expansion_js/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0082, edam:topic_0736 ; sc:citation , "pubmed:28263393" ; sc:description "Voronoi tessellation‐based Model Quality Assessment. Quality assessment of single protein structure models using inter-atomi contact areas derived from Voronoi diagram of atomic balls." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_2950 ; sc:name "VoroMQA" ; sc:softwareHelp ; sc:url "http://www.bti.vu.lt/en/departments/department-of-bioinformatics/software/voromqa" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0091, edam:topic_0154, edam:topic_0166, edam:topic_3047 ; sc:citation , "pmcid:PMC8265189", "pubmed:34107038" ; sc:description "Voronoia is a web tool which identifies cavities in a molecular structure and calculates the packing density of all atoms. This allows users to check for packing defects, which may be a sign of a wrongly resolved structure. The tool also helps in creating reliable simulations by finding cavities possibly missing internal water molecules in the structure, thereby enabling a more realistic modeling of proteins and nucleic acids. The results are visualized directly on the website with NGL. Voronoia also includes a database of precalculated structures from the Protein Data Bank which can be explored." ; sc:featureList edam:operation_0337, edam:operation_0387, edam:operation_3561 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Voronoia" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/krother/Voronoia" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0842 ; sc:encodingFormat edam:format_3016 ; sc:name "Identifier" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0199, edam:topic_3324, edam:topic_3474, edam:topic_3676 ; sc:citation , "pubmed:36528806" ; sc:description "A deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants." ; sc:featureList edam:operation_0331, edam:operation_3226, edam:operation_3461 ; sc:isAccessibleForFree true ; sc:name "VPatho" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://csbio.njust.edu.cn/bioinf/vpatho/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_0602, edam:topic_0781, edam:topic_2533, edam:topic_3336 ; sc:citation "pubmed:19654117" ; sc:description "The purpose of the tool is to generate a transition model showing the mutational pathways of drug resistance for viruses under drug pressure." ; sc:featureList edam:operation_3439 ; sc:name "vPhyloMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://vphylomm.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_2814, edam:topic_3510, edam:topic_3534 ; sc:citation "pubmed:26446136" ; sc:description "This uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, e.g. usually alpha helices and beta sheets) or ligand molecules while the edges model contacts and spatial relations between them." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "VPLG" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinformatik.uni-frankfurt.de/tools/vplg/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_0769, edam:topic_3673, edam:topic_3676 ; sc:citation , "pmcid:PMC8576923", "pubmed:34749640" ; sc:description "A test bench for variant prioritization methods" ; sc:featureList edam:operation_3225, edam:operation_3226, edam:operation_3227 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VPMBench" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/IDEA-PRIO/VPMBench" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0121, edam:topic_0154, edam:topic_0160, edam:topic_0601 ; sc:citation , "pubmed:33094321" ; sc:description """a viral posttranslational modification database. In viruses, posttranslational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for a better understanding of the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus-human interactions using comprehensive viral PTM datasets. To fill this gap, we developed the first comprehensive viral posttranslational modification database (VPTMdb) for collecting systematic information of PTMs in human viruses and infected host cells. The VPTMdb contains 1240 unique viral PTM sites with 8 modification types from 43 viruses (818 experimentally verified PTM sites manually extracted from 150 publications and 422 PTMs extracted from SwissProt) as well as 13 650 infected cells' PTMs extracted from seven global proteomics experiments in six human viruses""" ; sc:featureList edam:operation_0417, edam:operation_3755, edam:operation_3904 ; sc:name "VPTMdb" ; sc:url "http://vptmdb.com:8787/VPTMdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3384, edam:topic_3474 ; sc:citation , "pubmed:35727773" ; sc:description "Conditional Triplet Mixup for Medical Visual Question Answering." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VQAMix" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/haifangong/VQAMix" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0621, edam:topic_3174, edam:topic_3474, edam:topic_3697 ; sc:citation , "pubmed:35544285" ; sc:description "vRhyme enables binning of viral genomes from metagenomes." ; sc:featureList edam:operation_3192, edam:operation_3198, edam:operation_3216, edam:operation_3798 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "vRhyme" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/AnantharamanLab/vRhyme" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_3361, edam:topic_3474 ; sc:citation , "pubmed:31944959" ; sc:description """A Web-based Framework for Creating Immersive Analytics Experiences. visualization charts augmented-reality data-visualization virtual-reality webxr immersive-analytics.""" ; sc:featureList edam:operation_0337 ; sc:name "VRIA" ; sc:url "https://github.com/vriajs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0085, edam:topic_0092 ; sc:citation ; sc:description """VRMLGen is a free software package for 3D data visualisation on the web. It supports VRML and LiveGraphics3D formats. The package runs within the R environment for statistical computing and is available for download from CRAN. It is licensed under the terms of GNU GPL version 2 (or later). VRMLGen can be used to generate 3D line and bar charts, scatter plots with density estimation contour surfaces, visualizations of height maps, parametric functions and 3D object models.""" ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "VRMLGen" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.9" ; sc:url "https://ico2s.org/software/vrmlgen.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0154, edam:topic_0199, edam:topic_0209, edam:topic_2275 ; sc:citation , "pubmed:32745209" ; sc:description """VRmol: Virtual Reality for Molecular Structures. an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure. VRmol is an easy-to-use web-based tool capable of visualizing and integratively analyzing biomolecular structures in Virtual Reality environment.""" ; sc:featureList edam:operation_0337, edam:operation_3080, edam:operation_3938 ; sc:license "MIT" ; sc:name "VRmol" ; sc:softwareHelp ; sc:url "https://VRmol.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_0634, edam:topic_3168, edam:topic_3388 ; sc:citation , "pmcid:PMC8065164", "pubmed:33893283" ; sc:description "VRNetzer is a virtual reality framework for network visualization and analytics. The VRNetzer platform enables interactive network analysis in Virtual Reality." ; sc:featureList edam:operation_0276, edam:operation_2436, edam:operation_3226, edam:operation_3925 ; sc:license "MIT" ; sc:name "VRNetzer" ; sc:url "https://github.com/menchelab/VRNetzer" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0602, edam:topic_0769 ; sc:citation , "pubmed:36073903" ; sc:description "Bringing Virtual Reality into Pharmacophore-based Virtual Screening with Interactive Exploration and Realistic Visualization." ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VRPharmer" ; sc:operatingSystem "Windows" ; sc:url "https://github.com/VRPharmer/VRPharmer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:encodingFormat edam:format_1929 ; sc:name "Nucleic acid sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0798, edam:topic_3068, edam:topic_3305 ; sc:citation , "pmcid:PMC9252795", "pubmed:35524563" ; sc:description "Detection of antibiotic resistance-associated mobilome in bacterial pathogens." ; sc:featureList edam:operation_2422, edam:operation_3461, edam:operation_3482 ; sc:isAccessibleForFree true ; sc:name "VRprofile2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://tool2-mml.sjtu.edu.cn/VRprofile" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3173, edam:topic_3517 ; sc:citation , "pubmed:33270826" ; sc:description """vSampler is both a web-based tool and a local program to support matched control variant sampling. Given input variants, vSampler could randomly sample control variants with matched minor allele frequency (MAF), distance to closet transcription start site (DTCT), number of nearby genes, number of variants in LD, GC content and many other properties. These matched random controls could be used to construct null distribution for GWAS enrichment analysis to estimate significance of enrichment empirically or serve as negative training/test data for regulatory variant prediction methods. vSampler runs significantly faster than existing tools, supports both SNPs and indels and provides comprehensive state of art variant annotations as matching properties. A novel data structure and algorithm were developed to achieve this performance improvement.""" ; sc:featureList edam:operation_0282, edam:operation_2422, edam:operation_3227, edam:operation_3501 ; sc:name "vSampler" ; sc:url "http://mulinlab.org/vsampler" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3932 ; sc:encodingFormat edam:format_3752 ; sc:name "Q-value" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3768 ; sc:encodingFormat edam:format_3752 ; sc:name "Clustered expression profiles" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web service" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0622, edam:topic_2269, edam:topic_3172, edam:topic_3391, edam:topic_3473 ; sc:citation ; sc:description "Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance ." ; sc:featureList edam:operation_0313, edam:operation_0533, edam:operation_3664, edam:operation_3960 ; sc:isAccessibleForFree true ; sc:license "GPL-2.0" ; sc:name "VSClust" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://computproteomics.bmb.sdu.dk/Apps/VSClust/" ; biotools:primaryContact "Veit Schwämmle" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275, edam:topic_2814, edam:topic_3071, edam:topic_3343 ; sc:citation "pubmed:21826555" ; sc:description "Virtual Screening Data Management on an Integrated Platform  is divided in two parts: programs which actually do things (local packages) and program which translate those things to the database (cluster packages and cartridge)." ; sc:featureList edam:operation_0478, edam:operation_3431 ; sc:name "VSDMIP" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://ub.cbm.uam.es/software/vsdmip/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0622, edam:topic_3053, edam:topic_3517 ; sc:citation "pubmed:25170024" ; sc:description "Pipeline for investigating whether a set of gene/genomic intervals is enriched for genome wide association study (GWAS) p-values for a particular trait." ; sc:featureList edam:operation_3501 ; sc:name "VSEAMS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ollyburren/vseams/wiki" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0865 ; sc:name "Sequence similarity score" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:name "Sequence alignment" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3174 ; sc:citation , "pmcid:PMC5075697", "pubmed:27781170" ; sc:description "High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion." ; sc:featureList edam:operation_0450, edam:operation_2520 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VSEARCH" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "UiO" ; sc:softwareHelp ; sc:softwareVersion "1.9.0" ; sc:url "https://github.com/torognes/vsearch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0622, edam:topic_3673, edam:topic_3930 ; sc:citation , "pmcid:PMC7177155", "pubmed:32346552" ; sc:description "Comprehensive Computational Analysis of Viral Vectors in Gene Therapy." ; sc:featureList edam:operation_0266, edam:operation_3192, edam:operation_3219 ; sc:name "VSeq-Toolkit" ; sc:url "https://github.com/CompMeth/VSeq-Toolkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0209, edam:topic_2258, edam:topic_3343 ; sc:citation , "pmcid:PMC10064649", "pubmed:37004101" ; sc:description "Open-source ligand-based virtual screening tool." ; sc:featureList edam:operation_0245, edam:operation_0337, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VSFlow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/czodrowskilab/VSFlow" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2338 ; sc:name "Ontology identifier" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_3464 ; sc:name "Ontology data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2353 ; sc:encodingFormat edam:format_2376 ; sc:name "Ontology data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0219, edam:topic_0621, edam:topic_2259, edam:topic_3068, edam:topic_3307 ; sc:author ; sc:citation , , ; sc:description """General-purpose Interface for Biocuration and Knowledge Representation. — VSM is an intuitive and flexible method for entering and displaying knowledge on any topic, and with any contextual descriptions, in a form that is both semantically precise (for computer processing) and intuitive to read (for humans). VSM makes it practical to translate diverse research findings and their rich context (from literature) into a computable, readable form. — VSM defines: 1. a knowledge model that corresponds well to human thinking; 2. a user interface "vsm-box" to communicate knowledge in this form. This user interface is a JavaScript component that can be embedded in web apps with two lines of code. It may be filled with an entry template, and emits data upon user input. | https://vsm.github.io: all info on VSM | https://github.com/vsm: core modules | https://github.com/vsm/vsm-box: main user interface | https://github.com/vsm/vsm-to-rdf: output as RDF""" ; sc:featureList edam:operation_3559, edam:operation_3778 ; sc:license "AGPL-3.0" ; sc:name "VSM (Visual Syntax Method)" ; sc:softwareHelp ; sc:url "https://vsm.github.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3518 ; sc:citation , "pubmed:12169536" ; sc:description "The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format." ; sc:featureList edam:operation_2428, edam:operation_2495, edam:operation_3435 ; sc:license "Artistic-2.0" ; sc:name "vsn" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.46.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/vsn.html" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0108, edam:topic_3360, edam:topic_3474 ; sc:citation , "pubmed:36608930" ; sc:description "A variable-selection oriented LASSO bagging algorithm for biomarker discovery in omic-based translational research." ; sc:featureList edam:operation_3659, edam:operation_3936 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VSOLassoBag" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://seqworld.com/VSOLassoBag/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0659, edam:topic_0780, edam:topic_3170, edam:topic_3500, edam:topic_3512 ; sc:citation , "pubmed:36377755" ; sc:description "A novel method for identifying high-confidence viral small RNAs from small RNA-Seq data." ; sc:featureList edam:operation_3192, edam:operation_3222, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "vsRNAfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/ZenaCai/vsRNAfinder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0593, edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3452 ; sc:citation , , "pmcid:PMC7070820", "pubmed:32079305" ; sc:description """Variance-stabilized signals for sequencing-based genomic signals. Variance-stabilized signals (VSS) is a signal transformation approach used for eliminating the dependency of data variance from its mean. We generate VSS for sequencing-based genomic signals by learning the empirical relationship between the mean and variance of a given signal data set and producing transformed signals that normalize for this dependence.""" ; sc:featureList edam:operation_3435, edam:operation_3557, edam:operation_3659 ; sc:name "VSS" ; sc:url "https://github.com/faezeh-bayat/Variance-stabilized-units-for-sequencing-based-genomic-signals" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0196, edam:topic_0199, edam:topic_3315 ; sc:citation ; sc:description "Software tools to find optimal spaced seeds for a given genome sequence." ; sc:featureList edam:operation_3198, edam:operation_3359, edam:operation_3802 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "VSTseed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/vtman/VSTseed" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0160, edam:topic_3053, edam:topic_3168 ; sc:citation "pubmed:25701572" ; sc:description "Variant tool set that discovers short variants from Next Generation Sequencing data." ; sc:featureList edam:operation_3227 ; sc:name "vt" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://genome.sph.umich.edu/wiki/Vt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3308, edam:topic_3382 ; sc:citation , "pubmed:37054878" ; sc:description "Visualization toolbox for 3D transcriptomic data." ; sc:featureList edam:operation_0337 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "VT3D" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/BGI-Qingdao/VT3D" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3308 ; sc:citation ; sc:description "It is for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1." ; sc:featureList edam:operation_0310 ; sc:name "VTBuilder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.lstmed.ac.uk/vtbuilder" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3421, edam:topic_3474 ; sc:citation , "pubmed:37079979" ; sc:description "Machine learning prediction of venous thromboembolism after surgeries of major sellar region tumors." ; sc:featureList edam:operation_3503, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "VTE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://deepvep.shinyapps.io/VTEpred/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3305, edam:topic_3322, edam:topic_3324 ; sc:citation ; sc:description """a stochastic Python-based tool to simulate viral transmission. Repository for the code that simulates disease transmission among individuals.""" ; sc:featureList edam:operation_0337, edam:operation_2426 ; sc:name "VTES" ; sc:url "https://github.com/sstagg/disease-transmission" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0781, edam:topic_3308, edam:topic_3324, edam:topic_3500 ; sc:citation , "pmcid:PMC8728219", "pubmed:34634807" ; sc:description "A database for single-cell screening of virus target cells in the animal kingdom." ; sc:featureList edam:operation_0224, edam:operation_0314, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:name "VThunter" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://db.cngb.org/VThunter/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0769, edam:topic_3676 ; sc:citation ; sc:description "Software for annotating and tracking sequence variation for large-scale exome sequencing projects." ; sc:featureList edam:operation_3196, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:name "vtools" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://varianttools.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_2269 ; sc:citation ; sc:description "A package for analyzing variant-transcription factor-phenotype networks." ; sc:featureList edam:operation_2238, edam:operation_2497, edam:operation_3197 ; sc:license "Artistic-2.0" ; sc:name "vtpnet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.18.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/vtpnet.html" ; biotools:primaryContact "VJ Carey" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0621, edam:topic_0736, edam:topic_0821 ; sc:citation , , "pubmed:33375704" ; sc:description """Timely Reliability Analysis of Virtual Machines Considering Migration and Recovery in an Edge Server. VTR is a WebTool for contacts alignments between proteins and others macromolecules. an algorithm for identifying analogous contacts on protein structures and their complexes.""" ; sc:featureList edam:operation_0272, edam:operation_0295, edam:operation_0392, edam:operation_1839, edam:operation_3938 ; sc:name "VTR" ; sc:url "http://bioinfo.dcc.ufmg.br/vtr" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2259, edam:topic_3169 ; sc:citation , "pmcid:PMC5040167", "pubmed:27322546" ; sc:description "VirtUaL ChIP-Seq Analysis through Networks is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "LGPL-3.0" ; sc:name "vulcan" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/vulcan.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330 ; sc:name "Gene name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Gene name" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0984 ; sc:encodingFormat edam:format_2330, edam:format_3464 ; sc:name "Molecule name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2640, edam:topic_3053 ; sc:citation ; sc:description "Tool to prioritize therapeutic vulnerabilities in cancer." ; sc:featureList edam:operation_0463, edam:operation_3196, edam:operation_3501 ; 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168, edam:topic_3169 ; sc:citation "pubmed:21138948" ; sc:description "This employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks." ; sc:featureList edam:operation_2403 ; sc:name "W-ChIPeaks" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.uthscsa.edu/W-ChIPeaks/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3169, edam:topic_3511 ; sc:citation "pubmed:19797408" ; sc:description "Web application tool for de novo motif discovery from ChIP-based high throughput data." ; sc:featureList edam:operation_0238 ; sc:name "W-ChIPMotifs" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://compbio.uthscsa.edu/ChIPMotifs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3293, edam:topic_3299 ; sc:citation , "pmcid:PMC4987875", "pubmed:27084950" ; sc:description "A fast online phylogenetic tool for maximum likelihood analysis." ; sc:featureList edam:operation_0539 ; sc:name "W-IQ-TREE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://iqtree.cibiv.univie.ac.at/" ; biotools:primaryContact "Minh BQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622 ; sc:citation ; sc:description "An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes." ; sc:featureList edam:operation_0310, edam:operation_0525 ; sc:license "MIT" ; sc:name "w2rap-contigger" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/bioinfologics/w2rap-contigger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0097, edam:topic_0099, edam:topic_2828 ; sc:citation , "pmcid:PMC6602438", "pubmed:31114927" ; sc:description "Analysis, visualization, and modeling of 3D nucleic acid structures." ; sc:featureList edam:operation_0279, edam:operation_2518, edam:operation_3095 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "w3DNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://web.x3dna.org/" ; biotools:primaryContact "Wilma K Olson", "Xiang-Jun Lu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; 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sc:license "Not licensed" ; sc:name "WADDAICA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://bqflab.github.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269, edam:topic_3170, edam:topic_3518 ; sc:citation , "pubmed:33792651" ; sc:description "The waddR package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. 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WASP input can be either key searches (Section A) or SNPs with flanking sequences (Section B)." ; sc:featureList edam:operation_0308 ; sc:name "WASP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www4a.biotec.or.th/GI/tools/wasp" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3512 ; sc:citation , "pmcid:PMC7977290", "pubmed:33736596" ; sc:description "WASP is a versatile, web-accessible single cell RNA-Seq processing platform designed for the management, analysis and interpretation of scRNA-seq high-throughput data. The software addresses all aspects from initial quality control, demultiplexing and reference alignment to downstream statistical evaluation. 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Writhe Analysis Software Package (WASP) WASP is a software package for characterizing the topological development of ribbon structures particularly targeted at (but not limited to) use with molecular dynamics (MD) trajectories.""" ; sc:featureList edam:operation_0244, edam:operation_2476, edam:operation_3454 ; sc:name "WASP" ; sc:url "https://github.com/WereszczynskiGroup/WASP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2830, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pubmed:35674381" ; sc:description "Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq" ; sc:featureList edam:operation_0337, edam:operation_3695, edam:operation_3933 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "WAT3R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mainciburu/WAT3R" . a sc:SoftwareApplication ; 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Han" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3808 ; sc:encodingFormat edam:format_3547 ; sc:name "EM Micrograph" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3547 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0611, edam:topic_2259, edam:topic_3304 ; sc:citation ; sc:description """Visualize, share and annotate your large 3D images online. Upload your data and share links with collaborators. 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Shiny app to run MCP-counter and mMCP-counter.""" ; sc:featureList edam:operation_3799 ; sc:license "GPL-3.0" ; sc:name "webMCP-counter" ; sc:url "https://github.com/FPetitprez/webMCP-counter" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3591 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3546 ; sc:encodingFormat edam:format_3591 ; sc:name "Image metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:name "Image" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3382 ; sc:author "Mikael Lundin" ; sc:citation ; sc:description "Platform for virtual microscopy." ; sc:featureList edam:operation_3443, edam:operation_3552, edam:operation_3553 ; sc:name "WebMicroscope" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "FIMM" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://biomedbridges.webmicroscope.net" ; biotools:primaryContact "Johan Lundin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0749, edam:topic_3179, edam:topic_3656 ; sc:citation "pubmed:16332710", "pubmed:17584794" ; sc:description "WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. 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Elastic Network Model. Protein structure alignment and comparative flexibility analysis." ; sc:isAccessibleForFree true ; sc:name "WEBnma3" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3beta" ; sc:url "http://apps.cbu.uib.no/webnma3/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0166, edam:topic_0602, edam:topic_2814 ; sc:citation "pubmed:17919319", "pubmed:18420653", "pubmed:18463116" ; sc:description "webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. 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It is packaged as a Docker image that can be run anywhere." ; sc:name "webSalvador" ; sc:softwareHelp ; sc:url "https://websalvador.eeeeeric.com" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0654, edam:topic_2885, edam:topic_3360 ; sc:citation "pubmed:19255650" ; sc:description "Software for microsatellite molecular marker prediction and development. It allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification." ; sc:featureList edam:operation_0379 ; sc:name "WebSat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wsmartins.net/websat/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621, edam:topic_0623, edam:topic_3512 ; sc:citation "pubmed:18554390", "pubmed:18801164", "pubmed:21718515", "pubmed:21798037", "pubmed:23677611" ; sc:description "Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. 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This is a new release rewritten to be faster and optimized for large ChIP-Seq data." ; sc:featureList edam:operation_0238 ; sc:license "GPL-3.0" ; sc:name "Weeder" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://www.beaconlab.it/modtools" ; biotools:primaryContact "Federico Zambelli", "Giulio Pavesi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2070 ; sc:name "Sequence motif (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation ; sc:description "Identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs." ; sc:featureList edam:operation_0238 ; sc:license "GPL-3.0" ; sc:name "WeederH" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "ELIXIR-ITA-MILANO" ; sc:softwareHelp ; sc:softwareVersion "1.0" ; sc:url "http://www.beaconlab.it/modtools" ; biotools:primaryContact "Federico Zambelli", "Giulio Pavesi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation "pubmed:26582928" ; sc:description "WeGET is a computational tool to find mammalian genes that strongly co-express with a human query gene set of interest." ; sc:featureList edam:operation_0224, edam:operation_2495 ; sc:name "WeGet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://weget.cmbi.umcn.nl/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation "pubmed:16845012" ; sc:description "Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. 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It employs a weighted version of the neighbour-joining method in which longer distances in the matrix are given less weight." ; sc:featureList edam:operation_0289, edam:operation_0325, edam:operation_0546, edam:operation_0557 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "Weighbor" ; sc:operatingSystem "Linux" ; sc:softwareHelp , , ; sc:url "https://www.cs.mcgill.ca/~birch/birchdoc/program/weighbor.html" ; biotools:primaryContact "A. Halpern", "N. D. Socci", "W. Bruno" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2269 ; sc:citation , "pmcid:PMC3135688", "pubmed:21605215" ; sc:description "MATLAB script for Weighted Z-test for combining p-values across studies and datasets." ; sc:isAccessibleForFree true ; sc:name "Weighted Z-Test" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71671-weighted-z-test" ; biotools:primaryContact "Douglas Brubaker" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0602, edam:topic_2269, edam:topic_3053 ; sc:citation "pubmed:16400608" ; sc:description "Software to Apply Weighted False Discovery Rate for Multiple Testing. 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Researchers can utilize WellExplorer to study health outcomes related to exposure to fracturing chemicals in their population-based cohorts""" ; sc:featureList edam:operation_0533, edam:operation_2421, edam:operation_2422 ; sc:name "WellExplorer" ; sc:url "http://WellExplorer.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3519, edam:topic_3523, edam:topic_3934 ; sc:citation , "pmcid:PMC8088706", "pubmed:33933133" ; sc:description "wellmap is a file format for microplate layouts. The format is text-based and emphasizes being easy to read, write, and share. It is capable of describing any layout for any experiment. It is also accompanied by a tool for generating clear visualizations of layout files, and a simple API for parsing layout files in analysis scripts written in python or R. We have used wellmap in our own research to annotate data from a wide variety of experiments, including qPCR and flow cytometry." ; sc:featureList edam:operation_0335, edam:operation_0337, edam:operation_1812 ; sc:license "MIT" ; sc:name "wellmap" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://wellmap.rtfd.io" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3170, edam:topic_3320, edam:topic_3512 ; sc:citation "pubmed:25406327" ; sc:description "Software tool to quantify isoform expression and exon splicing ratios from RNA-seq data accurately and robustly." ; sc:featureList edam:operation_3680 ; sc:name "WemIQ" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www-rcf.usc.edu/~liangche/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3295, edam:topic_3399, edam:topic_3474 ; sc:citation , "pmcid:PMC6612879", "pubmed:31510704" ; sc:description "Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data | Weighted elastic net for domain adaptation | Wenda: Weighted Elastic Net for Unsupervised Domain Adaptation | This repository contains the source code for wenda, a method for unsupervised domain adaptation based on a weighted elastic net. 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This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. 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Modular implementation and framework for running weighted ensemble (WE) simulations in pure python, where the aim is to have simple things simple and complicated things possible. The latter being the priority. The deeper architecture of wepy is intended to be loosely coupled, so that unforeseen use cases can be accomodated, but tightly integrated for the most common of use cases, i.e. molecular dynamics. The goal of the architecture is that it should be highly modular to allow extension, but provide a “killer app” for most uses that just works, no questions asked.""" ; sc:featureList edam:operation_2476, edam:operation_3659, edam:operation_3891 ; sc:license "MIT" ; sc:name "wepy" ; sc:url "http://adicksonlab.github.io/wepy" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0082 ; sc:citation ; sc:description "Weighted Ensemble Solvent Accessibility. Meta-predictor based on a weighted ensemble of five methods, for solvent accessibility of residues, using the protein sequence as input. 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WEScall can also analyze WGS data.""" ; sc:featureList edam:operation_0484, edam:operation_0488, edam:operation_3196 ; sc:name "WEScall" ; sc:url "https://github.com/dwuab/WEScall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_0625, edam:topic_3512, edam:topic_3676 ; sc:citation , "pmcid:PMC8139020", "pubmed:34016036" ; sc:description "WEScover is a novel web application that provides an interface for discovering breadth and depth of coverage across population scale WES datasets, searching either by phenotype, by targeted gene panels and by genes. Moreover, the application shows metrics from the Genome Aggregation Database (gnomAD) to provide gene-centric view on breadth of coverage. Through the efficent querying of genes and phenotypes for exome coverage of associated exons, WEScover provides recommendations for gene panel tests of genes that are not well covered by whole exome sequencing." ; sc:featureList edam:operation_2421, edam:operation_3436, edam:operation_3920 ; sc:license "MIT" ; sc:name "WEScover" ; sc:url "https://tom.tch.harvard.edu/shinyapps/WEScover/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3168 ; sc:citation , "pubmed:32915952" ; sc:description """Fast gap-affine pairwise alignment using the wavefront algorithm. The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of. homologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s^2) memory. Moreover, the WFA exhibits simple data dependencies that can be easily vectorized, even by the automatic features of modern compilers, for different architectures, without the need to adapt the code.""" ; sc:featureList edam:operation_0491, edam:operation_0496, edam:operation_3198 ; sc:name "WFA" ; sc:url "https://github.com/smarco/WFA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0607, edam:topic_3572 ; sc:citation ; sc:description "Testing module for Galaxy workflows." ; sc:featureList edam:operation_0224, edam:operation_1812 ; sc:name "wft4galaxy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/phnmnl/wft4galaxy" ; biotools:primaryContact "Marco Enrico Piras" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_3295, edam:topic_3673, edam:topic_3674 ; sc:citation , "pmcid:PMC7195798", "pubmed:32357829" ; sc:description "wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline) can be utilised to analyse WGBS data. It performs alignment, qc, methylation calling, DMR calling, segmentation and annotation using a multitude of tools. First time using wg-blimp? We recommend having a look at our step-by-step guide" ; sc:featureList edam:operation_3186, edam:operation_3206, edam:operation_3218 ; sc:license "AGPL-3.0" ; sc:name "wg-blimp" ; sc:url "https://github.com/MarWoes/wg-blimp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0622, edam:topic_0769 ; sc:citation ; sc:description "WGA-LP is a pipeline for whole genome assembly that simplifies the usage of different tools and helps the user in evaluating his results." ; sc:featureList edam:operation_0525, edam:operation_3192, edam:operation_3216 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "WGA-LP" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/redsnic/WGA-LP" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3517 ; sc:citation "pubmed:18256235" ; sc:description "Suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study." ; sc:featureList edam:operation_0362, edam:operation_3208 ; sc:name "WGAViewer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://igm.cumc.columbia.edu/WGAViewer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Suite" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3168, edam:topic_3295, edam:topic_3524 ; sc:citation "pubmed:25777524" ; sc:description "Flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide." ; sc:featureList edam:operation_3204 ; sc:name "WGBSSuite" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.wgbssuite.org.uk/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203 ; sc:citation , ; sc:description "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization." ; sc:featureList edam:operation_3463 ; sc:name "WGCNA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://cran.r-project.org/web/packages/WGCNA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0769, edam:topic_0780 ; sc:citation , "pmcid:PMC6581438", "pubmed:30398564" ; sc:description """wgd-simple command line tools for the analysis of ancient whole-genome duplications. Copyright (C) 2018 Arthur Zwaenepoel. VIB/UGent center for plant systems biology - Bioinformatics & evolutionary genomics group http://bioinformatics.psb.ugent.be/beg/. wgd - simple command line tools for the analysis of ancient whole-genome duplications. Python package and command line interface (CLI) for the analysis of whole-genome duplications (WGDs). Tested with Python3 on Linux. If you don't have python or pip installed a simple sudo apt-get install python3-pip should do.""" ; sc:featureList edam:operation_3435 ; sc:license "GPL-3.0" ; sc:name "wgd" ; sc:softwareVersion "1.1.1" ; sc:url "https://github.com/arzwa/wgd" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_3175, edam:topic_3943 ; sc:citation ; sc:description "WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research." ; sc:featureList edam:operation_0553, edam:operation_3182, edam:operation_3745 ; sc:isAccessibleForFree true ; sc:license "BSD-2-Clause" ; sc:name "WGDI" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/SunPengChuan/wgdi" ; biotools:primaryContact "Xiyin Wang", "Zhenxiang Xi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2269, edam:topic_3293 ; sc:citation , "pmcid:PMC9701042", "pubmed:36434497" ; sc:description "A phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events." ; sc:featureList edam:operation_0544, edam:operation_0553, edam:operation_3942, edam:operation_3947 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "WGDTree" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cnickh/wgdtree" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3321 ; sc:citation , "pmcid:PMC4565030", "pubmed:25979474" ; sc:description "A CRISPR database for genome engineering." ; sc:featureList edam:operation_0224 ; sc:name "WGE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.sanger.ac.uk/htgt/wge/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0203, edam:topic_0622, edam:topic_2885, edam:topic_3168 ; sc:citation ; sc:description """reconstructing whole-genome viral haplotypes using L0 + L1-regularization. WgLink is a novel tool using regularized regression to stitch together regional haplotypes into global ones. The workflow of WgLink is briefed as follows: (A) WgLink first determines local haplotypes in tiling genomic windows by applying other tools: TenSQR or aBayesQR. (B) Regional haplotypes are then stitched together to generate all possible whole-genome haplotypes using a breadth-first search which could tolerate specified SNV mismatch when extending regions. (C) The final non-zero haplotype frequencies are estimated by L0L1 regularized regression.""" ; sc:featureList edam:operation_0487, edam:operation_3227, edam:operation_3659 ; sc:name "WgLink" ; sc:url "https://github.com/theLongLab/wglink" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3373, edam:topic_3474 ; sc:citation , "pmcid:PMC9205061", "pubmed:35715739" ; sc:description "Sequence-based drug-target affinity prediction using weighted graph neural networks." ; sc:featureList edam:operation_0272, edam:operation_0474, edam:operation_3092, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "WGNN-DTA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/595693085/WGNN-DTA" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0625 ; sc:citation , "pubmed:36575796" ; sc:description "A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3672 ; sc:isAccessibleForFree true ; sc:name "wGRN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://wheat.cau.edu.cn/wGRN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091 ; sc:citation ; sc:description "A workflow for standardized calling and filtering of structural variants, designed for whole genome sequencing projects." ; sc:featureList edam:operation_3227 ; sc:isAccessibleForFree true ; sc:name "wgs-structvar" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1" ; sc:url "https://github.com/NBISweden/wgs-structvar" ; biotools:primaryContact "Björn Nystedt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2885 ; sc:description """Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms. Wgsim outputs the simulated polymorphisms, and writes the true read coordinates as well as the number of polymorphisms and sequencing errors in read names. One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl that comes with the package.""" ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "wgsim" ; sc:url "https://github.com/lh3/wgsim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3168, edam:topic_3474 ; sc:citation , "pmcid:PMC10415921", "pubmed:37575187" ; sc:description "WGT is an open source Wheeler Graph suite for generating, recognizing, and visualizing Wheeler graphs. Central to WGT is \"Wheelie\", a fast Wheeler graph recognition algorithm that we proposed, which can recognize a graph with 1,000s of nodes in seconds." ; sc:featureList edam:operation_0224, edam:operation_0337, edam:operation_0524 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "WGT" ; sc:url "https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation ; sc:description "High-throughput sequence alignment tool." ; sc:featureList edam:operation_3198 ; sc:license "GPL-3.0" ; sc:name "WHAM" ; sc:softwareHelp , ; sc:url "http://www.cs.wisc.edu/wham/" ; biotools:primaryContact "Yinan Li" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3168, edam:topic_3574 ; sc:citation "pubmed:26625158" ; sc:description "A program for sequence alignment against human genome. It supports up to 5 mismatches." ; sc:featureList edam:operation_0346, edam:operation_0492, edam:operation_2429, edam:operation_3182, edam:operation_3227 ; sc:license "GPL-3.0" ; sc:name "Wham" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://zeeev.github.io/wham/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3517 ; sc:description "Designed for the calculation and association testing of stretches of homozygosity in genome-wide association data, as well as calculation of the intergrated haplotype score (iHS). Note that this tool is currently unpublished, and many of the website links are not fully updated." ; sc:featureList edam:operation_2429 ; sc:license "Not licensed" ; sc:name "Whamm" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://coruscant.itmat.upenn.edu/whamm/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0632, edam:topic_3474 ; sc:citation , "pubmed:31442996" ; sc:description "Interactive Probing of Machine Learning Models | Building effective machine learning models means asking a lot of questions. Look for answers using the What-if Tool, an interactive visual interface designed to probe your models better | you could inspect a machine learning model," ; sc:name "What-If Tool" ; sc:url "https://pair-code.github.io/what-if-tool/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2814 ; sc:description "A suite of programs to assess the \"stereochemical quality\" of a given protein structure." ; sc:featureList edam:operation_2406 ; sc:isAccessibleForFree true ; sc:name "WHAT_CHECK" ; sc:operatingSystem "Linux" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://swift.cmbi.ru.nl/gv/whatcheck/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2814, edam:topic_3542 ; sc:citation "pubmed:21071423" ; sc:description "PDB Related Datbases present a series of databases that run parallel to the PDB. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray." ; sc:featureList edam:operation_0267, edam:operation_0319, edam:operation_2416, edam:operation_2488 ; sc:name "WHAT IF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "http://swift.cmbi.ru.nl/servers/html/index.html" ; biotools:primaryContact "Gert Vriend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation ; sc:description "A molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc." ; sc:featureList edam:operation_0477 ; sc:isAccessibleForFree true ; sc:name "WHATIF" ; sc:operatingSystem "Linux" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://swift.cmbi.ru.nl/whatif/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_3308 ; sc:description "Web-based gene enrichment tools based on a huge underlying database of transcriptomic, proteomic (and other-omic) studies." ; sc:isAccessibleForFree true ; sc:name "Whatismygene" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://whatismygene.com" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:name "Report" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0972 ; sc:name "Text mining report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3473 ; sc:author "Dietrich Rebholz-Schuhmann", "Jee-Hyub Kim", "Johanna McEntyre", "Literature Services" ; sc:citation ; sc:description "A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases." ; sc:featureList edam:operation_0306 ; sc:name "Whatizit" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , , ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/webservices/whatizit/info.jsf" ; biotools:primaryContact "Jee-Hyub Kim" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0121, edam:topic_0199 ; sc:citation , "pmcid:PMC7059281", "pubmed:32138767" ; sc:description """a tool for identifying proteomic novelty. WhatsGNU utilizes the natural variation in public databases to rank protein sequences based on the number of observed exact protein matches (the GNU score) in all known genomes of a certain species & can quickly create whole protein reports.""" ; sc:featureList edam:operation_0224, edam:operation_3840 ; sc:license "GPL-3.0" ; sc:name "WhatsGNU" ; sc:url "https://github.com/ahmedmagds/WhatsGNU" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_2885 ; sc:citation , ; sc:description "Software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads." ; sc:featureList edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "WhatsHap" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "0.13" ; sc:url "http://whatshap.readthedocs.io" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0622, edam:topic_2269, edam:topic_3517, edam:topic_3676 ; sc:citation , "pubmed:34849577" ; sc:description "Focused goodness of fit tests for gene set analyses." ; sc:featureList edam:operation_2436, edam:operation_3196, edam:operation_3435, edam:operation_3659, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "wHC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/mqzhanglab/wHC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "Individual chromosome arms are being assembled and annotated. They are made publically available as they are produced using the genome viewer GBrowse2." ; sc:featureList edam:operation_0224 ; sc:name "Wheat Genome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "unimelb.edu.au" ; sc:softwareHelp ; sc:url "http://www.wheatgenome.info/wheat_genome_databases.php" ; biotools:primaryContact "Australia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_0780, edam:topic_3053 ; sc:citation "pubmed:23474942" ; sc:description "Fast and flexible on-line application to predict orthologus relationships with the model species Oryza sativa, Brachypodium dystachyon, and Sorghum bicolor." ; sc:featureList edam:operation_3209 ; sc:name "Wheat Zapper" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wge.ndsu.nodak.edu/wheatzapper/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1176 ; sc:name "GO concept ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:name "Sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1893 ; sc:name "Locus ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2757 ; sc:name "Pfam domain name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0659, edam:topic_0749, edam:topic_3173, edam:topic_3308 ; sc:citation , "pubmed:35660007" ; sc:description "A database for comparative co-expression networks analysis of allohexaploid wheat and its progenitors." ; sc:featureList edam:operation_0314, edam:operation_2436, edam:operation_3463, edam:operation_3927 ; sc:isAccessibleForFree true ; sc:name "WheatCENet" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bioinformatics.cau.edu.cn/WheatCENet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_0780, edam:topic_3517, edam:topic_3974 ; sc:citation , "pubmed:34115214" ; sc:description "WheatQTLdb is a manually curated QTL database for wheat that includes information about QTL identified through interval mapping and MTA identified using GWAS." ; sc:featureList edam:operation_0282, edam:operation_0305, edam:operation_3196 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "WheatQTLdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.wheatqtldb.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3304 ; sc:citation , "pubmed:32865525" ; sc:description """A Wheel Control-Based Gaming Platform for Studying Human Sensorimotor Control. Feedback control theory has been extensively implemented to theoretically model human sensorimotor control. However, experimental platforms capable of manipulating important components of multiple feedback loops lack development. This paper describes WheelCon, an open-source platform aimed at resolving such insufficiencies. Using only a computer, a standard display, and inexpensive gaming steering wheel equipped with a force feedback motor, WheelCon safely simulates the canonical sensorimotor task of riding a mountain bike down a steep, twisting, bumpy trail. The platform provides flexibility, as will be demonstrated in the demos provided, so that researchers may manipulate the disturbances, delay, and quantization (data rate) in the layered feedback loops, including a high-level advanced plan layer and a low-level delayed reflex layer""" ; sc:featureList edam:operation_2426 ; sc:name "WheelCon" ; sc:softwareHelp ; sc:url "https://github.com/Doyle-Lab/WheelCon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0154, edam:topic_0203, edam:topic_0632, edam:topic_3512 ; sc:citation "pubmed:17439966" ; sc:description "Resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design." ; sc:featureList edam:operation_0308, edam:operation_0314, edam:operation_2454, edam:operation_3233 ; sc:name "WhETS" ; sc:url "http://www.rothamsted.ac.uk/whets/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_3336, edam:topic_3534 ; sc:citation "pubmed:23740742" ; sc:description "Predicts which P450 isoform will bind/metabolize a molecule using simple yes/no classification models." ; sc:featureList edam:operation_0482 ; sc:name "WhichCyp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.farma.ku.dk/whichcyp/index.php" ; biotools:primaryContact "Contact form" . a sc:SoftwareApplication ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3077 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Search all sequence databases for an entry and retrieve it." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "whichdb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/whichdb.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3053, edam:topic_3500 ; sc:citation "pubmed:19406925" ; sc:description "WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifiers." ; sc:featureList edam:operation_2436, edam:operation_3223, edam:operation_3224 ; sc:name "WhichGenes" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.whichgenes.org/" ; biotools:primaryContact "Daniel González Peña", "Florentino Fernández Riverola" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0659, edam:topic_3320, edam:topic_3474, edam:topic_3512 ; sc:citation , "pubmed:33835461" ; sc:description "WHISTLE is a functionally annotated high-accuracy map of human m6A epitranscriptome." ; sc:featureList edam:operation_0224, edam:operation_0417, edam:operation_2429, edam:operation_3902 ; sc:name "WHISTLE" ; sc:url "http://www.xjtlu.edu.cn/biologicalsciences/whistle" ; biotools:primaryContact "Kunqi Chen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description """WhiteRabbit is a software tool to help prepare for ETLs (Extraction, Transformation, Loading) of longitudinal healthcare databases into the OMOP Common Data Model (CDM). The source data can be in comma-separated text files, or in a database (MySQL, SQL Server, ORACLE, PostgreSQL); the CDM will be in a database (MySQL, SQL Server, PostgreSQL). The main function of WhiteRabbit is to perform a scan of the source data, providing detailed information on the tables, fields, and values that appear in a field. This scan will generate a report that can be used as a reference when designing the ETL, for instance when using the Rabbit-In-a-Hat tool. Rabbit-In-a-Hat uses the scan document and displays source data information through a graphical user interface to allow a user to connect source data structure to the CDM data structure. The function of Rabbit-In-a-Hat is to generate documentation for the ETL process, not generate code to create an ETL.""" ; sc:featureList edam:operation_2409 ; sc:license "Apache-2.0" ; sc:name "White Rabbit" ; sc:softwareVersion "v0.10.7" ; sc:url "http://ohdsi.github.io/WhiteRabbit/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0091, edam:topic_0092 ; sc:citation "pubmed:25661541" ; sc:description "Class library implemented in C++, allowing for easy graphing any kind of data into any format. It provides all basic tool sets for drawing simple objects, as well as color manipulation methods, a rich set of compound graphs, and documentation." ; sc:featureList edam:operation_0337 ; sc:name "Whiteboard" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://whiteboard-class.sourceforge.net/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3063, edam:topic_3305 ; sc:citation ; sc:description "WHO Coronavirus (COVID-19) Dashboard With Vaccination Data presents official daily counts of COVID-19 cases and deaths worldwide, along with vaccination rates and other vaccination data, while providing a hub to other resources. Interactive tools, including maps, epidemic curves and other charts and graphics, with downloadable data, allow users to track and explore the latest trends, numbers and statistics at global, regional and country levels." ; sc:featureList edam:operation_3454 ; sc:name "WHO Coronavirus (COVID-19) Dashboard" ; sc:url "https://covid19.who.int" ; biotools:primaryContact "Muhammad Irfan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2815, edam:topic_3300, edam:topic_3444 ; sc:citation , "pubmed:35998568" ; sc:description "WHOle-brain CArdiac signal REgression from highly accelerated simultaneous multi-Slice fMRI acquisitions." ; sc:featureList edam:operation_2422, edam:operation_3443, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "WHOCARES" ; sc:operatingSystem "Linux" ; sc:url "https://github.com/gferrazzi/WHOCARES" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621, edam:topic_0780, edam:topic_3174, edam:topic_3500 ; sc:citation ; sc:description "Distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure." ; sc:featureList edam:operation_0310, edam:operation_2454, edam:operation_3460, edam:operation_3472 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Whokaryote" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://git.wageningenur.nl/lotte.pronk/whokaryote" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_3172, edam:topic_3174, edam:topic_3697, edam:topic_3941 ; sc:citation , "pmcid:PMC7382364", "pubmed:32765964" ; sc:description "a web application for global survey of surface water metabolites." ; sc:featureList edam:operation_0337, edam:operation_0387 ; sc:name "WHONDRS" ; sc:url "https://xmlin.shinyapps.io/whondrs/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0080 ; sc:citation , "pubmed:25273104" ; sc:description "High-Speed Processing of VCF, FASTA and Alignment Data. Also provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO. It is capable to read, modify and write PLINK .PED-format pedigree files." ; sc:featureList edam:operation_0260, edam:operation_0362, edam:operation_2409 ; sc:license "GPL-2.0" ; sc:name "WhopGenome" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "0.97" ; sc:url "https://cran.r-project.org/web/packages/WhopGenome/" ; biotools:primaryContact "Ulrich Wittelsbuerger" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0610, edam:topic_3382 ; sc:citation ; sc:description """WIAD: Wood Image Analysis and Dataset. open-access visual analysis tools to advance the ecological data revolution. The Wood Image Analysis and Dataset is a dynamic interface to extract, store and share data from images of tree rings, such as annual ring width. WIAD presents a dynamic interface for a wide range of scientists in archeology, ecology, geology, climatology and chronology disciplines to digitise and analyze their tree ring imagery easily, back up results and share them with collaborators and the public.""" ; sc:featureList edam:operation_0252, edam:operation_0337, edam:operation_3443 ; sc:name "WIAD" ; sc:url "http://wiad.science" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0605, edam:topic_3372 ; sc:citation ; sc:description """This packages enables users to build interactive widgets. Although the underlying implementation of any widget built is through the R tcltk package, users of widgetTools do not need to know all of the lowlevel Tcl/Tk commands, because the widget functionality is encapsulated in S4 classes which interact directly with standard R objects.""" ; sc:featureList edam:operation_2425, edam:operation_3436, edam:operation_3763 ; sc:license "GPL-3.0" ; sc:name "widgetTools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.56.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/widgetTools.html" ; biotools:primaryContact "Jianhua Zhang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654 ; sc:citation ; sc:description "Wavelet-based Identification of DNA focal genomic aberrations. Integrates array CGH data sets from multiple cancer samples and detects consistent aberrations across multiple samples." ; sc:featureList edam:operation_2495 ; sc:name "WIFA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "20110617" ; sc:url "http://www.gcancer.org/wifa/WIFA.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3710 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3652 ; sc:name "Mass spectrometry spectra" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation "pubmed:15507135" ; sc:description "Converts ABI WIFF to .dta." ; sc:featureList edam:operation_0335, edam:operation_1812 ; sc:name "wiff2dta" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://sourceforge.net/projects/protms" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3496 ; sc:encodingFormat edam:format_3006 ; sc:name "RNA sequence (raw)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:encodingFormat edam:format_3617 ; sc:name "Sequence composition plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_3170, edam:topic_3676 ; sc:citation ; sc:description "An R package to visualise RNA-seq read coverage across annotated exons. 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It can be used to generate signal density maps for ChIP-seq, DNase-seq, FAIRE-seq and MNase-seq data. 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Pico", "Martina Kutmon" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0602, edam:topic_3325 ; sc:citation , , "pmcid:PMC4168754", "pubmed:25254103" ; sc:description "Easy access to pathway content at WikiPathways.org from Cytoscape." ; sc:featureList edam:operation_0277, edam:operation_3083, edam:operation_3439, edam:operation_3562 ; sc:license "Apache-2.0" ; sc:name "WikiPathways App" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.3.1" ; sc:url "http://apps.cytoscape.org/apps/wikipathways" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2269, edam:topic_3172, edam:topic_3569, edam:topic_3570 ; sc:description "Does a Wilcoxon rank-sum test and creates box plot for genes etc in healthy vs. disease individuals" ; sc:featureList edam:operation_2943 ; sc:isAccessibleForFree true ; sc:name "Wilcoxon rank-sum test and box plots for genes compounds etc in healthy vs. disease" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/47381-wilcoxon-rank-sum-test-and-box-plots-for-genes-compounds-etc-in-healthy-vs-disease" ; biotools:primaryContact "Dr. Soumya Banerjee" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3068, edam:topic_3334, edam:topic_3409 ; sc:citation , "pmcid:PMC7270127", "pubmed:32493955" ; sc:description """WilsonGen a comprehensive clinically annotated genomic variant resource for Wilson's Disease. WilsonGen is a comprehensive resource of genetic variants in ATP7B gene manually curated from literature and data resources and systematically annotated using the ACMG & AMP guidelines for assessing pathogenicity of genetic variants. 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Manual modeling of complicated insect wings presents considerable practical challenges. To overcome these challenges, therefore, we developed WingMesh. This is an application for simple yet precise automatic modeling of insect wings. Using a series of examples, we showed the performance of our application in practice. We expect WingMesh to be particularly useful in comparative studies, especially where the modeling of a large number of insect wings is required within a short time.""" ; sc:featureList edam:operation_2426, edam:operation_3443 ; sc:name "WingMesh" ; sc:url "https://wingquest.org/wingmesh/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3053 ; sc:citation , ; sc:description "Haplotype phasing for large-scale population genotypes data. Significantly improved version of the WinHAP program that both process longer sequences with less computer memory usage and increases computing speed." ; sc:featureList edam:operation_3454 ; sc:name "WinHAP" ; sc:operatingSystem "Linux" ; sc:softwareVersion "2.0" ; sc:url "http://staff.ustc.edu.cn/~xuyun/winhap/WinHAP2.0.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , ; sc:description "Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats" ; sc:featureList edam:operation_0292 ; sc:license "Not licensed" ; sc:name "winnowmap" ; sc:softwareVersion "2.03" ; sc:url "https://github.com/marbl/Winnowmap" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3418 ; sc:citation , "pmcid:PMC7188201", "pubmed:32425496" ; sc:description """Efficacy of WINROP as a Screening Tool for Retinopathy of Prematurity in the East Coast of Malaysia. This online monitoring system, following weight gain, for predicting developing sight threatening ROP, was developed by the research group at The Sahlgrenska Center for Pediatric Ophthalmology Research.""" ; sc:name "WINROP" ; sc:url "http://winrop.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2259, edam:topic_2275 ; sc:citation "pubmed:14506622" ; sc:description "Windows oriented modeling program enabling the user to explore biological systems using mathematical models. Sophisticated modeling software is required to fit data to such models and to make predictions using these compartmental models." ; sc:featureList edam:operation_0337 ; sc:name "WinSAAM" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://www.winsaam.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0204, edam:topic_0749, edam:topic_3474 ; sc:citation , "pmcid:PMC7382975", "pubmed:31995498" ; sc:description """A New Weighted Imputed Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. Weighted, Imputed, Neighbor-regularized matrix TriFactorization, WINTF.""" ; sc:featureList edam:operation_2437, edam:operation_2492, edam:operation_3557, edam:operation_3695 ; sc:name "WINTF" ; sc:url "https://github.com/XieResearchGroup/WINTF" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0654, edam:topic_3391 ; sc:description "Workbench for Integrated Superfast Association study with Related Data is a comprehensive Statistical Analysis toolkit for omics data. Large-scale SNP, CNV and NGS data with related and unrelated samples can be analyzed in computationally optimized and efficient way by using muti-core system." ; sc:featureList edam:operation_2238 ; sc:name "WISARD" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://statgen.snu.ac.kr/wisard/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0654 ; sc:citation , "pmcid:PMC310858", "pubmed:10779496", "pubmed:15123596" ; sc:description "Compare a protein sequences or protein HMMs to a genomic DNA sequence, allowing for introns and frameshifting errors." ; sc:featureList edam:operation_0292, edam:operation_2479 ; sc:name "Wise2.4" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.4.1" ; sc:url "http://www.ebi.ac.uk/Tools/Wise2/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2977 ; sc:name "Nucleic acid sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1383 ; sc:name "Sequence alignment (nucleic acid)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application", "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:author "Ewan Birney" ; sc:citation , ; sc:description "Align two sequences assuming the sequences share colinear conserved blocks separated by gaps." ; sc:featureList edam:operation_0491, edam:operation_0495 ; sc:name "Wise2DBA (EBI)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "Retired" ; sc:url "http://www.ebi.ac.uk/Tools/psa/wise2dba/" ; biotools:primaryContact "Job Dispatcher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0634, edam:topic_2885, edam:topic_3360, edam:topic_3974 ; sc:citation , "pubmed:33733355" ; sc:description "WISH-R package (WISH-R) can calculate epistatic interactions using a linear or generalized linear model on a genome-wide level using genomic data and phenotype/disease data in a fully parallelized environment, and visualize genome-wide epistasis in many ways." ; sc:featureList edam:operation_0484, edam:operation_3196, edam:operation_3557, edam:operation_3766 ; sc:name "WISH-R" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/QSG-Group/WISH" ; biotools:primaryContact "Haja N. Kadarmideen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "MATLAB toolbox with reader/writer and analysis tools for WITec Project/Data (*.wip/*.wid) file." ; sc:featureList edam:operation_1812, edam:operation_2409, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:name "WIT Input Output" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/71956-wit-input-output" ; biotools:primaryContact "J. T. Holmi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "Toolbox can directly read/write WITec Project/Data (*.wip/*.wid) files in MATLAB with or without GUI. It also provides data analysis tools." ; sc:featureList edam:operation_2409 ; sc:isAccessibleForFree true ; sc:name "WITio" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.4.0.1" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/70983-wit_io" ; biotools:primaryContact "J. T. Holmi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0081, edam:topic_2275, edam:topic_2814, edam:topic_3307 ; sc:citation "pubmed:20501602" ; sc:description "Web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection has over 1600 different functions." ; sc:featureList edam:operation_0321, edam:operation_0474, edam:operation_0477, edam:operation_2406, edam:operation_2428 ; sc:name "WIWS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://swift.cmbi.ru.nl/" ; biotools:primaryContact "Gert Vriend" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3382, edam:topic_3474 ; sc:citation , "pmcid:PMC7691393", "pubmed:33294864" ; sc:description """A Web-Based Tool for Interactive Visualization of Big Data. Wiz is a web-based app for interactive data visualisation. Wiz is a convienient tool for interactively plotting data. Wiz allows users to quickly explore their data with fast switching between plot types and data series. Built-in features allow users to filter their data, edit plot layouts, and even print high quality images of their graphs. Check out our original publication , the help guide, the video, and the info below to get started!.""" ; sc:featureList edam:operation_0337, edam:operation_3096, edam:operation_3891 ; sc:license "MIT" ; sc:name "Wiz" ; sc:softwareHelp , ; sc:url "https://wiz.shef.ac.uk" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0622, edam:topic_0623 ; sc:citation "pubmed:27357839" ; sc:description "Integrated framework for the analysis and interpretation of the consequences of variants in the human kinome." ; sc:featureList edam:operation_2478 ; sc:name "wKinMut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://kinmut2.bioinfo.cnio.es/KinMut2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0634, edam:topic_0781, edam:topic_3169 ; sc:citation "pubmed:17531104" ; sc:description "Program that identifies viruses presented in a pathogen chip by analyzing and differentiating their signal intensity distribution with the background signal intensity distribution." ; sc:featureList edam:operation_3461 ; sc:name "WKL" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.gis.a-star.edu.sg/pathchip/WKL_readme.txt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0082, edam:topic_2275 ; sc:citation "pubmed:18763742" ; sc:description "A tool which allows to identify clusters of a structural water molecules in given superimposed 3D structures." ; sc:featureList edam:operation_0477 ; sc:name "wLake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/wLake/wLake.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654, edam:topic_3168 ; sc:description "Map high-throughput sequencing reads as well as methylated-C reads, enabling usage of such sequencing data to various fields of biological research." ; sc:featureList edam:operation_2429, edam:operation_2871 ; sc:name "WMap" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20091230" ; sc:url "http://systemsbio.ucsd.edu/wmap/manual.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0634, edam:topic_2259 ; sc:citation ; sc:description "Weighted MAXimum Clique. Method for identifying condition specific sub-network. Reveals a subset of genes which are closely related to a particular disease. It integrates gene expression data and protein-protein interaction information to construct molecular network, and then extracts the most density connected sub-network using an integration of a global search method and efficient projection procedure." ; sc:featureList edam:operation_2421 ; sc:name "WMAXC" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:softwareVersion "20131115" ; sc:url "http://combio.gist.ac.kr/WMAXC/WMAXC.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0203, edam:topic_2640, edam:topic_3170, edam:topic_3518 ; sc:citation , "pmcid:PMC7986389", "pubmed:33752597" ; sc:description "Weighted minimum feedback vertex sets (WMFVS) is a tool to predict cancer genes. WMFVS integrates the gene differential expression value with MFVS to select the maximum-weighted MFVS from all possible MFVSs in a protein interaction network." ; sc:featureList edam:operation_2436, edam:operation_2454, edam:operation_3223 ; sc:name "WMFVS" ; sc:url "https://github.com/lrming1993/WMFVS_codes" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3170 ; sc:citation , "pubmed:36179076" ; sc:description "A novel method for multiple sequence alignment of DNA sequences." ; sc:featureList edam:operation_0300, edam:operation_0491, edam:operation_0492 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "WMSA" ; sc:operatingSystem "Linux", "Windows" ; sc:url "https://github.com/malabz/WMSA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0625, edam:topic_0654, edam:topic_0781, edam:topic_3053 ; sc:citation "pubmed:24388930" ; sc:description "Server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution." ; sc:featureList edam:operation_3196 ; sc:name "WNV Typer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo.net.in/wnv/homepage.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1261 ; sc:name "Sequence composition report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3053 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Plot third base position variability in a nucleotide sequence." ; sc:featureList edam:operation_0287 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wobble" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/wobble.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_1775 ; sc:citation "pubmed:17517783" ; sc:description "WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction." ; sc:featureList edam:operation_0269, edam:operation_0474, edam:operation_2489, edam:operation_3092 ; sc:name "WoLF PSORT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://wolfpsort.hgc.jp/" ; biotools:primaryContact "Kenta Nakai" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3055 ; sc:citation , "pmcid:PMC2064953", "pubmed:17973343" ; sc:description "Program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML)." ; sc:featureList edam:operation_3664 ; sc:license "Not licensed" ; sc:name "Wombat" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://didgeridoo.une.edu.au/km/wombat.php" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0128, edam:topic_3534 ; sc:citation , "pmcid:PMC4621702", "pubmed:26387008" ; sc:description "Objective novel complex analysis for ensembles of protein–ligand structures." ; sc:featureList edam:operation_0482 ; sc:name "WONKA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wonka.sgc.ox.ac.uk/WONKA/" ; biotools:primaryContact "Anthony Bradley" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_3003 ; sc:name "Gene expression profile" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3511 ; sc:citation , "pubmed:28460063" ; sc:description "Webserver for Position Related data analysis of gene Expression in Prokaryotes is a web-tool for the analysis of bacteria transcriptomic data. Gene expression is integrated with genomic annotations to reveal connections between transcription regulation and structural organization of bacterial genomes. The analysis results include clusters of positionally proximal genes having the same trend of differential gene expression, along with graphical representations of the modulated clusters." ; sc:featureList edam:operation_3800 ; sc:name "WoPPER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://wopper.ba.itb.cnr.it/" ; biotools:primaryContact "Flavio Licciulli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Workflow for Open Reproducible Code in Science (WORCS) is a step-by-step procedure that researchers can follow to make a research project open and reproducible. The purpose of the workflow is to lower the threshold for adoption of open science principles. It is based on established best practices, and can be used either in parallel to, or in absence of, top-down requirements by journals, institutions, and funding bodies. To facilitate widespread adoption, the WORCS principles have been implemented in the R package worcs, which offers an RStudio project template and utility functions for specific workflow steps" ; sc:license "GPL-3.0" ; sc:name "WORCS" ; sc:url "https://github.com/cjvanlissa/worcs" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3168 ; sc:citation "pubmed:21261981" ; sc:description "Algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance." ; sc:featureList edam:operation_3472 ; sc:name "WordCluster" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioinfo2.ugr.es/wordCluster/wordCluster.php" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1261 ; sc:name "Sequence composition report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0157 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Count and extract unique words in molecular sequence(s)." ; sc:featureList edam:operation_0236 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wordcount" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/wordcount.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0874 ; sc:name "Comparison matrix" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Match large sequences against one or more other sequences." ; sc:featureList edam:operation_0288, edam:operation_2928 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wordfinder" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/wordfinder.html" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0849 ; sc:name "Sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1381 ; sc:name "Sequence alignment (pair)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1255 ; sc:name "Sequence features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0097 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find regions of identity (exact matches) of two sequences." ; sc:featureList edam:operation_0288 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wordmatch" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/wordmatch.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web service" ; sc:applicationSubCategory edam:topic_0080 ; sc:description "Finds all exact matches of a given minimum size between 2 sequences displaying the start points in each sequence and the match length." ; sc:featureList edam:operation_2403 ; sc:name "wordmatch WS (husar)" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://genius.embnet.dkfz-heidelberg.de/menu/hobit/embdoc/wordmatch.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0176, edam:topic_0593, edam:topic_3175 ; sc:citation , "pmcid:PMC9929209", "pubmed:36817953" ; sc:description "A user-friendly program for the analysis of molecular structures and conformational ensembles." ; sc:featureList edam:operation_2476, edam:operation_2939, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "Wordom" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://wordom.sf.net" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0203, edam:topic_0749, edam:topic_3125, edam:topic_3511 ; sc:citation "pubmed:15980501" ; sc:description "Allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. It employs this functionality as a means to search for transcription factor binding motifs." ; sc:featureList edam:operation_0238, edam:operation_0239, edam:operation_0438, edam:operation_0445, edam:operation_2454 ; sc:name "WordSpy" ; sc:url "http://cic.cs.wustl.edu/wordspy/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1807 ; sc:name "ORF name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation , "pmcid:PMC528921", "pubmed:15489327" ; sc:description "The Caenorhabditis elegans ORFeome cloning project." ; sc:featureList edam:operation_0224 ; sc:name "WORFDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://worfdb.dfci.harvard.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0769, edam:topic_3172, edam:topic_3390 ; sc:citation ; sc:description "A new workflow combining R packages for statistical analysis of metabolites." ; sc:featureList edam:operation_3435, edam:operation_3659 ; sc:name "workflow" ; sc:url "https://workflow4metabolomics.org/dataset_sacurine" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654, edam:format_3834 ; sc:name "Mass spectrum" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3488 ; sc:name "NMR spectrum" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Bioinformatics portal" ; sc:applicationSubCategory edam:topic_2259, edam:topic_3172, edam:topic_3307 ; sc:author , "Jean-François Martin", "Marion Landi", "Misharl Monsoor", "Mélanie Pétéra", "Pierre Pericard" ; sc:citation , ; sc:contributor "Alexis Delabrière", "Christophe Caron", "Sophie Goulitquer" ; sc:description "First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data." ; sc:featureList edam:operation_0226, edam:operation_0337, edam:operation_2238, edam:operation_3203, edam:operation_3214, edam:operation_3501, edam:operation_3694 ; sc:isAccessibleForFree true ; sc:name "Workflow4Metabolomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:url "https://workflow4metabolomics.org/" ; biotools:primaryContact , , , , "Marie Tremblay-Franco" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API", "Web application" ; sc:applicationSubCategory edam:topic_0769 ; sc:author ; sc:description """WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. The registry supports any workflow in its native repository. WorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. This is achieved through extensive use of open standards and tools, including Common Workflow Language (CWL), RO-Crate, BioSchemas and TRS, in accordance with the FAIR principles.""" ; sc:featureList edam:operation_0224, edam:operation_1812, edam:operation_2409, edam:operation_3431, edam:operation_3436, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "WorkflowHub" ; sc:operatingSystem "Linux" ; sc:softwareHelp , ; sc:url "https://workflowhub.eu" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_0769 ; sc:citation , "pmcid:PMC6833990", "pubmed:31723427" ; sc:description """Creating and sharing reproducible research code the workflowr way. Organize your project into a research website. workflowr: organized + reproducible + shareable data science in R. The workflowr R package helps researchers organize their analyses in a way that promotes effective project management, reproducibility, collaboration, and sharing of results. Workflowr combines literate programming (knitr and rmarkdown) and version control (Git, via git2r) to generate a website containing time-stamped, versioned, and documented results. Any R user can quickly and easily adopt workflowr. A Framework for Reproducible and Collaborative Data Science. Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results""" ; sc:featureList edam:operation_2422, edam:operation_3096, edam:operation_3454 ; sc:license "MIT" ; sc:name "workflowr" ; sc:url "https://github.com/jdblischak/workflowr" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1096 ; sc:name "Sequence accession (protein)" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2531 ; sc:encodingFormat edam:format_2331 ; sc:name "Experiment report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0121 ; sc:citation ; sc:description "A public repository, standards compliant, for proteomics image data published in the literature." ; sc:featureList edam:operation_0224 ; sc:name "The world-2DPAGE database" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://world-2dpage.expasy.org/repository/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0769, edam:topic_0780, edam:topic_3050 ; sc:citation ; sc:description """An R package for exact and fuzzy matching of plant names against the World Flora Online Taxonomic Backbone data. Standardize Plant Names According to World Flora Online Taxonomic Backbone. World Flora Online is an online flora of all known plants, available from . Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (), a working list of plant names that has become static since 2013.""" ; sc:featureList edam:operation_3435 ; sc:license "GPL-2.0" ; sc:name "WorldFlora" ; sc:url "https://cran.r-project.org/package=WorldFlora" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2295 ; sc:name "Gene ID" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0989 ; sc:name "Protein identifier" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web API" ; sc:applicationSubCategory edam:topic_0621 ; sc:citation ; sc:description "Caenorhabditis elegans genome database. International consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research." ; sc:featureList edam:operation_0224 ; sc:name "WormBase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.wormbase.org/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_3307, edam:topic_3500 ; sc:citation "pubmed:26421844" ; sc:description "Open-source software which designed for accurate quantification of sex ratio in Caenorhabditis elegans. 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sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "Find programs by EDAM topic." ; sc:featureList edam:operation_2422 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wosstopic" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://emboss.open-bio.org/rel/rel6/apps/wosstopic.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0194, edam:topic_2269 ; sc:citation ; sc:description """Statistically Consistent Genome-scale Species Tree Estimation from Weighted Quartets. wQFM is a quartet amalgamation method of estimating species tree. It takes a set of estimated gene trees as input and generates a set of weighted quartets and combines these weighted quartet trees into a tree on the full set of taxa using a heuristic aimed at finding a species tree of minimum distance to the set of weighted quartet trees.""" ; sc:featureList edam:operation_0544, edam:operation_0548, edam:operation_0556, edam:operation_3478, edam:operation_3942 ; sc:name "wQFM" ; sc:url "https://github.com/Mahim1997/wQFM-2020" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0128, edam:topic_0602, edam:topic_2258 ; sc:citation ; sc:description "Provides systematic prediction of multiple binding sites and modes of ligands on macromolecular targets at atomic resolution." ; sc:featureList edam:operation_0478 ; sc:license "CC-BY-4.0" ; sc:name "Wrap n Shake" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.wnsdock.xyz/" ; biotools:primaryContact "Mónika Bálint" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0080, edam:topic_0160 ; sc:citation "pubmed:24413524" ; sc:description "Software tool for amino acid motif searching using weighted regular expression and regular expressions with a Position-Specific Scoring Matrix" ; sc:featureList edam:operation_0239 ; sc:name "Wregex" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://wregex.ehubio.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3374, edam:topic_3934 ; sc:description "writeFCS is a MATLAB script that creates FCS file specified by Data File Standard for Flow Cytometry" ; sc:featureList edam:operation_1812 ; sc:isAccessibleForFree true ; sc:name "writeFCS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.2.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/42603-writefcs-fname-data-text-other" ; biotools:primaryContact "Jakub Nedbal" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0006 ; sc:encodingFormat edam:format_1975 ; sc:name "Data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2968 ; sc:encodingFormat edam:format_3547 ; sc:name "Image" ], [ a bsct:FormalParameter ; 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sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0659 ; sc:citation , ; sc:description "Write all ncRNAs analysis results into an HTML file (Only for ncRNAs analysis pipeline)." ; sc:featureList edam:operation_0335 ; sc:name "writerestohtml" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.0.0" ; sc:url "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/writeResToHTML/1.0.0" ; biotools:primaryContact "Galaxy Support Team" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0749, edam:topic_0769, edam:topic_3382 ; sc:citation , "pmcid:PMC9718391", "pubmed:36399491" ; sc:description "A modular package for high-throughput image analysis of parasitic and free-living worms." ; sc:featureList edam:operation_1812, edam:operation_3096, edam:operation_3443 ; 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sc:author ; sc:citation , , "pmcid:PMC3194195", "pubmed:19514061", "pubmed:21992054" ; sc:description "A web server for predicting disease associated variations from protein sequence and structure." ; sc:featureList edam:operation_3225 ; sc:isAccessibleForFree true ; sc:name "WS-SNPs-and-GO" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ELIXIR-ITA-BOLOGNA" ; sc:softwareHelp ; sc:softwareVersion "2.0" ; sc:url "http://snps.biofold.org/snps-and-go" ; biotools:primaryContact , "Rita Casadio" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2269, edam:topic_3474 ; sc:citation , "pmcid:PMC9037749", "pubmed:35480046" ; sc:description "Generalizable Beat-by-Beat Arrhythmia Detection by Using Weakly Supervised Deep Learning." ; sc:featureList edam:operation_3435, edam:operation_3436, edam:operation_3937 ; sc:isAccessibleForFree true ; sc:license "MIT" ; 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It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum." ; sc:featureList edam:operation_2403, edam:operation_2422 ; sc:name "SAS WS" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://www.ebi.ac.uk/thornton-srv/databases/WSsas/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0924 ; sc:encodingFormat edam:format_1929, edam:format_1930 ; sc:name "Sequence trace" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0925 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence assembly" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3168 ; sc:citation , "pmcid:PMC7004874", "pubmed:31819265" ; sc:description "Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy." ; sc:featureList edam:operation_0524, edam:operation_0525 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "wtdbg2" ; sc:softwareVersion "2.5" ; sc:url "https://github.com/ruanjue/wtdbg2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0654, edam:topic_3053, edam:topic_3517 ; sc:citation , "pmcid:PMC6929460", "pubmed:31874630" ; sc:description """an integrated R package for genetic epistasis testing. The W-Test for Genetic Interactions Testing. Perform the calculation of W-test, diagnostic checking, calculate minor allele frequency (MAF) and odds ratio""" ; sc:license "GPL-2.0" ; sc:name "wtest" ; sc:url "https://CRAN.R-project.org/package=wtest" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0089 ; sc:citation ; sc:description "Enrichment of genes associated with particular ontology terms. Implementation of both hypergeometric and model-based approaches, that can be published as a static site with computation run in JavaScript on the user's web browser client." ; sc:featureList edam:operation_3501 ; sc:license "BSD-3-Clause" ; sc:name "WTFgenes" ; sc:url "https://evoldoers.github.io/wtfgo/web/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3299, edam:topic_3500 ; sc:citation , "pmcid:PMC6350380", "pubmed:30691386" ; sc:description """Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. For more than a decade, gene expression data sets have been used as basis for the construction of co-expression networks used in systems biology investigations, leading to many important discoveries in a wide range of subjects spanning human disease to evolution and the development of organisms. A commonly encountered challenge in such investigations is first that of detecting, then subsequently removing, spurious correlations (i.e. links) in these networks. While access to a large number of measurements per gene would reduce this problem, often only a small number of measurements are available. The weighted Topological Overlap (wTO) measure, which incorporates information from the shared network-neighborhood of a given gene-pair into a single score, is a metric that is frequently used with the implicit expectation of producing higher-quality networks""" ; sc:featureList edam:operation_2437, edam:operation_3463, edam:operation_3766 ; sc:name "wTO" ; sc:url "https://github.com/andrevo/DiffCoEx-WTO" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0637, edam:topic_0769, edam:topic_3837 ; sc:citation ; sc:description "A scalable workflow for the identification and analysis of phage sequences." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "What the Phage" ; sc:url "https://github.com/replikation/What_the_Phage" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0622, edam:topic_3053, edam:topic_3678 ; sc:citation "pubmed:26521937" ; sc:description "The Washington University gRNA designer for CRISPR/Cas9 knockouts." ; sc:featureList edam:operation_3095 ; sc:name "WU-CRISPR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://crispr.wustl.edu/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3303 ; sc:citation , "pmcid:PMC7606381", "pubmed:32858282" ; sc:description """Neonatal EEG Analysis Toolbox (NEAT). A clinically validated, open-source MATLAB toolbox for limited-channel neonatal EEG analysis. Many qualitative and quantitative metrics have been developed to analyze the output of limited-channel EEG recordings in neonates. A significant roadblock in the widespread dissemination of these techniques is the device-specific, “black-box” nature of the analytic algorithms, preventing comparison between studies and the obsolescence of old recordings as software is abandoned. We have developed NEAT (Neonatal EEG Analysis Toolbox) as an open-source software platform to overcome these challenges. NEAT runs within MATLAB and is designed to work with any single-channel EEG input, regardless of source or sampling rate. The second release adds support for GNU Octave.""" ; sc:featureList edam:operation_2428, edam:operation_3435, edam:operation_3799 ; sc:name "WU-NEAT" ; sc:url "http://research.peds.wustl.edu/neat" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0166, edam:topic_0736, edam:topic_2814 ; sc:citation "pubmed:15215443" ; sc:description "Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures." ; sc:featureList edam:operation_0267, edam:operation_0268, edam:operation_0302, edam:operation_0474 ; sc:name "Wurst" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.zbh.uni-hamburg.de/wurst/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3343 ; sc:citation "pubmed:19429687" ; sc:description "The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. 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This library is primarily meant to calculate dihedral entropies from MD simulation data. For this, we use a KDE with automatic bandwidth selection as suggested by Z. Botev et al. We tried to keep the package as generalized as possible, therefore, the package can be used to calculate the entropy of any data, or also to simply calculate the KDE." ; sc:featureList edam:operation_0244, edam:operation_2476 ; sc:license "MIT" ; sc:name "X-Entropy" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/liedllab/X-Entropy" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0634, edam:topic_3053, edam:topic_3360 ; sc:citation "pubmed:18278816" ; sc:description "Suite of family-based tests for detecting association of X-chromosome genes. This is a likelihood-based approach which can perform hypothesis testing as well as estimation of disease-related marker relative risks under a case-parent design. This test uses nuclear family with a single affected proband and allows additional siblings and missing parental genotypes. This program can test both single marker and haplotypes association." ; sc:featureList edam:operation_3461 ; sc:name "X-LRT" ; sc:operatingSystem "Windows" ; sc:softwareHelp ; sc:url "http://dmpi.duke.edu/x-lrt" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0099, edam:topic_3168 ; sc:citation ; sc:description "An updated version of RNA-MATE capable of mapping both RNAseq and DNA sequence data." ; sc:featureList edam:operation_0292, edam:operation_2520 ; sc:license "Not licensed" ; sc:name "X-MATE" ; sc:softwareHelp ; sc:url "http://genomicbiology.org/2011/02/15/x-mate/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workflow" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3172, edam:topic_3173, edam:topic_3391, edam:topic_3474 ; sc:citation , "pmcid:PMC10787363", "pubmed:38217405" ; sc:description "This multi-omics data analysis workflow was developed as part of a case study investigating shared patterns between multi-omics data and childhood externalizing behaviour. The modular Nextflow workflow was implemented using FAIR practices. It comprises genome-wide DNA methylation, targeted metabolomics and behaviour data pre-processing, and integrative analysis methods. Individuals of a cohort are clustered using Similarity Network Fusion (SNF), latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) and Multiple Correspondence Analysis (MCA), and correlations between -omics and phenotype dimensions are determined in downstream analyses including results visualisation." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "X-omics ACTION demonstrator multi-omics analysis workflow" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "2.2", "2.3" ; sc:url "https://workflowhub.eu/workflows/402" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3070, edam:topic_3344, edam:topic_3382 ; sc:description "X-Ray Calculator is a MATLAB port and GUI to the mucal elemental x-ray properties calculator." ; sc:isAccessibleForFree true ; sc:name "X-Ray Calculator" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1.0.0.0" ; sc:url "https://www.mathworks.com/matlabcentral/fileexchange/34599-x-ray-calculator" ; biotools:primaryContact "Christopher Hall" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0128, edam:topic_0203, edam:topic_2259, edam:topic_3169, edam:topic_3308, edam:topic_3512 ; sc:citation "pubmed:22080467" ; sc:description "Method to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating ChIP-seq/chip and position-weight-matrices (PWMs) data, protein-protein interactions, and kinase-substrate phosphorylation reactions, it can better identify regulatory mechanisms upstream of genome-wide differences in gene expression." ; sc:featureList edam:operation_2495 ; sc:name "X2K" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.maayanlab.net/X2K" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0749 ; sc:citation , "pubmed:29800326" ; sc:description "Infers upstream regulatory networks from signatures of differentially expressed genes. By combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis, produces inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list." ; sc:featureList edam:operation_0314, edam:operation_3439, edam:operation_3501 ; sc:name "X2K Web" ; sc:url "http://amp.pharm.mssm.edu/X2K/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0625, edam:topic_3295 ; sc:citation ; sc:description "xQTLImp is an open source software that implements imputation of xQTL(such as eQTL, mQTL, haQTL et. al) statistics across the genome. xQTLImp accepts xQTL summary statistics (i.e., Z statistics) without the need of individual-level genotypes and molecular traits (such as gene expression profiles), and could accurately impute novel xQTL associations from known associations based on linkage disequilibrium (LD) among variants. Specifically, it models the statistics of variants associated with the same molecular trait by using a multivariate Gaussian model, and infers missing association statistics from nearby known association statistics by leveraging LD among variants (See Methods in the paper). Using multiple real datasets, we demonstrated that 1) xQTLImp can impute missing xQTL statistics with high accuracy, and 2) xQTLImp can effiectively reduce the lower bound of MAF in xQTL studies, leading to the discovery of novel xQTL signals to further enhance xQTL discoveries." ; sc:featureList edam:operation_3196, edam:operation_3232, edam:operation_3557 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "xQTLImp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/hitbc/xQTLimp" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0850 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence set" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3651 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3711 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Matches tandem mass spectra with library spectra from same organism." ; sc:featureList edam:operation_3631, edam:operation_3645, edam:operation_3767, edam:operation_3801 ; sc:name "X Hunter" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://www.thegpm.org/hunter/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0196, edam:topic_3174, edam:topic_3293 ; sc:citation "pubmed:26246894" ; sc:description "Novel method for targeting assembly of specific protein-coding genes using a graph structure combining both de Bruijn graphs and protein HMMs. The inclusion of HMM information guides the assembly, with concomitant gene annotation." ; sc:featureList edam:operation_0525 ; sc:name "Xander" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://github.com/rdpstaff/Xander_assembler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2828 ; sc:citation ; sc:description "XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼ atoms) of heterogeneous structural content." ; sc:featureList edam:operation_2476 ; sc:license "GPL-3.0" ; sc:name "XaNSoNS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/ElsevierSoftwareX/SOFTX-D-16-00083" ; biotools:primaryContact "V. S. Neverov" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0621, edam:topic_0622 ; sc:citation "pubmed:22116063" ; sc:description "Model organism database for the bacterium Myxococcus xanthus." ; sc:featureList edam:operation_0224, edam:operation_0362, edam:operation_3561 ; sc:name "Xanthusbase" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ecoliwiki.net/colipedia/index.php/XanthusBase" ; biotools:primaryContact "Roy D. Welch" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0081, edam:topic_3382, edam:topic_3474 ; sc:citation , "pubmed:33714842" ; sc:description "XAOM (X-ray Alignment and Orientation Method) is a method for automatic alignment and orientation of radiographs for computer-aided medical diagnosis. XAOM is a two-stage method for X-ray image alignment and orientation. The first stage of the XAOM is aligning images, while the second stage is orienting them by giving an orientation label (north, south, east, west)." ; sc:featureList edam:operation_3435, edam:operation_3960 ; sc:license "GPL-2.0" ; sc:name "XAOM" ; sc:url "https://github.com/fhrzic/XAOM" ; biotools:primaryContact "Ivan Štajduhar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_1317 ; sc:description "Generates Xaperones to facilitate the crystallization of proteins of interest." ; sc:featureList edam:operation_0250 ; sc:name "Xaperones" ; sc:provider "Instruct" ; sc:url "http://www.xaperones.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_2885, edam:topic_3168, edam:topic_3303 ; sc:citation , "pmcid:PMC9841152", "pubmed:36644891" ; sc:description "Scalable small variant calling across heterogeneous next-generation sequencing experiments." ; sc:featureList edam:operation_2939, edam:operation_3196, edam:operation_3227, edam:operation_3675, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "xAtlas" ; sc:url "https://github.com/jfarek/xatlas" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0769, edam:topic_2885, edam:topic_3174, edam:topic_3673 ; sc:citation ; sc:description "Comprehensive and accurate genetic variant identification from contaminated and low coverage Mycobacterium tuberculosis whole genome sequencing data." ; sc:featureList edam:operation_3192, edam:operation_3196, edam:operation_3227, edam:operation_3675 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "XBS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/TimHHH/XBS" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0863 ; sc:encodingFormat edam:format_2306, edam:format_2330 ; sc:name "Sequence alignment" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_2306, edam:format_2330 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3547 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation ; sc:description "This algorithm establishes an statistical model based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises that follow a Poisson distribution. 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It was initially written to support crystallographic fragment screening at beamline I04-1 at the Diamond Light Source, but it is a generic program that can be used to facilitate any structure-based drug design project." ; sc:featureList edam:operation_2406 ; sc:name "XChemExplorer" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://tkrojer.github.io/XChemExplorer/" ; biotools:primaryContact "Frank von Delft", "Rachael Skyner", "Tobias Krojer" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654 ; sc:name "Mass spectrometry data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_0943 ; sc:encodingFormat edam:format_3244, edam:format_3650, edam:format_3654 ; sc:name "Mass spectrometry spectra" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3248, edam:format_3650 ; sc:name "Mass spectrometry data" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0092, edam:topic_3172, edam:topic_3383 ; sc:citation , "pubmed:20671148" ; sc:description "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling." ; sc:featureList edam:operation_2428, edam:operation_3203, edam:operation_3215, edam:operation_3628, edam:operation_3634, edam:operation_3694, edam:operation_3695 ; sc:license "GPL-2.0" ; sc:name "xcms" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0.2" ; sc:url "http://bioconductor.org/packages/release/bioc/html/xcms.html" ; biotools:primaryContact . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_3483 ; sc:encodingFormat edam:format_3245 ; sc:name "Spectrum" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_2013 ; sc:name "Pathway or network" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2259, edam:topic_3172 ; sc:citation ; sc:description "A systems biology tool for analyzing metabolomic data. 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A website, where you can explore which amino acid residues in proteins that are predicted to be early folding, this in relation to the sequence fragment it occurs in, and the final secondary structure this fragment adopts in the protein (when folded)." ; sc:featureList edam:operation_0303, edam:operation_0474, edam:operation_2415, edam:operation_2488 ; sc:isAccessibleForFree true ; sc:name "XEFoldMine" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://xefoldmine.bio2byte.be/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0091, edam:topic_0219 ; sc:author "Benjamin Dartigues" ; sc:contributor "Alexis Groppi", "Cecile Cabasson", "Macha Nikolski", "Yves Gibon" ; sc:description "The web application Linda offers a complete tool for entering and managing metadata associated with a phenotyping experiment on plants. It thus makes it possible to intuitively describe experimental related information such as, for example, the experimental design, the growth protocols, the environmental variable measurements, etc. Linda is coupled with a database that stores this information in a structured manneer using oriented graphs. This database uses reference ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type of experiment such as the Minimal Information About Plant Phenotyping Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the FAIR principles (Findable Accessible Interoperable Reusable) and oon the other hand, by exporting this metadata relating to the experiment in tabulated formats or formatted for submission in the international databases (ISA-tab)." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Linda" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Centre de Bioinformatique de Bordeaux (CBiB)", "UMR 1332 - Biologie du Fruit et Pathologie" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://services.cbib.u-bordeaux.fr/linda/" ; biotools:primaryContact "Benjamin Dartigues" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3512 ; sc:citation "pubmed:19884130" ; sc:description "The model organism database for Xenopus laevis and X. 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Bush" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0602, edam:topic_3172, edam:topic_3375, edam:topic_3407 ; sc:citation , "pubmed:32525671" ; sc:description """Inference and Likelihood of Intermediate Metabolite Formation. XenoNet Web provides prediction web services for small molecule biochemistry. XenoNet Web can be used by medicinal chemists and biologists to make predictions about the human in vivo metabolism and reactivity of small molecules.""" ; sc:featureList edam:operation_3357, edam:operation_3660, edam:operation_3803, edam:operation_3929 ; sc:name "XenoNet" ; sc:url "https://swami.wustl.edu/xenonet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0154, edam:topic_0602, edam:topic_3292, edam:topic_3407, edam:topic_3524 ; sc:citation "pubmed:25411327" ; sc:description "It provides prediction web services for small molecule biochemistry. It can be used by medicinal chemists and biologists to make predictions about the human in vivo metabolism of small molecules." ; sc:featureList edam:operation_2492 ; sc:name "XenoSite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://swami.wustl.edu/xenosite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_2640, edam:topic_2815 ; sc:citation ; sc:description "The (Zebrafish) Xenograft Phenotype Interactive Repository (Xe.Ph.I.R) is an online database for describing how human cancer behaves when engrafted in zebrafish embryos. We provide representative images of the first days of cancer development post-engraftment and all the metadata required to recapitulate the experiments." ; sc:featureList edam:operation_3431 ; sc:isAccessibleForFree true ; sc:name "XePhIR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.xephir.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0108, edam:topic_0749, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7708984", "pubmed:33262392" ; sc:description """identification of N4-acetylcytidine (ac4C) in mRNA using eXtreme gradient boosting with electron-ion interaction pseudopotentials. XG-ac4C: Identification of N4-acetylcytidine (ac4C) in mRNA by using eXtreme Gradient Boosting method with electron-ion interaction pseudopotentials.""" ; sc:featureList edam:operation_3937 ; sc:name "XG-ac4C" ; sc:url "http://nsclbio.jbnu.ac.kr/tools/xgac4c/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3308, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC7533297", "pubmed:33230441" ; sc:description """An Interpretable Prediction Model for Identifying N7-Methylguanosine Sites Based on XGBoost and SHAP. Recent studies have increasingly shown that the chemical modification of mRNA plays an important role in the regulation of gene expression. N7< sup>-methylguanosine (m7G) is a type of positively-charged mRNA modification that plays an essential role for efficient gene expression and cell viability. However, the research on m7G has received little attention to date. Bioinformatics tools can be applied as auxiliary methods to identify m7G sites in transcriptomes. In this study, we develop a novel interpretable machine learning-based approach termed XG-m7G for the differentiation of m7G sites using the XGBoost algorithm and six different types of sequence-encoding schemes. 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Knight" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_2275, edam:topic_3047, edam:topic_3314, edam:topic_3474 ; sc:citation , "pubmed:34009965" ; sc:description "XGraphBoost is a tool for extracting Graph Neural Network-based features for a better prediction of molecular properties. 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Klau", "Jaap Heringa", "Lodewyk F. A. Wessels", "Macha Nikolski" ; sc:description "Software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions. Active subnetwork modules are sets of genes, one for each species, which: - induce a connected subnetwork in a species-specific interaction network, - show overall differential behavior, and - contain a large number of orthologous genes." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "xHeinz" ; sc:operatingSystem "Linux", "Mac" ; sc:provider "Bordeaux University, CBiB, France", "The Netherlands", "The Netherlands Cancer Institute, Amsterdam", "Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France,", "University Duisburg-Essen", "Würzburg University, Germany", "u-bordeaux.fr" ; sc:softwareHelp , ; sc:softwareVersion "1.0" ; sc:url "https://github.com/ls-cwi/xheinz" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0654, edam:topic_3518 ; sc:citation "pubmed:15333145" ; sc:description "Tool for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays." ; sc:featureList edam:operation_2495 ; sc:name "XHM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfo.no/tools/xhm/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2828 ; sc:citation ; sc:description "Automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable for immediately starting phasing and structure solution." ; sc:featureList edam:operation_0335, edam:operation_3445 ; sc:isAccessibleForFree true ; sc:name "XIA2" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "Instruct" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "https://xia2.github.io/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Workflow" ; sc:applicationSubCategory edam:topic_0099, edam:topic_0659, edam:topic_3170 ; sc:citation ; sc:description "Small RNAseq pipeline for paired-end reads" ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "XICRA" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "https://github.com/HCGB-IGTP/XICRA" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0121 ; sc:citation , "pubmed:27642655" ; sc:description "An algorithm to identify cross-linked peptides." ; sc:license "Apache-2.0" ; sc:name "Xilmass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "0.2" ; sc:url "https://github.com/compomics/xilmass" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2603 ; sc:encodingFormat edam:format_3752 ; sc:name "Expression data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3508 ; sc:name "Plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3308 ; sc:citation , "pubmed:30370770" ; sc:description "An R package for network analyses from multiplexed, time-resolved proteomics or trascriptomics data" ; sc:featureList edam:operation_2497 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "XINA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.1.1" ; sc:url "https://www.bioconductor.org/packages/devel/bioc/html/XINA.html" ; biotools:primaryContact "Lang Ho Lee", "Sasha A. Singh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0091, edam:topic_0769, edam:topic_3372 ; sc:citation "pubmed:23104885" ; sc:description "A flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run,construct and edit workflows. It allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed." ; sc:featureList edam:operation_3429 ; sc:name "XiP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://xip.hgc.jp/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application", "Web application" ; sc:applicationSubCategory edam:topic_3520 ; sc:citation ; sc:description "Next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments." ; sc:featureList edam:operation_3214 ; sc:license "Apache-2.0" ; sc:name "xiSPEC" ; sc:softwareHelp , ; sc:url "https://spectrumviewer.org" ; biotools:primaryContact "Colin Combe", "Lars Kolbowski", "Prof Juri Rappsilber" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0121, edam:topic_3520 ; sc:citation ; sc:description "Set of tools for analysis of data from crosslinked and digested protein complexes." ; sc:featureList edam:operation_2406, edam:operation_3092 ; sc:name "XLink" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://tools.proteomecenter.org/XLink.php" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0081, edam:topic_0128, edam:topic_2275 ; sc:citation "pubmed:25661704" ; sc:description "Interactive software for visualizing cross-links on structures and analyzing how the structures agree with the cross-links." ; sc:featureList edam:operation_2480 ; sc:name "Xlink Analyzer" ; sc:operatingSystem "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.beck.embl.de/XlinkAnalyzer.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0121, edam:topic_0128, edam:topic_0154, edam:topic_0601, edam:topic_0736, edam:topic_3520 ; sc:citation , , , "pubmed:33689356" ; sc:description """a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications. Using XlinkCyNET to visualize protein cross-links in Cytoscape software. Generate residue-to-residue connections provided by XL-MS in protein interaction networks. XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. Importantly, it provides an interactive interface for the exploration of cross-links and offers various options to display protein domains. XlinkCyNET works well in complex networks containing thousands of proteins.""" ; sc:featureList edam:operation_0276, edam:operation_3094, edam:operation_3925 ; sc:license "GPL-3.0" ; sc:name "XlinkCyNET" ; sc:url "https://www.theliulab.com/software/xlinkcynet" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0121, edam:topic_2814 ; sc:citation , "pubmed:30520642" ; sc:description "Database and tools to store, visualize and predict protein interaction topologies." ; sc:featureList edam:operation_0478, edam:operation_3083 ; sc:isAccessibleForFree true ; sc:license "Unlicense" ; sc:name "XLinkDB" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "3.0" ; sc:url "http://xlinkdb.gs.washington.edu/xlinkdb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_2814, edam:topic_3382, edam:topic_3520 ; sc:citation ; sc:description """Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures. An integrated tool to score model PDB structures based on crosslink and monolink data. Scoring for Crosslinks is performed using MNXL and Monolinks are scored by MoDS. If both crosslinks and monolinks are being scored the combination score XLMO is calculated.""" ; sc:featureList edam:operation_0244, edam:operation_0477, edam:operation_2950 ; sc:license "GPL-3.0" ; sc:name "XLM-Tools" ; sc:url "https://github.com/Topf-Lab/XLM-Tools" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_1317, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:26411867" ; sc:description "R package to visualize and score protein structure models based on sites of protein cross-linking." ; sc:featureList edam:operation_2406 ; sc:name "XLmap" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://brucelab.gs.washington.edu/software.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0659, edam:topic_3170, edam:topic_3474, edam:topic_3512 ; sc:citation , "pmcid:PMC9173695", "pubmed:35685437" ; sc:description "Interpretable Deep Learning Model Reveals Subsequences of Various Functions for Long Non-Coding RNA Identification." ; sc:featureList edam:operation_0269, edam:operation_0443, edam:operation_3216, edam:operation_3904 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "Xlnc1DCNN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cucpbioinfo/Xlnc1DCNN" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0654 ; sc:citation ; sc:description "Simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length." ; sc:featureList edam:operation_0224, edam:operation_2429 ; sc:name "xMAN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "20060925" ; sc:url "http://liulab.dfci.harvard.edu/WEBSITE/software.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0154, edam:topic_0199 ; sc:citation , "pubmed:31539018" ; sc:description "database of Homo sapiens mutated peptides | This script eliminates the hits reported from protein identification tools (proteomics) without the mutated amino acid in the sequence | Protein Descriptions contains the descriptions of the hits and these need to include the short sequence from the XMAn.v2 headers. (e.g. GN=CDC42BPB MRCKB_HUMAN Serine/threonine-protein kinase MRCK beta:c_C3625A:p_L1209I:VGIIEGL:Missense) | A file in EXCEL format (.xlsx) containing any columns but 2 columns with the exact following names: Sequence and Protein Descriptions" ; sc:featureList edam:operation_2929, edam:operation_3643, edam:operation_3767 ; sc:name "XMAn" ; sc:url "http://github.com/lazarlab/XMAnv2" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2887 ; sc:encodingFormat edam:format_3161 ; sc:name "Nucleic acid sequence record" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2166 ; sc:encodingFormat edam:format_3617 ; sc:name "Sequence composition plot" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0102 ; sc:citation , "pmcid:PMC2238884", "pubmed:17932061" ; sc:description "This package can plot graphs in the X:Map genome browser. It exports plotting files in a suitable format." ; sc:featureList edam:operation_3208 ; sc:license "GPL-3.0" ; sc:name "xmapbridge" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.32.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/xmapbridge.html" ; biotools:primaryContact "Chris Wirth" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092 ; sc:description "Visual tool for analyzing cross match alignments." ; sc:featureList edam:operation_0337 ; sc:license "GPL-3.0" ; sc:name "XMatchView" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.bcgsc.ca/platform/bioinfo/software/xmatchview" ; biotools:primaryContact "R. Warren" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0611, edam:topic_0769, edam:topic_1317, edam:topic_3452 ; sc:citation ; sc:description "A suite of image processing programs." ; sc:featureList edam:operation_0297, edam:operation_2409, edam:operation_3552 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "XMIPP" ; sc:operatingSystem "Linux" ; sc:provider "Instruct Image Processing Center (I2PC)" ; sc:softwareHelp ; sc:softwareVersion "3.22" ; sc:url "http://xmipp.i2pc.es/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0102 ; sc:description "XML2RAF is a Perl software to create RAF maps from PDB XML files.The Protein Data Bank provides XML files that include a mapping between the PDB-format records SEQRES (representing the sequence of the molecule used in an experiment) and ATOM (representing the atoms experimentally observed). These XML files (along with the PDB’s chemical dictionary) also provide information on the original identity of most residues prior to any post-translational modifications, including cyclizations." ; sc:featureList edam:operation_0335, edam:operation_2429 ; sc:name "XML2RAF 1.02 -Create RAF Maps from PDB XML files" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://scop.berkeley.edu/downloads/ver=1.75B" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3247, edam:format_3655 ; sc:name "Peptide identification" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0945 ; sc:encodingFormat edam:format_3475 ; sc:name "Peptide identification" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:description "Utility to convert peptide identifications from one format to another." ; sc:featureList edam:operation_3434 ; sc:name "xml2tsv" ; sc:url "https://github.com/bio-tools/biotoolsCompose/blob/master/msutils-poc-domainsetup/src/biotools/biotoolsCompose/poc/sib/xml2tsv.java" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:encodingFormat edam:format_2332 ; sc:name "Database metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:encodingFormat edam:format_2332 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071, edam:topic_3316 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "An Emboss tool that fetches XML entry from a file or a local or remote data resource, parses it and rewrites it in various formats" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3357 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "xmlget" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://www.bioinformatics.nl/cgi-bin/emboss/xmlget" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:encodingFormat edam:format_2332 ; sc:name "Database metadata" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0957 ; sc:encodingFormat edam:format_2330 ; sc:name "Database metadata" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0091, edam:topic_3071, edam:topic_3316 ; sc:citation , , ; sc:contributor "EMBOSS Contributors", "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:description "An Emboss tool that reads XML data and rewrites it as the original entry text" ; sc:featureList edam:operation_0335, edam:operation_2422, edam:operation_3357 ; sc:funder "UK BBSRC", "UK MRC", "Wellcome Trust" ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "xmltext" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI", "EMBOSS" ; sc:softwareHelp , , ; sc:softwareVersion "r6" ; sc:url "http://www.bioinformatics.nl/cgi-bin/emboss/xmltext" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_2275, edam:topic_2814 ; sc:citation "pubmed:7794836" ; sc:description "Desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server." ; sc:featureList edam:operation_0570, edam:operation_2406 ; sc:name "XmMol" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://bioserv.rpbs.univ-paris-diderot.fr/software/XmMol/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0622, edam:topic_2259, edam:topic_3053, edam:topic_3474 ; sc:citation ; sc:description "Fit Markov Networks to high-throughput genetics data." ; sc:featureList edam:operation_0296 ; sc:license "GPL-2.0" ; sc:name "XMRF" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/zhandong/XMRF" ; biotools:primaryContact "Ying-Wooi Wan" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library", "Web application" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0602, edam:topic_0625, edam:topic_2259 ; sc:citation ; sc:description "Data-driven integration and differential network analysis tool." ; sc:featureList edam:operation_0313, edam:operation_2497, edam:operation_3083 ; sc:name "xMWAS" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:url "https://kuppal.shinyapps.io/xmwas/" ; biotools:primaryContact "Karan Uppal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3071, edam:topic_3379, edam:topic_3384 ; sc:citation , "pmcid:PMC7343726", "pubmed:32642856" ; sc:description """Enabling FHIR on the Open-Source Research Platform XNAT. This plugin provides an additional REST API for XNAT 1.7, implementing the HL7 FHIR protocol.""" ; sc:featureList edam:operation_3435 ; sc:license "AGPL-3.0" ; sc:name "XNAT FHIR" ; sc:url "https://github.com/somnonetz/xnat-fhir-plugin" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3379, edam:topic_3384, edam:topic_3444, edam:topic_3452, edam:topic_3954 ; sc:citation , "pubmed:35304674" ; sc:description "XNAT for Preclinical Imaging Centers (XNAT-PIC) has been developed to expand XNAT's basic functionalities to preclinical imaging and consists of:" ; sc:featureList edam:operation_3435, edam:operation_3443, edam:operation_3553 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "XNAT-PIC" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/szullino/XNAT-PIC" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3056 ; sc:citation , "pmcid:PMC2687721", "pubmed:17943131" ; sc:description "Program to estimate the cross population extended haplotype homozygosity as an indicator of positive selection." ; sc:featureList edam:operation_3197 ; sc:license "Not licensed" ; sc:name "XP-EHH" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://hgdp.uchicago.edu/Software/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0097, edam:topic_3168 ; sc:citation "pubmed:8743701" ; sc:description "Program which computes a parameterized alignment of two sequences, displaying all of the optimal alignments for the two sequences when the costs of substitutions, gaps and insertions or deletions are varied. The user provides as input two sequences, an alignment type (global, local, end-gap free and substring), and selects which two of the alignment costs to vary." ; sc:featureList edam:operation_0292 ; sc:name "XPARAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.cs.ucdavis.edu/~gusfield/xparall/index.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_0654, edam:topic_3125 ; sc:description "DNA mapping program that draws plasmid or linear DNA maps showing features such as genes, multiple cloning sites and restriction sites. The maps are highly customizable. Fragments can be copied or cut, and inserted into different maps or turned into maps on their own (virtual cloning). FastA, text, and GenBank files can be imported directly, making maps of long and complex sequences (e.g. genomic sequences) quick and easy to prepare." ; sc:featureList edam:operation_2429, edam:operation_2520 ; sc:name "XPlasMap" ; sc:operatingSystem "Mac" ; sc:softwareVersion "0.99" ; sc:url "http://www.iayork.com/XPlasMap/index.shtml" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0928 ; sc:encodingFormat edam:format_1638, edam:format_2330, edam:format_3578 ; sc:name "Gene expression profile" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:encodingFormat edam:format_1929 ; sc:name "Protein sequence" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2536 ; sc:encodingFormat edam:format_3244 ; sc:name "Mass spectrometry data" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2884 ; sc:encodingFormat edam:format_3603 ; sc:name "Plot" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2048 ; sc:encodingFormat edam:format_3508 ; sc:name "Report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1448 ; sc:encodingFormat edam:format_3752 ; sc:name "Comparison matrix (nucleotide)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2600 ; sc:encodingFormat edam:format_3603 ; sc:name "Pathway or network" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_3754 ; sc:encodingFormat edam:format_3508, edam:format_3603, edam:format_3752 ; sc:name "GO-term enrichment data" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1449 ; sc:encodingFormat edam:format_3752 ; sc:name "Comparison matrix (amino acid)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_2343 ; sc:encodingFormat edam:format_2332, edam:format_3752 ; sc:name "Pathway ID (KEGG)" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_3764 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3391 ; sc:author "Dr. Michael Kohl" ; sc:citation , "pubmed:23501674" ; sc:description "It facilitates several steps that frequently occur in the context of multi-OMICS workflows like data conversion, quality control, data comparison, differential/statistical analyses, GO and pathway analyses. In the present version, CrossPlatformCommander enables Integration data obtained from Proteomics and Transcriptomics measurements." ; sc:featureList edam:operation_2997, edam:operation_2998, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:name "XPlatCom (Cross PLATform COMmander)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "1" ; sc:url "https://www.ruhr-uni-bochum.de/mpc/software/legacy/index.html.en#XPlatCom" ; biotools:primaryContact "PD Dr. Martin Eisenacher" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Workbench" ; sc:applicationSubCategory edam:topic_0092, edam:topic_0611, edam:topic_1317, edam:topic_3452 ; sc:description "Complete solution for 3D tomographic acquisition, reconstruction, and visualization into one integrated package." ; sc:featureList edam:operation_0297, edam:operation_0337, edam:operation_2426 ; sc:isAccessibleForFree true ; sc:name "Xplore3D" ; sc:operatingSystem "Windows" ; sc:provider "Instruct" ; sc:softwareVersion "1" ; sc:url "http://www.fei.com/applications/life-sciences/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0218, edam:topic_3068 ; sc:citation "pubmed:12824439" ; sc:description "Web tool that aids MEDLINE searching by summarizing the subjects contained in the results, thus allowing users to focus on subjects of interest." ; sc:featureList edam:operation_0305 ; sc:name "XplorMed" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://xplormed.ogic.ca/" ; biotools:primaryContact "XplorMed Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0203, edam:topic_2269 ; sc:citation ; sc:description "Cross-platform normalization method for combining gene expression data from different studies. 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The XyloTron platform integrates an imaging system built with off-the-shelf components, flexible illumination options with visible and UV light sources, software for camera control, and deep learning models for identification""" ; sc:featureList edam:operation_3946 ; sc:name "XyloTron" ; sc:url "https://github.com/fpl-xylotron" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0084, edam:topic_0625, edam:topic_2885, edam:topic_3056, edam:topic_3168 ; sc:citation , "pmcid:PMC7941695", "pubmed:33750289" ; sc:description "Y-LineageTracker is a high-throughput analysis framework for Y-chromosomal next-generation sequencing data. Y-LineageTracker provides a framework to fully analyze human Y-chromosome sequencing data. 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It uses a comparative approach with General mixture models similar to those used by nanocompore and xpore." ; sc:featureList edam:operation_0337, edam:operation_2495 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Yanocomp" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.github.com/bartongroup/yanocomp" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0769, edam:topic_3500 ; sc:citation ; sc:description """Opening the black box of high resolution fish tracking using yaps. YAPS - Yet Another Positioning Solver. YAPS - (Yet Another Positioning Solver). Welcome to the yaps repository. The yaps package is based on the original YAPS presented in Baktoft, Gjelland, Økland & Thygesen (2017): Positioning of aquatic animals based on time-of-arrival and random walk models using YAPS (Yet Another Positioning Solver)""" ; sc:license "GPL-3.0" ; sc:name "yaps" ; sc:url "http://github.com/baktoft/yaps" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_0199, edam:topic_2640, edam:topic_3473, edam:topic_3569 ; sc:citation ; sc:description "This package provides functions and routines useful in the analysis of somatic signatures. 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Yass ver. 2.0 has now been released and is available in the master branch.""" ; sc:featureList edam:operation_3432, edam:operation_3629, edam:operation_3802 ; sc:license "Apache-2.0" ; sc:name "YASS" ; sc:url "https://github.com/paninski-lab/yass" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_3070 ; sc:citation ; sc:description "The yeast deletion library represents a powerful resource for genome-wide identification of genes whose absence affects the cellular responses to a wide range of treatments." ; sc:featureList edam:operation_2409 ; sc:license "GPL-3.0" ; sc:name "Yeast-Deletion-Library-Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://yeastdb.org" ; biotools:primaryContact "Mark D. Temple" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1026 ; sc:name "Gene symbol" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0621 ; sc:citation , "pmcid:PMC1240090", "pubmed:16169922" ; sc:description "Tool for visualising the syntenic context of any gene from several yeast genomes." ; sc:featureList edam:operation_0224 ; sc:name "Yeast gene order browser" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ygob.ucd.ie/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_0621, edam:topic_3557 ; sc:citation "pubmed:21492431" ; sc:description "Contains high- and low-throughput data relevant to phosphorylation events. It includes 6,225 low-throughput and 21,990 high-throughput interactions, from greater than 35,000 experiments." ; sc:featureList edam:operation_2464, edam:operation_2949, edam:operation_3501, edam:operation_3561 ; sc:name "Yeast KID" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.moseslab.csb.utoronto.ca/KID/" ; biotools:primaryContact "Curation information", "Database interface related information" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0218, edam:topic_3068, edam:topic_3172 ; sc:citation "pubmed:21687783" ; sc:description "Yeast MetaboliNER is a tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome." ; sc:featureList edam:operation_0306, edam:operation_3280, edam:operation_3660, edam:operation_3778 ; sc:name "Yeast MetaboliNER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://nactem7.mib.man.ac.uk/metaboliner/" ; biotools:primaryContact "Web Service" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_3382, edam:topic_3512, edam:topic_3912 ; sc:citation , "pubmed:31612944" ; sc:description "Transcriptome visualization and data availability at the Saccharomyces Genome Database." ; sc:featureList edam:operation_2495, edam:operation_3208, edam:operation_3799 ; sc:name "yeastgenome" ; sc:url "http://www.yeastgenome.org" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1807 ; sc:name "ORF name" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_0916 ; sc:encodingFormat edam:format_2331 ; sc:name "Gene report" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0114, edam:topic_0621 ; sc:citation , "pubmed:14562095" ; sc:description "Yeast GFP fusion localization database." ; sc:featureList edam:operation_0224 ; sc:name "Yeast GFP fusion localization database (yeastgfp)" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://yeastgfp.yeastgenome.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description "YeastMate is a tool for the automated detection and segmentation of S. cerevisae cells and their mating and budding events, as well as a subclassification of the cells involved in these events into mother and daughter cells." ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "YeastMate" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://github.com/hoerlteam/YeastMate" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2229, edam:topic_3382 ; sc:citation ; sc:description """Deep Learning Enabled Accurate Segmentation of Budding Yeast Cells in Bright-field Microscopy. YeastNet: Deep Learning Semantic Segmentation for Budding Yeast Single Cell Analysis. YeastNet is a library for analysing live-cell fluorescence microscopy of budding yeast cells, written in Python3 using PyTorch 1.0.""" ; sc:featureList edam:operation_3443 ; sc:license "GPL-3.0" ; sc:name "YeastNet" ; sc:url "https://github.com/kaernlab/YeastNet" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749 ; sc:citation "pubmed:20972212" ; sc:description "The YEAst Search for Transcriptional Regulators And Consensus Tracking is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. It includes DISCOVERER and allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor." ; sc:featureList edam:operation_0224, edam:operation_0445, edam:operation_2422 ; sc:name "YEASTRACT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.yeastract.com" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0204, edam:topic_0602, edam:topic_0621, edam:topic_0749, edam:topic_3297 ; sc:citation , "pubmed:34427650" ; sc:description "YEASTRACT+ combines the existing database information of all yeast species, providing bioinformatics tools for the prediction and visualization of gene and genomic regulation based on orthologous regulatory associations described for other yeast species, based on comparative genomics." ; sc:featureList edam:operation_1781, edam:operation_2437, edam:operation_3663 ; sc:isAccessibleForFree true ; sc:name "Yeastract+" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://yeastract-plus.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3315, edam:topic_3318, edam:topic_3382, edam:topic_3474 ; sc:citation ; sc:description """A convolutional neural network for highly accurate, label-free segmentation of yeast microscopy images. Laboratory of the Physics of Biological Systems ‐ EPFL.""" ; sc:featureList edam:operation_3443, edam:operation_3553, edam:operation_3799 ; sc:name "yeaz" ; sc:url "https://lpbs-nn.epfl.ch/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0121, edam:topic_3170, edam:topic_3308, edam:topic_3520 ; sc:citation , "pubmed:36847572" ; sc:description "Multi-Omics Interactive Database for Yersinia Species." ; sc:featureList edam:operation_2422 ; sc:isAccessibleForFree true ; sc:name "Yersiniomics" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://yersiniomics.pasteur.fr/#bacnet.Yersinia" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "CLI tool to support building and maintaining Yevis workflow registry." ; sc:license "Apache-2.0" ; sc:name "Yevis-cli" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "0.5.4" ; sc:url "https://github.com/sapporo-wes/yevis-cli" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0769 ; sc:citation ; sc:description "Web application for browsing Yevis workflow registry." ; sc:license "Apache-2.0" ; sc:name "Yevis-web" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , , ; sc:softwareVersion "1.2.1" ; sc:url "https://github.com/sapporo-wes/yevis-web" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2044 ; sc:encodingFormat edam:format_1929 ; sc:name "Sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_2955 ; sc:encodingFormat edam:format_2333 ; sc:name "Sequence report" ], [ a bsct:FormalParameter ; sc:additionalType edam:data_1277 ; sc:encodingFormat edam:format_2330 ; sc:name "Protein features" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0160 ; sc:citation "pubmed:11928486" ; sc:description "Neural network predictions for O-Beta-GlcNAc attachment sites in eukaryotic protein sequences." ; sc:featureList edam:operation_0417 ; sc:isAccessibleForFree true ; sc:license "Other" ; sc:name "YinOYang" ; sc:operatingSystem "Linux" ; sc:provider "CBS" ; sc:softwareHelp ; sc:softwareVersion "1.2" ; sc:url "http://cbs.dtu.dk/services/YinOYang/" ; biotools:primaryContact "Ramneek Gupta" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_3500 ; sc:citation "pubmed:20507917" ; sc:description "Web server for the prediction of subcellular localization. Predictions are explained and biological properties used for the prediction highlighted. In addition, a confidence estimates rates the reliability of individual predictions." ; sc:featureList edam:operation_2489 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "YLoc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://abi-services.informatik.uni-tuebingen.de/yloc/webloc.cgi" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2299 ; sc:name "Gene name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0203, edam:topic_0621 ; sc:citation , "pubmed:36455295" ; sc:description "A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast." ; sc:featureList edam:operation_3501 ; sc:isAccessibleForFree true ; sc:name "YMLA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://cosbi7.ee.ncku.edu.tw/YMLA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_3656 ; sc:citation ; sc:description "Peak caller for HITS-CLIP data." ; sc:featureList edam:operation_3222 ; sc:license "GPL-3.0" ; sc:name "YODEL" ; sc:url "https://github.com/LancePalmerStJude/YODEL/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_0621, edam:topic_0623 ; sc:citation "pubmed:16845020" ; sc:description "Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved." ; sc:featureList edam:operation_0224, edam:operation_2422, edam:operation_2454 ; sc:name "YOGY" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://www.bahlerlab.info/YOGY/" ; biotools:primaryContact "Jürg Bähler" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0621, edam:topic_2269, edam:topic_3125, edam:topic_3474 ; sc:citation , "pubmed:33232970" ; sc:description """Computational prediction of species-specific yeast DNA replication origin via iterative feature representation. In yORIpred, 40 optimal baseline models were constructed by exploring eight different sequence-based encodings and five different machine learning classifiers, namely random forest, support vector machine, and extremely randomized tree. The predicted probability of 40 models was concatenated and considered as the novel features that enable us to learn the informative features from several sequential models in a supervised iterative mode. For a given sequence, the yORIpred predicts ORIs or non-ORIs and also the predicted probability value of ORIs.""" ; sc:featureList edam:operation_0324, edam:operation_3936, edam:operation_3937 ; sc:name "yORIpred" ; sc:url "http://thegleelab.org/yORIpred" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_3382, edam:topic_3383, edam:topic_3385 ; sc:citation "pubmed:22470060" ; sc:description "Open-source microscope control software compatible with most present-day automized microscopes. It allows to easily automatize complex microscopy protocols using an user-friendly graphical interface." ; sc:featureList edam:operation_3443 ; sc:name "YouScope 1.2 Beta" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.youscope.org/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3299, edam:topic_3379, edam:topic_3418, edam:topic_3419 ; sc:citation ; sc:description "Tools for mapping a range of measures routinely collected in youth mental health services to AQoL 6D utility" ; sc:featureList edam:operation_2422, edam:operation_3435, edam:operation_3659 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "youthu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "https://ready4-dev.github.io/youthu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_3125, edam:topic_3512 ; sc:citation "pubmed:21045055" ; sc:description "Database that collects promoter features in Saccharomyces cerevisiae. It integrates nine kinds of promoter features including promoter sequences, genes transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5’-UTRs) and three prime untranslated regions (3’-UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction." ; sc:featureList edam:operation_0372, edam:operation_0438, edam:operation_0440, edam:operation_0445 ; sc:name "YPA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://ypa.ee.ncku.edu.tw/" ; biotools:primaryContact "Wei-Sheng Wu" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_1009 ; sc:name "Protein name" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0153, edam:topic_0602, edam:topic_0621, edam:topic_0736, edam:topic_0820 ; sc:citation , "pmcid:PMC8261538", "pubmed:34285772" ; sc:description "YPIBP is an inclusive database consisting of all the members of phosphatidylinositols-binding proteins which are collected from high-throughput proteome and lipid array studies, QuickGO and a rigorous literature mining. Cumulatively, across all PI, total of 679 PI-binding proteins were collected. YPIBP also contains protein domain information which is categorized as lipid-binding, lipid-related and others, helping users to underpin the domain-based knowledge on lipid-protein interactions." ; sc:featureList edam:operation_0306, edam:operation_0478, edam:operation_3431, edam:operation_3501, edam:operation_3925 ; sc:isAccessibleForFree true ; sc:name "YPIBP" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cosbi7.ee.ncku.edu.tw/YPIBP/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0121, edam:topic_0203, edam:topic_0602, edam:topic_0621, edam:topic_3512 ; sc:citation , "pubmed:33186464" ; sc:description """YQFC: Yeast Quantitative Feature Comparator. A web tool to compare quantitative biological features between two yeast gene lists. For each quantitative feature, YQFC provides three statistical tests (t-test, U test, and KS test) to test whether this quantitative feature is significantly different between the two yeast gene lists.""" ; sc:featureList edam:operation_2238, edam:operation_2436, edam:operation_3799 ; sc:name "YQFC" ; sc:url "http://cosbi2.ee.ncku.edu.tw/YQFC/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0749, edam:topic_3305, edam:topic_3418 ; sc:citation , "pmcid:PMC7440204", "pubmed:32817611" ; sc:description """Overview and Methods for the Youth Risk Behavior Surveillance System. The Youth Risk Behavior Surveillance System (YRBSS) monitors six types of health-risk behaviors that contribute to the leading causes of death and disability among youth and adults, including behaviors that contribute to unintentional injuries and violence; sexual behaviors that contribute to unintended pregnancy and sexually transmitted disease, including HIV infection; alcohol and other drug use; tobacco; unhealthy dietary behaviors; inadequate physical activity. YRBSS also measures the prevalence of obesity and asthma among youth and young adults.""" ; sc:featureList edam:operation_3096, edam:operation_3436, edam:operation_3659 ; sc:name "YRBSS" ; sc:url "https://www.cdc.gov/healthyyouth/data/yrbs/index.htm" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0114 ; sc:citation , "pmcid:PMC1779557", "pubmed:16859520" ; sc:description "Web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes." ; sc:featureList edam:operation_0224 ; sc:license "Not licensed" ; sc:name "yrGATE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.plantgdb.org/prj/yrGATE/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3382 ; sc:citation , "pmcid:PMC7191716", "pubmed:32349658" ; sc:description """a video tracking and analysis program for bacterial motility. Bacterial video tracking and analysis. the gaussian-sum finite impulse response filter used by YSMR.""" ; sc:featureList edam:operation_3359, edam:operation_3695, edam:operation_3802 ; sc:license "GPL-3.0" ; sc:name "YSMR" ; sc:url "https://github.com/schwanbeck/YSMR" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0749, edam:topic_3068, edam:topic_3452, edam:topic_3656 ; sc:citation , "pmcid:PMC9449546", "pubmed:36090812" ; sc:description "Extracting yeast transcription factor-gene associations from the literature using automated literature readers." ; sc:featureList edam:operation_0438, edam:operation_2422, edam:operation_3625 ; sc:isAccessibleForFree true ; sc:license "Apache-2.0" ; sc:name "YTLR" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/cobisLab/YTLR/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0199, edam:topic_0632, edam:topic_3474 ; sc:citation ; sc:description "yuzu is a compressed-sensing based approach for quickly calculating in-silico mutagenesis saliency." ; sc:featureList edam:operation_0307, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:license "MIT" ; sc:name "Yuzu" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/kundajelab/yuzu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_3361 ; sc:citation , "pmcid:PMC7485551", "pubmed:32953459" ; sc:description "A novel client-integrating architecture for conducting z-Tree experiments over the Internet." ; sc:featureList edam:operation_3938 ; sc:name "z-Tree unleashed" ; sc:url "https://cler1.gitlab.io/ztree-unleashed-doc/docs/home/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0099, edam:topic_0128, edam:topic_0654 ; sc:description "A motif discovery software for CLIP-Seq high-throughput protein-RNA interaction data. Given the regions of significant enrichment for reads it can characterize the binding site for the given RBP." ; sc:featureList edam:operation_0238, edam:operation_3501 ; sc:name "Zagros" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "1.1.0" ; sc:url "http://smithlabresearch.org/software/zagros/" ; biotools:primaryContact "AD Smith" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0092, edam:topic_2275 ; sc:citation "pubmed:19254186" ; sc:description "Python object that takes input from a Protein Databank (PDB) file and converts it to a voxelised image.  The voxelised image can then expressed in terms of an expansion in a basis set of Zernike polynomials which can be used to make rapid comparisons between different protein shapes." ; sc:featureList edam:operation_0570 ; sc:name "ZClass" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.uea.ac.uk/computing/zclass-zernike-class-" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0622, edam:topic_0654, edam:topic_3053, edam:topic_3301 ; sc:citation "pubmed:25977299" ; sc:description "New system for recognizing protein coding genes in bacterial and archaeal genomes with highly accurate gene start prediction. The program is based on the Z curve theory of DNA sequence." ; sc:featureList edam:operation_2454 ; sc:name "ZCURVE" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cefg.uestc.edu.cn/zcurve/" ; biotools:primaryContact "Feng-Biao Guo" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0082, edam:topic_0128, edam:topic_2275 ; sc:citation "pubmed:24532726" ; sc:description "The tool performs a full rigid-body search of docking orientations between two proteins, it includes performance optimization and a novel pairwise statistical energy potential." ; sc:featureList edam:operation_0478 ; sc:name "ZDOCK" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://zlab.umassmed.edu/zdock/index.shtml" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0199, edam:topic_0602, edam:topic_0749, edam:topic_2640, edam:topic_3293 ; sc:citation , "pmcid:PMC6937862", "pubmed:31888434" ; sc:description "ZDOG: Zooming in on Dominating Genes with Mutations in Cancer Pathways ZDOG is an app for visualization of the extent to which mutated genes may affect cancer pathways using the dominating tree model. The dominator tree model allows us to examine conveniently the positional importance of a gene in cancer signalling pathways. This tool facilitates the identification of mutated “master” regulators even with low mutation frequency in deregulated signalling pathways." ; sc:featureList edam:operation_0331, edam:operation_3926, edam:operation_3927 ; sc:name "ZDOG" ; sc:url "https://github.com/rudi2013/ZDOG" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0108, edam:topic_2814 ; sc:citation , "pubmed:33772587" ; sc:description "ZEAL is a protein structure alignment based on shape similarity. ZEAL allows protein structures to be aligned based on their global shape similarity." ; sc:featureList edam:operation_0496, edam:operation_0510, edam:operation_2487, edam:operation_3899 ; sc:name "ZEAL" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://andrelab.org/zeal" ; biotools:primaryContact , "Ingemar André" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0637, edam:topic_3174, edam:topic_3697 ; sc:citation , "pubmed:36073806" ; sc:description "Filtering out false taxonomic hits from shotgun sequencing based on aggregated genome coverage of all samples in dataset." ; sc:featureList edam:operation_3436, edam:operation_3460, edam:operation_3695 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "Zebra" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/biocore/zebra_filter" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0130, edam:topic_0154, edam:topic_0623, edam:topic_0821, edam:topic_3299 ; sc:citation , "pmcid:PMC7319439", "pubmed:32313959" ; sc:description """advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. The Zebra parameters can be classified into three sections: (1) select positions (columns in the multiple alignment) that will be used to suggest classifications of proteins into functional subfamilies and to estimate the statistical significance of the corresponding subfamily-specific positions; (2) define parameters to improve the scoring and statistical assessment of the subfamily-specific positions; and, finally, (3) setup the algorithm to automatically classify proteins into functional subfamilies, or provide the manual classification file.""" ; sc:featureList edam:operation_0294, edam:operation_0492, edam:operation_0503, edam:operation_0504, edam:operation_2421 ; sc:name "Zebra2" ; sc:softwareHelp ; sc:url "https://biokinet.belozersky.msu.ru/zebra2" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0821, edam:topic_3299, edam:topic_3336, edam:topic_3474 ; sc:citation , "pmcid:PMC7933735", "pubmed:33738079" ; sc:description "Zebra3D is a tool for bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies. Zebra3D provides two types of useful results: a list of SSRs themselves and, for each such region, classification of proteins into subfamilies. Zebra3D implements statistical analysis in attempt to prioritize functionally significant 3D-variability observed among homologs and filter out functionally insignificant 3D-structural divergence which is due to random fluctuations in protein structures." ; sc:featureList edam:operation_3435, edam:operation_3664, edam:operation_4008, edam:operation_4009 ; sc:license "GPL-3.0" ; sc:name "Zebra3D" ; sc:softwareHelp , ; sc:url "https://biokinet.belozersky.msu.ru/Zebra3D" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3383 ; sc:citation ; sc:description "This work developed a fully automatic method to calculate heart rate, an important parameter to analyze cardiac function, from videos. It contains several filters to identify the heart region, to reduce video noise and to calculate heart rates." ; sc:featureList edam:operation_3443 ; sc:name "zebrafish" ; sc:softwareHelp ; sc:url "https://github.com/mbilab/zebrafish" ; biotools:primaryContact "Darby Tien-Hao Chang" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0625, edam:topic_0749, edam:topic_3068, edam:topic_3810 ; sc:citation , "pmcid:PMC8051354", "pubmed:33954026" ; sc:description "ZebraShare is intended to help establish fruitful collaborations by sharing mutant fish lines, and information about these mutants, particularly when authors do not otherwise see a clear path to publication." ; sc:featureList edam:operation_3196, edam:operation_3431, edam:operation_3435 ; sc:isAccessibleForFree true ; sc:name "ZebraShare" ; sc:url "https://zfin.org/action/zebrashare" ; biotools:primaryContact "April DeLaurier", "Jared C. Talbot" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0769, edam:topic_2229, edam:topic_3168, edam:topic_3172, edam:topic_3382 ; sc:citation ; sc:description "A 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari" ; sc:featureList edam:operation_0337, edam:operation_3436, edam:operation_3443, edam:operation_3799 ; sc:isAccessibleForFree true ; sc:license "BSD-3-Clause" ; sc:name "ZELDA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/RoccoDAnt/napari-zelda" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0749, edam:topic_3169, edam:topic_3170, edam:topic_3308, edam:topic_3512 ; sc:citation , "pmcid:PMC10440783", "pubmed:37608799" ; sc:description "Graphical web-portal builder for interactive visualization and dissemination of genome-scale data." ; sc:featureList edam:operation_0337, edam:operation_2422, edam:operation_2436, edam:operation_3891 ; sc:isAccessibleForFree true ; sc:license "CC-BY-4.0" ; sc:name "ZENBU-Reports" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://fantom.gsc.riken.jp/zenbu/reports" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0659, edam:topic_2640, edam:topic_3068, edam:topic_3382, edam:topic_3421 ; sc:citation , "pubmed:32931381" ; sc:description """A Database for Xenotransplantation Studies in Zebrafish. Rapidly accumulating literature has proven feasibility of the zebrafish xenograft models in cancer research. Nevertheless, online databases for searching the current zebrafish xenograft literature are in great demand. Herein, we have developed a manually curated database, called ZenoFishDb v1.1 (https: konulab.shinyapps.io zenofishdb), based on R Shiny platform aiming to provide searchable information on ever increasing collection of zebrafish studies for cancer cell line transplantation and patient-derived xenografts (PDXs). ZenoFishDb v1.1 user interface contains four modules: DataTable, Visualization, PDX Details, and PDX Charts""" ; sc:featureList edam:operation_0305, edam:operation_0337 ; sc:name "ZenoFishDb" ; sc:softwareVersion "1.1" ; sc:url "https://konulab.shinyapps.io/zenofishdb" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0108, edam:topic_0607, edam:topic_3383, edam:topic_3474 ; sc:citation ; sc:description """an open platform to use Deep-Learning in Microscopy. ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy. ZeroCostDL4Mic is a toolbox for the training and implementation of common Deep Learning approaches to microscopy imaging. It exploits the ease-of-use and access to GPU provided by Google Colab.""" ; sc:license "MIT" ; sc:name "ZeroCostDL4Mic" ; sc:url "https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_2640, edam:topic_3170, edam:topic_3308 ; sc:citation , "pmcid:PMC9310463", "pubmed:35879727" ; sc:description "Computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics." ; sc:featureList edam:operation_3435, edam:operation_3501 ; sc:isAccessibleForFree true ; sc:license "Not licensed" ; sc:name "ZetaSuite" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "https://github.com/YajingHao/ZetaSuite" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_2275 ; sc:description "A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics." ; sc:featureList edam:operation_0337, edam:operation_2421 ; sc:name "Zeus alpha" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.al-nasir.com/www/Jamie/Zeus/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0621, edam:topic_0625, edam:topic_0749 ; sc:citation "pubmed:21036866" ; sc:description "Central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. It manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations." ; sc:featureList edam:operation_0314, edam:operation_2495, edam:operation_3196, edam:operation_3223, edam:operation_3232 ; sc:name "ZFIN" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zfin.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0199, edam:topic_0602, edam:topic_0798, edam:topic_3512 ; sc:citation "pubmed:22067444" ; sc:description "Database of revertible protein trap gene-breaking transposon (GBT) insertional mutants in the zebrafish Danio rerio." ; sc:featureList edam:operation_0331, edam:operation_0427, edam:operation_2422, edam:operation_3553 ; sc:name "zfishbook" ; sc:url "http://zfishbook.org/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0160, edam:topic_0196, edam:topic_0654 ; sc:citation ; sc:description "ZFN-Scores searches a DNA sequence for good zinc finger nuclease target sites. The Extended Modular Assembly method has a 40-60% expected success rate" ; sc:featureList edam:operation_0310 ; sc:name "ZFN-Scores" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareVersion "v6" ; sc:url "http://zinc.genomecenter.ucdavis.edu:8080/Plone/zfn-scoresv6" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3170 ; sc:citation , "pmcid:PMC3870982", "pubmed:24215113" ; sc:description "This algorithm is based on the publication by Hart et al., 2013. Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data." ; sc:featureList edam:operation_2428, edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "zFPKM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp , ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/zFPKM.html" ; biotools:primaryContact , "Ron Ammar" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0622 ; sc:author ; sc:description """Prokaryotic genome assembly and annotation pipeline. Wide range of supported reads: Illumina, Oxford Nanopore, PacBio, BGI. Short read multi-threaded processing: QC, filtering, trimming, overlapped pairs merging. Assembling from short reads, long reads or hybrid assembly using modern and powerful assemblers: SPAdes, Unicycler or Flye. Quality control of assembly: completeness and contamination assessment with CheckM as well as PhiX detection. Fast annotation of bacterial and archeal genome assemblies with DFAST . No High Performance Computing needed. The pipeline works on laptop or desktop.""" ; sc:featureList edam:operation_0362, edam:operation_0525, edam:operation_3219 ; sc:isAccessibleForFree true ; sc:name "zga" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareVersion "0.0.8" ; sc:url "https://github.com/laxeye/zga/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0203, edam:topic_0602, edam:topic_3170, edam:topic_3512 ; sc:citation , "pubmed:32053182" ; sc:description """a quantile regression method for differential expression analysis of single-cell RNA-seq data. A statistical differential expression analysis method that accounts for both dropout rates and complex scRNA-seq data distributions in the same model.""" ; sc:featureList edam:operation_2495, edam:operation_3223, edam:operation_3659 ; sc:name "ZIAQ" ; sc:url "https://github.com/gefeizhang/ZIAQ" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0196, edam:topic_0654, edam:topic_3125 ; sc:citation "pubmed:17526515", "pubmed:20435679" ; sc:description "ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome." ; sc:featureList edam:operation_0224, edam:operation_0310, edam:operation_0420 ; sc:name "ZiFiT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://bindr.gdcb.iastate.edu/ZiFiT/" ; biotools:primaryContact "J.D. Sander" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0218, edam:topic_0602, edam:topic_3071, edam:topic_3324, edam:topic_3335 ; sc:citation ; sc:description """Informing epidemic (research) responses in a timely fashion by knowledge management. Zikv-CDB is a collaborative database. Our aim is to gather information about evidences and hypothesis that can lead researches about Zika virus. The database provides information about genes associated with the disease, their expression and interaction with sncRNA. Data will be inserted in ZIKV-CDB as they are released in public databases. If you want your data contextualized in our database, please contact us.""" ; sc:featureList edam:operation_0306, edam:operation_0337, edam:operation_2421 ; sc:name "Zika" ; sc:url "http://www.zikaknowledgebase.eu" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0602, edam:topic_0749, edam:topic_3512 ; sc:citation , "pubmed:31512145" ; sc:description "a new platform to analyze the molecular impact of Zika virus infection | ZIKV is a database that has been manually developed and cured by Brazilian researchers, experts in the fields of microbial infection and host-pathogen interaction, molecular biology, proteomics and neurochemistry. Our goal is to gather all information on gene expression alterations at mRNA and/or protein level promoted by Zika virus infection in different host models. The… | ZIKV is a database that has been manually developed and cured by Brazilian researchers, experts in the fields of microbial infection and host-pathogen interaction, molecular biology, proteomics and neurochemistry | The database provides information on genes which expression was experimentally measured after ZIKV infection" ; sc:featureList edam:operation_3431 ; sc:name "ZIKAVID" ; sc:url "https://zikavid.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Plug-in" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0092, edam:topic_0622, edam:topic_3168 ; sc:citation "pubmed:21787385" ; sc:description "Identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments" ; sc:featureList edam:operation_0564, edam:operation_2403, edam:operation_3501 ; sc:license "GPL-3.0" ; sc:name "ZINBA" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:softwareVersion "2.02.03" ; sc:url "https://code.google.com/archive/p/zinba/" ; biotools:primaryContact "Naim Rashid", "Paul Giresi" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3168, edam:topic_3170, edam:topic_3308 ; sc:citation ; sc:description "Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data." ; sc:featureList edam:operation_2945 ; sc:isAccessibleForFree true ; sc:license "Artistic-2.0" ; sc:name "zinbwave" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.2.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/zinbwave.html" ; biotools:primaryContact "Davide Risso" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0203, edam:topic_3047, edam:topic_3336 ; sc:citation , "pubmed:33667090" ; sc:description "ZINC Express is a virtual assistant for purchasing compounds annotated in the ZINC Database." ; sc:featureList edam:operation_0337, edam:operation_1812, edam:operation_2421 ; sc:name "ZINC Express" ; sc:url "http://zinc15.docking.org/substances/home/" ; biotools:primaryContact , . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_2275, edam:topic_3047, edam:topic_3314, edam:topic_3318 ; sc:citation , "pubmed:33118813" ; sc:description """Free Ultralarge-Scale Chemical Database for Ligand Discovery. ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 230 million purchasable compounds in ready-to-dock, 3D formats. ZINC also contains over 750 million purchasable compounds you can search for analogs in under a minute.""" ; sc:featureList edam:operation_2421, edam:operation_2422, edam:operation_3216, edam:operation_3938 ; sc:name "ZINC20" ; sc:url "http://zinc20.docking.org" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0078, edam:topic_0130, edam:topic_0140, edam:topic_0154 ; sc:citation "pubmed:10077584", "pubmed:11054286", "pubmed:11340073", "pubmed:12592412", "pubmed:16107335", "pubmed:16845061" ; sc:description "Provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them." ; sc:featureList edam:operation_0420, edam:operation_2489 ; sc:name "Zinc Finger Tools" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0078 ; sc:citation ; sc:description "Datasets and scripts used to apply the trained models to predict zinc-binding sites in proteins." ; sc:featureList edam:operation_2423, edam:operation_2479 ; sc:name "Zincidentifier" ; sc:operatingSystem "Linux", "Mac" ; sc:softwareHelp ; sc:url "http://protein.cau.edu.cn/zincidentifier/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0209, edam:topic_2258, edam:topic_2275, edam:topic_3343 ; sc:citation , "pubmed:33759118" ; sc:description "ZINClick is a virtual combinatorial database of over 16 million of 1,4-disubstituted-1,2,3-triazoles (Molecular Weight < 1000), each can be easily synthesized and it is at the same time new and patentable!" ; sc:featureList edam:operation_2421, edam:operation_3216, edam:operation_3938 ; sc:isAccessibleForFree true ; sc:name "ZINClick" ; sc:url "http://www.zinclick.org/" ; biotools:primaryContact "Alberto Massarotti" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0602, edam:topic_3336, edam:topic_3489 ; sc:citation "pubmed:22553363" ; sc:description "ZINCPharmer is webserver for screening the purchasable subset of the ZINC database (updates occur monthly). ZINCPharmer can import LigandScout and MOE pharmacophore definitions, as well as identify pharmacophore features directly from a molecular structure." ; sc:featureList edam:operation_0245, edam:operation_0360, edam:operation_0482, edam:operation_2421 ; sc:name "ZINCPharmer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zincpharmer.csb.pitt.edu" ; biotools:primaryContact "ZINCPharmer Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0199, edam:topic_3053, edam:topic_3673 ; sc:citation "pubmed:21989326" ; sc:description "A tool for detecting CNVs from low-pass WGS data." ; sc:featureList edam:operation_3233 ; sc:name "Zinfandel" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://www.cs.columbia.edu/~itsik/software/Zinfandel.html" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_2275 ; sc:citation , "pmcid:PMC7523679", "pubmed:31393558" ; sc:description "Integrating ab initio and template-based algorithms for protein-protein complex structure prediction | ZING is a method to identify and combine high-confidence protein-protein complex structure predictions of a template-free method (ZDOCK) with a template-based method (SPRING) | python ZING.py [-h] [-zdir zdres] [-sdir spres] | -h, --help show this help message and exit" ; sc:featureList edam:operation_0476, edam:operation_2492, edam:operation_3899 ; sc:name "ZING" ; sc:url "https://github.com/weng-lab/zing" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Library" ; sc:applicationSubCategory edam:topic_3316 ; sc:description "Library for very fast likelihood computations for hidden Markov models." ; sc:featureList edam:operation_0296 ; sc:name "zipHMM" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "birc.au.dk" ; sc:softwareHelp ; sc:softwareVersion "1.0.1" ; sc:url "http://birc.au.dk/software/ziphmm/" ; biotools:primaryContact "Andreas Sand Pedersen" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0622, edam:topic_0654 ; sc:citation "pubmed:26992782" ; sc:description "Tool for detected genomic islands by combining the homogeneity and heterogeneity properties." ; sc:featureList edam:operation_0415 ; sc:name "Zisland Explorer" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://cefg.uestc.edu.cn/Zisland_Explorer/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool", "Library" ; sc:applicationSubCategory edam:topic_3372, edam:topic_3569 ; sc:citation ; sc:description "This package creates libraries from the source code of zlib-1.2.5 for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package)." ; sc:featureList edam:operation_0335, edam:operation_3431, edam:operation_3763 ; sc:license "Artistic-2.0" ; sc:name "zlibbioc" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:softwareVersion "1.24.0" ; sc:url "http://bioconductor.org/packages/release/bioc/html/zlibbioc.html" ; biotools:primaryContact "BioConductor Package Maintainer" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0077, edam:topic_0078, edam:topic_0081, edam:topic_0154, edam:topic_2275 ; sc:citation "pubmed:20119653" ; sc:description "Molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes." ; sc:featureList edam:operation_0477 ; sc:name "ZMM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.zmmsoft.com/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0602, edam:topic_2640, edam:topic_3053 ; sc:citation , "pmcid:PMC4554190", "pubmed:25956356" ; sc:description "A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data." ; sc:featureList edam:operation_2421 ; sc:name "Zodiac" ; sc:softwareHelp ; sc:url "http://www.compgenome.org/zodiac2/" ; biotools:primaryContact "Support" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0780, edam:topic_3047, edam:topic_3172 ; sc:citation ; sc:description """Zodiac is a database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules. 1 Abstract The confident high-throughput identification of small molecules remains one of the most challenging tasks in mass spectrometry-based metabolomics. SIRIUS has become a powerful tool for the interpretation of tandem mass spectra and shows outstanding performance for identifying the molecular formula of a query compound, being the first step of structure identification. Nevertheless, the identification of both molecular formulas for large compounds above 500 Daltons and novel molecular formulas remains highly challenging. Here, we present ZODIAC, a network-based algorithm for the de novo estimation of molecular formulas.""" ; sc:featureList edam:operation_0224, edam:operation_2238, edam:operation_3801, edam:operation_3803 ; sc:name "ZODIAC" ; sc:url "https://bio.informatik.uni-jena.de/software/zodiac/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0848 ; sc:encodingFormat edam:format_2571 ; sc:name "Raw sequence" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_1274 ; sc:encodingFormat edam:format_2060, edam:format_2305, edam:format_3003 ; sc:name "Map" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Desktop application" ; sc:applicationSubCategory edam:topic_0102, edam:topic_0622, edam:topic_3569, edam:topic_3574 ; sc:citation "pubmed:18684737" ; sc:description "A software for mapping the human genome reads from Illumina/Solexa sequencing to the reference human genome." ; sc:featureList edam:operation_0253, edam:operation_2403, edam:operation_3198 ; sc:name "ZOOM" ; sc:operatingSystem "Linux", "Windows" ; sc:softwareHelp ; sc:url "http://www.bioinfor.com/zoom-1-3-gui-release-next-gen-seq/" ; biotools:primaryContact "Contact Form" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_0968 ; sc:name "Keyword" ] ; bsc:output [ a bsct:FormalParameter ; sc:additionalType edam:data_3509 ; sc:name "Ontology mapping" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0089, edam:topic_2259, edam:topic_3345 ; sc:author ; sc:citation , , "pmcid:PMC3194170", "pubmed:21995944" ; sc:description "ZOOMA 2 is a search engine for automatic curation and a repository of annotation knowledge. It facilitates automated data annotation against a variety of ontologies by exploring context and previous annotation efforts as well as lexical matching" ; sc:featureList edam:operation_0226 ; sc:name "Zooma" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "EMBL-EBI" ; sc:softwareHelp , ; sc:softwareVersion "1" ; sc:url "http://wwwdev.ebi.ac.uk/fgpt/zooma/" ; biotools:primaryContact . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0128, edam:topic_0602, edam:topic_2259 ; sc:citation "pubmed:26451833" ; sc:description "Web server in order to provide the research community with a tool for analysis, visualization and clustering of networks as a super network, based on their calculated feature properties." ; sc:featureList edam:operation_0276, edam:operation_3083 ; sc:name "ZoomOut" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://bioserver-3.bioacademy.gr/Bioserver/ZoomOut/" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2976 ; sc:name "Protein sequence" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0154, edam:topic_0166, edam:topic_0736, edam:topic_2275, edam:topic_3474 ; sc:citation , "pmcid:PMC8499977", "pubmed:34553747" ; sc:description "Residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features." ; sc:featureList edam:operation_0267, edam:operation_0321, edam:operation_0477 ; sc:isAccessibleForFree true ; sc:name "ZoomQA" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:url "http://zoomQA.renzhitech.com" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_3293, edam:topic_3305, edam:topic_3324, edam:topic_3500 ; sc:citation , "pmcid:PMC10351968", "pubmed:37465397" ; sc:description "Comprehensive web resource for zoonotic pathogens." ; sc:featureList edam:operation_0324, edam:operation_0337, edam:operation_2451 ; sc:isAccessibleForFree true ; sc:name "ZooPathWeb" ; sc:url "http://lab.malab.cn/~hrs/zoopathweb/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0622 ; sc:citation ; sc:description "ZORRO is an hybrid sequencing technology assembler. It takes to sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. The main caracteristic of Zorro is the treatment before and after assembly to avoid errors." ; sc:featureList edam:operation_0310 ; sc:license "GPL-3.0" ; sc:name "ZORRO" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "http://lge.ibi.unicamp.br/zorro/" ; biotools:primaryContact "Gustavo Lacerda", "Marcelo Carazzole", "Ramon Vidal" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Database portal", "Web application" ; sc:applicationSubCategory edam:topic_0621, edam:topic_0781, edam:topic_3305, edam:topic_3324, edam:topic_3500 ; sc:citation , "pmcid:PMC8728136", "pubmed:34634795" ; sc:description "The database of zoonotic and vector-borne viruses." ; sc:featureList edam:operation_0324, edam:operation_2421 ; sc:isAccessibleForFree true ; sc:name "ZOVER" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://www.mgc.ac.cn/ZOVER" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0203, edam:topic_0621, edam:topic_0749, edam:topic_3512 ; sc:citation "pubmed:14993211" ; sc:description "zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista." ; sc:featureList edam:operation_0448, edam:operation_0491, edam:operation_0492 ; sc:name "zPicture and multi-zPicture" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://zpicture.dcode.org/" ; biotools:primaryContact "Lisa Stubbs" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3524 ; sc:citation ; sc:description "A tool to optimize breeding programmes based on a deterministic approach. zplan evaluates the genetic and economic efficiency of breeding strategies considering one cycle of selection." ; sc:featureList edam:operation_2426 ; sc:license "Not licensed" ; sc:name "zplan" ; sc:operatingSystem "Linux" ; sc:softwareHelp ; sc:url "https://www.uni-hohenheim.de/en/organization/project/zplan-a-tool-to-optimize-breeding-programmes" . a sc:SoftwareApplication ; bsc:input [ a bsct:FormalParameter ; sc:additionalType edam:data_2082 ; sc:name "Matrix" ] ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_3473 ; sc:citation ; sc:description "Performs simple and partial Mantel tests." ; sc:featureList edam:operation_3438 ; sc:license "GPL-3.0" ; sc:name "ZT" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:provider "ugent.be" ; sc:softwareHelp ; sc:softwareVersion "1" ; sc:url "http://bioinformatics.psb.ugent.be/software/details/ZT" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Command-line tool" ; sc:applicationSubCategory edam:topic_0080, edam:topic_0102, edam:topic_3170 ; sc:citation ; sc:description "A fast and flexible pipeline to process RNA sequencing data with UMIs." ; sc:featureList edam:operation_2429, edam:operation_3680, edam:operation_3695 ; sc:license "GPL-3.0" ; sc:name "zUMIs" ; sc:softwareHelp ; sc:url "https://github.com/sdparekh/zUMIs" ; biotools:primaryContact "Ines Hellmann", "Swati Parekh" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Script" ; sc:applicationSubCategory edam:topic_0196, edam:topic_0659, edam:topic_0769, edam:topic_2229, edam:topic_3170, edam:topic_3174 ; sc:citation , "pmcid:PMC8376068", "pubmed:34370725" ; sc:description "The Zero Waste Algorithm (ZWA) is a pipeline comprised of various bioinformatic tools for context-based read trimming. The goal of this pipeline is to assist in viral genome assembly by retaining the viral part of reads and discarding any ribosomal hybrid bases the reads might contain." ; sc:featureList edam:operation_0524, edam:operation_0525, edam:operation_3192, edam:operation_3258, edam:operation_3431 ; sc:isAccessibleForFree true ; sc:license "GPL-3.0" ; sc:name "ZWA" ; sc:url "https://github.com/ndovro/ZWA/" . a sc:SoftwareApplication ; dcterms:conformsTo "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT" ; sc:additionalType "Web application" ; sc:applicationSubCategory edam:topic_0080, edam:topic_2269, edam:topic_3053 ; sc:citation ; sc:description "Processes convenient and accurate zygosity probability calculation." ; sc:featureList edam:operation_0236 ; sc:name "ZygProb" ; sc:operatingSystem "Linux", "Mac", "Windows" ; sc:softwareHelp ; sc:url "http://neurogenetics.qimrberghofer.edu.au/ZygProb/" . a schema:Person . a schema:Person . a schema:Person . a schema:Person . a 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